Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008150.1 Hibiscus syriacus cultivar Beakdansim tig00110716_pilon, whole genome shotgun sequence
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: 3012591
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:2858578 original size:2 final size:2
Alignment explanation
Indices: 2858571--2858615 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2858561 AATATGAATC
2858571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2858613 AT A
1 AT A
2858616 AATTAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2858848 original size:2 final size:2
Alignment explanation
Indices: 2858841--2858905 Score: 103
Period size: 2 Copynumber: 32.0 Consensus size: 2
2858831 CATATGCAAT
2858841 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
* *
2858883 TA TA CA TA TA TCA TA TA AA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA
2858906 GACACTTGAC
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 56 0.97
3 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2863567 original size:131 final size:130
Alignment explanation
Indices: 2863303--2863665 Score: 394
Period size: 131 Copynumber: 2.8 Consensus size: 130
2863293 CGATAGCGAG
* * * * * * * *
2863303 AATAATAATATCTTTTCA-TTC-AGTTGGAGTAATAAATGAAT-GCTCTAAAGCATGAGAGTTTA
1 AATAGTAATATCTCTTCATTTCGA-TCGGAGCAATAAATG-ATCGTTCTAAGGCATGAGAGGTCA
* * * * * * * *
2863365 TTTATTTTCGATTGGAAATAATACGATATTATCATTCTCCCTCGAATTAATATTGATTTTTAGGA
64 TTTATTCTCGATTGGAAATAATA-GATATTATTATTTTCACTAGAATCAATATTGAATTTTAAGA
*
2863430 TGA
128 CGA
* *
2863433 AATAGTGATATCTCTTCATTTCGATCGGAGCAATAAATG-TCTGCTTC-AAGGTATGAGAGGTCA
1 AATAGTAATATCTCTTCATTTCGATCGGAGCAATAAATGATC-G-TTCTAAGGCATGAGAGGTCA
* * *
2863496 TTAATTCTCGATTGGAAATCATCAGATATTATTATTTTCACTAGGATCAATATTGAATTTTAAGA
64 TTTATTCTCGATTGGAAATAAT-AGATATTATTATTTTCACTAGAATCAATATTGAATTTTAAGA
2863561 CGA
128 CGA
* * * *
2863564 AATAGTAATATCTCTTTATTTCGATTGGAGTAATAAATGATCGTTCTAAGGCATGAAAGGTCATT
1 AATAGTAATATCTCTTCATTTCGATCGGAGCAATAAATGATCGTTCTAAGGCATGAGAGGTCATT
2863629 TATTCTCGATTGGAAATAATTAGATATTATTATTTTC
66 TATTCTCGATTGGAAATAA-TAGATATTATTATTTTC
2863666 TCTATCAAAA
Statistics
Matches: 194, Mismatches: 30, Indels: 17
0.80 0.12 0.07
Matches are distributed among these distances:
129 1 0.01
130 18 0.09
131 168 0.87
132 7 0.04
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39
Consensus pattern (130 bp):
AATAGTAATATCTCTTCATTTCGATCGGAGCAATAAATGATCGTTCTAAGGCATGAGAGGTCATT
TATTCTCGATTGGAAATAATAGATATTATTATTTTCACTAGAATCAATATTGAATTTTAAGACGA
Found at i:2865654 original size:18 final size:18
Alignment explanation
Indices: 2865631--2865733 Score: 106
Period size: 16 Copynumber: 5.8 Consensus size: 18
2865621 AGGGATTATC
2865631 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
2865649 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
* * *
2865668 CAGTGGTCTTTCGAGATAT
1 -AGTGGTCCTTCGGGACAT
2865687 AGTGGTCCTTCGGGAC--
1 AGTGGTCCTTCGGGACAT
*
2865703 AGTGGTTCTTCGGGAC--
1 AGTGGTCCTTCGGGACAT
2865719 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
2865734 AAAATATTCA
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
16 29 0.41
18 27 0.38
19 4 0.06
20 11 0.15
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2865680 original size:20 final size:19
Alignment explanation
Indices: 2865628--2865680 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
2865618 TCGAGGGATT
* *
2865628 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCTTTCGGAAC
2865647 AT-AGTGGT-TCTTCGGAAC
1 ATCAGTGGTCT-TTCGGAAC
2865665 AATCAGTGGTCTTTCG
1 -ATCAGTGGTCTTTCG
2865681 AGATATAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 13 0.46
19 4 0.14
20 10 0.36
21 1 0.04
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (19 bp):
ATCAGTGGTCTTTCGGAAC
Found at i:2865992 original size:2 final size:2
Alignment explanation
Indices: 2865985--2866029 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2865975 AATGCATTGT
*
2865985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2866026 TA TA
1 TA TA
2866030 CCTCACTAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2870725 original size:64 final size:64
Alignment explanation
Indices: 2870593--2870748 Score: 181
Period size: 64 Copynumber: 2.4 Consensus size: 64
2870583 CAATGTGCAT
* * * * * * *
2870593 CGATGCACATGAAGTGTATCGATGCACTTCTTTAAAATAAAAACATCGAATGTCATTAGTGTAT
1 CGATGCACAAGTAGTGCATCGATGCACCTCCTTAAAATAAAAACATCGAATGGCATTAGTGTAC
* *
2870657 CGATGCACAAGTAGTGCATCGATGCACCTCCTTAAAATACAAACATCGAATGGGATTTA-TGTAC
1 CGATGCACAAGTAGTGCATCGATGCACCTCCTTAAAATAAAAACATCGAATGGCA-TTAGTGTAC
* *
2870721 CGATGCA-TAGATTGTGCATCGATGCACC
1 CGATGCACAAG-TAGTGCATCGATGCACC
2870749 CGTCAAGGGA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 2 0.03
64 74 0.94
65 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
CGATGCACAAGTAGTGCATCGATGCACCTCCTTAAAATAAAAACATCGAATGGCATTAGTGTAC
Found at i:2871364 original size:20 final size:19
Alignment explanation
Indices: 2871318--2871386 Score: 97
Period size: 18 Copynumber: 3.7 Consensus size: 19
2871308 TCGAGGGCTT
2871318 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
* *
2871337 AT-AGTGGTTCTTCGGTAC
1 ATCAGTGGTCCTTCGGGAC
2871355 AATCAGTGGTCCTTCGGGAC
1 -ATCAGTGGTCCTTCGGGAC
2871375 AT-AGTGGTCCTT
1 ATCAGTGGTCCTT
2871387 TAGGACAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
18 24 0.55
19 6 0.14
20 14 0.32
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.32
Consensus pattern (19 bp):
ATCAGTGGTCCTTCGGGAC
Found at i:2871651 original size:2 final size:2
Alignment explanation
Indices: 2871644--2871672 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2871634 AATTCATTGT
2871644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2871673 TATGCCTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2873275 original size:20 final size:20
Alignment explanation
Indices: 2873238--2873276 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2873228 TTTCCACCAC
**
2873238 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATAATCCTAA
*
2873258 ATGCATCTATATAATCCTA
1 ATGCAACTATATAATCCTA
2873277 TATGAGCTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATAATCCTAA
Found at i:2875139 original size:133 final size:134
Alignment explanation
Indices: 2874898--2875197 Score: 419
Period size: 133 Copynumber: 2.3 Consensus size: 134
2874888 AACATTGGGA
* * * *
2874898 CAGATCTAATTTTCCCTC-GGAAAGAAGCGGAACAAAACCCTCTCTTTCAAGATTTGATATTCCC
1 CAGATCTGATTTTCCCTCAGG-AAGAAGCGGAACATAACCATCTCTTTCAAGATTTAATATTCCC
* * * *
2874962 TGAGTAATTGTGGAACAAGTCTGCCTTGATTCAATCGTCTCTGAGTGA-AGTAGAATGAATCAAC
65 TGAGCAACTATGGAACAAGTCTGCCTTGATTCAATCGTCCCTGAGTGACAGTAGAATGAATCAAC
2875026 GTCCC
130 GTCCC
* **
