Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 17 of 22
Found at i:8493423 original size:6 final size:6
Alignment explanation
Indices: 8493412--8493437 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
8493402 TATTGCGTTT
8493412 GGGTTA GGGTTA GGGTTA GGGTTA GG
1 GGGTTA GGGTTA GGGTTA GGGTTA GG
8493438 TAAGAGGACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (6 bp):
GGGTTA
Found at i:8498549 original size:27 final size:27
Alignment explanation
Indices: 8498518--8498579 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
8498508 TTGTTGAGAT
8498518 AAGGTTTGAATGAAATTCTAAGTTGAA
1 AAGGTTTGAATGAAATTCTAAGTTGAA
8498545 AAGGTTTGAATGAAATTCTAAGTTGAA
1 AAGGTTTGAATGAAATTCTAAGTTGAA
8498572 AAGGTTTG
1 AAGGTTTG
8498580 GAACTCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (27 bp):
AAGGTTTGAATGAAATTCTAAGTTGAA
Found at i:8499442 original size:6 final size:6
Alignment explanation
Indices: 8499431--8499474 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
8499421 TAATGAAGAG
* *
8499431 GCCCCA GCCCCA GCCCCA GCCCCA GCACTA GCCCC- GTCCCCA GC
1 GCCCCA GCCCCA GCCCCA GCCCCA GCCCCA GCCCCA G-CCCCA GC
8499475 ATCCCCGCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 1 0.03
6 30 0.94
7 1 0.03
ACGTcount: A:0.16, C:0.61, G:0.18, T:0.05
Consensus pattern (6 bp):
GCCCCA
Found at i:8503094 original size:15 final size:16
Alignment explanation
Indices: 8503074--8503103 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8503064 AAATATAAAA
8503074 TAATAAATAA-AATTT
1 TAATAAATAATAATTT
8503089 TAATAAATAATAATT
1 TAATAAATAATAATT
8503104 AATTATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATAAATAATAATTT
Found at i:8512551 original size:8 final size:8
Alignment explanation
Indices: 8512528--8512583 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
8512518 AAAATAATAT
*
8512528 AATATTTT
1 AATATTTA
8512536 AATA-TTA
1 AATATTTA
*
8512543 ATTATTTA
1 AATATTTA
*
8512551 AATATTAA
1 AATATTTA
8512559 AATATTTA
1 AATATTTA
8512567 AA-ATTACTA
1 AATATT--TA
8512576 AATATTTA
1 AATATTTA
8512584 TTTTTAACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
7 8 0.21
8 24 0.62
9 4 0.10
10 3 0.08
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (8 bp):
AATATTTA
Found at i:8512578 original size:17 final size:16
Alignment explanation
Indices: 8512528--8512583 Score: 62
Period size: 15 Copynumber: 3.5 Consensus size: 16
8512518 AAAATAATAT
*
8512528 AATATTTTAATATT-A
1 AATATTTAAATATTAA
*
8512543 ATTATTTAAATATTAA
1 AATATTTAAATATTAA
8512559 AATATTTAAA-ATTACTA
1 AATATTTAAATATTA--A
8512576 AATATTTA
1 AATATTTA
8512584 TTTTTAACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 16 0.46
16 10 0.29
17 9 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATTTAAATATTAA
Found at i:8518821 original size:30 final size:30
Alignment explanation
Indices: 8518785--8518846 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
8518775 TTTAAATAAT
8518785 AATTT-AAAAAATT-AATTAAATATATATTAA
1 AATTTAAAAAAATTGAATTAAA-ATAT-TTAA
8518815 AATTTAAAAAAATTGAATTAAAATATTTAA
1 AATTTAAAAAAATTGAATTAAAATATTTAA
8518845 AA
1 AA
8518847 AATAACAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 11 0.37
31 12 0.40
32 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (30 bp):
AATTTAAAAAAATTGAATTAAAATATTTAA
Found at i:8518827 original size:22 final size:23
Alignment explanation
Indices: 8518788--8518850 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
8518778 AAATAATAAT
* **
8518788 TTAAAAAATTAATTAAATAT-ATA
1 TTAAAATATTAAAAAAATATGA-A
8518811 TTAAAAT-TTAAAAAAAT-TGAA
1 TTAAAATATTAAAAAAATATGAA
*
8518832 TTAAAATATTTAAAAAATA
1 TTAAAATATTAAAAAAATA
8518851 ACAACTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 9 0.27
22 18 0.55
23 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TTAAAATATTAAAAAAATATGAA
Found at i:8522266 original size:2 final size:2
Alignment explanation
Indices: 8522259--8522285 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8522249 AATTTAAAAT
8522259 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
8522286 TTAATACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8523882 original size:2 final size:2
Alignment explanation
Indices: 8523875--8523901 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8523865 AACCATTTTC
8523875 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
8523902 ATCAATAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8532664 original size:10 final size:10
Alignment explanation
Indices: 8532649--8532673 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
8532639 TGTCAGGTAA
8532649 TTTCTTTTAT
1 TTTCTTTTAT
8532659 TTTCTTTTAT
1 TTTCTTTTAT
8532669 TTTCT
1 TTTCT
8532674 GTTTTAATTG
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:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTCTTTTAT
Found at i:8536650 original size:22 final size:22
Alignment explanation
Indices: 8536606--8536650 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
8536596 AATCTCCAAT
* *
8536606 ATTCTAGTGTTTCTCTCATCTA
1 ATTCTAGTGTATCTATCATCTA
8536628 ATTCTAGTGTAT-TATCATACTA
1 ATTCTAGTGTATCTATCAT-CTA
8536650 A
1 A
8536651 GGCCTGGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.47
Consensus pattern (22 bp):
ATTCTAGTGTATCTATCATCTA
Found at i:8538247 original size:17 final size:17
Alignment explanation
Indices: 8538214--8538247 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8538204 AATATTTTAT
* *
8538214 TTATAATTTAAATATTA
1 TTATAATTAAAAGATTA
8538231 TTATAATTAAAAGATTA
1 TTATAATTAAAAGATTA
8538248 ATAATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTATAATTAAAAGATTA
Found at i:8538248 original size:43 final size:43
Alignment explanation
Indices: 8538175--8538265 Score: 116
Period size: 43 Copynumber: 2.1 Consensus size: 43
8538165 TAAAATTTTG
* *
8538175 TAATTTAATCATTAATATATTAAAATATTAAT-ATTTTATTTA
1 TAATTTAATCATTAATATATTAAAAGATTAATAATTTTAATTA
*
8538217 TAATTTAAAT-ATTATTATAATTAAAAGATTAATAATTTTAATTA
1 TAATTT-AATCATTAATAT-ATTAAAAGATTAATAATTTTAATTA
8538261 -AATTT
1 TAATTT
8538266 TATCTTTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 13 0.30
43 21 0.49
44 9 0.21
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (43 bp):
TAATTTAATCATTAATATATTAAAAGATTAATAATTTTAATTA
Found at i:8538250 original size:23 final size:21
Alignment explanation
Indices: 8538179--8538262 Score: 59
Period size: 23 Copynumber: 3.9 Consensus size: 21
8538169 ATTTTGTAAT
*
8538179 TTAATCATTAATATATTAAAATA
1 TTAAT-ATTATTATATTAAAA-A
* *
8538202 TTAATATT-TTAT-TTATAAT
1 TTAATATTATTATATTAAAAA
8538221 TTAAATATTATTATAATTAAAAGA
1 TT-AATATTATTAT-ATTAAAA-A
8538245 TTAATAATT-TTA-ATTAAA
1 TTAAT-ATTATTATATTAAA
8538263 TTTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
19 2 0.04
20 11 0.22
21 13 0.26
22 3 0.06
23 16 0.32
24 5 0.10
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (21 bp):
TTAATATTATTATATTAAAAA
Found at i:8544117 original size:42 final size:42
Alignment explanation
Indices: 8544070--8544150 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
8544060 GCTTTGTCCA
* * *
8544070 GCCCATTCTTCTGTCAAGTTTCCGAATGAGAAGTCTGGAAAT
1 GCCCATTCTTCAGTCAAGTTTCCAAATGAAAAGTCTGGAAAT
8544112 GCCCATTCTTCAGTCAAGTTTCCAAATGAAAAGTCTGGA
1 GCCCATTCTTCAGTCAAGTTTCCAAATGAAAAGTCTGGA
8544151 CGTTGCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (42 bp):
GCCCATTCTTCAGTCAAGTTTCCAAATGAAAAGTCTGGAAAT
Found at i:8547394 original size:2 final size:2
Alignment explanation
Indices: 8547389--8547416 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8547379 TGGAAGGTTT
8547389 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
8547417 GCTACTCAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8550384 original size:2 final size:2
Alignment explanation
Indices: 8550377--8550413 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8550367 AATGCTGTTT
8550377 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8550414 CAGTTTTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8552592 original size:33 final size:31
Alignment explanation
Indices: 8552555--8552616 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
8552545 ATAAGATTAG
*
8552555 TATTTTTCTAAGTAATATAAATGACAAAATTTT
1 TATTTTTCCAAG-AA-ATAAATGACAAAATTTT
* *
8552588 TATTTTTCCAAGCAATAAATGATAAAATT
1 TATTTTTCCAAGAAATAAATGACAAAATT
8552617 AGAGTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 14 0.54
32 1 0.04
33 11 0.42
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (31 bp):
TATTTTTCCAAGAAATAAATGACAAAATTTT
Found at i:8552629 original size:36 final size:36
Alignment explanation
Indices: 8552589--8552725 Score: 116
Period size: 36 Copynumber: 4.1 Consensus size: 36
8552579 CAAAATTTTT
*
8552589 ATTTTTCCAAGCAATAAATGATAAAATTAGAGTTAA
1 ATTTTTCTAAGCAATAAATGATAAAATTAGAGTTAA
* * *
8552625 ATTTTTCTAAGCAAAAAATGA-AAGATTAAGAGCTAA
1 ATTTTTCTAAGCAATAAATGATAAAATT-AGAGTTAA
8552661 A---TT-T-----ATAAATGATAAAATTAGAGTTAA
1 ATTTTTCTAAGCAATAAATGATAAAATTAGAGTTAA
* * * *
8552688 ATCTTTCTAAGTAA-AAATGATAAGATTAGAGTAAA
1 ATTTTTCTAAGCAATAAATGATAAAATTAGAGTTAA
8552723 ATT
1 ATT
8552726 AAAGAAATAA
Statistics
Matches: 80, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
27 15 0.19
28 5 0.06
30 2 0.03
31 1 0.01
32 1 0.01
33 2 0.03
35 26 0.32
36 28 0.35
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (36 bp):
ATTTTTCTAAGCAATAAATGATAAAATTAGAGTTAA
Found at i:8552676 original size:63 final size:61
Alignment explanation
Indices: 8552602--8552722 Score: 190
Period size: 63 Copynumber: 2.0 Consensus size: 61
8552592 TTTCCAAGCA
*
8552602 ATAAATGATAAAATTAGAGTTAAATTTTTCTAAGCAAAAAATGA-AAGATTAAGAGCTAAATTT
1 ATAAATGATAAAATTAGAGTTAAATCTTTCTAAG-AAAAAATGATAAGATT-AGAG-TAAATTT
*
8552665 ATAAATGATAAAATTAGAGTTAAATCTTTCTAAGTAAAAATGATAAGATTAGAGTAAA
