Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000893.1 Hibiscus syriacus cultivar Beakdansim tig00001750_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: 734264
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 3
Found at i:513067 original size:40 final size:40
Alignment explanation
Indices: 513020--513132 Score: 162
Period size: 36 Copynumber: 2.9 Consensus size: 40
513010 TTTGTATCGT
513020 TTCACTACTCTTTCATGAAGGTTGGATTACATTGCTTTAC
1 TTCACTACTCTTTCATGAAGGTTGGATTACATTGCTTTAC
** *
513060 TTCACTACTCTTTTGTGAAGGTTAGATT---TT-CTTTAC
1 TTCACTACTCTTTCATGAAGGTTGGATTACATTGCTTTAC
*
513096 TTCACTACTCTTCCATGAAGGTTGGATTACATTGCTT
1 TTCACTACTCTTTCATGAAGGTTGGATTACATTGCTT
513133 CACTACTCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
36 30 0.48
37 2 0.03
39 2 0.03
40 28 0.45
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.44
Consensus pattern (40 bp):
TTCACTACTCTTTCATGAAGGTTGGATTACATTGCTTTAC
Found at i:513077 original size:76 final size:76
Alignment explanation
Indices: 512981--513187 Score: 225
Period size: 76 Copynumber: 2.8 Consensus size: 76
512971 GATTTGTTCC
* *
512981 TACTTCACAACTCTTCTGTGAAGGCT-GAATTTGTAT-CGTTTCACTACTCTTTCATGAAGGTTG
1 TACTTCACAACTCTTCTGTGAAGGCTAGAATTTCTATAC--TTCACTACTCTTCCATGAAGGTTG
513044 GATTACATTGCTT
64 GATTACATTGCTT
* * * * *
513057 TACTTCACTACTCTTTTGTGAAGGTTAGATTTTCTTTACTTCACTACTCTTCCATGAAGGTTGGA
1 TACTTCACAACTCTTCTGTGAAGGCTAGAATTTCTATACTTCACTACTCTTCCATGAAGGTTGGA
513122 TTACATTG---
66 TTACATTGCTT
* * *
513130 --CTTCACTACTCTTCTGTGAAGGCTAAGAATGAT-T-TACTTCACTACTCTTCCGTGAAGG
1 TACTTCACAACTCTTCTGTGAAGGCT-AGAAT-TTCTATACTTCACTACTCTTCCATGAAGG
513188 CTAGATCCAA
Statistics
Matches: 115, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
71 45 0.39
72 5 0.04
73 1 0.01
76 56 0.49
77 7 0.06
78 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (76 bp):
TACTTCACAACTCTTCTGTGAAGGCTAGAATTTCTATACTTCACTACTCTTCCATGAAGGTTGGA
TTACATTGCTT
Found at i:513101 original size:36 final size:36
Alignment explanation
Indices: 513020--513193 Score: 145
Period size: 36 Copynumber: 4.8 Consensus size: 36
513010 TTTGTATCGT
* * *
513020 TTCACTACTCTTTCATGAAGGTTGGATTACATTGCTTTAC
1 TTCACTACTCTTCCGTGAAGGTTAGATT---TT-CTTTAC
**
513060 TTCACTACTCTTTTGTGAAGGTTAGATTTTCTTTAC
1 TTCACTACTCTTCCGTGAAGGTTAGATTTTCTTTAC
* * * * *
513096 TTCACTACTCTTCCATGAAGGTTGGA-TTACATTGC
1 TTCACTACTCTTCCGTGAAGGTTAGATTTTCTTTAC
* * * **
513131 TTCACTACTCTTCTGTGAAGGCTAAGA-ATGATTTAC
1 TTCACTACTCTTCCGTGAAGG-TTAGATTTTCTTTAC
*
513167 TTCACTACTCTTCCGTGAAGGCTAGAT
1 TTCACTACTCTTCCGTGAAGGTTAGAT
513194 CCAAGGTTGG
Statistics
Matches: 110, Mismatches: 22, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
35 28 0.25
36 55 0.50
37 2 0.02
40 25 0.23
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (36 bp):
TTCACTACTCTTCCGTGAAGGTTAGATTTTCTTTAC
Found at i:525990 original size:17 final size:17
Alignment explanation
Indices: 525964--526000 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
525954 AACCAGAATT
*
525964 ATAATTATATAATAATA
1 ATAATAATATAATAATA
*
525981 ATAATAATATAATTATA
1 ATAATAATATAATAATA
525998 ATA
1 ATA
526001 TAAAACGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATAATATAATAATA
Found at i:531873 original size:21 final size:21
Alignment explanation
Indices: 531847--531901 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
531837 CTCTACTTAT
531847 AGTATCGATACCCTAAGGTCA
1 AGTATCGATACCCTAAGGTCA
531868 AGTATCGATACCCTAAGGTCA
1 AGTATCGATACCCTAAGGTCA
531889 AGTATCGATACCC
1 AGTATCGATACCC
531902 CTATGAGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (21 bp):
AGTATCGATACCCTAAGGTCA
Found at i:533433 original size:22 final size:23
Alignment explanation
Indices: 533402--533444 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
533392 CATTTTCTCC
**
533402 TTTTTCTTAATTTAAAACAACCA
1 TTTTTCTTAATAAAAAACAACCA
533425 TTTTT-TTAATAAAAAACAAC
1 TTTTTCTTAATAAAAAACAAC
533445 TATAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTTTCTTAATAAAAAACAACCA
Found at i:542626 original size:2 final size:2
Alignment explanation
Indices: 542619--542679 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
542609 CAATTTAATT
542619 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
542661 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
542680 TATTTACAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:545216 original size:14 final size:14
Alignment explanation
Indices: 545188--545246 Score: 79
Period size: 14 Copynumber: 4.3 Consensus size: 14
545178 TTGGAGTACA
545188 AAAAGAA-AGAAAAG
1 AAAAGAAGA-AAAAG
545202 ATAAA-AAGAAAAAG
1 A-AAAGAAGAAAAAG
545216 AAAAGAAGAAAAAG
1 AAAAGAAGAAAAAG
545230 AAAAGAAG-AAAAG
1 AAAAGAAGAAAAAG
545243 AAAA
1 AAAA
545247 AGAAATTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.29
14 26 0.62
15 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAGAAGAAAAAG
Found at i:545217 original size:19 final size:18
Alignment explanation
Indices: 545187--545251 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 18
545177 ATTGGAGTAC
* *
545187 AAAAAG-AAAGAAAAGAT
1 AAAAAGAAAAGAAAAAAG
545204 AAAAAGAAAAAGAAAAGAAG
1 AAAAAG-AAAAGAAAA-AAG
545224 AAAAAGAAAAGAAGAAAAG
1 AAAAAGAAAAGAA-AAAAG
545243 AAAAAGAAA
1 AAAAAGAAA
545252 TTCAAAAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.14
19 27 0.64
20 9 0.21
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAAG
Found at i:545224 original size:8 final size:8
Alignment explanation
Indices: 545213--545244 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
545203 TAAAAAGAAA
545213 AAGAAAAG
1 AAGAAAAG
545221 AAG-AAA-
1 AAGAAAAG
545227 AAGAAAAG
1 AAGAAAAG
545235 AAGAAAAG
1 AAGAAAAG
545243 AA
1 AA
545245 AAAGAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 3 0.14
7 6 0.27
8 13 0.59
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AAGAAAAG
Found at i:549533 original size:19 final size:20
Alignment explanation
Indices: 549513--549548 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
549503 CTTTATTTAT
549513 TTTA-TTTCATT-CTTATTA
1 TTTATTTTCATTACTTATTA
549531 TTTATTTTCATTACTTAT
1 TTTATTTTCATTACTTAT
549549 ATTATTATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 7 0.44
20 5 0.31
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTTCATTACTTATTA
Found at i:549551 original size:19 final size:17
Alignment explanation
Indices: 549509--549551 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
549499 TATCCTTTAT
549509 TTAT-TTTATTTCATTC
1 TTATATTTATTTCATTC
549525 TTATTATTTATTTTCATTAC
1 TTA-TATTTA-TTTCATT-C
549545 TTATATT
1 TTATATT
549552 ATTATCCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.13
17 1 0.04
18 4 0.17
19 11 0.48
20 4 0.17
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATTTATTTCATTC
Found at i:553464 original size:2 final size:2
Alignment explanation
Indices: 553457--553505 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
553447 TCGACTTAAT
553457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
553499 TA TA TA T
1 TA TA TA T
553506 TATTTATGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:559873 original size:8 final size:8
Alignment explanation
Indices: 559860--559888 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
559850 GGTCGAGATT
559860 TTTTTTTC
1 TTTTTTTC
559868 TTTTTTTC
1 TTTTTTTC
559876 TTTTTTTC
1 TTTTTTTC
559884 TTTTT
1 TTTTT
559889 GAAAGGTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTC
Found at i:560253 original size:57 final size:57
Alignment explanation
Indices: 560179--560374 Score: 347
Period size: 57 Copynumber: 3.4 Consensus size: 57
560169 TATTAATATT
560179 TTAAAATAATATATTTTATAATAATATATTTATAATTATTTATTATATTTTAAACTA
1 TTAAAATAATATATTTTATAATAATATATTTATAATTATTTATTATATTTTAAACTA
* *
560236 TTAAATTAATATATTTTATAATAATATATTTATAATTATTTTTTATATTTTAAACTA
1 TTAAAATAATATATTTTATAATAATATATTTATAATTATTTATTATATTTTAAACTA
*
560293 TTAAAATAATGTATTTTATAATAATATATTTATAATTATTTATTATATTTTAAACTA
1 TTAAAATAATATATTTTATAATAATATATTTATAATTATTTATTATATTTTAAACTA
* *
560350 TTAAAATAATGTATTTTGTAATAAT
1 TTAAAATAATATATTTTATAATAAT
560375 TTAAATATTT
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 133 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (57 bp):
TTAAAATAATATATTTTATAATAATATATTTATAATTATTTATTATATTTTAAACTA
Found at i:560262 original size:15 final size:15
Alignment explanation
Indices: 560174--560328 Score: 96
Period size: 15 Copynumber: 10.8 Consensus size: 15
560164 GAATATATTA
*
560174 ATATTTTAAAATAAT
1 ATATTTTATAATAAT
560189 ATATTTTATAATAAT
1 ATATTTTATAATAAT
*
560204 ATA-TTTATAATTAT
1 ATATTTTATAATAAT
* * **
560218 TTATTATATTTTAA-
1 ATATTTTATAATAAT
560232 ACTA--TTA-AATTAAT
1 A-TATTTTATAA-TAAT
560246 ATATTTTATAATAAT
1 ATATTTTATAATAAT
560261 ATA-TTTATAAT--T
1 ATATTTTATAATAAT
* **
560273 ATTTTTTAT-ATTTT
1 ATATTTTATAATAAT
* * *
560287 AAACTATTAAAATAAT
1 ATA-TTTTATAATAAT
*
560303 GTATTTTATAATAAT
1 ATATTTTATAATAAT
560318 ATA-TTTATAAT
1 ATATTTTATAAT
560329 TATTTATTAT
Statistics
Matches: 105, Mismatches: 23, Indels: 25
0.69 0.15 0.16
Matches are distributed among these distances:
12 5 0.05
13 12 0.11
14 31 0.30
15 51 0.49
16 6 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (15 bp):
ATATTTTATAATAAT
Found at i:560391 original size:18 final size:18
Alignment explanation
Indices: 560361--560418 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 18
560351 TAAAATAATG
560361 TATTTTGTAATAATTTAAA
1 TATTTT-TAATAATTTAAA
*
560380 TATTTTTAATAATTAAAGAA
1 TATTTTTAATAATT-TA-AA
*
560400 TATATTTTAATAATATAAA
1 TAT-TTTTAATAATTTAAA
560419 AATAAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.24
19 9 0.27
20 6 0.18
21 10 0.30
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (18 bp):
TATTTTTAATAATTTAAA
Found at i:560406 original size:22 final size:21
Alignment explanation
Indices: 560377--560422 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
560367 GTAATAATTT
560377 AAATAT-TTTTAATAAT-TAA
1 AAATATATTTTAATAATATAA
560396 AGAATATATTTTAATAATATAA
1 A-AATATATTTTAATAATATAA
560418 AAATA
1 AAATA
560423 AAAATTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.04
20 5 0.21
21 14 0.58
22 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAATATATTTTAATAATATAA
Found at i:560656 original size:42 final size:42
Alignment explanation