2875031 CAGATCTGATTTTCCCTCAGGAAGAAGCGGAACATATCCATCTCTTTCAAGATTTAATATTCTTT
1 CAGATCTGATTTTCCCTCAGGAAGAAGCGGAACATAACCATCTCTTTCAAGATTTAATATTCCCT
* * *
2875096 GAGCAACTATGGAATAAGTCTGCCTTGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACG
66 GAGCAACTATGGAACAAGTCTGCCTTGATTCAATCGTCCCTGAGTGACAGTAGAATGAATCAACG
2875161 TCCC
131 TCCC
* *
2875165 CATATCTGATTTTCCCTCA-AAAGAAG-GGAACAT
1 CAGATCTGATTTTCCCTCAGGAAGAAGCGGAACAT
2875198 GTAACACTCA
Statistics
Matches: 149, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
132 7 0.05
133 102 0.68
134 40 0.27
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (134 bp):
CAGATCTGATTTTCCCTCAGGAAGAAGCGGAACATAACCATCTCTTTCAAGATTTAATATTCCCT
GAGCAACTATGGAACAAGTCTGCCTTGATTCAATCGTCCCTGAGTGACAGTAGAATGAATCAACG
TCCC
Found at i:2875919 original size:46 final size:46
Alignment explanation
Indices: 2875859--2876062 Score: 257
Period size: 46 Copynumber: 4.4 Consensus size: 46
2875849 TTTAAGCTGT
* * * * *
2875859 TAATACACTGTTATGTATTTTCATTTGTGGCATCCTTTCAT-TCCAA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATAT-CGA
* * * * *
2875905 TTATGCACCATTATGCATTTTCATTTATGGAATCCTTTCATGTTGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATATCGA
2875951 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATATCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATATCGA
* * **
2875997 TAATGCACCGTTATGCATTTTCATTTATGGCATCTTTTTATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATATCGA
*
2876043 TAATGCACCGGTATGCATTT
1 TAATGCACCGTTATGCATTT
2876063 AACTTTTCAT
Statistics
Matches: 138, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
46 137 0.99
47 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.43
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATATCGA
Found at i:2876121 original size:60 final size:60
Alignment explanation
Indices: 2876044--2876248 Score: 338
Period size: 60 Copynumber: 3.4 Consensus size: 60
2876034 TTATGCCGAT
* * *
2876044 AATGCACCGGTATGCATTTAACTTTTCATCTAACTTGCATTAATGGCACTTTTCTGCCAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACTTTTCTGCCAA
* *
2876104 AATGCACCGTTAGGCATTTAACTTTTCAACTAACTTGCATTAGTGACACTTTTCTGCCAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACTTTTCTGCCAA
* * *
2876164 AATTCACCGTTAGGTATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACTTTTCTGCCAA
2876224 AATGCACCGTTAGGCATTTAACTTT
1 AATGCACCGTTAGGCATTTAACTTT
2876249 CATTTTAGAG
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 133 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (60 bp):
AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACTTTTCTGCCAA
Found at i:2880581 original size:30 final size:29
Alignment explanation
Indices: 2880545--2880602 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2880535 AATGTTATGG
2880545 TATGTGACATAATTTAA-ATGATTATATGTA
1 TATGTGACAT-ATTTAACATG-TTATATGTA
* *
2880575 TATGTGATATGTTTAACATGTTATATGT
1 TATGTGACATATTTAACATGTTATATGT
2880603 GTTGTGTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (29 bp):
TATGTGACATATTTAACATGTTATATGTA
Found at i:2881211 original size:39 final size:39
Alignment explanation
Indices: 2881152--2881229 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
2881142 AGTCAAGGGT
*
2881152 TACAGTGGTCCTACGAGACATAGTGGTCCTTCGGGACAA
1 TACAGTGATCCTACGAGACATAGTGGTCCTTCGGGACAA
* *
2881191 TACAGTGATCCTACGTGACATAGTGGTCTTTCGGGACAA
1 TACAGTGATCCTACGAGACATAGTGGTCCTTCGGGACAA
2881230 ATTTCAGTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TACAGTGATCCTACGAGACATAGTGGTCCTTCGGGACAA
Found at i:2881228 original size:18 final size:18
Alignment explanation
Indices: 2881155--2881228 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
2881145 CAAGGGTTAC
* *
2881155 AGTGGTCCTACGAGACAT
1 AGTGGTCCTTCGGGACAT
2881173 AGTGGTCCTTCGGGACAAT
1 AGTGGTCCTTCGGGAC-AT
* * *
2881192 ACAGTGATCCTACGTGACAT
1 --AGTGGTCCTTCGGGACAT
*
2881212 AGTGGTCTTTCGGGACA
1 AGTGGTCCTTCGGGACA
2881229 AATTTCAGTG
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
18 27 0.61
19 2 0.05
20 2 0.05
21 13 0.30
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2881951 original size:12 final size:12
Alignment explanation
Indices: 2881934--2881980 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
2881924 TTTAACATTC
2881934 AGTACTGTTCAT
1 AGTACTGTTCAT
2881946 AGTACTGTTCAT
1 AGTACTGTTCAT
*
2881958 --TACTGTTCAC
1 AGTACTGTTCAT
* *
2881968 AGCACTGCTCAT
1 AGTACTGTTCAT
2881980 A
1 A
2881981 CCGTATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 9 0.31
12 20 0.69
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (12 bp):
AGTACTGTTCAT
Found at i:2881974 original size:22 final size:22
Alignment explanation
Indices: 2881931--2881979 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2881921 AAATTTAACA
* * *
2881931 TTCAGTACTGTTCATAGTACTG
1 TTCATTACTGTTCACAGCACTG
2881953 TTCATTACTGTTCACAGCACTG
1 TTCATTACTGTTCACAGCACTG
*
2881975 CTCAT
1 TTCAT
2881980 ACCGTATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (22 bp):
TTCATTACTGTTCACAGCACTG
Found at i:2890681 original size:46 final size:46
Alignment explanation
Indices: 2890602--2890805 Score: 273
Period size: 46 Copynumber: 4.4 Consensus size: 46
2890592 TTTATGTCGT
* * * * * * * *
2890602 TAATACACCATTATGTATTTTCATTTGTTGCATCATTTCATGCCAA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATACCGA
* *
2890648 TTATGCACTGTTATGCATTTTCATTTATGGCATCCTTTCATACCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATACCGA
* *
2890694 TAATGCACCGTTATGCATTTTCATTTATGGTATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATACCGA
* *
2890740 TAATGCACCATTATGAATTTTCATTTATGGCATCCTTTCATACCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATACCGA
*
2890786 TAATGCACCGTTATTCATTT
1 TAATGCACCGTTATGCATTT
2890806 AACTTTTCAT
Statistics
Matches: 137, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 137 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATACCGA
Found at i:2890995 original size:60 final size:60
Alignment explanation
Indices: 2890787--2890992 Score: 340
Period size: 60 Copynumber: 3.4 Consensus size: 60
2890777 TCATACCGAT
**
2890787 AATGCACCGTTATTCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
* * * *
2890847 AATGCACTGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGACACTTTTCTGCCAT
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
*
2890907 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTGGTGGCACCTTTCTGCCAAA
1 AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCC-AA
2890968 AATGCACCGTTAGGCATTTAACTTT
1 AATGCACCGTTAGGCATTTAACTTT
2890993 CATTTTAGAG
Statistics
Matches: 134, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
60 108 0.81
61 26 0.19
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.37
Consensus pattern (60 bp):
AATGCACCGTTAGGCATTTAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
Found at i:2891806 original size:3 final size:3
Alignment explanation
Indices: 2891798--2891862 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
2891788 TCCGCTTTTA
2891798 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2891846 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
2891863 CTACTACTAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2901237 original size:3 final size:3
Alignment explanation
Indices: 2901224--2901278 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
2901214 TTCGTTCGAG
*
2901224 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2901270 TTAA TTA TT
1 TT-A TTA TT
2901279 TGTAGGCCTG
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 41 0.87
4 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2902322 original size:30 final size:30
Alignment explanation
Indices: 2902286--2902350 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
2902276 AACCATTGTA
2902286 ATTTTGAGCATATGATTTTACCCTCATTTT
1 ATTTTGAGCATATGATTTTACCCTCATTTT
2902316 ATTTTGAGCATATGATTTTACCCTCATTTT
1 ATTTTGAGCATATGATTTTACCCTCATTTT
2902346 ATTTT
1 ATTTT
2902351 AGTCCTGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.23, C:0.15, G:0.09, T:0.52
Consensus pattern (30 bp):
ATTTTGAGCATATGATTTTACCCTCATTTT
Found at i:2906473 original size:18 final size:18
Alignment explanation
Indices: 2906452--2906486 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2906442 GTTTATTATT
*
2906452 TTAGCTTTTTTATTTTAA
1 TTAGCTTTTTTAATTTAA
*
2906470 TTAGTTTTTTTAATTTA
1 TTAGCTTTTTTAATTTA
2906487 TTCTTAGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.69
Consensus pattern (18 bp):
TTAGCTTTTTTAATTTAA
Found at i:2906599 original size:17 final size:17
Alignment explanation
Indices: 2906574--2906607 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2906564 GATTCGAATT
2906574 TTAAAATTTATTAAAAA
1 TTAAAATTTATTAAAAA
* *
2906591 TTAATATTTTTTAAAAA
1 TTAAAATTTATTAAAAA
2906608 CTCTAGGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAATTTATTAAAAA
Found at i:2907839 original size:51 final size:51
Alignment explanation
Indices: 2907743--2907853 Score: 161
Period size: 51 Copynumber: 2.2 Consensus size: 51
2907733 TGTTATGTGC
* *
2907743 TAAATTTGACTAGTGTAAGTCTATTATGAGTTCAATATGATAATTATAT-G
1 TAAATTTGACTAGTGTAAGTATATTATGAGTTCAATATGAGAATTATATGG
* * *
2907793 TAAAATTTGACTAGTGTAAGTATGTTATGAGTTCAATATGGGAATTATGTGG
1 T-AAATTTGACTAGTGTAAGTATATTATGAGTTCAATATGAGAATTATATGG
2907845 TAAATTTGA
1 TAAATTTGA
2907854 GTTCAATATG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 1 0.02
51 51 0.94
52 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.41
Consensus pattern (51 bp):
TAAATTTGACTAGTGTAAGTATATTATGAGTTCAATATGAGAATTATATGG
Found at i:2907858 original size:31 final size:31
Alignment explanation
Indices: 2907820--2907882 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
2907810 AAGTATGTTA
*
2907820 TGAGTTCAATATGGGAATTATGTGGTAAATT
1 TGAGTTCAATATGAGAATTATGTGGTAAATT
*
2907851 TGAGTTCAATATGAGAATTATGTGTTAAATT
1 TGAGTTCAATATGAGAATTATGTGGTAAATT
2907882 T
1 T
2907883 AGCTGGTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.41
Consensus pattern (31 bp):
TGAGTTCAATATGAGAATTATGTGGTAAATT
Found at i:2907870 original size:82 final size:82
Alignment explanation
Indices: 2907769--2907935 Score: 246
Period size: 82 Copynumber: 2.0 Consensus size: 82
2907759 AAGTCTATTA
*
2907769 TGAGTTCAATATGATAATTATATGTAAAATTT-GACTAGTGTAAGTATGTTATGAGTTCAATATG
1 TGAGTTCAATATGAGAATTATATGTAAAATTTAG-CTAGTGTAAGTATGTTATGAGTTCAATATG
* *
2907833 GGAATTATGTGGTAAATT
65 AGAATTATGTAGTAAATT
* * * * *
2907851 TGAGTTCAATATGAGAATTATGTGTTAAATTTAGCTGGTGTAAGTCTGTTATGAGTTCGATATGA
1 TGAGTTCAATATGAGAATTATATGTAAAATTTAGCTAGTGTAAGTATGTTATGAGTTCAATATGA
2907916 GAATTATGTAGTAAATT
66 GAATTATGTAGTAAATT
2907933 TGA
1 TGA
2907936 TTGGTGTAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
82 75 0.99
83 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (82 bp):
TGAGTTCAATATGAGAATTATATGTAAAATTTAGCTAGTGTAAGTATGTTATGAGTTCAATATGA
GAATTATGTAGTAAATT
Found at i:2907906 original size:51 final size:51
Alignment explanation
Indices: 2907851--2908002 Score: 227
Period size: 51 Copynumber: 3.0 Consensus size: 51
2907841 GTGGTAAATT
2907851 TGAGTTCAATATGAGAATTATGTGTTAAATTT-AGCTGGTGTAAGTCTGTTA
1 TGAGTTCAATATGAGAATTATGTGTTAAATTTGA-CTGGTGTAAGTCTGTTA
* * *
2907902 TGAGTTCGATATGAGAATTATGTAG-TAAATTTGATTGGTGTAAGTCTATTA
1 TGAGTTCAATATGAGAATTATGT-GTTAAATTTGACTGGTGTAAGTCTGTTA
* *
2907953 TGAGTTCAATATGGGAATTATGTGTTAAATTTGACTTGTGTAAGTCTGTT
1 TGAGTTCAATATGAGAATTATGTGTTAAATTTGACTGGTGTAAGTCTGTT
2908003 CTACGATCAA
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
50 1 0.01
51 87 0.97
52 2 0.02
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.42
Consensus pattern (51 bp):
TGAGTTCAATATGAGAATTATGTGTTAAATTTGACTGGTGTAAGTCTGTTA
Found at i:2907973 original size:133 final size:133
Alignment explanation
Indices: 2907735--2907986 Score: 373
Period size: 133 Copynumber: 1.9 Consensus size: 133
2907725 TGATGATATG
*
2907735 TTATGTGCTAAATTTGACTAGTGTAAGTCTATTATGAGTTCAATATGATAATTATATGTAAAATT
1 TTATGTGCTAAATTTGACTAGTGTAAGTCTATTATGAGTTCAATATGAGAATTATATGTAAAATT
*
2907800 TGACTAGTGTAAGTATGTTATGAGTTCAATATGGGAATTATGTGGTAAATTTGAGTTCAATATGA
66 TGACTAGTGTAAGTATATTATGAGTTCAATATGGGAATTATGTGGTAAATTTGAGTTCAATATGA
2907865 GAA
131 GAA
* * * * *
2907868 TTATGTGTTAAATTT-AGCTGGTGTAAGTCTGTTATGAGTTCGATATGAGAATTATGTAGT-AAA
1 TTATGTGCTAAATTTGA-CTAGTGTAAGTCTATTATGAGTTCAATATGAGAATTATAT-GTAAAA
* * * *
2907931 TTTGATTGGTGTAAGTCTATTATGAGTTCAATATGGGAATTATGTGTTAAATTTGA
64 TTTGACTAGTGTAAGTATATTATGAGTTCAATATGGGAATTATGTGGTAAATTTGA
2907987 CTTGTGTAAG
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
132 1 0.01
133 103 0.97
134 2 0.02
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (133 bp):
TTATGTGCTAAATTTGACTAGTGTAAGTCTATTATGAGTTCAATATGAGAATTATATGTAAAATT
TGACTAGTGTAAGTATATTATGAGTTCAATATGGGAATTATGTGGTAAATTTGAGTTCAATATGA
GAA
Found at i:2908033 original size:102 final size:101
Alignment explanation
Indices: 2907851--2908035 Score: 241
Period size: 102 Copynumber: 1.8 Consensus size: 101
2907841 GTGGTAAATT
* *
2907851 TGAGTTCAATATGAGAATTATGTGTTAAATTTAGCTGGTGTAAGTCTGTTATGAGTTCGATATGA
1 TGAGTTCAATATGAGAATTATGTGTTAAATTTAGCTGGTGTAAGTCTGTTATGAGATCAATATGA
*
2907916 GAATTATGTAGTAAATTTGATTGGTGTAAGTCTATTA
66 GAATCATGTA-TAAATTTGATTGGTGTAAGTCTATTA
* * *
2907953 TGAGTTCAATATGGGAATTATGTGTTAAATTT-GACTTGTGTAAGTCTGTTCT-ACGATCAATAT
1 TGAGTTCAATATGAGAATTATGTGTTAAATTTAG-CTGGTGTAAGTCTGTTATGA-GATCAATAT
*
2908016 GATAATAACATGT-TAAATTT
64 GAGAAT--CATGTATAAATTT
2908036 CACAACTGTA
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
101 2 0.03
102 66 0.92
104 4 0.06
