Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007978.1 Hibiscus syriacus cultivar Beakdansim tig00110415_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: 1479011
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 7
Found at i:510141 original size:24 final size:24
Alignment explanation
Indices: 510110--510163 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
510100 CAGTTTATAA
510110 TGCTGCTGTTGTTGTTGATGCTGC
1 TGCTGCTGTTGTTGTTGATGCTGC
*
510134 TGCTGCTGTTGTTGTTGTTGCTGC
1 TGCTGCTGTTGTTGTTGATGCTGC
510158 TGCTGC
1 TGCTGC
510164 AGTTTATTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.02, C:0.19, G:0.33, T:0.46
Consensus pattern (24 bp):
TGCTGCTGTTGTTGTTGATGCTGC
Found at i:514766 original size:11 final size:11
Alignment explanation
Indices: 514750--514779 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
514740 TTGACTGCTT
514750 TTTTTTAATTA
1 TTTTTTAATTA
514761 TTTTTTAATTA
1 TTTTTTAATTA
*
514772 TTATTTAA
1 TTTTTTAA
514780 CGTATTACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTTAATTA
Found at i:518111 original size:3 final size:3
Alignment explanation
Indices: 518103--518136 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
518093 TTTGAAAAAA
*
518103 TAT TAT TAT TAT TTT TAT TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
518137 CCACCAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:518293 original size:19 final size:19
Alignment explanation
Indices: 518269--518305 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
518259 GATTGATGAA
518269 CGGGAAATGCTCACGTGCC
1 CGGGAAATGCTCACGTGCC
518288 CGGGAAATGCTCACGTGC
1 CGGGAAATGCTCACGTGC
518306 GGCGTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.30, G:0.32, T:0.16
Consensus pattern (19 bp):
CGGGAAATGCTCACGTGCC
Found at i:520085 original size:31 final size:31
Alignment explanation
Indices: 520040--520120 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
520030 TTCGATAATA
* *
520040 TAATAATTATTTTTATAGT-ATTTAGATAAATT
1 TAATAAGTA-TTTTATAATCATTTA-ATAAATT
* *
520072 TATTAA-TAATTTTATAATCTTTTAATAAATT
1 TAATAAGT-ATTTTATAATCATTTAATAAATT
520103 TAATAAGTATTTTATAAT
1 TAATAAGTATTTTATAAT
520121 TTTTTAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 31 0.74
32 11 0.26
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (31 bp):
TAATAAGTATTTTATAATCATTTAATAAATT
Found at i:520098 original size:19 final size:20
Alignment explanation
Indices: 520074--520123 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
520064 GATAAATTTA
*
520074 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
520093 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
520114 TT-ATAATTTT
1 TTAATAATTTT
520124 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:520126 original size:31 final size:31
Alignment explanation
Indices: 520060--520127 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
520050 TTTTATAGTA
*
520060 TTTAGATAAATTTATTAATAATTTTATAATCT
1 TTTA-ATAAATTTAATAATAATTTTATAATCT
*
520092 TTTAATAAATTTAATAAGT-ATTTTATAATTT
1 TTTAATAAATTTAATAA-TAATTTTATAATCT
520123 TTTAA
1 TTTAA
520128 ACTTTATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTAATAAATTTAATAATAATTTTATAATCT
Found at i:542874 original size:28 final size:28
Alignment explanation
Indices: 542843--542896 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
542833 AAAATATCTA
*
542843 AATAAAATTAT-ATATATTAATGTATAAC
1 AATAAAATT-TGATAAATTAATGTATAAC
*
542871 AATAATATTTGATAAATTAATGTATA
1 AATAAAATTTGATAAATTAATGTATA
542897 GTGTTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (28 bp):
AATAAAATTTGATAAATTAATGTATAAC
Found at i:544542 original size:23 final size:23
Alignment explanation
Indices: 544512--544600 Score: 90
Period size: 23 Copynumber: 3.9 Consensus size: 23
544502 ATGTGAACTT
* *
544512 TGTCCCGAATGACTTATATACTA
1 TGTCCCGAAGGACTTATGTACTA
*
544535 TGTCCCGAAGGA-TCTGTGTACTA
1 TGTCCCGAAGGACT-TATGTACTA
* * *
544558 TGTCCCAAAGGACCTATGTACTG
1 TGTCCCGAAGGACTTATGTACTA
* *
544581 TGTCCCGAATGACCTATGTA
1 TGTCCCGAAGGACTTATGTA
544601 ACCCTTGACT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 1 0.02
23 54 0.98
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (23 bp):
TGTCCCGAAGGACTTATGTACTA
Found at i:544995 original size:14 final size:15
Alignment explanation
Indices: 544966--545003 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
544956 AACACCTAAA
544966 ATTCTTAT-TA-CAT
1 ATTCTTATATATCAT
544979 ATT-TTATATATCAT
1 ATTCTTATATATCAT
544993 ATTCTTATATA
1 ATTCTTATATA
545004 CTAATTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.18
13 5 0.23
14 6 0.27
15 7 0.32
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTCTTATATATCAT
Found at i:553367 original size:29 final size:29
Alignment explanation
Indices: 553327--553476 Score: 171
Period size: 29 Copynumber: 5.1 Consensus size: 29
553317 CCGGGTGACA
*
553327 TTTGAGAATTAATTCGAAATGA-GTGCTAT
1 TTTGAGAATTAATTCGAAA-AATGTGCTAT
*
553356 TTTGGGAATTAATTCG--AAATGGTGCTAT
1 TTTGAGAATTAATTCGAAAAAT-GTGCTAT
* * *
553384 TTTGGGAGTTTTATTCGAAAAATGTGCTATT
1 TTTGAGA-ATTAATTCGAAAAATGTGCTA-T
553415 TTTGAGAATTAATTCGAAAAATGTGCTAT
1 TTTGAGAATTAATTCGAAAAATGTGCTAT
* * *
553444 TTTGAGAATTAATTCAAAAAAGGTGTTAT
1 TTTGAGAATTAATTCGAAAAATGTGCTAT
553473 TTTG
1 TTTG
553477 GTAATTATTA
Statistics
Matches: 105, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 14 0.13
29 53 0.50
30 25 0.24
31 11 0.10
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.41
Consensus pattern (29 bp):
TTTGAGAATTAATTCGAAAAATGTGCTAT
Found at i:553464 original size:59 final size:57
Alignment explanation
Indices: 553327--553475 Score: 158
Period size: 59 Copynumber: 2.5 Consensus size: 57
553317 CCGGGTGACA
** *
553327 TTTGAGAATTAATTCGAAATGAGTGCTA-TTTTGGGAATTAATTCGAAATGGTGCTAT
1 TTTGAGAATTAATTC-AAAAAAGTGCTATTTTTGAGAATTAATTCGAAATGGTGCTAT
* * * *
553384 TTTGGGAGTTTTATTCGAAAAATGTGCTATTTTTGAGAATTAATTCGAAAAAT-GTGCTAT
1 TTTGAGA-ATTAATTC-AAAAAAGTGCTATTTTTGAGAATTAATTCG--AAATGGTGCTAT
*
553444 TTTGAGAATTAATTCAAAAAAGGTGTTATTTT
1 TTTGAGAATTAATTCAAAAAA-GTGCTATTTT
553476 GGTAATTATT
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
57 6 0.08
58 21 0.28
59 31 0.41
60 13 0.17
61 4 0.05
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (57 bp):
TTTGAGAATTAATTCAAAAAAGTGCTATTTTTGAGAATTAATTCGAAATGGTGCTAT
Found at i:553482 original size:29 final size:28
Alignment explanation
Indices: 553327--553501 Score: 124
Period size: 29 Copynumber: 6.1 Consensus size: 28
553317 CCGGGTGACA
* *
553327 TTTGAGAATTAATTC-GAAATGAGTGCTAT
1 TTTG-GAATTAATTCAAAAAAG-GTGCTAT
* *
553356 TTTGGGAATTAATTC-GAAATGGTGCTAT
1 TTT-GGAATTAATTCAAAAAAGGTGCTAT
* * * *
553384 TTTGGGAGTTTTATTCGAAAAATGTGCTATT
1 TTT-GGA-ATTAATTCAAAAAAGGTGCTA-T
* *
553415 TTTGAGAATTAATTCGAAAAATGTGCTAT
1 TTTG-GAATTAATTCAAAAAAGGTGCTAT
*
553444 TTTGAGAATTAATTCAAAAAAGGTGTTAT
1 TTTG-GAATTAATTCAAAAAAGGTGCTAT
* *
553473 TTTGGTAATT-ATT-AAAAAAAGTGATAT
1 TTTGG-AATTAATTCAAAAAAGGTGCTAT
553500 TT
1 TT
553502 CTTTAAAATG
Statistics
Matches: 128, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
27 14 0.11
28 18 0.14
29 60 0.47
30 30 0.23
31 6 0.05
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (28 bp):
TTTGGAATTAATTCAAAAAAGGTGCTAT
Found at i:554248 original size:15 final size:15
Alignment explanation
Indices: 554230--554262 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
554220 TGATATGTGA
554230 TTCCTGAATAT-TGAT
1 TTCCT-AATATCTGAT
554245 TTCCTAATATCTGAT
1 TTCCTAATATCTGAT
554260 TTC
1 TTC
554263 TGTATTTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.48
Consensus pattern (15 bp):
TTCCTAATATCTGAT
Found at i:554772 original size:18 final size:18
Alignment explanation
Indices: 554736--554783 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
554726 ATATCTATAT
** *
554736 TATTAATATTTTGTTTTG
1 TATTAATATAATGTATTG
554754 TATTAATATAATGTATTG
1 TATTAATATAATGTATTG
*
554772 TAATATATATAA
1 TATTA-ATATAA
554784 AAAAACATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
TATTAATATAATGTATTG
Found at i:556959 original size:142 final size:142
Alignment explanation
Indices: 556703--556986 Score: 525
Period size: 142 Copynumber: 2.0 Consensus size: 142
556693 CCCGGATAAT
*
556703 CGAAAGATTGTAATGATTGGGGAATGCCGTGGATTTCTGACGAATGTTGTATCTGCTTTGGTAGC
1 CGAAAGATTGTAATGATTGGGGAATGCCGTGGATTTCTGACGAATGTTGTATCTACTTTGGTAGC
556768 TGAGAAGATGATCAGGAAAGGTTCCGAGGTGTTTCTTGCTTATATATTGGATACTAGGAGTTCTC
66 TGAGAAGATGATCAGGAAAGGTTCCGAGGTGTTTCTTGCTTATATATTGGATACTAGGAGTTCTC
556833 AGTCTGATATTG
131 AGTCTGATATTG
*
556845 CGAAAGATTGTAATGATTGGGGAAAT-TCGTGGATTTCTGACGAATGTTGTATCTACTTTGGTAG
1 CGAAAGATTGTAATGATTGGGG-AATGCCGTGGATTTCTGACGAATGTTGTATCTACTTTGGTAG
*
556909 CTGAGAAGATGATCATGAAAGGTTCCGAGGTGTTTCTTGCTTATATATTGGATACTAGGAGTTCT
65 CTGAGAAGATGATCAGGAAAGGTTCCGAGGTGTTTCTTGCTTATATATTGGATACTAGGAGTTCT
556974 CAGTCTGATATTG
130 CAGTCTGATATTG
556987 AAGGTATCCG
Statistics
Matches: 138, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
142 135 0.98
143 3 0.02
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.35