Indices: 560601--560690 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
560591 AAAAATCCCT
560601 ATAA-TTTTAAATATTATATATATGTATAAAAAGATAAAATA
1 ATAATTTTTAAATATTATATATATGTATAAAAAGATAAAATA
560642 ATAATTTTTAAATATTATATATATGTATAAAAAGATAAAATA
1 ATAATTTTTAAATATTATATATATGTATAAAAAGATAAAATA
*
560684 AAAATTT
1 ATAATTT
560691 ATAAGGGTCG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (42 bp):
ATAATTTTTAAATATTATATATATGTATAAAAAGATAAAATA
Found at i:561416 original size:23 final size:23
Alignment explanation
Indices: 561386--561452 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
561376 TTAAAATAAA
*
561386 AATATAATATCTTATATTATTAT
1 AATATAATATATTATATTATTAT
*
561409 AATATAAT-TGATTATTTTATTAT
1 AATATAATAT-ATTATATTATTAT
*
561432 AATATTAAAATATTATATTAT
1 AATA-TAATATATTATATTAT
561453 ATTATTAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.03
23 23 0.62
24 12 0.32
25 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:561450 original size:21 final size:22
Alignment explanation
Indices: 561421--561468 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
561411 TATAATTGAT
*
561421 TATTTTATTATAATATTA-AAA
1 TATTATATTATAATATTAGAAA
*
561442 TATTATATTATATTATTAGAAA
1 TATTATATTATAATATTAGAAA
561464 TATTA
1 TATTA
561469 ATAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTATATTATAATATTAGAAA
Found at i:561450 original size:26 final size:26
Alignment explanation
Indices: 561364--561457 Score: 68
Period size: 26 Copynumber: 3.6 Consensus size: 26
561354 ATTAATAATT
* *
561364 TATTATATATTATTA-AA-ATAAAAA
1 TATTATATTTTATTATAATATTAAAA
* * * *
561388 TATAATATCTTATATTATTATAATATAA
1 TATTATAT-TT-TATTATAATATTAAAA
*
561416 T-TGATTATTTTATTATAATATTAAAA
1 TATTA-TATTTTATTATAATATTAAAA
*
561442 TATTATATTATATTAT
1 TATTATATTTTATTAT
561458 TAGAAATATT
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
24 7 0.13
25 1 0.02
26 29 0.56
27 7 0.13
28 8 0.15
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
TATTATATTTTATTATAATATTAAAA
Found at i:561476 original size:22 final size:21
Alignment explanation
Indices: 561338--561472 Score: 54
Period size: 21 Copynumber: 6.6 Consensus size: 21
561328 TGAAATTAAT
* *
561338 AAATAATATA-AATTTTATTA
1 AAATATTATATAATATTATTA
561358 ATAAT-TTAT-TATATATTATTA
1 A-AATATTATATA-ATATTATTA
** *
561379 AAATAAAAATATAATA-TCTT-
1 AAAT-ATTATATAATATTATTA
*
561399 --ATATTATTATAATATAATT-
1 AAATATTA-TATAATATTATTA
* * * * *
561418 GATTATTTTATTATAATATTA
1 AAATATTATATAATATTATTA
*
561439 AAATATTATATTATATTATTA
1 AAATATTATATAATATTATTA
561460 GAAATATTA-ATAA
1 -AAATATTATATAA
561473 ATATATTTTA
Statistics
Matches: 84, Mismatches: 19, Indels: 23
0.67 0.15 0.18
Matches are distributed among these distances:
17 2 0.02
18 9 0.11
19 2 0.02
20 17 0.20
21 39 0.46
22 13 0.15
23 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (21 bp):
AAATATTATATAATATTATTA
Found at i:561477 original size:29 final size:29
Alignment explanation
Indices: 561369--561479 Score: 76
Period size: 29 Copynumber: 4.0 Consensus size: 29
561359 TAATTTATTA
* *
561369 TATATTATTAAAATA-AAAATATAATATCT
1 TATATTATTAAAATATTAAA-ATAATATAT
* *
561398 TATATTATTATAATA-T--AAT--T-GAT
1 TATATTATTAAAATATTAAAATAATATAT
* * *
561421 TATTTTATTATAATATTAAAATATTATAT
1 TATATTATTAAAATATTAAAATAATATAT
*
561450 TATATTATTAGAAATATTAATA-AATATAT
1 TATATTATTA-AAATATTAAAATAATATAT
561479 T
1 T
561480 TTAAATATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
23 15 0.23
24 2 0.03
26 5 0.08
27 1 0.02
28 1 0.02
29 32 0.49
30 9 0.14
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (29 bp):
TATATTATTAAAATATTAAAATAATATAT
Found at i:561479 original size:21 final size:20
Alignment explanation
Indices: 561433--561542 Score: 59
Period size: 21 Copynumber: 5.4 Consensus size: 20
561423 TTTTATTATA
*
561433 ATATTAAAATATTATATTAT
1 ATATTAAAATATTATATAAT
561453 ATTATTAGAAATATTA-ATAAAT
1 A-TATTA-AAATATTATAT-AAT
*
561475 ATATTTTAAATATT-T-TAAT
1 ATA-TTAAAATATTATATAAT
* * *
561494 A-ATTAATATTTTGATTAAAAT
1 ATATTAAAATATT-A-TATAAT
* *
561515 GATATTAAAATATTTTATTA-
1 -ATATTAAAATATTATATAAT
561535 ATATTAAA
1 ATATTAAA
561543 TTTATAAAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 23
0.67 0.11 0.23
Matches are distributed among these distances:
17 7 0.10
18 1 0.01
19 12 0.18
20 3 0.04
21 22 0.32
22 14 0.21
23 9 0.13
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (20 bp):
ATATTAAAATATTATATAAT
Found at i:563578 original size:17 final size:18
Alignment explanation
Indices: 563542--563583 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
563532 TGACTGAAAG
563542 ATTTTTTTTATTAATTTTA
1 ATTTTTTTTATTAA-TTTA
563561 ATTTTTTTTATTAA-TTA
1 ATTTTTTTTATTAATTTA
563578 ATTTTT
1 ATTTTT
563584 CTATCCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 9 0.39
19 14 0.61
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTTTTTATTAATTTA
Found at i:564140 original size:19 final size:20
Alignment explanation
Indices: 564116--564165 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
564106 GATAAATTTA
*
564116 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
564135 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
564156 TT-ATAATTTT
1 TTAATAATTTT
564166 TTAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:564161 original size:11 final size:10
Alignment explanation
Indices: 564085--564176 Score: 52
Period size: 11 Copynumber: 9.2 Consensus size: 10
564075 CGATAATATA
564085 ATAATTATTTT
1 ATAA-TATTTT
* *
564096 ATAGTATTTAG
1 ATAATATTT-T
564107 ATAA-A-TTT
1 ATAATATTTT
564115 ATTAATAATTTT
1 A-TAAT-ATTTT
*
564127 ATAATCTTTT
1 ATAATATTTT
*
564137 AATAA-ATTTA
1 -ATAATATTTT
564147 ATAAGTATTTT
1 ATAA-TATTTT
564158 ATAAT-TTTT
1 ATAATATTTT
564167 -TAA-ATTTT
1 ATAATATTTT
564175 AT
1 AT
564177 TGACGAAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 22
0.68 0.09 0.24
Matches are distributed among these distances:
8 8 0.13
9 14 0.22
10 14 0.22
11 23 0.37
12 4 0.06
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (10 bp):
ATAATATTTT
Found at i:564168 original size:31 final size:30
Alignment explanation
Indices: 564083--564169 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
564073 TTCGATAATA
* *
564083 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
564114 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
564145 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
564170 ATTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:564264 original size:24 final size:24
Alignment explanation
Indices: 564231--564281 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 24
564221 ACTTTATTTG
564231 AAAATATAT-ATTAAACTTAGTAA
1 AAAATATATAATTAAACTTAGTAA
564254 AAAATATTATACAATTAAACTTAGTAA
1 AAAATA-TAT--AATTAAACTTAGTAA
564281 A
1 A
564282 CTTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 6 0.25
24 3 0.12
27 15 0.62
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (24 bp):
AAAATATATAATTAAACTTAGTAA
Found at i:564806 original size:31 final size:31
Alignment explanation
Indices: 564757--564831 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
564747 TTTAAAAAAA
* * * *
564757 TATAAAACACTTATTAAATTTAT-TAAAATAT
1 TATAAAATAATTAATAAATTTATCT-AAATAC
*
564788 TATAAAATTATTAATAAATTTATCTAAATAC
1 TATAAAATAATTAATAAATTTATCTAAATAC
564819 TATAAAATAATTA
1 TATAAAATAATTA
564832 TTATATTATC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (31 bp):
TATAAAATAATTAATAAATTTATCTAAATAC
Found at i:565134 original size:8 final size:8
Alignment explanation
Indices: 565121--565152 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
565111 CACCACCTAA
565121 ATATTTTT
1 ATATTTTT
565129 ATATTTTT
1 ATATTTTT
565137 ATA--TTT
1 ATATTTTT
565143 ATATTTTT
1 ATATTTTT
565151 AT
1 AT
565153 GCTATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.27
8 16 0.73
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
ATATTTTT
Found at i:565145 original size:14 final size:14
Alignment explanation
Indices: 565126--565152 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
565116 CCTAAATATT
565126 TTTATATTTTTATA
1 TTTATATTTTTATA
565140 TTTATATTTTTAT
1 TTTATATTTTTAT
565153 GCTATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATATTTTTATA
Found at i:565281 original size:19 final size:19
Alignment explanation
Indices: 565222--565281 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
565212 TACAAGCAAA
565222 TTTTAAAATATAAAAATAT
1 TTTTAAAATATAAAAATAT
** **
565241 CATTATAAATATTAAATTTAT
1 TTTTA-AAATA-TAAAAATAT
565262 TTTTAAAATATAAAAATAT
1 TTTTAAAATATAAAAATAT
565281 T
1 T
565282 AACTTTTGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
19 11 0.35
20 10 0.32
21 10 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTTAAAATATAAAAATAT
Found at i:565305 original size:27 final size:28
Alignment explanation
Indices: 565244--565321 Score: 106
Period size: 27 Copynumber: 2.8 Consensus size: 28
565234 AAAATATCAT
565244 TATAAATATTAAATTTATTTTTAAAATA
1 TATAAATATTAAATTTATTTTTAAAATA
* *
565272 TAAAAATATTAACTTT-TGTTTT-AAATA
1 TATAAATATTAAATTTAT-TTTTAAAATA
*
565299 TATAAATCTTAAATTTATTTTTA
1 TATAAATATTAAATTTATTTTTA
565322 TTGTAAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (28 bp):
TATAAATATTAAATTTATTTTTAAAATA
Found at i:566135 original size:16 final size:16
Alignment explanation
Indices: 566114--566145 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
566104 ATAATCTAAT
*
566114 TTTTGGGATTTTTTGG
1 TTTTGGGAGTTTTTGG
566130 TTTTGGGAGTTTTTGG
1 TTTTGGGAGTTTTTGG
566146 CTAGTTCCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.00, G:0.34, T:0.59
Consensus pattern (16 bp):
TTTTGGGAGTTTTTGG
Found at i:567096 original size:2 final size:2
Alignment explanation
Indices: 567089--567124 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
567079 TTAGTCTTGC
567089 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
567125 TTATTCTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:574371 original size:43 final size:42
Alignment explanation
Indices: 574122--574729 Score: 235
Period size: 43 Copynumber: 14.1 Consensus size: 42
574112 TATAACTTCA
* ** *
574122 TTTTTACTTTTATAATTGATGTTTCTAATTTTTTTCAATTTCAC
1 TTTTTACCTTTATAATTGA-GGCTCTAA-TTTTTTCAATCTCAC
** * * *
574166 TTTTTTATATTTATAGTTAAGG-TCTTAATTTTTTTCGATCAT-AC
1 -TTTTTACCTTTATAATTGAGGCTC-TAA-TTTTTTCAATC-TCAC
* * *