1 ATAAATGATAAAATTAGAGTTAAATCTTTCTAAGAAAAAATGATAAGATTAGAGTAAA
8552723 ATTAAAGAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
61 4 0.07
62 12 0.22
63 39 0.71
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.31
Consensus pattern (61 bp):
ATAAATGATAAAATTAGAGTTAAATCTTTCTAAGAAAAAATGATAAGATTAGAGTAAATTT
Found at i:8554146 original size:15 final size:15
Alignment explanation
Indices: 8554126--8554165 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
8554116 AAGTGATCTA
8554126 GATGATGATGAGGAT
1 GATGATGATGAGGAT
*
8554141 GATGATTATGAGGAT
1 GATGATGATGAGGAT
**
8554156 TTTGATGATG
1 GATGATGATG
8554166 GAGCTGTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (15 bp):
GATGATGATGAGGAT
Found at i:8562574 original size:11 final size:12
Alignment explanation
Indices: 8562552--8562585 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
8562542 ATTTTGCAAG
8562552 AAAATAATAAAA
1 AAAATAATAAAA
8562564 AAAATAA-AAAA
1 AAAATAATAAAA
*
8562575 AAGATAATAAA
1 AAAATAATAAA
8562586 TGAAAGATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAATAATAAAA
Found at i:8563272 original size:15 final size:16
Alignment explanation
Indices: 8563249--8563281 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
8563239 ACTTCGCTTT
8563249 AATATTTAAAATATTA
1 AATATTTAAAATATTA
*
8563265 AATA-TTAATATATTA
1 AATATTTAAAATATTA
8563280 AA
1 AA
8563282 ATGTTAGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATATTTAAAATATTA
Found at i:8564708 original size:9 final size:9
Alignment explanation
Indices: 8564694--8564755 Score: 72
Period size: 9 Copynumber: 6.8 Consensus size: 9
8564684 ATATAGATAG
8564694 AAAAATTTA
1 AAAAATTTA
8564703 AAAAATTTA
1 AAAAATTTA
8564712 AAAAATTT-
1 AAAAATTTA
8564720 AAAAATTTGA
1 AAAAATTT-A
* *
8564730 GTAAAATTGA
1 -AAAAATTTA
8564740 AAAAATTTA
1 AAAAATTTA
*
8564749 TAAAATT
1 AAAAATT
8564756 ATTTTATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
8 8 0.18
9 30 0.67
10 1 0.02
11 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (9 bp):
AAAAATTTA
Found at i:8564808 original size:13 final size:13
Alignment explanation
Indices: 8564790--8564826 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
8564780 ATTATTTAAA
8564790 TAAAAATTATTTT
1 TAAAAATTATTTT
8564803 TAAAAATTATTTT
1 TAAAAATTATTTT
8564816 TAAAAATTATT
1 TAAAAATTATT
8564827 AAAAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAAAAATTATTTT
Found at i:8570372 original size:32 final size:30
Alignment explanation
Indices: 8570336--8570415 Score: 83
Period size: 32 Copynumber: 2.6 Consensus size: 30
8570326 CTTAATTAAG
* *
8570336 TTTCTTTACATCTCTTTTTTTCTTTTCCTTTT
1 TTTCTTTAC-TCTCTTTTTGTCTTTT-CATTT
8570368 TTTCTTT-CTCTTCTATTTTGTCTTTTCATTT
1 TTTCTTTACTC-TCT-TTTTGTCTTTTCATTT
*
8570399 TTACTTTACTCT-TTTTT
1 TTTCTTTACTCTCTTTTT
8570416 CACCATTGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
29 4 0.10
30 3 0.07
31 15 0.36
32 20 0.48
ACGTcount: A:0.07, C:0.20, G:0.01, T:0.71
Consensus pattern (30 bp):
TTTCTTTACTCTCTTTTTGTCTTTTCATTT
Found at i:8570561 original size:16 final size:17
Alignment explanation
Indices: 8570530--8570567 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
8570520 CTTCTTCTTT
8570530 CTATTTATATTATTTAA
1 CTATTTATATTATTTAA
8570547 CTATTTATA-TATTTAA
1 CTATTTATATTATTTAA
*
8570563 TTATT
1 CTATT
8570568 GTGTGCAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
CTATTTATATTATTTAA
Found at i:8578829 original size:27 final size:27
Alignment explanation
Indices: 8578791--8578845 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
8578781 TGTGTGAGGT
8578791 AAATTAGTTCCATTCTCGAGCAATGCC
1 AAATTAGTTCCATTCTCGAGCAATGCC
8578818 AAATTAGTTCCATTCTCGAGCAATGCC
1 AAATTAGTTCCATTCTCGAGCAATGCC
8578845 A
1 A
8578846 TCAATGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (27 bp):
AAATTAGTTCCATTCTCGAGCAATGCC
Found at i:8593540 original size:53 final size:54
Alignment explanation
Indices: 8593476--8593587 Score: 190
Period size: 53 Copynumber: 2.1 Consensus size: 54
8593466 ATTTATAATT
* *
8593476 TTTTTTATTAGTATCTCGTTTGTCACATTCACATCAGGGAATGAACATTCAT-A
1 TTTTTTATTAGTAGCTCATTTGTCACATTCACATCAGGGAATGAACATTCATGA
*
8593529 TTTTTTATTAGTAGCTCATTTGTCACATTCACTTCAGGGAATGAACATTCATGA
1 TTTTTTATTAGTAGCTCATTTGTCACATTCACATCAGGGAATGAACATTCATGA
8593583 TTTTT
1 TTTTT
8593588 CATCAATAGC
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 49 0.89
54 6 0.11
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (54 bp):
TTTTTTATTAGTAGCTCATTTGTCACATTCACATCAGGGAATGAACATTCATGA
Found at i:8604300 original size:29 final size:29
Alignment explanation
Indices: 8604267--8604322 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
8604257 TTTTGTCAAC
**
8604267 GAAATTTTGTTGGAAAAGCATTTCCAATG
1 GAAATTTCATTGGAAAAGCATTTCCAATG
8604296 GAAATTTCATTGGAAAAGCATTTCCAA
1 GAAATTTCATTGGAAAAGCATTTCCAA
8604323 CATAAATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (29 bp):
GAAATTTCATTGGAAAAGCATTTCCAATG
Found at i:8604329 original size:29 final size:29
Alignment explanation
Indices: 8604263--8604352 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 29
8604253 GAATTTTTGT
**
8604263 CAAC-GAAATTTTGTTGGAAAAGCATTTC
1 CAACAGAAATTTCATTGGAAAAGCATTTC
**
8604291 CAATGGAAATTTCATTGGAAAAGCATTTC
1 CAACAGAAATTTCATTGGAAAAGCATTTC
* *
8604320 CAACATAAATTTCGTT-G-AAA--ATTTC
1 CAACAGAAATTTCATTGGAAAAGCATTTC
8604345 CAACAGAA
1 CAACAGAA
8604353 TTGATGCGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
25 12 0.23
27 3 0.06
28 4 0.08
29 34 0.64
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (29 bp):
CAACAGAAATTTCATTGGAAAAGCATTTC
Found at i:8605281 original size:35 final size:37
Alignment explanation
Indices: 8605235--8605319 Score: 111
Period size: 35 Copynumber: 2.3 Consensus size: 37
8605225 TTTCCCATTA
*
8605235 TGGGTTTTGGTTTCCCCATTGTTACT-GCCC-TATTG
1 TGGGTTTTGGTTTCCCCATTGTTACTACCCCATATTG
* *
8605270 TGGGTTTTGGTTTCCTCATTGTTGCTACCCCAATATTG
1 TGGGTTTTGGTTTCCCCATTGTTACTACCCC-ATATTG
*
8605308 TAGGTTTTGGTT
1 TGGGTTTTGGTT
8605320 GCTACCCCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
35 24 0.56
36 3 0.07
38 16 0.37
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (37 bp):
TGGGTTTTGGTTTCCCCATTGTTACTACCCCATATTG
Found at i:8605477 original size:20 final size:20
Alignment explanation
Indices: 8605441--8605478 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8605431 ATTATTTGAA
*
8605441 TGTTGTTTTGAATAATCTAT
1 TGTTGTTTTGAAGAATCTAT
8605461 TGTTGTTTT-AAGGAATCT
1 TGTTGTTTTGAA-GAATCT
8605479 GTCTTGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.24, C:0.05, G:0.18, T:0.53
Consensus pattern (20 bp):
TGTTGTTTTGAAGAATCTAT
Found at i:8620282 original size:28 final size:28
Alignment explanation
Indices: 8620251--8620318 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
8620241 AAAAATTTTG
8620251 GGGCTTAATTAAACACAATAAAAAGATA
1 GGGCTTAATTAAACACAATAAAAAGATA
8620279 GGGCTTAATTAAACACAATAAAAAGATA
1 GGGCTTAATTAAACACAATAAAAAGATA
8620307 GGGCTTAATTAA
1 GGGCTTAATTAA
8620319 CTTTTTTGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (28 bp):
GGGCTTAATTAAACACAATAAAAAGATA
Found at i:8622143 original size:16 final size:15
Alignment explanation
Indices: 8622110--8622151 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
8622100 AAGAATGTAG
*
8622110 AAAATTAAA-GAACT
1 AAAATTAAACTAACT
8622124 AAAATTAAACTAAGCT
1 AAAATTAAACTAA-CT
*
8622140 AAAATAAAACTA
1 AAAATTAAACTA
8622152 GCAAATACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 9 0.38
15 2 0.08
16 13 0.54
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (15 bp):
AAAATTAAACTAACT
Found at i:8624514 original size:30 final size:30
Alignment explanation
Indices: 8624475--8624534 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
8624465 TACATGGCCT
* *
8624475 ACATCTGGCTTTTATATACATGTGGTACAA
1 ACATCTGGCTCTCATATACATGTGGTACAA
* * *
8624505 ACATTTGGCTCTCATATACCTGTGTTACAA
1 ACATCTGGCTCTCATATACATGTGGTACAA
8624535 TGCCCCATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (30 bp):
ACATCTGGCTCTCATATACATGTGGTACAA
Found at i:8633073 original size:370 final size:368
Alignment explanation
Indices: 8632394--8633134 Score: 1412
Period size: 370 Copynumber: 2.0 Consensus size: 368
8632384 TGATTATAAC
*
8632394 AAAGTGGGACAATCACATTTAGGCATTGTGAATCTTTGAAATACTAAGATTCACTCAAATGTCCA
1 AAAGTGGGACAATCACATATAGGCATTGTGAATCTTTGAAATACTAAGATTCACTCAAATGTCCA
8632459 TTTAAAAATCCCCGCCTATGTTTTACATACAGTTAACGCCAAATGTGATGCGTAAAAACAAAAAT
66 TTTAAAAATCCCCGCCTATGTTTTACATACAGTTAACGCCAAATGTGATGCGTAAAAACAAAAAT
*
8632524 TTAGAAAAAAAAATACCTCCCGCTACAAGTATATGCAAATGAAATGCCATTTTCAGCAATAGATG
131 TTAGAAAAAAAAATACCTCCCACTACAAGTATATGCAAATGAAATGCCATTTTCAGCAATAGATG
8632589 TATAAAAAGGGAACCTTATTGAAGACCAATCAAGCACCACATGCACCATGTATCATTTGAGAACC
196 TATAAAAAGGGAACCTTATTGAAGACCAATCAAGCACCACATGCACCATGTATCATTTGAGAACC
*
8632654 ACGAACATGAAAGATGTAGAGACACCAAATTCTCTCAGCAAGTTCACCTGGGAAGACATCATGTA
261 ACGAACATGAAAGATGTAGAGACACCAAATTCTCTCAGCAAGTTCACCTGGAAAGACATCATGTA
8632719 TTTGATGTCCAATATCCAAAAAAAGATTAGAGTGCCTTTCAAA
326 TTTGATGTCCAATATCCAAAAAAAGATTAGAGTGCCTTTCAAA
*
8632762 AAAGTGGGACAATCACATATATGCATTGTGAATCTTTGAAATACTAAGATTCAACTCAAATGTCC
1 AAAGTGGGACAATCACATATAGGCATTGTGAATCTTTGAAATACTAAGATTC-ACTCAAATGTCC
8632827 ATTTAAAAATCCCCGCCTATGTTTTACATACAGTTAACGCCAAATGTGATGCGTAAAAACAAAAA
65 ATTTAAAAATCCCCGCCTATGTTTTACATACAGTTAACGCCAAATGTGATGCGTAAAAACAAAAA
8632892 TTTAGATAAAAAAAAATACCTCCCACTACAAGTATATGCAAATGAAATGCCATTTTCAGCAATAG
130 TTTAG--AAAAAAAAATACCTCCCACTACAAGTATATGCAAATGAAATGCCATTTTCAGCAATAG
8632957 ATGTAT-AAAAGGGAACCTTATTGAAGACCAATCAAGCACCACATGCACCATGTATCATTTGAGA
193 ATGTATAAAAAGGGAACCTTATTGAAGACCAATCAAGCACCACATGCACCATGTATCATTTGAGA
8633021 ACCACGAACATGAAAGATGTAGAGACACCAAATTCTCTCAGCAAGTTCACCTGGAAAGACATCAT
258 ACCACGAACATGAAAGATGTAGAGACACCAAATTCTCTCAGCAAGTTCACCTGGAAAGACATCAT