Consensus pattern (142 bp):
CGAAAGATTGTAATGATTGGGGAATGCCGTGGATTTCTGACGAATGTTGTATCTACTTTGGTAGC
TGAGAAGATGATCAGGAAAGGTTCCGAGGTGTTTCTTGCTTATATATTGGATACTAGGAGTTCTC
AGTCTGATATTG
Found at i:560281 original size:14 final size:14
Alignment explanation
Indices: 560262--560289 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
560252 TGAAACGTTG
560262 CCAAACGTCGAGAA
1 CCAAACGTCGAGAA
560276 CCAAACGTCGAGAA
1 CCAAACGTCGAGAA
560290 TTTCAAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.21, T:0.07
Consensus pattern (14 bp):
CCAAACGTCGAGAA
Found at i:560851 original size:29 final size:29
Alignment explanation
Indices: 560706--560882 Score: 171
Period size: 29 Copynumber: 6.1 Consensus size: 29
560696 ATCGGGTGAC
*
560706 ATTTTGGGAATTAATTCGAAATGGGTGTT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
** *
560735 ACATTGGGAATTAATTCGAAATGGGTGAT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
560764 ATTTTGGGAATTAATTCGAAAT--GTGCT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
* * **
560791 ATTTTGGGAATTTTATTCAAAAAAGGTGCT
1 ATTTTGGGAA-TTAATTCGAAATGGGTGCT
* *
560821 ATTTTAGGAATTAATTCGAAAAGGGAT-CT
1 ATTTTGGGAATTAATTCGAAATGGG-TGCT
** * ** *
560850 ATTTTGTTAATTATTTTAAAAAGGGTGCT
1 ATTTTGGGAATTAATTCGAAATGGGTGCT
560879 ATTT
1 ATTT
560883 CTGTAAAATG
Statistics
Matches: 124, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
27 14 0.11
28 10 0.08
29 85 0.69
30 15 0.12
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (29 bp):
ATTTTGGGAATTAATTCGAAATGGGTGCT
Found at i:561642 original size:14 final size:16
Alignment explanation
Indices: 561618--561650 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
561608 TGATACGTGA
561618 TTCCTGAATAT-TGAT
1 TTCCTGAATATCTGAT
561633 TTCCTG-ATATCTGAT
1 TTCCTGAATATCTGAT
561648 TTC
1 TTC
561651 TGTATTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.48
Consensus pattern (16 bp):
TTCCTGAATATCTGAT
Found at i:561908 original size:14 final size:13
Alignment explanation
Indices: 561886--561928 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
561876 AACAAACATG
561886 TTTAATGAAATGAT
1 TTTAATGAAATG-T
*
561900 TTTACTGAAATGT
1 TTTAATGAAATGT
* *
561913 TTTATTAAAATGT
1 TTTAATGAAATGT
561926 TTT
1 TTT
561929 TATACACTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (13 bp):
TTTAATGAAATGT
Found at i:562857 original size:23 final size:23
Alignment explanation
Indices: 562812--562886 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
562802 TTTGTTGTTT
* *
562812 GTTTATGTTCGTTTATTGGGTTC
1 GTTTATGTTCATTTATTAGGTTC
*
562835 -TATTATGTTCATTTATTATGTTC
1 GT-TTATGTTCATTTATTAGGTTC
* *
562858 GTTTATGTTCATTCATTTGTGTTC
1 GTTTATGTTCATTTATTAG-GTTC
562882 GTTTA
1 GTTTA
562887 CGTTTGTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.02
23 32 0.74
24 10 0.23
ACGTcount: A:0.15, C:0.09, G:0.17, T:0.59
Consensus pattern (23 bp):
GTTTATGTTCATTTATTAGGTTC
Found at i:562993 original size:16 final size:16
Alignment explanation
Indices: 562972--563004 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
562962 AAAAAAATTT
562972 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
562988 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
563004 T
1 T
563005 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:565757 original size:19 final size:16
Alignment explanation
Indices: 565720--565751 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
565710 CAAGTGAACG
565720 AAATGAAAAAAAGCAC
1 AAATGAAAAAAAGCAC
565736 AAATGAAAAAAAGCAC
1 AAATGAAAAAAAGCAC
565752 CACAAAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.12, G:0.12, T:0.06
Consensus pattern (16 bp):
AAATGAAAAAAAGCAC
Found at i:566283 original size:3 final size:3
Alignment explanation
Indices: 566272--566365 Score: 129
Period size: 3 Copynumber: 31.3 Consensus size: 3
566262 TTAAATAATA
566272 TAT TA- 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
* * *
566319 TACT TACT TAT TAT TAT TAT TA- TAT TAT TAA TAC TAT TAA TAT TAT
1 TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
566365 T
1 T
566366 TTTGCAGGCT
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
2 4 0.05
3 72 0.87
4 7 0.08
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:569979 original size:41 final size:42
Alignment explanation
Indices: 569919--570002 Score: 161
Period size: 41 Copynumber: 2.0 Consensus size: 42
569909 GCATTCTGTT
569919 TGAACTTTTTTTTTTCCACTTTTTCAAGTTTTTGTAAGAACG
1 TGAACTTTTTTTTTTCCACTTTTTCAAGTTTTTGTAAGAACG
569961 TGAAC-TTTTTTTTTCCACTTTTTCAAGTTTTTGTAAGAACG
1 TGAACTTTTTTTTTTCCACTTTTTCAAGTTTTTGTAAGAACG
570002 T
1 T
570003 TTGAATAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 37 0.88
42 5 0.12
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.52
Consensus pattern (42 bp):
TGAACTTTTTTTTTTCCACTTTTTCAAGTTTTTGTAAGAACG
Found at i:571868 original size:106 final size:106
Alignment explanation
Indices: 571711--573477 Score: 2996
Period size: 106 Copynumber: 16.7 Consensus size: 106
571701 ATATCGTGCC
* *
571711 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
571776 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
571817 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
571882 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
571923 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
571988 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
572029 ACTCCAGACAACGTATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCCACAAACAAATTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
572094 AATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
572135 ACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
572200 AATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
572241 ACTCTAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
572306 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
572347 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
572412 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
572453 ACTCCAGACAACTCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
572518 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
572559 ACTCCAGACAACGTATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCGC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
572624 AATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
572665 ACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
572730 AATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
572771 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
572836 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
572877 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
572942 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
572983 ACTCCAGACAACGTATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
573048 AATATCAGAGCCTATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
573089 ACTCCAGACAACGTATGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
573154 AATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
573195 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* *
573260 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
573301 ACTCCAGACAACGCGAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
* * * *
573366 AATTTCAGAGTCAATTTCAACTTCATAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
573407 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTT-TC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
*
573471 AACTTCA
66 AATTTCA
573478 CGACGAAGGA
Statistics
Matches: 1587, Mismatches: 74, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
105 7 0.00
106 1580 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:573639 original size:84 final size:83
Alignment explanation
Indices: 573524--573784 Score: 326
Period size: 84 Copynumber: 3.1 Consensus size: 83
573514 AAAGACCCCC
* * * * *
573524 GAGTTCGATTACGCTCAACTCTAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
573589 CTTCCAACCAAAGATCTTT
66 CTTCCAACCAAAGA-CTTT
* * * * *
573608 GAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAACATAGCTCAAGGCAAGAAGGGCTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
*
573673 -TTGCCAACCAAAGACCTTC
66 CTT-CCAACCAAAGA-CTTT
* * * *
573692 GAGTTTGACTACTCTCAGCTCCGAGGCACATCATTTGCAGCATAGCTTAAGTTGAGAAGGGCTAT
1 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
*
573757 CTGCCAACCAAAGACTTGAT
66 CTTCCAACCAAAGACTT--T
573777 GAGTTCGA
1 GAGTTCGA
573785 TTTCATTCAG
Statistics
Matches: 149, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
83 5 0.03
84 136 0.91
85 8 0.05
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (83 bp):
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
CTTCCAACCAAAGACTTT
Found at i:574025 original size:3 final size:3
Alignment explanation
Indices: 574014--574082 Score: 79
Period size: 3 Copynumber: 23.3 Consensus size: 3
574004 TTAAATAATA
*
574014 TAT TA- TAT TAT TAT TAT TAT TAT AAT TACT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * *
