Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008075.1 Hibiscus syriacus cultivar Beakdansim tig00110577_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: 1947163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:434081 original size:15 final size:13
Alignment explanation
Indices: 434045--434083 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
434035 TATATGGATA
434045 TTTTATTCATTCAT
1 TTTTATT-ATTCAT
434059 TTTTATTATTCAT
1 TTTTATTATTCAT
434072 GTTATTATTATT
1 -TT-TTATTATT
434084 ATATGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (13 bp):
TTTTATTATTCAT
Found at i:434277 original size:17 final size:17
Alignment explanation
Indices: 434255--434289 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
434245 ATAGTTTATT
*
434255 TATATACCTATTATTAA
1 TATATACATATTATTAA
*
434272 TATATATATATTATTAA
1 TATATACATATTATTAA
434289 T
1 T
434290 TATTTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATACATATTATTAA
Found at i:434343 original size:2 final size:2
Alignment explanation
Indices: 434338--434372 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
434328 CTTATAACTT
434338 TA TA TA 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 TA TA TA T
434373 TATTTTCGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:434587 original size:38 final size:40
Alignment explanation
Indices: 434536--434615 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
434526 AGTGAGAGGG
*
434536 TAGCTTTTCTATTTT-TAAATA-TTTGGTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
434574 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
434614 TA
1 TA
434616 TTTTCCTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:434690 original size:9 final size:9
Alignment explanation
Indices: 434669--434702 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
434659 ATTTTTTTCC
434669 TTTATCTTA-
1 TTTAT-TTAT
434678 TTTATTTAT
1 TTTATTTAT
434687 TTTATTTAT
1 TTTATTTAT
434696 TTTATTT
1 TTTATTT
434703 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:434691 original size:13 final size:14
Alignment explanation
Indices: 434669--434703 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
434659 ATTTTTTTCC
*
434669 TTTATCTTATTTA-
1 TTTATTTTATTTAT
434682 TTTATTTTATTTAT
1 TTTATTTTATTTAT
434696 TTTATTTT
1 TTTATTTT
434704 TCCCTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:435613 original size:2 final size:2
Alignment explanation
Indices: 435606--435663 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
435596 TAAGAAATAG
435606 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
435648 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
435664 GTAATCTGGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:441158 original size:5 final size:5
Alignment explanation
Indices: 441148--441188 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
441138 CTTTTTTGTG
*
441148 CTTTT CTTTT CTTTT CTTTT CTTTT CTTCTC CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTT-TT CTTTT CTTTT
441189 ACCATCTGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
CTTTT
Found at i:446082 original size:2 final size:2
Alignment explanation
Indices: 446032--446063 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
446022 CGTATGTAAG
*
446032 TA TA TG 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
446064 CACACACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:448082 original size:48 final size:49
Alignment explanation
Indices: 448022--448116 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 49
448012 GTTAAACCTT
*
448022 TAATGGTTTACTGACGTGGCATGATAAACATAT-AAAATTAAAATTATA
1 TAATGGTTTACTGACGTGGCATGATAAACAAATAAAAATTAAAATTATA
*
448070 TAATGGTTTACTGACGTGGCATGATAAATAAATAAAAATTAAAATTA
1 TAATGGTTTACTGACGTGGCATGATAAACAAATAAAAATTAAAATTA
448117 CATCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 31 0.70
49 13 0.30
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (49 bp):
TAATGGTTTACTGACGTGGCATGATAAACAAATAAAAATTAAAATTATA
Found at i:448291 original size:31 final size:31
Alignment explanation
Indices: 448214--448291 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
448204 AAAAAAAACA
* *
448214 TAAGTTTTAGTCACTTACGTTATCGTTTTAT
1 TAAGTTTTGGTCACTTACGTTATCATTTTAT
* *
448245 TAAATTATGGTCACTTACGTTATCATTTTAT
1 TAAGTTTTGGTCACTTACGTTATCATTTTAT
*
448276 TAAGTTTTGGCCACTT
1 TAAGTTTTGGTCACTT
448292 GGACGTTGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.49
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTATCATTTTAT
Found at i:449922 original size:30 final size:31
Alignment explanation
Indices: 449886--449961 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 31
449876 GTTAACATTT
* *
449886 AGTGACCACATCTTAATTAAAACGAAATG-A
1 AGTGACCAAATCTTAATTAAAACGAAACGAA
*
449916 AGTGACCAAATCTTAATTAAAATGAAACGAA
1 AGTGACCAAATCTTAATTAAAACGAAACGAA
449947 AGTGACCAAATCTTA
1 AGTGACCAAATCTTA
449962 TATTTTTCGA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 26 0.62
31 16 0.38
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (31 bp):
AGTGACCAAATCTTAATTAAAACGAAACGAA
Found at i:452156 original size:22 final size:23
Alignment explanation
Indices: 452106--452160 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
452096 AGTCTATCGG
452106 TATGACATGTTTTCATCTATCTT
1 TATGACATGTTTTCATCTATCTT
452129 TATGACATGTTTTC-T-TATACTT
1 TATGACATGTTTTCATCTAT-CTT
*
452151 TTTGACATGT
1 TATGACATGT
452161 ATTTTTGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 3 0.10
22 13 0.43
23 14 0.47
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.53
Consensus pattern (23 bp):
TATGACATGTTTTCATCTATCTT
Found at i:487230 original size:2 final size:2
Alignment explanation
Indices: 487225--487267 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
487215 ATTATTATCG
487225 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
487267 A
1 A
487268 GTTTTGAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:493178 original size:20 final size:22
Alignment explanation
Indices: 493153--493206 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
493143 AATAAGAGTT
*
493153 GGTATCGATAC-CCTAAT-TGG
1 GGTATCGATACTCCTAATCTAG
* *
493173 GGTATCAATACTTCTAATCTAG
1 GGTATCGATACTCCTAATCTAG
493195 GGTATCGATACT
1 GGTATCGATACT
493207 TGGGTGTCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.36
21 5 0.18
22 13 0.46
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (22 bp):
GGTATCGATACTCCTAATCTAG
Found at i:493488 original size:322 final size:325
Alignment explanation
Indices: 492878--493530 Score: 974
Period size: 322 Copynumber: 2.0 Consensus size: 325
492868 AAAGTAACTC
* * * *
492878 GGGTGTCCTGACTGTGTCTCGAGTATCAAACAAGGCTAGTTTTATGTCGTCCTAGTTGTTATTGT
1 GGGTGTCCTGACTGTGTCCCGACTATCAAACAAGACTAGTTTTATGTCATCCTAGTTGTTATTGT
492943 TTCTAACTGTTATGAGTTTAATCACTATTCTCACTTGTAGTTTTATTTCATGGTATTCTGGTATT
66 TTCTAACTGTTATGAGTTTAATCACTATTCTCACTTGTAGTTTTATTTC---G-ATTC-GGTATT
*
493008 ATGGGATCCCTCAATTCTCTCCTTTAAACTTTTGGAATTCTCTCCCAAAAACTGTATGTGGGTAC
126 ATGGGATCCCTCAATTCTATCCTTTAAACTTTTGGAATTCTCTCCCAAAAACTGTATGTGGGTAC
* ** * * *
493073 CGATACTAAGGCCTTCAATATCGGTACTGACCTCTGGGTATCGATACAACTGGAAAATTTTAGGC
191 CGATACTAAGGCCCTCAATATCAATACTAACCTATGGGTATCGATACAACTGGAAAATTTTAGGA
*
493138 TGAGAAATAAGAGTTGGTATCGATACCCTAATTGGGGTATCAATACTTCTAATCTAGGG-TATCG
256 TGAGAAATAAGAGTTGGTATCGATACCCTAATTGGGGTATCAATACTCCTAATCT-GGGATATCG
493202 ATACTT
320 ATACTT
*
493208 GGGTGTCCTGACTGTGTCCCGACTATCAAACAAGACTAGTTTTATGTCATCCTTGTTGTTATTGT
1 GGGTGTCCTGACTGTGTCCCGACTATCAAACAAGACTAGTTTTATGTCATCCTAGTTGTTATTGT
* *
493273 TTCTAACTGTTCTGAGTTTAATCACTATTCTCACTTGTAGTTTTATTTC-A-TC-GTATTCTGGG
66 TTCTAACTGTTATGAGTTTAATCACTATTCTCACTTGTAGTTTTATTTCGATTCGGTATTATGGG
* * *
493335 ATCCCTCAATTCTATCCTTTAAACTTTTAGG-ATTCTCTCCCAAAAACTGTCTGTGGGTTCTGAT
131 ATCCCTCAATTCTATCCTTTAAACTTTT-GGAATTCTCTCCCAAAAACTGTATGTGGGTACCGAT
* * * * *
493399 ACTAAGTCCCTCAGTATCAATACTAACCTATGGGTATTGATACTACTGGTAAATTTTAGGATGAG
195 ACTAAGGCCCTCAATATCAATACTAACCTATGGGTATCGATACAACTGGAAAATTTTAGGATGAG
** *
493464 AAATAAGAGTTGGTATCGATACCCTGGTTGGGGTATCAATACTCCTGATCTGGGATATCGATACT
260 AAATAAGAGTTGGTATCGATACCCTAATTGGGGTATCAATACTCCTAATCTGGGATATCGATACT
493529 T
325 T
493530 G
1 G
493531 TCTGAGTATC
Statistics
Matches: 295, Mismatches: 26, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
321 3 0.01
322 179 0.61
323 2 0.01
324 2 0.01
325 1 0.00
330 108 0.37
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (325 bp):
GGGTGTCCTGACTGTGTCCCGACTATCAAACAAGACTAGTTTTATGTCATCCTAGTTGTTATTGT
TTCTAACTGTTATGAGTTTAATCACTATTCTCACTTGTAGTTTTATTTCGATTCGGTATTATGGG
ATCCCTCAATTCTATCCTTTAAACTTTTGGAATTCTCTCCCAAAAACTGTATGTGGGTACCGATA
CTAAGGCCCTCAATATCAATACTAACCTATGGGTATCGATACAACTGGAAAATTTTAGGATGAGA
AATAAGAGTTGGTATCGATACCCTAATTGGGGTATCAATACTCCTAATCTGGGATATCGATACTT
Found at i:493500 original size:20 final size:22
Alignment explanation
Indices: 493475--493528 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
493465 AATAAGAGTT
*
493475 GGTATCGATAC-CCTGGT-TGG
1 GGTATCGATACTCCTGATCTGG
*
493495 GGTATCAATACTCCTGATCTGG
1 GGTATCGATACTCCTGATCTGG
*
493517 GATATCGATACT
1 GGTATCGATACT
493529 TGTCTGAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 10 0.36
