Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009591.1 Hibiscus syriacus cultivar Beakdansim tig00116970_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: 2451160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:317291 original size:21 final size:21
Alignment explanation
Indices: 317134--317292 Score: 126
Period size: 21 Copynumber: 7.7 Consensus size: 21
317124 GCGTTGCATT
* *
317134 TCGCGTTTCGATAATTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
317155 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
317175 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* *
317196 TCACGTTGCGATACTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
317217 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
* ** **
317237 TCGCGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATAGTTGAAAA
317257 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
317278 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
317293 CTACAGTTGT
Statistics
Matches: 111, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
20 49 0.44
21 62 0.56
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:317309 original size:22 final size:22
Alignment explanation
Indices: 317281--317352 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
317271 TTGAAAATCG
317281 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
317303 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
317322 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
317344 CGTTGCGAT
1 CGTTGCGAT
317353 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:317326 original size:19 final size:19
Alignment explanation
Indices: 317302--317370 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
317292 TCTACAGTTG
317302 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
317321 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
317342 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
317362 TCGTTGCGA
1 TCGTTGCGA
317371 AAATCGCGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 19 0.49
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:317326 original size:41 final size:41
Alignment explanation
Indices: 317281--317370 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
317271 TTGAAAATCG
317281 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
317322 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
317363 CGTTGCGA
1 CGTTGCGA
317371 AAATCGCGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:317326 original size:82 final size:81
Alignment explanation
Indices: 317158--317330 Score: 233
Period size: 82 Copynumber: 2.1 Consensus size: 81
317148 TTGAAAATCG
*
317158 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATACTTGAAAATCGCGT
1 CGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATACTTGAAAATCGCGT
*
317223 TGCGATTTTCCATTTC
66 TGCGATTTTCCAATTC
* * * * *
317239 GCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCT-ACAGTTGT
1 -CGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATACT-TGAAAATCG-
317303 CGTTGCGATTTTCCAAATT-
63 CGTTGCGATTTTCC-AATTC
317322 CGTTGCGAT
1 CGTTGCGAT
317331 AGTCTACAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
82 63 0.78
83 15 0.19
84 3 0.04
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (81 bp):
CGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCACGTTGCGATACTTGAAAATCGCGT
TGCGATTTTCCAATTC
Found at i:317425 original size:39 final size:40
Alignment explanation
Indices: 317370--317465 Score: 149
Period size: 39 Copynumber: 2.4 Consensus size: 40
317360 ATTCGTTGCG
*
317370 AAAATCGCGTTGCGATTTTCCAGTTCCCGTTGCGATAGTT
1 AAAATCGCGTTGCGATTTTCCAGTTCCCATTGCGATAGTT
*
317410 -AAATCGCGTTGCGATTTTCCAGTTCGCATTGCGATAGTT
1 AAAATCGCGTTGCGATTTTCCAGTTCCCATTGCGATAGTT
*
317449 GAAAATCACGTTGCGAT
1 -AAAATCGCGTTGCGAT
317466 AGTCTACAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
39 37 0.73
41 14 0.27
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (40 bp):
AAAATCGCGTTGCGATTTTCCAGTTCCCATTGCGATAGTT
Found at i:317481 original size:135 final size:135
Alignment explanation
Indices: 317237--317487 Score: 364
Period size: 135 Copynumber: 1.8 Consensus size: 135
317227 ATTTTCCATT
*
317237 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTTG
1 TCGCGTTGCGATTTTCCAGTTCCCGTTGCGATAGTT-AAAATCGCGTTGCGATA-TCTACAGTTG
* * * *
317302 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTT
64 TCATTGCGATGTTCAAAATACGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTT
317367 GCGAAAA
129 GCGAAAA
* *
317374 TCGCGTTGCGATTTTCCAGTTCCCGTTGCGATAGTT-AAATCGCGTTGCGAT-TTTCCAGTTCG-
1 TCGCGTTGCGATTTTCCAGTTCCCGTTGCGATAGTTAAAATCGCGTTGCGATATCTACAGTT-GT
*
317436 CATTGCGATAGTTGAAAATCACGTTGCGATAGTCTACAGTTGTCGTTGCGAT
65 CATTGCGAT-GTTCAAAAT-ACGTTGCGATAGTCTACAGTTGTCGTTGCGAT
317488 AGTCTACAGT
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
133 15 0.15
134 7 0.07
135 46 0.45
137 35 0.34
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (135 bp):
TCGCGTTGCGATTTTCCAGTTCCCGTTGCGATAGTTAAAATCGCGTTGCGATATCTACAGTTGTC
ATTGCGATGTTCAAAATACGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTTGC
GAAAA
Found at i:317485 original size:22 final size:22
Alignment explanation
Indices: 317457--317502 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
317447 TTGAAAATCA
317457 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
317479 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
317501 CG
1 CG
317503 ATTTTCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.35
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:317489 original size:43 final size:39
Alignment explanation
Indices: 317371--317490 Score: 116
Period size: 39 Copynumber: 3.0 Consensus size: 39
317361 TTCGTTGCGA
* * * *
317371 AAATCGCGTTGCGATTTTCCAGTTCCCGTTGCGATAGTT
1 AAATCACGTTGCGATTCTACAGTTCGCGTTGCGATAGTT
* * * *
317410 AAATCGCGTTGCGATTTTCCAGTTCGCATTGCGATAGTT
1 AAATCACGTTGCGATTCTACAGTTCGCGTTGCGATAGTT
317449 GAAAATCACGTTGCGATAGTCTACAGTT-GTCGTTGCGATAGT
1 --AAATCACGTTGCGAT--TCTACAGTTCG-CGTTGCGATAGT
317491 CTACAGTTGT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
39 37 0.53
41 14 0.20
42 1 0.01
43 18 0.26
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (39 bp):
AAATCACGTTGCGATTCTACAGTTCGCGTTGCGATAGTT
Found at i:317614 original size:6 final size:6
Alignment explanation
Indices: 317603--317645 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
317593 GACACGTATT
317603 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
317646 GACGGACGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:318271 original size:22 final size:22
Alignment explanation
Indices: 318245--318337 Score: 86
Period size: 22 Copynumber: 4.4 Consensus size: 22
318235 AATTTGGAAA
318245 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
318267 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * * **
318289 ATCTCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
318308 ATCGCAACGAC-ATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
318329 ATCGCAACG
1 ATCGCAACG
318338 CGAAATGAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
19 12 0.22
20 3 0.06
21 13 0.24
22 26 0.48
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:318350 original size:41 final size:41
Alignment explanation
Indices: 318302--318467 Score: 273
Period size: 41 Copynumber: 4.0 Consensus size: 41
318292 TCAACGAATT
*
318302 TGGAAAATCGCAACGAC-ATTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAA
* *
318343 TGAAAAATCGCAACGCGATTTTCAACTATAGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
318384 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
318425 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
318466 TG
1 TG
318468 CAACGCGAAT
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
40 1 0.01
41 116 0.98
42 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
Found at i:318354 original size:20 final size:20
Alignment explanation
Indices: 318329--318442 Score: 93
Period size: 20 Copynumber: 5.6 Consensus size: 20
318319 ATTGTAGACT
318329 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
** * **
318349 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
* *
318370 ATAGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
** * **
318390 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
318411 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
318431 ATCGCAACGCGA
1 ATCGCAACGCGA
318443 TTTTCAACTA
Statistics
Matches: 67, Mismatches: 25, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
20 39 0.58
21 28 0.42
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:318471 original size:21 final size:21
Alignment explanation
Indices: 318326--318471 Score: 127
Period size: 21 Copynumber: 7.1 Consensus size: 21
318316 GACATTGTAG
318326 ACTATCGCAACGCGAAATG-A
1 ACTATCGCAACGCGAAATGCA
** ** *
318346 AAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
* *
318367 ACTATAGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
318388 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
318408 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
318429 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
318449 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
318470 AC
1 AC
318472 GCGAATTTAC
Statistics
Matches: 91, Mismatches: 32, Indels: 5
0.71 0.25 0.04
Matches are distributed among these distances:
20 43 0.47
21 48 0.53
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:319121 original size:25 final size:25
