Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 157 of 295
Found at i:53346363 original size:18 final size:19
Alignment explanation
Indices: 53346340--53346376 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
53346330 ATAATACTAA
53346340 TTAAAAT-TTCGTAAAAAT
1 TTAAAATATTCGTAAAAAT
53346358 TTAAAATATTCGTAAAAAT
1 TTAAAATATTCGTAAAAAT
53346377 AAATACAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (19 bp):
TTAAAATATTCGTAAAAAT
Found at i:53349809 original size:17 final size:19
Alignment explanation
Indices: 53349784--53349818 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
53349774 TATCTTAAAT
53349784 AAATATATTAT-ATATTTA
1 AAATATATTATAATATTTA
53349802 AAAT-TATTATAATATTT
1 AAATATATTATAATATTT
53349819 TAATTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATATTATAATATTTA
Found at i:53352653 original size:22 final size:23
Alignment explanation
Indices: 53352618--53352663 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
53352608 TCATTAAAAC
* *
53352618 TAAGCATGATATAATCC-AATCA
1 TAAGCATGACATAAGCCTAATCA
*
53352640 TAAGCTTGACATAAGCCTAATCA
1 TAAGCATGACATAAGCCTAATCA
53352663 T
1 T
53352664 CATCCACAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (23 bp):
TAAGCATGACATAAGCCTAATCA
Found at i:53354433 original size:37 final size:37
Alignment explanation
Indices: 53354374--53354519 Score: 229
Period size: 37 Copynumber: 3.9 Consensus size: 37
53354364 AGCTCAGACG
* *
53354374 AAATCTCCACACGAAGTTATCGGGTCTTACCCGAACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
*
53354411 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
* *
53354448 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
* *
53354485 TAATCTCCATACGTAGTCATCGGGTCTTACCCGAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAA
53354520 ATATATTTCC
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 103 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
Found at i:53354778 original size:47 final size:47
Alignment explanation
Indices: 53354726--53354919 Score: 280
Period size: 47 Copynumber: 4.1 Consensus size: 47
53354716 CATACATATT
* * * *
53354726 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
53354773 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
53354820 TCGCATTGGCCATTCGGCCTTATCACATATATGCATGTTCGCATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
53354867 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
53354914 TCACAT
1 TCACAT
53354920 AAAATCCTAA
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 131 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:53357985 original size:12 final size:12
Alignment explanation
Indices: 53357968--53358004 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
53357958 CCAAAACCAC
53357968 TAAAAATATTTA
1 TAAAAATATTTA
53357980 TAAAAATATTTA
1 TAAAAATATTTA
53357992 TAAAAATATTTA
1 TAAAAATATTTA
53358004 T
1 T
53358005 GGCTCGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAAAAATATTTA
Found at i:53358145 original size:238 final size:240
Alignment explanation
Indices: 53357580--53358225 Score: 1066
Period size: 242 Copynumber: 2.7 Consensus size: 240
53357570 GGGTGTCACA
*
53357580 TAGGGTCTTACCACTTGAACTTAATTAATCATTCGAATAACCTAAATTACCATTTCAAAAATCTT
1 TAGGGTCTTACCACTTGAACTTAATTAATCATTCGAATAACCTAAATTACCATATCAAAAATCTT
*
53357645 TTAAAAACCATAATCGACTCGTAAATATTAAATAATAATATTTACGAACTTACTCATTGAATTTA
66 TTAAAAACCATAATCGACTCGTAAATATTAAATAATAATATTTACGAACTTACTCGTTGAATTTA
** *
53357710 GTGGCCCCAAAACCACTATTTCCAACACCACTAAAAATATTTATAAAAATCTTTATGGCTCGGTT
131 GTGGCCCCAAAACCACTA--TAAAACACCACTAAAAATATTTATAAAAATATTTATGGCTCGGTT
* *
53357775 TATAGAAACAAGGAATTGATACCTCATTTTCTAAAACCACTTGACCT
194 TATAGAAACAAGGAATCGATACCTCATTTTCTAAAACAACTTGACCT
53357822 TAGGGTCTTACCACTTGAACTTAATTAATCATTCGAATAACCTAAATTACCATATCAAAAATCTT
1 TAGGGTCTTACCACTTGAACTTAATTAATCATTCGAATAACCTAAATTACCATATCAAAAATCTT
*
53357887 TTAAAAACCATAACCGACTCGTAAATATTAAATAATAATATTTACGAACTTACTCGTTGAATTTA
66 TTAAAAACCATAATCGACTCGTAAATATTAAATAATAATATTTACGAACTTACTCGTTGAATTTA
* **
53357952 GTGGCCCCAAAACCACTA-AAAATATTTA-TAAAAATATTTATAAAAATATTTATGGCTCGGTTT
131 GTGGCCCCAAAACCACTATAAAACA-CCACTAAAAATATTTATAAAAATATTTATGGCTCGGTTT
*
53358015 ATAGAAACAAGGTATCGATACCTCATTTTCTAAAA-AACTTGACCT
195 ATAGAAACAAGGAATCGATACCTCATTTTCTAAAACAACTTGACCT
53358060 TAGGGTCTTACCACTTGAACTTAATTAATCATTCGAATAACCTAAATTACCATATCAAAAATCTT
1 TAGGGTCTTACCACTTGAACTTAATTAATCATTCGAATAACCTAAATTACCATATCAAAAATCTT
** *
53358125 TTAAAAACCATAATCGACTCGTAAATATTAAATAATAATATTTGTGAAC-TACTCGTTGAATTTT
66 TTAAAAACCATAATCGACTCGTAAATATTAAATAATAATATTTACGAACTTACTCGTTGAATTTA
**
53358189 GTGGCCCCAAAACCACTATTTCTAACACCACTAAAAA
131 GTGGCCCCAAAACCACTA--TAAAACACCACTAAAAA
53358226 ACAGGCTATT
Statistics
Matches: 378, Mismatches: 21, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
237 32 0.08
238 120 0.32
239 71 0.19
240 10 0.03
242 145 0.38
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (240 bp):
TAGGGTCTTACCACTTGAACTTAATTAATCATTCGAATAACCTAAATTACCATATCAAAAATCTT
TTAAAAACCATAATCGACTCGTAAATATTAAATAATAATATTTACGAACTTACTCGTTGAATTTA
GTGGCCCCAAAACCACTATAAAACACCACTAAAAATATTTATAAAAATATTTATGGCTCGGTTTA
TAGAAACAAGGAATCGATACCTCATTTTCTAAAACAACTTGACCT
Found at i:53360809 original size:56 final size:56
Alignment explanation
Indices: 53360561--53360807 Score: 370
Period size: 56 Copynumber: 4.4 Consensus size: 56
53360551 TCCCAGACAG
* *
53360561 GGTCTTACTCGCACACATATATCAAAATCACATATTGATGCCAACGTATTAAACGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGT
* * * * *
53360617 GCTCTTACTCGCACATATATATCAGAATCACATATTGATGCCAACTTATTAAATGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGT
* * *
53360673 GGTCTTACTCGCACACATATGTCAGAACCACATATCGATGCCAACGTATTAAATGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGT
**
53360729 GGTCTTACTCATACACATATATC-GAAATCACATATCGATGCCAACGTATTAAACGT
1 GGTCTTACTCGCACACATATATCAG-AATCACATATCGATGCCAACGTATTAAACGT
53360785 GGTCTTACTCGCACACATATATC
1 GGTCTTACTCGCACACATATATC
53360808 GATGCCATGG
Statistics
Matches: 172, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
55 1 0.01
56 171 0.99
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.30
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTATTAAACGT
Found at i:53361351 original size:29 final size:28
Alignment explanation
Indices: 53361319--53361386 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
53361309 TATTCATACA
* *
53361319 AGTCCATAATTTCATTTATTTC-ACATTTT
1 AGTCCCTAATTT-A-TTATTTCTACAATTT
53361348 AGTCCCTCAATTTATTATTTCTACAATTT
1 AGTCCCT-AATTTATTATTTCTACAATTT
53361377 AG-CCCTAATT
1 AGTCCCTAATT
53361387 ACTCAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 4 0.11
28 11 0.31
29 15 0.43
30 5 0.14
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.47
Consensus pattern (28 bp):
AGTCCCTAATTTATTATTTCTACAATTT
Found at i:53361368 original size:28 final size:27
Alignment explanation
Indices: 53361325--53361386 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
53361315 TACAAGTCCA
*
53361325 TAATTTCATTTATTTC-ACATTTTAGTCCC
1 TAATTT-A-TTATTTCTACAATTTAG-CCC
53361354 TCAATTTATTATTTCTACAATTTAGCCC
1 T-AATTTATTATTTCTACAATTTAGCCC
53361382 TAATT
1 TAATT
53361387 ACTCAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
27 4 0.13
28 11 0.37
29 10 0.33
30 5 0.17
ACGTcount: A:0.27, C:0.19, G:0.03, T:0.50
Consensus pattern (27 bp):
TAATTTATTATTTCTACAATTTAGCCC
Found at i:53361954 original size:13 final size:13
Alignment explanation
Indices: 53361936--53361960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53361926 ACAAACGATA
53361936 AAATTTTCACACG
1 AAATTTTCACACG
53361949 AAATTTTCACAC
1 AAATTTTCACAC
53361961 ATATAATATA
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:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:53364680 original size:27 final size:27
Alignment explanation
Indices: 53364642--53364696 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
53364632 TTAGATAATG
*
53364642 AGATTAAATACATGTCACATGTTCCAT
1 AGATTAAATACATGTCACACGTTCCAT
53364669 AGATTAAATACATGTCACACGTTCCAT
1 AGATTAAATACATGTCACACGTTCCAT
53364696 A
1 A
53364697 CTCTAGTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (27 bp):
AGATTAAATACATGTCACACGTTCCAT
Found at i:53367893 original size:18 final size:17
Alignment explanation
Indices: 53367870--53367903 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
53367860 TATATACACA
53367870 TAACATAACATTCATAAT
1 TAACATAACATT-ATAAT
53367888 TAACATAACATTATAA
1 TAACATAACATTATAA
53367904 ACATTTATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (17 bp):
TAACATAACATTATAAT
Found at i:53371471 original size:16 final size:18
Alignment explanation
Indices: 53371433--53371465 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
53371423 AACTAAAATC
53371433 TCAATGGTATCACATGAA
1 TCAATGGTATCACATGAA
53371451 TCAAT-GTAT-ACATGA
1 TCAATGGTATCACATGA
53371466 TCCAATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (18 bp):
TCAATGGTATCACATGAA
Found at i:53372920 original size:63 final size:63
Alignment explanation
Indices: 53372821--53372946 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
53372811 CCATTGATGC
*
53372821 ATATACATGAGTTTTGAAGTTTTATGATATAAAATGAATGGTTGTTGTTAGATAGACAACTTT