21 5 0.18
22 13 0.46
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (22 bp):
GGTATCGATACTCCTGATCTGG
Found at i:495543 original size:22 final size:23
Alignment explanation
Indices: 495513--495559 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
495503 TCGAATATAT
495513 AAACGAACAATAAACAAACACTA
1 AAACGAACAATAAACAAACACTA
* * *
495536 AAAC-AACACTAAACGAACATTA
1 AAACGAACAATAAACAAACACTA
495558 AA
1 AA
495560 TGAACACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.64, C:0.21, G:0.04, T:0.11
Consensus pattern (23 bp):
AAACGAACAATAAACAAACACTA
Found at i:495565 original size:22 final size:22
Alignment explanation
Indices: 495512--495566 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
495502 ATCGAATATA
* *
495512 TAAACGAACAATAAACAAACAC
1 TAAAAGAACACTAAACAAACAC
* * *
495534 TAAAACAACACTAAACGAACAT
1 TAAAAGAACACTAAACAAACAC
*
495556 TAAATGAACAC
1 TAAAAGAACAC
495567 ATTCGTGAAC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.60, C:0.22, G:0.05, T:0.13
Consensus pattern (22 bp):
TAAAAGAACACTAAACAAACAC
Found at i:495595 original size:24 final size:24
Alignment explanation
Indices: 495550--495653 Score: 99
Period size: 24 Copynumber: 4.5 Consensus size: 24
495540 AACACTAAAC
* **
495550 GAACAT-TAAATGAACACATTCGT
1 GAACATATAAACGAACATGTTCGT
* *
495573 GAACATATAAACAAATATGTTCGT
1 GAACATATAAACGAACATGTTCGT
*
495597 GGACATATAAACGAACATGTTC-T
1 GAACATATAAACGAACATGTTCGT
* *
495620 CAAACAT-TAAATGAACATGTTCGT
1 -GAACATATAAACGAACATGTTCGT
495644 GAACA-ATAAA
1 GAACATATAAA
495654 TAAACGAATA
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
23 29 0.45
24 36 0.55
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.26
Consensus pattern (24 bp):
GAACATATAAACGAACATGTTCGT
Found at i:507833 original size:126 final size:128
Alignment explanation
Indices: 507605--507977 Score: 325
Period size: 126 Copynumber: 2.9 Consensus size: 128
507595 GATGTCCATA
* *
507605 AATTTTTCAATCCCACCTTTTACATTTATAATTAAGACCCCTAATTTTTTCTATCTCACTTTCTA
1 AATTTTTTAATCCCACCTTTTACATTTATAATTAAGACCCCTAATTTTTTCAATCTCACTTTCTA
* * * * *
507670 CCTTTTTAATTGAAACCTCTAATTTTTTTAGTATCACTTTTTACATTTATAATTG-AGACCCCC
66 CCTTTATAATCGAAACCTCTAAATTTTTCAATATCACTTTTTACATTTATAATTGAAG-CCCCC
* * * * *
507733 AATTTTTTAATCCC-GCTTTCTACTTTTATAATTAAG-GCCCTGATTTTTT-AATCTCACTTTTT
1 AATTTTTTAATCCCACCTTT-TACATTTATAATTAAGACCCCTAATTTTTTCAATCTCACTTTCT
* ** * * *
507795 ACCTTTATAGTCG-AGGCTCCTAAATTTTTCAATCTCACTTTTTACCTTTATAATTGAAGCCCCT
65 ACCTTTATAATCGAAACCT-CTAAATTTTTCAATATCACTTTTTACATTTATAATTGAAGCCCCC
* * ** * * * * *
507859 AAATTTTTAAT-CTATTTTTTATATTTATAATTGAGGA-TCCTAATTTTTTCAAT-TGTACTTTT
1 AATTTTTTAATCCCACCTTTTACATTTATAATT-AAGACCCCTAATTTTTTCAATCT-CACTTTC
* * * * * *
507921 TAACTTTATAATTGAAA-CTCTTAATTTTTTAATATTAAC-TTTTACTTTTATAATTGA
64 TACCTTTATAATCGAAACCTCTAAATTTTTCAATA-TCACTTTTTACATTTATAATTGA
507978 GTCTCTTAAT
Statistics
Matches: 198, Mismatches: 37, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
125 15 0.08
126 112 0.57
127 42 0.21
128 29 0.15
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.49
Consensus pattern (128 bp):
AATTTTTTAATCCCACCTTTTACATTTATAATTAAGACCCCTAATTTTTTCAATCTCACTTTCTA
CCTTTATAATCGAAACCTCTAAATTTTTCAATATCACTTTTTACATTTATAATTGAAGCCCCC
Found at i:507879 original size:84 final size:84
Alignment explanation
Indices: 507584--508031 Score: 325
Period size: 84 Copynumber: 5.3 Consensus size: 84
507574 TTATTTTTTG
* * * * * * * * *
507584 CCTTTATAATTGATGTCCATAAATTTTTCAATCCCACCTTTTACATTTATAATTAAGACCCCTAA
1 CCTTTATAATTGAAGCCCCT-AATTTTTTAAT-CTACTTTTTACATTTATAATTGAGGCTCCTAA
* *
507649 TTTTTTCTATCTCACTTTCTA
64 ATTTTTCAATCTCACTTTCTA
* * * * **
507670 CCTTTTTAATTGAAACCTCTAATTTTTTTAGTATC-ACTTTTTACATTTATAATTGAGAC-CCCC
1 CCTTTATAATTGAAGCCCCTAA-TTTTTTA--ATCTACTTTTTACATTTATAATTGAGGCTCCTA
* * *
507733 AATTTTTTAATCCCGCTTTCTA
63 AATTTTTCAATCTCACTTTCTA
* * * * * *
507755 CTTTTATAATT-AAGGCCCTGATTTTTTAATCTCACTTTTTACCTTTATAGTCGAGGCTCCTAAA
1 CCTTTATAATTGAAGCCCCTAATTTTTTAATCT-ACTTTTTACATTTATAATTGAGGCTCCTAAA
*
507819 TTTTTCAATCTCACTTTTTA
65 TTTTTCAATCTCACTTTCTA
* * * * *
507839 CCTTTATAATTGAAGCCCCTAAATTTTTAATCTATTTTTTATATTTATAATTGAGGATCCTAATT
1 CCTTTATAATTGAAGCCCCTAATTTTTTAATCTACTTTTTACATTTATAATTGAGGCTCCTAAAT
* *
507904 TTTTCAAT-TGTACTTTTTA
66 TTTTCAATCT-CACTTTCTA
* * * * * * * *
507923 ACTTTATAATTGAAACTCTTAATTTTTTAATATTAAC-TTTTACTTTTATAATTGAGTCT-CTTA
1 CCTTTATAATTGAAGCCCCTAATTTTTTAAT-CT-ACTTTTTACATTTATAATTGAGGCTCCTAA
* * *
507986 A-TTTTCAATTTAACTTTTTTA
64 ATTTTTCAATCTCAC-TTTCTA
* * *
508007 CTTTTATAATTTAAACCCCTAATTT
1 CCTTTATAATTGAAGCCCCTAATTT
508032 AATCATTTTT
Statistics
Matches: 287, Mismatches: 63, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
81 3 0.01
83 38 0.13
84 133 0.46
85 67 0.23
86 43 0.15
87 1 0.00
88 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (84 bp):
CCTTTATAATTGAAGCCCCTAATTTTTTAATCTACTTTTTACATTTATAATTGAGGCTCCTAAAT
TTTTCAATCTCACTTTCTA
Found at i:507889 original size:41 final size:43
Alignment explanation
Indices: 507586--508028 Score: 264
Period size: 43 Copynumber: 10.5 Consensus size: 43
507576 ATTTTTTGCC
* * * * *
507586 TTTATAATTGATGTCCATAAATTTTTCAATCCCACCTTTTACA
1 TTTATAATTGAAGCCCCTAAATTTTTCAATCTCACTTTTTACA
* * * *
507629 TTTATAATT-AAGACCCCTAATTTTTTCTATCTCACTTTCTACC
1 TTTATAATTGAAG-CCCCTAAATTTTTCAATCTCACTTTTTACA
* * * * * * *
507672 TTTTTAATTGAAACCTCTAATTTTTTTAGTATCACTTTTTACA
1 TTTATAATTGAAGCCCCTAAATTTTTCAATCTCACTTTTTACA
* * * * * *
507715 TTTATAATTG-AGACCCC-CAATTTTTTAATCCCGCTTTCTACT
1 TTTATAATTGAAG-CCCCTAAATTTTTCAATCTCACTTTTTACA
* * * *
507757 TTTATAATT-AAGGCCCT-GATTTTTTAATCTCACTTTTTACC
1 TTTATAATTGAAGCCCCTAAATTTTTCAATCTCACTTTTTACA
* * * * *
507798 TTTATAGTCGAGGCTCCTAAATTTTTCAATCTCACTTTTTACC
1 TTTATAATTGAAGCCCCTAAATTTTTCAATCTCACTTTTTACA
* *
507841 TTTATAATTGAAGCCCCTAAATTTTT-AATCT-ATTTTTTATA
1 TTTATAATTGAAGCCCCTAAATTTTTCAATCTCACTTTTTACA
* ** * *
507882 TTTATAATTGAGGATCCTAATTTTTTCAAT-TGTACTTTTTA-A
1 TTTATAATTGAAGCCCCTAAATTTTTCAATCT-CACTTTTTACA
* * * * * * *
507924 CTTTATAATTGAA-ACTCTTAATTTTTTAATATTAAC-TTTTACT
1 -TTTATAATTGAAGCCCCTAAATTTTTCAAT-CTCACTTTTTACA
* * * * * *
507967 TTTATAATTG-AGTCTCTTAA-TTTTCAATTTAACTTTTTTACT
1 TTTATAATTGAAGCCCCTAAATTTTTCAATCTCAC-TTTTTACA
* *
508009 TTTATAATTTAAACCCCTAA
1 TTTATAATTGAAGCCCCTAA
508029 TTTAATCATT
Statistics
Matches: 313, Mismatches: 69, Indels: 36
0.75 0.17 0.09
Matches are distributed among these distances:
40 5 0.02
41 67 0.21
42 95 0.30
43 143 0.46
44 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (43 bp):
TTTATAATTGAAGCCCCTAAATTTTTCAATCTCACTTTTTACA
Found at i:507971 original size:42 final size:42
Alignment explanation
Indices: 507817--508031 Score: 158
Period size: 42 Copynumber: 5.1 Consensus size: 42
507807 GAGGCTCCTA
* * * * * *
507817 AATTTTTCAATCTCACTTTTTACCTTTATAATTGAAGCCCCTA
1 AATTTTTCAATTTAACTTTTTACTTTTATAATTGAA-ACTCTT
* * * *
507860 AATTTTT-AATCT-ATTTTTTA-TATTTATAATTGAGGA-TCCT
1 AATTTTTCAATTTAACTTTTTACT-TTTATAATTGA-AACTCTT
507900 AATTTTTTCAATTGT-ACTTTTTAAC-TTTATAATTGAAACTCTT
1 AA-TTTTTCAATT-TAACTTTTT-ACTTTTATAATTGAAACTCTT
* **
507943 AATTTTTTAATATTAAC-TTTTACTTTTATAATTGAGTCTCTT
1 AATTTTTCAAT-TTAACTTTTTACTTTTATAATTGAAACTCTT
* * *
507985 AA-TTTTCAATTTAACTTTTTTACTTTTATAATTTAAACCCCT
1 AATTTTTCAATTTAAC-TTTTTACTTTTATAATTGAAACTCTT
508027 AATTT
1 AATTT
508032 AATCATTTTT
Statistics
Matches: 138, Mismatches: 20, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
40 8 0.06
41 32 0.23
42 62 0.45
43 35 0.25
44 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.04, T:0.53
Consensus pattern (42 bp):
AATTTTTCAATTTAACTTTTTACTTTTATAATTGAAACTCTT
Found at i:507990 original size:21 final size:20
Alignment explanation
Indices: 507920--507990 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
507910 ATTGTACTTT
*
507920 TTAACTTTATAATTGAAACTC
1 TTAATTTTATAATTG-AACTC
* * *
507941 TTAATTTTTTAATATTAACTT
1 TTAATTTTATAAT-TGAACTC
* *
507962 TTACTTTTATAATTGAGTCTC
1 TTAATTTTATAATTGA-ACTC
507983 TTAATTTT
1 TTAATTTT
507991 CAATTTAACT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
20 2 0.05
21 35 0.92
22 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (20 bp):
TTAATTTTATAATTGAACTC
Found at i:516427 original size:177 final size:177
Alignment explanation
Indices: 516116--516466 Score: 621
Period size: 177 Copynumber: 2.0 Consensus size: 177
516106 TTTTCTTCTT
*
516116 AAAATTCACCTGAAAAGTTGGGTTCAAAATCCATCATAAAATAAGACCGGATTTCCTACTGTCTA
1 AAAACTCACCTGAAAAGTTGGGTTCAAAATCCATCATAAAATAAGACCGGATTTCCTACTGTCTA
* * **
516181 TCTGAAGTGGGATGCTTATAGGGTTGATATCTCCTATGTCATATGCTGTTGTCTTCACTGGGAAG
66 TCTGAAGTGGGATACTTATAGGGTTGATATCTCCTATGTCATATCCTGTTGTCTTCACCAGGAAG
516246 CCATTTTGTGGAGTCCTGCAACACTGATTACTATCCAAAGTTGTCTC
131 CCATTTTGTGGAGTCCTGCAACACTGATTACTATCCAAAGTTGTCTC
*
516293 AAAACTCACCTGAAAAGTTGGGTTCAAAATCTATCATAAAATAAGACCGGATTTCCTACTGTCTA
1 AAAACTCACCTGAAAAGTTGGGTTCAAAATCCATCATAAAATAAGACCGGATTTCCTACTGTCTA
* * *
516358 TCTGATGTGGGATACTTTTAGGGTTGATATCTCCTATGTCATATCCTGTTGTCTTCACCAGGTAG
66 TCTGAAGTGGGATACTTATAGGGTTGATATCTCCTATGTCATATCCTGTTGTCTTCACCAGGAAG
516423 CCATTTTGTGGAGTCCTGCAACACTGATTACTATCCAAAGTTGT
131 CCATTTTGTGGAGTCCTGCAACACTGATTACTATCCAAAGTTGT