Alignment explanation
Indices: 319093--319142 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
319083 ATTAATTAAC
* *
319093 TAAAATAAATTTAAAAGTAAAAAAT
1 TAAAATAAATATAAAAATAAAAAAT
*
319118 TAAAATTAATATAAAAATAAAAAAT
1 TAAAATAAATATAAAAATAAAAAAT
319143 GATTTCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (25 bp):
TAAAATAAATATAAAAATAAAAAAT
Found at i:323910 original size:15 final size:15
Alignment explanation
Indices: 323892--323921 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
323882 CGTTTGGATG
323892 GGGGAATGTGGAATT
1 GGGGAATGTGGAATT
323907 GGGGAATGTGGAATT
1 GGGGAATGTGGAATT
323922 CTCATGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.47, T:0.27
Consensus pattern (15 bp):
GGGGAATGTGGAATT
Found at i:330710 original size:24 final size:24
Alignment explanation
Indices: 330681--330765 Score: 84
Period size: 27 Copynumber: 3.5 Consensus size: 24
330671 AAATTGAACG
*
330681 ACCGGTTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTTACCGGATAAAAA
*
330705 ATCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTT---ACCGGATAAAAA
*
330732 ACCGGTTTTTTAACC-GA-AAAAA
1 ACCGGTTTTTTTACCGGATAAAAA
* *
330754 TCCAGTTTTTTT
1 ACCGGTTTTTTT
330766 TTAAAACTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
22 14 0.27
23 2 0.04
24 14 0.27
27 21 0.41
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (24 bp):
ACCGGTTTTTTTACCGGATAAAAA
Found at i:345731 original size:87 final size:87
Alignment explanation
Indices: 345529--345787 Score: 349
Period size: 87 Copynumber: 3.0 Consensus size: 87
345519 CATTTAACCG
* * * * * *
345529 GAAACATTATCAAGCACATTAACATATTAAGTACCGTTTATATAATATAATAGGTATCACTTATA
1 GAAACATTATCAAGCACAATAACATATTAGGTAACGTTTATATAATGTAATAGGTAGCGCTTATA
* *
345594 TAATAAAA-AAGTTAATTACTG
66 TAATAAAATAAGTTAATTATTA
* ***
345615 GAAACATTATCAAACACAATAACATATTAGGTAAAACTTATATAATGTAATAGGTAGCGCTTATA
1 GAAACATTATCAAGCACAATAACATATTAGGTAACGTTTATATAATGTAATAGGTAGCGCTTATA
*
345680 TAATAAAATAGGTTAATTATTA
66 TAATAAAATAAGTTAATTATTA
* * * *
345702 GAAATATTATCAAGCACAATAACATATTAGGTAGCGTTTATATAACGTAATAGGTAGTGCTTATA
1 GAAACATTATCAAGCACAATAACATATTAGGTAACGTTTATATAATGTAATAGGTAGCGCTTATA
*
345767 TAATAAAATATGTTAATTATT
66 TAATAAAATAAGTTAATTATT
345788 TAATTTGTTA
Statistics
Matches: 150, Mismatches: 22, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
86 63 0.42
87 87 0.58
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.34
Consensus pattern (87 bp):
GAAACATTATCAAGCACAATAACATATTAGGTAACGTTTATATAATGTAATAGGTAGCGCTTATA
TAATAAAATAAGTTAATTATTA
Found at i:345755 original size:23 final size:23
Alignment explanation
Indices: 345720--345769 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
345710 ATCAAGCACA
* *
345720 ATAACATATTAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
345743 ATAACGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
345766 ATAA
1 ATAA
345770 TAAAATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:346129 original size:155 final size:156
Alignment explanation
Indices: 345827--346140 Score: 524
Period size: 155 Copynumber: 2.0 Consensus size: 156
345817 CTCTTAAAAT
*
345827 ATTACCAATGATAATATAACCGATTATTTACTGGAAACATTATCAAGTATAATAATGTAAACGGT
1 ATTACCAATGATAACATAACCGATTATTTACTGGAAACATTATCAAGTATAATAATGTAAACGGT
** *
345892 AAAAAAAATAGGCGATAGTTATTACATTAAACTACTTACCAGATATGTTGAAAGTATCGATTCCA
66 AAAAAAAATAGGCGATACCTATTACATTAAACTACCTACCAGATATGTTGAAAGTATCGATTCCA
345957 TTTAAATAAGTATCGACACTTTTGGA
131 TTTAAATAAGTATCGACACTTTTGGA
* *
345983 ATTACCAATGATAACATAACCGGTTATTTACTGGAAACATTATCAAGTATAATAATGTAAATGGT
1 ATTACCAATGATAACATAACCGATTATTTACTGGAAACATTATCAAGTATAATAATGTAAACGGT
* *
346048 -AAAAAAATAGGCGCTACCTATTACATTAAACTACCTACC-GAATATGTTGAAAGTGTCGATTCC
66 AAAAAAAATAGGCGATACCTATTACATTAAACTACCTACCAG-ATATGTTGAAAGTATCGATTCC
*
346111 ATTTAAATAAGTATCGACATTTTTGGA
130 ATTTAAATAAGTATCGACACTTTTGGA
346138 ATT
1 ATT
346141 TAAAAGAAAA
Statistics
Matches: 148, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
154 1 0.01
155 85 0.57
156 62 0.42
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (156 bp):
ATTACCAATGATAACATAACCGATTATTTACTGGAAACATTATCAAGTATAATAATGTAAACGGT
AAAAAAAATAGGCGATACCTATTACATTAAACTACCTACCAGATATGTTGAAAGTATCGATTCCA
TTTAAATAAGTATCGACACTTTTGGA
Found at i:346321 original size:23 final size:23
Alignment explanation
Indices: 346286--346336 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
346276 CCAGTAATTA
**
346286 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
346309 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
346332 ACCTA
1 ACCTA
346337 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:346403 original size:87 final size:87
Alignment explanation
Indices: 346260--346423 Score: 301
Period size: 87 Copynumber: 1.9 Consensus size: 87
346250 ATATGTTGAA
*
346260 GTGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATAT
1 GTGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATAT
*
346325 AAGCGGTACCTAATATGTTATT
66 AAGCGCTACCTAATATGTTATT
*
346347 GTGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGTTACATATTACATTATAT
1 GTGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATAT
346412 AAGCGCTACCTA
66 AAGCGCTACCTA
346424 TTACATTATA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (87 bp):
GTGCTTGATAATGTTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACATATTACATTATAT
AAGCGCTACCTAATATGTTATT
Found at i:346408 original size:23 final size:23
Alignment explanation
Indices: 346373--346452 Score: 124
Period size: 23 Copynumber: 3.5 Consensus size: 23
346363 CCAGTAATTA
** *
346373 ACCTATTTTATTATATAAGCGTT
1 ACCTATTACATTATATAAGCGCT
*
346396 ACATATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
346419 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
346442 ACCTATTACAT
1 ACCTATTACAT
346453 CATAGTTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:347147 original size:274 final size:275
Alignment explanation
Indices: 346658--347209 Score: 1034
Period size: 274 Copynumber: 2.0 Consensus size: 275
346648 GTTTCAAAAT
*
346658 TTTTTAATAGTGTTTCATGTTTTCCACCAACAATATTAATTTAATAATTTCATTTATACAAAAAA
1 TTTTTAATAGTGTTTCATGTTTTCCACCAACAATATTAATTTAATAATTTCATTTACACAAAAAA
* *
346723 TTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAA
66 TTATTTGATTATTTTGATATTTTATAAAATATTATTTAAAATTTAAATTTAACAATTTTAACCAA
346788 AGATAATAATAAATATGTAATATCTATGTTTATTATTTTTAATTTAATAATAATATATATCGTAA
131 AGATAATAATAAATATGTAATATCTATGTTTATTATTTTTAATTTAATAATAATATATATCGTAA
*
346853 CATAAAAATAAACCATTAGACGTGTATAATTATTAAATTAATATCTTAAAACTCACTAAAAAA-A
196 CATAAAAATAAACCATTAGACGTGTATAATTACTAAATTAATATCTTAAAACTCACTAAAAAAGA
346917 TAACATAACCGATTA
261 TAACATAACCGATTA
*
346932 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
1 TTTTTAATAGTGTTTCATGTTTTCCACCAACAATATTAATTTAATAATTTCATTTACACAAAAAA
346997 TTATTTGATTATTTTGATATTTTATAAAATATTATTTAAAATTTAAATTTAACAATTTTAACCAA
66 TTATTTGATTATTTTGATATTTTATAAAATATTATTTAAAATTTAAATTTAACAATTTTAACCAA
*
347062 ATATAATAATAAATATGTAATATCTATGTTTATTATTTTTAATTTAATAATAATATATATCGTAA
131 AGATAATAATAAATATGTAATATCTATGTTTATTATTTTTAATTTAATAATAATATATATCGTAA
347127 CATAAAAATAAACCATTAGACGTGTATAATTACTAAATTAATATCTTAAAACTCACTAAAAAAGA
196 CATAAAAATAAACCATTAGACGTGTATAATTACTAAATTAATATCTTAAAACTCACTAAAAAAGA
*
347192 TAACATAACCGGTTA
261 TAACATAACCGATTA
347207 TTT
1 TTT
347210 ACTGGAAACA
Statistics
Matches: 270, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
274 252 0.93
275 18 0.07
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.42
Consensus pattern (275 bp):
TTTTTAATAGTGTTTCATGTTTTCCACCAACAATATTAATTTAATAATTTCATTTACACAAAAAA
TTATTTGATTATTTTGATATTTTATAAAATATTATTTAAAATTTAAATTTAACAATTTTAACCAA
AGATAATAATAAATATGTAATATCTATGTTTATTATTTTTAATTTAATAATAATATATATCGTAA
CATAAAAATAAACCATTAGACGTGTATAATTACTAAATTAATATCTTAAAACTCACTAAAAAAGA
TAACATAACCGATTA
Found at i:347568 original size:25 final size:23
Alignment explanation
Indices: 347506--347579 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
347496 CCAGTAATTA
**
347506 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
347529 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
* *
347552 ACCTATTACAGTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
347575 ACCTA
1 ACCTA
347580 ATATGTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:347651 original size:23 final size:23
Alignment explanation
Indices: 347616--347672 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
347606 CCAGTAATTA
**
347616 ACCTATTTTATTATATAAGCACT
1 ACCTATTACATTATATAAGCACT
*
347639 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCACT
347662 ACCTATTACAT
1 ACCTATTACAT
347673 CATAGTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCACT
Found at i:347841 original size:23 final size:23
Alignment explanation
Indices: 347809--347867 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
347799 TATGTTGAAA
*
347809 GTATATATACTTTTTATAAAAAT
1 GTATAGATACTTTTTATAAAAAT
347832 GTATAGATACTTTTTATAAAAAT
1 GTATAGATACTTTTTATAAAAAT
*
347855 GTATCGATACTTT
1 GTATAGATACTTT
347868 GTTGAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (23 bp):
GTATAGATACTTTTTATAAAAAT
Found at i:349340 original size:75 final size:75
Alignment explanation
Indices: 349249--349441 Score: 212
Period size: 75 Copynumber: 2.6 Consensus size: 75
349239 AATCATAAAT
* * * * * * *
349249 AATGTCAAATATCAAGACTCAAACAACAATATTAAATTTATAGCAGGAAAATCCATAA-ACAAA-
1 AATGTCAAATTTCAAGACTCAAACCATAATATTAAATCTAGAACAAGAAAATCCATAATA-AAAT