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.41
Consensus pattern (101 bp):
TGAGTTCAATATGAGAATTATGTGTTAAATTTAGCTGGTGTAAGTCTGTTATGAGATCAATATGA
GAATCATGTATAAATTTGATTGGTGTAAGTCTATTA
Found at i:2918625 original size:18 final size:18
Alignment explanation
Indices: 2918604--2918658 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
2918594 AGATAAGTAT
2918604 ATGATATAAGTTCTTGTC
1 ATGATATAAGTTCTTGTC
* *
2918622 ATG--A-AAGTTCATGTT
1 ATGATATAAGTTCTTGTC
2918637 ATGATATAAGTGT-TTGTC
1 ATGATATAAGT-TCTTGTC
2918655 ATGA
1 ATGA
2918659 AATTCCATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
15 12 0.41
16 1 0.03
17 1 0.03
18 14 0.48
19 1 0.03
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (18 bp):
ATGATATAAGTTCTTGTC
Found at i:2918645 original size:33 final size:33
Alignment explanation
Indices: 2918603--2918676 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 33
2918593 AAGATAAGTA
2918603 TATGATATAAGT-TCTTGTCATGAAAGTT-CATGT
1 TATGATATAAGTGT-TTGTCATGAAA-TTCCATGT
2918636 TATGATATAAGTGTTTGTCATGAAATTCCATGT
1 TATGATATAAGTGTTTGTCATGAAATTCCATGT
2918669 TATGATAT
1 TATGATAT
2918677 GTTCATTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
32 2 0.05
33 36 0.92
34 1 0.03
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (33 bp):
TATGATATAAGTGTTTGTCATGAAATTCCATGT
Found at i:2920694 original size:2 final size:2
Alignment explanation
Indices: 2920687--2920718 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2920677 CTTTATTATC
2920687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2920719 TTTAAATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2922734 original size:21 final size:22
Alignment explanation
Indices: 2922709--2922751 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2922699 ATCAATACTA
*
2922709 AAGAG-AGTATCGGTACAATAG
1 AAGAGAAGTATCGATACAATAG
*
2922730 AAGAGAAGTATCGATACTATAG
1 AAGAGAAGTATCGATACAATAG
2922752 TAGGGGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (22 bp):
AAGAGAAGTATCGATACAATAG
Found at i:2922741 original size:22 final size:21
Alignment explanation
Indices: 2922709--2922764 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
2922699 ATCAATACTA
*
2922709 AAGAGAGTATCGGTACAATAG
1 AAGAGAGTATCGATACAATAG
*
2922730 AAGAGAAGTATCGATACTATAG
1 AAGAG-AGTATCGATACAATAG
* *
2922752 TAG-GGGTATCGAT
1 AAGAGAGTATCGAT
2922765 CTATTTAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.27
21 6 0.20
22 16 0.53
ACGTcount: A:0.39, C:0.09, G:0.29, T:0.23
Consensus pattern (21 bp):
AAGAGAGTATCGATACAATAG
Found at i:2923430 original size:138 final size:138
Alignment explanation
Indices: 2923241--2923531 Score: 433
Period size: 138 Copynumber: 2.1 Consensus size: 138
2923231 GTTAAAGGTG
* * * *
2923241 CATTTCGACATA-AATTGTTTATAAAAGTTATCGATCGATTTTGTTTGATGCATAACGAT-CTAT
1 CATTTCGATATACAATTATGTATAAAAGTTATCGATCGATTTTGTTTAATGCATAACGATGC-AT
* * *
2923304 TTTCGTATCAATATTTTGTGCACTTTTGGCATTAGATGTGCAATCATGGTATTCATAACGAGTTT
65 TTTCGTATCAATATTGTGTGAACTTTTGGCACTAGATGTGCAATCATGGTATTCATAACGAGTTT
2923369 GTGAATTAC
130 GTGAATTAC
* *
2923378 CATTTCGATATACAATTATGTATAAAATTTATCGATCGATTTTGTTTAATGCATAACGGTGCATT
1 CATTTCGATATACAATTATGTATAAAAGTTATCGATCGATTTTGTTTAATGCATAACGATGCATT
* * *
2923443 TTCGTATCAGTGTTGTGTGAACTTTTGGCACTAGATGTGCAATCATGGTATTCATAATGAGTTTG
66 TTCGTATCAATATTGTGTGAACTTTTGGCACTAGATGTGCAATCATGGTATTCATAACGAGTTTG
2923508 TGAATTAC
131 TGAATTAC
* *
2923516 CATTTTGATATGCAAT
1 CATTTCGATATACAAT
2923532 CATTTTGATA
Statistics
Matches: 138, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
137 11 0.08
138 126 0.91
139 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.41
Consensus pattern (138 bp):
CATTTCGATATACAATTATGTATAAAAGTTATCGATCGATTTTGTTTAATGCATAACGATGCATT
TTCGTATCAATATTGTGTGAACTTTTGGCACTAGATGTGCAATCATGGTATTCATAACGAGTTTG
TGAATTAC
Found at i:2929389 original size:27 final size:27
Alignment explanation
Indices: 2929330--2929398 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
2929320 TTTGCATTGG
* *
2929330 GCTATGAAATGAAAAAGTGAATAGTATAT
1 GCTATGAAATG--AAAGTGAATAGTACAA
2929359 GCTATGAAATGAAAGTGAAT-GATACAA
1 GCTATGAAATGAAAGTGAATAG-TACAA
2929386 GCTATGAAATGAA
1 GCTATGAAATGAA
2929399 TAAAGTGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.03
27 25 0.68
29 11 0.30
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.25
Consensus pattern (27 bp):
GCTATGAAATGAAAGTGAATAGTACAA
Found at i:2932619 original size:40 final size:39
Alignment explanation
Indices: 2932575--2932652 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
2932565 AGTTTTCCCC
* *
2932575 TGTGCCCAAAACAAAAGGAGCTTACAGTAAGGACTTACCT
1 TGTGCACAAAAC-AAAGGAGCATACAGTAAGGACTTACCT
* *
2932615 TGTGCACAAAACAAAGGAGCATGCGGTAAGGACTTACC
1 TGTGCACAAAACAAAGGAGCATACAGTAAGGACTTACC
2932653 CTAGTCGAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 23 0.68
40 11 0.32
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (39 bp):
TGTGCACAAAACAAAGGAGCATACAGTAAGGACTTACCT
Found at i:2932644 original size:39 final size:39
Alignment explanation
Indices: 2932547--2932654 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 39
2932537 ATGCATGAAG
* * ** * *
2932547 CAAAGGGGCATGCGGTAAAGTTTTCCCCTGTGCCCAAAA
1 CAAAGGAGCATGCGGTAAGGACTTACCCTGTGCACAAAA
* * * *
2932586 CAAAAGGAGCTTACAGTAAGGACTTACCTTGTGCACAAAA
1 C-AAAGGAGCATGCGGTAAGGACTTACCCTGTGCACAAAA
2932626 CAAAGGAGCATGCGGTAAGGACTTACCCT
1 CAAAGGAGCATGCGGTAAGGACTTACCCT
2932655 AGTCGAAGTA
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
39 25 0.46
40 29 0.54
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.19
Consensus pattern (39 bp):
CAAAGGAGCATGCGGTAAGGACTTACCCTGTGCACAAAA
Found at i:2932987 original size:12 final size:12
Alignment explanation
Indices: 2932970--2932994 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2932960 GTAGGGAAAA
2932970 CAAAAAACTTAT
1 CAAAAAACTTAT
2932982 CAAAAAACTTAT
1 CAAAAAACTTAT
2932994 C
1 C
2932995 TAAATTGATA
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:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (12 bp):
CAAAAAACTTAT
Found at i:2938888 original size:32 final size:32
Alignment explanation
Indices: 2938847--2938910 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2938837 CACATAATTG
*
2938847 ATTAAAATTGACTAGGTTAATAATTAGAGCCT
1 ATTAAAATTGACTAGGTTAATAATTAAAGCCT
2938879 ATTAAAATTGACTAGGTTAATAATTAAAGCCT
1 ATTAAAATTGACTAGGTTAATAATTAAAGCCT
2938911 CCCTTTTAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (32 bp):
ATTAAAATTGACTAGGTTAATAATTAAAGCCT
Found at i:2938903 original size:16 final size:15
Alignment explanation
Indices: 2938848--2938903 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 15
2938838 ACATAATTGA
2938848 TTAAAATTGACTAGG
1 TTAAAATTGACTAGG
2938863 TTAATAATTAGAGCCTA--