516467 TGTACTCCCC
Statistics
Matches: 165, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
177 165 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (177 bp):
AAAACTCACCTGAAAAGTTGGGTTCAAAATCCATCATAAAATAAGACCGGATTTCCTACTGTCTA
TCTGAAGTGGGATACTTATAGGGTTGATATCTCCTATGTCATATCCTGTTGTCTTCACCAGGAAG
CCATTTTGTGGAGTCCTGCAACACTGATTACTATCCAAAGTTGTCTC
Found at i:522926 original size:21 final size:21
Alignment explanation
Indices: 522902--522941 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
522892 TTTATTTTAT
522902 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
522923 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
522942 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:522977 original size:32 final size:33
Alignment explanation
Indices: 522936--523033 Score: 155
Period size: 32 Copynumber: 3.0 Consensus size: 33
522926 TTTGTTTCAA
522936 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
522968 TTATCGAACTTGGAAG-TTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
523000 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
523033 T
1 T
523034 ATGTTGAGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 42 0.69
33 19 0.31
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:523062 original size:13 final size:13
Alignment explanation
Indices: 523019--523073 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
523009 TTGGAAGTAT
523019 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
523032 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
523046 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
523059 TTAAGTATTTGAA
1 TTAAGTATTTCAA
523072 TT
1 TT
523074 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:523494 original size:15 final size:15
Alignment explanation
Indices: 523469--523524 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
523459 ATCTGGAATA
*
523469 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
523484 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
523499 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
523516 TTAAAACCG
1 TTAAAACCG
523525 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:523533 original size:21 final size:18
Alignment explanation
Indices: 523488--523521 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
523478 GTTTTTTTAT
523488 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
523505 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
523522 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:523642 original size:15 final size:17
Alignment explanation
Indices: 523616--523647 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
523606 TTCTATGGGA
523616 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
523632 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
523648 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:526347 original size:5 final size:5
Alignment explanation
Indices: 526337--526370 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
526327 ATATGTTTCT
526337 TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCC
1 TTCCC TTCCC TTCCC TTCCC TTCCC TTCCC TTCC
526371 AGAAACTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
TTCCC
Found at i:527134 original size:21 final size:21
Alignment explanation
Indices: 527104--527143 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
527094 GAGTAGGAGC
527104 AGGAGCGCCAGTCCACGCCGA
1 AGGAGCGCCAGTCCACGCCGA
*
527125 AGGAGTGCCAGTCCACGCC
1 AGGAGCGCCAGTCCACGCC
527144 ACAGGCGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.33, T:0.07
Consensus pattern (21 bp):
AGGAGCGCCAGTCCACGCCGA
Found at i:530106 original size:20 final size:21
Alignment explanation
Indices: 530081--530132 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
530071 TTTTCCCAAT
*
530081 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
530101 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
530122 TCGCAATGCGA
1 TCGCAATGCGA
530133 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:530146 original size:20 final size:20
Alignment explanation
Indices: 530121--530234 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
530111 AATTGGGAAA
530121 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
530141 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
530161 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
530182 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * *
530202 TTCACAAAGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
530222 TTCGCAACGCGAT
1 ATCGCAATGCGAT
530235 TTACATAGCG
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
19 2 0.03
20 60 0.78
21 13 0.17
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:530165 original size:61 final size:61
Alignment explanation
Indices: 530118--530234 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
530108 GCGAATTGGG
* * * * * *
530118 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCACAAAGCGATACTGACTATCGCAACGCGATAATAC
* * *
530179 AAAATCGCAACGAGATACTGACTTTCACAAAGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCACAAAGCGATACTGACTATCGCAACGCGAT
530235 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCACAAAGCGATACTGACTATCGCAACGCGATAATAC
Found at i:530881 original size:33 final size:33
Alignment explanation
Indices: 530844--530931 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
530834 ATTGCGATTT
530844 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
530877 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
530910 TAATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
530932 ATTATCTCGT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
33 37 0.71
34 15 0.29
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:533129 original size:21 final size:21
Alignment explanation
Indices: 533105--533171 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
533095 TCATTCCTCG
533105 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * * * *
533126 AGAGGCCACTGCCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
533147 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
533168 AGAG
1 AGAG
533172 CCCGATTCAC
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.37, G:0.21, T:0.18
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:533129 original size:42 final size:42
Alignment explanation
Indices: 533053--533132 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
533043 GACTTGCCTG
* * *
533053 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
533095 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
533133 ACTGCCATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.21, C:0.39, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:534548 original size:14 final size:14
Alignment explanation
Indices: 534529--534564 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
534519 ATTGTTTAAT
534529 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
534543 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
534557 TGATTTGT
1 TGATTTGT
534565 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:534730 original size:19 final size:19
Alignment explanation
Indices: 534671--534737 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
534661 AAAAAGTACT
*
534671 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
534690 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
534704 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
534723 ATCGCAACGCAAAAT
1 ATCGCAACGCGAAAT
534738 TAAATTCGCG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:534788 original size:33 final size:32
Alignment explanation
Indices: 534746--534872 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
534736 ATTAAATTCG
534746 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
534779 CGTTGCGATTTTCATTTCGCATTGCAAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGC--GATTCCT
*
534812 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
534845 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
534873 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.04
33 76 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:534825 original size:66 final size:66
Alignment explanation
Indices: 534739--534869 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 66
534729 ACGCAAAATT
*
534739 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
534804 A
66 A
* *
534805 AAATTAGCGTTGTGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
534870 GATAGTAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
A
Found at i:537108 original size:12 final size:12
Alignment explanation
Indices: 537091--537115 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
537081 TCTTTGGGGA
537091 CTTTTTCTTCTT
1 CTTTTTCTTCTT
537103 CTTTTTCTTCTT
1 CTTTTTCTTCTT
537115 C
1 C
537116 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:538113 original size:20 final size:20
Alignment explanation
Indices: 538088--538138 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
538078 TGTATTATCT
538088 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
538108 CGTTGCAAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
538128 CGTTGCGAAAG