8633086 GTATTTGATGTCCAATATCCAAAAAAAGATTAGAGTGCCTTTCAAA
323 GTATTTGATGTCCAATATCCAAAAAAAGATTAGAGTGCCTTTCAAA
8633132 AAA
1 AAA
8633135 AAAAAAAACA
Statistics
Matches: 366, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
368 50 0.14
369 82 0.22
370 171 0.47
371 63 0.17
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (368 bp):
AAAGTGGGACAATCACATATAGGCATTGTGAATCTTTGAAATACTAAGATTCACTCAAATGTCCA
TTTAAAAATCCCCGCCTATGTTTTACATACAGTTAACGCCAAATGTGATGCGTAAAAACAAAAAT
TTAGAAAAAAAAATACCTCCCACTACAAGTATATGCAAATGAAATGCCATTTTCAGCAATAGATG
TATAAAAAGGGAACCTTATTGAAGACCAATCAAGCACCACATGCACCATGTATCATTTGAGAACC
ACGAACATGAAAGATGTAGAGACACCAAATTCTCTCAGCAAGTTCACCTGGAAAGACATCATGTA
TTTGATGTCCAATATCCAAAAAAAGATTAGAGTGCCTTTCAAA
Found at i:8639471 original size:30 final size:30
Alignment explanation
Indices: 8639454--8639561 Score: 83
Period size: 25 Copynumber: 3.9 Consensus size: 30
8639444 TAATTAAATA
8639454 AAAATATTAAAATAATATATAATATAAGAAT
1 AAAA-ATTAAAATAATATATAATATAAGAAT
*
8639485 AAAAATTAAAATAA-A-ATAA-ATAA-TA-
1 AAAAATTAAAATAATATATAATATAAGAAT
* * *
8639510 AAAAATTAACAT-TTATATAATAT-AG-GT
1 AAAAATTAAAATAATATATAATATAAGAAT
*
8639537 -AAAATT-AAATAAAATTATAATATAA
1 AAAAATTAAAATAATA-TATAATATAA
8639562 AAAATATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
25 15 0.24
26 13 0.21
27 14 0.23
28 5 0.08
29 1 0.02
30 10 0.16
31 4 0.06
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAAATTAAAATAATATATAATATAAGAAT
Found at i:8639557 original size:49 final size:54
Alignment explanation
Indices: 8639445--8639564 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 54
8639435 ATAATATTAT
8639445 AATTA-AATAAAAATATTAAAATAATATATAATATAAGAATAAAAATTAAAATAA
1 AATTATAATAAAAA-ATTAAAATAATATATAATATAAGAATAAAAATTAAAATAA
* * * *
8639499 AATAAATAATAAAAAATTAACAT-TTATATAATAT-AG-GT-AAAATT-AAATAA
1 AAT-TATAATAAAAAATTAAAATAATATATAATATAAGAATAAAAATTAAAATAA
8639549 AATTATAATATAAAAA
1 AATTATAATA-AAAAA
8639565 ATATTTTAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
49 6 0.10
50 14 0.24
51 6 0.10
52 1 0.02
53 2 0.03
54 13 0.22
55 8 0.14
56 8 0.14
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.31
Consensus pattern (54 bp):
AATTATAATAAAAAATTAAAATAATATATAATATAAGAATAAAAATTAAAATAA
Found at i:8639620 original size:15 final size:15
Alignment explanation
Indices: 8639580--8639620 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
8639570 TTAAGAAATG
8639580 AAAATAAAAT-ATAT
1 AAAATAAAATAATAT
*
8639594 AAAATTATAATAATAT
1 AAAA-TAAAATAATAT
8639610 AAAATAAAATA
1 AAAATAAAATA
8639621 TATGACATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 4 0.17
15 11 0.48
16 8 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATAAAATAATAT
Found at i:8639675 original size:29 final size:30
Alignment explanation
Indices: 8639642--8639939 Score: 99
Period size: 29 Copynumber: 10.0 Consensus size: 30
8639632 AAAATATTTT
*
8639642 AAAATTAT-ATTATAATAAAAATTAATATA
1 AAAATTATAATTATAATAAAAATAAATATA
* *
8639671 AAAA-TATAAATATATTAAAAATAAATATA
1 AAAATTATAATTATAATAAAAATAAATATA
* * *
8639700 ATATTTATAATTA-AATAAATA-AAATATA
1 AAAATTATAATTATAATAAAAATAAATATA
* * * * *
8639728 TGACATTAAAAATATATTTAAGAAATGATATTATATA
1 -AAAATTATAATTATA-ATAA-AAAT-A-A--ATATA
* * *
8639765 AAAA-TATAAATATAA-ATATATTAAA-AT-
1 AAAATTATAATTATAATA-AAAATAAATATA
* *
8639792 AAAATATAAAATTATAATAATAAATAAAAAT-
1 AAAAT-TATAATTATAATAA-AAATAAATATA
* * * *
8639823 AAAA-TAT-ATGATATTAAAAATATATTTA
1 AAAATTATAATTATAATAAAAATAAATATA
* *
8639851 AAATATGAT-ATTAT-AT-AAAATTAATAATA
1 AAA-ATTATAATTATAATAAAAATAAAT-ATA
* * * *
8639880 TAAA-TATAAATAT-TTAAATA-AAATATA
1 AAAATTATAATTATAATAAAAATAAATATA
*
8639907 AAATATTATAATAATAAATAAAAATAAAATATA
1 AAA-ATTATAATTAT-AATAAAAAT-AAATATA
8639940 TGAATTTAAA
Statistics
Matches: 191, Mismatches: 49, Indels: 54
0.65 0.17 0.18
Matches are distributed among these distances:
27 18 0.09
28 40 0.21
29 66 0.35
30 20 0.10
31 15 0.08
32 3 0.02
33 10 0.05
34 2 0.01
35 10 0.05
36 2 0.01
37 5 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAATTATAATTATAATAAAAATAAATATA
Found at i:8639676 original size:18 final size:17
Alignment explanation
Indices: 8639642--8639695 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
8639632 AAAATATTTT
* *
8639642 AAAATTATATTATAATA
1 AAAATTATATAAAAATA
8639659 AAAATTAATATAAAAATA
1 AAAATT-ATATAAAAATA
*
8639677 TAAA-TATATTAAAAATA
1 AAAATTATA-TAAAAATA
8639694 AA
1 AA
8639696 TATAATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 3 0.10
17 16 0.52
18 12 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTATATAAAAATA
Found at i:8639694 original size:23 final size:23
Alignment explanation
Indices: 8639668--8639831 Score: 72
Period size: 23 Copynumber: 6.8 Consensus size: 23
8639658 AAAAATTAAT
8639668 ATAAAAATATAAATATATTAAAA
1 ATAAAAATATAAATATATTAAAA
*
8639691 AT--AAATAT-AATATTTATAATTAA
1 ATAAAAATATAAATATAT-TAA--AA
* * *
8639714 ATAAATAAAATATATGACATTAAAA
1 ATAAA-AATATAAAT-ATATTAAAA
* *
8639739 ATATATTTAAGAAATGATATTATAT-AAAA
1 ATA-A---AA-ATAT-AAAT-ATATTAAAA
*
8639768 ATATAAATATAAATATATT-AAA
1 ATAAAAATATAAATATATTAAAA
*
8639790 AT-AAAATATAAAATTATAATAATAA
1 ATAAAAATAT-AAA-TATATTAA-AA
8639815 ATAAAAATA-AAATATAT
1 ATAAAAATATAAATATAT
8639832 GATATTAAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 40
0.67 0.08 0.25
Matches are distributed among these distances:
20 6 0.06
21 15 0.14
22 12 0.11
23 18 0.17
24 7 0.06
25 12 0.11
26 11 0.10
27 5 0.05
28 3 0.03
29 12 0.11
30 7 0.06
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (23 bp):
ATAAAAATATAAATATATTAAAA
Found at i:8639703 original size:18 final size:18
Alignment explanation
Indices: 8639660--8639704 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
8639650 ATTATAATAA
8639660 AAAT-TAATA-TAAAAAT
1 AAATATAATATTAAAAAT
8639676 ATAA-AT-ATATTAAAAAT
1 A-AATATAATATTAAAAAT
8639693 AAATATAATATT
1 AAATATAATATT
8639705 TATAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
16 6 0.25
17 13 0.54
18 5 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATATAATATTAAAAAT
Found at i:8639777 original size:6 final size:6
Alignment explanation
Indices: 8639766--8639939 Score: 62
Period size: 6 Copynumber: 28.2 Consensus size: 6
8639756 TATTATATAA
*
8639766 AAATAT AAATAT AAATAT -ATTA- AAATA- AAATAT AAA-ATT ATAATAAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATA-T A-AAT-AT
* * * * * *
8639813 AAATAA AAATA- AAATAT ATGATATT AAAAAT ATATTT AAA-AT ATGATAT
1 AAATAT AAATAT AAATAT A-AATA-T AAATAT AAATAT AAATAT A-AATAT
*
8639862 -TATAT AAA-ATT AATAATAT AAATAT AAATATTT AAATA- AAATAT AAAATATT
1 AAATAT AAATA-T -A-AATAT AAATAT AAATA--T AAATAT AAATAT -AAATA-T
*
8639914 ATAATAAT AAATAA AAATA- AAATAT A
1 A-AAT-AT AAATAT AAATAT AAATAT A
8639940 TGAATTTAAA
Statistics
Matches: 129, Mismatches: 15, Indels: 48
0.67 0.08 0.25
Matches are distributed among these distances:
5 34 0.26
6 50 0.39
7 23 0.18
8 19 0.15
9 3 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (6 bp):
AAATAT
Found at i:8639982 original size:107 final size:109
Alignment explanation
Indices: 8639581--8640112 Score: 668
Period size: 107 Copynumber: 5.0 Consensus size: 109
8639571 TAAGAAATGA
*
8639581 AAATAAAATATATAAA-ATTATAATAAT--AT-AAAATAAAATATATGACA-TTAAAAAATATTT
1 AAATAAAATATA-AAATATTATAATAATAAATAAAAATAAAATATATGACATTTAAAATATA-TT
*
8639641 TAA-AATTATATTATAATAAAAATTAAT-ATAAAAATATAAATATATT
64 TAAGAATGATATTAT-AT-AAAATTAATAATAAAAATATAAATATATT
* * *
8639687 AAAAATAAATATAATAT-TTATAAT--TAAAT--AAATAAAATATATGACATTAAAAATATATTT
1 AAATA-AAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTTAAAATATATTT
8639747 AAGAAATGATATTATAT-AAA--AAT-AT--AAATATAAATATATT
65 AAG-AATGATATTATATAAAATTAATAATAAAAATATAAATATATT
* *
8639787 AAAATAAAATAT-AAA-ATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTT
1 -AAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTTAAAATATATTT
* *
8639850 AAAATATGATATTATATAAAATTAATAATATAAATATAAATAT-TT
65 AAGA-ATGATATTATATAAAATTAATAATAAAAATATAAATATATT
8639895 AAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGA-ATTTAAAATATATTTA
1 AAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTTAAAATATATTTA
8639959 AGAATGATATTATATAAAATTAATAAT-AAAATATAAATATATT
66 AGAATGATATTATATAAAATTAATAATAAAAATATAAATATATT
* *
8640002 AAAAATAAATATAAAAT-TTAT-ATAATAAATAAAAAATAAAATATATGATA-TTAAAATATATT
1 AAATA-AAATATAAAATATTATAATAATAAAT-AAAAATAAAATATATGACATTTAAAATATATT
8640064 TAAGAATGATATTATATAAAAGTTAATAATAAAAA-ATATAATATATT
64 TAAGAATGATATTATATAAAA-TTAATAATAAAAATATA-AATATATT
8640111 AA
1 AA
8640113 CTTATATTTT
Statistics
Matches: 384, Mismatches: 13, Indels: 55
0.85 0.03 0.12
Matches are distributed among these distances:
99 9 0.02
100 21 0.05
101 9 0.02
102 6 0.02
103 44 0.11
104 7 0.02
105 22 0.06
106 49 0.13
107 114 0.30
108 45 0.12
109 58 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (109 bp):
AAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTTAAAATATATTTA
AGAATGATATTATATAAAATTAATAATAAAAATATAAATATATT
Found at i:8639989 original size:60 final size:59
Alignment explanation
Indices: 8639918--8640109 Score: 201
Period size: 56 Copynumber: 3.4 Consensus size: 59
8639908 AATATTATAA
8639918 TAATAAATAAAAATAAAATATATGAATTTAAAATATATTTAAGAATGATATTATATAAAAT
1 TAAT-AATAAAAATAAAATATATG-ATTTAAAATATATTTAAGAATGATATTATATAAAAT
* * * *
8639979 TAATAAT-AAAATATAA-ATAT-ATTAAAAATAAATAT-A-AA--AT-TTATAT--AAT
1 TAATAATAAAAATAAAATATATGATTTAAAATATATTTAAGAATGATATTATATAAAAT
*
8640028 AAAT-A-AAAAATAAAATATATGATATTAAAATATATTTAAGAATGATATTATATAAAAGT
1 TAATAATAAAAATAAAATATATGAT-TTAAAATATATTTAAGAATGATATTATATAAAA-T
*
8640087 TAATAATAAAAAATATAATATAT
1 TAATAAT-AAAAATAAAATATAT
8640110 TAACTTATAT
Statistics
Matches: 105, Mismatches: 11, Indels: 29
0.72 0.08 0.20
Matches are distributed among these distances:
48 9 0.09
49 10 0.10
50 2 0.02
51 16 0.15