574210 TTTTTACCTTTAT--TTGAGGAGGGTCCTAATTTTCTC--TCTCTC
1 TTTTTACCTTTATAATT---GAGGCT-CTAATTTTTTCAATCTCAC
* * * * * *
574252 TTTCTACTTTTATAGTTGAAGTCTGTAACGTTTTT-AATCTCAC
1 TTTTTACCTTTATAATTG-AGGCTCTAA-TTTTTTCAATCTCAC
* * * * * * *
574295 TTTTTTTACATTTATATTTGATGCCCCTGATTTTTTTAATCTTAC
1 --TTTTTACCTTTATAATTGA-GGCTCTAATTTTTTCAATCTCAC
* *
574340 TTTTTACCTTTATAATTGAGGCATCTAA-TTTTTCTATCTCGC
1 TTTTTACCTTTATAATTGAGGC-TCTAATTTTTTCAATCTCAC
* * * * * *
574382 TTTATAGCTTTATAATTAAAGCCCCTAATTTATTT-AATCCCAC
1 TTTTTACCTTTATAATT-GAGGCTCTAATTT-TTTCAATCTCAC
* ** ** *
574425 TTTTTACCTTTATAATTAACACTCCTAAAATTTTCAATCACAC
1 TTTTTACCTTTATAATTGAGGCT-CTAATTTTTTCAATCTCAC
* *
574468 TTCTTA-C--T-T--TTGAAGCTCCTAATTTTTTCAATCTCAC
1 TTTTTACCTTTATAATTGAGGCT-CTAATTTTTTCAATCTCAC
*** * *
574505 TTTTTGGTTTTATAATTGAGACCCATAA-TTTTTCAATC-CTAC
1 TTTTTACCTTTATAATTGAGGCTC-TAATTTTTTCAATCTC-AC
*
574547 TTTTTACCTTTATAATTGAGGCTCCTAATTTTTTCAATCACAC
1 TTTTTACCTTTATAATTGAGGCT-CTAATTTTTTCAATCTCAC
* * * *
574590 CTTTTACCTTTATAATTGAGACCCCTAATTTATTTTTTTTCAATCCCAC
1 TTTTTACCTTTATAATTGAG-GCTCT-A---A--TTTTTTCAATCTCAC
* * * *
574639 TTTTCACCTTGATAATTGAGACCCCTAATTTTTTTCAATCTCAC
1 TTTTTACCTTTATAATTGAG-GCTCTAA-TTTTTTCAATCTCAC
** * * * **
574683 TTCCTACATTTATAATTGAAGCCCTTAA-TTTTTCAATCAAAC
1 TTTTTACCTTTATAATTGAGGCTC-TAATTTTTTCAATCTCAC
574725 TTTTT
1 TTTTT
574730 TTCTTTTATA
Statistics
Matches: 429, Mismatches: 91, Indels: 89
0.70 0.15 0.15
Matches are distributed among these distances:
37 26 0.06
39 1 0.00
40 2 0.00
41 9 0.02
42 108 0.25
43 125 0.29
44 71 0.17
45 47 0.11
46 1 0.00
47 1 0.00
48 1 0.00
49 37 0.09
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (42 bp):
TTTTTACCTTTATAATTGAGGCTCTAATTTTTTCAATCTCAC
Found at i:574556 original size:122 final size:122
Alignment explanation
Indices: 574364--574589 Score: 294
Period size: 122 Copynumber: 1.9 Consensus size: 122
574354 ATTGAGGCAT
* * * *
574364 CTAATTTTTCTATCTCGCTTTATAGCTTTATAATTAAAGCCCCTAATTTATTTAATCCCACTTTT
1 CTAATTTTTCAATCTCACTTTATAGCTTTATAATTAAAGCCCATAATTTATTCAATCCCACTTTT
574429 TACCTTTATAATTAACACTCCTAAAATTTTCAATCACACTTCTTACTTTTGAAGCTC
66 TACCTTTATAATTAACACTCCTAAAATTTTCAATCACACTTCTTACTTTTGAAGCTC
* * * * *
574486 CTAATTTTTTCAATCTCACTTTTTGGTTTTATAATT-GAGACCCATAATTT-TTCAATCCTACTT
1 CTAA-TTTTTCAATCTCACTTTATAGCTTTATAATTAAAG-CCCATAATTTATTCAATCCCACTT
* ** **
574549 TTTACCTTTATAATTGAGGCTCCTAATTTTTTCAATCACAC
64 TTTACCTTTATAATTAACACTCCTAAAATTTTCAATCACAC
574590 CTTTTACCTT
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
122 53 0.60
123 35 0.40
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (122 bp):
CTAATTTTTCAATCTCACTTTATAGCTTTATAATTAAAGCCCATAATTTATTCAATCCCACTTTT
TACCTTTATAATTAACACTCCTAAAATTTTCAATCACACTTCTTACTTTTGAAGCTC
Found at i:574630 original size:49 final size:48
Alignment explanation
Indices: 574575--574673 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 48
574565 AGGCTCCTAA
*
574575 TTTTTTCAATCACACCTTTT-ACCTTTATAATTGAGACCCCTAATTTATT
1 TTTTTTCAATCACA-CTTTTCACCTTGATAATTGAGACCCCTAATTT-TT
*
574624 TTTTTTCAATCCCACTTTTCACCTTGATAATTGAGACCCCTAATTTTT
1 TTTTTTCAATCACACTTTTCACCTTGATAATTGAGACCCCTAATTTTT
574672 TT
1 TT
574674 CAATCTCACT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 9 0.19
49 38 0.81
ACGTcount: A:0.24, C:0.23, G:0.05, T:0.47
Consensus pattern (48 bp):
TTTTTTCAATCACACTTTTCACCTTGATAATTGAGACCCCTAATTTTT
Found at i:574641 original size:92 final size:93
Alignment explanation
Indices: 574533--574701 Score: 243
Period size: 92 Copynumber: 1.8 Consensus size: 93
574523 AGACCCATAA
* * * * * *
574533 TTTTTCAATCCTACTTTTTACCTTTATAATTGAGGCTCCTAA-TTTTTTCAATCACACCTT-TTA
1 TTTTTCAATCCCACTTTTCACCTTGATAATTGAGACCCCTAATTTTTTTCAATCACA-CTTCCTA
*
574596 CCTTTATAATTGAGACCCCTAATTTATTT
65 CATTTATAATTGAGACCCCTAATTTATTT
*
574625 TTTTTCAATCCCACTTTTCACCTTGATAATTGAGACCCCTAATTTTTTTCAATCTCACTTCCTAC
1 TTTTTCAATCCCACTTTTCACCTTGATAATTGAGACCCCTAATTTTTTTCAATCACACTTCCTAC
574690 ATTTATAATTGA
66 ATTTATAATTGA
574702 AGCCCTTAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
92 40 0.60
93 27 0.40
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.46
Consensus pattern (93 bp):
TTTTTCAATCCCACTTTTCACCTTGATAATTGAGACCCCTAATTTTTTTCAATCACACTTCCTAC
ATTTATAATTGAGACCCCTAATTTATTT
Found at i:575149 original size:16 final size:16
Alignment explanation
Indices: 575128--575173 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
575118 TTAATTCAAC
575128 TTAAATAATATTTAAA
1 TTAAATAATATTTAAA
*
575144 TTAAAT-AT-TTT-TA
1 TTAAATAATATTTAAA
575157 TTAAATAATATTTAAA
1 TTAAATAATATTTAAA
575173 T
1 T
575174 GAATAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 7 0.28
14 5 0.20
15 5 0.20
16 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATAATATTTAAA
Found at i:575193 original size:18 final size:19
Alignment explanation
Indices: 575158--575193 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
575148 ATATTTTTAT
*
575158 TAAATAATATTTAAATGAA
1 TAAATAATATTAAAATGAA
575177 TAAATAA-ATTAAAATGA
1 TAAATAATATTAAAATGA
575194 CAATTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (19 bp):
TAAATAATATTAAAATGAA
Found at i:575820 original size:29 final size:29
Alignment explanation
Indices: 575771--575826 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
575761 GATGTCTCAC
*
575771 AAAGTTTGAGGGCCTAATTAATATTTTAG
1 AAAGTTTGAGGACCTAATTAATATTTTAG
* * *
575800 AAAGTTTGAGGACTTATTTAATTTTTT
1 AAAGTTTGAGGACCTAATTAATATTTT
575827 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (29 bp):
AAAGTTTGAGGACCTAATTAATATTTTAG
Found at i:586065 original size:234 final size:232
Alignment explanation
Indices: 585630--586348 Score: 1041
Period size: 234 Copynumber: 3.1 Consensus size: 232
585620 TTTATAAGTA
* *
585630 AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGTAAAGTAAGAAAAGTTTC
1 AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTCGAAAAGTAAGAAAAGTTTC
* *
585695 TTACCTAGTAAACTATTTCCAAAATTGGTAGATCCTTCAGGTCATCAGTAAGTCTTCCGAGCATG
66 TTACCTAGTAAACTATTTCCAAAATTGGTAAATCCTTC-GGTCATCAGTAAGTCTTTCGAGCATG
* * * * *
585760 ATGCTTAAACCCTTCGGGTCATCTATAAGTCTTTCAAGAAAGGTGATAAGTTCTTCAGGCCATCA
130 ATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGGTGATAAGTCCTTCGGGCCATC-
585825 ATAAGACCTTTGGACAGGATGTTTTCACATGTTTTTT-G
194 ATAAGACCTTTGGACAGGATGTTTTCACATGTTTTTTCG
* *
585863 AAAAATGAGAAAAGGTTTCTCATTTAAATCTGAAAATTGAAATTTTTGAAAAGTAAGAAAAATTT
1 AAAAATGAGAAAA-GTTTCTCATTTAAATCTGAAAATTGAAATTTTCGAAAAGTAAGAAAAGTTT
* *
585928 ATTACCTAGTAAACTATTTCCAAAATTGGTAAATCCTTCGGATCATCAGTAAGTCTTTTGAGCAT
65 CTTACCTAGTAAACTATTTCCAAAATTGGTAAATCCTTCGG-TCATCAGTAAGTCTTTCGAGCAT
* *
585993 GATGCTTAAATCCTTCAGATCATCTATAAGTCTTTCGAGCAAGGTGATAAGTCCTTCGGGCCATT
129 GATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGGTGATAAGTCCTTCGGGCCA-T
*
586058 CATAAGACCTTTGGGCAGGATGTTTTCACATGTTTTTTCG
193 CATAAGACCTTTGGACAGGATGTTTTCACATGTTTTTTCG
* * * *
586098 TAAAATGAGAAAAATTTCTCATTTAAATCTGAAAATTGAAAATTTCAAAAAGTAAGAAAAGTTTC
1 AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTCGAAAAGTAAGAAAAGTTTC
* * * * *
586163 TTTCCTAGTAAACTATTTCTAAAATTGGTAAGTCCTTCGGGCCACCAGTAAGTCTTTCGAGCATG
66 TTACCTAGTAAACTATTTCCAAAATTGGTAAATCCTTC-GGTCATCAGTAAGTCTTTCGAGCATG
* * * * *
586228 ATGCTAAAATCCTTCGGGTCAGCTTTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
130 ATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGGTGATAAGTCCTTCGGGCCATCA
** * * *
586293 TAAGACCTTCAGCCAGGATGTTTTCACATG-TTTCTCA
195 TAAGACCTTTGGACAGGATGTTTTCACATGTTTTTTCG
586330 AAAAATGAG-AAAG-TTCTCA
1 AAAAATGAGAAAAGTTTCTCA
586349 AAAAATGAGA
Statistics
Matches: 440, Mismatches: 41, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
230 6 0.01
231 3 0.01
232 13 0.03
233 44 0.10
234 357 0.81
235 17 0.04
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (232 bp):
AAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTCGAAAAGTAAGAAAAGTTTC
TTACCTAGTAAACTATTTCCAAAATTGGTAAATCCTTCGGTCATCAGTAAGTCTTTCGAGCATGA
TGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGGTGATAAGTCCTTCGGGCCATCAT
AAGACCTTTGGACAGGATGTTTTCACATGTTTTTTCG
Found at i:586242 original size:42 final size:41
Alignment explanation
Indices: 586195--586289 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 41
586185 AATTGGTAAG
* *
586195 TCCTTCGGGCCACCAGTAAGTCTTTCGAGCATGATGCTAAAA
1 TCCTTCGGGCCACCAGTAAGTCTTTCGAGCAAGATGAT-AAA
* * ** *
586237 TCCTTCGGGTCAGCTTTAAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGCCACCAGTAAGTCTTTCGAGCAAGATGATAAA
586278 TCCTTCGGGCCA
1 TCCTTCGGGCCA
586290 TCCTAAGACC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 13 0.29
42 32 0.71
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.28
Consensus pattern (41 bp):
TCCTTCGGGCCACCAGTAAGTCTTTCGAGCAAGATGATAAA
Found at i:586367 original size:21 final size:20
Alignment explanation
Indices: 586322--586369 Score: 80
Period size: 19 Copynumber: 2.4 Consensus size: 20
586312 GTTTTCACAT
586322 GTTTCTCAAAAAATGAGAAA
1 GTTTCTCAAAAAATGAGAAA
586342 G-TTCTCAAAAAATGAGAAA
1 GTTTCTCAAAAAATGAGAAA
586361 GGTTTCTCA
1 -GTTTCTCA
586370 TTTAAATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 18 0.69
20 2 0.08
21 6 0.23
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (20 bp):
GTTTCTCAAAAAATGAGAAA
Found at i:590161 original size:22 final size:22
Alignment explanation
Indices: 590136--590178 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
590126 ATATAATAAA
*
590136 TATTATAATTTTTTAATTAATT
1 TATTATAATTTATTAATTAATT
* *
590158 TATTATTATTTATTAGTTAAT
1 TATTATAATTTATTAATTAAT
590179 ACTAACGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TATTATAATTTATTAATTAATT
Found at i:590458 original size:25 final size:25
Alignment explanation
Indices: 590416--590463 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
590406 TTTTCGAGTT
*
590416 TATTTAGGAAATTCGGTATTAATTA
1 TATTTAGGAAATTCGGTACTAATTA
*
590441 TATTTAGG-AATGTTGGTACTAAT
1 TATTTAGGAAAT-TCGGTACTAAT
590464 ATAAGATCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (25 bp):
TATTTAGGAAATTCGGTACTAATTA
Found at i:594052 original size:57 final size:58
Alignment explanation
Indices: 593955--594066 Score: 131
Period size: 57 Copynumber: 1.9 Consensus size: 58
593945 TATTTCACTT
* * *
593955 TAGAATCTTGTGTTGATTCTAACTTTGAAAATGAAATAAATTGTTAAATTTATTTTCA
1 TAGAATCTTGTGATGATTCTAACTTTGAAAATGAAATAAATCGTCAAATTTATTTTCA