1 CGTTGCGAAAG
538139 GCAATCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:538429 original size:19 final size:20
Alignment explanation
Indices: 538352--538440 Score: 171
Period size: 20 Copynumber: 4.5 Consensus size: 20
538342 TTCATTTGAT
538352 TATCGCAACGCGAAAATGGC
1 TATCGCAACGCGAAAATGGC
538372 TATCGCAACGCGAAAATGGC
1 TATCGCAACGCGAAAATGGC
538392 TATCGCAACGCGAAAATGGC
1 TATCGCAACGCGAAAATGGC
538412 TATCGCAACGCG-AAATGGC
1 TATCGCAACGCGAAAATGGC
538431 TATCGCAACG
1 TATCGCAACG
538441 ACAAAATCGC
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
19 17 0.25
20 52 0.75
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.16
Consensus pattern (20 bp):
TATCGCAACGCGAAAATGGC
Found at i:538490 original size:14 final size:14
Alignment explanation
Indices: 538471--538524 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
538461 GAAAATCGCA
538471 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
538485 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
538502 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
538518 TTGCGAT
1 TTGCGAT
538525 AGTCAGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:538490 original size:33 final size:33
Alignment explanation
Indices: 538453--538523 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
538443 AAAATCGCAA
*
538453 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
538486 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
538519 TGCGA
1 TGCGA
538524 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:538542 original size:20 final size:20
Alignment explanation
Indices: 538517--538555 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
538507 CGATTCTCTC
538517 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
538537 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
538556 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:538657 original size:14 final size:14
Alignment explanation
Indices: 538638--538674 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
538628 CATCAATTAA
538638 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
538652 ACAAATCATCTTTT
1 ACAAATCAACATTT
538666 ACAAATCAA
1 ACAAATCAA
538675 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:540595 original size:19 final size:20
Alignment explanation
Indices: 540540--540607 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
540530 GAAACTTAAA
540540 ATCGCAACGC-GAAAATGACT
1 ATCGCAACGCAG-AAATGACT
*
540560 ATCGCAACGCAGAAATGGCT
1 ATCGCAACGCAGAAATGACT
* * **
540580 ATCGTAATGC-GAAATGAAA
1 ATCGCAACGCAGAAATGACT
540599 ATCGCAACG
1 ATCGCAACG
540608 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 13 0.33
20 25 0.64
21 1 0.03
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCAGAAATGACT
Found at i:540615 original size:14 final size:14
Alignment explanation
Indices: 540596--540653 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
540586 ATGCGAAATG
540596 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
540610 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
540626 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
540642 AAAATCGCAACG
1 AAAATCGCAACG
540654 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:540638 original size:32 final size:33
Alignment explanation
Indices: 540580--540658 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
540570 AGAAATGGCT
*
540580 ATCGTAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
540613 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
540645 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
540659 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:540687 original size:19 final size:19
Alignment explanation
Indices: 540665--540746 Score: 104
Period size: 18 Copynumber: 4.6 Consensus size: 19
540655 GAAACACAAA
540665 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
540684 TCGCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
540702 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
540718 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
540735 TCGCATTGCGAT
1 TCGCATTGCGAT
540747 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.11
15 3 0.06
16 4 0.07
17 4 0.07
18 20 0.37
19 17 0.31
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:540765 original size:20 final size:19
Alignment explanation
Indices: 540731--540785 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
540721 TTGCGATTTT
*
540731 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
540750 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
540770 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
540786 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:540774 original size:39 final size:34
Alignment explanation
Indices: 540665--540766 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 34
540655 GAAACACAAA
540665 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTCATT
1 TCGCATTGCGA---TCATTTCGCGTTGCGATTTCATT
540702 TCGCATTGCGAT--TTT-GTCGTTGCGATTTTCATT
1 TCGCATTGCGATCATTTCG-CGTTGCGA-TTTCATT
540735 TCGCATTGCGATAGCCATTTCCGCGTTGCGAT
1 TCGCATTGCGAT---CATTT-CGCGTTGCGAT
540767 AGTCATTTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 17
0.77 0.00 0.23
Matches are distributed among these distances:
31 1 0.02
32 11 0.20
33 19 0.34
34 1 0.02
37 11 0.20
38 4 0.07
39 8 0.14
40 1 0.02
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.42
Consensus pattern (34 bp):
TCGCATTGCGATCATTTCGCGTTGCGATTTCATT
Found at i:541287 original size:18 final size:18
Alignment explanation
Indices: 541261--541305 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
541251 GTCGATCAGA
*
541261 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
541279 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
541297 TGATGGCTC
1 TGATGGCTC
541306 CCAAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:542658 original size:20 final size:20
Alignment explanation
Indices: 542625--542682 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
542615 AATAGTTTCT
**
542625 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACAC
**
542645 GAAAATGACTATCGCAATGC
1 GAAAATGACTATCGCAACAC
**
542665 GAATTTGACTATCGCAAC
1 GAAAATGACTATCGCAAC
542683 GAGAGAATCG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:542957 original size:23 final size:23
Alignment explanation
Indices: 542927--542971 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
542917 GATGGAGATA
542927 GACGGATTTCGCCAGAGATGGGG
1 GACGGATTTCGCCAGAGATGGGG
* *
542950 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
542972 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.44, T:0.20
Consensus pattern (23 bp):
GACGGATTTCGCCAGAGATGGGG
Found at i:543165 original size:21 final size:21
Alignment explanation
Indices: 543139--543234 Score: 90
Period size: 20 Copynumber: 4.7 Consensus size: 21
543129 CGCTTTGAAA
* * *
543139 ATCGCATTGCGATTATTTATT
1 ATCGCATTGCGATTAGTCAGT
*
543160 ATCGCATTGCGA-AAGTCAGT
1 ATCGCATTGCGATTAGTCAGT
* * * *
543180 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA-TTAGTCAGT
543201 ATCGCATTGCGA-TAGTCAGT
1 ATCGCATTGCGATTAGTCAGT
543221 ATCGCATTGCGATT
1 ATCGCATTGCGATT
543235 TTCCCAATTC
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
19 3 0.05
20 28 0.48
21 25 0.43
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.39
Consensus pattern (21 bp):
ATCGCATTGCGATTAGTCAGT
Found at i:543202 original size:41 final size:40
Alignment explanation
Indices: 543139--543236 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 40
543129 CGCTTTGAAA
543139 ATCGCATTGCGATTATTTATTATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATT-TTTATTATCGCATTGCGAAAGTCAGT
* * *
543180 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTT-TATTATCGCATTGCGAAAGTCAGT
543221 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
543237 CCCAATTCGC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 2 0.04
41 49 0.96
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.40
Consensus pattern (40 bp):
ATCGCATTGCGATTTTTATTATCGCATTGCGAAAGTCAGT
Found at i:543252 original size:41 final size:41
Alignment explanation
Indices: 543139--543254 Score: 119
Period size: 41 Copynumber: 2.8 Consensus size: 41
543129 CGCTTTGAAA
* * *
543139 ATCGCATTGCGATTATT-TATTATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATT-TTCCAATATCGCATTGCGATAGTCAGT
* * ** *
543180 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTCAGT
*
543221 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCATTGCGAT
543255 TTACTTATTC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
40 2 0.03
41 60 0.94
42 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTCAGT
Found at i:558499 original size:21 final size:20
Alignment explanation
Indices: 558472--558569 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
558462 AATCAGTGTC
558472 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
558493 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
558513 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
558533 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
558554 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