52 3 0.03
53 2 0.02
54 2 0.02
55 3 0.03
56 18 0.17
58 6 0.06
59 12 0.11
60 4 0.04
61 4 0.04
62 14 0.13
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (59 bp):
TAATAATAAAAATAAAATATATGATTTAAAATATATTTAAGAATGATATTATATAAAAT
Found at i:8640033 original size:215 final size:207
Alignment explanation
Indices: 8639580--8640110 Score: 708
Period size: 215 Copynumber: 2.5 Consensus size: 207
8639570 TTAAGAAATG
* *
8639580 AAAATAAAATATATAAAAT-TATAAT-AATATAAAATAAAATATATGACATTAAAAA-ATATTTT
1 AAAATAAAATATA-AAATTATATAATAAATA-AAAATAAAATATATGATATTAAAAATATA-TTT
*
8639642 AAAAT-T-ATATTATAATAAAAATTAAT-ATAAAAATATAAATATATTAAAAATAAATATAATAT
63 AAAATATGATATTAT-AT-AAAATTAATAATAAAAATATAAATAT-TTAAAAATAAATATAAAAT
8639704 TTATAATTAAATAAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAAAAA
125 TTATAATTAAATAAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAAAAA
8639769 TATAAATATAAATATATT
190 TATAAATATAAATATATT
8639787 AAAATAAAATATAAAATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAA
1 AAAATAAAATATAAAATTAT-ATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAA
* *
8639852 AATATGATATTATATAAAATTAATAATATAAATATAAATATTTAAATA-AAATATAAAATATTAT
65 AATATGATATTATATAAAATTAATAATAAAAATATAAATATTTAAAAATAAATATAAAAT-TTAT
*
8639916 AATAATAAATAAAAATAAAATATATGA-ATTTAAAATATATTTAAG-AATGATATTATATAAAAT
129 AAT--TAAAT--AAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATAT-AAA-
8639979 TAATAATAAAATATAAATATATT
188 -AAT-AT-AAATATAAATATATT
8640002 AAAA-ATAAATATAAAATTTATATAATAAATAAAAAATAAAATATATGATATT-AAAATATATTT
1 AAAATA-AAATATAAAA-TTATATAATAAAT-AAAAATAAAATATATGATATTAAAAATATATTT
*
8640065 AAGA-ATGATATTATATAAAAGTTAATAATAAAAAATATAATATATT
63 AAAATATGATATTATATAAAA-TTAATAAT-AAAAATATAA-ATATT
8640111 AACTTATATT
Statistics
Matches: 293, Mismatches: 8, Indels: 36
0.87 0.02 0.11
Matches are distributed among these distances:
206 4 0.01
207 24 0.08
208 59 0.20
209 25 0.09
210 25 0.09
211 20 0.07
212 15 0.05
213 3 0.01
214 19 0.06
215 60 0.20
216 34 0.12
217 5 0.02
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (207 bp):
AAAATAAAATATAAAATTATATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAAA
ATATGATATTATATAAAATTAATAATAAAAATATAAATATTTAAAAATAAATATAAAATTTATAA
TTAAATAAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAAAAATATAAA
TATAAATATATT
Found at i:8640280 original size:15 final size:15
Alignment explanation
Indices: 8640260--8640300 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
8640250 TTTTCCCTGT
*
8640260 AATCACATTGCTTGC
1 AATCACATTGCTTAC
* *
8640275 AATCACATTACTTAT
1 AATCACATTGCTTAC
8640290 AATCACATTGC
1 AATCACATTGC
8640301 ATTGTAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (15 bp):
AATCACATTGCTTAC
Found at i:8642496 original size:26 final size:23
Alignment explanation
Indices: 8642444--8642488 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
8642434 AATAGTTGAA
8642444 CTTA-TTATATTTATCTTGTAAT
1 CTTAGTTATATTTATCTTGTAAT
*
8642466 CTTAGTTATAGTTTATTTTGTAA
1 CTTAGTTATA-TTTATCTTGTAA
8642489 ACTCTTAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 5 0.25
24 11 0.55
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.58
Consensus pattern (23 bp):
CTTAGTTATATTTATCTTGTAAT
Found at i:8652460 original size:11 final size:11
Alignment explanation
Indices: 8652444--8652469 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8652434 ATTTGTCCCC
8652444 CCTTCTTTCTT
1 CCTTCTTTCTT
8652455 CCTTCTTTCTT
1 CCTTCTTTCTT
8652466 CCTT
1 CCTT
8652470 TATTTGGTGC
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:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (11 bp):
CCTTCTTTCTT
Found at i:8655801 original size:66 final size:66
Alignment explanation
Indices: 8655695--8655827 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
8655685 CAATGACACC
*
8655695 AGCATTATCTGCAAACAAATAAATAAACCCAAACTAAGTTTCCAACAAAAACAAATAAATTCTAG
1 AGCATTATCTGCAAACAAATAAATAAACCCAAACTAAGTTTCAAACAAAAACAAATAAATTCTAG
8655760 T
66 T
* * *
8655761 AGCATTATCTGCGAACAGATAAATAAACCCTAACTAAGTTTCAAACAAAAACAAATAAATTCTAG
1 AGCATTATCTGCAAACAAATAAATAAACCCAAACTAAGTTTCAAACAAAAACAAATAAATTCTAG
8655826 T
66 T
8655827 A
1 A
8655828 CTAAGTAACT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (66 bp):
AGCATTATCTGCAAACAAATAAATAAACCCAAACTAAGTTTCAAACAAAAACAAATAAATTCTAG
T
Found at i:8661526 original size:14 final size:15
Alignment explanation
Indices: 8661507--8661535 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
8661497 GATTGGTTGC
8661507 TAACAGTTT-ATTGT
1 TAACAGTTTCATTGT
8661521 TAACAGTTTCATTGT
1 TAACAGTTTCATTGT
8661536 GATTCCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (15 bp):
TAACAGTTTCATTGT
Found at i:8661568 original size:27 final size:26
Alignment explanation
Indices: 8661538--8661630 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 26
8661528 TTCATTGTGA
8661538 TTCCTATTTTTATTGTTAGTGGTAGTT
1 TTCC-ATTTTTATTGTTAGTGGTAGTT
* * *
8661565 TTCCATTTCATGTTGTTAGAGGTTGAG-T
1 TTCCATTT-TTATTGTTAGTGG-T-AGTT
*
8661593 CTCCACCCTATTTTATTGTTAGTGGTAGTT
1 TTCCA---T-TTTTATTGTTAGTGGTAGTT
8661623 TTCCATTT
1 TTCCATTT
8661631 CATGTTGTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 17
0.67 0.11 0.23
Matches are distributed among these distances:
26 6 0.12
27 15 0.30
28 6 0.12
29 4 0.08
30 6 0.12
31 11 0.22
32 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (26 bp):
TTCCATTTTTATTGTTAGTGGTAGTT
Found at i:8661610 original size:58 final size:59
Alignment explanation
Indices: 8661540--8661657 Score: 211
Period size: 58 Copynumber: 2.0 Consensus size: 59
8661530 CATTGTGATT
8661540 CCTATTTTTATTGTTAGTGGTAGTTTTCCATTTCATGTTGTTAGAGGTTGAGTCTCCAC
1 CCTATTTTTATTGTTAGTGGTAGTTTTCCATTTCATGTTGTTAGAGGTTGAGTCTCCAC
* *
8661599 CCTA-TTTTATTGTTAGTGGTAGTTTTCCATTTCATGTTGTTGGAGGTTGTGTCTCCAC
1 CCTATTTTTATTGTTAGTGGTAGTTTTCCATTTCATGTTGTTAGAGGTTGAGTCTCCAC
8661657 C
1 C
8661658 TTTCCACTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 53 0.93
59 4 0.07
ACGTcount: A:0.15, C:0.16, G:0.21, T:0.47
Consensus pattern (59 bp):
CCTATTTTTATTGTTAGTGGTAGTTTTCCATTTCATGTTGTTAGAGGTTGAGTCTCCAC
Found at i:8661638 original size:27 final size:27
Alignment explanation
Indices: 8661550--8661639 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 27
8661540 CCTATTTTTA
8661550 TTGTTAGTGGTAGTTTTCCATTTCATG
1 TTGTTAGTGGTAGTTTTCCATTTCATG
* * * *
8661577 TTGTTAGAGGTTGAG-TCTCCACCCTATT-TTA
1 TTGTTAGTGG-T-AGTTTTCCA---T-TTCATG
8661608 TTGTTAGTGGTAGTTTTCCATTTCATG
1 TTGTTAGTGGTAGTTTTCCATTTCATG
8661635 TTGTT
1 TTGTT
8661640 GGAGGTTGTG
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
26 2 0.04
27 16 0.34
28 6 0.13
29 4 0.09
30 6 0.13
31 11 0.23
32 2 0.04
ACGTcount: A:0.16, C:0.13, G:0.21, T:0.50
Consensus pattern (27 bp):
TTGTTAGTGGTAGTTTTCCATTTCATG
Found at i:8675481 original size:31 final size:31
Alignment explanation
Indices: 8675443--8675543 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 31
8675433 GGGAACATAT
8675443 ATACAACAAGAGCATAAGATGGATAACTAGA
1 ATACAACAAGAGCATAAGATGGATAACTAGA
*
8675474 ATACAACAAGAAGTTCAGTAAG-T---T-A-TA-T
1 ATACAACAAG-AG--CA-TAAGATGGATAACTAGA
*
8675502 ATACAACAAGAGCATAAGAAGGATAACTAGA
1 ATACAACAAGAGCATAAGATGGATAACTAGA
8675533 ATACAACAAGA
1 ATACAACAAGA
8675544 AGTTCAGTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 22
0.69 0.04 0.27
Matches are distributed among these distances:
24 4 0.07
25 2 0.04
27 2 0.04
28 11 0.20
29 3 0.05
30 3 0.05
31 22 0.39
32 2 0.04
34 3 0.05
35 4 0.07
ACGTcount: A:0.52, C:0.13, G:0.17, T:0.18
Consensus pattern (31 bp):
ATACAACAAGAGCATAAGATGGATAACTAGA
Found at i:8675530 original size:59 final size:59
Alignment explanation
Indices: 8675439--8675557 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
8675429 TTCTGGGAAC
*
8675439 ATATATACAACAAGAGCATAAGATGGATAACTAGAATACAACAAGAAGTTCAGTAAGTT
1 ATATATACAACAAGAGCATAAGAAGGATAACTAGAATACAACAAGAAGTTCAGTAAGTT
8675498 ATATATACAACAAGAGCATAAGAAGGATAACTAGAATACAACAAGAAGTTCAGTAAGTT
1 ATATATACAACAAGAGCATAAGAAGGATAACTAGAATACAACAAGAAGTTCAGTAAGTT
8675557 A
1 A
8675558 GGAGACGGAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (59 bp):
ATATATACAACAAGAGCATAAGAAGGATAACTAGAATACAACAAGAAGTTCAGTAAGTT
Found at i:8687585 original size:31 final size:31
Alignment explanation
Indices: 8687547--8687624 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
8687537 GTATCTGTAA
*
8687547 AACAAGTAAAAGGTGGTTACACGCCATGCAT
1 AACAAGTAAAAGGTGGTGACACGCCATGCAT
*
8687578 AACAAGTAAAAGGCGGTGACACGCCATGCAT
1 AACAAGTAAAAGGTGGTGACACGCCATGCAT
*
8687609 AACAAGTAAAAAGTGG
1 AACAAGTAAAAGGTGG
8687625 CGTGTGGGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.15
Consensus pattern (31 bp):
AACAAGTAAAAGGTGGTGACACGCCATGCAT
Found at i:8687678 original size:31 final size:31
Alignment explanation
Indices: 8687643--8687950 Score: 352
Period size: 31 Copynumber: 10.0 Consensus size: 31
8687633 TGGTGAGACA
* *
8687643 CCATGCATAACAAGTAAAAAGTCATGACACG
1 CCATGCATAACAAGTAAAATGTCGTGACACG
* * *
8687674 CCATGCATAATAAGTAAAAGGTGGTGACACG
1 CCATGCATAACAAGTAAAATGTCGTGACACG
* * **
8687705 GCATGCATAACAAGTAAAAGGTCGTGACATT
1 CCATGCATAACAAGTAAAATGTCGTGACACG
8687736 CCATGCATAACAAGTAAAA-GTCGTGACACG
1 CCATGCATAACAAGTAAAATGTCGTGACACG
* * *
8687766 CCATGTATAATAAGTAAAA-GTCATGACACG
1 CCATGCATAACAAGTAAAATGTCGTGACACG
* * * *
8687796 CCATGTATAATAAGTAAAAGGTCATGACACG
1 CCATGCATAACAAGTAAAATGTCGTGACACG
* *
8687827 CCATCCATAATAAGTAAAATG-CGGTGACACG
1 CCATGCATAACAAGTAAAATGTC-GTGACACG
* *
8687858 CCATGCATAACAAGTAAAATGTGGTCACACG
1 CCATGCATAACAAGTAAAATGTCGTGACACG
* * * *
8687889 TCATTCATAACAAGTCAAATGTTGTGACACG
1 CCATGCATAACAAGTAAAATGTCGTGACACG
* *
8687920 CTATGCATAACAAGTCAAATGTCGTGACACG
1 CCATGCATAACAAGTAAAATGTCGTGACACG
8687951 ATATGTAGAC
Statistics
Matches: 242, Mismatches: 32, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