1 TTAA-AATT-GA--CTAGG
2938880 TTAAAATTGACTAGG
1 TTAAAATTGACTAGG
2938895 TTAATAATT
1 TTAA-AATT
2938904 AAAGCCTCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
13 3 0.09
15 10 0.29
16 12 0.35
17 6 0.18
19 3 0.09
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (15 bp):
TTAAAATTGACTAGG
Found at i:2938993 original size:171 final size:170
Alignment explanation
Indices: 2938709--2939045 Score: 482
Period size: 171 Copynumber: 2.0 Consensus size: 170
2938699 TCGATAATTG
* * * *
2938709 ATTAAAATTGACTAGTTTAATAACTAGAGCCTTTATTTAGGCTTAATTTCAAACTTAGTCCTTAA
1 ATTAAAATTGACTAGGTTAATAACTAAAGCCTCTATTTAGGCTTAATTTCAAACCTAGTCCTTAA
*
2938774 ATTTAGGCGAATTTTTAATTTGGTACTCGCTTTTGCTCGAGGTTCCATTTTAATTATTCGAAT-C
66 ATTTAGGCGAATTTTTAATTTGGTACTCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAATAC
2938838 ACATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCT
131 -CATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCT
* * *
2938879 ATTAAAATTGACTAGGTTAATAATTAAAGCCTCCCT-TTTAGGCTTCATTTCAAACCTAG-CTTT
1 ATTAAAATTGACTAGGTTAATAACTAAAGCCT--CTATTTAGGCTTAATTTCAAACCTAGTC-CT
* * * *
2938942 TAAATTTAGGTGAATTTTTAATTTGGTCCTCATTTTTTCTCGAGGTTCCATTTTAATTATTCGAA
63 TAAATTTAGGCGAATTTTTAATTTGGTACTCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAA
*
2939007 TATGCCGTAATTGATTAAAATTGACTAGGTTAATAATTA
128 TA--CCATAATTGATTAAAATTGACTAGGTTAATAATTA
2939046 CAACCTCCAT
Statistics
Matches: 148, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
170 30 0.20
171 83 0.56
172 1 0.01
173 33 0.22
174 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (170 bp):
ATTAAAATTGACTAGGTTAATAACTAAAGCCTCTATTTAGGCTTAATTTCAAACCTAGTCCTTAA
ATTTAGGCGAATTTTTAATTTGGTACTCACTTTTGCTCGAGGTTCCATTTTAATTATTCGAATAC
CATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCT
Found at i:2939197 original size:139 final size:139
Alignment explanation
Indices: 2938891--2939204 Score: 350
Period size: 141 Copynumber: 2.2 Consensus size: 139
2938881 TAAAATTGAC
* * * * *
2938891 TAGGTTAATAATTAAAGCCTCCCTTTTAGGCTTCATTTCAAACCTAGCTTTTAAATTTAGGTGAA
1 TAGGTTAATAATTAAAACCTCCATTTTAGG-TTTATTTCAAACCTAGCTATTAAATTTAGGTAAA
* **
2938956 TTTTTAATTTGGTCCTCATTTTTTCTCGAGGTTCCATTTTAATTATTCGAATATGCCGTAATTGA
65 TTTTTAATTTGGTCCTCATTTTTCCTCGAGGTTCCATTTTAATTATTCGAATAT-CAATAATTGA
** *
2939021 TTAAAATTGAC
129 TTAAAATCAAA
* * * *
2939032 TAGGTTAATAATTACAACCTCCATTTTAGGTTTAGTTTCACACTTA-CTCATTAAATTTTGGTAA
1 TAGGTTAATAATTAAAACCTCCATTTTAGGTTTA-TTTCAAACCTAGCT-ATTAAATTTAGGT-A
* * *
2939096 AATTTTTAATTTGGTCAC-CGTTTTTGCCT-GATGTTCCATTTTAATTATTTGAAT-T-AATAAT
63 AATTTTTAATTTGGTC-CTCATTTTT-CCTCGAGGTTCCATTTTAATTATTCGAATATCAATAAT
2939157 TGATTAAAATCAAA
126 TGATTAAAATCAAA
* *
2939171 TAGGTTAATAATTAGATCCTCCATTTTAGGTTTA
1 TAGGTTAATAATTAAAACCTCCATTTTAGGTTTA
2939205 ATTGGGTCCT
Statistics
Matches: 148, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
139 47 0.32
140 5 0.03
141 48 0.32
142 45 0.30
143 3 0.02
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (139 bp):
TAGGTTAATAATTAAAACCTCCATTTTAGGTTTATTTCAAACCTAGCTATTAAATTTAGGTAAAT
TTTTAATTTGGTCCTCATTTTTCCTCGAGGTTCCATTTTAATTATTCGAATATCAATAATTGATT
AAAATCAAA
Found at i:2944573 original size:63 final size:64
Alignment explanation
Indices: 2944396--2944580 Score: 189
Period size: 68 Copynumber: 2.9 Consensus size: 64
2944386 AAATTTCGTA
2944396 TCACTTGAGACAA-TTTCCCTTGAAACACAAATTTTGAAATTGTTTCACTCGAAACAAATTTTTT
1 TCACTTGAGACAATTTTCCCTTGAAACACAAATTTTGAAATTGTTTCACTC---A-AAA-TTTTT
2944460 TATC
61 TATC
* * * * * ** ** * *
2944464 CCACTTGAGA-TATTTTCTCTTGGAATATGAATTTTGAAATCATTTCATTCAAAA-TTTTTGTC
1 TCACTTGAGACAATTTTCCCTTGAAACACAAATTTTGAAATTGTTTCACTCAAAATTTTTTATC
2944526 TCACTTGAGACAATTTTCCCTTGAAACACAAATTTT-AAGATTGTTTCACTCAAAA
1 TCACTTGAGACAATTTTCCCTTGAAACACAAATTTTGAA-ATTGTTTCACTCAAAA
2944581 CAAAATTTAT
Statistics
Matches: 93, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
62 18 0.19
63 32 0.34
64 3 0.03
65 1 0.01
67 1 0.01
68 38 0.41
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (64 bp):
TCACTTGAGACAATTTTCCCTTGAAACACAAATTTTGAAATTGTTTCACTCAAAATTTTTTATC
Found at i:2944893 original size:102 final size:102
Alignment explanation
Indices: 2944523--2944890 Score: 596
Period size: 102 Copynumber: 3.6 Consensus size: 102
2944513 CAAAATTTTT
* * *
2944523 GTCTCACTTGAGACAATTTTCCCTTGAAACACAAATTTTAAGATTGTTTCACTCAAAACAAAATT
1 GTCTCACTTGAGACAAGTTTCCCTTGAAACACAAATTTTAAGATCGTTTCACTCGAAACAAAATT
* *
2944588 TATCTCACTTGAGATTAG-TTTTCTTAAAACCGATTTC
66 GATCTCACTTGAGATT-GTTTTTCTTAAAACCAATTTC
*
2944625 GCCTCACTTGAGACAAGTTTCCCTTGAAACACAAATTTTAAGATCGTTTCACTCGAAACAAAATT
1 GTCTCACTTGAGACAAGTTTCCCTTGAAACACAAATTTTAAGATCGTTTCACTCGAAACAAAATT
*
2944690 GATCTCACTTGAGATTGTTATTCTTAAAACCAATTTC
66 GATCTCACTTGAGATTGTTTTTCTTAAAACCAATTTC
* * * * *
2944727 ATTTCGCTTGAGACAAGTTTCCCTTGAAACACAAATTTTATGATCGTTTCAGTCGAAACAAAATT
1 GTCTCACTTGAGACAAGTTTCCCTTGAAACACAAATTTTAAGATCGTTTCACTCGAAACAAAATT
*
2944792 GATCTCACTTAAGATTGTTTTTCTTAAAACCAATTTC
66 GATCTCACTTGAGATTGTTTTTCTTAAAACCAATTTC
2944829 GTCTCACTTGAGACAAGTTT-CCTTGAAACACAAATTTTAAGATCGTTTCACTCGAAACAAAA
1 GTCTCACTTGAGACAAGTTTCCCTTGAAACACAAATTTTAAGATCGTTTCACTCGAAACAAAA
2944891 ATTTATGAAA
Statistics
Matches: 245, Mismatches: 20, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
101 41 0.17
102 204 0.83
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (102 bp):
GTCTCACTTGAGACAAGTTTCCCTTGAAACACAAATTTTAAGATCGTTTCACTCGAAACAAAATT
GATCTCACTTGAGATTGTTTTTCTTAAAACCAATTTC
Found at i:2944902 original size:15 final size:15
Alignment explanation
Indices: 2944882--2944911 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2944872 CGTTTCACTC
2944882 GAAACAAAAATTTAT
1 GAAACAAAAATTTAT
2944897 GAAACAAAAATTTAT
1 GAAACAAAAATTTAT
2944912 CACTTGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (15 bp):
GAAACAAAAATTTAT
Found at i:2945738 original size:152 final size:152
Alignment explanation
Indices: 2945462--2945741 Score: 413
Period size: 152 Copynumber: 1.8 Consensus size: 152
2945452 ATTCATAATG
* * *
2945462 AGAAGAACTTGTTCACTATTTTGCTCGACTCTATCATAGAAAAAGGTAGATAATCATCAACATTT
1 AGAAGAACTTGTTCACCATTTTGCTCGACTCTAACACAGAAAAAGGTAGATAATCATCAACATTT
* * * * * *
2945527 TGTTTGATTCCATCACGGAAGGAGGTTGATCAAAATTTCTAATGGAAGGGTTTATAATGAGAAAA
66 TATTTGATTCCATCACAGAAGGAGGTGGATCAAAATTTCAAATGAAAGGGTTCATAATGAGAAAA
2945592 ACTCGTCTGAAAAAGGAGAAGA
131 ACTCGTCTGAAAAAGGAGAAGA
* *
2945614 AGAAGGAA-TTGTTCACCATTTTGCTCGACTTTAACACA-AAAAGATGTAGATCAA-CATCAACA
1 AGAA-GAACTTGTTCACCATTTTGCTCGACTCTAACACAGAAAA-AGGTAGAT-AATCATCAACA
2945676 TTTTATTTGATTCCATCACAGAAGGAGGTGGATCAAAATTTCAAATGAAAGGGTTCATAATGAGA
63 TTTTATTTGATTCCATCACAGAAGGAGGTGGATCAAAATTTCAAATGAAAGGGTTCATAATGAGA
2945741 A
128 A
2945742 GAATTCATTC
Statistics