349312 CAACAATATTAA
65 C-ACAATATTAA
* * * *
349324 AATGTCAAATTTCAAGATTCAAACCATAATATTAACTCTAGAATAATAAAATCCATAATAAAATC
1 AATGTCAAATTTCAAGACTCAAACCATAATATTAAATCTAGAACAAGAAAATCCATAATAAAATC
*
349389 ATAATATTAA
66 ACAATATTAA
* *
349399 AGTGTCAAATCTT-AAGACTCAAACCATAATATTAAGTCTAGAA
1 AATGTCAAAT-TTCAAGACTCAAACCATAATATTAAATCTAGAA
349442 AAATATTAAA
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
75 96 0.96
76 4 0.04
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (75 bp):
AATGTCAAATTTCAAGACTCAAACCATAATATTAAATCTAGAACAAGAAAATCCATAATAAAATC
ACAATATTAA
Found at i:349393 original size:11 final size:12
Alignment explanation
Indices: 349366--349394 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
349356 TAACTCTAGA
349366 ATAATAAAATCC
1 ATAATAAAATCC
349378 ATAATAAAAT-C
1 ATAATAAAATCC
349389 ATAATA
1 ATAATA
349395 TTAAAGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (12 bp):
ATAATAAAATCC
Found at i:352002 original size:11 final size:11
Alignment explanation
Indices: 351986--352011 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
351976 TTATAAAATG
351986 ATAACCATGTA
1 ATAACCATGTA
351997 ATAACCATGTA
1 ATAACCATGTA
352008 ATAA
1 ATAA
352012 GCATCATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (11 bp):
ATAACCATGTA
Found at i:356865 original size:10 final size:10
Alignment explanation
Indices: 356852--356876 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
356842 GTTCATTTGG
356852 TTTTAATTTT
1 TTTTAATTTT
356862 TTTTAATTTT
1 TTTTAATTTT
356872 TTTTA
1 TTTTA
356877 GAAAATAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:358866 original size:11 final size:11
Alignment explanation
Indices: 358850--358875 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
358840 TGATAAACCC
358850 TAAAATATACT
1 TAAAATATACT
358861 TAAAATATACT
1 TAAAATATACT
358872 TAAA
1 TAAA
358876 TGACAAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAATATACT
Found at i:359697 original size:36 final size:36
Alignment explanation
Indices: 359647--359723 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 36
359637 CGAATTAAAT
*
359647 GGGGACGGGAAAAAACCGTTTATGTTAAACGGAGAC
1 GGGGACGGGAAAAAACCGTTTATGCTAAACGGAGAC
*
359683 GGGGACGTGG-AAAAACCGTTTATGCTAAACGGGGAC
1 GGGGACG-GGAAAAAACCGTTTATGCTAAACGGAGAC
359719 GGGGA
1 GGGGA
359724 ATCCCCGCCC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 36 0.95
37 2 0.05
ACGTcount: A:0.32, C:0.14, G:0.38, T:0.16
Consensus pattern (36 bp):
GGGGACGGGAAAAAACCGTTTATGCTAAACGGAGAC
Found at i:368268 original size:6 final size:6
Alignment explanation
Indices: 368257--368296 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
368247 TGGCCATAAA
368257 CACTAG CACTAG CACTAG CACTAG CACTAG CACTAG CACT
1 CACTAG CACTAG CACTAG CACTAG CACTAG CACTAG CACT
368297 TGGGACTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.35, G:0.15, T:0.17
Consensus pattern (6 bp):
CACTAG
Found at i:370571 original size:21 final size:21
Alignment explanation
Indices: 370524--370572 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
370514 TCATTATTTG
*
370524 ATTTAATTTAAAATATAGATT
1 ATTTTATTTAAAATATAGATT
* *
370545 AATTTATTTAAAA-ATTGGATT
1 ATTTTATTTAAAATA-TAGATT
370566 ATTTTAT
1 ATTTTAT
370573 CTATTAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (21 bp):
ATTTTATTTAAAATATAGATT
Found at i:382106 original size:4 final size:4
Alignment explanation
Indices: 382099--382173 Score: 69
Period size: 4 Copynumber: 18.8 Consensus size: 4
382089 AAAACACATA
* * * * *
382099 CATG CATG CATG AATG CATA CATA CATA CATA CATG CATG CATG CATG
1 CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG
* * * *
382147 CATA CATA CATA CATA CATG CATG CAT
1 CATG CATG CATG CATG CATG CATG CAT
382174 ACATTTTTCA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 65 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.25
Consensus pattern (4 bp):
CATG
Found at i:382133 original size:32 final size:32
Alignment explanation
Indices: 382094--382173 Score: 151
Period size: 32 Copynumber: 2.5 Consensus size: 32
382084 TTATTAAAAC
382094 ACATACATGCATGCATGAATGCATACATACAT
1 ACATACATGCATGCATGAATGCATACATACAT
*
382126 ACATACATGCATGCATGCATGCATACATACAT
1 ACATACATGCATGCATGAATGCATACATACAT
382158 ACATACATGCATGCAT
1 ACATACATGCATGCAT
382174 ACATTTTTCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (32 bp):
ACATACATGCATGCATGAATGCATACATACAT
Found at i:384517 original size:2 final size:2
Alignment explanation
Indices: 384505--384556 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
384495 GGTTGCAAAT
*
384505 TA TA TA CA 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
*
384547 TA TT TA TA TA
1 TA TA TA TA TA
384557 CAGGGCCGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:385050 original size:2 final size:2
Alignment explanation
Indices: 385043--385088 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
385033 AAGCAATAGC
385043 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
385085 AT AT
1 AT AT
385089 TATGAAAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:393579 original size:18 final size:19
Alignment explanation
Indices: 393556--393600 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
393546 TTTTAATATT
393556 GATACTCAAGG-GAGTATC
1 GATACTCAAGGAGAGTATC
393574 GATACTCAAGGTAGAGTATC
1 GATACTCAAGG-AGAGTATC
393594 GATACTC
1 GATACTC
393601 TCCATAGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 11 0.44
20 14 0.56
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (19 bp):
GATACTCAAGGAGAGTATC
Found at i:403158 original size:20 final size:20
Alignment explanation
Indices: 403129--403171 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
403119 ATTCCACCAC
403129 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
403149 ATGCATCTATGTGGTCCTAA
1 ATGCAACTATATGCTCCTAA
403169 ATG
1 ATG
403172 AGCTCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:403338 original size:6 final size:6
Alignment explanation
Indices: 403323--403353 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
403313 CTCGCTCGGC
*
403323 TCGTGG TCGTGT TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
403354 AACACGTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.16, G:0.45, T:0.39
Consensus pattern (6 bp):
TCGTGG
Found at i:403635 original size:22 final size:23
Alignment explanation
Indices: 403582--403641 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 23
403572 GACAAGCTGT
* * *
403582 TAATATTAGGAGTTACATTGGTT
1 TAATATCAGGAGTTACATTGATA
*
403605 TAATTTCAGGAGTTACA-TGATA
1 TAATATCAGGAGTTACATTGATA
403627 TAATATCAGGAGTTA
1 TAATATCAGGAGTTA
403642 TAACAGCTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (23 bp):
TAATATCAGGAGTTACATTGATA
Found at i:409038 original size:22 final size:24
Alignment explanation
Indices: 408996--409049 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 24
408986 TCAGAAGTTG
*
408996 CAGGAGTTACATTGATTTAAT-TT
1 CAGGAGTTACATTGATATAATATT
409019 CAGGAGTTACA-TGATATAATATT
1 CAGGAGTTACATTGATATAATATT
409042 -AGGAGTTA
1 CAGGAGTTA
409050 TAACAGTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.37
Consensus pattern (24 bp):
CAGGAGTTACATTGATATAATATT
Found at i:416105 original size:21 final size:20
Alignment explanation
Indices: 416080--416119 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
416070 TTGTATTCCG
*
416080 AAAAATAAGGAAAAATAAAAT
1 AAAAATAAAG-AAAATAAAAT
416101 AAAAATAAAGAAAATAAAA
1 AAAAATAAAGAAAATAAAA
416120 ATTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (20 bp):
AAAAATAAAGAAAATAAAAT
Found at i:416120 original size:21 final size:22
Alignment explanation
Indices: 416080--416127 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
416070 TTGTATTCCG
*
416080 AAAAATAAGGAAAAATAAAA-T
1 AAAAATAAAGAAAAATAAAATT
416101 AAAAATAAAG-AAAATAAAAATT
1 AAAAATAAAGAAAAAT-AAAATT
416123 AAAAA
1 AAAAA
416128 AAAATTGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 13 0.54
22 6 0.25
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAAATAAAGAAAAATAAAATT
Found at i:423419 original size:153 final size:153
Alignment explanation
Indices: 423136--423450 Score: 578
Period size: 153 Copynumber: 2.1 Consensus size: 153
423126 ACATCGTGCT
*
423136 CACATAATTTCTAATTGAAATTGGGTTTAGGTGGGAGTTATGACCTCCACTAATTTAGGGTATAA
1 CACA-AATTTCTAATTGAAATTGGGTTTAGGTGGGAGTTATGACCCCCACTAATTTAGGGTATAA
* *
423201 TAAAAATAAATTAATTAAATGCGACTACACTGTTTTGGACAACACTTTCAATTAGAAATTATGTA
65 TAAAAATAAATAAATTAAATGCGACTACACTGTTTTGGACAACAATTTCAATTAGAAATTATGTA
423266 AGCACGATGTTGGTTTCTTTAGTA
130 AGCACGATGTTGGTTTCTTTAGTA
423290 CACAAATTTCTAATTGAAATTGGGTTTAGGTGGGAGTTATGACCCCCACTAATTTAGGGTATAAT
1 CACAAATTTCTAATTGAAATTGGGTTTAGGTGGGAGTTATGACCCCCACTAATTTAGGGTATAAT
423355 AAAAATAAATAAATTAAATGC-ATCTACACTGTTTTGGACAACAATTTCAATTAGAAATTATGTA
66 AAAAATAAATAAATTAAATGCGA-CTACACTGTTTTGGACAACAATTTCAATTAGAAATTATGTA
423419 AGCACGATGTTGGTTTCTTTAGTA
130 AGCACGATGTTGGTTTCTTTAGTA
423443 CACAAATT
1 CACAAATT
423451 CAATGCTTGG
Statistics
Matches: 157, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
152 1 0.01
153 152 0.97
154 4 0.03
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (153 bp):
CACAAATTTCTAATTGAAATTGGGTTTAGGTGGGAGTTATGACCCCCACTAATTTAGGGTATAAT
AAAAATAAATAAATTAAATGCGACTACACTGTTTTGGACAACAATTTCAATTAGAAATTATGTAA
GCACGATGTTGGTTTCTTTAGTA
Found at i:425967 original size:30 final size:30
Alignment explanation
Indices: 425931--425988 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