574058 TAT TAT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
574083 TTTGCAGGCT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:575991 original size:2 final size:2
Alignment explanation
Indices: 575979--576041 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
575969 CAAATATCTA
575979 AT AT A- 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
576020 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
576042 TTAAAATATT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:576064 original size:12 final size:13
Alignment explanation
Indices: 575979--576062 Score: 104
Period size: 12 Copynumber: 6.7 Consensus size: 13
575969 CAAATATCTA
575979 ATATAATATATAT
1 ATATAATATATAT
575992 ATAT-ATATATAT
1 ATATAATATATAT
576004 ATAT-ATATATAT
1 ATATAATATATAT
576016 ATAT-ATATATAT
1 ATATAATATATAT
576028 ATAT-ATATATAT
1 ATATAATATATAT
* * *
576040 ATTTAAAATATTT
1 ATATAATATATAT
576053 AATATAATAT
1 -ATATAATAT
576063 TTTTTTTATT
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
12 47 0.73
13 10 0.16
14 7 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:579642 original size:15 final size:15
Alignment explanation
Indices: 579620--579655 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
579610 TAACGGAATC
*
579620 TCTGAAGAATTGAAA
1 TCTGAAGAAATGAAA
*
579635 TTTGAAGAAATGAAA
1 TCTGAAGAAATGAAA
579650 TCTGAA
1 TCTGAA
579656 TCTTAAATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
TCTGAAGAAATGAAA
Found at i:579894 original size:21 final size:20
Alignment explanation
Indices: 579855--579894 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
579845 TTAAATATTA
* *
579855 ATTTTTTATTTTATTAATTG
1 ATTTTTTATTTAATAAATTG
579875 ATTTTTTATTTCAATAAATT
1 ATTTTTTATTT-AATAAATT
579895 ATAAAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (20 bp):
ATTTTTTATTTAATAAATTG
Found at i:580292 original size:27 final size:28
Alignment explanation
Indices: 580262--580322 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
580252 AAAACCCGAC
* * *
580262 CGACCCGTATATTACACTT-AAAAAACT
1 CGACCCGAATATCAAACTTAAAAAAACT
580289 CGACCCGAATATCAAACTTAAAAAAACT
1 CGACCCGAATATCAAACTTAAAAAAACT
*
580317 CTACCC
1 CGACCC
580323 TACCCGACCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.43, C:0.30, G:0.07, T:0.21
Consensus pattern (28 bp):
CGACCCGAATATCAAACTTAAAAAAACT
Found at i:593278 original size:25 final size:26
Alignment explanation
Indices: 593245--593306 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 26
593235 TAGGGGTTTT
*
593245 TATATTTTTAAATGTAT-TTTTAAAA
1 TATAATTTTAAATGTATATTTTAAAA
* * *
593270 TATAATTTT-TATTTTTATTTTAAAA
1 TATAATTTTAAATGTATATTTTAAAA
*
593295 TAAAATTTTAAA
1 TATAATTTTAAA
593307 AACTATAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 4 0.14
25 24 0.83
26 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TATAATTTTAAATGTATATTTTAAAA
Found at i:598731 original size:21 final size:22
Alignment explanation
Indices: 598681--598742 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
598671 AGAATTTCAG
* *
598681 CTTGATTTTGAAACCCCCTGTA
1 CTTGGTTTCGAAACCCCCTGTA
598703 CTTGGTTTCGAAACCCTCCTG-A
1 CTTGGTTTCGAAACCC-CCTGTA
*
598725 C-TGGTTTCGAAAACCCCT
1 CTTGGTTTCGAAACCCCCT
598743 TCCTGGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 3 0.08
21 13 0.36
22 16 0.44
23 4 0.11
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.32
Consensus pattern (22 bp):
CTTGGTTTCGAAACCCCCTGTA
Found at i:598751 original size:20 final size:21
Alignment explanation
Indices: 598691--598739 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
598681 CTTGATTTTG
*
598691 AAACCCCCTGTACTTGGTTTCGA
1 AAACCTCCTG-AC-TGGTTTCGA
*
598714 AACCCTCCTGACTGGTTTCGA
1 AAACCTCCTGACTGGTTTCGA
598735 AAACC
1 AAACC
598740 CCTTCCTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 2 0.09
23 8 0.35
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (21 bp):
AAACCTCCTGACTGGTTTCGA
Found at i:607746 original size:41 final size:39
Alignment explanation
Indices: 607701--607807 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 39
607691 GATTCGCAAC
*
607701 GCGATT-CTAACTATCGCATTGCGATTTTC-TAAATTCGCGTT
1 GCGATTCCTAA-T-TCGCATTGCGATTTACGT--ATTCGCGTT
607742 GCGATTTTCCTAATTCGCATTGCGATTTACGTATTCGCGTT
1 GCGA--TTCCTAATTCGCATTGCGATTTACGTATTCGCGTT
*
607783 GCGATTTTCCTAATTCGCAATGCGA
1 GCGA--TTCCTAATTCGCATTGCGA
607808 ATACGTAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
41 37 0.62
42 15 0.25
43 4 0.07
44 4 0.07
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (39 bp):
GCGATTCCTAATTCGCATTGCGATTTACGTATTCGCGTT
Found at i:607779 original size:20 final size:20
Alignment explanation
Indices: 607714--607807 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 20
607704 ATTCTAACTA
607714 TCGCATTGCGATTTTCTAAAT
1 TCGCATTGCGATTTTCT-AAT
*
607735 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTT-CTAAT
*
607756 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTC-TAAT
*
607776 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTT-CTAAT
*
607797 TCGCAATGCGA
1 TCGCATTGCGA
607808 ATACGTAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
20 17 0.27
21 43 0.69
22 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTTCTAAT
Found at i:607880 original size:20 final size:20
Alignment explanation
Indices: 607797--607870 Score: 105
Period size: 20 Copynumber: 3.6 Consensus size: 20
607787 TTTTCCTAAT
607797 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
607817 TCGCAATGTGAATTA-GGAACA
1 TCGCAATGCGAA-TACGTAA-A
607838 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
607858 TCGCAATGCGAAT
1 TCGCAATGCGAAT
607871 CTAACTATCG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
20 30 0.64
21 17 0.36
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:608151 original size:27 final size:27
Alignment explanation
Indices: 608095--608152 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
608085 CATCGCATGC
**
608095 GAAATCCCTCACAACCATTCACGGTAA
1 GAAATCCCTCACAACCATTCACGAAAA
*
608122 GAAATCCCTCACAATCATTCA-GAAATA
1 GAAATCCCTCACAACCATTCACGAAA-A
608149 GAAA
1 GAAA
608153 ATTAACCTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (27 bp):
GAAATCCCTCACAACCATTCACGAAAA
Found at i:610420 original size:95 final size:93
Alignment explanation
Indices: 610221--610597 Score: 537
Period size: 94 Copynumber: 4.1 Consensus size: 93
610211 TAGATTGCTT
* * *
610221 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAATACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
610282 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
* *
610311 AGTAAATTTATTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACATTTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACA-CTGTGAAGTTAG
*
610376 TATTTGTCTTTATTTTGTCTTTTGGTTGAA
65 TATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
610406 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTTTTTATCACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
610471 ATTTATCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
610500 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
610565 CTTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
610593 AGTAA
1 AGTAA
610598 TGCAATCCAT
Statistics
Matches: 258, Mismatches: 23, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
90 34 0.13
92 3 0.01
93 8 0.03
94 145 0.56
95 68 0.26
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.49
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:610537 original size:189 final size:183
Alignment explanation
Indices: 610221--610597 Score: 549
Period size: 189 Copynumber: 2.0 Consensus size: 183
610211 TAGATTGCTT
610221 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAATACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAATACTGTGAAGTTAGTATTT
* * * *
610286 GTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGTCAATTCTGCTAAACTGTG
66 ATCTTTTGTTTTATCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTA
* *
610351 TATTCTTTAACATTTGTGAAGTTAGTATTTGTCTTTATTTTGTCTTTTGGTTGAA
131 TATTCTTTAACA-CTCTGAAGTTAGTATTTGTCTTTATTTTGTCTTTTGGTTG-A
* * * *
610406 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTTTTTATCACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TTATTAAT-ACTGTGAAGTTAGT
* *
610471 ATTTATC-TTTGTTTTATCTTTTGGTTGAAAGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAA
62 ATTTATCTTTTGTTTTATCTTTTGGTTG-AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAA
* * *
610535 CTGTATATTCTTTAATACTCTGAAGTTAGTCTTTGTCTTTGTTTTGTCTTTTGGTTGA
126 CTGTATATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTATTTTGTCTTTTGGTTGA
610593 AGTAA
1 AGTAA
610598 TGCAATCCAT
Statistics
Matches: 172, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
185 34 0.20
187 9 0.05
188 61 0.35
189 68 0.40
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.49
Consensus pattern (183 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAATACTGTGAAGTTAGTATTT
ATCTTTTGTTTTATCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTA
TATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTATTTTGTCTTTTGGTTGA
Found at i:610735 original size:20 final size:20
Alignment explanation
Indices: 610710--610765 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
610700 GCAACGAGAG
610710 AATCGCAACGCGAAACCAAA
1 AATCGCAACGCGAAACCAAA
* *
610730 AATCGCAATGTGAAACCAAA
1 AATCGCAACGCGAAACCAAA
610750 AATCGCAACGCGAAAC
1 AATCGCAACGCGAAAC
610766 TATAATCGCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.48, C:0.27, G:0.16, T:0.09
Consensus pattern (20 bp):
AATCGCAACGCGAAACCAAA
Found at i:610793 original size:19 final size:19
Alignment explanation
Indices: 610771--610920 Score: 105
Period size: 19 Copynumber: 8.6 Consensus size: 19
610761 GAAACTATAA
*
610771 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* **
610790 TCGCTTTGCGA--TTC-CC
1 TCGCATTGCGATTTTCATT
610806 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
610823 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
610839 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
610856 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
*
610870 TCTCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
**
610889 TCGCATTGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
*
610908 TCTGCGTTGCGAT
1 TC-GCATTGCGAT
610921 AGATATTAAG
Statistics
Matches: 103, Mismatches: 12, Indels: 31
0.71 0.08 0.21
Matches are distributed among these distances:
14 22 0.21
16 16 0.16
17 16 0.16
19 40 0.39
20 9 0.09
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:610816 original size:33 final size:33
Alignment explanation
Indices: 610774--610900 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
610764 ACTATAATCG
* *
610774 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
610807 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
610840 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
610873 CATTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
610901 AGTCATTTCT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:610847 original size:14 final size:14
Alignment explanation
Indices: 610795--610882 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
610785 TCATTTCGCT
*
610795 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
610809 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
610826 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
610842 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
610859 CATTGCGATTCTCTCA
1 --TTGCGATTCTCTCG
610875 TTGCGATT
1 TTGCGATT
610883 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 13 0.22
17 13 0.22
19 12 0.21
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:613462 original size:24 final size:24
Alignment explanation
Indices: 613428--613481 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
613418 CTGAAAAATC
613428 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
613452 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
613476 ATCAAA
1 ATCAAA
613482 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:613495 original size:24 final size:24
Alignment explanation
Indices: 613428--613495 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
613418 CTGAAAAATC
* * *
613428 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
613452 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
613476 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
613496 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:614286 original size:21 final size:21
Alignment explanation
Indices: 614261--614400 Score: 203
Period size: 21 Copynumber: 6.7 Consensus size: 21
614251 TGCGATTTAC
614261 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCGAATTAGG
* *
614282 TAAATCACAATGCAAATTAGG
1 TAAATCGCAATGCGAATTAGG
*
614303 TAAATCGCAATGCG-ATTACG
1 TAAATCGCAATGCGAATTAGG
614323 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCGAATTAGG
*
614344 TAAATCGCAACGCGAATTAGG
1 TAAATCGCAATGCGAATTAGG
* *
614365 TAAATCGCAACGCGAATTTGAG
1 TAAATCGCAATGCGAATTAG-G
614387 -AAATCGCAATGCGA
1 TAAATCGCAATGCGA
614401 TAGTCAGAAG
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
20 19 0.18
21 88 0.81
22 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.22
Consensus pattern (21 bp):
TAAATCGCAATGCGAATTAGG
Found at i:614327 original size:62 final size:63
Alignment explanation
Indices: 614251--614400 Score: 218
Period size: 62 Copynumber: 2.4 Consensus size: 63
614241 AGAATCTCGT
*
614251 TGCGATTTAC-TAAATCGCAATGCGAATTAGGTAAATCACAATGCAAATTAGGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATTAGGTAAATCACAACGCAAATTAGGTAAATCGCAA
* *
614313 TGCGA-TTACGTAAATCGCAATGCGAATTAGGTAAATCGCAACGCGAATTAGGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATTAGGTAAATCACAACGCAAATTAGGTAAATCGCAA
*
614375 CGCGAATTTGA-G-AAATCGCAATGCGA
1 TGCG-ATTT-ACGTAAATCGCAATGCGA
614401 TAGTCAGAAG
Statistics
Matches: 80, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
61 4 0.05
62 57 0.71
63 15 0.19
64 3 0.04
65 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (63 bp):
TGCGATTTACGTAAATCGCAATGCGAATTAGGTAAATCACAACGCAAATTAGGTAAATCGCAA
Found at i:628108 original size:16 final size:16
Alignment explanation
Indices: 628089--628120 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
628079 TTAATTTTTT
*
628089 TTATTTATTCTTTTAA
1 TTATTTATTCGTTTAA
628105 TTATTTATTCGTTTAA
1 TTATTTATTCGTTTAA
628121 ATTTTACTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (16 bp):
TTATTTATTCGTTTAA
Found at i:629436 original size:16 final size:16
Alignment explanation
Indices: 629417--629450 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
629407 CAATATACGA
629417 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
629433 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
629449 AT
1 AT
629451 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:630191 original size:130 final size:130
Alignment explanation
Indices: 629987--630234 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
629977 AATTTTCTTC
* * *
629987 TAATTTGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** * *
630052 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTATGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
630117 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
630182 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
630235 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:630681 original size:35 final size:35
Alignment explanation
Indices: 630631--630706 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
630621 AATTGAATTC
* *
630631 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
630666 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
630701 AATTGA
1 AATTGA
630707 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:634596 original size:2 final size:2
Alignment explanation
Indices: 634589--634664 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
634579 CTTCTTTTTC
634589 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
634631 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
634665 GTGAGCAGAC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:637268 original size:6 final size:6
Alignment explanation
Indices: 637259--637286 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
637249 TATATATATA
637259 TATTTG TATTTG TATTTG TATTTG TATT
1 TATTTG TATTTG TATTTG TATTTG TATT
637287 GATTTCAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.68
Consensus pattern (6 bp):
TATTTG
Found at i:639347 original size:35 final size:35
Alignment explanation
Indices: 639298--639407 Score: 107
Period size: 35 Copynumber: 3.1 Consensus size: 35
639288 TGTGTATTTT
* * *
639298 AAGTAGAACAGAAGGAATCATCACACTTTCGATTC
1 AAGTAAAACGGAAGGAATCATCGCACTTTCGATTC
* *
639333 AAGTAAAATGGAAGGAAGT-ATCGCACTTTCTG-TTT
1 AAGTAAAACGGAAGGAA-TCATCGCACTTTC-GATTC
** * *
639368 AAGTGGAACGAAAGGAAGCATCGCACTTTCGATTC
1 AAGTAAAACGGAAGGAATCATCGCACTTTCGATTC
639403 AAGTA
1 AAGTA
639408 TTCATATTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
34 1 0.02
35 56 0.95
36 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (35 bp):
AAGTAAAACGGAAGGAATCATCGCACTTTCGATTC
Found at i:648470 original size:81 final size:82
Alignment explanation
Indices: 648326--648490 Score: 287
Period size: 81 Copynumber: 2.0 Consensus size: 82
648316 ACGACAAAAA
* *
648326 CATACATAAATCATAAATAAACTATATGAACATAATAAAGTCTTAAAGTTAATTTTTTCAACAAA
1 CATACACAAATCATAAATAAACTATATGAACATAATAAAGTCTTAAAGTTAATTTGTTCAACAAA
*
648391 ACAATCTTCTTGAAATC
66 ACAATCTTCTTAAAATC
*
648408 CATACACAAATCATAAATAAACTATATGAATAT-ATAAAGTCTTAAAGTTAATTTGTTCAACAAA
1 CATACACAAATCATAAATAAACTATATGAACATAATAAAGTCTTAAAGTTAATTTGTTCAACAAA
648472 ACAATCTTCTTAAAATC
66 ACAATCTTCTTAAAATC
648489 CA
1 CA
648491 AACAACTTCA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 48 0.61
82 31 0.39
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (82 bp):
CATACACAAATCATAAATAAACTATATGAACATAATAAAGTCTTAAAGTTAATTTGTTCAACAAA
ACAATCTTCTTAAAATC
Found at i:650341 original size:113 final size:112
Alignment explanation
Indices: 650143--650367 Score: 405