** *
594013 TAGAATCTTGT-ATGATTCT-GTTTTGTAAAA-GAAATTAAATCGTCAGATTTATTT
1 TAGAATCTTGTGATGATTCTAACTTTG-AAAATGAAA-TAAATCGTCAAATTTATTT
594067 CTTGAGAATC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
56 8 0.17
57 27 0.59
58 11 0.24
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (58 bp):
TAGAATCTTGTGATGATTCTAACTTTGAAAATGAAATAAATCGTCAAATTTATTTTCA
Found at i:597514 original size:14 final size:16
Alignment explanation
Indices: 597475--597515 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
597465 GAATTTGACC
597475 AAAAATCATTATGATG
1 AAAAATCATTATGATG
* *
597491 AACAACCATT-T-ATG
1 AAAAATCATTATGATG
597505 AAAAATCATTA
1 AAAAATCATTA
597516 AAACTTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 11 0.55
15 1 0.05
16 8 0.40
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.29
Consensus pattern (16 bp):
AAAAATCATTATGATG
Found at i:601379 original size:83 final size:84
Alignment explanation
Indices: 601239--601392 Score: 247
Period size: 83 Copynumber: 1.8 Consensus size: 84
601229 GTGTATATAT
* *
601239 GTTTAATATTTTAAATTTTAAAAGATATTATTATCTATTTAAATTTAAATATTAAAAGATATCTG
1 GTTTAATATTTTAAATTTTAAAAGATATTATTATATATTTAAATTTAAATATTAAAAGATATCTA
601304 GTTGGAGTAAATCTCTCAA
66 GTTGGAGTAAATCTCTCAA
* * * *
601323 GTTTAATATTTTAAA-TTTAAATGATATTATTATATGTTTAAATTTAGATATTAAAAGATATTTA
1 GTTTAATATTTTAAATTTTAAAAGATATTATTATATATTTAAATTTAAATATTAAAAGATATCTA
601387 GTTGGA
66 GTTGGA
601393 AAGAACTCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
83 49 0.77
84 15 0.23
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.46
Consensus pattern (84 bp):
GTTTAATATTTTAAATTTTAAAAGATATTATTATATATTTAAATTTAAATATTAAAAGATATCTA
GTTGGAGTAAATCTCTCAA
Found at i:601421 original size:83 final size:83
Alignment explanation
Indices: 601241--601410 Score: 189
Period size: 83 Copynumber: 2.0 Consensus size: 83
601231 GTATATATGT
* * * *
601241 TTAATATTTTAAATTTTAAAAGATATTATTATCTATTTAAATTTAAATATTAAAAGATATCTGGT
1 TTAATACTATAAA-TTTAAAAGATATTATTATATATTTAAATTTAAATATTAAAAGATATCTAGT
**
601306 TGGAGTAAATCTCTCAAGT
65 TGGAGTAAATCTCTCAAAA
* * * * * *
601325 TTAATATTTTAAATTTAAATGATATTATTATATGTTTAAATTTAGATATTAAAAGATATTTAGTT
1 TTAATACTATAAATTTAAAAGATATTATTATATATTTAAATTTAAATATTAAAAGATATCTAGTT
*
601390 GGAAAG-AACTCTCTCAAAA
66 GG--AGTAAATCTCTCAAAA
601409 TT
1 TT
601411 CTCCTATAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
83 48 0.64
84 25 0.33
85 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.44
Consensus pattern (83 bp):
TTAATACTATAAATTTAAAAGATATTATTATATATTTAAATTTAAATATTAAAAGATATCTAGTT
GGAGTAAATCTCTCAAAA
Found at i:603745 original size:133 final size:132
Alignment explanation
Indices: 603569--603808 Score: 369
Period size: 133 Copynumber: 1.8 Consensus size: 132
603559 AGGAACACAC
*
603569 ATTATTATGGTATTTCCGATTAAAGAAAAACTAATTCCCTAATTTTTATTAAGGTAATTATTTCT
1 ATTATTATGGTATTTCCGATTAAAGAAAAACTAATTCCCTAATTTTTATTAAGGCAATTATTTCT
*
603634 TATTTTTTTAATTTAAATAATAAAATATTGTCATTTC-TTAAAAGTTTAGAAAATAAGAAAAAAC
66 TA--TTTTTAATTTAAATAATAAAATATTGACATTTCATTAAAAGTTTAGAAAATAAGAAAAAAC
603698 GTAA
129 GTAA
* * * *
603702 ATTATTAT-TTATTTCC-AGTTAAAGAAGAAATTAGTTTCCTAATTTTTATTAAGGCAATTATTT
1 ATTATTATGGTATTTCCGA-TTAAAGAA-AAACTAATTCCCTAATTTTTATTAAGGCAATTATTT
603765 CTTATTTTTAATTTAAATAATAAAATATTGACATTTCATTAAAA
64 CTTATTTTTAATTTAAATAATAAAATATTGACATTTCATTAAAA
603809 ATTAAAATAA
Statistics
Matches: 98, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
131 33 0.34
132 21 0.21
133 44 0.45
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (132 bp):
ATTATTATGGTATTTCCGATTAAAGAAAAACTAATTCCCTAATTTTTATTAAGGCAATTATTTCT
TATTTTTAATTTAAATAATAAAATATTGACATTTCATTAAAAGTTTAGAAAATAAGAAAAAACGT
AA
Found at i:604332 original size:20 final size:20
Alignment explanation
Indices: 604309--604352 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
604299 CCATTCCTGT
604309 TTTCTGGAAAATTTTCCAGA
1 TTTCTGGAAAATTTTCCAGA
604329 TTTCTGGAAAATTTTCCAGA
1 TTTCTGGAAAATTTTCCAGA
604349 TTTC
1 TTTC
604353 CCCTCTCCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
TTTCTGGAAAATTTTCCAGA
Found at i:604926 original size:13 final size:13
Alignment explanation
Indices: 604904--604948 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
604894 AACCAGACCC
*
604904 GACCCAACCCGTT
1 GACCCGACCCGTT
*
604917 TACCCGACCCGTT
1 GACCCGACCCGTT
* *
604930 GGCCCGACCCATT
1 GACCCGACCCGTT
604943 GACCCG
1 GACCCG
604949 TTGACTCGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:604966 original size:15 final size:16
Alignment explanation
Indices: 604941--604979 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
604931 GCCCGACCCA
604941 TTGACCCGTTGACT-CG
1 TTGA-CCGTTGACTGCG
604957 TTGACCGTTGACTGGCG
1 TTGACCGTTGACT-GCG
604974 TTGACC
1 TTGACC
604980 ACTATTAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 4 0.19
17 8 0.38
ACGTcount: A:0.13, C:0.28, G:0.28, T:0.31
Consensus pattern (16 bp):
TTGACCGTTGACTGCG
Found at i:607431 original size:24 final size:23
Alignment explanation
Indices: 607404--607488 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 23
607394 TCCGACTTGA
*
607404 ATTCTATTCTGATACATGACCTGG
1 ATTCTGTTCTGATAC-TGACCTGG
* * *
607428 ATTCTGTTATGATTTCTGATCTGG
1 ATTCTGTTCTGA-TACTGACCTGG
** *
607452 ATTCTGTTCTGATATCTGATTTGA
1 ATTCTGTTCTGATA-CTGACCTGG
*
607476 ATTCTGTTTTGAT
1 ATTCTGTTCTGAT
607489 TCTTGATATC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
23 1 0.02
24 47 0.94
25 2 0.04
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (23 bp):
ATTCTGTTCTGATACTGACCTGG
Found at i:607486 original size:12 final size:11
Alignment explanation
Indices: 607427--607491 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 11
607417 ACATGACCTG
*
607427 GATTCTGTTAT
1 GATTCTGTTCT
*
607438 GATTTCTGATCT
1 GA-TTCTGTTCT
607450 GGATTCTGTTCT
1 -GATTCTGTTCT
607462 GATATCTGATT-T
1 GAT-TCTG-TTCT
*
607474 GAATTCTGTTTT
1 G-ATTCTGTTCT
607486 GATTCT
1 GATTCT
607492 TGATATCTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 12 0.27
12 27 0.60
13 6 0.13
ACGTcount: A:0.17, C:0.12, G:0.18, T:0.52
Consensus pattern (11 bp):
GATTCTGTTCT
Found at i:609578 original size:17 final size:17
Alignment explanation
Indices: 609553--609586 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
609543 ACCGGTCATA
*
609553 ACCCGACCCGACCCGTT
1 ACCCAACCCGACCCGTT
609570 ACCCAACCCGACCCGTT
1 ACCCAACCCGACCCGTT
609587 GGCCCGACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.53, G:0.15, T:0.12
Consensus pattern (17 bp):
ACCCAACCCGACCCGTT
Found at i:609594 original size:13 final size:13
Alignment explanation
Indices: 609575--609605 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
609565 CCGTTACCCA
609575 ACCCGACCCGTTG
1 ACCCGACCCGTTG
*
609588 GCCCGACCCGTTG
1 ACCCGACCCGTTG
609601 ACCCG
1 ACCCG
609606 TTGACTGGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.48, G:0.26, T:0.13
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:612129 original size:12 final size:12
Alignment explanation
Indices: 612108--612174 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
612098 ATGACCTGGA
*
612108 TTCTGTTCTGAT
1 TTCTGATCTGAT
612120 TTCTGATCTGGA-
1 TTCTGATCT-GAT
*
612132 TTCTGTTCTGAT
1 TTCTGATCTGAT
* * *
612144 ATCTGATTTGAA
1 TTCTGATCTGAT
* *
612156 TTCTGTTTTGAT
1 TTCTGATCTGAT
612168 TTCTGAT
1 TTCTGAT
612175 ATCTCCGTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.15, C:0.13, G:0.18, T:0.54
Consensus pattern (12 bp):
TTCTGATCTGAT
Found at i:612172 original size:24 final size:24
Alignment explanation
Indices: 612066--612174 Score: 105
Period size: 24 Copynumber: 4.5 Consensus size: 24
612056 AAATATTTTA
* *
612066 TCTGATTTCCGA-CTTGAATTCTAT
1 TCTGATTTCTGATC-TGAATTCTGT
* * *
612090 TCTGA-TACATGACCTGGATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
*
612114 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
612138 TCTGATATCTGATTTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
612162 TTTGATTTCTGAT
1 TCTGATTTCTGAT
612175 ATCTCCGTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
23 2 0.03
24 66 0.93
25 3 0.04
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:616411 original size:98 final size:98
Alignment explanation
Indices: 616228--616411 Score: 219
Period size: 98 Copynumber: 1.9 Consensus size: 98
616218 GCAACAACTG
* * * *
616228 CCATGACAAACTCTAAATTAAATCTATGACGACGATGACAATGAAGACAATTACTATGACAAACT
1 CCATGACAAACTCTAAATTAAATCTATGACGACGACGACAATCAAGACAACTACCATGACAAACT
**
616293 CCAAATTCAGACTATGACGACGATTATGATTTA
66 CCAAATTCAGACTACAACGACGATTATGATTTA
* ** * **
616326 CCATGAC-AACTTCTAAATTTAATCTATGACGATTACGACAATCACGACAACTACCATGATGAAC
1 CCATGACAAAC-TCTAAATTAAATCTATGACGACGACGACAATCAAGACAACTACCATGACAAAC
*
616390 TCTAAATTCA-ATCTACAACGAC
65 TCCAAATTCAGA-CTACAACGAC
616412 TACCATGTCT
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
97 4 0.06
98 67 0.94
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (98 bp):
CCATGACAAACTCTAAATTAAATCTATGACGACGACGACAATCAAGACAACTACCATGACAAACT
CCAAATTCAGACTACAACGACGATTATGATTTA
Found at i:618708 original size:15 final size:15
Alignment explanation
Indices: 618688--618723 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
618678 CTCGGGAGGC
618688 CGTGGAGAAGGCGAT
1 CGTGGAGAAGGCGAT
618703 CGTGGAGAAGGCGAT
1 CGTGGAGAAGGCGAT
618718 CG-GGAG
1 CGTGGAG
618724 CGCGCTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.25, C:0.14, G:0.50, T:0.11
Consensus pattern (15 bp):
CGTGGAGAAGGCGAT
Found at i:621758 original size:19 final size:20
Alignment explanation
Indices: 621715--621758 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
621705 AAAGGTACAA
621715 AAAATAACATATAAAAAGAT
1 AAAATAACATATAAAAAGAT
* *
621735 -TAATAA-ATATAAAAAGCT
1 AAAATAACATATAAAAAGAT
621753 AAAATA
1 AAAATA
621759 TAAATAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAATAACATATAAAAAGAT
Found at i:621773 original size:12 final size:12
Alignment explanation
Indices: 621736--621778 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
621726 TAAAAAGATT
*
621736 AATAAATATAAA
1 AATAAATATATA
621748 AAGCTAAA-ATATA
1 AA--TAAATATATA
621761 AATAAATATATA
1 AATAAATATATA
621773 AATAAA
1 AATAAA
621779 ACTAAACATG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 4 0.15
12 13 0.48
13 6 0.22
14 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (12 bp):
