Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 118 of 126
Found at i:23318028 original size:2 final size:2
Alignment explanation
Indices: 23318021--23318061 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
23318011 TGCCTTTCCC
23318021 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23318062 CAATCCCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23326076 original size:2 final size:2
Alignment explanation
Indices: 23326069--23326112 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
23326059 ATTCTGCAAA
* *
23326069 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23326111 AT
1 AT
23326113 TACGAGTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:23329317 original size:6 final size:6
Alignment explanation
Indices: 23329306--23329337 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
23329296 GGTCTATGGT
23329306 AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG AA
1 AAAGTG AAAGTG AAAGTG AAAGTG AAAGTG AA
23329338 TGCAAAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.31, T:0.16
Consensus pattern (6 bp):
AAAGTG
Found at i:23329661 original size:22 final size:22
Alignment explanation
Indices: 23329619--23329663 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
23329609 AATTTTTATC
* *
23329619 TTTAATTTTAGAGATACAAATA
1 TTTAATTTTAAAAATACAAATA
*
23329641 TTTAATTTTAAAAATATAAATA
1 TTTAATTTTAAAAATACAAATA
23329663 T
1 T
23329664 AAATATATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
TTTAATTTTAAAAATACAAATA
Found at i:23333652 original size:22 final size:22
Alignment explanation
Indices: 23333627--23333669 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
23333617 TTTTTTATCT
23333627 TTAATTCTAGAGATACAAATAC
1 TTAATTCTAGAGATACAAATAC
*
23333649 TTAATTCTAGATATACAAATA
1 TTAATTCTAGAGATACAAATA
23333670 TAAATATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (22 bp):
TTAATTCTAGAGATACAAATAC
Found at i:23336516 original size:15 final size:17
Alignment explanation
Indices: 23336496--23336529 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
23336486 AAAGCTCTTG
23336496 AAAA-TTTATTTTT-AA
1 AAAATTTTATTTTTGAA
23336511 AAAATTTTATTTTTGAA
1 AAAATTTTATTTTTGAA
23336528 AA
1 AA
23336530 TATAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 9 0.53
17 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AAAATTTTATTTTTGAA
Found at i:23336530 original size:15 final size:15
Alignment explanation
Indices: 23336493--23336530 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
23336483 GTTAAAGCTC
23336493 TTGAAAA-TTTATTT
1 TTGAAAATTTTATTT
*
23336507 TTAAAAAATTTTATTT
1 TT-GAAAATTTTATTT
23336523 TTGAAAAT
1 TTGAAAAT
23336531 ATAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 2 0.10
15 9 0.45
16 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (15 bp):
TTGAAAATTTTATTT
Found at i:23340142 original size:15 final size:16
Alignment explanation
Indices: 23340122--23340154 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
23340112 TTAATTAAAT
23340122 AATAAA-TATATTTTA
1 AATAAATTATATTTTA
23340137 AATAAATTATATTTTA
1 AATAAATTATATTTTA
23340153 AA
1 AA
23340155 CTTTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAAATTATATTTTA
Found at i:23340335 original size:19 final size:20
Alignment explanation
Indices: 23340297--23340335 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
23340287 ATTTGGATTA
*
23340297 TTTAATATTTCAATTAAATT
1 TTTAATATTTAAATTAAATT
*
23340317 TTTAAT-TTTAAATTTAATT
1 TTTAATATTTAAATTAAATT
23340336 AATTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATATTTAAATTAAATT
Found at i:23341312 original size:17 final size:17
Alignment explanation
Indices: 23341280--23341312 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23341270 GTGGGTATTT
23341280 TATATAGAAAATACAAA
1 TATATAGAAAATACAAA
23341297 TATATTAGAAAA-ACAA
1 TATA-TAGAAAATACAA