558570 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:558522 original size:41 final size:41
Alignment explanation
Indices: 558413--558569 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
558403 AAATGACCAA
* **
558413 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
558452 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
558493 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
558534 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
558570 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:558579 original size:20 final size:20
Alignment explanation
Indices: 558556--558726 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 20
558546 GCGAATATGA
558556 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
558576 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
558596 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
558616 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
558636 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
558656 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* **
558676 AAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGTAA-CCAT
* *
558696 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
558716 AAATCGCAACG
1 AAATCGCAACG
558727 AGAATCTGTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 127 0.97
21 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:558621 original size:60 final size:58
Alignment explanation
Indices: 558536--558745 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 58
558526 CGATTTTCCA
* ** * *
558536 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAA-GCGTATCCGT
* ** *
558596 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAA-GCGTATCCGT
* *
558656 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAAGCG-T-ATCCGT
* * *
558716 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
558746 ACTTAAATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 120 0.96
61 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACCGTAAATCGCAAGCGTATCCGT
Found at i:558727 original size:20 final size:20
Alignment explanation
Indices: 558590--558745 Score: 174
Period size: 20 Copynumber: 7.8 Consensus size: 20
558580 CGCAATGCGT
*
558590 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
558610 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
558630 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
558650 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
558670 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
558690 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
558710 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
558730 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
558746 ACTTAAATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:558727 original size:40 final size:40
Alignment explanation
Indices: 558556--558745 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
558546 GCGAATATGA
* *
558556 AAATCGCAACGCGAA-CACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAA--CGATAATCCGT
* * * *
558596 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
558636 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
558676 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
558716 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
558746 ACTTAAATTT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 129 0.97
41 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:559467 original size:24 final size:24
Alignment explanation
Indices: 559428--559474 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
559418 AAATTTGGTC
559428 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
559452 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
559475 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:559666 original size:12 final size:12
Alignment explanation
Indices: 559649--559673 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
559639 ATATAATCCT
559649 GAAGAAGAAAAA
1 GAAGAAGAAAAA
559661 GAAGAAGAAAAA
1 GAAGAAGAAAAA
559673 G
1 G
559674 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:561972 original size:19 final size:19
Alignment explanation
Indices: 561950--562223 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
561940 CGGAAATTAC
*
561950 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
561969 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
561983 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
562003 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
562017 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
562036 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
562055 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
562069 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
562088 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
562107 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
562126 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
562145 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
562164 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
562183 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
562197 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
562216 AATCGCAA
1 AATCGCAA
562224 CGAGAGAATC
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 40 0.18
15 2 0.01
16 11 0.05
17 10 0.04
18 3 0.01
19 147 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:562122 original size:38 final size:38
Alignment explanation
Indices: 561950--562245 Score: 354
Period size: 33 Copynumber: 8.4 Consensus size: 38
561940 CGGAAATTAC
* *
561950 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
561983 AATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
562017 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
562055 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
562088 AATCGCAATGCGAAATGAAAATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
562126 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
562164 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
562197 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
562230 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
562246 TATAAACGCA
Statistics
Matches: 241, Mismatches: 8, Indels: 28
0.87 0.03 0.10
Matches are distributed among these distances:
31 2 0.01
33 100 0.41
34 30 0.12
35 6 0.02
36 7 0.03
37 2 0.01
38 94 0.39
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (38 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:562202 original size:14 final size:14
Alignment explanation
Indices: 562183--562237 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
562173 GCGAAATGAA
562183 AATCGCAACGAAAG
1 AATCGCAACGAAAG
562197 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
562214 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
562230 AATCGCAA
1 AATCGCAA
562238 TGCGAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 5 0.14
19 8 0.23
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:562261 original size:52 final size:52
Alignment explanation
Indices: 561978--562245 Score: 375
Period size: 52 Copynumber: 5.0 Consensus size: 52
561968 AAATCCCAAC
561978 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
562031 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
562083 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGTGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
562140 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
562195 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
562244 AT
1 AT
562246 TATAAACGCA
Statistics
Matches: 203, Mismatches: 4, Indels: 19
0.90 0.02 0.08
Matches are distributed among these distances:
47 10 0.05
48 1 0.00
49 5 0.02
50 2 0.01
52 95 0.47
53 16 0.08
54 2 0.01
55 5 0.02
56 1 0.00
57 66 0.33
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:562296 original size:19 final size:19
Alignment explanation
Indices: 562252--562353 Score: 133
Period size: 19 Copynumber: 5.6 Consensus size: 19
562242 AAATTATAAA
562252 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
562271 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
562291 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
562307 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
*
562324 CGCATTGTGATTTTCATTT
1 CGCATTGCGATTTTCATTT
*
562343 CACATTGCGAT
1 CGCATTGCGAT
562354 AGTCATTTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 33 0.46
20 19 0.26
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:562359 original size:19 final size:19
Alignment explanation
Indices: 562318--562361 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
562308 GTTGCGATTT
* * **
562318 TCATTTCGCATTGTGATTT
1 TCATTTCACATTGCGATAG
562337 TCATTTCACATTGCGATAG
1 TCATTTCACATTGCGATAG
562356 TCATTT
1 TCATTT
562362 TTGCCTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (19 bp):
TCATTTCACATTGCGATAG
Found at i:562479 original size:14 final size:14
Alignment explanation
Indices: 562460--562496 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
562450 CATCAATTAC
562460 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
562474 ACAAATCATCTTTT