Period size: 113 Copynumber: 2.0 Consensus size: 112
650133 ACCGACTCGG
*
650143 AACTCTTCAGCCAAAAGATGCATGTGTAATTTAACCGGTGAGCATCAGTACCAATGAAATGAGAA
1 AACTCTTCAGCCAAAAGATGCATGTGTAATTTAACCGGTGAGCATCAGCACCAATGAAATGAGAA
650208 ATGACCTACAAGTTATTACAAATGAGATCCCACACATGCAAAGAGATT
66 ATGACCTACAAGTTATTAC-AATGAGATCCCACACATGCAAAGAGATT
* *
650256 AACTCTTCAGCCAAAAGATGCATGTGTAATTTAACCGGTGAGCATCAGCACCGATGAAATGAGGA
1 AACTCTTCAGCCAAAAGATGCATGTGTAATTTAACCGGTGAGCATCAGCACCAATGAAATGAGAA
*
650321 ATGACCTACAAGTTATTACAATGAGATCCCACGCATGCAAAGAGATT
66 ATGACCTACAAGTTATTACAATGAGATCCCACACATGCAAAGAGATT
650368 GATTACTTTC
Statistics
Matches: 108, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
112 27 0.25
113 81 0.75
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (112 bp):
AACTCTTCAGCCAAAAGATGCATGTGTAATTTAACCGGTGAGCATCAGCACCAATGAAATGAGAA
ATGACCTACAAGTTATTACAATGAGATCCCACACATGCAAAGAGATT
Found at i:652185 original size:21 final size:20
Alignment explanation
Indices: 652151--652193 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
652141 AAATATTTAA
652151 TAAATATTTATATTTATATTT
1 TAAATATTTATATTTAT-TTT
652172 TAAAT-TTTACTATTTATTTT
1 TAAATATTTA-TATTTATTTT
652192 TA
1 TA
652194 CATGAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TAAATATTTATATTTATTTT
Found at i:652989 original size:24 final size:24
Alignment explanation
Indices: 652962--653012 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
652952 TTTTATGTTA
*
652962 AAGGATGCG-AACGTATAAAAATTT
1 AAGGATGAGTAACGTAT-AAAATTT
* *
652986 AAGGGTGAGTAACTTATAAAATTT
1 AAGGATGAGTAACGTATAAAATTT
653010 AAG
1 AAG
653013 AGACGAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.27
Consensus pattern (24 bp):
AAGGATGAGTAACGTATAAAATTT
Found at i:656130 original size:18 final size:19
Alignment explanation
Indices: 656097--656146 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
656087 CCCTACTTGA
*
656097 TTAAATATTTA--ATAAAT
1 TTAAATATTTATTTTAAAT
*
656114 TTTAATATTT-TTTTAAAT
1 TTAAATATTTATTTTAAAT
656132 TTAAATATTTATTTT
1 TTAAATATTTATTTT
656147 TACATGAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 9 0.33
18 14 0.52
19 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAAATATTTATTTTAAAT
Found at i:658564 original size:25 final size:25
Alignment explanation
Indices: 658536--658586 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
658526 TCGAGTATTG
* * *
658536 TTAAATTTGACTCAATTCGAAAATT
1 TTAAAGTTAACTCAACTCGAAAATT
*
658561 TTAAAGTTAATTCAACTCGAAAATT
1 TTAAAGTTAACTCAACTCGAAAATT
658586 T
1 T
658587 GTGTGATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (25 bp):
TTAAAGTTAACTCAACTCGAAAATT
Found at i:660397 original size:21 final size:20
Alignment explanation
Indices: 660371--660503 Score: 83
Period size: 20 Copynumber: 6.5 Consensus size: 20
660361 CAGTTCCCAT
660371 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
660391 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
660412 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
660434 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
660454 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
660474 AATCGCAACGCGATTTTGAC
1 AATCGCAACGCGATTATGAA
*
660494 TATCGCAACG
1 AATCGCAACG
660504 AGTATCCGTA
Statistics
Matches: 87, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
19 2 0.02
20 46 0.53
21 35 0.40
22 3 0.03
23 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:660459 original size:20 final size:20
Alignment explanation
Indices: 660434--660725 Score: 257
Period size: 20 Copynumber: 14.5 Consensus size: 20
660424 GATTTTCCAG
* *
660434 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
660454 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
* **
660474 AATCGCAACGCGATTTTG-A
1 AATCGCAACGCGAATACGTA
* * * *
660493 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
660515 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
660535 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
660556 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
660576 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
660596 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
660616 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
* * *
660636 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
660656 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
660676 AATCGTAATGCGAATACATA
1 AATCGCAACGCGAATACGTA
*
660696 AATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
660716 AATCGCAACG
1 AATCGCAACG
660726 AGATTCTGAC
Statistics
Matches: 232, Mismatches: 33, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 195 0.84
21 34 0.15
22 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:660656 original size:60 final size:60
Alignment explanation
Indices: 660495--660728 Score: 297
Period size: 60 Copynumber: 3.9 Consensus size: 60
660485 GATTTTGACT
* * *
660495 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGT-AAATCGCAACGCGAATCCGTAAATCGCAACGAGAATACGT-AA
* *
660557 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGCGAATCCGTAAATCGCAACGAGAATACGTAA
* * * * *
660617 ATCGCAATGCGTATCCGTAAATCGCAATGCGTATCCGTAAATCGCAATGCGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGCGAATCCGTAAATCGCAACGAGAATACGTAA
* * * * * * *
660677 ATCGTAATGCGAATACATAAATCGCAATGCGAATCTGTAAATCGCAACGAGA
1 ATCGCAACGCGTATCCGTAAATCGCAACGCGAATCCGTAAATCGCAACGAGA
660729 TTCTGACTAT
Statistics
Matches: 152, Mismatches: 20, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
60 99 0.65
61 36 0.24
62 17 0.11
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (60 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGCGAATCCGTAAATCGCAACGAGAATACGTAA
Found at i:661635 original size:24 final size:24
Alignment explanation
Indices: 661584--661637 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
661574 GTATTCAAAA
*
661584 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGAAC
* *
661608 TTTGATCTTGGTCAATACTCGAAT
1 TTTGATCTTGGTCAATACCCGAAC
661632 TTTGAT
1 TTTGAT
661638 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGAAC
Found at i:664250 original size:53 final size:52
Alignment explanation
Indices: 664188--664302 Score: 167
Period size: 53 Copynumber: 2.2 Consensus size: 52
664178 GCAACGAGAG
* * *
664188 AATCGCAATGCGAAATGAAAATCGTAACGTGAAAATCGCAACGCGGAAATGAC
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGC-GAAATGAA
* * *
664241 TATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAATGAA
664293 AATCGCAATG
1 AATCGCAATG
664303 AGGGAATCGC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
52 16 0.29
53 39 0.71
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAATGAA
Found at i:664257 original size:19 final size:19
Alignment explanation
Indices: 664188--664339 Score: 109
Period size: 19 Copynumber: 8.7 Consensus size: 19
664178 GCAACGAGAG
664188 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
664207 AATCGTAA--CG---TGAA
1 AATCGCAATGCGAAATGAA
* *
664221 AATCGCAACGCGGAAATGAC
1 AATCGCAATGC-GAAATGAA
*
664241 TATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
664260 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
664274 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
664293 AATCGCAAT--G--A-GGG
1 AATCGCAATGCGAAATGAA
*
664307 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
*
664326 AATCGCAACGCGAA
1 AATCGCAATGCGAA
664340 TTTAGTTTCC
Statistics
Matches: 102, Mismatches: 15, Indels: 32
0.68 0.10 0.21
Matches are distributed among these distances:
14 31 0.30
15 2 0.02
16 4 0.04
17 6 0.06
18 2 0.02
19 45 0.44
20 12 0.12
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:664284 original size:33 final size:33
Alignment explanation
Indices: 664242--664335 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
664232 GGAAATGACT
664242 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
664275 ATCGCAATGCGAAATGAAAATCGCAATGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
664308 ATCGCAATACGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
664336 CGAATTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:664311 original size:86 final size:87
Alignment explanation
Indices: 664148--664337 Score: 240
Period size: 86 Copynumber: 2.2 Consensus size: 87
664138 CAATCATCTT
* * ** *
664148 AATGTCTATCGCAACGCGGAAATTACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGT
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
*
664213 AACGTGAAAATCGCAACGCGGA
66 AACGAGAAAATCGCAACGCGGA
*
664235 AATGACTATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
* ** **
664299 AATGAGGGAATCGCAATAC-GA
66 AACGAGAAAATCGCAACGCGGA
**
664320 AATGAAAATCGCAACGCG
1 AATGACTATCGCAACGCG
664338 AATTTAGTTT
Statistics
Matches: 87, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
85 16 0.18
86 56 0.64
87 15 0.17
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (87 bp):
AATGACTATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
AACGAGAAAATCGCAACGCGGA
Found at i:664377 original size:19 final size:19
Alignment explanation