Matches: 114, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
151 4 0.04
152 105 0.92
153 5 0.04
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (152 bp):
AGAAGAACTTGTTCACCATTTTGCTCGACTCTAACACAGAAAAAGGTAGATAATCATCAACATTT
TATTTGATTCCATCACAGAAGGAGGTGGATCAAAATTTCAAATGAAAGGGTTCATAATGAGAAAA
ACTCGTCTGAAAAAGGAGAAGA
Found at i:2954348 original size:13 final size:13
Alignment explanation
Indices: 2954324--2954356 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2954314 GTTTTGTTTC
2954324 ATTATAATTATATT
1 ATTAT-ATTATATT
2954338 ATTATATTATATT
1 ATTATATTATATT
2954351 ATTATA
1 ATTATA
2954357 ACTTGTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTATATTATATT
Found at i:2956056 original size:75 final size:75
Alignment explanation
Indices: 2955907--2956114 Score: 256
Period size: 75 Copynumber: 2.8 Consensus size: 75
2955897 CAAAGCCAAA
* * * * **
2955907 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
2955972 TTGGCTCCGAG
65 TTGGCTCCGAG
* * *
2955983 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACTGATTCCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
2956048 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
2956058 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
2956115 GTTCAACGGT
Statistics
Matches: 114, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
75 83 0.73
76 31 0.27
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:2962583 original size:2 final size:2
Alignment explanation
Indices: 2962576--2962629 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
2962566 TTTTCGTGAT
2962576 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
2962618 TA TA TA TA TA TA
1 TA TA TA TA TA TA
2962630 CTCTTGATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2964261 original size:31 final size:31
Alignment explanation
Indices: 2964226--2964289 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
2964216 AGTCAAAAAG
2964226 TAGTAAAATGGAGTGCAATAGCTGAATTTAT
1 TAGTAAAATGGAGTGCAATAGCTGAATTTAT
2964257 TAGTAAAATGGAGTGCAATAGCTGAATTTAT
1 TAGTAAAATGGAGTGCAATAGCTGAATTTAT
2964288 TA
1 TA
2964290 CAAGTAGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (31 bp):
TAGTAAAATGGAGTGCAATAGCTGAATTTAT
Found at i:2967002 original size:43 final size:43
Alignment explanation
Indices: 2966954--2967107 Score: 136
Period size: 43 Copynumber: 3.5 Consensus size: 43
2966944 AAGCCTAGTA
*
2966954 TTCACGGAAGAGTAGTGGAATCAAATCAACCTTGAATCTGATC
1 TTCACGGAAGAGTAGTGGAAACAAATCAACCTTGAATCTGATC
* * **
2966997 TTCACGGAAGAGTAGT-GAAACAGATTCTTTTTAA--TTTAATCCAATC
1 TTCACGGAAGAGTAGTGGAAACA-AATC-----AACCTTGAATCTGATC
* * * *
2967043 TCCACGGAAGAATAGTGGAAGCAAATCAACCTCGAATCTGATC
1 TTCACGGAAGAGTAGTGGAAACAAATCAACCTTGAATCTGATC
*
2967086 TTCACGAAAGAGTAGT-GAAACA
1 TTCACGGAAGAGTAGTGGAAACA
2967108 GATTCTTCTC
Statistics
Matches: 85, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
41 2 0.02
42 10 0.12
43 40 0.47
46 26 0.31
47 5 0.06
48 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (43 bp):
TTCACGGAAGAGTAGTGGAAACAAATCAACCTTGAATCTGATC
Found at i:2967162 original size:89 final size:89
Alignment explanation
Indices: 2966961--2967123 Score: 236
Period size: 89 Copynumber: 1.8 Consensus size: 89
2966951 GTATTCACGG
* * * *
2966961 AAGAGTAGTGGAATCAAATCAACCTTGAATCTGATCTTCACGGAAGAGTAGTGAAACAGATTCTT
1 AAGAATAGTGGAAGCAAATCAACCTCGAATCTGATCTTCACGAAAGAGTAGTGAAACAGATTCTT
* * * * **
2967026 TTTAATTTAATCCAATCTCCACGG
66 CTCAAATCAATCCAATCTCCACAA
2967050 AAGAATAGTGGAAGCAAATCAACCTCGAATCTGATCTTCACGAAAGAGTAGTGAAACAGATTCTT
1 AAGAATAGTGGAAGCAAATCAACCTCGAATCTGATCTTCACGAAAGAGTAGTGAAACAGATTCTT
2967115 CTCAAATCA
66 CTCAAATCA
2967124 TTTTCATTCT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 66 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (89 bp):
AAGAATAGTGGAAGCAAATCAACCTCGAATCTGATCTTCACGAAAGAGTAGTGAAACAGATTCTT
CTCAAATCAATCCAATCTCCACAA
Found at i:2967178 original size:35 final size:37
Alignment explanation
Indices: 2967132--2967223 Score: 127
Period size: 36 Copynumber: 2.6 Consensus size: 37
2967122 CATTTTCATT
*
2967132 CTTCACAAAAGAGTAGTGAAGAC-ATGC-AACCCAAC
1 CTTCACAAAAGAGTAGTGAAGACAATACAAACCCAAC
*
2967167 CTTCACAAAAGAGTAGTGAA-ACAATACAAATCCAAC
1 CTTCACAAAAGAGTAGTGAAGACAATACAAACCCAAC
* *
2967203 CTTTACAATAGAGTAGTGAAG
1 CTTCACAAAAGAGTAGTGAAG
2967224 CAAGATCAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 2 0.04
35 23 0.46
36 25 0.50
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (37 bp):
CTTCACAAAAGAGTAGTGAAGACAATACAAACCCAAC
Found at i:2967425 original size:13 final size:14
Alignment explanation
Indices: 2967402--2967435 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
2967392 GTTTTGTTTC
2967402 ATTATAATTATATT
1 ATTATAATTATATT
2967416 ATTA-AATTATATT
1 ATTATAATTATATT
2967429 ATTATAA
1 ATTATAA
2967436 CTTGTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTATAATTATATT
Found at i:2970696 original size:23 final size:22
Alignment explanation
Indices: 2970646--2970698 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
2970636 ATTTTCTTTG
*
2970646 ATATTGAAAATAAATATACATT
1 ATATTTAAAATAAATATACATT
* *
2970668 ATTATTTAAAATATATATATATAT
1 A-TATTTAAAATAAATATACAT-T
2970692 ATATTTA
1 ATATTTA
2970699 TTTATTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 23 0.88
24 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATTTAAAATAAATATACATT
Found at i:2970735 original size:17 final size:17
Alignment explanation
Indices: 2970713--2970746 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2970703 TTTATGTGAC
2970713 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
2970730 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
2970747 CAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:2970773 original size:16 final size:16
Alignment explanation
Indices: 2970752--2970784 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2970742 AATAACAAAT
2970752 TAATATTAAAAATAAA
1 TAATATTAAAAATAAA
*
2970768 TAATATTTAAAATAAA
1 TAATATTAAAAATAAA
2970784 T
1 T
2970785 TTAAAAGCAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATATTAAAAATAAA
Found at i:2971990 original size:3 final size:3
Alignment explanation
Indices: 2971965--2972019 Score: 69
Period size: 3 Copynumber: 18.0 Consensus size: 3
2971955 ATTGGGCTTG
2971965 TAA T-A TAA TAA -AA TTAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
2972010 TAAA TAA TAA
1 T-AA TAA TAA
2972020 AAAACCAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 4 0.09
3 35 0.74
4 8 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2974355 original size:114 final size:114
Alignment explanation
Indices: 2974156--2974492 Score: 577
Period size: 114 Copynumber: 3.0 Consensus size: 114
2974146 GATCATGCAG
* * * * *