1 ACAAATCAACTTTT
562488 ACAAATCAA
1 ACAAATCAA
562497 TTAAATAAGC
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:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:564443 original size:19 final size:19
Alignment explanation
Indices: 564403--564513 Score: 98
Period size: 19 Copynumber: 6.3 Consensus size: 19
564393 TAGTTTACTT
* *
564403 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
564423 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
564442 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
**
564456 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
564475 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
564489 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
564508 TCGCAA
1 TCGCAA
564514 TCGTTGCGAT
Statistics
Matches: 75, Mismatches: 6, Indels: 21
0.74 0.06 0.21
Matches are distributed among these distances:
14 16 0.21
16 10 0.13
17 10 0.13
19 27 0.36
20 12 0.16
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:564459 original size:14 final size:14
Alignment explanation
Indices: 564440--564496 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
564430 GCGAAATGAA
564440 AATCGCAACGACAG
1 AATCGCAACGACAG
*
564454 AATCGCAACGCGAAACCAA
1 AATCGCAA--CG--A-CAG
*
564473 AATCGCAACGAAAG
1 AATCGCAACGACAG
564487 AATCGCAACG
1 AATCGCAACG
564497 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.28, G:0.19, T:0.07
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:564463 original size:33 final size:33
Alignment explanation
Indices: 564421--564513 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
564411 CGAAACTTAA
*
564421 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
564454 AATCGCAACGCGAAACCAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
564487 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
564514 TCGTTGCGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.25, G:0.19, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:564558 original size:20 final size:19
Alignment explanation
Indices: 564515--564561 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
564505 AAATCGCAAT
**
564515 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTACTTTCG
564534 CGTTGCGATTTTAACTTTCG
1 CGTTGCGATTTT-ACTTTCG
*
564554 TGTTGCGA
1 CGTTGCGA
564562 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.11, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTACTTTCG
Found at i:564725 original size:93 final size:93
Alignment explanation
Indices: 564609--565076 Score: 895
Period size: 93 Copynumber: 5.1 Consensus size: 93
564599 ATGGATTGCA
* *
564609 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATAAAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
564673 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
564701 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
564766 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
564794 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAG-ATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
564858 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
564886 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
564951 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
564979 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
565044 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
565072 TTACT
1 TTACT
565077 AAGCAATCTA
Statistics
Matches: 371, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
92 96 0.26
93 275 0.74
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:564926 original size:185 final size:186
Alignment explanation
Indices: 564609--565076 Score: 895
Period size: 185 Copynumber: 2.5 Consensus size: 186
564599 ATGGATTGCA
* *
564609 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATAAAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
564673 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
564738 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
564794 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAG-ATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
564858 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
564923 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
564979 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
565044 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
565077 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
185 187 0.67
186 91 0.33
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:566796 original size:14 final size:14
Alignment explanation
Indices: 566777--566866 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
566767 TTGAAATGAA
566777 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
566791 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
566810 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
566824 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
566843 AATCGCAACGAGAG
1 AATCGCAACGAGAG
566857 AATCGCAACG
1 AATCGCAACG
566867 CGAAATAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:566814 original size:33 final size:33
Alignment explanation
Indices: 566769--566883 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
566759 TCTTTTGGTT
566769 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
566802 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
566835 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
566868 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
566884 TGCGATTTGG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.47, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:566815 original size:19 final size:19
Alignment explanation
Indices: 566791--566888 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
566781 GCAACGAGAG
*
566791 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
566810 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
566824 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
566843 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
566857 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
566876 AATCGCAATGCGA
1 AATCGCAACGCGA
566889 TTTGGTTTCG
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:566918 original size:14 final size:14
Alignment explanation
Indices: 566899--566955 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
566889 TTTGGTTTCG
566899 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
566913 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
566932 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
566946 CGTTGCGATT
1 CGTTGCGATT
566956 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:566937 original size:19 final size:19
Alignment explanation
Indices: 566913--567001 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
566903 GCGATTCTCT
566913 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
566932 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
566946 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
566965 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
566985 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
567002 ATCTCGTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 25 0.45
20 15 0.27
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:566993 original size:39 final size:33
Alignment explanation
Indices: 566894--567001 Score: 153
Period size: 33 Copynumber: 3.1 Consensus size: 33
566884 TGCGATTTGG
566894 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
566927 TTTCGCGTTGCGATTCTCTCGTTGCGATTGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
566960 TTTCGCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTT--G-C-G--ATTCTCTCGTTGCGATTTTCA
566999 TTT
1 TTT
567002 ATCTCGTTGC
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
33 41 0.61
35 1 0.01
36 1 0.01
37 1 0.01
39 23 0.34
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.44
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:567135 original size:33 final size:33
Alignment explanation
Indices: 567093--567163 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
567083 AATACTAACT
567093 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
567126 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
567159 TGAAA
1 TGAAA
567164 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:567397 original size:22 final size:22
Alignment explanation
Indices: 567345--567399 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
567335 TGGTTGTGAG
**
567345 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
567367 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
567389 GGATTTCTTCG
1 GGATTTCTTCG
567400 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:567571 original size:20 final size:20
Alignment explanation
Indices: 567546--567739 Score: 194
Period size: 20 Copynumber: 9.7 Consensus size: 20
567536 CTTTAAATAT
567546 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
567566 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
567588 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
567607 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
567627 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