425921 GTTTTGTTAC
425931 AACTTATTCAAGACCCTTTGATTATTGCGT
1 AACTTATTCAAGACCCTTTGATTATTGCGT
*
425961 AACTTATTCAAGACCCTTTGATTGTTGC
1 AACTTATTCAAGACCCTTTGATTATTGC
425989 ATTTTGTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (30 bp):
AACTTATTCAAGACCCTTTGATTATTGCGT
Found at i:431927 original size:22 final size:23
Alignment explanation
Indices: 431884--431928 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
431874 AATCTGTATA
*
431884 TTTATTAAATAAAAGTAATATTT
1 TTTAATAAATAAAAGTAATATTT
*
431907 TTTAATAAATATAA-TAATATTT
1 TTTAATAAATAAAAGTAATATTT
431929 ATGGTCGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTAATAAATAAAAGTAATATTT
Found at i:436770 original size:22 final size:22
Alignment explanation
Indices: 436742--436786 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
436732 CTATCATGTA
*
436742 ATTAATACACTAACATTAACCT
1 ATTAATACACTAACACTAACCT
*
436764 ATTAATATACTAACACTAACCT
1 ATTAATACACTAACACTAACCT
436786 A
1 A
436787 AAACATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (22 bp):
ATTAATACACTAACACTAACCT
Found at i:442628 original size:21 final size:22
Alignment explanation
Indices: 442604--442651 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
442594 ACCCGACCCG
442604 AAATAATATATTTATT-AAAAA
1 AAATAATATATTTATTCAAAAA
* * *
442625 AAATATTATTTTTATTCAATAA
1 AAATAATATATTTATTCAAAAA
442647 AAATA
1 AAATA
442652 GGGATTTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAATATATTTATTCAAAAA
Found at i:443201 original size:29 final size:29
Alignment explanation
Indices: 443159--443272 Score: 192
Period size: 29 Copynumber: 3.9 Consensus size: 29
443149 GAATGAGTTG
* * * *
443159 AGTCTATGTTTATCTCAAACAAAAGCCTT
1 AGTCGATGTTTATCTCAAACTACAGCCCT
443188 AGTCGATGTTTATCTCAAACTACAGCCCT
1 AGTCGATGTTTATCTCAAACTACAGCCCT
443217 AGTCGATGTTTATCTCAAACTACAGCCCT
1 AGTCGATGTTTATCTCAAACTACAGCCCT
443246 AGTCGATGTTTATCTCAAACTACAGCC
1 AGTCGATGTTTATCTCAAACTACAGCC
443273 TTAGCCTTAG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (29 bp):
AGTCGATGTTTATCTCAAACTACAGCCCT
Found at i:444012 original size:16 final size:16
Alignment explanation
Indices: 443993--444026 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
443983 CAATATACGA
443993 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
444009 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
444025 AT
1 AT
444027 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:444100 original size:16 final size:18
Alignment explanation
Indices: 444068--444101 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
444058 TATTAATGTA
444068 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
444086 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
444102 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:444775 original size:130 final size:130
Alignment explanation
Indices: 444571--444818 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
444561 AATTTTCTTC
* *
444571 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
444636 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
444701 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
444766 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
444819 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:445263 original size:35 final size:35
Alignment explanation
Indices: 445215--445288 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
445205 TTGAATTTAG
* *
445215 TTGAATTATTTTGGAATTTAGGGTTTAGAATGAAA
1 TTGAATTACTTTGGAAATTAGGGTTTAGAATGAAA
*
445250 TTGAATTACTTTGGAAATTGGGGTTTAGAATGAAA
1 TTGAATTACTTTGGAAATTAGGGTTTAGAATGAAA
445285 TTGA
1 TTGA
445289 GGACTGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.01, G:0.24, T:0.41
Consensus pattern (35 bp):
TTGAATTACTTTGGAAATTAGGGTTTAGAATGAAA
Found at i:446325 original size:19 final size:19
Alignment explanation
Indices: 446257--446337 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
446247 TTAAATAACT
446257 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
446276 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
446295 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
446315 TTATTAATAAT-TTAGTAA
1 TTATTAATAATATTATTAA
446333 -TATTA
1 TTATTA
446338 TTTCTATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:446360 original size:27 final size:26
Alignment explanation
Indices: 446288--446362 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 26
446278 ATTATATTAA
446288 TATTAAA-TATATAAATAATATTATTC
1 TATTAAATTA-ATAAATAATATTATTC
446314 -ATT--ATTAATAATTTAGTAATATTATTTC
1 TATTAAATTAATAA---A-TAATATTA-TTC
446342 TATTAAATTAATAAATAATAT
1 TATTAAATTAATAAATAATAT
446363 AAATTTATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 17
0.70 0.00 0.30
Matches are distributed among these distances:
23 5 0.12
24 2 0.05
25 3 0.08
26 1 0.03
27 14 0.35
28 4 0.10
29 3 0.08
31 8 0.20
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (26 bp):
TATTAAATTAATAAATAATATTATTC
Found at i:446409 original size:21 final size:22
Alignment explanation
Indices: 446348--446409 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
446338 TTTCTATTAA
446348 ATTAATAA-ATAATATAA-ATTT
1 ATTAATAATATAATATAATA-TT
* *
446369 ATTAATAATTTATTAT-ATATT
1 ATTAATAATATAATATAATATT
446390 ATTAA-AATATAATATAATAT
1 ATTAATAATATAATATAATAT
446410 CTTATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 8 0.24
21 20 0.59
22 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTAATAATATAATATAATATT
Found at i:446423 original size:23 final size:23
Alignment explanation
Indices: 446397--446450 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
446387 ATTATTAAAA
*
446397 TATAATATAATAT-CTTATATTAT
1 TATAATATAAT-TGATTATATTAT
*
446420 TATAATATAATTGATTATTTTAT
1 TATAATATAATTGATTATATTAT
446443 TATAATAT
1 TATAATAT
446451 TAAAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TATAATATAATTGATTATATTAT
Found at i:446431 original size:53 final size:53
Alignment explanation
Indices: 446373--446477 Score: 124
Period size: 53 Copynumber: 2.0 Consensus size: 53
446363 AAATTTATTA
* * *
446373 ATAATTTATTATATATTATTAAAATA-T-AATATAATATCTTATATTATTATAAT
1 ATAATTGATTAT-T-TTATTAAAATATTAAAAATAATATATTATATTATTATAAT
* * *
446426 ATAATTGATTATTTTATTATAATATTAAAAATATTGTATTATATTATTATAA
1 ATAATTGATTATTTTATTAAAATATTAAAAATAATATATTATATTATTATAA
446478 ATATTAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
51 10 0.23
52 2 0.05
53 32 0.73
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (53 bp):
ATAATTGATTATTTTATTAAAATATTAAAAATAATATATTATATTATTATAAT
Found at i:446442 original size:28 final size:28
Alignment explanation
Indices: 446378--446497 Score: 79
Period size: 28 Copynumber: 4.3 Consensus size: 28
446368 TATTAATAAT
*
446378 TTATTATATATTATTAAAATATAATATA
1 TTATTTTATATTATTAAAATATAATATA
* * *
446406 ATATCTTATATTATTATAATATAAT-TGA
1 TTATTTTATATTATTAAAATATAATAT-A
* *
446434 TTA-TTT-TATTA-TAATAT-TAAAAATA
1 TTATTTTATATTATTAAAATAT-AATATA
* * *
446459 TTGTATTATATTATTATAAATATTAATAAA
1 TTATTTTATATTATTA-AAATA-TAATATA
446489 TATATTTTA
1 T-TATTTTA
446498 AATATTTTAA
Statistics
Matches: 66, Mismatches: 16, Indels: 17
0.67 0.16 0.17
Matches are distributed among these distances:
24 1 0.02
25 9 0.14
26 8 0.12
27 8 0.12
28 26 0.39
29 3 0.05
30 5 0.08
31 6 0.09
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52
Consensus pattern (28 bp):
TTATTTTATATTATTAAAATATAATATA
Found at i:446465 original size:22 final size:22
Alignment explanation
Indices: 446435--446482 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
446425 TATAATTGAT
*
446435 TATTTTATTATAATATTAAAAA
1 TATTGTATTATAATATTAAAAA
* *
446457 TATTGTATTATATTATTATAAA
1 TATTGTATTATAATATTAAAAA
446479 TATT
1 TATT
446483 AATAAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TATTGTATTATAATATTAAAAA
Found at i:447937 original size:12 final size:12
Alignment explanation
Indices: 447922--447956 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
447912 TCTGGCCTGA
447922 TTAAAAGCCTAT
1 TTAAAAGCCTAT
* *
447934 TTAAAAGCTTGT
1 TTAAAAGCCTAT
447946 TTAAAAGCCTA
1 TTAAAAGCCTA
447957 ATTTTTAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (12 bp):
TTAAAAGCCTAT
Found at i:449150 original size:3 final size:3
Alignment explanation
Indices: 449142--449236 Score: 100
Period size: 3 Copynumber: 29.0 Consensus size: 3
449132 ATAAAAAATC
*
449142 AAT AAT AAT AAT AAT AAT AGAT AAT AGAT AAT AAT ATT AACT AAAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AA-T -AAT AAT
*
449191 AAT AAT AAT AGAT AAT AAT AAT ATT AAAT AAGT AAAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT -AAT AA-T -AAT AAT AAT AAT
449237 TTATAAATCC
Statistics
Matches: 80, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
3 61 0.76
4 15 0.19
5 4 0.05
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:449189 original size:40 final size:40
Alignment explanation
Indices: 449145--449236 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 40
449135 AAAAATCAAT
*
449145 AATAATAATAATAATAGATAATAGATAATAAT-ATTAACTA
1 AATAATAATAATAATAGATAATA-ATAATAATAAATAACTA
* *
449185 AATAATAATAATAATAGATAATAATAATATTAAATAAGTA
1 AATAATAATAATAATAGATAATAATAATAATAAATAACTA
449225 AATAATAATAAT
1 AATAATAATAAT
449237 TTATAAATCC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
39 7 0.15
40 41 0.85
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (40 bp):
AATAATAATAATAATAGATAATAATAATAATAAATAACTA
Found at i:449209 original size:43 final size:40
Alignment explanation