Indices: 664335--664380 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
664325 AAATCGCAAC
*
664335 GCGAATTTAGTTTCCCGTT
1 GCGATTTTAGTTTCCCGTT
*
664354 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCCCGTT
664373 GCGATTTT
1 GCGATTTT
664381 GTCGTTGCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCCCGTT
Found at i:664419 original size:33 final size:33
Alignment explanation
Indices: 664350--664443 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 33
664340 TTTAGTTTCC
* * ***
664350 CGTTGCGATTTTAGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCACT
* *
664383 CGTTGCGATTTTAATTTCGTATTGTGATTCACT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCACT
* *
664416 CGTTGCAATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTAATTTCGCATTGCGAT
664444 AGTCATTTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTCGCATTGCGATTCACT
Found at i:664576 original size:14 final size:14
Alignment explanation
Indices: 664559--664585 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
664549 AACAAACAAA
664559 CTTTTACAAATCAT
1 CTTTTACAAATCAT
664573 CTTTTACAAATCA
1 CTTTTACAAATCA
664586 ATTAAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTTTACAAATCAT
Found at i:665967 original size:21 final size:20
Alignment explanation
Indices: 665901--665967 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
665891 GTGAATCGGG
*
665901 CTCTTGAATGGTGGGAGGGA
1 CTCTTGAACGGTGGGAGGGA
* * ** *
665921 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAG-GGA
665943 CTCTTGAACGGTGGGAGAGGA
1 CTCTTGAACGGTGGGAG-GGA
665964 CTCT
1 CTCT
665968 CGAGGAACGA
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGA
Found at i:668003 original size:20 final size:20
Alignment explanation
Indices: 667978--668073 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 20
667968 TTTTGGTTGA
667978 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
667998 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
668017 AAATGACTATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
668036 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
668051 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
668071 AAT
1 AAT
668074 CACAATGCGA
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 8 0.13
16 4 0.06
17 2 0.03
18 1 0.02
19 14 0.23
20 33 0.53
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:668062 original size:33 final size:33
Alignment explanation
Indices: 667976--668097 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 33
667966 TCTTTTGGTT
667976 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
**
668015 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
668049 GAAATGAAAATCGCAACGAGAGAATCACAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
668082 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
668098 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
33 45 0.59
34 11 0.14
36 1 0.01
37 1 0.01
38 3 0.04
40 15 0.20
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:668146 original size:33 final size:33
Alignment explanation
Indices: 668098--668190 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
668088 AAAATCGCAA
**
668098 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
668131 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
**
668164 TGCGATAGTCATTTCCGCGTTGCGATT
1 TGCGATTTTCATTT-CGCGTTGCGATT
668191 TTCATTCTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 42 0.78
34 12 0.22
ACGTcount: A:0.11, C:0.22, G:0.25, T:0.43
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:668195 original size:20 final size:19
Alignment explanation
Indices: 668128--668232 Score: 85
Period size: 20 Copynumber: 5.6 Consensus size: 19
668118 GCGATTATCT
668128 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
668147 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
**
668161 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
*
668181 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
* *
668201 CGTTGTGATTTTCATTTTCA
1 CGTTGCGATTTTCA-TTTCG
*
668221 TGTTGCGATTTT
1 CGTTGCGATTTT
668233 AAGTTTAGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 3 0.04
19 9 0.13
20 41 0.60
21 3 0.04
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:668216 original size:40 final size:40
Alignment explanation
Indices: 668154--668232 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
668144 TCGCGTTGCG
*
668154 ATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATAGTCATTTCCACGTTGCGATTTTC
* ** * *
668194 ATTCTCTCGTTGTGATTTTCATTTTCATGTTGCGATTTT
1 ATTCTCTCGTTGCGATAGTCATTTCCACGTTGCGATTTT
668233 AAGTTTAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.13, C:0.20, G:0.18, T:0.49
Consensus pattern (40 bp):
ATTCTCTCGTTGCGATAGTCATTTCCACGTTGCGATTTTC
Found at i:668832 original size:20 final size:20
Alignment explanation
Indices: 668798--668988 Score: 154
Period size: 20 Copynumber: 9.5 Consensus size: 20
668788 TTAAAAATCG
*
668798 CGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGTATTCT
* * *
668819 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCT
* *
668839 CTTTGAGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCT
* *
668859 CGTTGCGATTTACAG-ATACG
1 CGTTGCGATTTAC-GTATTCT
668879 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCT
* *
668899 CGTTGCGATTTACGGATACT
1 CGTTGCGATTTACGTATTCT
* * *
668919 CGTTGCGATAGT-CAG-AATCG
1 CGTTGCGAT-TTAC-GTATTCT
** *
668939 CGTTGCGATTTATATATTCG
1 CGTTGCGATTTACGTATTCT
* * *
668959 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATTCT
668979 CGTTGCGATT
1 CGTTGCGATT
668989 ATGGAAAATC
Statistics
Matches: 137, Mismatches: 27, Indels: 13
0.77 0.15 0.07
Matches are distributed among these distances:
19 2 0.01
20 124 0.91
21 11 0.08
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCT
Found at i:668924 original size:40 final size:40
Alignment explanation
Indices: 668796--668988 Score: 210
Period size: 40 Copynumber: 4.8 Consensus size: 40
668786 CTTTAAAAAT
*
668796 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
* * *
668837 CGCTTTGAGATTTACGTATTCTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
668877 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* * * * *** *
668917 CTCGTTGCGATAGT-CAG-AATCGCGTTGCGATTTATATATT
1 CGCGTTGCGAT-TTAC-GTATTCTCGTTGCGATTTACGGATA
* * *
668957 CGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATT
668989 ATGGAAAATC
Statistics
Matches: 129, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.01
40 118 0.91
41 10 0.08
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (40 bp):
CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:668957 original size:60 final size:60
Alignment explanation
Indices: 668819--668969 Score: 171
Period size: 60 Copynumber: 2.5 Consensus size: 60
668809 TACGTATTGT
** * * * * * *
668819 CGTTGCGATTTACGGATACGCTTTGAGATTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACATATTCGCGTTGCGATTTACGGATACTCGTTGCGATGTACAGATACG
* *
668879 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACTCGTTGCGATAGT-CAGA-ATCG
1 CGTTGCGATTTACATATTCGCGTTGCGATTTACGGATACTCGTTGCGAT-GTACAGATA-CG
*
668939 CGTTGCGATTTATATATTCGCGTTGCGATTT
1 CGTTGCGATTTACATATTCGCGTTGCGATTT
668970 TCATATTCGC
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 1 0.01
60 76 0.97
61 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (60 bp):
CGTTGCGATTTACATATTCGCGTTGCGATTTACGGATACTCGTTGCGATGTACAGATACG
Found at i:668983 original size:60 final size:60
Alignment explanation
Indices: 668877--669050 Score: 154
Period size: 60 Copynumber: 2.9 Consensus size: 60
668867 TTTACAGATA
** * * ** * * *
668877 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACTCGTTGCGATA-GTCAGAAT
1 CGCGTTGCGATTTATATATTCGCGTTGCGATTTTCATATTCGCGTTGCGATATG-CAAAAT
*
668937 CGCGTTGCGATTTATATATTCGCGTTGCGATTTTCATATTCGCGTTGCGATTATGGAAAAT
1 CGCGTTGCGATTTATATATTCGCGTTGCGATTTTCATATTCGCGTTGCGA-TATGCAAAAT
** * * *
668998 CGCAATGCGAATTTGTACTA-TCGCATTGCGATTCTTCATAATCGCGTTGCGAT
1 CGCGTTGCG-ATTTATA-TATTCGCGTTGCGATT-TTCATATTCGCGTTGCGAT
669051 TCTGGGAACT
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
60 42 0.45
61 13 0.14
62 20 0.21
63 19 0.20
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTATATATTCGCGTTGCGATTTTCATATTCGCGTTGCGATATGCAAAAT
Found at i:669087 original size:20 final size:19
Alignment explanation
Indices: 669038--669091 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
669028 ATTCTTCATA
*
669038 ATCGCGTTGCGATTCTGGG
1 ATCGTGTTGCGATTCTGGG
*
669057 AAC-TGATTTGCGATTCTGGAG
1 ATCGTG--TTGCGATTCTGG-G
669078 ATCGTGTTGCGATT
1 ATCGTGTTGCGATT
669092 TTTATTTCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 1 0.04
19 2 0.07
20 20 0.71
21 3 0.11
22 2 0.07
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (19 bp):
ATCGTGTTGCGATTCTGGG
Found at i:671347 original size:9 final size:9
Alignment explanation
Indices: 671298--671348 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
671288 ACCCTGACAA
671298 AAATAATAAT
1 AAATAA-AAT
*
671308 -AATAAATT
1 AAATAAAAT
*
