Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 18 of 316
Found at i:5453968 original size:268 final size:268
Alignment explanation
Indices: 5453490--5454028 Score: 938
Period size: 268 Copynumber: 2.0 Consensus size: 268
5453480 GTGAAAAATC
*
5453490 AAGAAAAAGAATTTGGTATCTTGATAATTGCGCCAACAATCACATGTGTGGCCGAAAAGACTTAT
1 AAGAAAAAGAATTTGGTATCTTGATAATTGCACCAACAATCACATGTGTGGCCGAAAAGACTTAT
*
5453555 TTTCAGAGTTAGATGAGAATATTCATGGACAAGTAACGTTTGGAGATGAATCGCATACCACGGTC
66 TTTCAAAGTTAGATGAGAATATTCATGGACAAGTAACGTTTGGAGATGAATCGCATACCACGGTC
*
5453620 AAAAGCAACGGCAAAGTCACTATTACAAAAAAGAATGGAAAAAAGAAGTTAATTTCAAATGTTTA
131 AAAAGCAAAGGCAAAGTCACTATTACAAAAAAGAATGGAAAAAAGAAGTTAATTTCAAATGTTTA
* * *
5453685 TTACGTACTAGCTTTGAAAAGCAACATTATCAGCTTTAGACAGCTTTTAAAAAAAAGATATGAAG
196 TTACGTACCAGCTTTGAAAAGCAACATTATCAGCTTTAGACAGCTTCTAAAAAAAAGATATAAAG
5453750 TACATATG
261 TACATATG
*
5453758 AAGAAAAA-ATATTTGGTATCTTGATAATTGCACCAGCAATCACATGTGTGGCCGAAAAGACTTA
1 AAGAAAAAGA-ATTTGGTATCTTGATAATTGCACCAACAATCACATGTGTGGCCGAAAAGACTTA
* *
5453822 TTTTCAAAGTTGGATGAGAATATTCATGGACAAGTAACGTTTGGAGATGAATCGCATGCCACGGT
65 TTTTCAAAGTTAGATGAGAATATTCATGGACAAGTAACGTTTGGAGATGAATCGCATACCACGGT
* *
5453887 CAAAGGCAAAGGCAAAGTCACTATTACAAAAAAGAATGGAAAAAAGAAGTTCATTT-AAGATGTT
130 CAAAAGCAAAGGCAAAGTCACTATTACAAAAAAGAATGGAAAAAAGAAGTTAATTTCAA-ATGTT
*
5453951 TATTACGTACCAGCTTTGAAAAGCAACATTATCAGCTTTAGACAGCTTCTAAAAAAAGGATATAA
194 TATTACGTACCAGCTTTGAAAAGCAACATTATCAGCTTTAGACAGCTTCTAAAAAAAAGATATAA
5454016 AGTACATATG
259 AGTACATATG
5454026 AAG
1 AAG
5454029 GATTCCATGC
Statistics
Matches: 257, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
267 3 0.01
268 254 0.99
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (268 bp):
AAGAAAAAGAATTTGGTATCTTGATAATTGCACCAACAATCACATGTGTGGCCGAAAAGACTTAT
TTTCAAAGTTAGATGAGAATATTCATGGACAAGTAACGTTTGGAGATGAATCGCATACCACGGTC
AAAAGCAAAGGCAAAGTCACTATTACAAAAAAGAATGGAAAAAAGAAGTTAATTTCAAATGTTTA
TTACGTACCAGCTTTGAAAAGCAACATTATCAGCTTTAGACAGCTTCTAAAAAAAAGATATAAAG
TACATATG
Found at i:5459196 original size:17 final size:16
Alignment explanation
Indices: 5459174--5459218 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
5459164 ACATATTTTA
5459174 AAAATAATTAATTACAT
1 AAAATAATTAATTA-AT
*
5459191 AAAATAATTAATTATT
1 AAAATAATTAATTAAT
*
5459207 TAAATAATTAAT
1 AAAATAATTAAT
5459219 ATTAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATAATTAATTAAT
Found at i:5462517 original size:16 final size:17
Alignment explanation
Indices: 5462486--5462518 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5462476 TTCATAAGTA
5462486 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
5462503 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
5462519 GTTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:5463052 original size:138 final size:138
Alignment explanation
Indices: 5462814--5463062 Score: 410
Period size: 138 Copynumber: 1.8 Consensus size: 138
5462804 TGCCATAGTG
* *
5462814 TCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACTATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
** *
5462879 TTCATTTCATGTCACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTG
66 CACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTG
5462944 CCATGGCA
131 CCATGGCA
*
5462952 TCTTTCAAGC-ATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTT
1 TCTTTCAA-CTATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTT
* *
5463016 ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTA
65 ACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTA
5463063 CACATTTCAT
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
138 101 0.99
139 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.41
Consensus pattern (138 bp):
TCTTTCAACTATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
CACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTG
CCATGGCA
Found at i:5463077 original size:46 final size:46
Alignment explanation
Indices: 5462799--5463072 Score: 361
Period size: 46 Copynumber: 6.0 Consensus size: 46
5462789 TTATCTTTGA
* * * *
5462799 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
*
5462845 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * * **
5462891 CACGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * * **
5462937 CATGTTGCCATGGCATCTTTCAAGCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
5462983 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
5463029 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
5463073 ATCAGAGAGC
Statistics
Matches: 206, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.02
46 202 0.98
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:5464496 original size:17 final size:17
Alignment explanation
Indices: 5464474--5464512 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
5464464 ACACCCTTAT
5464474 TTTCTTTTTCTACACTA
1 TTTCTTTTTCTACACTA
5464491 TTTCTTTTTCTACACTA
1 TTTCTTTTTCTACACTA
5464508 TTTCT
1 TTTCT
5464513 CATCACTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTCTTTTTCTACACTA
Found at i:5466474 original size:45 final size:45
Alignment explanation
Indices: 5466383--5466475 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
5466373 GACTGTTAAC
* * * *
5466383 AGAAAAAGGTGGCTGTGCAACAGTATCACCTGAAGCACTGGTTGG
1 AGAAAAAGATGGCTGTGCAACAATATCACCGGAAGCACTGGATGG
* *
5466428 AGAAAAAGATGGTTGTGCAACAATATCACCGGGAGCA-TGGGATGG
1 AGAAAAAGATGGCTGTGCAACAATATCACCGGAAGCACT-GGATGG
5466473 AGA
1 AGA
5466476 TGAGCTGGTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 1 0.02
45 40 0.98
ACGTcount: A:0.34, C:0.15, G:0.32, T:0.18
Consensus pattern (45 bp):
AGAAAAAGATGGCTGTGCAACAATATCACCGGAAGCACTGGATGG
Found at i:5467592 original size:25 final size:25
Alignment explanation
Indices: 5467558--5467609 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
5467548 GGAGACCCAG
5467558 AGCTTGAAGC-AGATTTATTAAAAGT
1 AGCTTGAAGCAAG-TTTATTAAAAGT
*
5467583 AGCTTGAAGCAAGTTTATTGAAAGT
1 AGCTTGAAGCAAGTTTATTAAAAGT
5467608 AG
1 AG
5467610 GTCGAGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (25 bp):
AGCTTGAAGCAAGTTTATTAAAAGT
Found at i:5468570 original size:63 final size:63
Alignment explanation
Indices: 5468471--5468592 Score: 235
Period size: 63 Copynumber: 1.9 Consensus size: 63
5468461 GGAAGGCCAG
5468471 CCAAGATAACGCTGATCTGTTCTTGCTTCGTAACCAGGCTACCAGCGGCAGTCAGACTACCCA
1 CCAAGATAACGCTGATCTGTTCTTGCTTCGTAACCAGGCTACCAGCGGCAGTCAGACTACCCA
*
5468534 CCAAGATAACGCTGATCTGTTCTTGCTTCGTAACCAGGCTACTAGCGGCAGTCAGACTA
1 CCAAGATAACGCTGATCTGTTCTTGCTTCGTAACCAGGCTACCAGCGGCAGTCAGACTA
5468593 TCACTTAAAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (63 bp):
CCAAGATAACGCTGATCTGTTCTTGCTTCGTAACCAGGCTACCAGCGGCAGTCAGACTACCCA
Found at i:5493288 original size:30 final size:31
Alignment explanation
Indices: 5493252--5493315 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
5493242 TAACGTTCTT
*
5493252 TTATTATTATCATG-TAATAATAGTAATA-AA
1 TTATTATTATAATGTTAAT-ATAGTAATATAA
* *
5493282 TTATTATTCTAATGTTAATTTAGTAATATAA
1 TTATTATTATAATGTTAATATAGTAATATAA
5493313 TTA
1 TTA
5493316 ACAATGAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 20 0.69
31 9 0.31
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (31 bp):
TTATTATTATAATGTTAATATAGTAATATAA
Found at i:5500533 original size:21 final size:21
Alignment explanation
Indices: 5500509--5500550 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5500499 ATCTGCTCAA
* *
5500509 ACTCCACCTGTTTTGGAGTAT
1 ACTCCACCTGCTGTGGAGTAT
5500530 ACTCCACCTGCTGTGGAGTAT
1 ACTCCACCTGCTGTGGAGTAT
5500551 TGCTCGTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.33
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAT
Found at i:5504381 original size:16 final size:16
Alignment explanation
Indices: 5504352--5504388 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
5504342 AATTACAACT
*
5504352 CTATTTCATTACAGCC
1 CTATTGCATTACAGCC
*
5504368 CTATTGCATTACAGTC
1 CTATTGCATTACAGCC
5504384 CTATT
1 CTATT
5504389 CTATTAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (16 bp):
CTATTGCATTACAGCC
Found at i:5504394 original size:16 final size:15
Alignment explanation
Indices: 5504356--5504405 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
5504346 ACAACTCTAT
*
5504356 TTCATTACAGCCCTA
1 TTCATTACAGTCCTA
5504371 TTGCATTACAGTCCTA
1 TT-CATTACAGTCCTA
*
5504387 TTCTATTAAAGTCCTA
1 TTC-ATTACAGTCCTA
5504403 TTC
1 TTC
5504406 CATTCCACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
15 3 0.10
16 28 0.90
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.40
Consensus pattern (15 bp):
TTCATTACAGTCCTA
Found at i:5505645 original size:15 final size:15
Alignment explanation
Indices: 5505615--5505643 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5505605 CATGTATCTC
5505615 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
5505630 ATTTTTT-AATATTT
1 ATTTTTTAAATATTT
5505644 TACTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:5525558 original size:13 final size:13
Alignment explanation
Indices: 5525501--5525559 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
5525491 CAAAACAATA
5525501 AAAATATAATATT
1 AAAATATAATATT
*
5525514 AAAAGATATATATAT
1 AAAATATA-ATAT-T
* *
5525529 AAAATGT-ATA-C
1 AAAATATAATATT
*
5525540 ATAATATAATATT
1 AAAATATAATATT
5525553 AAAATAT
1 AAAATAT
5525560 TTACATGGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
11 5 0.15
12 3 0.09
13 16 0.47
14 4 0.12
15 6 0.18
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (13 bp):
AAAATATAATATT
Found at i:5525564 original size:24 final size:24
Alignment explanation
Indices: 5525519--5525565 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5525509 ATATTAAAAG
*
5525519 ATATATATATAAAATGTATACATA
1 ATATATATATAAAATATATACATA
*
5525543 ATATA-ATATTAAAATATTTACAT