30 56 0.23
31 186 0.77
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (31 bp):
CCATGCATAACAAGTAAAATGTCGTGACACG
Found at i:8687876 original size:122 final size:123
Alignment explanation
Indices: 8687643--8687950 Score: 368
Period size: 122 Copynumber: 2.5 Consensus size: 123
8687633 TGGTGAGACA
** *
8687643 CCATGCATAACAAGTAAAAAGTCATGACACGCCATGCATAATAAGTAAAAGGTGGTGACACGGCA
1 CCATGCATAACAAGTAAAAAGTCATGACACGCCATGCATAATAAGTAAAAGGTCATGACACGCCA
* **
8687708 TGCATAACAAGTAAAAGGTCGTGACATTCCATGCATAACAAGTAAAAGTCGTGACACG
66 TCCATAACAAGTAAAAGGTCGTGACACGCCATGCATAACAAGTAAAAGTCGTGACACG
* * *
8687766 CCATGTATAATAAGT-AAAAGTCATGACACGCCATGTATAATAAGTAAAAGGTCATGACACGCCA
1 CCATGCATAACAAGTAAAAAGTCATGACACGCCATGCATAATAAGTAAAAGGTCATGACACGCCA
* * * *
8687830 TCCATAATAAGTAAAATG-CGGTGACACGCCATGCATAACAAGTAAAATGTGGTCACACG
66 TCCATAACAAGTAAAAGGTC-GTGACACGCCATGCATAACAAGTAAAA-GTCGTGACACG
* * * * ** * * * * *
8687889 TCATTCATAACAAGTCAAATGTTGTGACACGCTATGCATAACAAGTCAAATGTCGTGACACG
1 CCATGCATAACAAGTAAAAAGTCATGACACGCCATGCATAATAAGTAAAAGGTCATGACACG
8687951 ATATGTAGAC
Statistics
Matches: 156, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
121 1 0.01
122 85 0.54
123 33 0.21
124 37 0.24
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (123 bp):
CCATGCATAACAAGTAAAAAGTCATGACACGCCATGCATAATAAGTAAAAGGTCATGACACGCCA
TCCATAACAAGTAAAAGGTCGTGACACGCCATGCATAACAAGTAAAAGTCGTGACACG
Found at i:8688612 original size:47 final size:46
Alignment explanation
Indices: 8688548--8689360 Score: 642
Period size: 47 Copynumber: 17.4 Consensus size: 46
8688538 CTTTCATTGT
* * * *
8688548 CGTGTCACTAACTCTGAACACTGACTTGTCATAGATTCCCTCCATGA
1 CGTGTCACAAACTCTGAACACT-ACGTGTCACAGATTCCCTCCATGC
* * * * *
8688595 CGTGTCACAAACCCTGAACCCTACCATGTCACAAATTCCCTCCATGG
1 CGTGTCACAAACTCTGAACACTA-CGTGTCACAGATTCCCTCCATGC
* * *
8688642 CGTGTCACAAACTCTGAATACCGT-CGTGTCACAAATTCCATCCATGC
1 CGTGTCACAAACTCTGAACA-C-TACGTGTCACAGATTCCCTCCATGC
* * * *
8688689 CGTGTCACAAACCCTGAACCCTACCGTGTCACAAATTCCCTCCATGG
1 CGTGTCACAAACTCTGAACACTA-CGTGTCACAGATTCCCTCCATGC
* * * *
8688736 CGTGTCACAAACTCTGAATACCATCGTGTCATAGATTCCATCCATGC
1 CGTGTCACAAACTCTGAACACTA-CGTGTCACAGATTCCCTCCATGC
* * *
8688783 CATGT--CAAACTCTGAACTCTAGCATGTCACAGATTCCCTCCATGC
1 CGTGTCACAAACTCTGAACACTA-CGTGTCACAGATTCCCTCCATGC
* * *
8688828 CGTGTCACCAACTCTGAACACTAGTGTGTCACAGATTCCCTCCATGG
1 CGTGTCACAAACTCTGAACACTA-CGTGTCACAGATTCCCTCCATGC
* * *
8688875 CGTGTCACAAACCCTAAATCA-TACCGTGTCACAGATTCCCTCCATGG
1 CGTGTCACAAACTCTGAA-CACTA-CGTGTCACAGATTCCCTCCATGC
* * * ** * *
8688922 CGTGTCACAATCTCTAAATACTGTTGTGTCACAGATTCCATCCATGT
1 CGTGTCACAAACTCTGAACACT-ACGTGTCACAGATTCCCTCCATGC
* * *** * * *
8688969 CGTGT--CAAACTTTAAATTTTGGCTTATCACAGATTCCCTCCATGC
1 CGTGTCACAAACTCTGAACACT-ACGTGTCACAGATTCCCTCCATGC
* * * *
8689014 CGTGTCACCAACTCTGAACTCTAGAGTGTCACAGATTTCCTCCATTG-
1 CGTGTCACAAACTCTGAACACTA-CGTGTCACAGATTCCCTCCA-TGC
* * * * * *
8689061 TGTGTCACAAACCCTGAACCCTATCATGTCATAGATTCCCTCCATGA
1 CGTGTCACAAACTCTGAACACTA-CGTGTCACAGATTCCCTCCATGC
* * * *
8689108 CATGTCACAAACCCTGAACCCTATCGTGTCACAGATTCCCTCCATGA
1 CGTGTCACAAACTCTGAACACTA-CGTGTCACAGATTCCCTCCATGC
* * * * *
8689155 CATGTCACAAACTCTGAATACTGTCGTGTCACAGATTCCATCCATGT
1 CGTGTCACAAACTCTGAACACT-ACGTGTCACAGATTCCCTCCATGC
* * *
8689202 CATGT--CAAACTTTGAACTCTAGCGTGTCACAGATTCCCTCCATGC
1 CGTGTCACAAACTCTGAACACTA-CGTGTCACAGATTCCCTCCATGC
* * * ** *
8689247 CTTGTCATAAACTCTGAA-ATCTGGA-GTTTCACAGATTCTATCCATGG
1 CGTGTCACAAACTCTGAACA-CT--ACGTGTCACAGATTCCCTCCATGC
* *
8689294 CGTGTCACAAACTCTGAACTCTGGA-GTGTCACAGATTCCCTCCATGG
1 CGTGTCACAAACTCTGAACACT--ACGTGTCACAGATTCCCTCCATGC
* *
8689341 CATGTCATGAAACTCTGAAC
1 CGTGTCA-CAAACTCTGAAC
8689361 CTTGTCGTGT
Statistics
Matches: 628, Mismatches: 114, Indels: 47
0.80 0.14 0.06
Matches are distributed among these distances:
45 110 0.18
46 5 0.01
47 495 0.79
48 16 0.03
49 2 0.00
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (46 bp):
CGTGTCACAAACTCTGAACACTACGTGTCACAGATTCCCTCCATGC
Found at i:8688651 original size:23 final size:23
Alignment explanation
Indices: 8688582--8688746 Score: 90
Period size: 23 Copynumber: 7.0 Consensus size: 23
8688572 CTTGTCATAG
*
8688582 ATTCCCTCCATGACGTGTCACAA
1 ATTCCCTCCATGCCGTGTCACAA
* * *
8688605 A--CCCTGAACCCTACCATGTCACAA
1 ATTCCCT---CCATGCCGTGTCACAA
*
8688629 ATTCCCTCCATGGCGTGTCACAA
1 ATTCCCTCCATGCCGTGTCACAA
* ** *
8688652 A--CTCTGAATACCGTCGTGTCACAA
1 ATTCCCTCCAT---GCCGTGTCACAA
*
8688676 ATTCCATCCATGCCGTGTCACAA
1 ATTCCCTCCATGCCGTGTCACAA
* *
8688699 A--CCCTGAACCCTACCGTGTCACAA
1 ATTCCCT---CCATGCCGTGTCACAA
*
8688723 ATTCCCTCCATGGCGTGTCACAA
1 ATTCCCTCCATGCCGTGTCACAA
8688746 A
1 A
8688747 CTCTGAATAC
Statistics
Matches: 104, Mismatches: 23, Indels: 30
0.66 0.15 0.19
Matches are distributed among these distances:
21 12 0.12
23 40 0.38
24 40 0.38
26 12 0.12
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (23 bp):
ATTCCCTCCATGCCGTGTCACAA
Found at i:8688720 original size:24 final size:24
Alignment explanation
Indices: 8688595--8688723 Score: 74
Period size: 24 Copynumber: 5.5 Consensus size: 24
8688585 CCCTCCATGA
*
8688595 CGTGTCACAAACCCTGAACCCTAC
1 CGTGTCACAAACCCTGAACCATAC
* **
8688619 CATGTCACAAATTCCCT---CCATGG
1 CGTGTCACAAA--CCCTGAACCATAC
* *
8688642 CGTGTCACAAACTCTGAATACCGT--
1 CGTGTCACAAACCCTG-A-ACCATAC
* * *
8688666 CGTGTCACAAATTCC--ATCCATGC
1 CGTGTCACAAA-CCCTGAACCATAC
*
8688689 CGTGTCACAAACCCTGAACCCTAC
1 CGTGTCACAAACCCTGAACCATAC
8688713 CGTGTCACAAA
1 CGTGTCACAAA
8688724 TTCCCTCCAT
Statistics
Matches: 78, Mismatches: 15, Indels: 24
0.67 0.13 0.21
Matches are distributed among these distances:
21 6 0.08
22 3 0.04
23 24 0.31
24 37 0.47
25 1 0.01
26 7 0.09
ACGTcount: A:0.29, C:0.36, G:0.14, T:0.22
Consensus pattern (24 bp):
CGTGTCACAAACCCTGAACCATAC
Found at i:8688844 original size:186 final size:187
Alignment explanation
Indices: 8688548--8689360 Score: 759
Period size: 186 Copynumber: 4.3 Consensus size: 187
8688538 CTTTCATTGT
* * * * * * * *
8688548 CGTGTCACTAACTCTGAACACTGA-CTTGTCATAGATTCCCTCCATGACGTGTCACAAACCCTGA
1 CGTGTCACAAACTCTGAATAC-CATCGTGTCACAGATTCCATCCATGACATGT-ACAAACTCTGA
* * * * * *
8688612 ACCCTACCATGTCACAAATTCCCTCCATGGCGTGTCACAAACTCTGAA-TAC-CGTCGTGTCACA
64 ACTCTAGCATGTCACAGATTCCCTCCATGCCGTGTCACCAACTCTGAACT-CTAG-CGTGTCACA
* *
8688675 AATTCCATCCATGCCGTGTCACAAACCCTGAACCCTACCGTGTCACAAATTCCCTCCATGG
127 AATTCCCTCCATGCCGTGTCACAAACCCTGAACCCTACCGTGTCACAGATTCCCTCCATGG
* *
8688736 CGTGTCACAAACTCTGAATACCATCGTGTCATAGATTCCATCCATGCCATGT-CAAACTCTGAAC
1 CGTGTCACAAACTCTGAATACCATCGTGTCACAGATTCCATCCATGACATGTACAAACTCTGAAC
* * *
8688800 TCTAGCATGTCACAGATTCCCTCCATGCCGTGTCACCAACTCTGAACACTAGTGTGTCACAGATT
66 TCTAGCATGTCACAGATTCCCTCCATGCCGTGTCACCAACTCTGAACTCTAGCGTGTCACAAATT
* * * *
8688865 CCCTCCATGGCGTGTCACAAACCCTAAATCATACCGTGTCACAGATTCCCTCCATGG
131 CCCTCCATGCCGTGTCACAAACCCTGAACCCTACCGTGTCACAGATTCCCTCCATGG
* * ** * * * * * *
8688922 CGTGTCACAATCTCTAAATACTGTTGTGTCACAGATTCCATCCATGTCGTGT-CAAACTTTAAAT
1 CGTGTCACAAACTCTGAATACCATCGTGTCACAGATTCCATCCATGACATGTACAAACTCTGAAC
* * * * * *
8688986 TTTGGCTTATCACAGATTCCCTCCATGCCGTGTCACCAACTCTGAACTCTAGAGTGTCACAGATT
66 TCTAGCATGTCACAGATTCCCTCCATGCCGTGTCACCAACTCTGAACTCTAGCGTGTCACAAATT
* * * * * *
8689051 TCCTCCATTG-TGTGTCACAAACCCTGAACCCTATCATGTCATAGATTCCCTCCATGA
131 CCCTCCA-TGCCGTGTCACAAACCCTGAACCCTACCGTGTCACAGATTCCCTCCATGG
* * * *
8689108 CATGTCACAAACCCTGAA-CCCTATCGTGTCACAGATTCCCTCCATGACATGTCACAAACTCTGA
1 CGTGTCACAAACTCTGAATACC-ATCGTGTCACAGATTCCATCCATGACATGT-ACAAACTCTGA
* * * * *
8689172 A-TACT-GTCGTGTCACAGATTCCATCCATGTCATGTCA--AACTTTGAACTCTAGCGTGTCACA
64 ACT-CTAG-CATGTCACAGATTCCCTCCATGCCGTGTCACCAACTCTGAACTCTAGCGTGTCACA
* * * * ** *** * **
8689233 GATTCCCTCCATGCCTTGTCATAAACTCTGAAATCTGGAGTTTCACAGATTCTATCCATGG
127 AATTCCCTCCATGCCGTGTCACAAACCCTGAACCCTACCGTGTCACAGATTCCCTCCATGG
**** * * *
8689294 CGTGTCACAAACTCTGAACT-CTGGAGTGTCACAGATTCCCTCCATGGCATGTCATGAAACTCTG
1 CGTGTCACAAACTCTGAA-TACCATCGTGTCACAGATTCCATCCATGACATGT-A-CAAACTCTG
8689358 AAC
63 AAC
8689361 CTTGTCGTGT
Statistics
Matches: 517, Mismatches: 94, Indels: 28
0.81 0.15 0.04
Matches are distributed among these distances:
185 3 0.01
186 419 0.81
187 17 0.03
188 78 0.15
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (187 bp):
CGTGTCACAAACTCTGAATACCATCGTGTCACAGATTCCATCCATGACATGTACAAACTCTGAAC
TCTAGCATGTCACAGATTCCCTCCATGCCGTGTCACCAACTCTGAACTCTAGCGTGTCACAAATT
CCCTCCATGCCGTGTCACAAACCCTGAACCCTACCGTGTCACAGATTCCCTCCATGG
Found at i:8688882 original size:23 final size:23
Alignment explanation
Indices: 8688853--8688930 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
8688843 GAACACTAGT
8688853 GTGTCACAGATTCCCTCCATGGC
1 GTGTCACAGATTCCCTCCATGGC
* * **
8688876 GTGTCACA-A-ACCCTAAATCATACC
1 GTGTCACAGATTCCCT---CCATGGC
8688900 GTGTCACAGATTCCCTCCATGGC
1 GTGTCACAGATTCCCTCCATGGC
8688923 GTGTCACA
1 GTGTCACA
8688931 ATCTCTAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
21 4 0.10
22 1 0.02
23 20 0.48
24 12 0.29
25 1 0.02
26 4 0.10
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.24
Consensus pattern (23 bp):
GTGTCACAGATTCCCTCCATGGC
Found at i:8688975 original size:233 final size:229
Alignment explanation
Indices: 8688557--8689347 Score: 822
Period size: 233 Copynumber: 3.4 Consensus size: 229
8688547 TCGTGTCACT
* * * **
8688557 AACTCTGAACACTG-ACTTGTCATAGATTCCCTCCATGACGTGTCACAAACCCTGAACCCTACCA
1 AACTCTGAACTCTGCA-GTGTCACAGATTCCCTCCATG-CGTGTCACAAACCCTGAACCCTAGTA
* * * * * *
8688621 TGTCACAAATTCCCTCCATGGCGTGTCACAAACTCTGAAT-A-CCGTCGTGTCACAAATTCCATC
64 TGTCACAGATTCCCTCCATGGCATGTCACAAACCCTGAATCATAC--CGTGTCACAGATTCCCTC
* * ** ** * * *
8688684 CATGCCGTGTCACAAACCCTGAACCCTACCGTGTCACAAATTCCCTCCATGGCGTGTCACAAACT
127 CATGACGTGTCACAAACTCTGAATACTGTCGTGTCACAGATTCCATCCATGTCGTGT--CAAACT
* * * * *