567647 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
567667 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * * *
567687 CGCATTGCAATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
567707 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
567727 CGCGTTGCGATTT
1 CGCGTTGCGATTT
567740 TGGAAAATCG
Statistics
Matches: 141, Mismatches: 28, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
19 2 0.01
20 122 0.87
21 15 0.11
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:567733 original size:60 final size:60
Alignment explanation
Indices: 567546--567739 Score: 226
Period size: 60 Copynumber: 3.2 Consensus size: 60
567536 CTTTAAATAT
* * ** *
567546 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATACGCATTGC-AATTTATGTATTCGCGTTGCGATTTACAGATA
* * *** * *
567607 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCATTGCAATTTATGTATTCGCGTTGCGATTTACAGATA
* * * * *
567667 CACGTTGCGATTTACGGATACGCATTGCAATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCATTGCAATTTATGTATTCGCGTTGCGATTTACAGATA
567727 CGCGTTGCGATTT
1 CGCGTTGCGATTT
567740 TGGAAAATCG
Statistics
Matches: 109, Mismatches: 24, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 83 0.76
61 26 0.24
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCATTGCAATTTATGTATTCGCGTTGCGATTTACAGATA
Found at i:567756 original size:21 final size:20
Alignment explanation
Indices: 567706--567803 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
567696 ATTTATGTGT
* * * *
567706 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
567726 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
567747 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
567767 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
567788 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
567804 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:567798 original size:41 final size:41
Alignment explanation
Indices: 567706--567803 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
567696 ATTTATGTGT
* * *
567706 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
567747 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
567788 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
567804 GAAACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.04
41 42 0.91
42 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:569199 original size:22 final size:21
Alignment explanation
Indices: 569166--569227 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
569156 CTTAGCATTA
*
569166 TTAAA-AAAAATAAAGAAACCT
1 TTAAAGAAAAATAAAGAAA-AT
569187 TTAAAGAAAAATAAAGAAAAT
1 TTAAAGAAAAATAAAGAAAAT
* * *
569208 GTAAAGAAAAAGAAAAAAAA
1 TTAAAGAAAAATAAAGAAAA
569228 AAGAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 23 0.64
22 13 0.36
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.15
Consensus pattern (21 bp):
TTAAAGAAAAATAAAGAAAAT
Found at i:569236 original size:11 final size:11
Alignment explanation
Indices: 569214--569240 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
569204 AAATGTAAAG
569214 AAAAAGAAAAA
1 AAAAAGAAAAA
569225 AAAAAGAAAAA
1 AAAAAGAAAAA
569236 AAAAA
1 AAAAA
569241 CTTTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:569735 original size:27 final size:26
Alignment explanation
Indices: 569705--569764 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
569695 TTATTATAAT
*
569705 TTAATATATTTTCTTTTTTTAATAAAA
1 TTAATATATTTTCTATTTTTAA-AAAA
*
569732 TTAAT-T-GTTTCTATTTTTAAAAAA
1 TTAATATATTTTCTATTTTTAAAAAA
*
569756 TTATTATAT
1 TTAATATAT
569765 ACGCTATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
24 8 0.30
25 13 0.48
26 1 0.04
27 5 0.19
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (26 bp):
TTAATATATTTTCTATTTTTAAAAAA
Found at i:572754 original size:16 final size:17
Alignment explanation
Indices: 572723--572755 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
572713 TAAAATTTTA
572723 AAAATGATAAAATTAAT
1 AAAATGATAAAATTAAT
*
572740 AAAAT-ATATAATTAAT
1 AAAATGATAAAATTAAT
572756 CGGGAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATGATAAAATTAAT
Found at i:573816 original size:23 final size:22
Alignment explanation
Indices: 573768--573817 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
573758 TCCGTCTCAT
* * * *
573768 TAAATTTATTTCTTTTGATTTT
1 TAAAATTATTTCATTTAATTTA
573790 TAAAATTATTTCATTTAATATTA
1 TAAAATTATTTCATTTAAT-TTA
573813 TAAAA
1 TAAAA
573818 GTCAACAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TAAAATTATTTCATTTAATTTA
Found at i:575060 original size:18 final size:17
Alignment explanation
Indices: 575037--575079 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
575027 ATATATATAT
575037 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
575055 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
575072 ATAA-AATA
1 ATAATAATA
575080 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:576418 original size:105 final size:105
Alignment explanation
Indices: 576231--576954 Score: 1158
Period size: 105 Copynumber: 7.0 Consensus size: 105
576221 GCATTGTTCA
* * **
576231 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
576291 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
576331 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
576396 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
576436 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
576501 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
576541 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
576606 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
576646 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA---GTTATTGACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
576708 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
576748 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTAACAGG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
576813 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
576853 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAA
* ** * *
576918 CCAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
576955 CCTCGAGTGC
Statistics
Matches: 586, Mismatches: 29, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
100 36 0.06
101 1 0.00
102 101 0.17
103 2 0.00
104 2 0.00
105 404 0.69
106 40 0.07
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:576759 original size:207 final size:208
Alignment explanation
Indices: 576231--576954 Score: 1150
Period size: 207 Copynumber: 3.5 Consensus size: 208
576221 GCATTGTTCA
* * ** *
576231 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AATTTTGTTGACAAGCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
*
576293 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTT
* *
576358 GAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
576423 CTTGCATTGTCTG
196 CTTGCGTTGTCTG
** *
576436 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA--TGTTGTTGACAAG
576501 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAG
576566 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
129 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
576631 AACTTGCGTTGTCTG
194 AACTTGCGTTGTCTG
* * * * *
576646 AAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGAGAA-GTTATTGACAGGCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
*
576710 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTT
* *
576775 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTAACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
576840 CTTGCGTTGTCTG
196 CTTGCGTTGTCTG
576853 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA--TG-TTGTTGACAA
* ** * *
576918 CCAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
63 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
576955 CCTCGAGTGC
Statistics
Matches: 478, Mismatches: 32, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
205 36 0.08
206 1 0.00
207 201 0.42
208 2 0.00
210 198 0.41
211 40 0.08
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (208 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAATGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTG
Found at i:576848 original size:312 final size:313
Alignment explanation
Indices: 576232--576954 Score: 1152
Period size: 312 Copynumber: 2.3 Consensus size: 313
576222 CATTGTTCAG
* * **
576232 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
576292 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGT
* * *
576357 TGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGAAATTGAGAA--TGTTATTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
* * ** *
576422 ACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAG
194 ACTTGCATTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
*
576487 TTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
259 TTGTTGTTAACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
576542 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
576607 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGT
* *
576672 TGAAATTGGTTCTGAAATTGAGAA-GTTATTGACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 TGAAATTGGCTCTGAAATTGAGAATGTTATTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