1 ATATATATA-TAAAATATATACAT
5525566 GGTATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
ATATATATATAAAATATATACATA
Found at i:5526129 original size:38 final size:38
Alignment explanation
Indices: 5526075--5526214 Score: 172
Period size: 38 Copynumber: 3.6 Consensus size: 38
5526065 GATTCCATTC
* *
5526075 CCCCTATGCTACTTTGTTTTATTATTAATCAAAACCACT
1 CCCC-ATGCTATTTTGTTTTATTATTAATTAAAACCACT
*
5526114 CCCCATGCTATTTTGTTTTATTGTTAATTAAAACCACT
1 CCCCATGCTATTTTGTTTTATTATTAATTAAAACCACT
* * * *
5526152 CCCCATGCTATTTTGTTTTATTTTTTATTAAAACTATTT
1 CCCCATGCTATTTTGTTTTATTATTAATTAAAACCA-CT
* * *
5526191 TCCCATACTATTTTGTTTTTTTAT
1 CCCCATGCTATTTTGTTTTATTAT
5526215 CATAAAAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 64 0.72
39 25 0.28
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.50
Consensus pattern (38 bp):
CCCCATGCTATTTTGTTTTATTATTAATTAAAACCACT
Found at i:5530718 original size:41 final size:40
Alignment explanation
Indices: 5530663--5530748 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 40
5530653 ATATAATCAC
* *
5530663 TTTTTTTATATTTTTAATTTGTGTATTATTTTAAAAATTG
1 TTTTATTATATTTTTAATTTATGTATTATTTTAAAAATTG
* * * * *
5530703 TTTTATTATTATTTTTCATTTATTTTTTCTTTTAATAATTG
1 TTTTATTA-TATTTTTAATTTATGTATTATTTTAAAAATTG
5530744 TTTTA
1 TTTTA
5530749 AGTGTATTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 7 0.18
41 31 0.82
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (40 bp):
TTTTATTATATTTTTAATTTATGTATTATTTTAAAAATTG
Found at i:5543568 original size:21 final size:22
Alignment explanation
Indices: 5543538--5543579 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5543528 TTGATAAATT
5543538 ATATACATTTA-AATATTTTTC
1 ATATACATTTATAATATTTTTC
* *
5543559 ATATATATTTATAATCTTTTT
1 ATATACATTTATAATATTTTT
5543580 TTTTGTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATACATTTATAATATTTTTC
Found at i:5561807 original size:13 final size:13
Alignment explanation
Indices: 5561789--5561815 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5561779 ATATATTGTT
5561789 AAATTATCACAGA
1 AAATTATCACAGA
5561802 AAATTATCACAGA
1 AAATTATCACAGA
5561815 A
1 A
5561816 TATATACACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
AAATTATCACAGA
Found at i:5563232 original size:13 final size:13
Alignment explanation
Indices: 5563201--5563225 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5563191 CCATATTTTT
5563201 TTTATATATATAG
1 TTTATATATATAG
5563214 TTTATATATATA
1 TTTATATATATA
5563226 TTATATACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTATATATATAG
Found at i:5563500 original size:36 final size:37
Alignment explanation
Indices: 5563459--5563532 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
5563449 ATAATTCATG
* *
5563459 TGTACACACATATGT-TTTTTTATATTTTCATAATTT
1 TGTACACACATATATGTCTTTTATATTTTCATAATTT
* * *
5563495 TGTACATATATATATGTCTTTTATCTTTTCATAATTT
1 TGTACACACATATATGTCTTTTATATTTTCATAATTT
5563532 T
1 T
5563533 TTTTTGGATC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
36 12 0.38
37 20 0.62
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (37 bp):
TGTACACACATATATGTCTTTTATATTTTCATAATTT
Found at i:5569873 original size:86 final size:86
Alignment explanation
Indices: 5569728--5570077 Score: 574
Period size: 86 Copynumber: 4.1 Consensus size: 86
5569718 AGTAAAAATT
* * * * * *
5569728 GAAGATAAACCTTGCCTCTCTCGGTCGTAGCAGAGCTGGTTGAAGTTATCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
5569793 GCATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
*
5569814 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
5569879 GCATTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
*
5569900 GAAGACAAACCTTGCCACTCTCGTTTGTAGTAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
*
5569965 GCACTGACAGCGAAGCAGATC
66 GCATTGACAGCGAAGCAGATC
* *
5569986 GAAGACAAACCTTGCCTCTCTCGTTTGTAGCAGAGCTGGTTGAAGATATCAGATCTTGCCTTCCT
1 GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
* *
5570051 GTATTTGGCAGCGAAGCAGATC
66 GCA-TTGACAGCGAAGCAGATC
5570073 GAAGA
1 GAAGA
5570078 TGGCAGATTT
Statistics
Matches: 249, Mismatches: 14, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
86 228 0.92
87 21 0.08
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (86 bp):
GAAGACAAACCTTGCCACTCTCGTTTGTAGCAGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
GCATTGACAGCGAAGCAGATC
Found at i:5569915 original size:42 final size:42
Alignment explanation
Indices: 5569782--5570002 Score: 107
Period size: 42 Copynumber: 5.2 Consensus size: 42
5569772 GTTATCAGAT
5569782 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
* * * * * * * * *
5569824 CTTGCC-ACTCT-CGTTTG-TAG-TAGAGCTGGTTGAAGATAGCAGAT
1 CTTGCCTTC-CTGC-ATTGACAGCGA-AGCAGATCGAAG--A-CAAAC
5569868 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
* * * * * * * * *
5569910 CTTGCC-ACTCT-CGTTTG-TAG-TAGAGCTGGTTGAAGATAGCAGAT
1 CTTGCCTTC-CTGC-ATTGACAGCGA-AGCAGATCGAAG--A-CAAAC
*
5569954 CTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
5569996 CTTGCCT
1 CTTGCCT
5570003 CTCTCGTTTG
Statistics
Matches: 122, Mismatches: 37, Indels: 40
0.61 0.19 0.20
Matches are distributed among these distances:
40 2 0.02
41 26 0.21
42 35 0.29
43 4 0.03
44 27 0.22
45 26 0.21
46 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (42 bp):
CTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACAAAC
Found at i:5570085 original size:46 final size:46
Alignment explanation
Indices: 5570035--5570496 Score: 120
Period size: 46 Copynumber: 10.3 Consensus size: 46
5570025 TTGAAGATAT
*
5570035 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGG
1 CAGATCTTGCCTCCCTGTATTTGGCAGCGAAGCAGATCGAAGATGG
* * * * * * * * * ** *
5570081 CAGATTTTACCTCCCTG-A-CT-ACAGTGGAGTACATTGAAGCCGA
1 CAGATCTTGCCTCCCTGTATTTGGCAGCGAAGCAGATCGAAGATGG
* * * * *
5570124 TA-ATTCTAT--CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATTG
1 CAGA-TCT-TGCCTCCCTGTATTTGGCAG-CGAAGCAGATCGAAGATGG
* *
5570169 CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGG
1 CAGATCTTGCCTCCCTGTATTTGGCAGCGAAGCAGATCGAAGATGG
* * * * * * * * * ** *
5570215 CAGATTTTACCTCCCTG-A-CT-ACAGAGGAGTACATTGAAGCCGA
1 CAGATCTTGCCTCCCTGTATTTGGCAGCGAAGCAGATCGAAGATGG
* * * * *
5570258 TA-ACTCTAT--CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATTG
1 CAGA-TCT-TGCCTCCCTGTATTTGGCAG-CGAAGCAGATCGAAGATGG
** ** *
5570303 CAGATCTTGTTTTTCTGTATTTGGCAGCAAAGCAGATCGAAGATGG
1 CAGATCTTGCCTCCCTGTATTTGGCAGCGAAGCAGATCGAAGATGG
* * * * * * * * * ** *
5570349 CAGATTTTACCTCCCTG-A-CT-ACAGAGGAGTACATTGAAGCCGA
1 CAGATCTTGCCTCCCTGTATTTGGCAGCGAAGCAGATCGAAGATGG
* * * * *
5570392 TA-ACTCTAT--CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATTG
1 CAGA-TCT-TGCCTCCCTGTATTTGGCAG-CGAAGCAGATCGAAGATGG
* * *
5570437 CAGATCTTGCTTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGG
1 CAGATCTTGCCTCCCTGTATTTGGCAGCGAAGCAGATCGAAGATGG
* *
5570483 CAGATTTTACCTCC
1 CAGATCTTGCCTCC
5570497 ATGTGACTAC
Statistics
Matches: 281, Mismatches: 105, Indels: 60
0.63 0.24 0.13
Matches are distributed among these distances:
42 24 0.09
43 52 0.19
44 12 0.04
45 59 0.21
46 134 0.48
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (46 bp):
CAGATCTTGCCTCCCTGTATTTGGCAGCGAAGCAGATCGAAGATGG
Found at i:5570266 original size:134 final size:134
Alignment explanation
Indices: 5570025--5570570 Score: 950
Period size: 134 Copynumber: 4.1 Consensus size: 134
5570015 GCAGAGCTGG
*
5570025 TTGAAGATAT-CAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTT
1 TTGAAGAT-TGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTT
* *
5570089 ACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAATTCTATCTCCCTGTATTTGGCAGTGGA
65 ACCTCCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGA
5570154 ATAGA
130 ATAGA
5570159 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTA
5570224 CCTCCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
66 CCTCCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
5570289 TAGA
131 TAGA
** * * *
5570293 TTGAAGATTGCAGATCTTGTTTTTCTGTATTTGGCAGCAAAGCAGATCGAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTA
5570358 CCTCCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
66 CCTCCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
5570423 TAGA
131 TAGA
*
5570427 TTGAAGATTGCAGATCTTGCTTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTA
* * *
5570492 CCTCCATGTGACTACAGTGGAGTACATTGAAGCCAATAACTCTATCTCCCTGTATTTGGCAGTGG
66 CCTCC--CTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGG
5570557 AATAGA
129 AATAGA
5570563 TTGAAGAT
1 TTGAAGAT
5570571 CGAAGATGGC
Statistics
Matches: 394, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
133 1 0.00
134 324 0.82
136 69 0.18
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (134 bp):
TTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGATTTTA
CCTCCCTGACTACAGAGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGAA
TAGA
Found at i:5570616 original size:50 final size:49
Alignment explanation
Indices: 5570551--5570713 Score: 133
Period size: 50 Copynumber: 3.4 Consensus size: 49
5570541 CTGTATTTGG
*
5570551 CAGTGGAATAGATTGAAGATCGAAGATGGCAGATTTTACCTCCCTGACTA
1 CAGTGGAATACATTGAAGATC-AAGATGGCAGATTTTACCTCCCTGACTA
* * * * * * *
5570601 CAGTGGAGTACATTGAAG--C-CGAT---A-ACTCTATCTCCCTGTATTTGG
1 CAGTGGAATACATTGAAGATCAAGATGGCAGATTTTACCTCCCTG-A-CT-A
* *
5570646 CAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCCTGACCA
1 CAGTGGAATACATTGAAGATC-AAGATGGCAGATTTTACCTCCCTGACTA
*
5570696 CAGTGGAGTACATTGAAG
1 CAGTGGAATACATTGAAG
5570714 CCGATAACTC
Statistics
Matches: 83, Mismatches: 19, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
42 11 0.13
43 2 0.02
44 1 0.01
45 16 0.19
46 3 0.04
47 1 0.01
48 1 0.01
49 3 0.04
50 32 0.39
52 2 0.02
53 11 0.13
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (49 bp):