8688749 CTGAATACCATCGTGTCATAGATTCCATCCATGCCATGTCA
190 TTGAAT-CTAGCGTGTCACAGATTCCCTCCATGCCATGTCA
* * * *
8688790 AACTCTGAACTCTAGCA-TGTCACAGATTCCCTCCATGCCGTGTCACCAACTCTGAACACTAGTG
1 AACTCTGAACTCT-GCAGTGTCACAGATTCCCTCCATG-CGTGTCACAAACCCTGAACCCTAGTA
* *
8688854 TGTCACAGATTCCCTCCATGGCGTGTCACAAACCCTAAATCATACCGTGTCACAGATTCCCTCCA
64 TGTCACAGATTCCCTCCATGGCATGTCACAAACCCTGAATCATACCGTGTCACAGATTCCCTCCA
* * * * *
8688919 TGGCGTGTCACAATCTCTAAATACTGTTGTGTCACAGATTCCATCCATGTCGTGTCAAACTTTAA
129 TGACGTGTCACAAACTCTGAATACTGTCGTGTCACAGATTCCATCCATGTCGTGTCAAACTTTGA
* * * * *
8688984 ATTTTGGCTTATCACAGATTCCCTCCATGCCGTGTCA
194 A-TCTAGCGTGTCACAGATTCCCTCCATGCCATGTCA
* *
8689021 CCAACTCTGAACTCTAG-AGTGTCACAGATTTCCTCCATTGTGTGTCACAAACCCTGAACCCTA-
1 --AACTCTGAACTCT-GCAGTGTCACAGATTCCCTCCA-TGCGTGTCACAAACCCTGAACCCTAG
* * * * *
8689084 TCATGTCATAGATTCCCTCCATGACATGTCACAAACCCTGAACCCTATCGTGTCACAGATTCCCT
62 T-ATGTCACAGATTCCCTCCATGGCATGTCACAAACCCTGAATCATACCGTGTCACAGATTCCCT
* *
8689149 CCATGACATGTCACAAACTCTGAATACTGTCGTGTCACAGATTCCATCCATGTCATGTCAAACTT
126 CCATGACGTGTCACAAACTCTGAATACTGTCGTGTCACAGATTCCATCCATGTCGTGTCAAACTT
*
8689214 TGAACTCTAGCGTGTCACAGATTCCCTCCATGCCTTGTCATA
191 TGAA-TCTAGCGTGTCACAGATTCCCTCCATGCCATGTC--A
* * * ** * * *
8689256 AACTCTGAAATCTGGAGTTTCACAGATTCTATCCATGGCGTGTCACAAACTCTGAACTCT-GGAG
1 AACTCTGAACTCTGCAGTGTCACAGATTCCCTCCAT-GCGTGTCACAAACCCTGAACCCTAGTA-
8689320 TGTCACAGATTCCCTCCATGGCATGTCA
64 TGTCACAGATTCCCTCCATGGCATGTCA
8689348 TGAAACTCTG
Statistics
Matches: 467, Mismatches: 75, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
231 34 0.07
232 6 0.01
233 420 0.90
234 4 0.01
235 3 0.01
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (229 bp):
AACTCTGAACTCTGCAGTGTCACAGATTCCCTCCATGCGTGTCACAAACCCTGAACCCTAGTATG
TCACAGATTCCCTCCATGGCATGTCACAAACCCTGAATCATACCGTGTCACAGATTCCCTCCATG
ACGTGTCACAAACTCTGAATACTGTCGTGTCACAGATTCCATCCATGTCGTGTCAAACTTTGAAT
CTAGCGTGTCACAGATTCCCTCCATGCCATGTCA
Found at i:8689163 original size:23 final size:23
Alignment explanation
Indices: 8689085--8689163 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
8689075 TGAACCCTAT
*
8689085 CATGTCATAGATTCCCTCCATGA
1 CATGTCACAGATTCCCTCCATGA
* *
8689108 CATGTCACA-A-ACCCTGAACCCT-A
1 CATGTCACAGATTCCCT---CCATGA
*
8689131 TCGTGTCACAGATTCCCTCCATGA
1 -CATGTCACAGATTCCCTCCATGA
8689155 CATGTCACA
1 CATGTCACA
8689164 AACTCTGAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
21 4 0.10
22 1 0.02
23 20 0.48
24 12 0.29
25 1 0.02
26 4 0.10
ACGTcount: A:0.28, C:0.34, G:0.13, T:0.25
Consensus pattern (23 bp):
CATGTCACAGATTCCCTCCATGA
Found at i:8689207 original size:23 final size:23
Alignment explanation
Indices: 8689134--8689208 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
8689124 AACCCTATCG
* *
8689134 TGTCACAGATTCCCTCCATGACA
1 TGTCACAGATTCCATCCATGTCA
* ** * *
8689157 TGTCACAAACTCTGAATAC-TGTCG
1 TGTCACAGA-T-TCCATCCATGTCA
8689181 TGTCACAGATTCCATCCATGTCA
1 TGTCACAGATTCCATCCATGTCA
8689204 TGTCA
1 TGTCA
8689209 AACTTTGAAC
Statistics
Matches: 37, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
22 4 0.11
23 18 0.49
24 12 0.32
25 3 0.08
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (23 bp):
TGTCACAGATTCCATCCATGTCA
Found at i:8689323 original size:24 final size:24
Alignment explanation
Indices: 8689249--8689326 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 24
8689239 CTCCATGCCT
* *
8689249 TGTCATAAACTCTGAAATCTGGAG
1 TGTCACAAACTCTGAACTCTGGAG
* * * * *
8689273 TTTCACAGATTCT-ATC-CATGGCG
1 TGTCACAAACTCTGAACTC-TGGAG
8689296 TGTCACAAACTCTGAACTCTGGAG
1 TGTCACAAACTCTGAACTCTGGAG
8689320 TGTCACA
1 TGTCACA
8689327 GATTCCCTCC
Statistics
Matches: 39, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
22 1 0.03
23 15 0.38
24 22 0.56
25 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
TGTCACAAACTCTGAACTCTGGAG
Found at i:8692436 original size:68 final size:68
Alignment explanation
Indices: 8692327--8692460 Score: 196
Period size: 68 Copynumber: 2.0 Consensus size: 68
8692317 TCTACGATAT
** ** *
8692327 AGAGTTATTTGGGCTTAATTTTAATAATAATTTTGCTTAGTTCTTGTATTAATGCATAGAAATTA
1 AGAGTTATTTAAGCTTAATTTTAATAATAATTTAACTTAGTTCTTGTAGTAATGCATAGAAATTA
8692392 GTA
66 GTA
* * *
8692395 AGAGTTATTTAAGCTTAATTTTTATAGTAATTTAACTTAGTTCTTGTGGTAATGCATAGAAATTA
1 AGAGTTATTTAAGCTTAATTTTAATAATAATTTAACTTAGTTCTTGTAGTAATGCATAGAAATTA
8692460 G
66 G
8692461 AAAGTTTTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (68 bp):
AGAGTTATTTAAGCTTAATTTTAATAATAATTTAACTTAGTTCTTGTAGTAATGCATAGAAATTA
GTA
Found at i:8699794 original size:15 final size:16
Alignment explanation
Indices: 8699775--8699829 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
8699765 AAGAAGAACA
*
8699775 GAAAGAAAGGAGGAA-
1 GAAAGAAAGGAAGAAG
8699790 GAAAGAAAGGAAGAAG
1 GAAAGAAAGGAAGAAG
8699806 GAGAA-AAAGGAAGAAG
1 GA-AAGAAAGGAAGAAG
8699822 GAAAGAAA
1 GAAAGAAA
8699830 AAGTTAAGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
15 16 0.44
16 18 0.50
17 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
GAAAGAAAGGAAGAAG
Found at i:8700688 original size:106 final size:106
Alignment explanation
Indices: 8700503--8700710 Score: 364
Period size: 106 Copynumber: 2.0 Consensus size: 106
8700493 CGTGTTGATT
*
8700503 TACTTTAAATGCAAAGTTGTGGAAAGCATAAGCAGATAGAAATCATAGGTATTTTATGGGTGCTT
1 TACTTTAAATGCAAAGTTGTGGAAAGCATAAGCAGATAGAAATCATAGGTATTTTATGGATGCTT
* *
8700568 AAATATTTGAAAGTGTTTTGATTATGTACGTATATAAACTA
66 AAATATTTGAAAGTGTTTTGATTATATACATATATAAACTA
*
8700609 TACTTTAAATGCAAAGTTGTGGAAAGCATAAGCA-AGTAGAAATCATAGGTATTTTGTGGATGCT
1 TACTTTAAATGCAAAGTTGTGGAAAGCATAAGCAGA-TAGAAATCATAGGTATTTTATGGATGCT
8700673 TAAATATTTGAAAGTGTTTTGATTATATACATATATAA
65 TAAATATTTGAAAGTGTTTTGATTATATACATATATAA
8700711 GTTATAGATG
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
105 1 0.01
106 96 0.99
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (106 bp):
TACTTTAAATGCAAAGTTGTGGAAAGCATAAGCAGATAGAAATCATAGGTATTTTATGGATGCTT
AAATATTTGAAAGTGTTTTGATTATATACATATATAAACTA
Found at i:8707456 original size:7 final size:7
Alignment explanation
Indices: 8707444--8707468 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8707434 TTCCAAATCT
8707444 TAAACCC
1 TAAACCC
8707451 TAAACCC
1 TAAACCC
8707458 TAAACCC
1 TAAACCC
8707465 TAAA
1 TAAA
8707469 TTCTTCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:8709667 original size:23 final size:24
Alignment explanation
Indices: 8709632--8709688 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
8709622 AATAGAGATT
8709632 AATAAACAA-AATT-AAATAAATAA-
1 AATAAA-AATAATTGAAATAAA-AAG
*
8709655 AATAAAAATAATTGGAATAAAAAG
1 AATAAAAATAATTGAAATAAAAAG
8709679 AA-AAAAATAA
1 AATAAAAATAA
8709689 GAGTTTCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.07
23 20 0.67
24 8 0.27
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (24 bp):
AATAAAAATAATTGAAATAAAAAG
Found at i:8720781 original size:20 final size:20
Alignment explanation
Indices: 8720753--8720801 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
8720743 TTTTTCTTAG
* *
8720753 TTTAGTTTAAATCATGTTGA
1 TTTATTTTAAATCAAGTTGA
* * *
8720773 TTTATTTTAATTTAAGTTGT
1 TTTATTTTAAATCAAGTTGA
8720793 TTTATTTTA
1 TTTATTTTA
8720802 GTTTTATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (20 bp):
TTTATTTTAAATCAAGTTGA
Found at i:8720848 original size:26 final size:27
Alignment explanation
Indices: 8720773--8720850 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 27
8720763 ATCATGTTGA
* *
8720773 TTTATTTTAAT-TTAAGTT-GTTTTAT
1 TTTAGTTTAATATTAAATTAGTTTTAT
* *
8720798 TTTAGTTTTATATTAAATTACTTTTAT
1 TTTAGTTTAATATTAAATTAGTTTTAT
* *
8720825 TTT-GTTTAATATTGATTTAGTTTTAT
1 TTTAGTTTAATATTAAATTAGTTTTAT
8720851 GCATTTGCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
25 9 0.21
26 25 0.58
27 9 0.21
ACGTcount: A:0.26, C:0.01, G:0.08, T:0.65
Consensus pattern (27 bp):
TTTAGTTTAATATTAAATTAGTTTTAT
Found at i:8724638 original size:17 final size:17
Alignment explanation
Indices: 8724609--8724642 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
8724599 AGAATGTTCT
8724609 ATACACTATCCCATTAA
1 ATACACTATCCCATTAA
8724626 ATAC-CTATACCCATTAA
1 ATACACTAT-CCCATTAA
8724643 TTATCCGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.41, C:0.29, G:0.00, T:0.29
Consensus pattern (17 bp):
ATACACTATCCCATTAA
Found at i:8742211 original size:48 final size:45
Alignment explanation
Indices: 8742123--8742213 Score: 121
Period size: 47 Copynumber: 2.0 Consensus size: 45
8742113 TTACAATTTC
8742123 TTAAAAATAAAAATTATTTCTATTTTTTATTGTTCTAGAATTTTT
1 TTAAAAATAAAAATTATTTCTATTTTTTATTGTTCTAGAATTTTT
* *
8742168 TTAAACAATTAAAAATTATTT-TATATTTTATATTTTTTTAGAATTT
1 TTAAA-AA-TAAAAATTATTTCTAT-TTTT-TATTGTTCTAGAATTT
8742214 CTAAAATACA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 5 0.12
46 5 0.12
47 16 0.40
48 14 0.35
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (45 bp):
TTAAAAATAAAAATTATTTCTATTTTTTATTGTTCTAGAATTTTT
Found at i:8742273 original size:28 final size:27
Alignment explanation
Indices: 8742242--8742298 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
8742232 TTTTAAATTT
*
8742242 TTAAATTTTATTATTTAAAAATTTAAAA
1 TTAAATTTAATT-TTTAAAAATTTAAAA
* * *
8742270 TTAACTTTAATTTTTAAAACTTTTAAA
1 TTAAATTTAATTTTTAAAAATTTAAAA
8742297 TT
1 TT
8742299 GATAAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAAATTTAATTTTTAAAAATTTAAAA
Found at i:8746496 original size:21 final size:21
Alignment explanation
Indices: 8746470--8746514 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
8746460 CACTAAAATA
8746470 GCCTTTATCTACTGGCAATCT
1 GCCTTTATCTACTGGCAATCT
8746491 GCCTTTATCTACTGGCAATCT
1 GCCTTTATCTACTGGCAATCT
8746512 GCC
1 GCC
8746515 ATGAAGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.36
Consensus pattern (21 bp):
GCCTTTATCTACTGGCAATCT
Found at i:8752396 original size:2 final size:2