Indices: 449142--449236 Score: 129
Period size: 43 Copynumber: 2.3 Consensus size: 40
449132 ATAAAAAATC
449142 AATAATAATAATAATAATAGATAATAGATAATAATATTAACTA
1 AATAATAATAATAATAATAGATAATA-ATAATAA-A-TAACTA
* *
449185 AATAATAATAATAATAGATA-ATAATAATATTAAATAAGTA
1 AATAATAATAATAATA-ATAGATAATAATAATAAATAACTA
449225 AATAATAATAAT
1 AATAATAATAAT
449237 TTATAAATCC
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
40 17 0.35
41 1 0.02
42 6 0.12
43 22 0.45
44 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (40 bp):
AATAATAATAATAATAATAGATAATAATAATAAATAACTA
Found at i:450347 original size:21 final size:21
Alignment explanation
Indices: 450308--450350 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
450298 ACCATATACA
* * *
450308 ATATATATATTTTTGTATTAT
1 ATATATATATATATATATTAT
450329 ATATATATATATATATATTAT
1 ATATATATATATATATATTAT
450350 A
1 A
450351 CAAAGTCAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATATATATATATATATTAT
Found at i:454272 original size:20 final size:19
Alignment explanation
Indices: 454244--454286 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
454234 AATCTAAAAA
*
454244 AAAAT-TAT-TTTTATTTT
1 AAAATATATATTTTATATT
454261 AAAATATATATTTTATATT
1 AAAATATATATTTTATATT
454280 AAAATAT
1 AAAATAT
454287 TTTGAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 15 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAAATATATATTTTATATT
Found at i:454343 original size:22 final size:23
Alignment explanation
Indices: 454301--454345 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
454291 AAATTAAGTA
454301 AAATATATTTAATATATTTTTAT
1 AAATATATTTAATATATTTTTAT
*
454324 AAATAT-TTTATTATTATTTTTA
1 AAATATATTTAATA-TATTTTTA
454346 CTTTTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
AAATATATTTAATATATTTTTAT
Found at i:454376 original size:30 final size:30
Alignment explanation
Indices: 454324--454397 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 30
454314 ATATTTTTAT
*
454324 AAATATTTTATTATTA-TTTTTACTTTTCA
1 AAATATATTATTATTATTTTTTACTTTTCA
454353 AAATATATTATTATTATTTTTTACTTTTCA
1 AAATATATTATTATTATTTTTTACTTTTCA
454383 AAATATA-TATT-TTAT
1 AAATATATTATTATTAT
454398 CTTAATTTAC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
28 4 0.09
29 19 0.44
30 20 0.47
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (30 bp):
AAATATATTATTATTATTTTTTACTTTTCA
Found at i:454443 original size:30 final size:31
Alignment explanation
Indices: 454408--454469 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
454398 CTTAATTTAC
*
454408 TAAATATATTATATTATTACTTTC-AAATAT
1 TAAATATATTATATTATTAATTTCAAAATAT
* *
454438 TAAATATATTTTATTCTTAATTTCAAAATAT
1 TAAATATATTATATTATTAATTTCAAAATAT
454469 T
1 T
454470 TTGAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (31 bp):
TAAATATATTATATTATTAATTTCAAAATAT
Found at i:460159 original size:23 final size:26
Alignment explanation
Indices: 460104--460180 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
460094 TAAATACAAT
*
460104 AAATAATATTATTTATCATAAA-ACTTA
1 AAATAAT-TTATTTATTATAAATA-TTA
*
460131 ATATAA-TTATTT-TTA-AAATATTA
1 AAATAATTTATTTATTATAAATATTA
460154 AAATAATTTATTTATTATTAAATATTA
1 AAATAATTTATTTATTA-TAAATATTA
460181 TCTTTATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
23 11 0.26
24 9 0.21
25 9 0.21
27 13 0.31
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
AAATAATTTATTTATTATAAATATTA
Found at i:460252 original size:31 final size:31
Alignment explanation
Indices: 460145--460253 Score: 83
Period size: 31 Copynumber: 3.7 Consensus size: 31
460135 AATTATTTTT
*
460145 AAAATATTAAAATAATT-TA-TTTATT-AT-
1 AAAATATTAATATAATTATATTTTATTAATA
* *
460172 TAAATATT-ATCT--TTATAATTTTATTAATA
1 AAAATATTAATATAATTAT-ATTTTATTAATA
* *
460201 AAAATATTAATATTAGTATATTTTATTGAAATA
1 AAAATATTAATATAATTATATTTTATT--AATA
460234 AAAATATT-ATA-AATTATATT
1 AAAATATTAATATAATTATATT
460254 AATTATTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
24 2 0.03
25 1 0.02
26 3 0.05
27 13 0.20
28 2 0.03
29 7 0.11
30 3 0.05
31 15 0.23
32 6 0.09
33 12 0.19
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (31 bp):
AAAATATTAATATAATTATATTTTATTAATA
Found at i:460313 original size:23 final size:23
Alignment explanation
Indices: 460283--460334 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
460273 AGTGTTATAT
460283 TATATTTTAAAAATATTAATTAA
1 TATATTTTAAAAATATTAATTAA
* * *
460306 TATATTTTAAATATCTTTATTAA
1 TATATTTTAAAAATATTAATTAA
*
460329 AATATT
1 TATATT
460335 ATTATATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAA
Found at i:461883 original size:9 final size:9
Alignment explanation
Indices: 461869--461895 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
461859 ATAGAGGTAT
461869 CTCTTCTCC
1 CTCTTCTCC
461878 CTCTTCTCC
1 CTCTTCTCC
461887 CTCTTCTCC
1 CTCTTCTCC
461896 TTTTTAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (9 bp):
CTCTTCTCC
Found at i:473530 original size:2 final size:2
Alignment explanation
Indices: 473523--473559 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
473513 GTCCTAAACC
*
473523 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
473560 GAGTTAGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:474785 original size:21 final size:22
Alignment explanation
Indices: 474759--474799 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
474749 CCAGGACAGG
474759 GAGTATCGGTACTT-CTTTAAT
1 GAGTATCGGTACTTCCTTTAAT
*
474780 GAGTATCGGTATTTCCTTTA
1 GAGTATCGGTACTTCCTTTA
474800 TAATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.44
Consensus pattern (22 bp):
GAGTATCGGTACTTCCTTTAAT
Found at i:475015 original size:20 final size:20
Alignment explanation
Indices: 474990--475038 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
474980 TTACCTTTGA
474990 TATCGGTACCACGTGAACAG
1 TATCGGTACCACGTGAACAG
**
475010 TATCGGTATTACGTGAACAG
1 TATCGGTACCACGTGAACAG
475030 TATCGGTAC
1 TATCGGTAC
475039 TATGTACCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (20 bp):
TATCGGTACCACGTGAACAG
Found at i:477614 original size:20 final size:23
Alignment explanation
Indices: 477570--477616 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
477560 TATATTATAA
477570 AAATAAGTTATTTGTGTAGTATT
1 AAATAAGTTATTTGTGTAGTATT
*
477593 AAATAGGTTATTT-T-TA-TATT
1 AAATAAGTTATTTGTGTAGTATT
477613 AAAT
1 AAAT
477617 TTAAATAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 2 0.09
22 1 0.04
23 12 0.52
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (23 bp):
AAATAAGTTATTTGTGTAGTATT
Found at i:483017 original size:29 final size:29
Alignment explanation
Indices: 482979--483042 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
482969 AAATACACGA
*
482979 CAAAATTAGAAGAATAGGAGGGGGAATCC
1 CAAACTTAGAAGAATAGGAGGGGGAATCC
483008 CAAACTTAGAAGAATAGGAGGGGGAATCC
1 CAAACTTAGAAGAATAGGAGGGGGAATCC
483037 CAAACT
1 CAAACT
483043 AAAGGTGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.44, C:0.14, G:0.28, T:0.14
Consensus pattern (29 bp):
CAAACTTAGAAGAATAGGAGGGGGAATCC
Found at i:487183 original size:5 final size:5
Alignment explanation
Indices: 487173--487288 Score: 133
Period size: 5 Copynumber: 23.2 Consensus size: 5
487163 TCAGTAAAAT
* * * * * * *
487173 ATATA ATATA ATATA ATACA ATACA ATACA ATACA ATACA ATACA ATACA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * *
487223 ATACA ATACA ATACA ATACA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
487273 ATATA ATATA ATATA A
1 ATATA ATATA ATATA A
487289 AAAAATAAAA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 109 1.00
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (5 bp):
ATATA
Found at i:487295 original size:15 final size:15
Alignment explanation
Indices: 487247--487305 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
487237 AATACAATAT
* *
487247 AATATAATATAATAT
1 AATATAATATAAAAA
* *
487262 AATATAATATAATAT
1 AATATAATATAAAAA
487277 AATATAATATAAAAA
1 AATATAATATAAAAA
*
487292 AATA-AAAATAAAAA
1 AATATAATATAAAAA
487306 CTTTTACTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 9 0.22
15 32 0.78
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATATAATATAAAAA
Found at i:502170 original size:57 final size:57
Alignment explanation
Indices: 502085--502199 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
502075 CTCGCTTTCT
502085 TTTTCTGGATCTGAGTATGCTTGCCAATGTTACAAATAAATAATTAAGCTATCCTTC
1 TTTTCTGGATCTGAGTATGCTTGCCAATGTTACAAATAAATAATTAAGCTATCCTTC
502142 TTTTCTGGATCTGAGTATGCTTGCCAATGTTACAAATAAATAATTAAGCTATCCTTC
1 TTTTCTGGATCTGAGTATGCTTGCCAATGTTACAAATAAATAATTAAGCTATCCTTC
502199 T
1 T
502200 AAAAAAACAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (57 bp):
TTTTCTGGATCTGAGTATGCTTGCCAATGTTACAAATAAATAATTAAGCTATCCTTC
Found at i:509490 original size:18 final size:17
Alignment explanation
Indices: 509445--509491 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
509435 TTTTTTAAAG
*
509445 AAAATATA-AATATTTT
1 AAAATATATAATATTAT
* *
509461 AAAATTTGTAATATTAT
1 AAAATATATAATATTAT
509478 ACAAATATATAATA
1 A-AAATATATAATA
509492 AGGATAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 6 0.25
17 8 0.33
18 10 0.42
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AAAATATATAATATTAT
Found at i:510020 original size:225 final size:224
Alignment explanation
Indices: 509635--510223 Score: 1008
Period size: 225 Copynumber: 2.6 Consensus size: 224
509625 AATAATTTGG
509635 TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
1 TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