AATAAATATATA
Found at i:626722 original size:19 final size:22
Alignment explanation
Indices: 626680--626722 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
626670 ACAAATGAAA
*
626680 GTATAAATGCGTTAGATGGTAT
1 GTATAAATGCGTTAGATGGAAT
626702 GTATAAATG-G-TA-ATGGAAT
1 GTATAAATGCGTTAGATGGAAT
626721 GT
1 GT
626723 TATGGTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 2 0.10
21 1 0.05
22 9 0.45
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (22 bp):
GTATAAATGCGTTAGATGGAAT
Found at i:638313 original size:17 final size:19
Alignment explanation
Indices: 638293--638327 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
638283 CCTGAAAAAG
638293 AAGT-AAAC-AAAAACAAT
1 AAGTAAAACTAAAAACAAT
638310 AAGTAAAACTAAAAACAA
1 AAGTAAAACTAAAAACAA
638328 AAACTAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.71, C:0.11, G:0.06, T:0.11
Consensus pattern (19 bp):
AAGTAAAACTAAAAACAAT
Found at i:641256 original size:22 final size:24
Alignment explanation
Indices: 641223--641267 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
641213 AGGATGATGC
641223 ATTATCTTTTAGG-ATT-AGATTT
1 ATTATCTTTTAGGAATTAAGATTT
641245 ATTAT-TTATTAGGAATTAAGATT
1 ATTATCTT-TTAGGAATTAAGATT
641268 GGGTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.10
22 10 0.50
23 3 0.15
24 5 0.25
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.51
Consensus pattern (24 bp):
ATTATCTTTTAGGAATTAAGATTT
Found at i:642146 original size:23 final size:21
Alignment explanation
Indices: 642107--642155 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
642097 ATTTTTTTCT
* *
642107 CAAAAAAACAAAAAAAAAAGG
1 CAAAAAAAAAAAAAAAAAAGC
642128 CAAAAAAAAAAAACCAAAAAAGC
1 CAAAAAAAAAAAA--AAAAAAGC
642151 CAAAA
1 CAAAA
642156 TTTCAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.50
23 12 0.50
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAAAAAAAAAAAGC
Found at i:642147 original size:15 final size:14
Alignment explanation
Indices: 642108--642148 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
642098 TTTTTTTCTC
642108 AAAAAAA-C-AAAA
1 AAAAAAACCAAAAA
**
642120 AAAAAAGGCAAAAA
1 AAAAAAACCAAAAA
642134 AAAAAAACCAAAAA
1 AAAAAAACCAAAAA
642148 A
1 A
642149 GCCAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 6 0.25
13 1 0.04
14 17 0.71
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (14 bp):
AAAAAAACCAAAAA
Found at i:656593 original size:13 final size:12
Alignment explanation
Indices: 656566--656600 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
656556 TCAAAGAAGA
656566 TTAAAAAGAAAT
1 TTAAAAAGAAAT
656578 TTAAAAAGAAAGT
1 TTAAAAAGAAA-T
656591 TT-AAAAGAAA
1 TTAAAAAGAAA
656601 ATTCAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 19 0.86
13 3 0.14
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (12 bp):
TTAAAAAGAAAT
Found at i:657142 original size:16 final size:16
Alignment explanation
Indices: 657121--657151 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
657111 CGGCTTGAAA
*
657121 GAAAATTAAAGAAAAT
1 GAAAATAAAAGAAAAT
657137 GAAAATAAAAGAAAA
1 GAAAATAAAAGAAAA
657152 AGAATTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (16 bp):
GAAAATAAAAGAAAAT
Found at i:659307 original size:35 final size:34
Alignment explanation
Indices: 659217--659296 Score: 124
Period size: 34 Copynumber: 2.4 Consensus size: 34
659207 TTTTTTTCTC
* * *
659217 TTACTGTTCGAACCAAAATTGTACTACTATTTTT
1 TTACTGTTCGAAACAAAACTATACTACTATTTTT
*
659251 TTACTGTTCGAAACAAAACTATACTGCTATTTTT
1 TTACTGTTCGAAACAAAACTATACTACTATTTTT
659285 TTACTGTTCGAA
1 TTACTGTTCGAA
659297 TAGTGAACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (34 bp):
TTACTGTTCGAAACAAAACTATACTACTATTTTT
Found at i:660218 original size:12 final size:13
Alignment explanation
Indices: 660203--660232 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
660193 TCAAACAAGA
660203 TAAAAAGAAA-TT
1 TAAAAAGAAAGTT
660215 TAAAAAGAAAGTT
1 TAAAAAGAAAGTT
660228 TAAAA
1 TAAAA
660233 GAATATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (13 bp):
TAAAAAGAAAGTT
Found at i:665459 original size:13 final size:13
Alignment explanation
Indices: 665438--665518 Score: 51
Period size: 13 Copynumber: 5.8 Consensus size: 13
665428 CAAATGTTAG
*
665438 ATAATAAATAAAT
1 ATAAAAAATAAAT
*
665451 ATAAAAAATAATAGA
1 ATAAAAAATAA-A-T
665466 ATAATAAAAT-AAT
1 ATAA-AAAATAAAT
665479 GA-ATAAAAATAAAT
1 -ATA-AAAAATAAAT
665493 A-ATAAAAATAAAT
1 ATA-AAAAATAAAT
665506 AAATAAAAAATAA
1 --ATAAAAAATAA
665519 TAAAAATGAT
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
13 29 0.52
14 7 0.12
15 14 0.25
16 6 0.11
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (13 bp):
ATAAAAAATAAAT
Found at i:665500 original size:42 final size:42
Alignment explanation
Indices: 665438--665519 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
665428 CAAATGTTAG
665438 ATAATAAATAAATATAAAAAAT-AATAGAATAATAAAATAATGA
1 ATAATAAATAAATATAAAAAATAAATA-AATAA-AAAATAATGA
665481 ATAA-AAATAAATA-ATAAAAATAAATAAATAAAAAATAAT
1 ATAATAAATAAATATA-AAAAATAAATAAATAAAAAATAAT
665520 AAAAATGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
41 9 0.24
42 20 0.54
43 8 0.22
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (42 bp):
ATAATAAATAAATATAAAAAATAAATAAATAAAAAATAATGA
Found at i:665531 original size:36 final size:37
Alignment explanation
Indices: 665438--665536 Score: 64
Period size: 37 Copynumber: 2.6 Consensus size: 37
665428 CAAATGTTAG
* *
665438 ATAATAA-ATAAATATAAAAAATAATAGAATAAT--AAA
1 ATAATAATAAAAATATAATAAA-AA-AGAATAATAAAAA
*
665474 ATAATGAATAAAAATA-AATAATAAA-AATAAATAAATAA
1 ATAAT-AATAAAAATATAATAAAAAAGAAT-AATAAA-AA
* *
665512 AAAATAATAAAAATGATAATGAAAA
1 ATAATAATAAAAAT-ATAATAAAAA
665537 CAAAAATCAG
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
34 3 0.06
35 4 0.08
36 7 0.14
37 16 0.33
38 13 0.27
39 6 0.12
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (37 bp):
ATAATAATAAAAATATAATAAAAAAGAATAATAAAAA
Found at i:665541 original size:27 final size:25
Alignment explanation
Indices: 665465--665543 Score: 76
Period size: 24 Copynumber: 3.1 Consensus size: 25
665455 AAAATAATAG
*
665465 AATAAT-AAAATAATGAAT-AAAAATA
1 AATAATAAAAAT-AT-AATGAAAAAAA
665490 AATAATAAAAATA-AAT-AAATAAAA
1 AATAATAAAAATATAATGAAA-AAAA
665514 AATAATAAAAATGATAATGAAAACAAA
1 AATAATAAAAAT-ATAATGAAAA-AAA
665541 AAT
1 AAT
665544 CAGAGAGGGG
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
23 6 0.13
24 15 0.32
25 8 0.17
26 9 0.19
27 9 0.19
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (25 bp):
AATAATAAAAATATAATGAAAAAAA
Found at i:665593 original size:121 final size:122
Alignment explanation
Indices: 665442--665664 Score: 273
Period size: 124 Copynumber: 1.8 Consensus size: 122
665432 TGTTAGATAA
* *
665442 TAAATAAATATAAAAAATAATAGAATAATAA-AATAATGAATAA-AA-ATAAATAATA-AAAATA
1 TAAATAAATATAAAAAATAATAGAAAAATAATAATAAT-AATAATAATAAAAATAATAGAAAATA
665503 AATAAATAAAAAATA-ATAAAAATGATAAT-GAAAACAAAAATCAGAGAGGGGAAAAAAGAT
65 AA-AAATAAAAAATAGA-AAAAATGA-AATAGAAAA-AAAAATCAGAGAGGGGAAAAAAGAT
* * *
665563 TAAATAAATA-AAAATATAAGTCA-AAAAATAATGATAATAATAATAATAAAAATAATATGAGAA
1 TAAATAAATATAAAAAATAA-T-AGAAAAATAATAATAATAATAATAATAAAAATAATA-GAAAA
665626 TAAAAAATAAAAAATAGAAAAAATGAAATAGAAAAAAAA
63 TAAAAAATAAAAAATAGAAAAAATGAAATAGAAAAAAAA
665665 TTAAAATAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 16
0.81 0.05 0.15
Matches are distributed among these distances:
120 8 0.09
121 23 0.26
122 8 0.09
123 16 0.18
124 25 0.28
125 8 0.09
ACGTcount: A:0.70, C:0.01, G:0.08, T:0.20
Consensus pattern (122 bp):
TAAATAAATATAAAAAATAATAGAAAAATAATAATAATAATAATAATAAAAATAATAGAAAATAA
AAAATAAAAAATAGAAAAAATGAAATAGAAAAAAAAATCAGAGAGGGGAAAAAAGAT
Found at i:665634 original size:24 final size:26
Alignment explanation
Indices: 665585--665639 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
665575 AATATAAGTC
*
665585 AAAAAATAATGATAATAATAATAATA
1 AAAAAATAATGAGAATAATAATAATA
665611 AAAATAAT-ATGAGAATAA-AA-AATA
1 AAAA-AATAATGAGAATAATAATAATA
665635 AAAAA
1 AAAAA
665640 TAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 8 0.30
25 2 0.07
26 13 0.48
27 3 0.11
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (26 bp):
AAAAAATAATGAGAATAATAATAATA
Found at i:665663 original size:17 final size:16
Alignment explanation
Indices: 665627--665677 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
665617 ATATGAGAAT
*
665627 AAAAAATAAAA-AATAG
1 AAAAAATAAAATAA-AA
*
665643 AAAAAATGAAATAGAAA
1 AAAAAATAAAATA-AAA
*
665660 AAAAATTAAAATAAAA
1 AAAAAATAAAATAAAA
665676 AA
1 AA
665678 GGTTAACTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 15 0.52
17 13 0.45
18 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (16 bp):
AAAAAATAAAATAAAA
Found at i:666916 original size:36 final size:36
Alignment explanation
Indices: 666849--666946 Score: 117
Period size: 36 Copynumber: 2.6 Consensus size: 36
666839 TGTCAATAAT
*
666849 AAAAATATTTTCCAAAAACCTATATAATATATATTTTTAA
1 AAAAATATTTT-C-AAAA-TTATATAATATATATTTTT-A
* *
666889 AAAAATATTTT-AAAATTATATATTATATATTTTTT
1 AAAAATATTTTCAAAATTATATAATATATATTTTTA
*
666924 AAAAATGTTTTCAAAATTATATA
1 AAAAATATTTTCAAAATTATATA
666947 GTTTTCAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
35 10 0.19
36 28 0.53
37 4 0.08
40 11 0.21
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (36 bp):
AAAAATATTTTCAAAATTATATAATATATATTTTTA
Found at i:666956 original size:29 final size:29
Alignment explanation
Indices: 666910--667009 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
666900 AAAATTATAT
* *
666910 ATTATATATTTTTTAAAAATGTTTTCAAA
1 ATTATATAGTTTTCAAAAATGTTTTCAAA
*
666939 ATTATATAGTTTTCAAAAATGTTTTTAAA
1 ATTATATAGTTTTCAAAAATGTTTTCAAA
*
666968 ACTAAATATTATAAGTTTTC-AAAATGATTTCAAA
1 A-T---TA-TAT-AGTTTTCAAAAATGTTTTCAAA
*
667002 ACTATATA
1 ATTATATA
667010 ATATATATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
28 1 0.02
29 30 0.51
30 3 0.05
33 2 0.03
34 16 0.27
35 7 0.12
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTATATAGTTTTCAAAAATGTTTTCAAA
Found at i:666957 original size:65 final size:63
Alignment explanation
Indices: 666876--667009 Score: 153
Period size: 65 Copynumber: 2.1 Consensus size: 63
666866 ACCTATATAA
* * * * *
666876 TATATATTTTTAAAAAAAT-ATTTTAAAATTATATATTATATATTTTTTAAAAATGTTTTCAAAA
1 TATATAGTTTT-AAAAAATGATTTTAAAACTAAATATTATA-A-GTTTTAAAAATGATTTCAAAA