1 ATATACATGAGTTTTGAAGTTTTATGATATAAAATGAATGGTTGTTGTTAGATAAACAACTTT
*
53372884 ATATACATGATTTTTGAAGTTTTATGATATAAAATGAATGGTTGTTGTTAGATAAACAACTTT
1 ATATACATGAGTTTTGAAGTTTTATGATATAAAATGAATGGTTGTTGTTAGATAAACAACTTT
53372947 TGTAAAGAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (63 bp):
ATATACATGAGTTTTGAAGTTTTATGATATAAAATGAATGGTTGTTGTTAGATAAACAACTTT
Found at i:53372959 original size:63 final size:63
Alignment explanation
Indices: 53372832--53372963 Score: 212
Period size: 63 Copynumber: 2.1 Consensus size: 63
53372822 TATACATGAG
* * *
53372832 TTTTGAAGTTTTATGATATAAAATGAATGGTTGTTGTTAGATAGACAACTTTATATACATGAT
1 TTTTGAAGTTTTATGATATAAAATGAATGGTTGTTGTTAGATAAACAACTTTATATAAAAGAT
*
53372895 TTTTGAAGTTTTATGATATAAAATGAATGGTTGTTGTTAGATAAACAACTTT-TGTAAAGAGAT
1 TTTTGAAGTTTTATGATATAAAATGAATGGTTGTTGTTAGATAAACAACTTTATATAAA-AGAT
53372958 TTTTGA
1 TTTTGA
53372964 TGAAATTATC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 4 0.06
63 60 0.94
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (63 bp):
TTTTGAAGTTTTATGATATAAAATGAATGGTTGTTGTTAGATAAACAACTTTATATAAAAGAT
Found at i:53375529 original size:12 final size:11
Alignment explanation
Indices: 53375487--53375521 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
53375477 ATTGGTCATG
*
53375487 AGAGTTTCAAT
1 AGAGTTTGAAT
53375498 AGAGTTTGAAT
1 AGAGTTTGAAT
53375509 AGAGTTTGAAT
1 AGAGTTTGAAT
53375520 AG
1 AG
53375522 GTGTTTGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (11 bp):
AGAGTTTGAAT
Found at i:53375886 original size:16 final size:16
Alignment explanation
Indices: 53375865--53375897 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53375855 CGGCATAAGC
*
53375865 TACCTTTCTAATTCTA
1 TACCTTCCTAATTCTA
53375881 TACCTTCCTAATTCTA
1 TACCTTCCTAATTCTA
53375897 T
1 T
53375898 CTTCTTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.48
Consensus pattern (16 bp):
TACCTTCCTAATTCTA
Found at i:53377783 original size:29 final size:29
Alignment explanation
Indices: 53377743--53377852 Score: 121
Period size: 29 Copynumber: 3.8 Consensus size: 29
53377733 GGCCCATCTT
*
53377743 ATTCATATGGCCCATCAGGCCCAATTCAC
1 ATTCATATGGCCCATCAGGCCCAAATCAC
* * *
53377772 ATTCATATGGCCTATCAGGCCCAACTCAT
1 ATTCATATGGCCCATCAGGCCCAAATCAC
** *
53377801 ATTCATATGGCATATTAGGCCCAAATCAC
1 ATTCATATGGCCCATCAGGCCCAAATCAC
* * * *
53377830 CTTTATATGGCCCGTTAGGCCCA
1 ATTCATATGGCCCATCAGGCCCA
53377853 GTCGCATTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
ATTCATATGGCCCATCAGGCCCAAATCAC
Found at i:53377850 original size:58 final size:58
Alignment explanation
Indices: 53377742--53377852 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 58
53377732 TGGCCCATCT
* * *
53377742 TATTCATATGGCCCATCAGGCCCAATTCACATTCATATGGCCTATCAGGCCCAACTCA
1 TATTCATATGGCACATCAGGCCCAAATCACATTCATATGGCCCATCAGGCCCAACTCA
* * * * * *
53377800 TATTCATATGGCATATTAGGCCCAAATCACCTTTATATGGCCCGTTAGGCCCA
1 TATTCATATGGCACATCAGGCCCAAATCACATTCATATGGCCCATCAGGCCCA
53377853 GTCGCATTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (58 bp):
TATTCATATGGCACATCAGGCCCAAATCACATTCATATGGCCCATCAGGCCCAACTCA
Found at i:53378110 original size:16 final size:16
Alignment explanation
Indices: 53378076--53378110 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
53378066 GTAGCCAAAC
*
53378076 TTTCAGCTTTTTGGCA
1 TTTCAGCTTTTCGGCA
*
53378092 TTTCAGCTTTTCGGTA
1 TTTCAGCTTTTCGGCA
53378108 TTT
1 TTT
53378111 TGGCATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.54
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:53379708 original size:18 final size:19
Alignment explanation
Indices: 53379682--53379722 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
53379672 AGCCTCTCGG
53379682 CGGTAGCTG-ACCACC-CCT
1 CGGTAGCTGCA-CACCACCT
*
53379700 CGGTGGCTGCACACCACCT
1 CGGTAGCTGCACACCACCT
53379719 CGGT
1 CGGT
53379723 CAACGACTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.15, C:0.41, G:0.27, T:0.17
Consensus pattern (19 bp):
CGGTAGCTGCACACCACCT
Found at i:53382329 original size:29 final size:29
Alignment explanation
Indices: 53382276--53382399 Score: 108
Period size: 29 Copynumber: 4.3 Consensus size: 29
53382266 TAGCCCATCT
* * *
53382276 CATTCATATAGCCCATCAAGTCCAATTCA
1 CATTCATATGGCCCATCAGGCCCAATTCA
53382305 CATTCATATGGCCCATCAGGCCCAACTT-A
1 CATTCATATGGCCCATCAGGCCCAA-TTCA
* * * *
53382334 TATTCATATGGCCTATTAGGCCCAAATCA
1 CATTCATATGGCCCATCAGGCCCAATTCA
* * * * * *
53382363 CCTTTATATGGCCCGTTAGG-CCTAGTCA
1 CATTCATATGGCCCATCAGGCCCAATTCA
53382391 CATTCATAT
1 CATTCATAT
53382400 TCATGCTCAC
Statistics
Matches: 77, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
28 14 0.18
29 61 0.79
30 2 0.03
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (29 bp):
CATTCATATGGCCCATCAGGCCCAATTCA
Found at i:53385327 original size:17 final size:16
Alignment explanation
Indices: 53385300--53385331 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
53385290 TGGTTGGAGT
53385300 AAACTGAAACTGTAGG
1 AAACTGAAACTGTAGG
53385316 AAACTAGAAACTGTAG
1 AAACT-GAAACTGTAG
53385332 TGAGCCTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (16 bp):
AAACTGAAACTGTAGG
Found at i:53392053 original size:24 final size:25
Alignment explanation
Indices: 53392016--53392063 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
53392006 TTGCCACATA
* *
53392016 TACTGATACTGGCAGCTTTGCTGCT
1 TACTGATACTGGCAACCTTGCTGCT
53392041 TACTG-TACTGGCAACCTTGCTGC
1 TACTGATACTGGCAACCTTGCTGC
53392064 GATATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (25 bp):
TACTGATACTGGCAACCTTGCTGCT
Found at i:53394182 original size:40 final size:40
Alignment explanation
Indices: 53394135--53394319 Score: 293
Period size: 40 Copynumber: 4.6 Consensus size: 40
53394125 ACTACTTGCT
* *
53394135 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
*
53394175 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
53394215 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
*
53394255 CAAATGCCTTC-GGAGCTTAGCCCGGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATA-TAGTAACTAGCA
*
53394295 AAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
53394320 TTATCATCCG
Statistics
Matches: 138, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
39 4 0.03
40 131 0.95
41 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
Found at i:53397158 original size:40 final size:39
Alignment explanation
Indices: 53396927--53397151 Score: 292
Period size: 40 Copynumber: 5.6 Consensus size: 39
53396917 TTGAATGATG
* * * *
53396927 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
*
53396967 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
53397007 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
53397047 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
*
53397087 TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTA-AA
*
53397127 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
53397152 AACGAGTAGC
Statistics
Matches: 171, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
39 35 0.20
40 128 0.75
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53397181 original size:79 final size:78
Alignment explanation
Indices: 53396940--53397184 Score: 282
Period size: 79 Copynumber: 3.1 Consensus size: 78
53396930 GGGCTAAGTC
* * * * *
53396940 CCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTAC
1 CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTAC
*
53397003 TAAATCCGGACTAAGAT
64 TAAATCCGG-TTAA-AT
*
53397020 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
*
53397085 AATCCGGGTTAAGT
66 AATCC-GGTTAAAT
* **
53397099 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-C
*
53397162 TATATCCGGTTAAATT
64 TAAATCCGGTTAAA-T
53397178 CCGAAGG
1 CCGAAGG
53397185 TACGTGATTT
Statistics
Matches: 145, Mismatches: 14, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
78 8 0.06
79 69 0.48
80 59 0.41
81 9 0.06
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
AATCCGGTTAAAT
Found at i:53399449 original size:77 final size:81
Alignment explanation
Indices: 53399315--53399497 Score: 234
Period size: 77 Copynumber: 2.3 Consensus size: 81
53399305 TTGAATGATG
*
53399315 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
53399379 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
53399394 TCCGGGCTAAGT-CC-AAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
*
53399455 TTGTGCGAGTTACTATA
65 TTGTGCGAGATACTATA
* *
53399472 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53399498 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
76 1 0.01
77 45 0.50
78 20 0.22
79 14 0.16
80 10 0.11
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:53399462 original size:40 final size:40
Alignment explanation
Indices: 53399315--53399497 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
53399305 TTGAATGATG
* * * *
53399315 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
53399355 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
53399394 TCCGGGCTAAGT-CC-AAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
53399432 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
53399473 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53399498 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
37 20 0.16
38 16 0.13
39 13 0.10