23341313 TTTCCTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
TATATAGAAAATACAAA
Found at i:23342368 original size:18 final size:17
Alignment explanation
Indices: 23342341--23342387 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
23342331 TATTCAAATG
* *
23342341 ATTATGATTTTTTGTGTA
1 ATTATAATTTTTTATG-A
23342359 ATTATAA-TTTTTATGA
1 ATTATAATTTTTTATGA
*
23342375 ATAATAATTTTTT
1 ATTATAATTTTTT
23342388 TATATTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 7 0.28
17 12 0.48
18 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (17 bp):
ATTATAATTTTTTATGA
Found at i:23342413 original size:18 final size:18
Alignment explanation
Indices: 23342390--23342468 Score: 54
Period size: 18 Copynumber: 4.3 Consensus size: 18
23342380 AATTTTTTTA
23342390 TATTTAAATAATTATAAT
1 TATTTAAATAATTATAAT
* *
23342408 TATTT-ATTATATGATAAT
1 TATTTAAATA-ATTATAAT
** *
23342426 TATTTTTATTTAAATATAAT
1 TA--TTTAAATAATTATAAT
* *
23342446 TATTTTAATAATTAAAAT
1 TATTTAAATAATTATAAT
23342464 T-TTTA
1 TATTTA
23342469 TTTAATATAA
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
17 6 0.13
18 26 0.57
20 11 0.24
21 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (18 bp):
TATTTAAATAATTATAAT
Found at i:23342435 original size:20 final size:20
Alignment explanation
Indices: 23342378--23342451 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 20
23342368 TTTATGAATA
*
23342378 ATAATTTTTTTATATTTAAAT
1 ATAATTATTTT-TATTTAAAT
* * *
23342399 AATTATAATTATTTA-TTATAT
1 -ATAATTATT-TTTATTTAAAT
23342420 GATAATTATTTTTATTTAAAT
1 -ATAATTATTTTTATTTAAAT
23342441 ATAATTATTTT
1 ATAATTATTTT
23342452 AATAATTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 15 0.36
21 17 0.40
22 8 0.19
23 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (20 bp):
ATAATTATTTTTATTTAAAT
Found at i:23342479 original size:18 final size:18
Alignment explanation
Indices: 23342427--23342481 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
23342417 TATGATAATT
*
23342427 ATTTTTATTTAA-ATATA
1 ATTTTTATTTAATATAAA
*
23342444 A-TTAT-TTTAATAATTAAA
1 ATTTTTATTTAAT-A-TAAA
23342462 ATTTTTATTTAATATAAA
1 ATTTTTATTTAATATAAA
23342480 AT
1 AT
23342482 ACATTACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
15 5 0.17
16 3 0.10
17 2 0.07
18 10 0.33
19 4 0.13
20 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTTATTTAATATAAA
Found at i:23344269 original size:25 final size:23
Alignment explanation
Indices: 23344196--23344299 Score: 70
Period size: 24 Copynumber: 4.4 Consensus size: 23
23344186 AGATTTAAGG
*
23344196 TAATAATAACGATAAAATT-AAT-
1 TAATAATAA-AATAAAATTAAATA
* * *
23344218 TAAT-TTAATAATAAGATTAAATT
1 TAATAATAA-AATAAAATTAAATA
*
23344241 TAATGATAAAATAAAAATATAAATA
1 TAATAATAAAAT-AAAAT-TAAATA
* *
23344266 TAATAATAATGATAAAATTGAATA
1 TAATAATAA-AATAAAATTAAATA
*
23344290 TAATCATAAA
1 TAATAATAAA
23344300 TTGTTTCATT
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
21 10 0.16
22 7 0.11
23 7 0.11
24 20 0.31
25 18 0.28
26 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.34
Consensus pattern (23 bp):
TAATAATAAAATAAAATTAAATA
Found at i:23348816 original size:20 final size:20
Alignment explanation
Indices: 23348775--23348817 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
23348765 TTATTTAAAT
* * *
23348775 TATCATATTAATAAAGTGAA
1 TATCACATTAATAAAATCAA
23348795 TATCACATTAATAAAATCAA
1 TATCACATTAATAAAATCAA
23348815 TAT
1 TAT
23348818 TTATGTCATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (20 bp):
TATCACATTAATAAAATCAA
Found at i:23349708 original size:11 final size:11
Alignment explanation
Indices: 23349692--23349743 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
23349682 CGGTGATAAA
23349692 ATATAAAAACG
1 ATATAAAAACG
**
23349703 ATATAATAAAAA
1 ATATAA-AAACG
* *
23349715 ATATAGACACG
1 ATATAAAAACG
*
23349726 ATATAAAAATG
1 ATATAAAAACG
23349737 ATATAAA
1 ATATAAA