671316 AAATTAAAT
1 AAATAAAAT
*
671325 TAATAAAAT
1 AAATAAAAT
671334 GAAATAAAAT
1 -AAATAAAAT
671344 AAATA
1 AAATA
671349 TTAATATAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
8 2 0.06
9 23 0.70
10 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (9 bp):
AAATAAAAT
Found at i:671590 original size:16 final size:16
Alignment explanation
Indices: 671569--671601 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
671559 TAATAAATAG
671569 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
671585 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
671601 A
1 A
671602 AAAAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:671682 original size:10 final size:10
Alignment explanation
Indices: 671667--671741 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
671657 CATTTAATAA
671667 ATAAACGAAC
1 ATAAACGAAC
671677 ATAAACGAAC
1 ATAAACGAAC
671687 ----ACGAAC
1 ATAAACGAAC
671693 ATAAACGAAC
1 ATAAACGAAC
** *
671703 ACGAAC-ATAA
1 ATAAACGA-AC
671713 ATGAACACGAAC
1 AT-AA-ACGAAC
671725 ATAAACGAAC
1 ATAAACGAAC
671735 ATAAACG
1 ATAAACG
671742 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:671692 original size:16 final size:16
Alignment explanation
Indices: 671671--671735 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
671661 TAATAAATAA
671671 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
671687 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
671703 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
671719 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
671735 A
1 A
671736 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:672503 original size:14 final size:14
Alignment explanation
Indices: 672486--672541 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
672476 AATGAACATA
672486 AACGAACATAATCG
1 AACGAACATAATCG
672500 AACGAACAT-A---
1 AACGAACATAATCG
* *
672510 AACAAACATAACCG
1 AACGAACATAATCG
672524 AACGAACATAATCG
1 AACGAACATAATCG
672538 AACG
1 AACG
672542 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:672506 original size:24 final size:24
Alignment explanation
Indices: 672466--672540 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
672456 GATTGAGTTA
*
672466 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
672490 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* *
672514 AACATAACCGAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
672538 AAC
1 AAC
672541 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:672853 original size:63 final size:58
Alignment explanation
Indices: 672712--672871 Score: 157
Period size: 61 Copynumber: 2.6 Consensus size: 58
672702 TTTACAGGCC
*
672712 TAAAACTATATATTATATAAATTTTCCAAAAATGTTTTTAAAAAATTATATATTATATTTT
1 TAAAACTATATAATATAT-AATTTT-C-AAAATGTTTTTAAAAAATTATATATTATATTTT
* *
672773 TAAAACTATATACTATATAATTTTCAAAATG-TTTT-AAAACTTATATATTGTACATAAGTTTT
1 TAAAACTATATAATATATAATTTTCAAAATGTTTTTAAAAAATTATATA-T-T--AT-A-TTTT
672835 TAAAAACTATATAATATAT-A-TTTCAAAAATGTATTTT
1 T-AAAACTATATAATATATAATTTTC-AAAATGT-TTTT
672872 TTAAAAACAT
Statistics
Matches: 86, Mismatches: 3, Indels: 17
0.81 0.03 0.16
Matches are distributed among these distances:
56 11 0.13
57 5 0.06
58 7 0.08
59 1 0.01
60 8 0.09
61 22 0.26
62 12 0.14
63 16 0.19
64 4 0.05
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (58 bp):
TAAAACTATATAATATATAATTTTCAAAATGTTTTTAAAAAATTATATATTATATTTT
Found at i:678412 original size:29 final size:30
Alignment explanation
Indices: 678379--678447 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 30
678369 ATTAATATTT
678379 ATAATAATAAAATACTCA-A-TTATATTATA
1 ATAATAATAAAATA-TCATATTTATATTATA
* * *
678408 ATAAT-ATAAGATATTATATTTTTATTATA
1 ATAATAATAAAATATCATATTTATATTATA
678437 ATAATATATAA
1 ATAATA-ATAA
678448 TAAATTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 2 0.06
28 8 0.24
29 19 0.58
31 4 0.12
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (30 bp):
ATAATAATAAAATATCATATTTATATTATA
Found at i:678459 original size:21 final size:20
Alignment explanation
Indices: 678431--678471 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
678421 TTATATTTTT
*
678431 ATTATAATAATATATAATAA
1 ATTATAATAATAAATAATAA
*
678451 ATTATTAATGATAAATAATAA
1 ATTA-TAATAATAAATAATAA
678472 TATTTATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATTATAATAATAAATAATAA
Found at i:683848 original size:21 final size:22
Alignment explanation
Indices: 683808--683848 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
683798 GAGCCAGAAC
683808 CAGAAAGGTGGGGAAGGGGAGG
1 CAGAAAGGTGGGGAAGGGGAGG
683830 CAGAAA-GTCGGGG-AGGGGA
1 CAGAAAGGT-GGGGAAGGGGA
683849 AGGGGAGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.32, C:0.07, G:0.56, T:0.05
Consensus pattern (22 bp):
CAGAAAGGTGGGGAAGGGGAGG
Found at i:688997 original size:22 final size:21
Alignment explanation
Indices: 688946--688998 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
688936 AATAAAAATA
*
688946 TTATATTATATTTTAAATTAT
1 TTATAATATATTTTAAATTAT
*
688967 TAATAAATATATTTTAAGGATT-T
1 TTAT-AATATATTTTAA--ATTAT
688990 TTATAATAT
1 TTATAATAT
688999 TATTAGACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.12
22 16 0.62
23 4 0.15
24 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
TTATAATATATTTTAAATTAT
Found at i:689233 original size:23 final size:23
Alignment explanation
Indices: 689191--689246 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
689181 ATTATTATAT
689191 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* * *
689215 TATATTTTAAACATGTTAATAAT
1 TATATTTTAAAAATATTAATAAA
689238 TAATATTTT
1 T-ATATTTT
689247 TTATTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:689764 original size:51 final size:51
Alignment explanation
Indices: 689687--689888 Score: 334
Period size: 51 Copynumber: 4.0 Consensus size: 51
689677 TATTATTGAT
* *
689687 GAGGCATGTCGAAGGAGACCCAAAAAAACGACGGATTTTGTACGATAGGAC
1 GAGGCATATCGAAGGAGACCCTAAAAAACGACGGATTTTGTACGATAGGAC
689738 GAGGCATATCGAAGGAGACCCTAAAAAACGACGGATTTTGTACGATAGGAC
1 GAGGCATATCGAAGGAGACCCTAAAAAACGACGGATTTTGTACGATAGGAC
*
689789 GAGGCATATCGAAGGAGACCCTAAAAAACGACGGATTTTGTACGATAGGAT
1 GAGGCATATCGAAGGAGACCCTAAAAAACGACGGATTTTGTACGATAGGAC
* * * *
689840 GAGGCATATCGAAGGACACCC-AATAAACGAAGGATTTTGTTCGATAGGA
1 GAGGCATATCGAAGGAGACCCTAAAAAACGACGGATTTTGTACGATAGGA
689889 ATGGATTGAG
Statistics
Matches: 144, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
50 25 0.17
51 119 0.83
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (51 bp):
GAGGCATATCGAAGGAGACCCTAAAAAACGACGGATTTTGTACGATAGGAC
Found at i:692232 original size:24 final size:25
Alignment explanation
Indices: 692193--692239 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
692183 TTCTGGCTAT
* *
692193 TTATATGATATGTATAATGTAATAA
1 TTATATGATATATATAAAGTAATAA
692218 TTATAT-ATATATATAAAGTAAT
1 TTATATGATATATATAAAGTAAT
692240 TTTATACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (25 bp):
TTATATGATATATATAAAGTAATAA
Found at i:693675 original size:21 final size:23
Alignment explanation
Indices: 693650--693696 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
693640 TCTATAAAAA
*
693650 TAAAAATATT-AT-ATTATATTT
1 TAAAAATATTAATAAATATATTT
*
693671 TAAAATTATTAATAAATATATTT
1 TAAAAATATTAATAAATATATTT
693694 TAA
1 TAA
693697 GGATTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAAAATATTAATAAATATATTT
Found at i:693711 original size:23 final size:22
Alignment explanation
Indices: 693650--693712 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
693640 TCTATAAAAA
* *
693650 TAAAAATA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
693671 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
* *
693694 TAAGGATTTTTTATAATAT
1 TAA-AATTATTTATAATAT
693713 TATTAGACTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.48
24 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:693892 original size:26 final size:26
Alignment explanation
Indices: 693846--693902 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
693836 TTAAAATAAG
693846 AATATAATAGTATCATATATTATTAT
1 AATATAATAGTATCATATATTATTAT
*
693872 AATATAATTGAGTAT-AT-TATTGTTAT
1 AATATAA-T-AGTATCATATATTATTAT
693898 AATAT
1 AATAT
693903 TATTATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 20 0.71
27 3 0.11
28 5 0.18
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (26 bp):
AATATAATAGTATCATATATTATTAT
Found at i:693904 original size:14 final size:14
Alignment explanation
Indices: 693885--693921 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
693875 ATAATTGAGT
*
693885 ATATTATTGTTATA
1 ATATTATTATTATA
*
693899 ATATTATTATTATT
1 ATATTATTATTATA
693913 ATATTATTA
1 ATATTATTA
693922 AAAATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
ATATTATTATTATA
Found at i:693908 original size:17 final size:17
Alignment explanation
Indices: 693886--693921 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
693876 TAATTGAGTA
*
693886 TATTATTGTTATAATAT
1 TATTATTATTATAATAT
*
693903 TATTATTATTATATTAT
1 TATTATTATTATAATAT
693920 TA
1 TA