40 67 0.53
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53407485 original size:40 final size:40
Alignment explanation
Indices: 53407255--53407478 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
53407245 TTGAATGATG
* * * *
53407255 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
53407295 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAG-TACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
53407333 TCCGGGCTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
53407373 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
53407413 TCCGAGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
53407454 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53407479 AACGAGTAGC
Statistics
Matches: 167, Mismatches: 11, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
38 32 0.19
39 7 0.04
40 118 0.71
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53422786 original size:42 final size:42
Alignment explanation
Indices: 53422680--53422844 Score: 199
Period size: 43 Copynumber: 3.9 Consensus size: 42
53422670 TCGGAAGCTC
* * * *
53422680 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAA
1 ATACGATGCCAACGTCCCAGACATGGTCTTACACGAAATCAA
* *
53422722 ATATTGATGCC-ACTATCCCAGACATGGTCTTACACGAAATCAA
1 ATA-CGATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCAA
*
53422765 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCATA
1 ATACGATGCCAACGTCCCAGACATGGTCTTACACG-AAATCA-A
*
53422809 AGT-CGATGCCAACGTCCCAGACGTGGTCTTACACGA
1 A-TACGATGCCAACGTCCCAGACATGGTCTTACACGA
53422845 TAACATAGAT
Statistics
Matches: 106, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
42 32 0.30
43 41 0.39
44 32 0.30
45 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (42 bp):
ATACGATGCCAACGTCCCAGACATGGTCTTACACGAAATCAA
Found at i:53428498 original size:54 final size:54
Alignment explanation
Indices: 53428291--53428499 Score: 170
Period size: 53 Copynumber: 3.9 Consensus size: 54
53428281 TTTCCTTTTT
* ** * * * *
53428291 AAACTTACCATTGCCATTTCATGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 AAACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTACCTTATA
* * * * * *
53428344 GAACTCACCATTGCCATGCCTTGGCGTGGTCTTACATGGGATCTTTACCTTATCA
1 AAACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTACCTTAT-A
* ** * * * * * *
53428399 TAGTTTATCAATGCCATGTCC-TGACAGGGTCTTACATGATTTCCTTACCTTGTA
1 AAACTTACCAATGCCATG-CCTTGGCATGGTCTTACATGGTATCCTTACCTTATA
* *
53428453 AAACTTACCAATGCCATGCCTTGGCTTGGTCTTACTTGGTATCCTTA
1 AAACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTA
53428500 AACCCTAATG
Statistics
Matches: 117, Mismatches: 35, Indels: 7
0.74 0.22 0.04
Matches are distributed among these distances:
53 44 0.38
54 35 0.30
55 36 0.31
56 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
AAACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCCTTACCTTATA
Found at i:53437327 original size:47 final size:47
Alignment explanation
Indices: 53437254--53437384 Score: 147
Period size: 47 Copynumber: 2.8 Consensus size: 47
53437244 AACAATCGAT
** * * *
53437254 AAGTACCTATACCATGGCTTGGAGCCAAACCAAGGTAACT-TAACCCG
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCT-ACCCA
* * * *
53437301 GAGTACCTATACCATGGCCCGTAGCCAAATCAAGTTAACTCTTCTCA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCTACCCA
* *
53437348 AAATACCTATATCATGGCCCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
53437385 TTATTCGTAC
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
47 69 0.99
48 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCTACCCA
Found at i:53444850 original size:47 final size:47
Alignment explanation
Indices: 53444773--53444903 Score: 165
Period size: 47 Copynumber: 2.8 Consensus size: 47
53444763 CATAATCGAT
* * *
53444773 AAGTACCTATACCATGGCCCGTAGCAAAATCAAGGTAACTTATC-CTG
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTC-A
* ** *
53444820 GAGTACCTATACCATGGCCTATAGCCAAATCAAGGTAACTCCTCTCA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCA
* *
53444867 AAATACCTATATCATGGCCCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
53444904 TTATTCACAC
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
47 70 0.99
48 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCA
Found at i:53452334 original size:24 final size:24
Alignment explanation
Indices: 53452263--53452336 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
53452253 TTCGAGTTAT
* *
53452263 GAACAGTAAGCTCCTCCTGAGCTGA
1 GAACAGTAAGCTCTTAC-GAGCTGA
* *
53452288 TAGACAGTAAGCT-TTGACAAGCTGA
1 GA-ACAGTAAGCTCTT-ACGAGCTGA
53452313 GAACAGTAAGCTCTTACGAGCTGA
1 GAACAGTAAGCTCTTACGAGCTGA
53452337 TATATCAGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
24 18 0.45
25 11 0.28
26 11 0.28
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (24 bp):
GAACAGTAAGCTCTTACGAGCTGA
Found at i:53454420 original size:12 final size:12
Alignment explanation
Indices: 53454403--53454427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53454393 CTAGTATGAG
53454403 TATAAGGAATAT
1 TATAAGGAATAT
53454415 TATAAGGAATAT
1 TATAAGGAATAT
53454427 T
1 T
53454428 CGGCCTAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (12 bp):
TATAAGGAATAT
Found at i:53457677 original size:12 final size:12
Alignment explanation
Indices: 53457660--53457685 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53457650 CATTCCGAAG
53457660 TATATATATACA
1 TATATATATACA
53457672 TATATATATACA
1 TATATATATACA
53457684 TA
1 TA
53457686 AGTATGCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:53458215 original size:27 final size:28
Alignment explanation
Indices: 53458131--53458228 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
53458121 CATGAGATTG
* * * *
53458131 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
53458160 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
53458188 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
53458215 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
53458229 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:53458239 original size:27 final size:27
Alignment explanation
Indices: 53458159--53458241 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
53458149 TAAATTGTAC
* *
53458159 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
53458187 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
53458214 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
53458241 A
1 A
53458242 CTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:53465953 original size:12 final size:12
Alignment explanation
Indices: 53465936--53465961 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53465926 CATTCCGAAG
53465936 TATATATATACA
1 TATATATATACA
53465948 TATATATATACA
1 TATATATATACA
53465960 TA
1 TA
53465962 AGTATGCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:53466490 original size:27 final size:28
Alignment explanation
Indices: 53466406--53466503 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
53466396 CATGAGATTG
* * * *
53466406 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
53466435 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
53466463 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
53466490 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
53466504 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:53466514 original size:27 final size:27
Alignment explanation
Indices: 53466434--53466516 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
53466424 TAAATTGTAC
* *
53466434 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
53466462 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
53466489 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
53466516 A
1 A
53466517 CTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:53530099 original size:20 final size:20
Alignment explanation
Indices: 53530074--53530114 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
53530064 CTTTGATATC
53530074 ACATAAACTATGCTTATGAG
1 ACATAAACTATGCTTATGAG
*
53530094 ACATAAACTGTGCTTATGAG
1 ACATAAACTATGCTTATGAG
53530114 A
1 A
53530115 TACGGACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (20 bp):
ACATAAACTATGCTTATGAG
Found at i:53530401 original size:47 final size:48
Alignment explanation
Indices: 53530284--53530414 Score: 158
Period size: 48 Copynumber: 2.8 Consensus size: 48
53530274 GTGCGAGTGA
* * * * *
53530284 TACCATGATTTGGCTATAGGCCATGGTATAGGTATTTCGGAGTGGAGT
1 TACCTTGATTTGGATACAGGCCATGGTATAGGTACTTCGGAGTGAAGT
*
53530332 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTTCAGGA-T-AAGT
1 TACCTTGATTTGGATACAGGCCATGGTATAGGTACTTC-GGAGTGAAGT
* * *
53530379 TATCTTGATTTGGATTCGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGATACAGGCCATGGTATAGGTACT
53530415 CATTGATTGA
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
47 35 0.47
48 36 0.49
49 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (48 bp):
TACCTTGATTTGGATACAGGCCATGGTATAGGTACTTCGGAGTGAAGT
Found at i:53532826 original size:10 final size:10
Alignment explanation
Indices: 53532811--53532849 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
53532801 CTGATTTGTA
53532811 CATGATATGC
1 CATGATATGC
53532821 CATGATATGC
1 CATGATATGC
*
53532831 ACATGATATTC