CAGTGGAATACATTGAAGATCAAGATGGCAGATTTTACCTCCCTGACTA
Found at i:5570620 original size:95 final size:95
Alignment explanation
Indices: 5570470--5570760 Score: 528
Period size: 95 Copynumber: 3.0 Consensus size: 95
5570460 GCAGCGAAGC
* *
5570470 AGATCAAAGATGGCAGATTTTACCTCCATGTGACTACAGTGGAGTACATTGAAGCCAATAACTCT
1 AGATCAAAGATGGCAGATTTTACCTCC--CTGACTACAGTGGAGTACATTGAAGCCGATAACTCT
5570535 ATCTCCCTGTATTTGGCAGTGGAATAGATTGA
64 ATCTCCCTGTATTTGGCAGTGGAATAGATTGA
*
5570567 AGATCGAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
5570632 CTCCCTGTATTTGGCAGTGGAATAGATTGA
66 CTCCCTGTATTTGGCAGTGGAATAGATTGA
*
5570662 AGATCAAAGATGGCAGATTTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
5570727 CTCCCTGTATTTGGCAGTGGAATAGATTGA
66 CTCCCTGTATTTGGCAGTGGAATAGATTGA
5570757 AGAT
1 AGAT
5570761 TGCAGATCTT
Statistics
Matches: 189, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
95 163 0.86
97 26 0.14
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (95 bp):
AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
CTCCCTGTATTTGGCAGTGGAATAGATTGA
Found at i:5570652 original size:45 final size:45
Alignment explanation
Indices: 5570601--5570758 Score: 124
Period size: 45 Copynumber: 3.4 Consensus size: 45
5570591 TCCCTGACTA
*
5570601 CAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGG
1 CAGTGGAATACATTGAAGCCGATAACTCTATCTCCCTGTATTTGG
* * * * * ***
5570646 CAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCCTG-A--CCA
1 CAGTGGAATACATTGAAG--C--CGAT---A-ACTCTATCTCCCTGTATTTGG
*
5570696 CAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGG
1 CAGTGGAATACATTGAAGCCGATAACTCTATCTCCCTGTATTTGG
*
5570741 CAGTGGAATAGATTGAAG
1 CAGTGGAATACATTGAAG
5570759 ATTGCAGATC
Statistics
Matches: 82, Mismatches: 20, Indels: 22
0.66 0.16 0.18
Matches are distributed among these distances:
42 11 0.13
43 2 0.02
45 32 0.39
46 3 0.04
47 1 0.01
48 1 0.01
49 3 0.04
50 16 0.20
52 2 0.02
53 11 0.13
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (45 bp):
CAGTGGAATACATTGAAGCCGATAACTCTATCTCCCTGTATTTGG
Found at i:5570923 original size:46 final size:46
Alignment explanation
Indices: 5570727--5570923 Score: 145
Period size: 46 Copynumber: 4.4 Consensus size: 46
5570717 ATAACTCTAT
*
5570727 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTAC
* ** * ** * *
5570773 CTTCCTGTATTTGGCA-ACGAAGCAGATCAAAGATGGCAGATTTTAC
1 CTCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATTGCAGATCTTAC
*** * * ** * * *
5570819 CTCCCTG-A--CCACAGTGGAGTACATTGAAG-CCG-ATAACTCTAT
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCT-TAC
*
5570861 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGC
1 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTAC
*
5570907 CTTCCTGTATTTGGCAG
1 CTCCCTGTATTTGGCAG
5570924 CAAAGCAGGT
Statistics
Matches: 105, Mismatches: 38, Indels: 16
0.66 0.24 0.10
Matches are distributed among these distances:
41 3 0.03
42 10 0.10
43 9 0.09
44 2 0.02
45 20 0.19
46 57 0.54
47 4 0.04
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (46 bp):
CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTAC
Found at i:5570999 original size:134 final size:134
Alignment explanation
Indices: 5570662--5570982 Score: 570
Period size: 134 Copynumber: 2.4 Consensus size: 134
5570652 AATAGATTGA
5570662 AGATCAAAGATGGCAGATTTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTAT
*
5570727 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAACG
66 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAACA
5570792 AAGC
131 AAGC
5570796 AGATCAAAGATGGCAGATTTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTAT
*
5570861 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCA
66 CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAACA
5570926 AAGC
131 AAGC
* ** * **
5570930 AGGTTGAAGACGGCAGATTTTACCTCCCTGATTACAGTGGAGTACATTGAAGC
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACCACAGTGGAGTACATTGAAGC
5570983 TAATAGTTCT
Statistics
Matches: 179, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
134 179 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (134 bp):
AGATCAAAGATGGCAGATTTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTAT
CTCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAACA
AAGC
Found at i:5571244 original size:132 final size:132
Alignment explanation
Indices: 5571007--5572306 Score: 2188
Period size: 132 Copynumber: 9.8 Consensus size: 132
5570997 CCCGGGGCAA
* * *
5571007 GAAGTAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGA
* *
5571072 TCTTATCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
5571137 GT
131 GT
* * * *
5571139 GAAGTAGATCGAAGATAGCTGATCCTATCTTCTTATATTGGTAGGAAATGGATCGAAGATGCAGA
1 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGA
5571204 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
5571269 GT
131 GT
*
5571271 GAAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATT-AGTAGGAAGTGGATCGAAGATGCAG
1 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGA-TAGGAAGTGGATCGAAGATGCAG
*
5571335 ATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGA
65 ATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGG
5571400 CGT
130 CGT
* * * * *
5571403 GAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATAATGATTGGAAGTGGATCGACGACGCAGA
1 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGA
*
5571468 TCTTGTCTTCCCATATTAGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
5571533 GT
131 GT
* * *
5571535 GAAGTAGATCGAAGATAGCAGGTCCTATCTTCCAATATTGATAGGAAGTGGATCCAAGATGCAGA
1 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGA
*
5571600 TCTTGTCTTTCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
5571665 GT
131 GT
* * * * *
5571667 GAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATAATGATTGGAAGTGGATCGACGACGCAGA
1 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGA
*
5571732 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTAGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
5571797 GT
131 GT
* * * * *
5571799 GAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATAATGATTGGAAGTGGATCGACGACGCAGA
1 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGA
*
5571864 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATATATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
5571929 GT
131 GT
* * *
5571931 GAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATACAGA
1 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGA
5571996 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
5572061 GT
131 GT
* * *
5572063 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCCACGACGCAGA
1 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGA
5572128 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
5572193 GT
131 GT
* *
5572195 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATACAGA
1 GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGA
* * *
5572260 TCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATC
5572307 GACGATGGCG
Statistics
Matches: 1114, Mismatches: 52, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
132 1113 1.00
133 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (132 bp):
GAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGATAGGAAGTGGATCGAAGATGCAGA
TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
GT
Found at i:5573656 original size:3 final size:3
Alignment explanation
Indices: 5573631--5573688 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
5573621 GTTTTTTAGT
* *
5573631 TTA TT- TTA TTA ATA -TA GTTA TTA TTA TTA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
5573675 TTA TT- TT- TTA TTA T
1 TTA TTA TTA TTA TTA T
5573689 ACTTACATAC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
2 8 0.17
3 38 0.79
4 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5573812 original size:13 final size:12
Alignment explanation
Indices: 5573796--5573829 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
5573786 CCATATTTTT
5573796 TTTATATATATA
1 TTTATATATATA
5573808 GTTTATATATATA
1 -TTTATATATATA
5573821 TATTATATA
1 T-TTATATA
5573830 CATTCATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 19 0.95
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
TTTATATATATA
Found at i:5589444 original size:13 final size:14
Alignment explanation
Indices: 5589402--5589445 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
5589392 TTTTATCCTG
*
5589402 AATCTCGAATCTTA
1 AATCTCGAACCTTA
*
5589416 AATCTCGAACCCTA
1 AATCTCGAACCTTA
*
5589430 AA-CTTGAACCTTA
1 AATCTCGAACCTTA
5589443 AAT
1 AAT
5589446 TTAAATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.30
Consensus pattern (14 bp):
AATCTCGAACCTTA
Found at i:5591454 original size:18 final size:19
Alignment explanation
Indices: 5591431--5591466 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5591421 CATTTCGATA
*
5591431 TTTAATTTCG-TATTTAAG
1 TTTAATTACGATATTTAAG
5591449 TTTAATTACGATATTTAA
1 TTTAATTACGATATTTAA
5591467 TTTGATGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (19 bp):
TTTAATTACGATATTTAAG
Found at i:5591671 original size:22 final size:22
Alignment explanation
Indices: 5591625--5591706 Score: 101
Period size: 22 Copynumber: 3.5 Consensus size: 22
5591615 AACAAAAGAG
5591625 AAAAACTCAAATATTAAATTGAA
1 AAAAACTCAAATATTAAATT-AA
*
5591648 AAAAACCCAAATATTAAATTAA
1 AAAAACTCAAATATTAAATTAA
* *
5591670 AAAAATTCAAGTATTAAATTAA
1 AAAAACTCAAATATTAAATTAA
5591692 ATATTAAACTCAAAT
1 A-A--AAACTCAAAT
5591707 TCAAGCATCA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.44
23 20 0.40
25 8 0.16
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAAACTCAAATATTAAATTAA
Found at i:5592938 original size:22 final size:22
Alignment explanation
Indices: 5592919--5592981 Score: 94