*
509700 ATTAAAAGAATTGAAACATAAATTACATGACTTTAAAAGAAGTATATATCATTTTTATAAAAGTG
66 ATTAAAA-AATTGAAACATAAATTACATAACTTT-AAA-AAGTATATATCATTTTTATAAAAGTG
509765 TACATACTTATTTCACGGTTGAAAACATATTTATTATTATATTTGGTTAATATTATTAAATTTAA
128 T-CATACTTATTTCACGGTTGAAAACATATTTATTATTATATTTGGTTAATATTATTAAATTTAA
509830 ATTCTAAATAATATTTTATAAAATATCAAAACAA
192 ATTCTAAATAATATTTTATAAAATATCAAAA-AA
509864 TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTA-GTGG-AAACATGAAACACT
1 TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
509927 ATTAAAAAATTGAAACATAAATTACATAACTTTCAAAAAGTATATATCATTTTTATAAAAGTGTC
66 ATTAAAAAATTGAAACATAAATTACATAACTTT-AAAAAGTATATATCATTTTTATAAAAGTGTC
* *
509992 TATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGGTTAATATTGTTAAATTTAAAT
130 -ATACTTATTTCACGGTTGAAAACATATTTATTATTATATTTGGTTAATATTATTAAATTTAAAT
510057 TCTAAATAATATTTTATAAAATATCAAAAAA
194 TCTAAATAATATTTTATAAAATATCAAAAAA
* *
510088 TCAAATAATATTTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
1 TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
*
510153 ATTAAATAAATTGAAACATAAATTACATAACTTTAAAAA--A-GTATCATTTTTATAAAAGTGTC
66 ATTAAA-AAATTGAAACATAAATTACATAACTTTAAAAAGTATATATCATTTTTATAAAAGTGT-
510215 CATACTTAT
129 CATACTTAT
510224 AAAAGTAGGT
Statistics
Matches: 348, Mismatches: 7, Indels: 16
0.94 0.02 0.04
Matches are distributed among these distances:
223 28 0.08
224 48 0.14
225 122 0.35
226 53 0.15
227 48 0.14
228 4 0.01
229 45 0.13
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.39
Consensus pattern (224 bp):
TCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACT
ATTAAAAAATTGAAACATAAATTACATAACTTTAAAAAGTATATATCATTTTTATAAAAGTGTCA
TACTTATTTCACGGTTGAAAACATATTTATTATTATATTTGGTTAATATTATTAAATTTAAATTC
TAAATAATATTTTATAAAATATCAAAAAA
Found at i:510209 original size:17 final size:18
Alignment explanation
Indices: 510184--510230 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
510174 ATTACATAAC
* *
510184 TTTAAAAAAGTAT-CATT
1 TTTATAAAAGTATCCATA
*
510201 TTTATAAAAGTGTCCATA
1 TTTATAAAAGTATCCATA
*
510219 CTTATAAAAGTA
1 TTTATAAAAGTA
510231 GGTCTAAGTC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (18 bp):
TTTATAAAAGTATCCATA
Found at i:510504 original size:20 final size:19
Alignment explanation
Indices: 510481--510527 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
510471 CGATATACCA
510481 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
510501 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
510521 GGTAAAA
1 GGTAAAA
510528 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:510670 original size:180 final size:181
Alignment explanation
Indices: 510278--510740 Score: 646
Period size: 180 Copynumber: 2.6 Consensus size: 181
510268 CCGTTTCGTG
* * * *
510278 TCGATCCAAAACGATATAACAGGTAAAACTAGGACAAAACCGGTATA-GAAATGATAAAACCGGT
1 TCGATCC-AAACGATATAACAGGTAAAAATATGATAAAACCGGTA-ACAAAATGATAAAACCGGT
* * * * * *
510342 CAAGCGCTACCGAATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTCGTGAATTT
64 AAAACGATACCGGATATATTTAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTT
* * * *
510407 AAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTAAAAATGTA
129 AAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAAAAAATATA
*
510460 TCGATCCAACACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATAAAACCGGTA
1 TCGATCCAA-ACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATAAAACCGGTA
* * *
510525 AAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTTGTGAATTT-
65 AAACGATACCGGATATATTTAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTA
** *
510588 AAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTAAAAAATATA
130 AAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAAAAAATATA
*
510640 TCGATCCACAACGATATAACA-GTAAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGT
1 TCGATCCA-AACGATATAACAGGT-AAAAATATGATAAAACCGGTAACAAAATGATAAAACCGGT
*
510704 AAAATGATACCGGATATATTTAAAGTGTCGATACTTT
64 AAAACGATACCGGATATATTTAAAGTGTCGATACTTT
510741 CGTAAGTACG
Statistics
Matches: 252, Mismatches: 25, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
179 2 0.01
180 136 0.54
181 30 0.12
182 84 0.33
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (181 bp):
TCGATCCAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATAAAACCGGTAA
AACGATACCGGATATATTTAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTAA
AAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAAAAAATATA
Found at i:510709 original size:17 final size:19
Alignment explanation
Indices: 510670--510712 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
510660 AGTAAAAAAT
510670 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
510690 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
510707 ATGATA
1 ATGATA
510713 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:512805 original size:230 final size:226
Alignment explanation
Indices: 512368--512824 Score: 862
Period size: 230 Copynumber: 2.0 Consensus size: 226
512358 GAATTCAATT
512368 GGGCTGATATATCCATTCGAGATTGATTGAATCAATAATCACCTTTAAAAAGGGCAGCCAGAGAT
1 GGGCTGATATATCCATTCGAGATTGATTGAATCAATAATCACCTTTAAAAAGGGCAGCCAGAGAT
512433 ACCTCAAAGGGTGCATAGCAATCTTAGAGGTAATGAGTTGAATCACTTTTTGTGTTTTTATATAA
66 ACCTCAAAGGGTGCATAGCAATCTTAGAGGTAATGAGTTGAATCACTTTTTGTGTTTTTATATAA
512498 AATATAAATTTATTATAAATGCAGGTTGCACTGTTCGATTTTTGGTCTGGCTGTGAGGCAGTGCC
131 AATATAAATTTATTATAAATGCAGGTTGCACTGTTCGATTTTTGGTCTGGCTGTGAGGCAGTGCC
512563 GGCTTATGAAAGAACCGGAGTGGCACGCATCC
196 GGCTTATGAAAGAACC-GAGTGGCACGCATCC
512595 GGGCTGATATATCCATTCGAGATTGATTGAATCAATAATCACCTTT-AAAAGGGCAGCCAGAGAT
1 GGGCTGATATATCCATTCGAGATTGATTGAATCAATAATCACCTTTAAAAAGGGCAGCCAGAGAT
512659 ACCTCAAAGGGTGCATAGCAATCTTAGAGGTAAATGAGTTGAATCACTTTTTTGTGTTTTTATAT
66 ACCTCAAAGGGTGCATAGCAATCTTAGAGGT-AATGAGTTGAATCAC-TTTTTGTGTTTTTATAT
512724 AAAAATATAAATTTTATTATAAATGCAGGTTGCACTGTTCGATTTTTGGTCTGGCTGTGAGGCAG
129 -AAAATATAAA-TTTATTATAAATGCAGGTTGCACTGTTCGATTTTTGGTCTGGCTGTGAGGCAG
512789 TGCCGGCTTATGAAAGAACCGAGTGGCACGCATCC
192 TGCCGGCTTATGAAAGAACCGAGTGGCACGCATCC
512824 G
1 G
512825 TGCATGGGGG
Statistics
Matches: 226, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
226 49 0.22
227 61 0.27
228 17 0.08
229 26 0.12
230 73 0.32
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (226 bp):
GGGCTGATATATCCATTCGAGATTGATTGAATCAATAATCACCTTTAAAAAGGGCAGCCAGAGAT
ACCTCAAAGGGTGCATAGCAATCTTAGAGGTAATGAGTTGAATCACTTTTTGTGTTTTTATATAA
AATATAAATTTATTATAAATGCAGGTTGCACTGTTCGATTTTTGGTCTGGCTGTGAGGCAGTGCC
GGCTTATGAAAGAACCGAGTGGCACGCATCC
Found at i:513052 original size:15 final size:15
Alignment explanation
Indices: 513032--513060 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
513022 GTTGTATTGG
513032 GGGATGACGGTGAGT
1 GGGATGACGGTGAGT
513047 GGGATGACGGTGAG
1 GGGATGACGGTGAG
513061 GGAAAATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.55, T:0.17
Consensus pattern (15 bp):
GGGATGACGGTGAGT
Found at i:513168 original size:20 final size:21
Alignment explanation
Indices: 513142--513193 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
513132 AAGACAATCA
*
513142 AGAGTCGAAGAGAAACT-GAT
1 AGAGTCGAAGAGAAACTCGAG
* *
513162 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
513183 AGAGTCGAAGA
1 AGAGTCGAAGA
513194 TACACTTGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.40, C:0.13, G:0.33, T:0.13
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:513281 original size:33 final size:33
Alignment explanation
Indices: 513239--513304 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
513229 AAATAGATGG
*
513239 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
513272 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
513305 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:515091 original size:18 final size:19
Alignment explanation
Indices: 515047--515094 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
515037 AATGTAGGGT
515047 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
515066 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
515085 T-ATTTTGTAT
1 TAATTTTGTAT
515095 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:516323 original size:191 final size:196
Alignment explanation
Indices: 515212--516732 Score: 2431
Period size: 191 Copynumber: 7.9 Consensus size: 196
515202 CAATATGGCC
* * * *
515212 AACAGGGTGAACCCATAAA--GTCGATCCATATAT-AAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
* * * * *
515274 TC-AAAGTATAATGT-A-ATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAAA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTTATGAGA
*
515336 AAATATGTCTAAATAATGTGTCGACACTAATATAG-TTGTGTCGATATTTCTTTTCCAGAATGAA
130 TAATATGT-TAAATAATGTGTCGA-ACTAATATAGTTTGTGTCGATATTT-TTTTCCAGAATGAA
515400 TGGAA
192 TGGAA
515405 AACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
515468 CAAAAG--T-A--T--TATGTAATTTTTCAATCTAACCGGTACAATTATACATGTTTTATGAGAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTTATGAGAT
*
515526 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATAAATG
131 AATATGT-TAAATAATGTGTCGA-ACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
515591 GAA
194 GAA
*
515594 AATAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
515659 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTG-TTTATGAGAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTTATGAGAT
515723 AATATGTATAAAT-ATGTGTCGACACTAATATAGTTTGTGTCGAT-TTTTTTTCCAGAATGAATG