576736 TTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT
196 TTGCATTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT
* *
576801 GTTGTTAACAGGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
261 GTTGTTAACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
*
576854 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
** * *
576919 CAGTTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
576955 CCTCGAGTGC
Statistics
Matches: 382, Mismatches: 25, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
310 35 0.09
311 2 0.01
312 203 0.53
313 44 0.12
314 2 0.01
315 96 0.25
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (313 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGT
TGAAATTGGCTCTGAAATTGAGAATGTTATTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCATTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT
GTTGTTAACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
Found at i:577686 original size:67 final size:65
Alignment explanation
Indices: 577597--577753 Score: 199
Period size: 67 Copynumber: 2.4 Consensus size: 65
577587 AAGATATCTG
* * * ** *
577597 TTGTTTCATGAGAAACGGTCTCAAGGGA-AACAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATT-TGTTTTAAGGGAAATAAATTCAAAG-G
577661 TT
64 TT
* *
577663 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGAAAAAATTTGTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTTAAGGGAAATAAATTCAAAGGT
577728 T
65 T
*
577729 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
577754 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 22 0.28
66 4 0.05
67 46 0.58
68 7 0.09
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTTAAGGGAAATAAATTCAAAGGTT
Found at i:577780 original size:36 final size:36
Alignment explanation
Indices: 577729--577852 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
577719 TTCAAAGGTT
*
577729 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
* *
577765 TTGTTTCAAGAGAAACTGTCTTAAGAGAGAC-AAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
* * *
577800 CTTAGTTCCAAGGGAAACTATCTCAAGAGAGACGAAAT
1 -TT-GTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
*
577838 TTATTTCAAGGGAAA
1 TTGTTTCAAGGGAAA
577853 TGTTTTCAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 27 0.36
38 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA
Found at i:578843 original size:22 final size:22
Alignment explanation
Indices: 578818--578860 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
578808 ATTTTTGTTT
578818 ATTTGATGCT-AAATGGTTTGAC
1 ATTTGATGCTCAAA-GGTTTGAC
578840 ATTTGATGCTCAAAGGTTTGA
1 ATTTGATGCTCAAAGGTTTGA
578861 TGGGGTAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (22 bp):
ATTTGATGCTCAAAGGTTTGAC
Found at i:579518 original size:16 final size:15
Alignment explanation
Indices: 579473--579543 Score: 67
Period size: 15 Copynumber: 4.7 Consensus size: 15
579463 TTCTTTTTGA
579473 TTTTTGTTCTTTAT-T
1 TTTTTGTTCTTT-TCT
579488 TTTTTGTT-TTCTTCT
1 TTTTTGTTCTT-TTCT
579503 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
* *
579519 TTTTTCTT-TTTGCT
1 TTTTTGTTCTTTTCT
579533 CTTTTTGTTCT
1 -TTTTTGTTCT
579544 GATTGAATCT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
14 8 0.17
15 25 0.53
16 12 0.26
17 2 0.04
ACGTcount: A:0.01, C:0.14, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:580696 original size:8 final size:8
Alignment explanation
Indices: 580680--580718 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
580670 ATTGTAGATG
580680 AAAATGCA
1 AAAATGCA
*
580688 AAAAGGCA
1 AAAATGCA
580696 AAAATGC-
1 AAAATGCA
580703 AAAATGCA
1 AAAATGCA
*
580711 AGAATGCA
1 AAAATGCA
580719 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:580706 original size:15 final size:15
Alignment explanation
Indices: 580680--580718 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
580670 ATTGTAGATG
580680 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
580696 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
580711 AGAATGCA
1 AAAATGCA
580719 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:583329 original size:12 final size:12
Alignment explanation
Indices: 583312--583376 Score: 85
Period size: 12 Copynumber: 5.4 Consensus size: 12
583302 AAAAAGGAAA
*
583312 AAATATAAATAT
1 AAATATATATAT
583324 AAATATATATAT
1 AAATATATATAT
*
583336 ATATATATATAT
1 AAATATATATAT
*
583348 ATATATATATAT
1 AAATATATATAT
*
583360 ATATATATATAT
1 AAATATATATAT
*
583372 TAATA
1 AAATA
583377 AATAAGCTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AAATATATATAT
Found at i:583390 original size:2 final size:2
Alignment explanation
Indices: 583314--583371 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
583304 AAAGGAAAAA
* *
583314 AT AT AA AT AT AA 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
583356 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
583372 TAATAAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:583878 original size:18 final size:17
Alignment explanation
Indices: 583857--583899 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
583847 ATATATACAT
583857 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
583875 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
583892 ATAA-AATA
1 ATAATAATA
583900 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:592904 original size:2 final size:2
Alignment explanation
Indices: 592897--592933 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
592887 TATATTTCAT
592897 TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
592934 GGCACTGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:593882 original size:68 final size:66
Alignment explanation
Indices: 593798--594013 Score: 249
Period size: 68 Copynumber: 3.2 Consensus size: 66
593788 TACACGGAAC
* *
593798 ACCTAATCATATTATTCTAGGTGACTCGCACGGGAGCCTCGAGGGATTAGAGTGACTTGCACGGA
1 ACCTAATCATATTATTC-AGGTGACTCGCAAGGGAGCCTCGAGGGATTAGAGTGACTCGCAC-GA
593863 AGA
64 AGA
* * *
593866 ACCTAATCATATTATTCCGGATGACTCGCAAGGGAG-TTCGAAGGATTAGAGTGACTCGCACGAG
1 ACCTAATCATATTATTCAGG-TGACTCGCAAGGGAGCCTCGAGGGATTAGAGTGACTCGCACGA-
*
593930 AGC
64 AGA
* * * *
593933 ACTTAATCATATTATTCCAGGTGACTAGCATGGGAGCC-CTGAGGAATTAGAGTGACTCGCACG-
1 ACCTAATCATATTATT-CAGGTGACTCGCAAGGGAGCCTC-GAGGGATTAGAGTGACTCGCACGA
593996 AGA
64 AGA
593999 ACACTTAATCATATT
1 AC-C-TAATCATATT
594014 TATTTTTAGG
Statistics
Matches: 126, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
66 6 0.05
67 55 0.44
68 65 0.52
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (66 bp):
ACCTAATCATATTATTCAGGTGACTCGCAAGGGAGCCTCGAGGGATTAGAGTGACTCGCACGAAG
A
Found at i:594151 original size:70 final size:69
Alignment explanation
Indices: 593910--594135 Score: 269
Period size: 70 Copynumber: 3.3 Consensus size: 69
593900 AGTTCGAAGG
* ** * *
593910 ATTAGAGTGACTCGCACGAGAGCACTTAATCATA-TTATTCCAGGTGACT-AGCATGGGAGCCCT
1 ATTAGAGTGACTCGCACGAGAACACTTAATCATATTTATTTTAGGTGACTCA-TATGGGATCCCT
593973 G-AGGA
65 GTA-GA
* *
593978 ATTAGAGTGACTCGCACGAGAACACTTAATCATATTTATTTTTAGGTCACTCATACGGGATCCCT
1 ATTAGAGTGACTCGCACGAGAACACTTAATCATATTTA-TTTTAGGTGACTCATATGGGATCCCT
*
594043 GTAGG
65 GTAGA
* * * *
594048 TTTAGAGTGACTCACACGGGAACACCTAATCATATTTATTTTAGGGTGACTCATATGGGATCCCT
1 ATTAGAGTGACTCGCACGAGAACACTTAATCATATTTATTTTA-GGTGACTCATATGGGATCCCT
*
594113 GTATA
65 GTAGA
*
594118 ATTAGAGTGACTTGCACG
1 ATTAGAGTGACTCGCACG
594136 GGAGAGCCTA
Statistics
Matches: 134, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
68 33 0.25
69 8 0.06
70 91 0.68
71 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (69 bp):
ATTAGAGTGACTCGCACGAGAACACTTAATCATATTTATTTTAGGTGACTCATATGGGATCCCTG
TAGA
Found at i:594310 original size:2 final size:2
Alignment explanation
Indices: 594303--594343 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
594293 TATAGTACTT
594303 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
594344 CTTAAGATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:598758 original size:21 final size:21
Alignment explanation
Indices: 598690--598768 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 21
598680 TCGAAATGGA
** *
598690 GTGCATGGATGCACTACA-TG
1 GTGCATGGATGCACTGTAGGG
*
598710 GTGCATCGATGCACTAGT-GGCAG
1 GTGCATGGATGCACT-GTAGG--G
598733 GTGCATGGATGCACTGTAGGG
1 GTGCATGGATGCACTGTAGGG
598754 GTGCATGGATGCACT
1 GTGCATGGATGCACT
598769 TTGACACCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
20 14 0.29
21 16 0.33
22 2 0.04
23 17 0.35
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (21 bp):
GTGCATGGATGCACTGTAGGG
Found at i:602106 original size:38 final size:40
Alignment explanation
Indices: 602030--602106 Score: 115
Period size: 38 Copynumber: 2.0 Consensus size: 40
602020 TTAAATAATA
602030 AAAAATTTCAAAAACATCCACATGTTTCTTCTTCTTCTTC
1 AAAAATTTCAAAAACATCCACATGTTTCTTCTTCTTCTTC
*
602070 AAAAA-TTCAAAAACA-CCACGT-TCTTCTTCTTCTTCTT
1 AAAAATTTCAAAAACATCCACATGT-TTCTTCTTCTTCTT
602107 TAAATTCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
37 1 0.03
38 19 0.54
39 10 0.29
40 5 0.14
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (40 bp):
AAAAATTTCAAAAACATCCACATGTTTCTTCTTCTTCTTC
Done.