Period size: 20 Copynumber: 3.0 Consensus size: 22
5592909 TCTTTCAATA
5592919 TTCTCTCAAATTTCTCTCAAAT
1 TTCTCTCAAATTTCTCTCAAAT
5592941 TTCTCTCAAA--TCTCTCAAAT
1 TTCTCTCAAATTTCTCTCAAAT
* *
5592961 TTCTCTTAAATTCCTCTCAAA
1 TTCTCTCAAATTTCTCTCAAA
5592982 ACTCTCATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 19 0.51
22 18 0.49
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (22 bp):
TTCTCTCAAATTTCTCTCAAAT
Found at i:5592947 original size:13 final size:11
Alignment explanation
Indices: 5592919--5592981 Score: 94
Period size: 11 Copynumber: 5.9 Consensus size: 11
5592909 TCTTTCAATA
5592919 TTCTCTCAAAT
1 TTCTCTCAAAT
5592930 TTCTCTCAAAT
1 TTCTCTCAAAT
5592941 TTCTCTCAAA-
1 TTCTCTCAAAT
5592951 -TCTCTCAAAT
1 TTCTCTCAAAT
*
5592961 TTCTCTTAAAT
1 TTCTCTCAAAT
*
5592972 TCCTCTCAAA
1 TTCTCTCAAA
5592982 ACTCTCATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
9 9 0.19
11 38 0.81
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:5592958 original size:31 final size:31
Alignment explanation
Indices: 5592920--5592988 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
5592910 CTTTCAATAT
*
5592920 TCTCTCAAATTTCTCTCAAATTTCTCTCAAA
1 TCTCTCAAATTTCTCTCAAATTCCTCTCAAA
*
5592951 TCTCTCAAATTTCTCTTAAATTCCTCTCAAA
1 TCTCTCAAATTTCTCTCAAATTCCTCTCAAA
*
5592982 ACTCTCA
1 TCTCTCA
5592989 TTAATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.29, C:0.30, G:0.00, T:0.41
Consensus pattern (31 bp):
TCTCTCAAATTTCTCTCAAATTCCTCTCAAA
Found at i:5592994 original size:22 final size:22
Alignment explanation
Indices: 5592920--5592992 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
5592910 CTTTCAATAT
* * **
5592920 TCTCTCAAATTTCTCTCAAATT
1 TCTCTTAAATTCCTCTCAAAAC
* **
5592942 TCTCTCAAA-T-CTCTCAAATT
1 TCTCTTAAATTCCTCTCAAAAC
5592962 TCTCTTAAATTCCTCTCAAAAC
1 TCTCTTAAATTCCTCTCAAAAC
5592984 TCTCATTAA
1 TCTC-TTAA
5592993 TTTTTTCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
20 18 0.40
21 2 0.04
22 21 0.47
23 4 0.09
ACGTcount: A:0.30, C:0.29, G:0.00, T:0.41
Consensus pattern (22 bp):
TCTCTTAAATTCCTCTCAAAAC
Found at i:5593037 original size:16 final size:15
Alignment explanation
Indices: 5593008--5593038 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5592998 TCAAAAAAGC
*
5593008 TCTAATTTTATTTTT
1 TCTAAATTTATTTTT
5593023 TCTAAATTTATTTTT
1 TCTAAATTTATTTTT
5593038 T
1 T
5593039 AAAATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTAAATTTATTTTT
Found at i:5594365 original size:496 final size:496
Alignment explanation
Indices: 5593432--5594424 Score: 1986
Period size: 496 Copynumber: 2.0 Consensus size: 496
5593422 CACTATCTGT
5593432 AACACCCCTTACCCGTATCCAACACCGGAATAGGGTACGAGGCATTACCAAAACACATACACTTG
1 AACACCCCTTACCCGTATCCAACACCGGAATAGGGTACGAGGCATTACCAAAACACATACACTTG
5593497 TAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATTAAAACTTTCAAAATAATTAACATGTT
66 TAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATTAAAACTTTCAAAATAATTAACATGTT
5593562 TCTATAACTTTTCCCAATATATCCTCAAAATATTATAATCATAATAATTAGGGCCTGCGAGACCC
131 TCTATAACTTTTCCCAATATATCCTCAAAATATTATAATCATAATAATTAGGGCCTGCGAGACCC
5593627 GATACATACTCATGCAATTTAATGCTTCATTTCCATTTCATTCAATTCGCAATTTCTCATGCTCA
196 GATACATACTCATGCAATTTAATGCTTCATTTCCATTTCATTCAATTCGCAATTTCTCATGCTCA
5593692 TAATTTAAATCATATCACTAGCAATTTCCATTTAATTCACGTGCAATTCAATGACATCAAATTCA
261 TAATTTAAATCATATCACTAGCAATTTCCATTTAATTCACGTGCAATTCAATGACATCAAATTCA
5593757 AAACTAATACGTATTTACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTAT
326 AAACTAATACGTATTTACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTAT
5593822 GAAATTCTCAATTTAGCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAA
391 GAAATTCTCAATTTAGCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAA
5593887 TACACTACCACTTATCCATTTACTTTAATTCTTTTGGGCCC
456 TACACTACCACTTATCCATTTACTTTAATTCTTTTGGGCCC
5593928 AACACCCCTTACCCGTATCCAACACCGGAATAGGGTACGAGGCATTACCAAAACACATACACTTG
1 AACACCCCTTACCCGTATCCAACACCGGAATAGGGTACGAGGCATTACCAAAACACATACACTTG
5593993 TAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATTAAAACTTTCAAAATAATTAACATGTT
66 TAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATTAAAACTTTCAAAATAATTAACATGTT
5594058 TCTATAACTTTTCCCAATATATCCTCAAAATATTATAATCATAATAATTAGGGCCTGCGAGACCC
131 TCTATAACTTTTCCCAATATATCCTCAAAATATTATAATCATAATAATTAGGGCCTGCGAGACCC
5594123 GATACATACTCATGCAATTTAATGCTTCATTTCCATTTCATTCAATTCGCAATTTCTCATGCTCA
196 GATACATACTCATGCAATTTAATGCTTCATTTCCATTTCATTCAATTCGCAATTTCTCATGCTCA
5594188 TAATTTAAATCATATCACTAGCAATTTCCATTTAATTCACGTGCAATTCAATGACATCAAATTCA
261 TAATTTAAATCATATCACTAGCAATTTCCATTTAATTCACGTGCAATTCAATGACATCAAATTCA
5594253 AAACTAATACGTATTTACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTAT
326 AAACTAATACGTATTTACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTAT
5594318 GAAATTCTCAATTTAGCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAA
391 GAAATTCTCAATTTAGCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAA
5594383 TACACTACCACTTATCCATTTACTTTAATTCTTTTGGGCCC
456 TACACTACCACTTATCCATTTACTTTAATTCTTTTGGGCCC
5594424 A
1 A
5594425 TTTGTCACTT
Statistics
Matches: 497, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
496 497 1.00
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.34
Consensus pattern (496 bp):
AACACCCCTTACCCGTATCCAACACCGGAATAGGGTACGAGGCATTACCAAAACACATACACTTG
TAAACGTATTTAACCGAGTTATAAAATTTCATCAAAATTAAAACTTTCAAAATAATTAACATGTT
TCTATAACTTTTCCCAATATATCCTCAAAATATTATAATCATAATAATTAGGGCCTGCGAGACCC
GATACATACTCATGCAATTTAATGCTTCATTTCCATTTCATTCAATTCGCAATTTCTCATGCTCA
TAATTTAAATCATATCACTAGCAATTTCCATTTAATTCACGTGCAATTCAATGACATCAAATTCA
AAACTAATACGTATTTACCATTTAACTCAATGTTTATTGATTATACCATTCAATAACACATTTAT
GAAATTCTCAATTTAGCAATGAAAATATCACTTTAGTTTGAATAACAACATCGTCCTGATATAAA
TACACTACCACTTATCCATTTACTTTAATTCTTTTGGGCCC
Found at i:5594586 original size:37 final size:37
Alignment explanation
Indices: 5594525--5594744 Score: 381
Period size: 37 Copynumber: 6.0 Consensus size: 37
5594515 TACGTATGAT
* *
5594525 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
5594560 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
5594597 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
5594634 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
5594671 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
5594708 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
5594745 TAAAGCTATC
Statistics
Matches: 176, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
35 9 0.05
36 3 0.02
37 164 0.93
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:5594787 original size:52 final size:52
Alignment explanation
Indices: 5594708--5595074 Score: 461
Period size: 52 Copynumber: 7.2 Consensus size: 52
5594698 TAAGTGTAGC
* * **
5594708 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
5594761 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
5594813 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
5594859 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
5594911 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* * *
5594957 CACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
5595009 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
5595061 CACTTTGTCACTTG
1 CACTTT-TCACTTG
5595075 ATCAGAAGTA
Statistics
Matches: 276, Mismatches: 25, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
46 83 0.30
49 1 0.00
52 177 0.64
53 15 0.05
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:5594874 original size:98 final size:98
Alignment explanation
Indices: 5594708--5595066 Score: 520
Period size: 98 Copynumber: 3.6 Consensus size: 98
5594698 TAAGTGTAGC
* * * *
5594708 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
5594773 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
5594806 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
** *
5594871 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
5594904 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
*
5594969 GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * * *
5595002 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTT
5595067 GTCACTTGAT
Statistics
Matches: 236, Mismatches: 19, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
98 192 0.81
100 1 0.00
104 43 0.18
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:5595075 original size:150 final size:144
Alignment explanation
Indices: 5594719--5595080 Score: 580
Period size: 150 Copynumber: 2.4 Consensus size: 144
5594709 ACTTATCACT
* *
5594719 TTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTTGTCACTTGATC
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC---T---TTGTCACTTGATC
*
5594784 AGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
60 AGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
5594849 TATTACTTATCACTTTCCAC
125 TATTACTTATCACTTTCCAC
5594869 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
*
5594934 GTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGC
66 GTATAGCCGAAGCTATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGC
5594999 TATTACTTATCACTTTCCAC
125 TATTACTTATCACTTTCCAC
5595019 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
5595081 AGTACTCAAA
Statistics
Matches: 202, Mismatches: 4, Indels: 12
0.93 0.02 0.06
Matches are distributed among these distances:
144 43 0.21
146 1 0.00
147 1 0.00
150 157 0.78
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (144 bp):
TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
GTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTAC
TTATCACTTTCCAC
Found at i:5603085 original size:24 final size:24
Alignment explanation
Indices: 5603053--5603100 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5603043 CATTATGTAT
5603053 TTCATCTATTTTAAAACAAATAAA
1 TTCATCTATTTTAAAACAAATAAA
5603077 TTCATCTATTTTAAAACAAATAAA