1 -CATGATATGC
53532842 CATGATAT
1 CATGATAT
53532850 ATTCATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (10 bp):
CATGATATGC
Found at i:53532826 original size:21 final size:21
Alignment explanation
Indices: 53532810--53532849 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53532800 ACTGATTTGT
53532810 ACATGATATGCCATGATATGC
1 ACATGATATGCCATGATATGC
*
53532831 ACATGATATTCCATGATAT
1 ACATGATATGCCATGATAT
53532850 ATTCATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (21 bp):
ACATGATATGCCATGATATGC
Found at i:53534222 original size:22 final size:22
Alignment explanation
Indices: 53534194--53534238 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
53534184 ATGAGACAGT
*
53534194 AGCTAGGCTACACTGTTGCGAA
1 AGCTAGGCTACAATGTTGCGAA
53534216 AGCTAGGCTACAATGTTGCGAA
1 AGCTAGGCTACAATGTTGCGAA
53534238 A
1 A
53534239 ACAATCCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (22 bp):
AGCTAGGCTACAATGTTGCGAA
Found at i:53538261 original size:27 final size:27
Alignment explanation
Indices: 53538228--53538371 Score: 180
Period size: 27 Copynumber: 5.3 Consensus size: 27
53538218 TACAGAAATG
* *
53538228 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
* * * * * *
53538255 CCTTCGATTTATAGATTTACCGTTTCA
1 CCCTCGATTTACAAAATTACCATTTTA
* *
53538282 CCCTCGATTTACAAAATTATCGTTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
*
53538309 CCCTCAATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
*
53538336 CCCTCAATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
53538363 CCCTCGATT
1 CCCTCGATT
53538372 GTGAAATTAC
Statistics
Matches: 103, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 103 1.00
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTACAAAATTACCATTTTA
Found at i:53538433 original size:27 final size:28
Alignment explanation
Indices: 53538403--53538579 Score: 190
Period size: 27 Copynumber: 6.6 Consensus size: 28
53538393 TGTAGGATAG
*
53538403 AATTAGCAAAATACCCCTTA-TTTGTAA
1 AATTACCAAAATACCCCTTAGTTTGTAA
53538430 AATTACCAAAATACCCC-TAGTTTGTAA
1 AATTACCAAAATACCCCTTAGTTTGTAA
53538457 AATTACCAAAATA-CCCTTAGTTTGTAA
1 AATTACCAAAATACCCCTTAGTTTGTAA
* *
53538484 AATTACCAAAATACCAC-TAGTTTGTGA
1 AATTACCAAAATACCCCTTAGTTTGTAA
* * * *
53538511 AATTATC-GAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCTTAGTTTGTAA
* * **
53538537 AATTACGAAAATACCCC-TAATTTACAA
1 AATTACCAAAATACCCCTTAGTTTGTAA
53538564 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
53538580 TTGACTTTCT
Statistics
Matches: 127, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
25 2 0.02
26 22 0.17
27 98 0.77
28 5 0.04
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (28 bp):
AATTACCAAAATACCCCTTAGTTTGTAA
Found at i:53538444 original size:54 final size:54
Alignment explanation
Indices: 53538370--53538555 Score: 189
Period size: 54 Copynumber: 3.5 Consensus size: 54
53538360 TTACCCTCGA
* ** * *
53538370 TTGTGAAATTACTGAAATACCCCT-GTAGGATAGAATTAGCAAAATACCCCTTA-T
1 TTGTAAAATTACCAAAATACCCCTAGTAGG-TAAAATTACCAAAATA-CCCTTAGT
**
53538424 TTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTAGT
1 TTGTAAAATTACCAAAATACCCCTAGTAGGTAAAATTACCAAAATACCCTTAGT
* ** * * * * *
53538478 TTGTAAAATTACCAAAATACCACTAGTTTGTGAAATTATC-GAATACCCTCAAT
1 TTGTAAAATTACCAAAATACCCCTAGTAGGTAAAATTACCAAAATACCCTTAGT
*
53538531 TTGTAAAATTACGAAAATACCCCTA
1 TTGTAAAATTACCAAAATACCCCTA
53538556 ATTTACAAAA
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
53 39 0.34
54 73 0.63
55 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (54 bp):
TTGTAAAATTACCAAAATACCCCTAGTAGGTAAAATTACCAAAATACCCTTAGT
Found at i:53538602 original size:29 final size:27
Alignment explanation
Indices: 53538557--53538642 Score: 102
Period size: 27 Copynumber: 3.1 Consensus size: 27
53538547 ATACCCCTAA
* *
53538557 TTTACAAAATTACAGAAATACCCTTGAC
1 TTTACAAAATTATAGAAATACCCTTG-G
*
53538585 TTT-CTAAAAATTATAGAAATACCATTGG
1 TTTAC--AAAATTATAGAAATACCCTTGG
*
53538613 TTTACAAAATTATTGAAATACCCTTGG
1 TTTACAAAATTATAGAAATACCCTTGG
53538640 TTT
1 TTT
53538643 GTAGATTTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
27 24 0.48
28 6 0.12
29 20 0.40
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (27 bp):
TTTACAAAATTATAGAAATACCCTTGG
Found at i:53538726 original size:27 final size:27
Alignment explanation
Indices: 53538683--53538756 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
53538673 AAATGACTAA
*
53538683 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
53538710 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
53538737 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
53538757 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:53538760 original size:27 final size:27
Alignment explanation
Indices: 53538696--53538760 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
53538686 ACCCCTAATA
*
53538696 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
53538723 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
53538750 GGTAAAATGAC
1 GGTAAAATGAC
53538761 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:53539112 original size:20 final size:22
Alignment explanation
Indices: 53539073--53539113 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
53539063 GTGCACGATG
*
53539073 GTAAGTTGGGCCTCAATGGGCA
1 GTAAGTTGGGCCTAAATGGGCA
53539095 GTAA-TTGGGCC-AAATGGGC
1 GTAAGTTGGGCCTAAATGGGC
53539114 TTTTGGGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.22
Consensus pattern (22 bp):
GTAAGTTGGGCCTAAATGGGCA
Found at i:53539603 original size:25 final size:25
Alignment explanation
Indices: 53539570--53539639 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
53539560 AGGAAGTGCT
*
53539570 AAAAGGGCTATGCCCCAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
53539595 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
53539620 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
53539640 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:53539652 original size:24 final size:25
Alignment explanation
Indices: 53539570--53539664 Score: 113
Period size: 25 Copynumber: 3.8 Consensus size: 25
53539560 AGGAAGTGCT
*
53539570 AAAAGGGCTATGCCCCAGTTTACCA
1 AAAAGGGCTATGCCCCAGTTTATCA
*
53539595 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTATGCCCCAGTTTATCA
* *
53539620 AAAAGGGCTTTGCCCCAG-TTAT-T
1 AAAAGGGCTATGCCCCAGTTTATCA
*
53539643 AAAAGAGGCTAGGCCTCCAGTT
1 AAAAG-GGCTATGCC-CCAGTT
53539665 ATATGATAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.08
24 11 0.18
25 45 0.73
26 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTATGCCCCAGTTTATCA
Found at i:53539897 original size:31 final size:31
Alignment explanation
Indices: 53539859--53540035 Score: 266
Period size: 31 Copynumber: 5.7 Consensus size: 31
53539849 CGTTTACAGT
*
53539859 AAAGGCTTCGGCCCAGAGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
53539890 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
53539921 AAAGGCTTCAGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* * *
53539952 AAAGGCTTTGGCCCAATGATATGATTTATTA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* * * *
53539983 AAAGGCTTCAGCCTATTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
53540014 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
53540036 TCAAGACTAA
Statistics
Matches: 131, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 5 0.04
31 126 0.96
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.30
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:53541685 original size:27 final size:27
Alignment explanation
Indices: 53541642--53541715 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
53541632 AAATGACTAA
*
53541642 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
53541669 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
53541696 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
53541716 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:53541719 original size:27 final size:27
Alignment explanation
Indices: 53541655--53541719 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
53541645 ACCCCTAATA
*
53541655 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
53541682 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
53541709 GGTAAAATGAC
1 GGTAAAATGAC
53541720 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:53542071 original size:20 final size:22
Alignment explanation
Indices: 53542032--53542072 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
53542022 GTGCACGATG
*
53542032 GTAAGTTGGGCCTCAATGGGCA
1 GTAAGTTGGGCCTAAATGGGCA
53542054 GTAA-TTGGGCC-AAATGGGC
1 GTAAGTTGGGCCTAAATGGGC
53542073 TTTTGGCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.22
Consensus pattern (22 bp):
GTAAGTTGGGCCTAAATGGGCA
Found at i:53542604 original size:24 final size:25
Alignment explanation
Indices: 53542528--53542604 Score: 102
Period size: 25 Copynumber: 3.1 Consensus size: 25
53542518 AGGAAGTGCT
* * * *
53542528 AAAAGGGCTATGCCCTAGTTTACTG
1 AAAAGGGCTTTGCCCCAGTTTATTA
*
53542553 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATTA
53542578 AAAAGGGCTTTGCCCCAG-TTATTA
1 AAAAGGGCTTTGCCCCAGTTTATTA
53542602 AAA
1 AAA
53542605 GAGGCTAGGC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 8 0.17