*
666940 T
63 C
* * *
666941 TATATAGTTTTCAAAAATGTTTTTAAAACTAAATATTATAAGTTTTCAAAATGATTTCAAAAC
1 TATATAGTTTTAAAAAATGATTTTAAAACTAAATATTATAAGTTTTAAAAATGATTTCAAAAC
667004 TATATA
1 TATATA
667010 ATATATATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
63 24 0.41
64 7 0.12
65 28 0.47
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (63 bp):
TATATAGTTTTAAAAAATGATTTTAAAACTAAATATTATAAGTTTTAAAAATGATTTCAAAAC
Found at i:667025 original size:103 final size:100
Alignment explanation
Indices: 666862--667148 Score: 313
Period size: 100 Copynumber: 2.9 Consensus size: 100
666852 AATATTTTCC
* * *
666862 AAAAACCTATATAATATATAT-TTTT-AAAAAAATATTTTAAAATTATATAT-TATATATTTTTT
1 AAAAA-CTAAATAATATATATATTTTCAAAAAAA-ATTTAAAAACTATATATATATATATTTTTT
* * *
666924 AAAAATGTTTTCAAAATTATATAGTTTTCAAAAATGTTTT
64 TAAAATGTTTTAAAAACTATATA-TTTTC-AAAATG-TTT
* ** *
666964 TAAAACTAAAT-AT-TATA-AGTTTTC-AAAATGATTTCAAAACTATATAATATATATATGTTTT
1 AAAAACTAAATAATATATATA-TTTTCAAAAAAAATTTAAAAACTATAT-ATATATATAT-TTTT
667025 TTAAAATGTTTTTAAAAACTATATATTTTCAAAATGTTT
63 TTAAAATG-TTTTAAAAACTATATATTTTCAAAATGTTT
* *
667064 AAAAACTATATAATATATATATTTTCAAAAAAAATTTAAAAACTATATAT-TATAT-TTATTTTC
1 AAAAACTAAATAATATATATATTTTCAAAAAAAATTTAAAAACTATATATATATATATT-TTTTT
667127 AAAATGTTTTAAAAACTATATA
65 AAAATGTTTTAAAAACTATATA
667149 ATATATAAAT
Statistics
Matches: 158, Mismatches: 15, Indels: 27
0.79 0.08 0.14
Matches are distributed among these distances:
99 34 0.22
100 35 0.22
101 25 0.16
102 31 0.20
103 33 0.21
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (100 bp):
AAAAACTAAATAATATATATATTTTCAAAAAAAATTTAAAAACTATATATATATATATTTTTTTA
AAATGTTTTAAAAACTATATATTTTCAAAATGTTT
Found at i:667085 original size:37 final size:36
Alignment explanation
Indices: 667044--667234 Score: 217
Period size: 37 Copynumber: 5.2 Consensus size: 36
667034 TTTTAAAAAC
667044 TATATATTTTCAAAATGTTTAAAAACTATATA-ATA
1 TATATATTTTCAAAATGTTTAAAAACTATATATATA
**
667079 TATATATTTTCAAAAAAAATTTAAAAACTATATAT-TA
1 TATATATTTTC--AAAATGTTTAAAAACTATATATATA
*
667116 TATTTATTTTCAAAATGTTTTAAAAACTATATAATATA
1 TATATATTTTCAAAATG-TTTAAAAACTATAT-ATATA
* * *
667154 TAAATGTTTTCAAACATGTTTTCAAAACTATATAT-TA
1 TATATATTTTCAAA-ATG-TTTAAAAACTATATATATA
* * *
667191 TATATGTTTTAAAAATGTTTATAAACTATAATATATA
1 TATATATTTTCAAAATGTTTAAAAACTAT-ATATATA
667228 TATATAT
1 TATATAT
667235 ATATATATAT
Statistics
Matches: 133, Mismatches: 14, Indels: 16
0.82 0.09 0.10
Matches are distributed among these distances:
35 25 0.19
36 21 0.16
37 55 0.41
38 15 0.11
39 17 0.13
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.45
Consensus pattern (36 bp):
TATATATTTTCAAAATGTTTAAAAACTATATATATA
Found at i:667145 original size:139 final size:137
Alignment explanation
Indices: 666941--667189 Score: 342
Period size: 139 Copynumber: 1.8 Consensus size: 137
666931 TTTTCAAAAT
*** * *
666941 TATATAGTTTTCAAAAATGTTTTTAAAACTAAATATTATAAGTTTTCAAAATGATTTCAAAACTA
1 TATATAGTTTTCAAAAAAAATTTAAAAACTAAATATTATAAGTTTTCAAAATGATTTAAAAACTA
* *
667006 TATAATATATATATGTTTTTTAAA-ATGTTTTTAAAAACTATATATTTTCAAAATGTTTAAAAAC
66 TATAATATATAAATG-TTTTCAAACATG-TTTTAAAAACTATATATTTTCAAAATGTTTAAAAAC
667070 TATATAATA
129 TATATAATA
* *
667079 TATATA-TTTTCAAAAAAAATTTAAAAACTATATATTATATTTA-TTTTCAAAATGTTTTAAAAA
1 TATATAGTTTTCAAAAAAAATTTAAAAACTAAATATTATA---AGTTTTCAAAATGATTTAAAAA
*
667142 CTATATAATATATAAATGTTTTCAAACATGTTTTCAAAACTATATATT
63 CTATATAATATATAAATGTTTTCAAACATGTTTTAAAAACTATATATT
667190 ATATATGTTT
Statistics
Matches: 97, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
137 28 0.29
138 30 0.31
139 38 0.39
140 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (137 bp):
TATATAGTTTTCAAAAAAAATTTAAAAACTAAATATTATAAGTTTTCAAAATGATTTAAAAACTA
TATAATATATAAATGTTTTCAAACATGTTTTAAAAACTATATATTTTCAAAATGTTTAAAAACTA
TATAATA
Found at i:667185 original size:75 final size:73
Alignment explanation
Indices: 667044--667236 Score: 244
Period size: 75 Copynumber: 2.6 Consensus size: 73
667034 TTTTAAAAAC
667044 TATATATTTTCAAAATGTTTAAAAACTATATAATATAT-ATATTTTCAAAAAAAATTTAAAAACT
1 TATATATTTTCAAAATGTTTAAAAACTATATAATATATAATATTTTCAAAAAAAATTTAAAAACT
667108 ATATATTA
66 ATATATTA
* * * *** *
667116 TATTTATTTTCAAAATGTTTTAAAAACTATATAATATATAAATGTTTTCAAACATGTTTTCAAAA
1 TATATATTTTCAAAATG-TTTAAAAACTATATAATATAT-AATATTTTCAAAAAAAATTTAAAAA
667181 CTATATATTA
64 CTATATATTA
* * *
667191 TATATGTTTTAAAAATGTTTATAAACTATAATATATATATATATAT
1 TATATATTTTCAAAATGTTTAAAAACTAT-ATA-ATATATA-ATAT
667237 ATATATATAT
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
72 16 0.16
73 21 0.20
74 11 0.11
75 46 0.45
76 9 0.09
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.45
Consensus pattern (73 bp):
TATATATTTTCAAAATGTTTAAAAACTATATAATATATAATATTTTCAAAAAAAATTTAAAAACT
ATATATTA
Found at i:667228 original size:2 final size:2
Alignment explanation
Indices: 667217--667289 Score: 112
Period size: 2 Copynumber: 37.0 Consensus size: 2
667207 GTTTATAAAC
*
667217 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
667258 TA TA TA TA TG TG 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
667290 AATGGGACGA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:668096 original size:84 final size:83
Alignment explanation
Indices: 667814--668467 Score: 518
Period size: 84 Copynumber: 7.8 Consensus size: 83
667804 ACAAATTTAT
* * * * * * *
667814 TGACAGATAGCCCTTCTTGCCTTGAGTTATGCTGTAAATTTGATTTGCCTTTG-AGCTGAGTGTA
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAA--TGATATGCC-TTGAAGCTGAGCGTA
* * *
667878 ATCGAACTCGAAGGTATTTTCG
63 GTCGAACTCGAAGGT-CTTTGG
* * * * * * * *
667900 TGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGAAGCTGAGCGTAGT
* *
667965 CGAACTTGAGGGTCTTTGG
65 CGAACTCGAAGGTCTTTGG
* * *
667984 T-A-A-ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATACGCCTTGAAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGAAGCTGAGCGTAGTC
668046 GAACTCGAAGGTCTTTGG
66 GAACTCGAAGGTCTTTGG
* * * * * *
668064 TTGACAAATAACCATTCTCGACTTAAGTTATGCTGCAAATGATATG-CTTGGGAGCTTAGAGTAG
1 -TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTT-GAAGCTGAGCGTAG
*
668128 TCGAACTCGAAGGTATTTTGG
64 TCGAACTCGAAGGT-CTTTGG
* * * * ** ** * ** *
668149 TTACAGATAACCCTTCTAGCCTTGATTTATGCTATAAATGATGCGCCCTCGAAGCTGAGTATAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGAAGCTGAGCGTAGT
*
668214 CAAACTCG-AGGATCTTT-G
65 CGAACTCGAAGG-TCTTTGG
* * * *
668232 -G-CATATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGAAGCTGAGCGTAGTC
*
668295 GAACTCGAAGGTCTTTAG
66 GAACTCGAAGGTCTTTGG
** * * * *
668313 TGGTAGATAACCCTTCTAGCCTTGAGTAATGCTGCAAATGATATGCCTT-AGAGTTGAGCGTAGT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGA-AGCTGAGCGTAGT
* *
668377 TGAACTCGAAGGTCTTTTAG
65 CGAACTCGAAGGTC-TTTGG
* * * * * * * * * * *
668397 TTACAGATAACCTTTCTAGCCTTGAGTTATGTTGTAAATAATGTTCCTTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTT-GAAGCTGAGCGTAGT
668462 CGAACT
65 CGAACT
668468 TGTTGAAAAC
Statistics
Matches: 462, Mismatches: 87, Indels: 39
0.79 0.15 0.07
Matches are distributed among these distances:
80 59 0.13
81 70 0.15
82 3 0.01
83 70 0.15
84 158 0.34
85 64 0.14
86 38 0.08
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (83 bp):
TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGAAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGG
Found at i:668106 original size:165 final size:161
Alignment explanation
Indices: 667824--668467 Score: 542
Period size: 165 Copynumber: 3.9 Consensus size: 161
667814 TGACAGATAG
* * ** *
667824 CCCTTCTTGCCTTGAGTTATGCTGTAAATTTGATTTGCCTTTG-AGCTGAGTGTAATCGAACTCG
1 CCCTTCTAGCCTTGAG-TATGCTGCAAA--TGATACGCC-TTGAAGCTGAGCGTAATCGAACTCG
* * * * *
667888 AAGGTATTTTCGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAA
62 AAGGT-CTTT-GTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTCGAA
* *
667953 GCTGAGTGTAATCGAACTTGAGGGTCTTTGGTAAATAA
124 GCTGAGTGTAATCGAACTCGAAGGTCTTTGGTAAATAA
* * * *
667991 CCCTTCTCGACTTAAGCTATGCTGCAAATGATACGCCTTGAAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAG-TATGCTGCAAATGATACGCCTTGAAGCTGAGCGTAATCGAACTCGAAG
* * * * * * * *
668056 GTCTTTGGTTGACAAATAACCATTCTCGACTTAAGTTATGCTGCAAATGATATGCTTGGGAGCTT
65 GTCTTT-G-TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTCGAAGCTG
* * *
668121 AGAGTAGTCGAACTCGAAGGTATTTTGGTTACAGATAA
128 AGTGTAATCGAACTCGAAGGT-CTTTGG-TA-A-ATAA
* ** * * ** *
668159 CCCTTCTAGCCTTGATTTATGCTATAAATGATGCGCCCTCGAAGCTGAGTATAATCAAACTCG-A
1 CCCTTCTAGCCTTGA-GTATGCTGCAAATGATACG-CCTTGAAGCTGAGCGTAATCGAACTCGAA
* * * *
668223 GGATCTTTG-G-CATATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTG
64 GG-TCTTTGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTCGAAGCTG
* * *
668286 AGCGTAGTCGAACTCGAAGGTCTTTAGTGGTAGATAA
128 AGTGTAATCGAACTCGAAGGTC-TT--TGGTAAATAA
* * * *
668323 CCCTTCTAGCCTTGAGTAATGCTGCAAATGATATGCCTT-AGAGTTGAGCGTAGTTGAACTCGAA
1 CCCTTCTAGCCTTGAGT-ATGCTGCAAATGATACGCCTTGA-AGCTGAGCGTAATCGAACTCGAA
* * * * * * * *
668387 GGTCTTTTAGTTACAGATAACCTTTCTAGCCTTGAGTTATGTTGTAAATAATGTTCCTTCGAAGC
64 GGTC-TTT-GTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TCGAAGC
668452 TGAGTGTAATCGAACT
126 TGAGTGTAATCGAACT
668468 TGTTGAAAAC
Statistics
Matches: 380, Mismatches: 77, Indels: 39
0.77 0.16 0.08
Matches are distributed among these distances:
162 1 0.00
163 21 0.06
164 69 0.18
165 141 0.37
166 5 0.01
167 62 0.16
168 54 0.14
169 27 0.07
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (161 bp):
CCCTTCTAGCCTTGAGTATGCTGCAAATGATACGCCTTGAAGCTGAGCGTAATCGAACTCGAAGG
TCTTTGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTCGAAGCTGAGT
GTAATCGAACTCGAAGGTCTTTGGTAAATAA
Found at i:668246 original size:249 final size:248
Alignment explanation
Indices: 667854--668467 Score: 818
Period size: 249 Copynumber: 2.5 Consensus size: 248
667844 GCTGTAAATT
* * * * * * *
667854 TGATTTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTCGTGACAGATAACCCTTCTAG
1 TGATATGCCTTAGAGTTGAGAGTAGTCGAACTCGAAGGTATTTTAGTTACAGATAACCCTTCTAG
* *
667919 CCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGG
66 CCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGATCTTTGG
* *
667984 TAAATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATACGCCTTGAAGCTGAGCGTAGTCGAA
131 CAAATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATACGCCTTGAAGCTGAGCGTAGTCGAA