1 TTCATCTATTTTAAAACAAATAAA
5603101 CGTGTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (24 bp):
TTCATCTATTTTAAAACAAATAAA
Found at i:5604798 original size:43 final size:43
Alignment explanation
Indices: 5604750--5604832 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
5604740 TTTATTTTAA
* *
5604750 TAAGGGTACAACTCCTAAAAGTACAACTCTCTCACCCTTCCAC
1 TAAGGGTACAACTCCTAAAAGTACAACTCCCACACCCTTCCAC
* * *
5604793 TAAGGGTACGACTCCTAAATGTGCAACTCCCACACCCTTC
1 TAAGGGTACAACTCCTAAAAGTACAACTCCCACACCCTTC
5604833 TAAGGATCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.30, C:0.35, G:0.12, T:0.23
Consensus pattern (43 bp):
TAAGGGTACAACTCCTAAAAGTACAACTCCCACACCCTTCCAC
Found at i:5605744 original size:17 final size:18
Alignment explanation
Indices: 5605696--5605733 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5605686 ATGTGGGTAA
5605696 AAAATAAAA--TTAATAT
1 AAAATAAAATTTTAATAT
5605712 AAAATAAAATTTTAATAT
1 AAAATAAAATTTTAATAT
5605730 AAAA
1 AAAA
5605734 GAATTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATAAAATTTTAATAT
Found at i:5607413 original size:15 final size:14
Alignment explanation
Indices: 5607377--5607403 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5607367 TATTAGATTC
5607377 AAAAAATAAATTTT
1 AAAAAATAAATTTT
5607391 AAAAAATAAATTT
1 AAAAAATAAATTT
5607404 ATTTAAAATA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAAATAAATTTT
Found at i:5607551 original size:14 final size:15
Alignment explanation
Indices: 5607534--5607567 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5607524 ATATAACACA
*
5607534 TAAAATATTATT-TT
1 TAAAATAATATTATT
5607548 TAAAATAATATTATT
1 TAAAATAATATTATT
5607563 TAAAA
1 TAAAA
5607568 ATATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAATAATATTATT
Found at i:5607559 original size:17 final size:16
Alignment explanation
Indices: 5607537--5607575 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5607527 TAACACATAA
*
5607537 AATATTATTTTTAAAAT
1 AATATTA-TTTAAAAAT
5607554 AATATTATTTAAAAAT
1 AATATTATTTAAAAAT
5607570 -ATATTA
1 AATATTA
5607576 ATATTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 8 0.38
17 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATTATTTAAAAAT
Found at i:5607573 original size:15 final size:14
Alignment explanation
Indices: 5607534--5607575 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
5607524 ATATAACACA
5607534 TAAAATATTATT-TT
1 TAAAATA-TATTATT
5607548 TAAAATAATATTATT
1 TAAAAT-ATATTATT
5607563 TAAAAATATATTA
1 T-AAAATATATTA
5607576 ATATTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.40
15 10 0.40
16 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAAATATATTATT
Found at i:5610776 original size:38 final size:38
Alignment explanation
Indices: 5610695--5610778 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 38
5610685 GCAACCTCAG
*
5610695 TTTGTGAATACAATTATGATAATTCTTACTAGAGTGCA
1 TTTGTTAATACAATTATGATAATTCTTACTAGAGTGCA
5610733 TTTGTTAATACAATTATGATAATTCTTACTAGAGTGCA
1 TTTGTTAATACAATTATGATAATTCTTACTAGAGTGCA
5610771 TTTGTTAA
1 TTTGTTAA
5610779 GGTTTATAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (38 bp):
TTTGTTAATACAATTATGATAATTCTTACTAGAGTGCA
Found at i:5613144 original size:27 final size:28
Alignment explanation
Indices: 5613098--5613160 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
5613088 CACTAAATAG
*
5613098 TAAAAAT-AAATCATAATTTTTTA-AAA
1 TAAAAATAAAATCATAATTTTCTATAAA
*
5613124 TAAAAATAAAAT-ACTATTTTTCTATAAA
1 TAAAAATAAAATCA-TAATTTTCTATAAA
5613152 -AAAAATAAA
1 TAAAAATAAA
5613161 TTTCCCCCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 8 0.25
27 21 0.66
28 3 0.09
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (28 bp):
TAAAAATAAAATCATAATTTTCTATAAA
Found at i:5616612 original size:79 final size:79
Alignment explanation
Indices: 5616473--5616623 Score: 212
Period size: 79 Copynumber: 1.9 Consensus size: 79
5616463 CTGTAGTAAG
* * * * * *
5616473 AAATGGCACTTCAAGTTAAGCTGCAAAGAGTGAAATGATTACCTAGTCACTAGGGGAAAATGTAT
1 AAATGACACTTCAAGTCAAGCTGCAAAGAGGGAAACGATTACCTAGTCACTAAGGAAAAATGTAT
*
5616538 GGAACTCCTATAAA
66 GAAACTCCTATAAA
** *
5616552 AAATGACACTTCAAGTCAATTTGTAAAGAGGGAAACGATTACCTAGTCACTAAGGAAAAATGTAT
1 AAATGACACTTCAAGTCAAGCTGCAAAGAGGGAAACGATTACCTAGTCACTAAGGAAAAATGTAT
5616617 GAAACTC
66 GAAACTC
5616624 TTTAATATGA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 62 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (79 bp):
AAATGACACTTCAAGTCAAGCTGCAAAGAGGGAAACGATTACCTAGTCACTAAGGAAAAATGTAT
GAAACTCCTATAAA
Found at i:5621574 original size:23 final size:19
Alignment explanation
Indices: 5621528--5621565 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5621518 ATAAAGAACG
5621528 ATTAGTCTGAATTTAAACA
1 ATTAGTCTGAATTTAAACA
5621547 ATTAGTCTGAATTTAAACA
1 ATTAGTCTGAATTTAAACA
5621566 TAAAATTAGA
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:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
ATTAGTCTGAATTTAAACA
Found at i:5624561 original size:60 final size:60
Alignment explanation
Indices: 5624468--5624588 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
5624458 ACTGACTATG
5624468 GACTCGATCATCTTTAGAGCATAAGCCTCCACTTATATCAAAGCACCATGAGTTATATAT
1 GACTCGATCATCTTTAGAGCATAAGCCTCCACTTATATCAAAGCACCATGAGTTATATAT
5624528 GACTCGATCATCTTTAGAGCATAAGCCTCCACTTATATCAAAGCACCATGAGTTATATAT
1 GACTCGATCATCTTTAGAGCATAAGCCTCCACTTATATCAAAGCACCATGAGTTATATAT
5624588 G
1 G
5624589 CATGGCCAGT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (60 bp):
GACTCGATCATCTTTAGAGCATAAGCCTCCACTTATATCAAAGCACCATGAGTTATATAT
Found at i:5625195 original size:19 final size:19
Alignment explanation
Indices: 5625152--5625188 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5625142 TATTAAAAAT
*
5625152 AATTTTTTATAATATTTAA
1 AATTTTTGATAATATTTAA
5625171 AATTTTTGATAAT-TTTAA
1 AATTTTTGATAATATTTAA
5625189 TGATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
AATTTTTGATAATATTTAA
Found at i:5629935 original size:128 final size:129
Alignment explanation
Indices: 5629702--5629937 Score: 393
Period size: 128 Copynumber: 1.8 Consensus size: 129
5629692 AAATTCCTTA
* * *
5629702 AAACGAAGGCAATATTTGATGCTTGGAAATTCGGGGAATCGTGCCTTATCGTGCTGGGTTTCGAT
1 AAACGAAGGCAATATTTGATACTTGAAAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTTCGAT
5629767 TTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTTGTGTTTTTCTAAATTCTG
66 TTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTTGTGTTTTTCTAAATTCTG
* * *
5629831 AAAC-AAGGCAATGTTTGATATTTGAAAATTCGGGGAATCGTGCCCTATTGTGCTGGGTTTCGAT
1 AAACGAAGGCAATATTTGATACTTGAAAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTTCGAT
* *
5629895 TTCTCGTTTGTTCAAAATAATCGAATATTCTTTTAGAATTTCA
66 TTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCA
5629938 TTCGTATTCT
Statistics
Matches: 99, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
128 95 0.96
129 4 0.04
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (129 bp):
AAACGAAGGCAATATTTGATACTTGAAAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTTCGAT
TTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTCACTTGTGTTTTTCTAAATTCTG
Found at i:5630029 original size:127 final size:128
Alignment explanation
Indices: 5629728--5630018 Score: 379
Period size: 128 Copynumber: 2.3 Consensus size: 128
5629718 TGATGCTTGG
* * *
5629728 AAATTCGGGGAATCGTGCCTTATCGTGCTGGGTTTCGATTTCCCGTTTGTTCAAAATAATCGAAT
1 AAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCGATTTCTCGTTTGTTCAAAATAATCGAAT
* * * * **
5629793 ATTCCTTTAGAATTTCACTTGTGTTTTTCTAAATTCTGAAACAAGGCAATGTTTGATATTTGA
66 ATTCCTTTAGAATTTCACTTGTATTCTTCTAAATTCTAAAACAAAGCAATGTTCAATATTTGA
* *
5629856 AAATTCGGGGAATCGTGCCCTATTGTGCTGGGTTTCGATTTCTCGTTTGTTCAAAATAATCGAAT
1 AAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCGATTTCTCGTTTGTTCAAAATAATCGAAT
* * * * *
5629921 ATTCTTTTAGAATTTCA-TTCGTATTCTT-TAAATTTTAAAATAAAGCAATGTTCAATGTTTGG
66 ATTCCTTTAGAATTTCACTT-GTATTCTTCTAAATTCTAAAACAAAGCAATGTTCAATATTTGA
* * * *
5629983 AAGTTTGAGGAATCGTGCCCTACCGTGTTGGGTTTC
1 AAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTC
5630019 AGTTTTTCGT
Statistics
Matches: 142, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
127 58 0.41
128 84 0.59
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (128 bp):
AAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCGATTTCTCGTTTGTTCAAAATAATCGAAT
ATTCCTTTAGAATTTCACTTGTATTCTTCTAAATTCTAAAACAAAGCAATGTTCAATATTTGA
Found at i:5633021 original size:3 final size:3
Alignment explanation
Indices: 5633010--5633097 Score: 72
Period size: 3 Copynumber: 29.3 Consensus size: 3
5633000 ATTATTTTGT
* *
5633010 TTA TT- TTA TTA TTA TTA TTA TTA TTTA CTA TTA TTA TCT- TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA
* * * * * *
5633055 TTA TTG TTA GTA TTA TTA CTA CTA TTA TTA TTA CTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5633098 ATTTATACCT
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
2 3 0.04
3 60 0.90
4 4 0.06
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5633030 original size:12 final size:12
Alignment explanation
Indices: 5633015--5633097 Score: 85
Period size: 12 Copynumber: 6.6 Consensus size: 12
5633005 TTTGTTTATT
*
5633015 TTATTATTATTA
1 TTATTATTACTA
5633027 TTATTATTTACTA
1 TTATTA-TTACTA
5633040 TTATTATCTTTACTA
1 TTATTA---TTACTA
* *
5633055 TTATTGTTAGTA
1 TTATTATTACTA
*
5633067 TTATTACTACTA
1 TTATTATTACTA
5633079 TTATTATTACTA
1 TTATTATTACTA
*
5633091 TCATTAT
1 TTATTAT
5633098 ATTTATACCT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
12 37 0.62
13 11 0.18
15 12 0.20
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.59
Consensus pattern (12 bp):
TTATTATTACTA
Found at i:5633409 original size:6 final size:6
Alignment explanation
Indices: 5633398--5633440 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