23349744 TAAAAAATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
11 23 0.74
12 8 0.26
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.23
Consensus pattern (11 bp):
ATATAAAAACG
Found at i:23349712 original size:21 final size:22
Alignment explanation
Indices: 23349689--23349731 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
23349679 ACACGGTGAT
23349689 AAAATATAAAAACGATATAATAA
1 AAAATATAAAAACGATATAAT-A
* *
23349712 AAAATATAGACACGATATAA
1 AAAATATAAAAACGATATAA
23349732 AAATGATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.21
Consensus pattern (22 bp):
AAAATATAAAAACGATATAATA
Found at i:23349765 original size:35 final size:34
Alignment explanation
Indices: 23349691--23349766 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 34
23349681 ACGGTGATAA
* *
23349691 AATATAAAAACGATATAATAAAAAATATAGACAC
1 AATATAAAAACGATATAATAAAAAATATAAAAAC
* * *
23349725 GATATAAAAATGATATAAATAAAAAATATAAAAAT
1 AATATAAAAACGATAT-AATAAAAAATATAAAAAC
23349760 AATATAA
1 AATATAA
23349767 TTTAAATTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
34 14 0.40
35 21 0.60
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.24
Consensus pattern (34 bp):
AATATAAAAACGATATAATAAAAAATATAAAAAC
Found at i:23350245 original size:43 final size:43
Alignment explanation
Indices: 23350182--23350263 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 43
23350172 ATACGCATAT
* *
23350182 AATTGTATTTTAATATTTTTATTATATTATTA-ATTTAATTTTG
1 AATTGTATTTTAATATTTTTAGTAT-TAATTATATTTAATTTTG
23350225 AATTGT-TTATTAGATA-TTTTAGTATTAATTATATTTAAT
1 AATTGTATT-TTA-ATATTTTTAGTATTAATTATATTTAAT
23350264 AATATATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 7 0.21
43 24 0.71
44 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (43 bp):
AATTGTATTTTAATATTTTTAGTATTAATTATATTTAATTTTG
Found at i:23363652 original size:2 final size:2
Alignment explanation
Indices: 23363645--23363670 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23363635 CATATACGTG
23363645 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
23363671 GGAAAAATGT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23364109 original size:35 final size:34
Alignment explanation
Indices: 23364070--23364135 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
23364060 TACTAAATAC
23364070 ATTTTTTAGAAAACAAAAAATAAAAAATAAAAAAT
1 ATTTTTTAGAAAAC-AAAAATAAAAAATAAAAAAT
*
23364105 ATTTTTTATAAAACAAAAATAAAAAATAAAA
1 ATTTTTTAGAAAACAAAAATAAAAAATAAAA
23364136 CCGGTAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (34 bp):
ATTTTTTAGAAAACAAAAATAAAAAATAAAAAAT
Found at i:23369421 original size:29 final size:30
Alignment explanation
Indices: 23369383--23369443 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
23369373 AAATTTAGAT
* *
23369383 AAATCAAATCGAATTTAAATA-TAAAAATA
1 AAATAAAATCAAATTTAAATATTAAAAATA
23369412 AAATAAAATCAAATTTAAATATTAAAAATA
1 AAATAAAATCAAATTTAAATATTAAAAATA
23369442 AA
1 AA
23369444 TATCATGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (30 bp):
AAATAAAATCAAATTTAAATATTAAAAATA
Found at i:23370758 original size:242 final size:236
Alignment explanation
Indices: 23370339--23370809 Score: 683
Period size: 242 Copynumber: 2.0 Consensus size: 236
23370329 ACTCTCTAGC
***
23370339 TTATGGTTTGATTAATCTAGCCACAAGATCCTATGTCAAGTTTAATATAAAATGTCTAATGACTC
1 TTATGGTTTGATTAATCTAGCCACAAGATCCTACACCAAGTTTAATATAAAATGTCTAATGACTC
* * * *
23370404 CTCCCATCGTATATGCTAAGCACAGTCCAATAATATATCGTAAGCACACAATTGATCCTGAAATT
66 CTCCCATCATATATGCTAAGCACAGTCCAATAATACATCATAAGCACACAATTCATCCTGAAATT
** * * * *
23370469 CTGAACCACATTCCAGAGGAAGTAAGTATAATGATCATTTTTGAAGCATTCAACTGACAAAGACA
131 CTGAACCACATTCCAGAAAAAGTAAATATAATGATAATTTTTGAAGCATGCAACAGACAAAGACA
*
23370534 AGATATTCAAACAAAAATGTCATTGATCTCATCAAAGTAAG
196 AGATATTCAAACAAAAATGCCATTGATCTCATCAAAGTAAG
23370575 TTATGGTTTGATTAATCTAGCCACAAGATCCTACACCAAGTTTAATATAAAAGTAAAATGTCTAA