* * *
668049 CTCGAAGGTCTTTGGTTGACAAATAACCATTCTCGACTTAAGTTATGCTGCAAA
196 CTCGAAGGTCTTTAG-TGACAAATAACCATTCTAGACTTAAGTAATGCTGCAAA
* *
668103 TGATATG-CTTGGGAGCTT-AGAGTAGTCGAACTCGAAGGTATTTTGGTTACAGATAACCCTTCT
1 TGATATGCCTT-AGAG-TTGAGAGTAGTCGAACTCGAAGGTATTTTAGTTACAGATAACCCTTCT
* * * * * *
668166 AGCCTTGATTTATGCTATAAATGATGCGCCCTCGAAGCTGAGTATAATCAAACTCGAGGATCTTT
64 AGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGATCTTT
* * * ** *
668231 GGCATATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG
129 GGCAAATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATACGCCTTGAAGCTGAGCGTAGTCG
** * * * *
668296 AACTCGAAGGTCTTTAGTGGTAGATAACCCTTCTAGCCTTGAGTAATGCTGCAAA
194 AACTCGAAGGTCTTTAGTGACAAATAACCATTCTAGACTTAAGTAATGCTGCAAA
* * * *
668351 TGATATGCCTTAGAGTTGAGCGTAGTTGAACTCGAAGGTCTTTTAGTTACAGATAACCTTTCTAG
1 TGATATGCCTTAGAGTTGAGAGTAGTCGAACTCGAAGGTATTTTAGTTACAGATAACCCTTCTAG
* * *
668416 CCTTGAGTTATGTTGTAAATAATGTTCCTTCGAAGCTGAGTGTAATCGAACT
66 CCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
668468 TGTTGAAAAC
Statistics
Matches: 314, Mismatches: 47, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
247 2 0.01
248 128 0.41
249 183 0.58
250 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (248 bp):
TGATATGCCTTAGAGTTGAGAGTAGTCGAACTCGAAGGTATTTTAGTTACAGATAACCCTTCTAG
CCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGATCTTTGG
CAAATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATACGCCTTGAAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTAGTGACAAATAACCATTCTAGACTTAAGTAATGCTGCAAA
Found at i:668547 original size:20 final size:21
Alignment explanation
Indices: 668510--668549 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
668500 AAATTAAGTT
668510 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
668531 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
668550 TATTCTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:668923 original size:64 final size:65
Alignment explanation
Indices: 668798--668924 Score: 193
Period size: 64 Copynumber: 2.0 Consensus size: 65
668788 GAAGCATTCT
* * *
668798 CCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTGATGCATCGATGCACAAG
1 CCATGCATCGATACACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCATCGATGCACAAG
** *
668863 CCATGCATCGATACACTCAGGCTATTTTC-AAACATCGAATGCATTTCATGCATCGGTGCACA
1 CCATGCATCGATACACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCATCGATGCACA
668925 CTTGGTGCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
64 31 0.55
65 25 0.45
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (65 bp):
CCATGCATCGATACACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCATCGATGCACAAG
Found at i:674689 original size:20 final size:19
Alignment explanation
Indices: 674660--674715 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 19
674650 TTTGTGCTTC
*
674660 ATGCACCGATGCATTTAACA
1 ATGCATCGATGCATTTAA-A
*
674680 ATGCATCGATGCATCCTTTAAT
1 ATGCATCGATGCA---TTTAAA
674702 ATGCATCGATGCAT
1 ATGCATCGATGCAT
674716 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 1 0.03
20 12 0.39
22 13 0.42
23 5 0.16
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (19 bp):
ATGCATCGATGCATTTAAA
Found at i:676272 original size:21 final size:21
Alignment explanation
Indices: 676230--676273 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
676220 AACCCCGGAG
*
676230 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
676251 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
676272 CT
1 CT
676274 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:677327 original size:19 final size:17
Alignment explanation
Indices: 677283--677330 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
677273 ATTAATTGAA
677283 ACATCGAATGCATTCCAT
1 ACATCG-ATGCATTCCAT
* *
677301 GCACCGATGCATTATCCAT
1 ACATCGATGCA-T-TCCAT
677320 ACATCGATGCA
1 ACATCGATGCA
677331 CTCTGAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 5 0.21
18 5 0.21
19 14 0.58
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (17 bp):
ACATCGATGCATTCCAT
Found at i:677374 original size:63 final size:64
Alignment explanation
Indices: 677234--677438 Score: 225
Period size: 63 Copynumber: 3.2 Consensus size: 64
677224 ATTTGAGGTG
* * * * * *
677234 ATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCATTC
1 ATGCACCGATGCATAAACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATTT
677298 C
64 C
* * * *
677299 ATGCACCGATGCATTATCCATACATCGATGCACTCTGAATATTTTCAAA-ATCGAATGCATTTG
1 ATGCACCGATGCATAAACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
* * * * **
677362 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCATAAACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
*
677426 ATGCATCGATGCA
1 ATGCACCGATGCA
677439 CACTTGGTGC
Statistics
Matches: 120, Mismatches: 18, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
63 53 0.44
64 36 0.30
65 31 0.26
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (64 bp):
ATGCACCGATGCATAAACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:678152 original size:32 final size:33
Alignment explanation
Indices: 678095--678160 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
678085 TTTAATTGCC
678095 AATTCACCCCCTCTTGGCTAATTCCGTCGATCG
1 AATTCACCCCCTCTTGGCTAATTCCGTCGATCG
678128 AATTCACCCCCTCTT-GCTAATTCCGTCGATCG
1 AATTCACCCCCTCTTGGCTAATTCCGTCGATCG
678160 A
1 A
678161 TTAACTCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 18 0.55
33 15 0.45
ACGTcount: A:0.20, C:0.36, G:0.14, T:0.30
Consensus pattern (33 bp):
AATTCACCCCCTCTTGGCTAATTCCGTCGATCG
Found at i:684309 original size:54 final size:54
Alignment explanation
Indices: 684246--684366 Score: 188
Period size: 54 Copynumber: 2.2 Consensus size: 54
684236 TACCTCTAAG
684246 GGGGTATCGGTACCCAATCGACATTCTATTTTTCTCGGAGCCAAAATTGGCATA
1 GGGGTATCGGTACCCAATCGACATTCTATTTTTCTCGGAGCCAAAATTGGCATA
* * * * * *
684300 GGGGTATCGGTACCCATTTGGCATTTTGTTTTTCTTGGAGCCAAAATTGGCATA
1 GGGGTATCGGTACCCAATCGACATTCTATTTTTCTCGGAGCCAAAATTGGCATA
684354 GGGGTATCGGTAC
1 GGGGTATCGGTAC
684367 ACCCTATGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.32
Consensus pattern (54 bp):
GGGGTATCGGTACCCAATCGACATTCTATTTTTCTCGGAGCCAAAATTGGCATA
Found at i:686505 original size:19 final size:19
Alignment explanation
Indices: 686473--686512 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
686463 AGTTTTCATG
686473 AAAACAACATAATTAAATAAA
1 AAAACAACA-AATTAAA-AAA
686494 AAAACAAC-AATTAAAAAA
1 AAAACAACAAATTAAAAAA
686512 A
1 A
686513 TCATAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 7 0.37
21 8 0.42
ACGTcount: A:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAACAACAAATTAAAAAA
Found at i:687018 original size:21 final size:23
Alignment explanation
Indices: 686945--687007 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
686935 ATCTTTATAG
686945 GGGTATCGATACACATTCAAAGA
1 GGGTATCGATACACATTCAAAGA
686968 GGGTATCGATACACATTCAAAGA
1 GGGTATCGATACACATTCAAAGA
*
686991 GGGTATCTATACACATT
1 GGGTATCGATACACATT
687008 GAAGGGGTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (23 bp):
GGGTATCGATACACATTCAAAGA
Found at i:703310 original size:237 final size:238
Alignment explanation
Indices: 702693--703315 Score: 898
Period size: 236 Copynumber: 2.6 Consensus size: 238
702683 GTGATTTTCA
* * *
702693 AAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATCATTTTTAAAAATGAAATTTTTGAAA
1 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTT-AATGATTTTTAAAAATGAAATTTTTGAAA
* * * *
702758 AGTAATAAAGAGATTTCCAAAGTTTCTTACTTAGTAAGTCCTT-TGAGCCATCAGAAAGTCTTTT
65 AGTAAAAAAGTGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGA-CCATCAGTAAGT-TTTT
* *
702822 -GAGCATGATGATTAAAT-CTTTCGGGTCATCTATAAGTCTTTCGAGCAAGATAATAAGTCCTTT
128 CGAGCATGATGATTAAATCCTTTCGGGTCATCTATAAGTCTTTCGAGCAAGATAATAAGTCATTC
* * *
702885 GGGCCATCCATGAGACCTTCAGGCATGATGTTTTTACATGAATTTG
193 GGGCCATCCATAAGACCTTCAGGCAAGATATTTTTACATGAATTTG
* * *
702931 -AAAATTAGAAAGCGATTTTCAAAGTTTCTCATTTAATGATTTTTGAAAATGAAATATTTGAAAA
1 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGATTTTTAAAAATGAAATTTTTGAAAA
* * * * *
702995 GTAAGAAAA-TGATTTCCAAAGTTTCTTACTTAGTAAGTCATTCGGGCCATCAATAAGTCTTTCG
66 GTAA-AAAAGTGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGACCATCAGTAAGTTTTTCG
* *
703059 AGCATGATGATTAAATCCTTT-GGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCATTCGG
130 AGCATGATGATTAAATCCTTTCGGGTCATCTATAAGTCTTTCGAGCAAGATAATAAGTCATTCGG
*
703123 GCCATCCATAAGACCTTCGGGCAAGATATTTTTACATGAATTTG
195 GCCATCCATAAGACCTTCAGGCAAGATATTTTTACATGAATTTG
* * * *
703167 AAAAATGAGAAAGCGGTTTTCAAAGTTTCTCATTTAATGTTTTTTTAAGATGAAATTTTTGAAAA
1 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGATTTTTAAAAATGAAATTTTTGAAAA
* *
703232 GTAAAAAAGTGATTTCCAAAGTTTCTTACTTAGTAAGACCTTCAGACCATCAGTACGTTTTTCGA
66 GTAAAAAAGTGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGACCATCAGTAAGTTTTTCGA
*
703297 GCATGACGATTAAATCCTT
131 GCATGATGATTAAATCCTT
703316 CCCGTTATCT
Statistics
Matches: 343, Mismatches: 36, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
235 3 0.01
236 172 0.50
237 168 0.49
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (238 bp):
AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGATTTTTAAAAATGAAATTTTTGAAAA
GTAAAAAAGTGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCAGACCATCAGTAAGTTTTTCGA
GCATGATGATTAAATCCTTTCGGGTCATCTATAAGTCTTTCGAGCAAGATAATAAGTCATTCGGG
CCATCCATAAGACCTTCAGGCAAGATATTTTTACATGAATTTG
Found at i:703404 original size:37 final size:37
Alignment explanation
Indices: 703363--703437 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
703353 TCTTTGGGCT
*
703363 ATCTTAAGCCTTCACAGAAGGGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCA
* *
703400 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAACTCA
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCA
703437 A
1 A
703438 GACCGAGTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (37 bp):
ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCA
Found at i:706988 original size:3 final size:3
Alignment explanation
Indices: 706982--707052 Score: 90
Period size: 3 Copynumber: 23.7 Consensus size: 3
706972 TTCCATTTAC
* *
706982 TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT GAT TAT TAT TAT GAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