5633388 AATATCACTA
*
5633398 TTTATT TTTA-T TTTA-T TTTATT TTTATT TGTTATT ATTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT T-TTATT TTTATT TT
5633441 CAAATTTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 10 0.30
6 18 0.55
7 5 0.15
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:5633419 original size:16 final size:18
Alignment explanation
Indices: 5633398--5633440 Score: 63
Period size: 16 Copynumber: 2.4 Consensus size: 18
5633388 AATATCACTA
5633398 TTTATTTTTA-TT-TTAT
1 TTTATTTTTATTTGTTAT
5633414 TTTATTTTTATTTGTTAT
1 TTTATTTTTATTTGTTAT
5633432 TATTATTTT
1 T-TTATTTT
5633441 CAAATTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.42
17 2 0.08
18 5 0.21
19 7 0.29
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTATTTTTATTTGTTAT
Found at i:5650248 original size:132 final size:133
Alignment explanation
Indices: 5650076--5650376 Score: 364
Period size: 132 Copynumber: 2.3 Consensus size: 133
5650066 TTGAATTTCT
* * * *
5650076 AAACATCGAGCATTGCCTT-GTTTTATAGAATTTTTAAG-AAACATGAGGGAAATTCTAAAGGGG
1 AAACATCGAACATTGCCTTCGTTTTAAAGAATTTTTAAGAAAACATGAAGGAAATTCCAAA-GGG
** *
5650139 ATGTTCGATTATTTTGAACCAATA-G-GAAATTGCAACCCAGCACGATAGGGCACAATTCCCCGA
65 ACATTCGATTATTTTGAA-CAA-ACGAGAAATTGCAACCCAGCACGATAGGGCACAATTCCACGA
5650202 ATTGCC
128 ATTGCC
* * *
5650208 AAACATCGAACATTACCTTCGTTTTAAAGAGTTTTT-AGAAAACATGAATGAAATTCCAAAGGGA
1 AAACATCGAACATTGCCTTCGTTTTAAAGAATTTTTAAGAAAACATGAAGGAAATTCCAAAGGGA
* * * *
5650272 CATTCGATTGTTTTGAACAAACGAGAAATTGCAACCTAGCACGTTAGGGCACGATTCCACGAATT
66 CATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAGCACGATAGGGCACAATTCCACGAATT
5650337 GCC
131 GCC
*
5650340 AAATATC-AA-ATCTCGCCTTCGTTTTTAAAGAATTTTT
1 AAACATCGAACAT-T-GCCTTCG-TTTTAAAGAATTTTT
5650377 GAACGAATAA
Statistics
Matches: 145, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
130 3 0.02
131 7 0.05
132 89 0.61
133 46 0.32
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (133 bp):
AAACATCGAACATTGCCTTCGTTTTAAAGAATTTTTAAGAAAACATGAAGGAAATTCCAAAGGGA
CATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAGCACGATAGGGCACAATTCCACGAATT
GCC
Found at i:5661317 original size:18 final size:18
Alignment explanation
Indices: 5661291--5661365 Score: 114
Period size: 18 Copynumber: 4.2 Consensus size: 18
5661281 TACGACCGTT
5661291 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
5661309 TACGATACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
5661327 TATGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
5661345 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
5661363 TAC
1 TAC
5661366 AGTAGTTGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:5666409 original size:2 final size:2
Alignment explanation
Indices: 5666402--5666443 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
5666392 TCCAAAGTGT
*
5666402 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5666444 GAAGTGTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5669681 original size:20 final size:20
Alignment explanation
Indices: 5669656--5669695 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5669646 TAACATGTGC
5669656 ATAATACGA-TATTAAAAAAT
1 ATAATA-GAGTATTAAAAAAT
*
5669676 ATAATATAGTATTAAAAAAT
1 ATAATAGAGTATTAAAAAAT
5669696 GTATACATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAATAGAGTATTAAAAAAT
Found at i:5669705 original size:21 final size:20
Alignment explanation
Indices: 5669665--5669708 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5669655 CATAATACGA
*
5669665 TATTAAAAAATATAATATAG
1 TATTAAAAAATATAACATAG
*
5669685 TATTAAAAAATGTATACATAG
1 TATTAAAAAATATA-ACATAG
5669706 TAT
1 TAT
5669709 ATATACTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (20 bp):
TATTAAAAAATATAACATAG
Found at i:5669828 original size:24 final size:25
Alignment explanation
Indices: 5669780--5669831 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
5669770 ATAGTAATAG
* *
5669780 TATATACATAATATAGTTATTAAAAA
1 TATATACATAACATAG-TATGAAAAA
5669806 TATATACATAACATA-TATGAAAAA
1 TATATACATAACATAGTATGAAAAA
5669830 TA
1 TA
5669832 CAATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 10 0.42
26 14 0.58
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (25 bp):
TATATACATAACATAGTATGAAAAA
Found at i:5669939 original size:21 final size:22
Alignment explanation
Indices: 5669915--5670000 Score: 56
Period size: 21 Copynumber: 4.0 Consensus size: 22
5669905 ATGATATTAC
*
5669915 ATAAATATATACAT-ATATATT
1 ATAAATATATACATAACATATT
5669936 ATAAATGA-ATACATGATA-ATATT
1 ATAAAT-ATATACAT-A-ACATATT
* *
5669959 A-AAAGTATGTACATAACATATA
1 ATAAA-TATATACATAACATATT
* *
5669981 AAAAATATATATAT-ACATAT
1 ATAAATATATACATAACATAT
5670001 ATACACATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
21 19 0.36
22 18 0.34
23 15 0.28
24 1 0.02
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.35
Consensus pattern (22 bp):
ATAAATATATACATAACATATT
Found at i:5669984 original size:22 final size:21
Alignment explanation
Indices: 5669917--5670001 Score: 55
Period size: 22 Copynumber: 3.9 Consensus size: 21
5669907 GATATTACAT
* * *
5669917 AAATATATACATATATATTAT
1 AAATATATACATACATATAAA
* *
5669938 AAATGA-ATACATGATAATATTAA
1 AAAT-ATATACAT-A-CATATAAA
* *
5669961 AAGTATGTACATAACATATAAA
1 AAATATATACAT-ACATATAAA
*
5669983 AAATATATATATACATATA
1 AAATATATACATACATATA
5670002 TACACATAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
21 17 0.34
22 18 0.36
23 15 0.30
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATATATACATACATATAAA
Found at i:5670059 original size:37 final size:37
Alignment explanation
Indices: 5669982--5670060 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 37
5669972 TAACATATAA
*
5669982 AAAATATATATATACATATATACACATAATATAGTGTT
1 AAAATATATACATACATATATACACATAATATA-TGTT
* *
5670020 AAAATATTTACATA-ATATATACATATAAGTAT-TGATT
1 AAAATATATACATACATATATACACATAA-TATATG-TT
5670057 AAAA
1 AAAA
5670061 AATAATACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
36 2 0.06
37 19 0.53
38 15 0.42
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (37 bp):
AAAATATATACATACATATATACACATAATATATGTT
Found at i:5670201 original size:16 final size:17
Alignment explanation
Indices: 5670182--5670216 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5670172 TTAGTAACGT
*
5670182 TATATATA-TGTAAACA
1 TATATATATTGAAAACA
5670198 TATATATATTGAAAACA
1 TATATATATTGAAAACA
5670215 TA
1 TA
5670217 CATACATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (17 bp):
TATATATATTGAAAACA
Found at i:5670409 original size:24 final size:24
Alignment explanation
Indices: 5670331--5670468 Score: 74
Period size: 24 Copynumber: 5.7 Consensus size: 24
5670321 CATTAGACAC
* *
5670331 ATATATATAT-ATGATAACATAAAA
1 ATATATACATAAT-ATAATATAAAA
* *
5670355 ATATATA-ACTAATA-ATATTTAAGA
1 ATATATACA-TAATATA-ATATAAAA
*
5670379 ATGTATACATAATATAATATAAAAA
1 ATATATACATAATATAATAT-AAAA
* *
5670404 TATATATACGTAATATAGA-ATTTAAA
1 -ATATATACATAATATA-ATA-TAAAA
*
5670430 ATATAT--ATAATATATTA-AAAGA
1 ATATATACATAATATAATATAAA-A
*
5670452 ATATATACATATTATAA
1 ATATATACATAATATAA
5670469 AGTTAAGAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
21 2 0.02
22 7 0.08
23 10 0.11
24 35 0.40
25 13 0.15
26 18 0.21
27 2 0.02
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (24 bp):
ATATATACATAATATAATATAAAA
Found at i:5670580 original size:22 final size:22
Alignment explanation
Indices: 5670561--5670617 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
5670551 ATACTAATGC
5670561 TAATAAATAAT-AAATATAATAA
1 TAAT-AATAATAAAATATAATAA
* *
5670583 TAATAGTAATAAAATATAATAG
1 TAATAATAATAAAATATAATAA
5670605 TATATATATAATA
1 TA-ATA-ATAATA
5670618 TTAAAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 5 0.17
22 16 0.55
23 3 0.10
24 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (22 bp):
TAATAATAATAAAATATAATAA
Found at i:5670617 original size:19 final size:18
Alignment explanation
Indices: 5670561--5670618 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 18
5670551 ATACTAATGC
*
5670561 TAATA-AATAATAA-ATA
1 TAATATAATAGTAATATA
5670577 TAATAATAATAGTAATA-A
1 TAAT-ATAATAGTAATATA
5670595 -AATATAATAGTATATATA
1 TAATATAATAGTA-ATATA
5670613 TAATAT
1 TAATAT
5670619 TAAAATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 13 0.37
17 7 0.20
18 9 0.26
19 6 0.17
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TAATATAATAGTAATATA
Found at i:5672243 original size:16 final size:16
Alignment explanation
Indices: 5672222--5672278 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
5672212 TATTTCTTCC
5672222 AAAAATTCTAAATTCT
1 AAAAATTCTAAATTCT
5672238 AAAAATTC-AAA---T
1 AAAAATTCTAAATTCT
*
5672250 AAGAAAATCTAAATTTCT
1 AA-AAATTCTAAA-TTCT
5672268 AAAAATT-TAAA
1 AAAAATTCTAAA
5672279 ACTTTATTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
12 3 0.09
13 5 0.15
14 3 0.09
15 3 0.09
16 12 0.36
17 4 0.12
18 3 0.09
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.32
Consensus pattern (16 bp):
AAAAATTCTAAATTCT
Found at i:5672455 original size:17 final size:18
Alignment explanation
Indices: 5672430--5672467 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5672420 TCAAAAGTTA
*
5672430 TATACTTTTTT-AATTCT
1 TATAATTTTTTCAATTCT
*
5672447 TATAATTTTTTCAATTTT
1 TATAATTTTTTCAATTCT
5672465 TAT
1 TAT
5672468 CTAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (18 bp):
TATAATTTTTTCAATTCT
Found at i:5672502 original size:28 final size:29
Alignment explanation
Indices: 5672450--5672505 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
5672440 TAATTCTTAT
*
5672450 AATTTTTTCAATTTTTATCTAATATTTTG
1 AATTTTTTCAATTTATATCTAATATTTTG
5672479 AATTTTTT-AATTTATAT-TATATATTTT
1 AATTTTTTCAATTTATATCTA-ATATTTT
5672506 ATCATTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 2 0.08