25 38 0.83
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATTA
Found at i:53542610 original size:24 final size:24
Alignment explanation
Indices: 53542527--53542622 Score: 95
Period size: 25 Copynumber: 3.9 Consensus size: 24
53542517 GAGGAAGTGC
*
53542527 TAAAAGGGCTATGCCCTAGTTTACT
1 TAAAAGGGCTATGCCCCAGTTTA-T
* *
53542552 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTATGCCCCAGTTTAT
* *
53542576 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTATGCCCCAGTTTAT
*
53542600 TAAAAGAGGCTAGGCCTCCAGTT
1 TAAAAG-GGCTATGCC-CCAGTT
53542623 ATATGATAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
23 5 0.08
24 12 0.20
25 42 0.70
26 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
TAAAAGGGCTATGCCCCAGTTTAT
Found at i:53542621 original size:50 final size:50
Alignment explanation
Indices: 53542528--53542622 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
53542518 AGGAAGTGCT
* **
53542528 AAAAGGGCTATGCCCTAGTTTACTGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTATGCCCCAGTTTACTGAAAAGGGCTAGGCCCCAGTTTATCA
* *
53542578 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTATGCCCCAGTTTACTGAAAAG-GGCTAGGCC-CCAGTT
53542623 ATATGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 6 0.16
49 10 0.26
50 22 0.58
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.26
Consensus pattern (50 bp):
AAAAGGGCTATGCCCCAGTTTACTGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:53542853 original size:31 final size:31
Alignment explanation
Indices: 53542817--53542931 Score: 178
Period size: 31 Copynumber: 3.7 Consensus size: 31
53542807 CGTTTACAAT
*
53542817 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
53542848 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* * * *
53542879 AAAGGCTTTGGCCTATTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
53542910 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
53542932 TCAAGACTAA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
30 5 0.07
31 71 0.93
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:53546246 original size:22 final size:22
Alignment explanation
Indices: 53546219--53546263 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
53546209 TGAATAATGA
53546219 TTGTATGATTTGATCGAATGTG
1 TTGTATGATTTGATCGAATGTG
53546241 TTGTATGATTTGATCGAATGTG
1 TTGTATGATTTGATCGAATGTG
53546263 T
1 T
53546264 GAGAAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.04, G:0.27, T:0.47
Consensus pattern (22 bp):
TTGTATGATTTGATCGAATGTG
Found at i:53552556 original size:25 final size:26
Alignment explanation
Indices: 53552516--53552573 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
53552506 AATAAGGAAG
* *
53552516 TTTTCTTTTCTTTCTTT-CTTTT-TC
1 TTTTCTTTTCTCTCTTTGCTTTTCTA
53552540 TTTTCTTATTCTCTCTTTGCTTTTCTA
1 TTTTCTT-TTCTCTCTTTGCTTTTCTA
53552567 TTTTCTT
1 TTTTCTT
53552574 GAGAACTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 7 0.24
25 9 0.31
26 5 0.17
27 8 0.28
ACGTcount: A:0.03, C:0.21, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTTCTTTTCTCTCTTTGCTTTTCTA
Found at i:53557337 original size:16 final size:16
Alignment explanation
Indices: 53557316--53557375 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
53557306 TCATATAATT
53557316 TAATTATTTAATTTAA
1 TAATTATTTAATTTAA
*
53557332 TAATTATCTTTAACTTAAA
1 TAATTA--TTTAA-TTTAA
**
53557351 TAA-TAAGTAATTTAA
1 TAATTATTTAATTTAA
53557366 TAATTTATTT
1 TAA-TTATTT
53557376 TACAATTGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
15 7 0.21
16 9 0.27
17 3 0.09
18 7 0.21
19 7 0.21
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (16 bp):
TAATTATTTAATTTAA
Found at i:53563484 original size:40 final size:40
Alignment explanation
Indices: 53563410--53563711 Score: 446
Period size: 40 Copynumber: 7.6 Consensus size: 40
53563400 AACCCAAGTA
* * *
53563410 CCTTCGGGATTTAG-CCGGATAT-AGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAA-TAGCACAAATG
* * *
53563449 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
* *
53563489 CCTCCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
* *
53563529 CCTTCGGGACTTAGCCCAGATATAATCAATAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
* *
53563569 CCTTCGGGACTTAGCCCAGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
53563609 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
* *
53563649 CCTTCGGGACTTAGCCCGGATATAATCACTAGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
*
53563689 CCTTCGGGACTTAACCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
53563712 CATTCGAATA
Statistics
Matches: 239, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
39 12 0.05
40 224 0.94
41 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAATCAATAGCACAAATG
Found at i:53571869 original size:29 final size:28
Alignment explanation
Indices: 53571837--53571904 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
53571827 ATAATATCAT
53571837 TATAATTTAATTATCATAAATTCA-T-ATTA
1 TATAATTTAATT-T-ATAAA-TCATTAATTA
* *
53571866 TATAAATTATATTTATATATCATTAATTA
1 TATAATTTA-ATTTATAAATCATTAATTA
53571895 TATAATTTAA
1 TATAATTTAA
53571905 AACAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 3 0.09
28 6 0.18
29 21 0.64
30 3 0.09
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (28 bp):
TATAATTTAATTTATAAATCATTAATTA
Found at i:53571870 original size:15 final size:14
Alignment explanation
Indices: 53571837--53571899 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
53571827 ATAATATCAT
*
53571837 TATAATTTA-ATTA
1 TATAAATTATATTA
53571850 TCATAAATTCATATTA
1 T-ATAAATT-ATATTA
53571866 TATAAATTATATTTA
1 TATAAATTATA-TTA
*
53571881 TATATCATTA-ATTA
1 TATA-AATTATATTA
53571895 TATAA
1 TATAA
53571900 TTTAAAACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
13 1 0.02
14 16 0.38
15 16 0.38
16 9 0.21
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (14 bp):
TATAAATTATATTA
Found at i:53577468 original size:40 final size:40
Alignment explanation
Indices: 53577424--53577499 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
53577414 TAGTGCCTCA
*
53577424 TATAGCCGAAGCTATTT-CAATTCGCACACTAAGTGCTATT
1 TATAGCCGAAGCTATTTCCAA-ACGCACACTAAGTGCTATT
53577464 TATAGCCGAAGCTATTTCCAAACGCACACTAAGTGC
1 TATAGCCGAAGCTATTTCCAAACGCACACTAAGTGC
53577500 CAAACATCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 31 0.91
41 3 0.09
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (40 bp):
TATAGCCGAAGCTATTTCCAAACGCACACTAAGTGCTATT
Found at i:53577791 original size:72 final size:72
Alignment explanation
Indices: 53577674--53577822 Score: 289
Period size: 72 Copynumber: 2.1 Consensus size: 72
53577664 CCTCGTTCTA
53577674 AATCCTAATTCTCTCTTTCCTGATCTATATGTATTCAAAATTAACCCATTTAATCACCAATTCAT
1 AATCCTAATTCTCTCTTTCCTGATCTATATGTATTCAAAATTAACCCATTTAATCACCAATTCAT
53577739 TCAATTT
66 TCAATTT
*
53577746 AATCCTAATTCTCTCTTTCTTGATCTATATGTATTCAAAATTAACCCATTTAATCACCAATTCAT
1 AATCCTAATTCTCTCTTTCCTGATCTATATGTATTCAAAATTAACCCATTTAATCACCAATTCAT
53577811 TCAATTT
66 TCAATTT
53577818 AATCC
1 AATCC
53577823 ACAAACACAT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (72 bp):
AATCCTAATTCTCTCTTTCCTGATCTATATGTATTCAAAATTAACCCATTTAATCACCAATTCAT
TCAATTT
Found at i:53578042 original size:28 final size:29
Alignment explanation
Indices: 53577983--53578047 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
53577973 CATTCATTTA
* *
53577983 TTTCACAATTTAACCCCTCAATTTACACT
1 TTTCTCAAATTAACCCCTCAATTTACACT
*
53578012 TTTCTCAAATTAATCCCT-AATTTACA-T
1 TTTCTCAAATTAACCCCTCAATTTACACT
*
53578039 TTTTTCAAA
1 TTTCTCAAA
53578048 AAAACTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 9 0.28
28 8 0.25
29 15 0.47
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (29 bp):
TTTCTCAAATTAACCCCTCAATTTACACT
Found at i:53589545 original size:55 final size:55
Alignment explanation
Indices: 53589461--53589572 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
53589451 ATGTTAAATG
53589461 TATGTTAAATACTTGTTTAGATAGCATGTTATTTGCATATGGACTTACTAAGCTT
1 TATGTTAAATACTTGTTTAGATAGCATGTTATTTGCATATGGACTTACTAAGCTT
53589516 TATGTTAAATACTTGTTTAGATAGCATGTTATTTGCATATGGACTTACTAAGCTT
1 TATGTTAAATACTTGTTTAGATAGCATGTTATTTGCATATGGACTTACTAAGCTT
53589571 TA
1 TA
53589573 ATGCTTACCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (55 bp):
TATGTTAAATACTTGTTTAGATAGCATGTTATTTGCATATGGACTTACTAAGCTT
Found at i:53590630 original size:38 final size:39
Alignment explanation
Indices: 53590573--53590650 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
53590563 TCATGATAAT
*
53590573 TTTCTAAGTTTTCCCAAAAATTTTTAAAGTTCAGTTTAG
1 TTTCTAAGTTTTCCCAAAAAATTTTAAAGTTCAGTTTAG
53590612 TTTCTAAG-TTTCCCAAAAAATTTTAAAGTTCAGTTTAG
1 TTTCTAAGTTTTCCCAAAAAATTTTAAAGTTCAGTTTAG
53590650 T
1 T
53590651 CCCGAACTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 30 0.79
39 8 0.21
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (39 bp):
TTTCTAAGTTTTCCCAAAAAATTTTAAAGTTCAGTTTAG
Found at i:53605526 original size:88 final size:87
Alignment explanation
Indices: 53605424--53605586 Score: 236
Period size: 87 Copynumber: 1.9 Consensus size: 87
53605414 CAGCGCATTG
* * * *
53605424 CGGTAAACCGCTGTATAGACAGGTTGCAGTTTAAACTACCAGATTAGATAATAGTACGCAACAAA
1 CGGTAAACCACTGTACAGACAAGTTGCAG-TTAAACTACCAGATCAGATAATAGTACGCAACAAA