2974156 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTC-TACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
2974220 ACACTTCCAAAAGATACTATTGGGTCTCCTTATTTCTACTACGAGCAAA
66 ACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTACGAGCAAA
*
2974269 TTCATCTTTTAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
2974334 ACACTTCCAAAAGAGGCTATTGGGTCTCCTTATTTCTACTACGAGCAAA
66 ACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTACGAGCAAA
2974383 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* *
2974448 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTGCTACGAG
66 ACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTACGAG
2974493 AACGTGACAC
Statistics
Matches: 211, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
113 32 0.15
114 179 0.85
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTACGAGCAAA
Found at i:2976783 original size:21 final size:21
Alignment explanation
Indices: 2976757--2976796 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2976747 CTTGATTCAA
* *
2976757 TTTTCCTTTTTTTTTTTTTGC
1 TTTTCCATTTTTCTTTTTTGC
2976778 TTTTCCATTTTTCTTTTTT
1 TTTTCCATTTTTCTTTTTT
2976797 CCTTCTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (21 bp):
TTTTCCATTTTTCTTTTTTGC
Found at i:2979245 original size:6 final size:6
Alignment explanation
Indices: 2979218--2979263 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
2979208 CAAACGTAAA
* * * *
2979218 AAATGC AAAGGT AAATGC AAATGT AAATGT AAATGC AAATGT AAAT
1 AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAATGT AAAT
2979264 ATATATGAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.24
Consensus pattern (6 bp):
AAATGT
Found at i:2979249 original size:18 final size:18
Alignment explanation
Indices: 2979218--2979263 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2979208 CAAACGTAAA
* *
2979218 AAATGCAAAGGTAAATGC
1 AAATGTAAATGTAAATGC
2979236 AAATGTAAATGTAAATGC
1 AAATGTAAATGTAAATGC
2979254 AAATGTAAAT
1 AAATGTAAAT
2979264 ATATATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.24
Consensus pattern (18 bp):
AAATGTAAATGTAAATGC
Found at i:2981549 original size:21 final size:21
Alignment explanation
Indices: 2981511--2981568 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
2981501 TAAATAAATG
*
2981511 AATAAAACATTT-TCTTAAGAT
1 AATAAAA-ATTTATTTTAAGAT
*
2981532 AATAAAAATTTATTTTAATAT
1 AATAAAAATTTATTTTAAGAT
* *
2981553 AGTAAGATATTTATTT
1 AATAA-AAATTTATTT
2981569 ATTCAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 4 0.13
21 18 0.58
22 9 0.29
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (21 bp):
AATAAAAATTTATTTTAAGAT
Found at i:2981793 original size:2 final size:2
Alignment explanation
Indices: 2981786--2981811 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2981776 TTATTATTTA
2981786 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2981812 GTGACTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2981872 original size:16 final size:16
Alignment explanation
Indices: 2981853--2981885 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2981843 AATAACAAAT
2981853 TAATA-TTATAAATAAA
1 TAATATTTA-AAATAAA
2981869 TAATATTTAAAATAAA
1 TAATATTTAAAATAAA
2981885 T
1 T
2981886 TTAAAAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATATTTAAAATAAA
Found at i:2987276 original size:25 final size:26
Alignment explanation
Indices: 2987235--2987316 Score: 84
Period size: 25 Copynumber: 3.3 Consensus size: 26
2987225 TTTTGCTTGA
*
2987235 AGAAAAAAA-G-AAGAAGAAAAAATG
1 AGAAAAAAATGAAAAAAGAAAAAATG
** *
2987259 AG-TGAAAATGAAAAAAGAAAAAA-A
1 AGAAAAAAATGAAAAAAGAAAAAATG
*
2987283 AGAAAAAAATGAAAAATGAAAAAATG
1 AGAAAAAAATGAAAAAAGAAAAAATG
2987309 -GAAAAAAA
1 AGAAAAAAA
2987317 GAAGGGTTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
23 4 0.09
24 5 0.11
25 37 0.80
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (26 bp):
AGAAAAAAATGAAAAAAGAAAAAATG
Found at i:2987283 original size:9 final size:9
Alignment explanation
Indices: 2987269--2987298 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2987259 AGTGAAAATG
2987269 AAAAAAGAA
1 AAAAAAGAA
2987278 AAAAAAGAA
1 AAAAAAGAA
*
2987287 AAAAATGAA
1 AAAAAAGAA
2987296 AAA
1 AAA
2987299 TGAAAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:2987306 original size:9 final size:8
Alignment explanation
Indices: 2987263--2987315 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
2987253 AAAATGAGTG
2987263 AAAATGAA
1 AAAATGAA
2987271 AAAA-GAAA
1 AAAATG-AA
*
2987279 AAAAAGAAA
1 AAAATG-AA
2987288 AAAATG-A
1 AAAATGAA
2987295 AAAATGAA
1 AAAATGAA
2987303 AAAATGGAA
1 AAAAT-GAA
2987312 AAAA
1 AAAA
2987316 AGAAGGGTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
7 8 0.20
8 16 0.40
9 16 0.40
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (8 bp):
AAAATGAA
Found at i:2993064 original size:16 final size:16
Alignment explanation
Indices: 2993043--2993080 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
2993033 AACCTTATTC
2993043 ACATGATATCTACCCA
1 ACATGATATCTACCCA
2993059 ACATGATATCTACCCA
1 ACATGATATCTACCCA
2993075 ATCATG
1 A-CATG
2993081 CTTTAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (16 bp):
ACATGATATCTACCCA
Found at i:2997005 original size:108 final size:107
Alignment explanation
Indices: 2996816--2997415 Score: 776
Period size: 108 Copynumber: 5.6 Consensus size: 107
2996806 GAACTCGAAT
* * * *
2996816 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCAAACAATCTTCAACA
1 ATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCATCA
* * *
2996881 ATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACA
65 ATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACA
* *
2996924 ATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAAT-
1 ATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTC-ATC
* * *
2996988 GATTGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACA
64 AATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACA
* * *
2997032 ATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-CCACAATCTTCATCAA
1 ATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCATCAA
* * *
2997096 TTGCGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACA
66 TTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACA
* * *
2997140 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGA-TCCACAATCTTCATCAA
1 ATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCATCAA
* * * *
2997204 TCGCGTCTCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACG
66 TTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACA
* * * * *
2997248 ATCTTCAACGATTGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGAC-CCACAATCTTCATCAA
1 ATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCATCAA
*
2997312 TTACGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACA
66 TTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACA
* * * * *
2997354 ATCTTCATCAATTGCGTTTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCA
1 ATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCA
2997416 ATAATTGTTG
Statistics
Matches: 438, Mismatches: 46, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
105 2 0.00
106 85 0.19
107 4 0.01
108 346 0.79
109 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (107 bp):
ATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCATCAA
TTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACA
Found at i:2997083 original size:161 final size:163
Alignment explanation
Indices: 2996808--2997415 Score: 818
Period size: 161 Copynumber: 3.8 Consensus size: 163
2996798 GGAGAATAGA
* * * * * *
2996808 ACTCGAA-TATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCAAACAA
1 ACTCGAACAATCTTCAATAATTGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAA
* * * *
2996872 TCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAA
64 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAA
*
2996935 TCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
129 TTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
2996970 ACTCGAACGATCTTCAATGATTGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAATAATTGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
* *
2997035 TTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATT
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATT
* *
2997098 GCGTCTGCTCCCTATTTCTTCAGAGAGTATGAG
131 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * * *
2997131 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGATCCACAATC
1 ACTCGAACAATCTTCAATAATTGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
* * * *
2997196 TTCATCAATCGCGTCTCCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACGATT
66 TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATT
* *
2997261 GTGTCTGCCCCCTATATCTTCAGAGAGTATAAG
131 GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* **
2997294 AC-C-CACAATCTTC-ATCAATTACGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAAT
1 ACTCGAACAATCTTCAAT-AATTGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAAT
* * * *
2997356 CTTCATCAATTGCGTTTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCA
65 CTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCA
2997416 ATAATTGTTG
Statistics
Matches: 397, Mismatches: 45, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
160 1 0.00
161 300 0.76
162 10 0.03
163 86 0.22
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (163 bp):
ACTCGAACAATCTTCAATAATTGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATC
TTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATT
GCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:2997142 original size:269 final size:269
Alignment explanation
Indices: 2996816--2997416 Score: 1121
Period size: 269 Copynumber: 2.2 Consensus size: 269
2996806 GAACTCGAAT
* * * *
2996816 ATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCAAACAATCTTCAACA
1 ATCTTCATCAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACA
*
2996881 ATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCC
66 ATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTCCC
*
2996946 CCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAATGATTGTGTCTGCCCCCTATATCT
131 CCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCT
*
2997011 TCAGAGAGTATAAGACCCACAATCTTCATCAATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATA
196 TCAGAGAGTATAAGACCCACAATCTTCATCAATTACGTCTGCCCCCTATTTCTTCAGAGAGTATA
2997076 AGACCCACA
261 AGACCCACA
2997085 ATCTTCATCAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACA
1 ATCTTCATCAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACA
*
2997150 ATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGATCCACAATCTTCATCAATCGCGTCTCCC
66 ATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTCCC
2997215 CCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCT
131 CCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCT
2997280 TCAGAGAGTATAAGACCCACAATCTTCATCAATTACGTCTGCCCCCTATTTCTTCAGAGAGTATA
196 TCAGAGAGTATAAGACCCACAATCTTCATCAATTACGTCTGCCCCCTATTTCTTCAGAGAGTATA
2997345 AGACCCACA
261 AGACCCACA
*
2997354 ATCTTCATCAATTGCGTTTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 ATCTTCATCAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
2997417 TAATTGTTGG
Statistics
Matches: 323, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
269 323 1.00
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (269 bp):
ATCTTCATCAATTGCGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACA
ATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTCCC
CCCTATTTCTTCAGAGAGTATAAGACTCGAACGATCTTCAACGATTGTGTCTGCCCCCTATATCT
TCAGAGAGTATAAGACCCACAATCTTCATCAATTACGTCTGCCCCCTATTTCTTCAGAGAGTATA
AGACCCACA
Found at i:2998361 original size:8 final size:8
Alignment explanation
Indices: 2998343--2998395 Score: 56
Period size: 7 Copynumber: 6.5 Consensus size: 8
2998333 GAACCCTTCT
2998343 TTTTTTCCA
1 TTTTTT-CA
2998352 TTTTTTCA
1 TTTTTTCA
2998360 -TTTTTCA
1 TTTTTTCA
*
2998367 TTTTTTCTTT
1 TTTTTTC--A
2998377 TTTTTTCA
1 TTTTTTCA
2998385 -TTTTTCA
1 TTTTTTCA
2998392 TTTT
1 TTTT
2998396 CACTCATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 14 0.37
8 11 0.29
9 6 0.16
10 7 0.18
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:2998371 original size:25 final size:26
Alignment explanation
Indices: 2998342--2998395 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
2998332 TGAACCCTTC
2998342 TTTTTTTC-CATTTTTTCATTTTTCA
1 TTTTTTTCTCATTTTTTCATTTTTCA
**
2998367 -TTTTTTCTTTTTTTTTCATTTTTCA
1 TTTTTTTCTCATTTTTTCATTTTTCA
2998392 TTTT
1 TTTT
2998396 CACTCATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 15 0.60
26 3 0.12
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTTTCTCATTTTTTCATTTTTCA
Found at i:2998405 original size:25 final size:25
Alignment explanation
Indices: 2998350--2998407 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
2998340 TCTTTTTTTC
**
2998350 CATTTTTTCATTTTTCATTTTTTCT
1 CATTTTTTCATTTTTCATTTTCACT
**
2998375 TTTTTTTTCATTTTTCATTTTCACT
1 CATTTTTTCATTTTTCATTTTCACT
2998400 CATTTTTT
1 CATTTTTT
2998408 TTCTTCTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (25 bp):
CATTTTTTCATTTTTCATTTTCACT
Found at i:3008086 original size:16 final size:16
Alignment explanation
Indices: 3008065--3008102 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
3008055 AACCTTATTC
3008065 ACATGATATCTACCCA
1 ACATGATATCTACCCA
3008081 ACATGATATCTACCCA
1 ACATGATATCTACCCA
3008097 ATCATG
1 A-CATG
3008103 CTTTAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (16 bp):
ACATGATATCTACCCA
Done.