Alignment explanation
Indices: 8752389--8752418 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8752379 TCCTTGAGGT
8752389 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
8752419 ATGCGCATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:8752945 original size:55 final size:55
Alignment explanation
Indices: 8752847--8752951 Score: 151
Period size: 55 Copynumber: 1.9 Consensus size: 55
8752837 CCCTTTTCTA
* *
8752847 TCTTGAGTTTGTTTGAGGATGTTTCTCTCAAGTTTGTGAATGCTGTTTGAAAATG
1 TCTTGAGTTTGTTTGAAGATGTTTCTCTCAAGATTGTGAATGCTGTTTGAAAATG
*
8752902 TCTTGAGTTTGTTTGAAGACTTTTTCTCGT-AAGATTGTG-ATGCTGTTTGA
1 TCTTGAGTTTGTTTGAAGA-TGTTTCTC-TCAAGATTGTGAATGCTGTTTGA
8752952 GACGCTGAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
55 29 0.64
56 15 0.33
57 1 0.02
ACGTcount: A:0.19, C:0.10, G:0.25, T:0.47
Consensus pattern (55 bp):
TCTTGAGTTTGTTTGAAGATGTTTCTCTCAAGATTGTGAATGCTGTTTGAAAATG
Found at i:8755819 original size:26 final size:27
Alignment explanation
Indices: 8755787--8755839 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
8755777 TTTATAAGAG
8755787 TATTTAAATAAATTTTT-AATTTTTAT
1 TATTTAAATAAATTTTTGAATTTTTAT
* *
8755813 TATTTAATTAAATTTTTGTATTTTTAT
1 TATTTAAATAAATTTTTGAATTTTTAT
8755840 GTTACATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTTAAATAAATTTTTGAATTTTTAT
Found at i:8756168 original size:30 final size:30
Alignment explanation
Indices: 8756127--8756191 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
8756117 ATAATTAACG
* *
8756127 ATAAGAATTTATTTGATTCAAAATAAAAAT
1 ATAAAAATTTATTTCATTCAAAATAAAAAT
*
8756157 ATAAAAATTTATTTCATTTAAAATAAAAAT
1 ATAAAAATTTATTTCATTCAAAATAAAAAT
8756187 ATAAA
1 ATAAA
8756192 TGTTTGATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (30 bp):
ATAAAAATTTATTTCATTCAAAATAAAAAT
Found at i:8756403 original size:2 final size:2
Alignment explanation
Indices: 8756398--8756430 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
8756388 TGTATGCTAT
8756398 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
8756431 TTTTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:8762673 original size:57 final size:57
Alignment explanation
Indices: 8762585--8762692 Score: 198
Period size: 57 Copynumber: 1.9 Consensus size: 57
8762575 ACTATTAAGC
* *
8762585 TTTATCTACTACATGTACAATTTGCTTCAATGCTTCCCTTATTATGTGTCCCTTTGA
1 TTTATCTAATACATGGACAATTTGCTTCAATGCTTCCCTTATTATGTGTCCCTTTGA
8762642 TTTATCTAATACATGGACAATTTGCTTCAATGCTTCCCTTATTATGTGTCC
1 TTTATCTAATACATGGACAATTTGCTTCAATGCTTCCCTTATTATGTGTCC
8762693 AAGCTAGCTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (57 bp):
TTTATCTAATACATGGACAATTTGCTTCAATGCTTCCCTTATTATGTGTCCCTTTGA
Found at i:8764999 original size:2 final size:2
Alignment explanation
Indices: 8764994--8765032 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
8764984 TGCGTGTGTG
* *
8764994 TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8765033 CCTCTCTAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:8765733 original size:13 final size:14
Alignment explanation
Indices: 8765704--8765733 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
8765694 AAGTTTCCGA
8765704 AAATGAATTTTTGT
1 AAATGAATTTTTGT
8765718 AAATGAATTTTT-T
1 AAATGAATTTTTGT
8765731 AAA
1 AAA
8765734 ATTGTTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (14 bp):
AAATGAATTTTTGT
Found at i:8767014 original size:215 final size:214
Alignment explanation
Indices: 8766618--8767033 Score: 586
Period size: 215 Copynumber: 1.9 Consensus size: 214
8766608 TCCATAATTA
* * *
8766618 TATAAATATAATTAATGATAGAACTTATATGTTAAAATGTTTTATATCAAAGTTTATATAAATAA
1 TATAAATATAATTAATGATACAAATTAAATGTTAAAATGTTTTATATCAAAGTTTATATAAATAA
* * * *
8766683 TAACTAATTATAAATAATATGTTATAAAATCTAAAATGATGATTAATAAACTTATTAAGTGTAAT
66 TAACTAATTATAAATAATATATTATAAAATCTAAAATGATAACTAATAAACTCATTAAGTGTAAT
* * * * *
8766748 CATATGAATAAAATTTATTACAAGTTATAGTAATGCTTATGTATAAATTAAATATA-AGTATATA
131 CAAATAAATAAAATTTACTACAAATTATAGTAATACTTATGTATAAATTAAATATATA-TA-ATA
8766812 TATTATACATGACTTTATTTTT
194 T-TTATACATGACTTTATTTTT
* * *
8766834 TATATATATAATTAATGATACAAATTAAATGTTAAAATGTTTTATATTAAAGTTTGTATAAATAA
1 TATAAATATAATTAATGATACAAATTAAATGTTAAAATGTTTTATATCAAAGTTTATATAAATAA
** * *
8766899 TAGTTAATTAT-AATAATATATTATAAAATCTAACATGATAACTAATAAAGTCATTAAGTGTAAT
66 TAACTAATTATAAATAATATATTATAAAATCTAAAATGATAACTAATAAACTCATTAAGTGTAAT
* *
8766963 CAAATAAATAAAGTTTACTATAAATTATAGTAATACTTATG-ACTAAATTAAATATATATAATAT
131 CAAATAAATAAAATTTACTACAAATTATAGTAATACTTATGTA-TAAATTAAATATATATAATAT
8767027 TTATACA
195 TTATACA
8767034 ATTATATATA
Statistics
Matches: 177, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
213 7 0.04
214 5 0.03
215 96 0.54
216 69 0.39
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (214 bp):
TATAAATATAATTAATGATACAAATTAAATGTTAAAATGTTTTATATCAAAGTTTATATAAATAA
TAACTAATTATAAATAATATATTATAAAATCTAAAATGATAACTAATAAACTCATTAAGTGTAAT
CAAATAAATAAAATTTACTACAAATTATAGTAATACTTATGTATAAATTAAATATATATAATATT
TATACATGACTTTATTTTT
Found at i:8774271 original size:24 final size:22
Alignment explanation
Indices: 8774223--8774272 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
8774213 TATTTAACAA
*
8774223 TTTATATTTTATGTACTATAGT
1 TTTATATTTTATGTACTATAAT
* *
8774245 TTTATATTTATTTCGTATTATAAT
1 TTTATATTT-TAT-GTACTATAAT
8774269 TTTA
1 TTTA
8774273 AATAGAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 9 0.39
23 2 0.09
24 12 0.52
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (22 bp):
TTTATATTTTATGTACTATAAT
Found at i:8774288 original size:11 final size:11
Alignment explanation
Indices: 8774272--8774304 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
8774262 TTATAATTTT
8774272 AAATAGAAATA
1 AAATAGAAATA
8774283 AAATAGAAATA
1 AAATAGAAATA
*
8774294 AAATAAAAATA
1 AAATAGAAATA
8774305 TTGGAGATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (11 bp):
AAATAGAAATA
Found at i:8779181 original size:24 final size:24
Alignment explanation
Indices: 8779154--8779201 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
8779144 CAGAACAATG
8779154 ATATGATGTAAGATATGTATGTTC
1 ATATGATGTAAGATATGTATGTTC
*
8779178 ATATGATGTGAGATATGTATGTTC
1 ATATGATGTAAGATATGTATGTTC
8779202 CGTTCATGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.23, T:0.42
Consensus pattern (24 bp):
ATATGATGTAAGATATGTATGTTC
Found at i:8779678 original size:36 final size:35
Alignment explanation
Indices: 8779575--8779682 Score: 135
Period size: 35 Copynumber: 3.1 Consensus size: 35
8779565 ATGACTTTGA
* * *
8779575 GACTCCGTCGTTTGCTCAGCAATGAGGCATGACAA
1 GACTCCATCGTTTGCTCAGCAATGAGGCGTGACAT
*
8779610 GACTCCATCGTTTGCTCAGCAATGAAGCGTGACAT
1 GACTCCATCGTTTGCTCAGCAATGAGGCGTGACAT
* * * *
8779645 GACTCTATCGTTTGCTATAGCAATGGGGTGTGACAT
1 GACTCCATCGTTTGCT-CAGCAATGAGGCGTGACAT
8779681 GA
1 GA
8779683 TATTGTATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
35 46 0.73
36 17 0.27
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (35 bp):
GACTCCATCGTTTGCTCAGCAATGAGGCGTGACAT
Found at i:8790797 original size:15 final size:17
Alignment explanation
Indices: 8790773--8790804 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
8790763 GGCAAATGAG
8790773 TTTTCTTTTCT-TTTTT
1 TTTTCTTTTCTATTTTT
8790789 TTTTC-TTTCTATTTTT
1 TTTTCTTTTCTATTTTT
8790805 CACATCAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTCTTTTCTATTTTT
Found at i:8792078 original size:18 final size:18
Alignment explanation
Indices: 8792055--8792096 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
8792045 CTCTAGCTAA
**
8792055 TTGTTTTCATTATTTAAG
1 TTGTTTTCACCATTTAAG
*
8792073 TTGTTTTCACCATTTACG
1 TTGTTTTCACCATTTAAG
8792091 TTGTTT
1 TTGTTT
8792097 ATGATTTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.60
Consensus pattern (18 bp):
TTGTTTTCACCATTTAAG
Found at i:8794764 original size:17 final size:17
Alignment explanation
Indices: 8794742--8794801 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
8794732 TTTAGAACAT
8794742 TAATAATTAAACATAAA
1 TAATAATTAAACATAAA
* * * *
8794759 TAATAATCAACAAATGAT
1 TAATAATTAA-ACATAAA
8794777 TAA-AA-TAAACATAAA
1 TAATAATTAAACATAAA
*
8794792 TATTAATTAA
1 TAATAATTAA
8794802 CATTATCAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
15 6 0.19
16 4 0.13
17 14 0.45
18 7 0.23
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.30
Consensus pattern (17 bp):
TAATAATTAAACATAAA
Found at i:8795044 original size:2 final size:2
Alignment explanation
Indices: 8795031--8795062 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8795021 ACTTCTCATG
*
8795031 AT AT AT AG 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
8795063 TGGAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8796671 original size:52 final size:53
Alignment explanation
Indices: 8796615--8796714 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 53
8796605 TGTGTAGTAT
* * **
8796615 TTCATCACGTCACTTATCACATGTTTTGCCA-AGTTTATCTTTTATGTTGTGC
1 TTCATCACATCACTTATCACATGCTTCACCACAGTTTATCTTTTATGTTGTGC
*
8796667 TTCATCACATCACTTATCACATGCTTCACCACATTTTATCTTTTATGT
1 TTCATCACATCACTTATCACATGCTTCACCACAGTTTATCTTTTATGT
8796715 CATATTTCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 27 0.64
53 15 0.36
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.45
Consensus pattern (53 bp):
TTCATCACATCACTTATCACATGCTTCACCACAGTTTATCTTTTATGTTGTGC
Found at i:8798054 original size:21 final size:21
Alignment explanation
Indices: 8798028--8798071 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
8798018 AGAAAGTATT
*
8798028 TTATGTGATAAGTATCGATAC
1 TTATGTGAGAAGTATCGATAC
*
8798049 TTATGTTAGAAGTATCGATAC
1 TTATGTGAGAAGTATCGATAC
8798070 TT
1 TT
8798072 GAGGCATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (21 bp):
TTATGTGAGAAGTATCGATAC
Found at i:8799155 original size:37 final size:37
Alignment explanation