*
53605489 GTTGACGTACATGTGGTACAGTA
65 GATGACGTACATGTGGTACAGTA
* * * *
53605512 CGGTAAACTACTGTACAGATAAGTTGCAGTTAAACTGCCAGATCAGATAATAGTACGCAGCAAAG
1 CGGTAAACCACTGTACAGACAAGTTGCAGTTAAACTACCAGATCAGATAATAGTACGCAACAAAG
53605577 ATGACGTACA
66 ATGACGTACA
53605587 AGCGATATAG
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
87 42 0.64
88 24 0.36
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (87 bp):
CGGTAAACCACTGTACAGACAAGTTGCAGTTAAACTACCAGATCAGATAATAGTACGCAACAAAG
ATGACGTACATGTGGTACAGTA
Found at i:53605564 original size:87 final size:87
Alignment explanation
Indices: 53605446--53605639 Score: 253
Period size: 87 Copynumber: 2.2 Consensus size: 87
53605436 GTATAGACAG
* * * * * *
53605446 GTTGCAGTTTAAACTACCAGATTAGATAATAGTACGCAACAAAGTTGACGTACATGTGGTACAGT
1 GTTGCAG-TTAAACTGCCAGATCAGATAATAGTACGCAACAAAGATGACGTACAAGCGATACAGT
*
53605511 ACGGTAAACTACTGTACAGATAA
65 ACAGTAAACTACTGTACAGATAA
* * *
53605534 GTTGCAGTTAAACTGCCAGATCAGATAATAGTACGCAGCAAAGATGACGTACAAGCGATATAGTG
1 GTTGCAGTTAAACTGCCAGATCAGATAATAGTACGCAACAAAGATGACGTACAAGCGATACAGTA
* * *
53605599 CAGTAAATTGCTGTACCGATAA
66 CAGTAAACTACTGTACAGATAA
*
53605621 GTTGTAGTTAAACTGCCAG
1 GTTGCAGTTAAACTGCCAG
53605640 TTCAAAACAT
Statistics
Matches: 92, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
87 85 0.92
88 7 0.08
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (87 bp):
GTTGCAGTTAAACTGCCAGATCAGATAATAGTACGCAACAAAGATGACGTACAAGCGATACAGTA
CAGTAAACTACTGTACAGATAA
Found at i:53606941 original size:15 final size:15
Alignment explanation
Indices: 53606921--53606962 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
53606911 AAATCCAAAC
*
53606921 TAAATACATATTTAA
1 TAAATAAATATTTAA
53606936 TAAATAAATATTTAA
1 TAAATAAATATTTAA
*
53606951 CAAATAAATATT
1 TAAATAAATATT
53606963 AAATTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAATAAATATTTAA
Found at i:53612132 original size:48 final size:48
Alignment explanation
Indices: 53612058--53612286 Score: 167
Period size: 48 Copynumber: 4.8 Consensus size: 48
53612048 TGAATTACCG
* * * * *
53612058 ATGCCATGTTCCAAACATGGTCTTACACTGGCTTACATGTCGAGGCCA
1 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATCTCAAGGCCA
* ** * *
53612106 ATTCCATGTCCCTGACATGGTCTTACACTAGCTCGCATCTCAATGCCA
1 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATCTCAAGGCCA
* * * ** *
53612154 ATGCCATGTTCCAAACATGGTCTTACA-TTGTCTCTCAT-TACATTGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTAG-CTCACATCT-CAAGGCCA
* * * * * ** *
53612202 ATGCCATGTCCTAGACATGGCCTTACACT-GCTCTCATATCGTGGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATCTCAAGGCCA
* * * *
53612249 ATGCCATGACCCAGACATGGTCTTGCACTAGCACACAT
1 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCACAT
53612287 ATCACCCAAA
Statistics
Matches: 146, Mismatches: 30, Indels: 10
0.78 0.16 0.05
Matches are distributed among these distances:
47 41 0.28
48 104 0.71
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (48 bp):
ATGCCATGTCCCAAACATGGTCTTACACTAGCTCACATCTCAAGGCCA
Found at i:53612227 original size:96 final size:95
Alignment explanation
Indices: 53612058--53612234 Score: 227
Period size: 96 Copynumber: 1.9 Consensus size: 95
53612048 TGAATTACCG
*
53612058 ATGCCATGTTCCAAACATGGTCTTACACTGGCTTACATGTCGAGGCCAATTCCATGTCCCTGACA
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTTACATGTCGAGGCCAATGCCATGTCCCTGACA
*
53612123 TGGTCTTACACTAGCTCGCATCTCAATGCCA
66 TGGCCTTACACT-GCTCGCATCTCAATGCCA
* * * *
53612154 ATGCCATGTTCCAAACATGGTCTTACATTGTCTCT-CAT-TAC-ATTGCCGATGCCATGT-CCTA
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCT-TACATGT-CGA-GGCCAATGCCATGTCCCT-
53612215 GACATGGCCTTACACTGCTC
62 GACATGGCCTTACACTGCTC
53612235 TCATATCGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
95 9 0.13
96 61 0.86
97 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (95 bp):
ATGCCATGTTCCAAACATGGTCTTACACTGGCTTACATGTCGAGGCCAATGCCATGTCCCTGACA
TGGCCTTACACTGCTCGCATCTCAATGCCA
Found at i:53614637 original size:43 final size:42
Alignment explanation
Indices: 53614590--53614756 Score: 115
Period size: 43 Copynumber: 3.9 Consensus size: 42
53614580 AACATATAAA
* * *
53614590 ATGCCAACATCCCAGACGTGGTCTTACATGTAATCAAACATCG
1 ATGCCAACATCCCAAACGTGGTCTTACACGAAATCAAA-ATCG
* * * *
53614633 ATGCC-ACTATCCCAAACAG-GATCTTACATGAAAT-TAGATACG
1 ATGCCAAC-ATCCCAAAC-GTGGTCTTACACGAAATCAAAAT-CG
* ** * * * *
53614675 ATGTCAATGTCCCAAACATGGTCTTACACATAAAACAGAAATCA
1 ATGCCAACATCCCAAACGTGGTCTTACAC-GAAATCA-AAATCG
* *
53614719 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATCAAA
1 ATGCCAACATCCCAAACGTGGTCTTACACGAAATCAAA
53614757 TAACAAAATC
Statistics
Matches: 94, Mismatches: 22, Indels: 17
0.71 0.17 0.13
Matches are distributed among these distances:
41 2 0.02
42 27 0.29
43 35 0.37
44 27 0.29
45 3 0.03
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (42 bp):
ATGCCAACATCCCAAACGTGGTCTTACACGAAATCAAAATCG
Found at i:53615064 original size:26 final size:26
Alignment explanation
Indices: 53615034--53615100 Score: 109
Period size: 26 Copynumber: 2.5 Consensus size: 26
53615024 TAATTCTTGA
53615034 TCTATATAAATTCAAATTTAACTTAT
1 TCTATATAAATTCAAATTTAACTTAT
53615060 TCTATATAAATTCAAATTTAACTTAT
1 TCTATATAAATTCAAATTTAACTTAT
53615086 T-TAATCATAAATTCA
1 TCT-AT-ATAAATTCA
53615101 TTCAAAACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
25 1 0.03
26 29 0.74
27 9 0.23
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (26 bp):
TCTATATAAATTCAAATTTAACTTAT
Found at i:53623829 original size:47 final size:47
Alignment explanation
Indices: 53623607--53624105 Score: 701
Period size: 47 Copynumber: 10.4 Consensus size: 47
53623597 CAGCCAAGAG
* *
53623607 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53623654 AGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTA--TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53623703 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
53623754 AGTGTATGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
53623805 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
53623852 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
53623899 AGTGTATATATGTAATAAGGCCTAATGGCTGATGTGATGAATATGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
53623946 AGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
53623993 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * * *
53624040 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
53624087 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
53624106 TCCCGAAAGG
Statistics
Matches: 416, Mismatches: 30, Indels: 12
0.91 0.07 0.03
Matches are distributed among these distances:
47 279 0.67
49 41 0.10
51 92 0.22
53 4 0.01
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:53624280 original size:37 final size:37
Alignment explanation
Indices: 53624224--53624302 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
53624214 CCGAGCTCTA
* * *
53624224 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
53624261 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
53624298 AAGAC
1 AAGAC
53624303 TTTGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:53633199 original size:45 final size:45
Alignment explanation
Indices: 53633135--53633225 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
53633125 AATCTTGTCA
*
53633135 CCCTATCTCTAGGCGTGCAATCAACTCCGCTTAATTATTTAAGAT
1 CCCTATCTCTAGGCGTGCAATCAACTCCGCTCAATTATTTAAGAT
* *
53633180 CCCTATCTCTAGGTGTGCAATCAACTTCGCTCAATTATTTAAGAT
1 CCCTATCTCTAGGCGTGCAATCAACTCCGCTCAATTATTTAAGAT
53633225 C
1 C
53633226 TACTCTTAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (45 bp):
CCCTATCTCTAGGCGTGCAATCAACTCCGCTCAATTATTTAAGAT
Found at i:53639096 original size:37 final size:37
Alignment explanation
Indices: 53639032--53639107 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
53639022 TTACAAGCCA
53639032 AAATCATTATAAGCCACATCTCATGGCTACAT-ACAAC
1 AAATCATTATAAGCCACATCTCATGGCTA-ATCACAAC
*
53639069 AAATCATTATAAGCCA-ATACAT-TTGGCTAATCACAAC
1 AAATCATTATAAGCCACAT-C-TCATGGCTAATCACAAC
53639106 AA
1 AA
53639108 CATCGATCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 4 0.11
37 30 0.86
38 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (37 bp):
AAATCATTATAAGCCACATCTCATGGCTAATCACAAC
Found at i:53657185 original size:18 final size:18
Alignment explanation
Indices: 53657162--53657202 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
53657152 ATAAGTATAA
53657162 AATTAAACGAATTAACTG
1 AATTAAACGAATTAACTG
* *
53657180 AATTAATCGAATTACCTG
1 AATTAAACGAATTAACTG
53657198 AATTA
1 AATTA
53657203 CCCAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (18 bp):
AATTAAACGAATTAACTG
Found at i:53657219 original size:9 final size:9
Alignment explanation
Indices: 53657162--53657220 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
53657152 ATAAGTATAA
*
53657162 AATTAAACG
1 AATTAACCG
*
53657171 AATTAACTG
1 AATTAACCG
*
53657180 AATTAATCG
1 AATTAACCG
53657189 AATT-ACCTG
1 AATTAACC-G
* *
53657198 AATTACCCA
1 AATTAACCG
53657207 AATTAACCG
1 AATTAACCG
53657216 AATTA
1 AATTA
53657221 TTTGTATAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
8 2 0.05
9 35 0.90
10 2 0.05
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:53657256 original size:5 final size:6