131 AATATGT-TAAATAATGTGTCGA-ACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
515786 GAA
194 GAA
515789 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
515854 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACATGTTTTATGAGAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTTATGAGAT
515919 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTCTTTTCCAGAATGAAT
131 AATATGT-TAAATAATGTGTCGA-ACTAATATAGTTTGTGTCGATATTT-TTTTCCAGAATGAAT
515984 GGAA
193 GGAA
*
515988 AACAGGGTGCACCCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
516053 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACATGTTTTATGAGAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTTATGAGAT
516118 AATATG-TAAATAATGTGTCG-ACTAA-ATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGA
131 AATATGTTAAATAATGTGTCGAACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGA
516180 A
196 A
516181 AACAGGGTGCACCC-TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
516245 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTTATGAGAC
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTTATGAGAT
516309 AATATG-TAAATAATGTGTCGACACT-A-ATAGTTT-TGTCGATA-TTTTTTCCAGAATGAATGG
131 AATATGTTAAATAATGTGTCGA-ACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGG
516369 AA
195 AA
516371 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
516436 CAAAAGTATAATGTAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTTATGAGAT
*
516500 AATATATATAAA-AATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCC---A-GAATG
131 AATATGT-TAAATAATGTGTCGA-ACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
516559 GAA
194 GAA
516562 AACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
516625 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTTATGAGAT
516690 AATATGTATAAATAA--TGTCGACACT-ATATAGTTTGTGTCGATA
131 AATATGT-TAAATAATGTGTCGA-ACTAATATAGTTTGTGTCGATA
516733 CTAATTTAAA
Statistics
Matches: 1272, Mismatches: 26, Indels: 65
0.93 0.02 0.05
Matches are distributed among these distances:
188 18 0.01
189 195 0.15
190 96 0.08
191 259 0.20
192 101 0.08
193 67 0.05
194 54 0.04
195 167 0.13
196 54 0.04
197 67 0.05
198 40 0.03
199 154 0.12
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (196 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTTATGAGAT
AATATGTTAAATAATGTGTCGAACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGA
A
Found at i:516393 original size:582 final size:586
Alignment explanation
Indices: 515212--516732 Score: 2528
Period size: 582 Copynumber: 2.6 Consensus size: 586
515202 CAATATGGCC
* * * *
515212 AACAGGGTGAACCCATAAA--GTCGATCCATATAT-AAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
* * * *
515274 TC-AAAGTATAATGT-A-ATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAAA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
515336 AAATATGTCTAAATAATGTGTCGACACTAATATAG-TTGTGTCGATATTTCTTTTCCAGAATGAA
130 TAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTCTTTTCCAGAATGAA
515400 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGA
195 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGA
515465 ACCCAAAAG--T-A--T--TATGTAATTTTTCAATCTAACCGGTACAATTATACATGTTTTATGA
260 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACATGTTTTATGA
515523 GATAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATAA
325 GATAATATGT-TAAATAATGTGTCG--ACTAA-ATAGTTTGTGTCGATATTTTTTTCCAGAATAA
*
515588 ATGGAAAATAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
386 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
515653 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTAT
451 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTAT
* *
515718 GAGATAATATGTATAAATATGTGTCGACACTAATATAGTTTGTGTCGATTTTTTTTCCAGAATGA
516 GAGACAATATGTATAAATATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCAGAATGA
515783 ATGGAA
581 ATGGAA
515789 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
**
515854 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACATGTTTTATGAGAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAT
515919 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTCTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTCTTTTCCAGAATGAAT
*
515984 GGAAAACAGGGTGCACCCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCG
516049 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACATGTTTTATG
259 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACATGTTTTATG
*
516114 AGATAATATG-TAAATAATGTGTCGACTAAATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
324 AGATAATATGTTAAATAATGTGTCGACTAAATAGTTTGTGTCGATATTTTTTTCCAGAATAAATG
516178 GAAAACAGGGTGCACCC-TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
389 GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
516242 ACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTTATGA
454 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTG-TTTATGA
516306 GACAATATG--TAAATAATGTGTCGACACT-A-ATAGTTT-TGTCGATATTTTTTCCAGAATGAA
518 GACAATATGTATAAAT-ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCAGAATGAA
516366 TGGAA
582 TGGAA
516371 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
516436 CAAAAGTATAATGTAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAT
* *
516500 AATATATATAAA-AATGTGTCGACACTAATATAGTTTGTGTCGATA-TT-TTTTCC---A-GAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTCTTTTCCAGAATGAAT
516558 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAA
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAA
**
516623 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
261 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACATGTTTTATGAG
* *
516688 ATAATATGTATAAATAATGTCGAC-ACTATATAGTTTGTGTCGATA
326 ATAATATGT-TAAATAATGT-GTCGACTAAATAGTTTGTGTCGATA
516733 CTAATTTAAA
Statistics
Matches: 898, Mismatches: 25, Indels: 45
0.93 0.03 0.05
Matches are distributed among these distances:
572 103 0.11
574 66 0.07
575 3 0.00
577 18 0.02
578 6 0.01
579 19 0.02
580 68 0.08
581 45 0.05
582 197 0.22
583 69 0.08
584 6 0.01
585 105 0.12
586 66 0.07
587 51 0.06
588 6 0.01
590 15 0.02
592 55 0.06
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (586 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAT
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTCTTTTCCAGAATGAAT
GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAA
CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACATGTTTTATGAG
ATAATATGTTAAATAATGTGTCGACTAAATAGTTTGTGTCGATATTTTTTTCCAGAATAAATGGA
AAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAC
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCTGTTTATGAGAC
AATATGTATAAATATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCAGAATGAATGGA
A
Found at i:518094 original size:12 final size:12
Alignment explanation
Indices: 518077--518180 Score: 100
Period size: 12 Copynumber: 8.4 Consensus size: 12
518067 CGTCGCAGAA
*
518077 GATGAAGCTGAC
1 GATGAAGATGAC
518089 GATGAAGATGAC
1 GATGAAGATGAC
*
518101 GATGATGATGAC
1 GATGAAGATGAC
* *
518113 GATGAAGCTGGC
1 GATGAAGATGAC
518125 GATGAAGATGATGAC
1 GATG-A-A-GATGAC
*
518140 GATGATGATGAC
1 GATGAAGATGAC
* *
518152 GATGATGATGAT
1 GATGAAGATGAC
* *
518164 GATGATGATGAT
1 GATGAAGATGAC
518176 GATGA
1 GATGA
518181 TCCAAACAAG
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
12 69 0.86
13 1 0.01
14 2 0.03
15 8 0.10
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.23
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:518097 original size:18 final size:18
Alignment explanation
Indices: 518074--518135 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
518064 AAGCGTCGCA
518074 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
518092 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
518110 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
518128 GAAGATGA
1 GAAGATGA
518136 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:518098 original size:6 final size:6
Alignment explanation
Indices: 518074--518180 Score: 61
Period size: 6 Copynumber: 17.3 Consensus size: 6
518064 AAGCGTCGCA
* * * * * *
518074 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * *
518122 GGCGAT GAAGAT GATGACGAT GATGAT GACGAT GATGAT GATGAT GATGAT
1 GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
518173 GATGAT GA
1 GAAGAT GA
518181 TCCAAACAAG
Statistics
Matches: 81, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
6 75 0.93
8 1 0.01
9 5 0.06
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.22
Consensus pattern (6 bp):
GAAGAT
Found at i:518109 original size:3 final size:3
Alignment explanation
Indices: 518089--518181 Score: 96
Period size: 3 Copynumber: 31.0 Consensus size: 3
518079 TGAAGCTGAC
* * * * * ** *
518089 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
518137 GAC GAT GAT GAT GAC GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
518182 CCAAACAAGT
Statistics
Matches: 71, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.34, C:0.06, G:0.34, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:519312 original size:20 final size:20
Alignment explanation
Indices: 519287--519325 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
519277 TAATATATTG
*
519287 TAAAGTATCTATCCTTTTTA
1 TAAAGTATCTATACTTTTTA
*
519307 TAAAGTGTCTATACTTTTT
1 TAAAGTATCTATACTTTTT
519326 CCACTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (20 bp):
TAAAGTATCTATACTTTTTA
Found at i:520050 original size:179 final size:179
Alignment explanation
Indices: 519623--520099 Score: 763