1 TTATGGTTTGATTAATCTAGCCACAAGATCCTACACCAAGTTT-A-AT---A-TAAAATGTCTAA
*
23370640 TGACTCCTCCCATCATATGTGCTAAGCACAGTCCAATAATACATCATAAGCACACAATTCATCCT
60 TGACTCCTCCCATCATATATGCTAAGCACAGTCCAATAATACATCATAAGCACACAATTCATCCT
* ** *
23370705 GAAA-TCTTGAGCCACATTCCAGAAAAAGTAAATATGCTGATAATTTTTGAAGCATGCGACAGAC
125 GAAATTC-TGAACCACATTCCAGAAAAAGTAAATATAATGATAATTTTTGAAGCATGCAACAGAC
* *
23370769 AAAGACAAGATATTCAAATAAACATGCCATTGATCTCATCA
189 AAAGACAAGATATTCAAACAAAAATGCCATTGATCTCATCA
23370810 TCAAAATAAG
Statistics
Matches: 207, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
236 40 0.19
237 1 0.00
238 2 0.01
241 3 0.01
242 161 0.78
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (236 bp):
TTATGGTTTGATTAATCTAGCCACAAGATCCTACACCAAGTTTAATATAAAATGTCTAATGACTC
CTCCCATCATATATGCTAAGCACAGTCCAATAATACATCATAAGCACACAATTCATCCTGAAATT
CTGAACCACATTCCAGAAAAAGTAAATATAATGATAATTTTTGAAGCATGCAACAGACAAAGACA
AGATATTCAAACAAAAATGCCATTGATCTCATCAAAGTAAG
Found at i:23384697 original size:3 final size:3
Alignment explanation
Indices: 23384684--23384713 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
23384674 AACCAAAGCC
23384684 CTT CTTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CT
23384714 ACTGCTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:23390394 original size:2 final size:2
Alignment explanation
Indices: 23390387--23390415 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23390377 GATTCAATCC
23390387 AT 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 AT A
23390416 AATTTGGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23391455 original size:19 final size:19
Alignment explanation
Indices: 23391427--23391463 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
23391417 ATAACTAGTT
23391427 AATATATTTAATTGTATTA
1 AATATATTTAATTGTATTA
* *
23391446 AATATGTTTAATTTTATT
1 AATATATTTAATTGTATT
23391464 TAGAAAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
AATATATTTAATTGTATTA
Found at i:23392299 original size:24 final size:24
Alignment explanation
Indices: 23392272--23392338 Score: 116
Period size: 24 Copynumber: 2.8 Consensus size: 24
23392262 TGCAAGATGA
23392272 ACAATGATTGGAACCCATTCGAGG
1 ACAATGATTGGAACCCATTCGAGG
23392296 ACAATGATTGGAACCCATTCGAGG
1 ACAATGATTGGAACCCATTCGAGG
* *
23392320 ACAATGGTTGGAGCCCATT
1 ACAATGATTGGAACCCATT
23392339 ACGTGTCGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.22
Consensus pattern (24 bp):
ACAATGATTGGAACCCATTCGAGG
Found at i:23392393 original size:27 final size:27
Alignment explanation
Indices: 23392349--23392401 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
23392339 ACGTGTCGTA
* *
23392349 GACCTTGAGGGTTGTACAACTGAACCG
1 GACCTTGAGGCTTATACAACTGAACCG
*
23392376 GACCTTGAGGCTTATACATCTGAACC
1 GACCTTGAGGCTTATACAACTGAACC
23392402 AAATGACGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (27 bp):
GACCTTGAGGCTTATACAACTGAACCG
Found at i:23393066 original size:17 final size:17
Alignment explanation
Indices: 23393014--23393066 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
23393004 TTTAGTTCTA
23393014 AATCTAATTACTAGTTT
1 AATCTAATTACTAGTTT
* * * * *
23393031 GATTTCATTTC-ACTTT
1 AATCTAATTACTAGTTT
23393047 AATCTAATTACTAGTTT
1 AATCTAATTACTAGTTT
23393064 AAT
1 AAT
23393067 GTTGACTTTG
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (17 bp):
AATCTAATTACTAGTTT
Found at i:23396584 original size:24 final size:24
Alignment explanation
Indices: 23396557--23396604 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
23396547 TTTATTTAAT
* *
23396557 TAAAATTTTATTAATATGTAAAAA
1 TAAAATTTTATTAAAATATAAAAA
* *
23396581 TAAATTTTTGTTAAAATATAAAAA
1 TAAAATTTTATTAAAATATAAAAA
23396605 CTTTTCATAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
TAAAATTTTATTAAAATATAAAAA
Found at i:23399072 original size:17 final size:17
Alignment explanation
Indices: 23399020--23399072 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