Alignment explanation
Indices: 53657241--53657281 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
53657231 ATTATATGTT
*
53657241 TTTTTA TTTTTA TTTTTA GTTTTATA TTTTTA TTATTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
53657282 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 21 0.68
7 8 0.26
8 2 0.06
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:53657317 original size:5 final size:5
Alignment explanation
Indices: 53657307--53657355 Score: 62
Period size: 5 Copynumber: 9.2 Consensus size: 5
53657297 ATTTTTATGA
*
53657307 TTGGG TTGGG TAATTGGG TTGGG TTGGG TTGGG TTCGG TTGGG TTGGG
1 TTGGG TTGGG T---TGGG TTGGG TTGGG TTGGG TTGGG TTGGG TTGGG
53657355 T
1 T
53657356 ACTTGGGTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 34 0.87
8 5 0.13
ACGTcount: A:0.04, C:0.02, G:0.53, T:0.41
Consensus pattern (5 bp):
TTGGG
Found at i:53662581 original size:27 final size:26
Alignment explanation
Indices: 53662543--53662654 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
53662533 CAGCATGGAT
* *
53662543 ACCAGAACAGATAATGTGACAGAGTC
1 ACCAGAACAGATAATGTGGCAGAGCC
53662569 ACCAGATACAGATAATCGTGGCAGAGCC
1 ACCAGA-ACAGATAAT-GTGGCAGAGCC
*
53662597 ACCAGAACAGATATATGTGGCAAAGCC
1 ACCAGAACAGATA-ATGTGGCAGAGCC
* * *
53662624 ACCAGATCAGATATTTGTGGCATAGCC
1 ACCAGAACAGATA-ATGTGGCAGAGCC
53662651 ACCA
1 ACCA
53662655 AAACGCTTCC
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
26 6 0.08
27 54 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (26 bp):
ACCAGAACAGATAATGTGGCAGAGCC
Found at i:53662607 original size:54 final size:54
Alignment explanation
Indices: 53662543--53662654 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
53662533 CAGCATGGAT
* *
53662543 ACCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCC
1 ACCAGAACAGATATATGTGACAAAGCCACCAGAT-CAGATAATCGTGGCAGAGCC
* * * *
53662597 ACCAGAACAGATATATGTGGCAAAGCCACCAGATCAGATATTTGTGGCATAGCC
1 ACCAGAACAGATATATGTGACAAAGCCACCAGATCAGATAATCGTGGCAGAGCC
53662651 ACCA
1 ACCA
53662655 AAACGCTTCC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (54 bp):
ACCAGAACAGATATATGTGACAAAGCCACCAGATCAGATAATCGTGGCAGAGCC
Found at i:53664362 original size:25 final size:26
Alignment explanation
Indices: 53664268--53664376 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
53664258 CATGAAATTC
53664268 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
53664294 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
53664320 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
53664346 TTATCATG-AACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
53664371 TTATCA
1 TTATCA
53664377 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
25 23 0.28
26 58 0.72
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:53668383 original size:27 final size:26
Alignment explanation
Indices: 53668346--53668460 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
53668336 AGCATGGCTG
* *
53668346 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
53668372 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
* *
53668400 CCAGAACAAATATATGTGGCAAAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
53668427 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
53668454 CCAGAAC
1 CCAGAAC
53668461 GCTTCCTCCA
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
26 5 0.06
27 55 0.71
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:53668405 original size:54 final size:54
Alignment explanation
Indices: 53668346--53668460 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
53668336 AGCATGGCTG
* * *
53668346 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAAATATATGTGACAAAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
53668400 CCAGAACAAATATATGTGGCAAAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAAATATATGTGACAAAGCCACCAGATCAGATAATCGTGGCAGAGCCA
53668454 CCAGAAC
1 CCAGAAC
53668461 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 36 0.68
55 17 0.32
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (54 bp):
CCAGAACAAATATATGTGACAAAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:53670106 original size:26 final size:26
Alignment explanation
Indices: 53670070--53670179 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
53670060 CATGAAATTC
53670070 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
53670096 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
53670122 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
53670148 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
53670174 TTATCA
1 TTATCA
53670180 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:53673631 original size:44 final size:45
Alignment explanation
Indices: 53673564--53673694 Score: 169
Period size: 45 Copynumber: 3.0 Consensus size: 45
53673554 TCGAATTTAT
* * *
53673564 TCACCGGCATT-TTGCCTGCTAGGCTC-GAGGCCCGAAA-AATATC
1 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCC-AAATAATATC
*
53673607 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAATGTC
1 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAATATC
* * *
53673652 TCCCTAGCATTATAGCCTGCTAGGCTCCAAGGCCCAAATAATA
1 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAATA
53673695 CTGTACAACA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
43 10 0.13
44 17 0.22
45 50 0.65
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (45 bp):
TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAATATC
Found at i:53681682 original size:45 final size:44
Alignment explanation
Indices: 53681584--53681712 Score: 152
Period size: 45 Copynumber: 2.9 Consensus size: 44
53681574 CCAAATTTAT
* * * * *
53681584 TCACCAGCATT-TTGCTTGCTAGGCTCGAGGCTCGAAAAATATC
1 TCACCAGCATTATAGCCTGCTAGGCTCAAGGCTCGAATAAGATC
** * *
53681627 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAAGGTC
1 TCACCAGCATTATAGCCTGCTAGGCTC-AAGGCTCGAATAAGATC
53681672 TCACCAGCATTATAGCCTGCTAGGCTCCAAGGCTCGAATAA
1 TCACCAGCATTATAGCCTGCTAGGCT-CAAGGCTCGAATAA
53681713 TACTGTACAA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
43 9 0.13
44 13 0.18
45 48 0.68
46 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (44 bp):
TCACCAGCATTATAGCCTGCTAGGCTCAAGGCTCGAATAAGATC
Found at i:53684442 original size:13 final size:14
Alignment explanation
Indices: 53684424--53684453 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
53684414 ATGGACTTGC
53684424 TTGTACCTAA-GGA
1 TTGTACCTAAGGGA
53684437 TTGTACCTAAGGGA
1 TTGTACCTAAGGGA
53684451 TTG
1 TTG
53684454 CAATTTGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (14 bp):
TTGTACCTAAGGGA
Found at i:53685462 original size:53 final size:53
Alignment explanation
Indices: 53685399--53685504 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
53685389 CTTGACCTAC
53685399 AAGCTCATGTAACCTTATTTAAATATATAAAATGTAATAAAAACTACTAGAAA
1 AAGCTCATGTAACCTTATTTAAATATATAAAATGTAATAAAAACTACTAGAAA
53685452 AAGCTCATGTAACCTTATTTAAATATATAAAATGTAATAAAAACTACTAGAAA
1 AAGCTCATGTAACCTTATTTAAATATATAAAATGTAATAAAAACTACTAGAAA
53685505 GCATAAATTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (53 bp):
AAGCTCATGTAACCTTATTTAAATATATAAAATGTAATAAAAACTACTAGAAA
Found at i:53688054 original size:24 final size:24
Alignment explanation
Indices: 53688027--53688079 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
53688017 TTTAAGCTAC
* * * *
53688027 ATGTTAGTGGTTACTTCTACTTTT
1 ATGTCAGTGGCTACATCTACTATT
53688051 ATGTCAGTGGCTACATCTACTATT
1 ATGTCAGTGGCTACATCTACTATT
53688075 ATGTC
1 ATGTC
53688080 TAATTCTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (24 bp):
ATGTCAGTGGCTACATCTACTATT
Found at i:53689141 original size:17 final size:20
Alignment explanation
Indices: 53689105--53689142 Score: 55
Period size: 17 Copynumber: 2.0 Consensus size: 20
53689095 CGCGAGTTCC
53689105 TTTAGCCTAGATTCAATTAT
1 TTTAGCCTAGATTCAATTAT
53689125 TTTA-CCTA-ATT-AATTAT
1 TTTAGCCTAGATTCAATTAT
53689142 T
1 T
53689143 GATGTAGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 4 0.22
20 4 0.22
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTAGCCTAGATTCAATTAT
Found at i:53691444 original size:22 final size:22
Alignment explanation
Indices: 53691419--53691477 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
53691409 GATTTTAATT
53691419 TAGTTTTATTTTCTTCGAAAAA
1 TAGTTTTATTTTCTTCGAAAAA
*
53691441 TAGTTTTATTTTCTTCTAAAAA
1 TAGTTTTATTTTCTTCGAAAAA
53691463 TAGTTTTATTTTCTT
1 TAGTTTTATTTTCTT
53691478 ATTCTTCAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.58
Consensus pattern (22 bp):
TAGTTTTATTTTCTTCGAAAAA
Found at i:53693729 original size:56 final size:56
Alignment explanation
Indices: 53693664--53693770 Score: 214
Period size: 56 Copynumber: 1.9 Consensus size: 56
53693654 ATTTGAGCAT
53693664 AATGATGCATGTTTGGAAATGTCTAATTAGTTGAAATGTATATGTGAATTTTTTTG
1 AATGATGCATGTTTGGAAATGTCTAATTAGTTGAAATGTATATGTGAATTTTTTTG
53693720 AATGATGCATGTTTGGAAATGTCTAATTAGTTGAAATGTATATGTGAATTT
1 AATGATGCATGTTTGGAAATGTCTAATTAGTTGAAATGTATATGTGAATTT
53693771 GGTATAAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (56 bp):
AATGATGCATGTTTGGAAATGTCTAATTAGTTGAAATGTATATGTGAATTTTTTTG
Found at i:53701644 original size:48 final size:48
Alignment explanation