Period size: 178 Copynumber: 2.7 Consensus size: 179
519613 CTTTCAACAT
* * *
519623 ATATAAATATACCGGTTTTTTGTGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTTGT
1 ATATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACAC-TTTTAATATTGT
* *
519688 GTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACATT
65 GTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTATCGACATT
519753 TACACATCGGAACCCTAATTATAATGTAATAGATAATTTTGTAATATACCG
129 TACACATCGGAACCCTAATTATAATGTAATAGATAATTTTGTAATATACCG
519804 ATATAAATATA-CGGTTTTATGCA-CGAATAGGTCTACAACCTATATCGACACTTTTAATATTGT
1 ATATAAATATACCGGTTTTATG-AGCGAATAGGTCTACAACCTATATCGACACTTTTAATATTGT
*
519867 GTCGGTACTTTATGTCCATA-TGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACATT
65 GTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTATCGACATT
519931 TACACATCGGAACCC-AGATTTATAATGTAATAG-TAATTTTGTAATA-ACCG
129 TACACATCGGAACCCTA-A-TTATAATGTAATAGATAATTTTGTAATATACCG
*
519981 GTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGT
1 ATATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTT-TAATATTGT
520046 GTCGGTACTTTATGTCCAGATTGGAAG--AAATGTGTCGATACCATTTAAAAAAGT
65 GTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGT
520100 GTCGGTAATT
Statistics
Matches: 279, Mismatches: 8, Indels: 21
0.91 0.03 0.07
Matches are distributed among these distances:
177 16 0.06
178 133 0.48
179 76 0.27
180 43 0.15
181 11 0.04
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (179 bp):
ATATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTAATATTGTG
TCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTATCGACATTTA
CACATCGGAACCCTAATTATAATGTAATAGATAATTTTGTAATATACCG
Found at i:522588 original size:25 final size:25
Alignment explanation
Indices: 522560--522624 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
522550 TTATCATTAA
522560 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
522585 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
522610 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
522625 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:523001 original size:23 final size:23
Alignment explanation
Indices: 522970--523032 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
522960 ATAGGTAAAC
*
522970 ATATGATGTAATAGGT-TGCGCTT
1 ATATAATGTAATAGGTAT-CGCTT
*
522993 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGCTT
523016 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
523033 GTGGTTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 36 0.97
24 1 0.03
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGCTT
Found at i:523040 original size:23 final size:23
Alignment explanation
Indices: 522970--523042 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
522960 ATAGGTAAAC
* * *
522970 ATATGATGTAATAGGTTGCGCTT
1 ATATAATGTAATAGGTAGTGCTT
*
522993 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
523016 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
523039 ATAT
1 ATAT
523043 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:523486 original size:18 final size:18
Alignment explanation
Indices: 523465--523501 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
523455 GTAATTGGAG
523465 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
523483 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
523501 T
1 T
523502 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:523509 original size:24 final size:24
Alignment explanation
Indices: 523457--523503 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
523447 TTTCATATGT
* *
523457 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
523481 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
523504 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:523813 original size:34 final size:34
Alignment explanation
Indices: 523775--523840 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
523765 AAATCCAAAG
*
523775 CTCATATGGTGCCAAGCAAAAGGAAATCAAAAAT
1 CTCATATGATGCCAAGCAAAAGGAAATCAAAAAT
523809 CTCATATGATGCCAAGCAAAAGGAAATCAAAA
1 CTCATATGATGCCAAGCAAAAGGAAATCAAAA
523841 TCTACAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.48, C:0.18, G:0.17, T:0.17
Consensus pattern (34 bp):
CTCATATGATGCCAAGCAAAAGGAAATCAAAAAT
Found at i:524288 original size:23 final size:23
Alignment explanation
Indices: 524257--524329 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
524247 ATAGGTAAAC
*
524257 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
524280 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
524303 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
524326 ATAT
1 ATAT
524330 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:524960 original size:15 final size:15
Alignment explanation
Indices: 524931--524959 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
524921 GTACTAAACC
524931 TGTTTAACTTTAAAA
1 TGTTTAACTTTAAAA
524946 TGTTTAA-TTTAAAA
1 TGTTTAACTTTAAAA
524960 AGAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (15 bp):
TGTTTAACTTTAAAA
Found at i:529959 original size:28 final size:28
Alignment explanation
Indices: 529923--530001 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 28
529913 AAAAACTAGT
* *
529923 AACCGAGACGAGAAAAAAACCAACTCAC
1 AACCAAGACGAGAAAAAAACCAACACAC
** * *
529951 GCCCAAGACGAGAAAACATAAGCATCACAC
1 AACCAAGACGAGAAAA-A-AACCAACACAC
529981 AACCAAGACGAGAAAAAAACC
1 AACCAAGACGAGAAAAAAACC
530002 TAAGCATCAC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
28 16 0.40
29 2 0.05
30 22 0.55
ACGTcount: A:0.53, C:0.28, G:0.15, T:0.04
Consensus pattern (28 bp):
AACCAAGACGAGAAAAAAACCAACACAC
Found at i:530006 original size:33 final size:33
Alignment explanation
Indices: 529923--530013 Score: 99
Period size: 33 Copynumber: 3.0 Consensus size: 33
529913 AAAAACTAGT
* *
529923 AACCGAGACGAGAAAAAAACC-AA-C-TCACGC
1 AACCAAGACGAGAAAAAAACCTAAGCATCACAC
*
529953 --CCAAGACGAG---AAAACATAAGCATCACAC
1 AACCAAGACGAGAAAAAAACCTAAGCATCACAC
529981 AACCAAGACGAGAAAAAAACCTAAGCATCACAC
1 AACCAAGACGAGAAAAAAACCTAAGCATCACAC
530014 CTAGGGCTCC
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
25 5 0.10
26 2 0.04
27 1 0.02
28 14 0.29
30 10 0.20
33 17 0.35
ACGTcount: A:0.52, C:0.29, G:0.14, T:0.05
Consensus pattern (33 bp):
AACCAAGACGAGAAAAAAACCTAAGCATCACAC
Found at i:535340 original size:21 final size:21
Alignment explanation
Indices: 535316--535374 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
535306 GTACTAAAGC
*
535316 TTTTCATATTTGTTTTCTTTT-
1 TTTTCAT-TTTGCTTTCTTTTA
535337 TTTTCACTTTTGCTTTCTTTTA
1 TTTTCA-TTTTGCTTTCTTTTA
535359 TGTTTCATTTT-CTTTC
1 T-TTTCATTTTGCTTTC
535375 AGCAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 23 0.68
22 6 0.18
23 5 0.15
ACGTcount: A:0.08, C:0.15, G:0.05, T:0.71
Consensus pattern (21 bp):
TTTTCATTTTGCTTTCTTTTA
Found at i:540666 original size:31 final size:32
Alignment explanation
Indices: 540602--540679 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 32
540592 CGGTAAAGTC
* *
540602 AATGACCATTTAGTACCAGTTAGATAAAATTT
1 AATGACCATTTTGTAACAGTTAGATAAAATTT
* *
540634 AATGATCATTTTGTAACAGTTTGAT-AAATTT
1 AATGACCATTTTGTAACAGTTAGATAAAATTT
540665 AATGACCA-TTTGTAA
1 AATGACCATTTTGTAA
540680 TTTTTTAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 7 0.17
31 13 0.32
32 21 0.51
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (32 bp):
AATGACCATTTTGTAACAGTTAGATAAAATTT
Found at i:544744 original size:3 final size:3
Alignment explanation
Indices: 544736--544764 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
544726 TATTCTTATA
544736 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
544765 CTACATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:551652 original size:16 final size:17
Alignment explanation
Indices: 551622--551661 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
551612 TCCGTATCCG
551622 ATCCGAAAAAATCGGAT
1 ATCCGAAAAAATCGGAT
*
551639 ATCC-AAAAATTCGGAT
1 ATCCGAAAAAATCGGAT
551655 ATCCGAA
1 ATCCGAA
551662 TATCCGAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (17 bp):
ATCCGAAAAAATCGGAT
Found at i:558438 original size:18 final size:19
Alignment explanation
Indices: 558409--558445 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
558399 TATGTCTCTC
558409 TCTCTCACTGAAAATTGTT
1 TCTCTCACTGAAAATTGTT
*
558428 TCTCT-ACTGAAACTTGTT
1 TCTCTCACTGAAAATTGTT
558446 GATCACACTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (19 bp):
TCTCTCACTGAAAATTGTT
Found at i:569265 original size:18 final size:18
Alignment explanation
Indices: 569242--569304 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
569232 TTATAAATAT
569242 ATTATTAAAATATTGAAA
1 ATTATTAAAATATTGAAA
* *
569260 ATTATTAGAGTATTTGTAAA
1 ATTATTAAAATA-TTG-AAA
569280 ATTATTAAAATAATT-AAA
1 ATTATTAAAAT-ATTGAAA
*
569298 AATATTA
1 ATTATTA
569305 TAAAATAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 19 0.51
19 3 0.08
20 14 0.38
21 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.41
Consensus pattern (18 bp):
ATTATTAAAATATTGAAA
Found at i:569320 original size:15 final size:17
Alignment explanation
Indices: 569295--569338 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
569285 TAAAATAATT
569295 AAAAATATTATAAA-AT-
1 AAAAAT-TTATAAATATA
*
569311 AATAATTTATAAATATA
1 AAAAATTTATAAATATA
569328 AAAAATTTATA
1 AAAAATTTATA
569339 TCCAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 7 0.29
17 10 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAATTTATAAATATA
Done.