Indices: 8799100--8799187 Score: 158
Period size: 37 Copynumber: 2.4 Consensus size: 37
8799090 GTAACCATCA
* *
8799100 CAAGAATGGTGGTATTTTCTCGCTTGTGAGTGGTAAG
1 CAAGGATGGTGGTATTTTCTCGCTTGTGAATGGTAAG
8799137 CAAGGATGGTGGTATTTTCTCGCTTGTGAATGGTAAG
1 CAAGGATGGTGGTATTTTCTCGCTTGTGAATGGTAAG
8799174 CAAGGATGGTGGTA
1 CAAGGATGGTGGTA
8799188 AGTGGGGACA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.23, C:0.10, G:0.34, T:0.33
Consensus pattern (37 bp):
CAAGGATGGTGGTATTTTCTCGCTTGTGAATGGTAAG
Found at i:8800085 original size:22 final size:22
Alignment explanation
Indices: 8800033--8800086 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
8800023 TTCCCCAGTG
8800033 TTCACATTTCCATATCAAAGCCC
1 TTCAC-TTTCCATATCAAAGCCC
*
8800056 TCTC-CTTTACCATA-CAAATCCC
1 T-TCACTTT-CCATATCAAAGCCC
8800078 TTCACTTTC
1 TTCACTTTC
8800087 ACCTTTTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
21 3 0.11
22 15 0.56
23 7 0.26
24 2 0.07
ACGTcount: A:0.26, C:0.37, G:0.02, T:0.35
Consensus pattern (22 bp):
TTCACTTTCCATATCAAAGCCC
Found at i:8800350 original size:17 final size:15
Alignment explanation
Indices: 8800294--8800362 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 15
8800284 ATTTAAATTA
8800294 TTTT-TTTTTTTCATC
1 TTTTCTTTTTTTC-TC
8800309 -TTTCTATTTTTT-TC
1 TTTTCT-TTTTTTCTC
* *
8800323 TTTT-GTTTTCTC-C
1 TTTTCTTTTTTTCTC
8800336 ATTTTCTTTTTTTCTC
1 -TTTTCTTTTTTTCTC
8800352 TTTT-TTTTTTT
1 TTTTCTTTTTTT
8800363 TTTTTTTCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 15
0.69 0.06 0.24
Matches are distributed among these distances:
13 6 0.14
14 16 0.37
15 14 0.33
16 7 0.16
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTTTCTC
Found at i:8800355 original size:10 final size:9
Alignment explanation
Indices: 8800309--8800367 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
8800299 TTTTTTCATC
8800309 TTTCTATTTT
1 TTTCT-TTTT
8800319 TTTCTTTTGT
1 TTTCTTTT-T
***
8800329 TTTCTCCAT
1 TTTCTTTTT
8800338 TTTCTTTTT
1 TTTCTTTTT
8800347 TTCTCTTTTT
1 TT-TCTTTTT
8800357 TTT-TTTTT
1 TTTCTTTTT
8800365 TTT
1 TTT
8800368 TTCAAAAGGC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
8 8 0.20
9 13 0.32
10 20 0.49
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:8800359 original size:19 final size:18
Alignment explanation
Indices: 8800309--8800367 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
8800299 TTTTTTCATC
8800309 TTTCTATTTTTTTCTTTTGT
1 TTTCT-TTTTTTTCTTTT-T
***
8800329 TTTCTCCATTTTCTTTTT
1 TTTCTTTTTTTTCTTTTT
8800347 TTCTCTTTTTTTT-TTTTT
1 TT-TCTTTTTTTTCTTTTT
8800365 TTT
1 TTT
8800368 TTCAAAAGGC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 1 0.03
18 10 0.31
19 16 0.50
20 5 0.16
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTCTTTTTTTTCTTTTT
Found at i:8800896 original size:8 final size:7
Alignment explanation
Indices: 8800877--8800955 Score: 67
Period size: 7 Copynumber: 11.3 Consensus size: 7
8800867 CTTCAATTTA
8800877 TTCTTTT
1 TTCTTTT
8800884 TTCTTTT
1 TTCTTTT
8800891 TCTCTTTT
1 T-TCTTTT
8800899 TT-TTTT
1 TTCTTTT
*
8800905 CTTC-TGT
1 -TTCTTTT
8800912 TTCTTTT
1 TTCTTTT
8800919 TT-TTTT
1 TTCTTTT
8800925 CTT-TTTCT
1 -TTCTTT-T
8800933 TTCTTTT
1 TTCTTTT
* *
8800940 TTGTTCT
1 TTCTTTT
8800947 TTCTTTT
1 TTCTTTT
8800954 TT
1 TT
8800956 TTTCCTTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
6 11 0.19
7 37 0.63
8 11 0.19
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (7 bp):
TTCTTTT
Found at i:8800902 original size:17 final size:16
Alignment explanation
Indices: 8800882--8800965 Score: 80
Period size: 17 Copynumber: 4.9 Consensus size: 16
8800872 ATTTATTCTT
8800882 TTTTCTTTTTCTCTTTT-
1 TTTT-TTTTTCT-TTTTC
* *
8800899 TTTTTTCTTCTGTTTC
1 TTTTTTTTTCTTTTTC
8800915 TTTTTTTTTTCTTTTTC
1 -TTTTTTTTTCTTTTTC
*
8800932 TTTCTTTTTTGTTCTTTC
1 TTT-TTTTTTCTT-TTTC
8800950 TTTTTTTTTCCTTTTT
1 TTTTTTTTT-CTTTTT
8800966 TCTCATACTT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
15 3 0.05
16 9 0.16
17 35 0.62
18 9 0.16
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTCTTTTTC
Found at i:8800904 original size:14 final size:13
Alignment explanation
Indices: 8800877--8800966 Score: 83
Period size: 14 Copynumber: 6.7 Consensus size: 13
8800867 CTTCAATTTA
*
8800877 TTCTTTTTTCTTT
1 TTCTTTTTTTTTT
*
8800890 TTCTCTTTTTTTT
1 TTCTTTTTTTTTT
* *
8800903 TTCTTCTGTTTCTT
1 TTCTT-TTTTTTTT
*
8800917 TT-TTTTTTCTTT
1 TTCTTTTTTTTTT
*
8800929 TTCTTTCTTTTTTG
1 TTCTTT-TTTTTTT
8800943 TTCTTTCTTTTTTT
1 TTCTTT-TTTTTTT
8800957 TTCCTTTTTT
1 TT-CTTTTTT
8800967 CTCATACTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
12 7 0.11
13 20 0.32
14 31 0.50
15 4 0.06
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:8800914 original size:22 final size:20
Alignment explanation
Indices: 8800880--8800968 Score: 74
Period size: 21 Copynumber: 4.4 Consensus size: 20
8800870 CAATTTATTC
*
8800880 TTTTTTCTTTTTCTCTTTTTT
1 TTTTTTCTGTTTCT-TTTTTT
8800901 TTTTCTTCTGTTTCTTTTTTT
1 TTTT-TTCTGTTTCTTTTTTT
* * *
8800922 TTTCTTTTTCTTTCTTTTTTG
1 TTT-TTTCTGTTTCTTTTTTT
* **
8800943 TTCTTTCT-TTT-TTTTTCC
1 TTTTTTCTGTTTCTTTTTTT
8800961 TTTTTTCT
1 TTTTTTCT
8800969 CATACTTACT
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
18 12 0.21
19 3 0.05
20 4 0.07
21 28 0.49
22 10 0.18
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTTTCTGTTTCTTTTTTT
Found at i:8800916 original size:20 final size:18
Alignment explanation
Indices: 8800880--8800968 Score: 108
Period size: 18 Copynumber: 4.8 Consensus size: 18
8800870 CAATTTATTC
8800880 TTTTTTCTTTTTCTCTTTT
1 TTTTTTCTTTTT-TCTTTT
8800899 TTTTTTCTTCTGTTTCTTTT
1 TTTTTTCTT-T-TTTCTTTT
*
8800919 TTTTTTC-TTTTTCTTTC
1 TTTTTTCTTTTTTCTTTT
* *
8800936 TTTTTTGTTCTTTCTTTT
1 TTTTTTCTTTTTTCTTTT
*
8800954 TTTTTCCTTTTTTCT
1 TTTTTTCTTTTTTCT
8800969 CATACTTACT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
17 13 0.22
18 21 0.35
19 10 0.17
20 14 0.23
21 2 0.03
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (18 bp):
TTTTTTCTTTTTTCTTTT
Found at i:8800918 original size:35 final size:32
Alignment explanation
Indices: 8800877--8800968 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 32
8800867 CTTCAATTTA
8800877 TTCTTTTTTCTTTTTCTCTTTTTTT-TTTCTTCTG
1 TTCTTTTTT-TTTTTCTCTTTTTTTCTTT-TT-TG
8800911 TT-TCTTTTTTTTTTCT-TTTTCTTTCTTTTTTG
1 TTCT-TTTTTTTTTTCTCTTTT-TTTCTTTTTTG
*
8800943 TTCTTTCTTTTTTTT-TCCTTTTTTCT
1 TTCTTT-TTTTTTTTCTCTTTTTTTCT
8800969 CATACTTACT
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
32 16 0.31
33 25 0.49
34 10 0.20
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (32 bp):
TTCTTTTTTTTTTTCTCTTTTTTTCTTTTTTG
Found at i:8813009 original size:20 final size:21
Alignment explanation
Indices: 8812980--8813019 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
8812970 CCTATTTGGT
8812980 TTAAAATAAAAAT-ATAAAAA
1 TTAAAATAAAAATAATAAAAA
* *
8813000 TTAAATTAAACATAATAAAA
1 TTAAAATAAAAATAATAAAA
8813020 TAATAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
TTAAAATAAAAATAATAAAAA
Found at i:8826348 original size:12 final size:12
Alignment explanation
Indices: 8826301--8826348 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
8826291 TCTGCTGATG
*
8826301 CTTCTTCATCTC
1 CTTCTTCATCTT
* *
8826313 CTTCTCCATCAT
1 CTTCTTCATCTT
*
8826325 CTTCGTCATCTT
1 CTTCTTCATCTT
*
8826337 CTTCTTCTTCTT
1 CTTCTTCATCTT
8826349 GTTTAAGTAG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.08, C:0.38, G:0.02, T:0.52
Consensus pattern (12 bp):
CTTCTTCATCTT
Found at i:8828365 original size:12 final size:13
Alignment explanation
Indices: 8828336--8828368 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
8828326 TGGGAGTACG
8828336 TATA-ATTTCACT
1 TATACATTTCACT
8828348 TATACATTTCACT
1 TATACATTTCACT
8828361 T-TACATTT
1 TATACATTT
8828369 TAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (13 bp):
TATACATTTCACT
Found at i:8835872 original size:2 final size:2
Alignment explanation
Indices: 8835865--8835891 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8835855 TTATATTTCA
8835865 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
8835892 AGGACTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8841031 original size:2 final size:2
Alignment explanation
Indices: 8841024--8841049 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8841014 GAGGCCTCGT
8841024 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
8841050 CCGAGTCTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:8846771 original size:30 final size:32
Alignment explanation
Indices: 8846682--8846776 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 32
8846672 TAAATTGTTC
*
8846682 GTTGATGTGTTTTAGTATAAGTCTATTATA-AA
1 GTTGATGTGTTTTAGTATAACTCTATTA-AGAA
* *
8846714 CTTGATATGTTTTAGTATAACTCTATTAAGAA
1 GTTGATGTGTTTTAGTATAACTCTATTAAGAA
* *
8846746 GTTGATGTGTTTTACTAT-A-TCTATTAGGAA
1 GTTGATGTGTTTTAGTATAACTCTATTAAGAA
8846776 G
1 G
8846777 ACTTTTTTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
30 11 0.20
31 2 0.04
32 42 0.76
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (32 bp):
GTTGATGTGTTTTAGTATAACTCTATTAAGAA
Found at i:8849119 original size:3 final size:3
Alignment explanation
Indices: 8849111--8849158 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
8849101 GGCTCACTTG
8849111 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
8849159 TATCCCTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8852355 original size:21 final size:22
Alignment explanation
Indices: 8852331--8852375 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
8852321 AAAAAATTTT
* *
8852331 AAATTTTTTTAAATA-ATTCAA
1 AAATATTTTCAAATATATTCAA
8852352 AAATATTTTCAAATATTATTCAA
1 AAATATTTTCAAATA-TATTCAA
8852375 A
1 A
8852376 GTTTCAGTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATATTTTCAAATATATTCAA
Done.