Indices: 53701563--53701756 Score: 217
Period size: 48 Copynumber: 4.0 Consensus size: 48
53701553 TAGGGTTATG
* * * * *
53701563 TGTGATCCCAGGAAAGAGCATGTCTAGGACATGGCATTGGCATTGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* * * *
53701611 TGTGATCCCATGTAAGACCAGGTCTGGGGCATGGCATTGGGATCGATT
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* * * *
53701659 TGTGATCTCATGTAAAACCATGTCTGGGACATGGCATTGGTATCAATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* * * * * *
53701707 TTTGATCTCATGTAAGACCATATCTGGGATATGGCATTAGTATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
53701755 TG
1 TG
53701757 AGACATCGTA
Statistics
Matches: 123, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 123 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
Found at i:53701771 original size:48 final size:48
Alignment explanation
Indices: 53701589--53701776 Score: 135
Period size: 48 Copynumber: 3.9 Consensus size: 48
53701579 AGCATGTCTA
* * ** * * * **
53701589 GGACATGGCATTGGCATTGATATGTGATCCCATGTAAGACCAGGTCTG
1 GGACATGGCATTAGTATCAATATGAGATCTCATATAAGACCATATCTG
* * * * * * * * *
53701637 GGGCATGGCATTGGGATCGATTTGTGATCTCATGTAAAACCATGTCTG
1 GGACATGGCATTAGTATCAATATGAGATCTCATATAAGACCATATCTG
* ** *
53701685 GGACATGGCATTGGTATCAATATTTGATCTCATGTAAGACCATATCTG
1 GGACATGGCATTAGTATCAATATGAGATCTCATATAAGACCATATCTG
* * *
53701733 GGATATGGCATTAGTATCGATATGAGA-CATCGTATAAGACCATA
1 GGACATGGCATTAGTATCAATATGAGATC-TCATATAAGACCATA
53701777 GATGGGCTAT
Statistics
Matches: 118, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
47 1 0.01
48 117 0.99
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (48 bp):
GGACATGGCATTAGTATCAATATGAGATCTCATATAAGACCATATCTG
Found at i:53705079 original size:45 final size:45
Alignment explanation
Indices: 53705009--53705119 Score: 177
Period size: 45 Copynumber: 2.5 Consensus size: 45
53704999 GCCGATATCT
* * *
53705009 AGACATGGTCTTACACATAACCACATATATCGATGCCAATGTCCC
1 AGACGTGGTCTTACACAAAATCACATATATCGATGCCAATGTCCC
*
53705054 AGACGTGGTCTTACACAAAATCACATATATCGATGCCAATGTCCT
1 AGACGTGGTCTTACACAAAATCACATATATCGATGCCAATGTCCC
*
53705099 AGATGTGGTCTTACACAAAAT
1 AGACGTGGTCTTACACAAAAT
53705120 AAAATATTGG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (45 bp):
AGACGTGGTCTTACACAAAATCACATATATCGATGCCAATGTCCC
Found at i:53706236 original size:14 final size:15
Alignment explanation
Indices: 53706219--53706247 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53706209 GAACAAAAAT
53706219 TTCACACAT-ATAAA
1 TTCACACATAATAAA
53706233 TTCACACATAATAAA
1 TTCACACATAATAAA
53706248 CACAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:53710225 original size:41 final size:41
Alignment explanation
Indices: 53710168--53710249 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
53710158 TTTTGTAAGA
53710168 GTGACTCTTCCTACAATTGACAAAGCACATGCCTCCCAACC
1 GTGACTCTTCCTACAATTGACAAAGCACATGCCTCCCAACC
* * *
53710209 GTGACTTTTCCTACAATTGACAAAGCACGTGCCTTCCAACC
1 GTGACTCTTCCTACAATTGACAAAGCACATGCCTCCCAACC
53710250 ATTTAGTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.28, C:0.34, G:0.13, T:0.24
Consensus pattern (41 bp):
GTGACTCTTCCTACAATTGACAAAGCACATGCCTCCCAACC
Found at i:53713131 original size:17 final size:19
Alignment explanation
Indices: 53713105--53713147 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
53713095 CAATATAAAC
53713105 ATTAAAATAA-A-TTTAAT
1 ATTAAAATAACACTTTAAT
*
53713122 ATTAAGATAATCACTTTAAT
1 ATTAAAATAA-CACTTTAAT
53713142 ATTAAA
1 ATTAAA
53713148 TTAATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 9 0.43
19 1 0.05
20 11 0.52
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
ATTAAAATAACACTTTAAT
Found at i:53713573 original size:9 final size:9
Alignment explanation
Indices: 53713550--53713580 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
53713540 AAAATATCAT
53713550 ATTAATTTCA
1 ATTAATTT-A
53713560 ATTAATTTA
1 ATTAATTTA
53713569 ATTAATTTA
1 ATTAATTTA
53713578 ATT
1 ATT
53713581 TTACTTAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (9 bp):
ATTAATTTA
Found at i:53716791 original size:29 final size:29
Alignment explanation
Indices: 53716728--53716795 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
53716718 TAATCAACCA
53716728 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
53716757 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
53716786 CGCACACTTA
1 CGCACACTTA
53716796 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:53716935 original size:29 final size:30
Alignment explanation
Indices: 53716896--53716974 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
53716886 CTTAATAATC
53716896 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
53716926 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
53716955 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
53716975 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:53716940 original size:173 final size:174
Alignment explanation
Indices: 53716617--53716943 Score: 541
Period size: 173 Copynumber: 1.9 Consensus size: 174
53716607 AACTCAAGGT
* *
53716617 ACTTACCTTTTTCCACTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTAT
1 ACTTACCTTTTTCCACTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
* *
53716682 AGAAAATATATATTGGGTTGCACACATAACGTTTAGTAATCAACCACGCACACTTAGTGCCATGC
66 AGAAAATATATATTGGGTTGCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATGC
53716747 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
53716791 ACTTACC-TTTTCCGCTGT-CAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
1 ACTTACCTTTTTCCACTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
** *
53716854 AGAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATG
66 AGAAAATATATATTGGGTT-GCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATG
* *
53716919 TACTTTAAACTCGCACACTTAGTGC
130 CACTTTAAACTCACACACTTAGTGC
53716944 TGTACAATTT
Statistics
Matches: 142, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
172 62 0.44
173 73 0.51
174 7 0.05
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTTCCACTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTAT
AGAAAATATATATTGGGTTGCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:53728861 original size:18 final size:18
Alignment explanation
Indices: 53728838--53728880 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
53728828 GATATGGTGT
53728838 ATATTTTG-ATTTTTCAAA
1 ATATTTTGAATTTTT-AAA
*
53728856 ATATTTAGAATTTTTAAA
1 ATATTTTGAATTTTTAAA
*
53728874 TTATTTT
1 ATATTTT
53728881 TTTTAATTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (18 bp):
ATATTTTGAATTTTTAAA
Found at i:53734112 original size:22 final size:22
Alignment explanation
Indices: 53734086--53734128 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
53734076 GACGCAGCGA
* * *
53734086 TACTCCACAGACAGGTTGGAGG
1 TACTCCAAAAACAGGCTGGAGG
53734108 TACTCCAAAAACAGGCTGGAG
1 TACTCCAAAAACAGGCTGGAG
53734129 TTTGAGCCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.16
Consensus pattern (22 bp):
TACTCCAAAAACAGGCTGGAGG
Found at i:53742400 original size:15 final size:15
Alignment explanation
Indices: 53742380--53742429 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
53742370 ATCTAGATAT
53742380 TTATTTGACCCATAC
1 TTATTTGACCCATAC
* * *
53742395 TTATTT-ATCTAGAC
1 TTATTTGACCCATAC
*
53742409 CTATTTGACCCATAC
1 TTATTTGACCCATAC
53742424 TTATTT
1 TTATTT
53742430 ATTAACTGAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.26, C:0.22, G:0.06, T:0.46
Consensus pattern (15 bp):
TTATTTGACCCATAC
Found at i:53745264 original size:36 final size:37
Alignment explanation
Indices: 53745181--53745331 Score: 252
Period size: 36 Copynumber: 4.1 Consensus size: 37
53745171 TTATTACGAA
* * * *
53745181 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
53745218 GTCTTACCCGGACAAAATCCCCACACGTAGTCATC-G
1 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
53745254 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
53745291 GTCTTACCCGGAC-AAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
53745327 GTCTT
1 GTCTT
53745332 TAGAGCTCGG
Statistics
Matches: 109, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
36 64 0.59
37 45 0.41
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.22
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
Found at i:53745300 original size:73 final size:73
Alignment explanation
Indices: 53745181--53745331 Score: 250
Period size: 73 Copynumber: 2.1 Consensus size: 73
53745171 TTATTACGAA
* * *
53745181 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGGGTCTTACCCGGACAAAATCCCCACACGT
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGGGTCTTACCCGGAC-AAATCCCCACACGT
53745246 AGTCATC-G
65 AGTCATCGG
*
53745254 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGGGTCTTACCCGGACAAATCCCCACACGTA
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGGGTCTTACCCGGACAAATCCCCACACGTA
53745319 GTCATCGG
66 GTCATCGG
53745327 GTCTT
1 GTCTT
53745332 TAGAGCTCGG
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 21 0.29
73 52 0.71
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.22
Consensus pattern (73 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGGGTCTTACCCGGACAAATCCCCACACGTA
GTCATCGG
Done.