23399010 TTTAGTTCTA
23399020 AATCTAATTACTAGTTT
1 AATCTAATTACTAGTTT
* * * * *
23399037 GATTTCATTTC-ACTTT
1 AATCTAATTACTAGTTT
23399053 AATCTAATTACTAGTTT
1 AATCTAATTACTAGTTT
23399070 AAT
1 AAT
23399073 GTTGACTTTG
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (17 bp):
AATCTAATTACTAGTTT
Found at i:23401334 original size:20 final size:20
Alignment explanation
Indices: 23401294--23401334 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
23401284 AAAAATCTAC
* *
23401294 AAAAATTATAAAAACACAAT
1 AAAAATTATAAAAAAAAAAT
*
23401314 AAAAGTTATAAAAAAAAAAT
1 AAAAATTATAAAAAAAAAAT
23401334 A
1 A
23401335 GTAAAATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAAATTATAAAAAAAAAAT
Found at i:23409110 original size:6 final size:6
Alignment explanation
Indices: 23409094--23409128 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
23409084 ATAAGTCTAC
*
23409094 AAAAAT TAAAAT AAAAAT AAAAAT AAAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAA
23409129 CTCAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:23411922 original size:100 final size:99
Alignment explanation
Indices: 23411744--23411926 Score: 235
Period size: 100 Copynumber: 1.8 Consensus size: 99
23411734 CACGGTTTTA
* * * *
23411744 AAAAAAATAAATTGTAAATATTAAATTTAAAATTTAAAAACTTAATAGATATATTTTTTAAGAAT
1 AAAAAAATAAATTATAAATATTAAATTTAAAATTTAAAAACTTAATAAATATATATTTTAAAAAT
* ** *
23411809 TATTGTATGAATTAATTAATTTAAATTTTAAATT
66 AATTACATAAATTAATTAATTTAAATTTTAAATT
* *
23411843 AAAAAAATAAATTATAAAATATTGAGA-TTCAAATTT-AAAACTTAATAAATATTATATTTTAAA
1 AAAAAAATAAATTAT-AAATATT-AAATTTAAAATTTAAAAACTTAATAAATA-TATATTTTAAA
23411906 AATAATTACATAAATTAATTA
63 AATAATTACATAAATTAATTA
23411927 TTTTGCGTTC
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
99 28 0.39
100 41 0.58
101 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (99 bp):
AAAAAAATAAATTATAAATATTAAATTTAAAATTTAAAAACTTAATAAATATATATTTTAAAAAT
AATTACATAAATTAATTAATTTAAATTTTAAATT
Found at i:23413874 original size:18 final size:20
Alignment explanation
Indices: 23413829--23413874 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
23413819 TATTTTTATT
*
23413829 TTTTATTAAATTTATTACAA
1 TTTTATTAAAATTATTACAA
23413849 TCTTTATTAAAATT-TTA-AA
1 T-TTTATTAAAATTATTACAA
23413868 TTTTATT
1 TTTTATT
23413875 TTTTTCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
19 3 0.12
20 4 0.17
21 11 0.46
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATTAAAATTATTACAA
Found at i:23413944 original size:24 final size:24
Alignment explanation
Indices: 23413870--23413950 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
23413860 ATTTTAAATT
23413870 TTATTTTT-T-TCATTTTT-TTATA
1 TTATTTTTATATC-TTTTTATTATA
** * *
23413892 TTATTTTTATATAATATTATTGTA
1 TTATTTTTATATCTTTTTATTATA
* *
23413916 GTATTTTTATATCTTTTTATTATT
1 TTATTTTTATATCTTTTTATTATA
23413940 TTA-TTTTATAT
1 TTATTTTTATAT
23413951 TATTCATGCT
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
22 8 0.18
23 12 0.27
24 25 0.56
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (24 bp):
TTATTTTTATATCTTTTTATTATA
Found at i:23413953 original size:18 final size:18
Alignment explanation
Indices: 23413932--23413991 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
23413922 TTATATCTTT
*
23413932 TTATTATTTTATTTTATA
1 TTATTATTTTATTTTAAA
*
23413950 TTATTCATGCTTTCTTTTAAA
1 TTATT-AT--TTTATTTTAAA
**
23413971 TTATTAAATTATTTTAAA
1 TTATTATTTTATTTTAAA
23413989 TTA
1 TTA
23413992 ACAAAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 17 0.50
19 2 0.06
20 1 0.03
21 14 0.41
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATTATTTTATTTTAAA
Found at i:23414277 original size:21 final size:21
Alignment explanation
Indices: 23414235--23414278 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
23414225 AAAATGATAA
*
23414235 TTAAAAGTTTAAAATTATATC
1 TTAAAAGTTTAAAATTAAATC