28 15 0.60
29 8 0.32
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (29 bp):
AATTTTTTCAATTTATATCTAATATTTTG
Found at i:5674362 original size:21 final size:23
Alignment explanation
Indices: 5674319--5674362 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5674309 TGATGGAGTT
5674319 ATAAATATTATTTTTACAAAGTA
1 ATAAATATTATTTTTACAAAGTA
5674342 ATAAATATTA-TTTTA-AAAGTA
1 ATAAATATTATTTTTACAAAGTA
5674363 TTTTTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 5 0.24
23 10 0.48
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (23 bp):
ATAAATATTATTTTTACAAAGTA
Found at i:5675029 original size:18 final size:19
Alignment explanation
Indices: 5675001--5675036 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5674991 TGAAATTTCA
5675001 ATTGAAATCGAATTAATTG
1 ATTGAAATCGAATTAATTG
*
5675020 ATTG-AATCGATTTAATT
1 ATTGAAATCGAATTAATT
5675037 CGGTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.42
Consensus pattern (19 bp):
ATTGAAATCGAATTAATTG
Found at i:5676400 original size:29 final size:29
Alignment explanation
Indices: 5676348--5676407 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
5676338 TTAATTTTCA
5676348 TTTTAAATAAAAATAAAAATAATTAAATT
1 TTTTAAATAAAAATAAAAATAATTAAATT
* *
5676377 TTTTGAAATAAAAGTAGAAA-AATTAAATT
1 TTTT-AAATAAAAATAAAAATAATTAAATT
5676406 TT
1 TT
5676408 ATATATGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (29 bp):
TTTTAAATAAAAATAAAAATAATTAAATT
Found at i:5684792 original size:18 final size:18
Alignment explanation
Indices: 5684771--5684815 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
5684761 ACCAATATGT
* * *
5684771 GGCCCAATACCATTCTTC
1 GGCCCAATACCACTATTA
*
5684789 GGCCCAACACCACTATTA
1 GGCCCAATACCACTATTA
5684807 GGCCCAATA
1 GGCCCAATA
5684816 GTACCATCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.38, G:0.13, T:0.20
Consensus pattern (18 bp):
GGCCCAATACCACTATTA
Found at i:5685001 original size:18 final size:17
Alignment explanation
Indices: 5684978--5685023 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
5684968 AGCATACCAC
*
5684978 TTTTGACCACAATCATAA
1 TTTTGACCACAA-AATAA
5684996 TTTTGACCAGCAAAATAA
1 TTTTGACCA-CAAAATAA
*
5685014 TTCTGACCAC
1 TTTTGACCAC
5685024 TTCCATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 21 0.84
19 3 0.12
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (17 bp):
TTTTGACCACAAAATAA
Found at i:5685055 original size:21 final size:21
Alignment explanation
Indices: 5685006--5685065 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
5684996 TTTTGACCAG
* *
5685006 CAAAATAATTCTGACCACTTC
1 CAAAATAATTTTGACCATTTC
** *
5685027 CATTATAATTTTGACCATTTT
1 CAAAATAATTTTGACCATTTC
5685048 CAAAATAATTTTGACCAT
1 CAAAATAATTTTGACCAT
5685066 GGTTAGAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (21 bp):
CAAAATAATTTTGACCATTTC
Found at i:5701430 original size:21 final size:21
Alignment explanation
Indices: 5701404--5701444 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5701394 AGACGAGCAA
* *
5701404 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5701425 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
5701445 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5705245 original size:17 final size:17
Alignment explanation
Indices: 5705196--5705247 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
5705186 TCAACTGTTT
*
5705196 ATAAAATATATTTTTTA
1 ATAAAATATATATTTTA
*
5705213 ATAAAATATATTTTTTA
1 ATAAAATATATATTTTA
* *
5705230 ATGAAATATGTATTTTA
1 ATAAAATATATATTTTA
5705247 A
1 A
5705248 CAAGTTTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
ATAAAATATATATTTTA
Found at i:5705245 original size:19 final size:17
Alignment explanation
Indices: 5705196--5705238 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
5705186 TCAACTGTTT
5705196 ATAAAATATATTTTTTA
1 ATAAAATATATTTTTTA
5705213 ATAAAATATATTTTTTA
1 ATAAAATATATTTTTTA
*
5705230 ATGAAATAT
1 ATAAAATAT
5705239 GTATTTTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
ATAAAATATATTTTTTA
Found at i:5705702 original size:22 final size:22
Alignment explanation
Indices: 5705677--5705728 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
5705667 GTCATACCGT
5705677 TGCCAATCGTCCATATCTAAAG
1 TGCCAATCGTCCATATCTAAAG
*
5705699 TGCCAATCGTCCATATCTGAAG
1 TGCCAATCGTCCATATCTAAAG
*
5705721 TACCAATC
1 TGCCAATC
5705729 CCTTCCACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (22 bp):
TGCCAATCGTCCATATCTAAAG
Found at i:5711400 original size:46 final size:46
Alignment explanation
Indices: 5711350--5711525 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
5711340 TGGTTGAGCA
*
5711350 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
5711396 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
5711443 TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
5711489 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5711526 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 63 0.58
47 28 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:5711506 original size:93 final size:93
Alignment explanation
Indices: 5711347--5711518 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
5711337 GGATGGTTGA
* * *
5711347 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
5711412 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
5711440 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
5711505 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
5711519 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:5716793 original size:10 final size:10
Alignment explanation
Indices: 5716772--5716850 Score: 51
Period size: 10 Copynumber: 7.8 Consensus size: 10
5716762 CAACCCAATC
5716772 TTTATTTTTA
1 TTTATTTTTA
5716782 TTT-TTATTTA
1 TTTATT-TTTA
*
5716792 -TTATTTTTC
1 TTTATTTTTA
*
5716801 TTTCTTTTCT-
1 TTTATTTT-TA
5716811 TTTATTATTTA
1 TTTATT-TTTA
5716822 -TTATTTATTA
1 TTTATTT-TTA
5716832 TTT-TATTTTA
1 TTTAT-TTTTA
5716842 TTTTATTTT
1 -TTTATTTT
5716851 AGTTAAATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 21
0.70 0.04 0.27
Matches are distributed among these distances:
9 8 0.15
10 33 0.60
11 13 0.24
12 1 0.02
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:5716851 original size:37 final size:36
Alignment explanation
Indices: 5716772--5716851 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 36
5716762 CAACCCAATC
*
5716772 TTTA-TTT-TTATTTTTATTTATTATTTTTCTTTCT
1 TTTATTTTATTATTTTTATTTATTATTTTTCTTTAT
*
5716806 TTTCTTTTATTATTTATTATTTATTATTTTAT-TTTAT
1 TTTATTTTATTATTT-TTATTTATTATTTT-TCTTTAT
5716843 TTTATTTTA
1 TTTATTTTA
5716852 GTTAAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
34 3 0.08
35 3 0.08
36 6 0.15
37 26 0.67
38 1 0.03
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (36 bp):
TTTATTTTATTATTTTTATTTATTATTTTTCTTTAT
Found at i:5717976 original size:118 final size:118
Alignment explanation
Indices: 5717768--5718003 Score: 445
Period size: 118 Copynumber: 2.0 Consensus size: 118
5717758 TGTTTTCCAT
*
5717768 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGCCATT
1 GGTTATGAGTACAGCTTAGATCGTAACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGCCATT
*
5717833 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAACCGA
*
5717886 GGTTATGAGTACAGCTTAGATCGTAACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTTAGATCGTAACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGCCATT
5717951 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAACCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAACCGA
5718004 AAATAAATAA
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 115 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (118 bp):
GGTTATGAGTACAGCTTAGATCGTAACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGCCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAACCGA
Found at i:5718146 original size:19 final size:19
Alignment explanation
Indices: 5718111--5718147 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5718101 GTAAATAAAT
**
5718111 AATAAAAAAATTTAAAAAA
1 AATAAAAAAATCAAAAAAA
5718130 AATAAAAAAATCAAAAAA
1 AATAAAAAAATCAAAAAA
5718148 GGGAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (19 bp):
AATAAAAAAATCAAAAAAA
Found at i:5719956 original size:70 final size:69
Alignment explanation
Indices: 5719846--5719977 Score: 210
Period size: 70 Copynumber: 1.9 Consensus size: 69
5719836 ATTGAAATAC
* * *
5719846 CATACCTACATTTCATACTCGGTATGGAAAATACCATACCTACGTTTCGCAACTCGGTATGGGAA
1 CATACCTACATTTCATACTCAGTATGGAAAATACCATACCTACATTTCACAACTCGGTATGGGAA
5719911 ATGT
66 ATGT
* *
5719915 CATACCTACATTTCTTAACTCAGTATGGATAATACCATACCTACATTTCACAACTCGGTATGG
1 CATACCTACATTTCAT-ACTCAGTATGGAAAATACCATACCTACATTTCACAACTCGGTATGG
5719978 ATGATCACAA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
69 15 0.26
70 42 0.74
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (69 bp):
CATACCTACATTTCATACTCAGTATGGAAAATACCATACCTACATTTCACAACTCGGTATGGGAA
ATGT
Found at i:5719978 original size:35 final size:35
Alignment explanation
Indices: 5719841--5719979 Score: 174
Period size: 35 Copynumber: 4.0 Consensus size: 35
5719831 TCCTCATTGA
* *
5719841 AATACCATACCTACATTTCA-TACTCGGTATGGAA
1 AATACCATACCTACATTTCACAACTCGGTATGGAT
* *
5719875 AATACCATACCTACGTTTCGCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCGGTAT-GGAT
** ** *
5719910 AATGTCATACCTACATTTCTTAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCGGTATGGAT
5719945 AATACCATACCTACATTTCACAACTCGGTATGGAT
1 AATACCATACCTACATTTCACAACTCGGTATGGAT
5719980 GATCACAACT
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
34 21 0.24
35 64 0.73
36 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCGGTATGGAT
Found at i:5719987 original size:20 final size:20
Alignment explanation
Indices: 5719962--5720002 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5719952 TACCTACATT