693922 AAAATATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TATTATTATTATAATAT
Found at i:693938 original size:22 final size:22
Alignment explanation
Indices: 693919--693965 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
693909 TATTATATTA
693919 TTAAAAATATTAATAAATATAT
1 TTAAAAATATTAATAAATATAT
* * *
693941 TTAAACATGTTAATAATTAATAT
1 TTAAAAATATTAATAAAT-ATAT
693964 TT
1 TT
693966 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
TTAAAAATATTAATAAATATAT
Found at i:694619 original size:35 final size:36
Alignment explanation
Indices: 694580--694658 Score: 124
Period size: 38 Copynumber: 2.2 Consensus size: 36
694570 TCTAGCAATA
694580 ATTGAT-TAAAACCAACATACATGTGATTATATATT
1 ATTGATATAAAACCAACATACATGTGATTATATATT
*
694615 ATTGATGAATAAGACCAACATACATGTGATTATATATT
1 ATTGAT--ATAAAACCAACATACATGTGATTATATATT
694653 ATTGAT
1 ATTGAT
694659 GAAGCATCTC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 6 0.15
38 34 0.85
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (36 bp):
ATTGATATAAAACCAACATACATGTGATTATATATT
Found at i:701180 original size:21 final size:21
Alignment explanation
Indices: 701151--701196 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
701141 ATTCTGACTA
701151 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
701172 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
701193 TCGC
1 TCGC
701197 TATGTGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:701225 original size:20 final size:20
Alignment explanation
Indices: 701202--701286 Score: 107
Period size: 20 Copynumber: 4.2 Consensus size: 20
701192 TTCGCTATGT
*
701202 GAATACGTAAATCGCAACGC
1 GAATACGTAAATCGCAATGC
** * *
701222 GAATTTGGAAAATCGCAATAC
1 GAA-TACGTAAATCGCAATGC
*
701243 GATTACGTAAATCGCAATGC
1 GAATACGTAAATCGCAATGC
701263 GAATACGTAAATCGCAATGC
1 GAATACGTAAATCGCAATGC
701283 GAAT
1 GAAT
701287 CTGACTATCG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 39 0.74
21 14 0.26
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (20 bp):
GAATACGTAAATCGCAATGC
Found at i:701506 original size:22 final size:22
Alignment explanation
Indices: 701481--701542 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
701471 GGCGACATCC
701481 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
701503 GTCCCCA----CGACGATAA-CA
1 GTCCCCATCTCCGACGA-AATCA
*
701521 GTCTCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
701543 TTCACGGTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
18 14 0.42
19 2 0.06
21 2 0.06
22 15 0.45
ACGTcount: A:0.29, C:0.39, G:0.15, T:0.18
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:701937 original size:20 final size:20
Alignment explanation
Indices: 701914--701964 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
701904 CGAATTTGAC
701914 TGTTGCGATTTTCATTTTCG
1 TGTTGCGATTTTCATTTTCG
**
701934 TGTTGCGATAGTCATTTTCG
1 TGTTGCGATTTTCATTTTCG
701954 TGTTGCGATTT
1 TGTTGCGATTT
701965 AATGTGGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.14, G:0.24, T:0.51
Consensus pattern (20 bp):
TGTTGCGATTTTCATTTTCG
Found at i:702130 original size:21 final size:21
Alignment explanation
Indices: 702104--702149 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
702094 TTTGTGGGTG
702104 TTTTCTATGAATTTCTTTTTA
1 TTTTCTATGAATTTCTTTTTA
702125 TTTTCTATGAATTTCTTTTTA
1 TTTTCTATGAATTTCTTTTTA
702146 TTTT
1 TTTT
702150 GTTCCGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTCTATGAATTTCTTTTTA
Found at i:708389 original size:2 final size:2
Alignment explanation
Indices: 708384--708448 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
708374 TTTTTGATTT
708384 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
708426 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
708449 GATGTTTTCT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:710707 original size:20 final size:20
Alignment explanation
Indices: 710670--710707 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
710660 GAATAGAGTG
**
710670 AAGTATCGATACTTAAGGTA
1 AAGTATCGATACCCAAGGTA
710690 AAGTATCGATACCCAAGG
1 AAGTATCGATACCCAAGG
710708 GGTCAATACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (20 bp):
AAGTATCGATACCCAAGGTA
Found at i:715090 original size:364 final size:364
Alignment explanation
Indices: 714421--715144 Score: 1430
Period size: 364 Copynumber: 2.0 Consensus size: 364
714411 CAGGTTTAAA
714421 GTGCCATTTGTAGGGAATTTCATTCGGTTAATCTAGTATTCTGCTCTTTTAATTATTTGATCTTT
1 GTGCCATTTGTAGGGAATTTCATTCGGTTAATCTAGTATTCTGCTCTTTTAATTATTTGATCTTT
*
714486 GCATCAGGTTGCACTCCTCTCCATTGGGCAGCTATTAGGGGTAATCTAGAAGCTTGCACAGTCCT
66 GCACCAGGTTGCACTCCTCTCCATTGGGCAGCTATTAGGGGTAATCTAGAAGCTTGCACAGTCCT
714551 AGTAAAGGCGGGTAAGATGGAGGACTTGTTGGTCACTGATAGTAGTGGCCCTACACCTGAACAGC
131 AGTAAAGGCGGGTAAGATGGAGGACTTGTTGGTCACTGATAGTAGTGGCCCTACACCTGAACAGC
714616 TTGCTTCTGATCAAAATCACAGACAAGTTGTTTTTCTCCTTGTAGGTGCCTTAACATATTTACTT
196 TTGCTTCTGATCAAAATCACAGACAAGTTGTTTTTCTCCTTGTAGGTGCCTTAACATATTTACTT
714681 TGGTAATAATTATTCTTCTGATATTTATTTGTTTTTGTTTTCAATCTTGCACTGTTCCAGCTCTT
261 TGGTAATAATTATTCTTCTGATATTTATTTGTTTTTGTTTTCAATCTTGCACTGTTCCAGCTCTT
714746 TCTTTTTAGTGATGACTGATAAACGCCCTGTGCAGGACT
326 TCTTTTTAGTGATGACTGATAAACGCCCTGTGCAGGACT
714785 GTGCCATTTGTAGGGAATTTCATTCGGTTAATCTAGTATTCTGCTCTTTTAATTATTTGATCTTT
1 GTGCCATTTGTAGGGAATTTCATTCGGTTAATCTAGTATTCTGCTCTTTTAATTATTTGATCTTT
714850 GCACCAGGTTGCACTCCTCTCCATTGGGCAGCTATTAGGGGTAATCTAGAAGCTTGCACAGTCCT
66 GCACCAGGTTGCACTCCTCTCCATTGGGCAGCTATTAGGGGTAATCTAGAAGCTTGCACAGTCCT
*
714915 AGTAAAGGCGGGTAAGATGGAGGACTTGTTGGTCACTGATAGTAGTGGCCTTACACCTGAACAGC
131 AGTAAAGGCGGGTAAGATGGAGGACTTGTTGGTCACTGATAGTAGTGGCCCTACACCTGAACAGC
714980 TTGCTTCTGATCAAAATCACAGACAAGTTGTTTTTCTCCTTGTAGGTGCCTTAACATATTTACTT
196 TTGCTTCTGATCAAAATCACAGACAAGTTGTTTTTCTCCTTGTAGGTGCCTTAACATATTTACTT
715045 TGGTAATAATTATTCTTCTGATATTTATTTGTTTTTGTTTTCAATCTTGCACTGTTCCAGCTCTT
261 TGGTAATAATTATTCTTCTGATATTTATTTGTTTTTGTTTTCAATCTTGCACTGTTCCAGCTCTT
715110 TCTTTTTAGTGATGACTGATAAACGCCCTGTGCAG
326 TCTTTTTAGTGATGACTGATAAACGCCCTGTGCAG
715145 AATGAAAGAC
Statistics
Matches: 358, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
364 358 1.00
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (364 bp):
GTGCCATTTGTAGGGAATTTCATTCGGTTAATCTAGTATTCTGCTCTTTTAATTATTTGATCTTT
GCACCAGGTTGCACTCCTCTCCATTGGGCAGCTATTAGGGGTAATCTAGAAGCTTGCACAGTCCT
AGTAAAGGCGGGTAAGATGGAGGACTTGTTGGTCACTGATAGTAGTGGCCCTACACCTGAACAGC
TTGCTTCTGATCAAAATCACAGACAAGTTGTTTTTCTCCTTGTAGGTGCCTTAACATATTTACTT
TGGTAATAATTATTCTTCTGATATTTATTTGTTTTTGTTTTCAATCTTGCACTGTTCCAGCTCTT
TCTTTTTAGTGATGACTGATAAACGCCCTGTGCAGGACT
Found at i:725689 original size:22 final size:23
Alignment explanation
Indices: 725671--725724 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
725661 AGAGGGAATT
725671 GATACCCCC-TTGAAGGGGAACC
1 GATACCCCCTTTGAAGGGGAACC
* *
725693 GATTCCCCCTTTGTAGGGGAACC
1 GATACCCCCTTTGAAGGGGAACC
725716 GATACCCCC
1 GATACCCCC
725725 ATGGGGTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 8 0.29
23 20 0.71
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.19
Consensus pattern (23 bp):
GATACCCCCTTTGAAGGGGAACC
Found at i:729353 original size:12 final size:12
Alignment explanation
Indices: 729336--729360 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
729326 ATCAAAGACG
729336 ATGATACACCCA
1 ATGATACACCCA
729348 ATGATACACCCA
1 ATGATACACCCA
729360 A
1 A
729361 ATTGTTATGT
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:0.44, C:0.32, G:0.08, T:0.16
Consensus pattern (12 bp):
ATGATACACCCA
Found at i:738844 original size:20 final size:20
Alignment explanation
Indices: 738819--738872 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
738809 GACCAACAAA
738819 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
738839 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
738859 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
738873 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:739031 original size:22 final size:22
Alignment explanation
Indices: 739006--739048 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
738996 CATCTCCATC
739006 CGTTCATATATCCAACGACATA
1 CGTTCATATATCCAACGACATA
*
739028 CGTTCCTATATCCAACGACAT
1 CGTTCATATATCCAACGACAT
739049 CCTTCTCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.30, G:0.09, T:0.28
Consensus pattern (22 bp):
CGTTCATATATCCAACGACATA
Found at i:739672 original size:12 final size:12
Alignment explanation
Indices: 739651--739684 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
739641 ACCACATTTC
*
739651 CAATACCAAACA
1 CAATATCAAACA
739663 CAATATCAAACA
1 CAATATCAAACA
*
739675 CAATCTCAAA
1 CAATATCAAA
739685 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:742148 original size:18 final size:18
Alignment explanation
Indices: 742115--742150 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
742105 AAGCAAAAGG
**
742115 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
742133 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
742151 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Done.