707028 TTT TTT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
707053 CAAACGGGCC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:707131 original size:27 final size:27
Alignment explanation
Indices: 707071--707131 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
707061 CCAAGTCTGG
* **
707071 CCCAACCAGTTAACCCAAATACAATGG
1 CCCAAACAGTTAACCCAAATACAATAA
*
707098 CCCAAACAGTTAACCCAAATA-TATAA
1 CCCAAACAGTTAACCCAAATACAATAA
707124 CCCTAAAC
1 CCC-AAAC
707132 CCGTTTAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.44, C:0.33, G:0.07, T:0.16
Consensus pattern (27 bp):
CCCAAACAGTTAACCCAAATACAATAA
Found at i:708352 original size:27 final size:27
Alignment explanation
Indices: 708300--708358 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
708290 TAAATAGATA
*
708300 TAATAAATAATTATTTATATATTTTTT
1 TAATAAATAATTATTAATATATTTTTT
*
708327 TAATAAATTATT-TTAATAT-TTATTTT
1 TAATAAATAATTATTAATATATT-TTTT
708353 TCAATA
1 T-AATA
708359 TCGAAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 2 0.07
26 11 0.39
27 15 0.54
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
TAATAAATAATTATTAATATATTTTTT
Found at i:719620 original size:10 final size:10
Alignment explanation
Indices: 719605--719643 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
719595 ATGCTTGAAG
719605 AAAAGAAAAA
1 AAAAGAAAAA
719615 AAAAGAAAAA
1 AAAAGAAAAA
*
719625 AAAAG-AGAA
1 AAAAGAAAAA
719634 AAAAGAAAAA
1 AAAAGAAAAA
719644 GGGGGGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:720936 original size:83 final size:83
Alignment explanation
Indices: 720797--721585 Score: 1381
Period size: 83 Copynumber: 9.5 Consensus size: 83
720787 ATGCAATGTA
*
720797 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACATAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
720862 ATTTGGAAGATGAATATG
66 ATTTGGAAGATGAATATG
720880 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
*
720945 ATTTGGAAGATGAATGTG
66 ATTTGGAAGATGAATATG
720963 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTG
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCATTG
721027 AATTTGGAAGATGAATATG
65 AATTTGGAAGATGAATATG
*
721046 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACATAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
*
721111 ATTTGGAAGATGAATGTG
66 ATTTGGAAGATGAATATG
*
721129 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACATAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
721194 ATTTGGAAGATGAATATG
66 ATTTGGAAGATGAATATG
*
721212 CTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
*
721277 ATTTGGAAGATGAATGTG
66 ATTTGGAAGATGAATATG
*
721295 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGG-CAGAACCAATCATTG
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GGTTGGACAGAACCAATCATTG
721359 AATTTGGAAGATGAATATG
65 AATTTGGAAGATGAATATG
*
721378 CTCATAGCAACTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
*
721443 ATTTGGAAGATGAATGTG
66 ATTTGGAAGATGAATATG
* *
721461 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-TA-AACCAATTATTG
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCATTG
* *
721524 AATTTAGAAGATGAATTTG
65 AATTTGGAAGATGAATATG
721543 C-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
721586 ATTTGATATA
Statistics
Matches: 680, Mismatches: 20, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
81 1 0.00
82 78 0.11
83 588 0.86
84 13 0.02
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGA
ATTTGGAAGATGAATATG
Found at i:722726 original size:231 final size:228
Alignment explanation
Indices: 722309--723092 Score: 1215
Period size: 225 Copynumber: 3.5 Consensus size: 228
722299 GCAAAGATTT
** * * * * *
722309 AAATCCATCATTCAATGGATCAGCATTGCCAG-GTAGAGTTCATAATAAGAAGAACTCGTCATCT
1 AAATCCATCATTTGATGAATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCT
722373 GAAGAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTT
62 GAAGAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTT
722438 GATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAGA
127 GATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCT---GAAGAAGAAGA
722503 AGAAGTTCATAATGAGAAGAATTTGTTCAATCTTTTGCTC
189 AGAAGTTCATAATGAGAAGAATTTGTTCAATCTTTTGCTC
*
722543 AAATCCATCATTTGATGAATCAGCTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGAATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
722608 AAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATG
66 AAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATG
722673 GATTAACATTGCCAGGTAGAGTTCATAATGAG-A-AACTCGTCATCTG-AGAAGAAGAAGAAGTT
131 GATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAGAAGTT
722735 CATAATGAGAAGAATTTGTTCAATCTTTTGCTC
196 CATAATGAGAAGAATTTGTTCAATCTTTTGCTC
722768 AAATCCATCATTTGATGAATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGAATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
722833 AAGG-A-AATAAGTTCATAATGAG-A-AATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATG
66 AAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATG
*
722894 GATTAACA-TGCCAGGTAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAG-A-AA-TT
131 GATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAGAAGTT
* *
722955 CATAATGAGAAGAATTTGTTCAATTTTTTGCTT
196 CATAATGAGAAGAATTTGTTCAATCTTTTGCTC
* * * *
722988 AAATCCATCACTTGATGGAGCAGTTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTTGATGAATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* ** *
723052 AA-GAAG---AAGTTCATAATAAGAAGAGCTTGTTCAACTTTTTG
66 AAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
723093 CATAATTCTA
Statistics
Matches: 522, Mismatches: 20, Indels: 31
0.91 0.03 0.05
Matches are distributed among these distances:
217 13 0.02
218 2 0.00
219 48 0.09
220 85 0.16
221 49 0.09
222 15 0.03
223 25 0.05
224 1 0.00
225 117 0.22
226 1 0.00
229 12 0.02
230 1 0.00
231 107 0.20
232 1 0.00
234 44 0.08
235 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (228 bp):
AAATCCATCATTTGATGAATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGATG
GATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAGAAGTT
CATAATGAGAAGAATTTGTTCAATCTTTTGCTC
Found at i:723074 original size:17 final size:17
Alignment explanation
Indices: 723020--723075 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
723010 GTTTTTCCAG
*
723020 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATAAGA
* *
723037 AGAA-CTCATCTGAAGAAGA
1 AGAAGTTCA--T-AATAAGA
723056 AGAAGTTCATAATAAGA
1 AGAAGTTCATAATAAGA
723073 AGA
1 AGA
723076 GCTTGTTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 3 0.10
17 13 0.43
18 2 0.07
19 9 0.30
20 3 0.10
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.20
Consensus pattern (17 bp):
AGAAGTTCATAATAAGA
Found at i:723212 original size:84 final size:82
Alignment explanation
Indices: 723058--723241 Score: 208
Period size: 84 Copynumber: 2.2 Consensus size: 82
723048 GAAGAAGAAG
* * * * * * *
723058 AAGTTCATAATAAGAAGAGCTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTA
1 AAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCA
*
723123 GCATCAGCCTTTCCAG-AGA
66 ACATCAGCC---CCAGCAGA
* * *
723142 AAGTTCATAATGAGAAGAGCTTATTTAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCA
1 AAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCA
*
723207 ACATCATCCCCAGCAGA
66 ACATCAGCCCCAGCAGA
* *
723224 AGGTTCATAATGAAAAGA
1 AAGTTCATAATGAGAAGA
723242 ACTCATCTGA
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
81 4 0.05
82 19 0.22
84 62 0.73
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (82 bp):
AAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCA
ACATCAGCCCCAGCAGA
Found at i:723411 original size:3 final size:3
Alignment explanation
Indices: 723403--723476 Score: 114
Period size: 3 Copynumber: 24.7 Consensus size: 3
723393 TTCCATTTAC
* *
723403 TAT TAT TAT TATT TAT TAT TAT TAA TAT GAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
723449 TAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
723477 CAAACGGGCC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 60 0.92
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:724891 original size:23 final size:23
Alignment explanation
Indices: 724865--724915 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
724855 AGATATAATA
724865 AATAATTATTTATATATATTTTT-
1 AATAATTATTTA-ATATATTTTTC
*
724888 AATAAATTATTTAATATTTTTTTC
1 AAT-AATTATTTAATATATTTTTC
724912 AATA
1 AATA
724916 TCGAAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
AATAATTATTTAATATATTTTTC
Found at i:724900 original size:24 final size:24
Alignment explanation
Indices: 724868--724915 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
724858 TATAATAAAT
724868 AATTATTTATATATATTTTT-AATA
1 AATTATTTA-ATATATTTTTCAATA
*
724892 AATTATTTAATATTTTTTTCAATA
1 AATTATTTAATATATTTTTCAATA
724916 TCGAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
AATTATTTAATATATTTTTCAATA
Found at i:730129 original size:21 final size:21
Alignment explanation
Indices: 730103--730160 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
730093 ATTTACCATG
* * *
730103 ATTGCGGCCGTCGTGGGCGCT
1 ATTGCGGCCGCCGCGGACGCT
*
730124 ATTGCGGCCGCCGCGGACTCT
1 ATTGCGGCCGCCGCGGACGCT
730145 ATTGCGGCCGCCGCGG
1 ATTGCGGCCGCCGCGG
730161 GTAAATCGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.07, C:0.34, G:0.40, T:0.19
Consensus pattern (21 bp):
ATTGCGGCCGCCGCGGACGCT
Found at i:732070 original size:95 final size:94
Alignment explanation
Indices: 731892--732081 Score: 317
Period size: 95 Copynumber: 2.0 Consensus size: 94
731882 GTCATGAAGA
* *
731892 TATAAGGTTTGTCAAAATTATATGCATATTTCTTGGAATTATGGAGTAATCTTTTTGTTTTGGTT
1 TATAAGGTTTGTCAAAATCATATGCATATTTCATGGAATTATGGAGTAATCTTTTTGTTTTGGTT
* * * *
731957 AAAAGAGTAATGGGCTTTTGGTGAATTAG
66 AAAAGAGTAAAGGACTTTTAGCGAATTAG
731986 TATAAGGTTTGTCAAAATCATATGCATATTTCATGGAATTTATGGAGTAATCTTTTTGTTTTGGT
1 TATAAGGTTTGTCAAAATCATATGCATATTTCATGGAA-TTATGGAGTAATCTTTTTGTTTTGGT
732051 TAAAAGAGTAAAGGACTTTTAGCGAATTAG
65 TAAAAGAGTAAAGGACTTTTAGCGAATTAG
732081 T
1 T
732082 CAAGATTTAC
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 36 0.40
95 53 0.60
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (94 bp):
TATAAGGTTTGTCAAAATCATATGCATATTTCATGGAATTATGGAGTAATCTTTTTGTTTTGGTT
AAAAGAGTAAAGGACTTTTAGCGAATTAG
Done.