* * *
23414256 TTAAAATTTTGAATTTAAATC
1 TTAAAAGTTTAAAATTAAATC
23414277 TT
1 TT
23414279 GAAACGAATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (21 bp):
TTAAAAGTTTAAAATTAAATC
Found at i:23415759 original size:66 final size:66
Alignment explanation
Indices: 23415626--23415794 Score: 238
Period size: 66 Copynumber: 2.6 Consensus size: 66
23415616 GAGGAGAAAG
* * * *
23415626 AAAAGAGATTCGAAGATGTGAGAAAGGAG-ATGCAAA-G--GTTACGCCGCCAATTAGAGGAGAT
1 AAAAGAAATTAGAAGATATGAGAAAGGAGAAT-CAAAGGTTGTTACACCGCCAATTAGAGGAGAT
*
23415687 GG
65 GA
* *
23415689 AAAAGAAATTAGAAGATACGAGAAAGGAGAATCAAAGGTTGTTACACCGCCCATTAGAGGAGATG
1 AAAAGAAATTAGAAGATATGAGAAAGGAGAATCAAAGGTTGTTACACCGCCAATTAGAGGAGATG
23415754 A
66 A
23415755 AAAAGAAATTAGAAGATATGAGAAAGGAGAATCAAAGGTT
1 AAAAGAAATTAGAAGATATGAGAAAGGAGAATCAAAGGTT
23415795 AAAGAAGAGT
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
63 29 0.31
64 3 0.03
66 62 0.66
ACGTcount: A:0.46, C:0.09, G:0.28, T:0.17
Consensus pattern (66 bp):
AAAAGAAATTAGAAGATATGAGAAAGGAGAATCAAAGGTTGTTACACCGCCAATTAGAGGAGATG
A
Found at i:23415775 original size:21 final size:21
Alignment explanation
Indices: 23415741--23415780 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
23415731 TACACCGCCC
*
23415741 ATTAGAGGAGATGAAAAAGAA
1 ATTAGAAGAGATGAAAAAGAA
* *
23415762 ATTAGAAGATATGAGAAAG
1 ATTAGAAGAGATGAAAAAG
23415781 GAGAATCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (21 bp):
ATTAGAAGAGATGAAAAAGAA
Found at i:23415938 original size:30 final size:30
Alignment explanation
Indices: 23415902--23415958 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
23415892 TGTTTATATA
*
23415902 AGGCGGCTCTCTCATTTACAAATCCTTATT
1 AGGCGGCCCTCTCATTTACAAATCCTTATT
23415932 AGGCGGCCCTCTCATTTACAAATCCTT
1 AGGCGGCCCTCTCATTTACAAATCCTT
23415959 GTAGTAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (30 bp):
AGGCGGCCCTCTCATTTACAAATCCTTATT
Found at i:23422724 original size:29 final size:28
Alignment explanation
Indices: 23422650--23422725 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
23422640 AAATAATTTA
*
23422650 ATAATTATTTAAATATTTAATATTTTATT
1 ATAATTAATTAAAT-TTTAATATTTTATT
** *
23422679 ATAATTAAGCAAGATTTTAATTTTTTATT
1 ATAATTAATTAA-ATTTTAATATTTTATT
23422708 -TCAACTTAATTAAATTTT
1 AT-AA-TTAATTAAATTTT
23422726 TAAATGAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 1 0.03
29 29 0.76
30 8 0.21
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (28 bp):
ATAATTAATTAAATTTTAATATTTTATT
Found at i:23428145 original size:21 final size:21
Alignment explanation
Indices: 23428121--23428165 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
23428111 TTCTAAACTC
*
23428121 AAAGAAGCATAAATTACCAAA
1 AAAGAAGCAAAAATTACCAAA
23428142 AAAGAAGCAAAAATTACCAAA
1 AAAGAAGCAAAAATTACCAAA
23428163 AAA
1 AAA
23428166 AATGGAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.67, C:0.13, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAGAAGCAAAAATTACCAAA
Found at i:23430896 original size:10 final size:9
Alignment explanation
Indices: 23430879--23430929 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 9
23430869 TGGTGCATAA
23430879 TTTTATTTT
1 TTTTATTTT
23430888 TTATTATTTGT
1 TT-TTATTT-T
23430899 TTTTATTTTT
1 TTTTA-TTTT
23430909 TATTTATTTT
1 T-TTTATTTT
23430919 ATTTTATTTT
1 -TTTTATTTT
23430929 T
1 T
23430930 AATTTTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
9 3 0.08
10 23 0.62
11 11 0.30
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (9 bp):
TTTTATTTT
Found at i:23430913 original size:17 final size:17
Alignment explanation
Indices: 23430886--23430935 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
23430876 TAATTTTATT
*
23430886 TTTTATTATTTGTTTTTA
1 TTTTATTATTT-ATTTTA
23430904 TTTT-TTATTTATTTTA
1 TTTTATTATTTATTTTA
23430920 TTTTATT-TTTAATTTT
1 TTTTATTATTT-ATTTT
23430936 TCTTACAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 12 0.41