5719962 TCACAACTCGGTATGGATGA
1 TCACAACTCGGTATGGATGA
5719982 TCACAACTCGGTATGGATGA
1 TCACAACTCGGTATGGATGA
5720002 T
1 T
5720003 ACCATACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (20 bp):
TCACAACTCGGTATGGATGA
Found at i:5722200 original size:20 final size:20
Alignment explanation
Indices: 5722177--5722216 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5722167 TTATTCAAAC
5722177 AATATTACT-TGAATAATTAT
1 AATATTA-TATGAATAATTAT
5722197 AATATTATATGAATAATTAT
1 AATATTATATGAATAATTAT
5722217 GTCTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
AATATTATATGAATAATTAT
Found at i:5732210 original size:17 final size:17
Alignment explanation
Indices: 5732185--5732217 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5732175 TTGTTGAAGA
5732185 ATCTATTTGGATTTTGC
1 ATCTATTTGGATTTTGC
*
5732202 ATCTGTTTGGATTTTG
1 ATCTATTTGGATTTTG
5732218 TATCAGTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.21, T:0.55
Consensus pattern (17 bp):
ATCTATTTGGATTTTGC
Found at i:5735522 original size:11 final size:11
Alignment explanation
Indices: 5735495--5735547 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
5735485 TGACCTTTCC
5735495 AAGGTATGGG-
1 AAGGTATGGGA
*
5735505 TAGGTATGGGA
1 AAGGTATGGGA
5735516 AAGGTATGGGCA
1 AAGGTATGGG-A
*
5735528 AA-GTATGGGC
1 AAGGTATGGGA
*
5735538 AAGGAATGGG
1 AAGGTATGGG
5735548 TATATTCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 11 0.31
11 22 0.61
12 3 0.08
ACGTcount: A:0.32, C:0.04, G:0.45, T:0.19
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:5739639 original size:18 final size:18
Alignment explanation
Indices: 5739592--5739648 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
5739582 CCCAACTATT
* * *
5739592 GTATACGTGAACAGTATC
1 GTATACATGAATAGTGTC
*
5739610 GTATATATGAATAGTGTC
1 GTATACATGAATAGTGTC
*
5739628 GTATACATGAATAGTGCC
1 GTATACATGAATAGTGTC
5739646 GTA
1 GTA
5739649 AATGGTCGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (18 bp):
GTATACATGAATAGTGTC
Found at i:5740208 original size:21 final size:22
Alignment explanation
Indices: 5740182--5740239 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
5740172 TGACCTTTCC
*
5740182 AAGGTATGGG-TAGGTATGGGA
1 AAGGTATGGGCAAGGTATGGGA
5740203 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGGCAAGGTATGGGA
*
5740225 AAGGTATGGGGAAGG
1 AAGGTATGGGCAAGG
5740240 AATAGGTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 10 0.29
22 24 0.71
ACGTcount: A:0.31, C:0.02, G:0.48, T:0.19
Consensus pattern (22 bp):
AAGGTATGGGCAAGGTATGGGA
Found at i:5740209 original size:11 final size:11
Alignment explanation
Indices: 5740182--5740239 Score: 82
Period size: 11 Copynumber: 5.4 Consensus size: 11
5740172 TGACCTTTCC
5740182 AAGGTATGGG-
1 AAGGTATGGGA
*
5740192 TAGGTATGGGA
1 AAGGTATGGGA
*
5740203 AAGGTATGGGC
1 AAGGTATGGGA
5740214 AAGGTATGGGA
1 AAGGTATGGGA
*
5740225 AAGGTATGGGG
1 AAGGTATGGGA
5740236 AAGG
1 AAGG
5740240 AATAGGTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
10 9 0.21
11 33 0.79
ACGTcount: A:0.31, C:0.02, G:0.48, T:0.19
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:5740907 original size:29 final size:29
Alignment explanation
Indices: 5740861--5740917 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
5740851 TTTAATGTGG
* *
5740861 TGTAATATTAGTTATGCACTTGGACAATA
1 TGTAATAATAATTATGCACTTGGACAATA
*
5740890 TGTAATAATAATTGTGCACTTGGACAAT
1 TGTAATAATAATTATGCACTTGGACAAT
5740918 GTTGTTATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (29 bp):
TGTAATAATAATTATGCACTTGGACAATA
Found at i:5741895 original size:3 final size:3
Alignment explanation
Indices: 5741887--5741914 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5741877 TTTTGATGCT
5741887 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5741915 AAATGATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5742675 original size:16 final size:16
Alignment explanation
Indices: 5742648--5742701 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
5742638 CGACACCAAT
5742648 GTATATATTTATTTATA
1 GTATA-ATTTATTTATA
* *
5742665 GTATAATTTATTTTTT
1 GTATAATTTATTTATA
*
5742681 GGATAATTTATTTATA
1 GTATAATTTATTTATA
5742697 GTATA
1 GTATA
5742702 GGGTGTATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
16 26 0.84
17 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.57
Consensus pattern (16 bp):
GTATAATTTATTTATA
Found at i:5749207 original size:24 final size:23
Alignment explanation
Indices: 5749155--5749210 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
5749145 TGAAACCTTT
*
5749155 ACTAAAATTAAGTTCATTAATAA
1 ACTAAAATTAAGTTAATTAATAA
* * *
5749178 AATAAAATTTATTTAATTAAATAA
1 ACTAAAATTAAGTTAATT-AATAA
5749202 ACTAAAATT
1 ACTAAAATT
5749211 GTATATTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (23 bp):
ACTAAAATTAAGTTAATTAATAA
Found at i:5750142 original size:59 final size:58
Alignment explanation
Indices: 5750032--5750173 Score: 149
Period size: 59 Copynumber: 2.4 Consensus size: 58
5750022 TTTTGATTTC
* * * * * *
5750032 ATTTTATTATTATATTACTACTATTTTGTTGTTATTATTTGGGTATTGTATAATTCTT
1 ATTTTATTATTATATTACTACCATATTGTTGTTATTATTTAGATATAGTATAACTCTT
** *
5750090 ATTTTATTATTAATATTGTTACCATATTGTTGTTATTGTTTAGATATAGTATAACTCTT
1 ATTTTATTATT-ATATTACTACCATATTGTTGTTATTATTTAGATATAGTATAACTCTT
* * * *
5750149 GTTATATTACTAAATTTACTACCAT
1 ATTTTATTATTATA-TTACTACCAT
5750174 TTTATAGGCA
Statistics
Matches: 67, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
58 13 0.19
59 54 0.81
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (58 bp):
ATTTTATTATTATATTACTACCATATTGTTGTTATTATTTAGATATAGTATAACTCTT
Found at i:5753927 original size:30 final size:31
Alignment explanation
Indices: 5753872--5753929 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
5753862 AAATTTTAAA
*
5753872 ATTCGAAAAGAATAGGGACTAAAATTGACTG
1 ATTCGAAAAGAACAGGGACTAAAATTGACTG
* *
5753903 ATTCGAAAAGTACATGGA-TAAAATTGA
1 ATTCGAAAAGAACAGGGACTAAAATTGA
5753930 TCAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (31 bp):
ATTCGAAAAGAACAGGGACTAAAATTGACTG
Found at i:5755561 original size:11 final size:10
Alignment explanation
Indices: 5755533--5755588 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 10
5755523 TCTCAACAAA
5755533 AATTTAAAAT
1 AATTTAAAAT
5755543 AA-TTAAAAT
1 AATTTAAAAT
5755552 AATTTTAAAAT
1 AA-TTTAAAAT
5755563 --TTTAAAAT
1 AATTTAAAAT
5755571 -ATTTATAAA-
1 AATTTA-AAAT
5755580 AATTCTAAA
1 AATT-TAAA
5755589 TTTTATATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
8 8 0.20
9 13 0.32
10 10 0.25
11 9 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:5755566 original size:28 final size:28
Alignment explanation
Indices: 5755530--5755593 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
5755520 TTCTCTCAAC
* *
5755530 AAAAATTTAAAATAATTA-AAATAATTTT
1 AAAATTTTAAAATAATTATAAA-AATTCT
*
5755558 AAAATTTTAAAATATTTATAAAAATTCT
1 AAAATTTTAAAATAATTATAAAAATTCT
5755586 -AAATTTTA
1 AAAATTTTA
5755594 TATTTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 8 0.25
28 21 0.66
29 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAATTTTAAAATAATTATAAAAATTCT
Found at i:5755567 original size:19 final size:19
Alignment explanation
Indices: 5755535--5755580 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5755525 TCAACAAAAA
5755535 TTTAAAATAATTAAAATAAT
1 TTTAAAATAATTAAAAT-AT
*
5755555 TTTAAAAT-TTTAAAATAT
1 TTTAAAATAATTAAAATAT
5755573 TTATAAAA
1 TT-TAAAA
5755581 ATTCTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 12 0.50
20 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAAAATAATTAAAATAT
Found at i:5757217 original size:38 final size:37
Alignment explanation
Indices: 5757125--5757217 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 37
5757115 GTTTTCTTTT
*
5757125 AATTTTAATATTTTTTTACAATGTTTTATAATTTCGAA
1 AATTTTAATA-TTTTTTACAATATTTTATAATTTCGAA
* * * *
5757163 AAATTTAATAACTTTTTACAATATTTTATAGTTTCTAA
1 AATTTTAAT-ATTTTTTACAATATTTTATAATTTCGAA
* *
5757201 TCATTTTTATATTTTTT
1 -AATTTTAATATTTTTT
5757218 GATATTTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
38 37 0.84
39 7 0.16
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.57
Consensus pattern (37 bp):
AATTTTAATATTTTTTACAATATTTTATAATTTCGAA
Found at i:5757714 original size:11 final size:11
Alignment explanation
Indices: 5757693--5757723 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
5757683 TTTATAAAAA
5757693 TTATATTTTTTT
1 TTAT-TTTTTTT
5757705 TTATTTTTTTT
1 TTATTTTTTTT
5757716 TTATTTTT
1 TTATTTTT
5757724 AAACCAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (11 bp):
TTATTTTTTTT
Found at i:5757984 original size:21 final size:21
Alignment explanation
Indices: 5757958--5757997 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5757948 TAAATTAAAT
*
5757958 AAAATTGA-TTATTTTTATTAA
1 AAAATT-ATTTATTTGTATTAA
5757979 AAAATTATTTATTTGTATT
1 AAAATTATTTATTTGTATT
5757998 GTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
AAAATTATTTATTTGTATTAA
Found at i:5760484 original size:27 final size:26
Alignment explanation
Indices: 5760426--5760563 Score: 159
Period size: 27 Copynumber: 5.1 Consensus size: 26
5760416 TGGTTGCCAA
* *
5760426 AACAGATAATGTGACAGAGTCACCAG
1 AACAGATAATGTGGCAGAGCCACCAG
5760452 ATACAGATAATCGTGGCAGAGCCACCAG
1 A-ACAGATAAT-GTGGCAGAGCCACCAG
5760480 AACAGATATATGTGGCAGAGCCACCAG
1 AACAGATA-ATGTGGCAGAGCCACCAG
* *
5760507 ATCAGATATTTGTGGCAGAGCCACCAG
1 AACAGATA-ATGTGGCAGAGCCACCAG
* * * *
5760534 ATCATATATTTGTGGCATAGCCACCAG
1 AACAGATA-ATGTGGCAGAGCCACCAG
5760561 AAC
1 AAC
5760564 GCTTCCTCCA
Statistics
Matches: 102, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
26 1 0.01
27 84 0.82
28 17 0.17
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (26 bp):
AACAGATAATGTGGCAGAGCCACCAG
Done.