17 13 0.45
18 4 0.14
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTATTATTTATTTTA
Found at i:23430915 original size:21 final size:21
Alignment explanation
Indices: 23430878--23430934 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
23430868 TTGGTGCATA
23430878 ATTTTATTTTTTA-TTATTTGT
1 ATTTTATTTTTTATTTATTT-T
23430899 -TTTTATTTTTTATTTATTTT
1 ATTTTATTTTTTATTTATTTT
*
23430919 ATTTTATTTTTAATTT
1 ATTTTATTTTTTATTT
23430935 TTCTTACAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (21 bp):
ATTTTATTTTTTATTTATTTT
Found at i:23431390 original size:14 final size:14
Alignment explanation
Indices: 23431368--23431416 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
23431358 TATTTTTGCG
*
23431368 ATTTGAAAAAATGT
1 ATTTAAAAAAATGT
23431382 ATTT--AAAAATGT
1 ATTTAAAAAAATGT
23431394 -TGTTAAAAAAATGT
1 AT-TTAAAAAAATGT
23431408 AGTTTAAAA
1 A-TTTAAAA
23431417 TTCTAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
11 1 0.03
12 10 0.33
14 12 0.40
15 6 0.20
16 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (14 bp):
ATTTAAAAAAATGT
Found at i:23433948 original size:7 final size:7
Alignment explanation
Indices: 23433923--23433975 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
23433913 TTTATTAAGT
23433923 TAAAATAA
1 TAAAAT-A
*
23433931 TTAAATAA
1 TAAAAT-A
23433939 TAAAATA
1 TAAAATA
23433946 TAAAATA
1 TAAAATA
*
23433953 TAAATTA
1 TAAAATA
23433960 -AAAATTA
1 TAAAA-TA
23433967 TAAAATA
1 TAAAATA
23433974 TA
1 TA
23433976 TTTTACATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
6 3 0.08
7 20 0.51
8 16 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TAAAATA
Found at i:23438534 original size:15 final size:13
Alignment explanation
Indices: 23438505--23438529 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23438495 AATAAGCATT
23438505 TATTTTTTAAAAC
1 TATTTTTTAAAAC
23438518 TATTTTTTAAAA
1 TATTTTTTAAAA
23438530 AACTAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTTTTAAAAC
Found at i:23445293 original size:21 final size:21
Alignment explanation
Indices: 23445260--23445308 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
23445250 ACCATAACTC
*
23445260 TTTTTATATATTAT-TTATAT
1 TTTTTATACATTATATTATAT
*
23445280 TTTTTGATACATTATATTATTT
1 TTTTT-ATACATTATATTATAT
23445302 TATTTTA
1 T-TTTTA
23445309 AAAAGGGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 5 0.21
21 8 0.33
22 7 0.29
23 4 0.17
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTTATACATTATATTATAT
Found at i:23451110 original size:30 final size:30
Alignment explanation
Indices: 23451046--23451179 Score: 112
Period size: 30 Copynumber: 4.5 Consensus size: 30
23451036 GAACTTTATC
* *
23451046 ATTT-TATTTAAATAAATTTTTATTTTTTT
1 ATTTATATTTAAATAAATTTTTAATTTTTA
**
23451075 A-TTATATTTAAATTGATTTTTAATTTTTA
1 ATTTATATTTAAATAAATTTTTAATTTTTA
* * **
23451104 ATTTATATTCAAATAAACTTTTAACATTTA
1 ATTTATATTTAAATAAATTTTTAATTTTTA
* * * *
23451134 ATTTGTATCTAAAT-AATCTTCTAACTTTTA
1 ATTTATATTTAAATAAAT-TTTTAATTTTTA
* *
23451164 ATTTGTAATTAAATAA
1 ATTTATATTTAAATAA
23451180 CCTCTAATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
28 2 0.02
29 25 0.30
30 55 0.66
31 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.55
Consensus pattern (30 bp):
ATTTATATTTAAATAAATTTTTAATTTTTA
Found at i:23451196 original size:29 final size:30
Alignment explanation
Indices: 23451099--23451197 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 30
23451089 GATTTTTAAT
* * * *
23451099 TTTTAATTTATAT-TCAAATAAACTTTTAAC
1 TTTTAATTTGTATCT-AAATAATCCTCTAAC
* *
23451129 ATTTAATTTGTATCTAAATAATCTTCTAAC
1 TTTTAATTTGTATCTAAATAATCCTCTAAC
*
23451159 TTTTAATTTGTAAT-TAAATAA-CCTCTAAT
1 TTTTAATTTGT-ATCTAAATAATCCTCTAAC
*
23451188 TTTTCATTTG
1 TTTTAATTTG
23451198 AAATAAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.25
30 41 0.69
31 3 0.05
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.51
Consensus pattern (30 bp):
TTTTAATTTGTATCTAAATAATCCTCTAAC
Found at i:23454283 original size:14 final size:13
Alignment explanation
Indices: 23454259--23454287 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
23454249 AATTTATTTT
23454259 TTAAAATAAAATA
1 TTAAAATAAAATA
23454272 TTAAAATAAAA-A
1 TTAAAATAAAATA
23454284 TTAA
1 TTAA
23454288 CATATACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAAATAAAATA
Found at i:23456018 original size:6 final size:6
Alignment explanation
Indices: 23456017--23456062 Score: 56
Period size: 6 Copynumber: 7.0 Consensus size: 6
23456007 AATAAATTTA
23456017 AAAATT AAAATT AAAATTT AATCAATT AAAATT AAAAATT AAAATT
1 AAAATT AAAATT AAAA-TT AA--AATT AAAATT -AAAATT AAAATT
23456063 TTTTTGAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 20 0.56
7 10 0.28
8 4 0.11
9 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (6 bp):
AAAATT
Found at i:23456025 original size:13 final size:13
Alignment explanation
Indices: 23456017--23456062 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
23456007 AATAAATTTA
23456017 AAAATT-AAAATT
1 AAAATTAAAAATT
*
23456029 AAAATTTAATCAATT
1 AAAA-TTAA-AAATT
23456044 AAAATTAAAAATT
1 AAAATTAAAAATT
23456057 AAAATT
1 AAAATT
23456063 TTTTTGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 5 0.17
15 8 0.28
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:23456026 original size:7 final size:7
Alignment explanation
Indices: 23456014--23456060 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
23456004 TTTAATAAAT
23456014 TTAAAAA
1 TTAAAAA
23456021 TT-AAAA
1 TTAAAAA
*
23456027 TTAAAAT
1 TTAAAAA
*
23456034 TTAATCAA
1 TTAA-AAA
23456042 TT-AAAA
1 TTAAAAA
23456048 TTAAAAA
1 TTAAAAA
23456055 TTAAAA
1 TTAAAA
23456061 TTTTTTTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 10 0.30
7 20 0.61
8 3 0.09
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (7 bp):
TTAAAAA
Found at i:23456029 original size:28 final size:27
Alignment explanation
Indices: 23455998--23456059 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
23455988 TTTTTTAATC
*
23455998 ATTAATTTTAATAAATTTAAAAATT-AAA
1 ATTAAATTTAATAAA-TT-AAAATTAAAA
*
23456026 ATTAAAATTTAATCAATTAAAATTAAAA
1 ATT-AAATTTAATAAATTAAAATTAAAA
23456054 ATTAAA
1 ATTAAA
23456060 ATTTTTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 9 0.30
28 11 0.37
29 10 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
ATTAAATTTAATAAATTAAAATTAAAA
Found at i:23456045 original size:21 final size:20
Alignment explanation
Indices: 23456010--23456060 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
23456000 TAATTTTAAT
23456010 AAATTTAAAAATTAAAATTA
1 AAATTTAAAAATTAAAATTA
*
23456030 AAATTTAATCAATTAAAATTA
1 AAATTTAA-AAATTAAAATTA
*
23456051 AAAATTAAAA
1 AAATTTAAAA
23456061 TTTTTTTGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTTAAAAATTAAAATTA
Found at i:23457951 original size:35 final size:35
Alignment explanation
Indices: 23457905--23457974 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
23457895 CATATTGGTG
*
23457905 GGTTGAAATAAGCT-GTTTTAGGGATTTTGTAAAGA
1 GGTTGAAATAAGCTGGTTTAAGGG-TTTTGTAAAGA
23457940 GGTTGAAATAAGCTGGTTTAAGGGTTTTGTAAAGA
1 GGTTGAAATAAGCTGGTTTAAGGGTTTTGTAAAGA
23457975 AAGCTAAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 25 0.76
36 8 0.24
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (35 bp):
GGTTGAAATAAGCTGGTTTAAGGGTTTTGTAAAGA
Found at i:23474498 original size:22 final size:23
Alignment explanation
Indices: 23474449--23474506 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 23
23474439 TGGTTGGTGC
*
23474449 ATAATATT-ATATTA-AAATATA
1 ATAAAATTAATATTATAAATATA
23474470 ATAAAA-TAATATTATAAAT-TAA
1 ATAAAATTAATATTATAAATAT-A
*
23474492 ATTAAATTAA-ATTAT
1 ATAAAATTAATATTAT
23474507 TTTATTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 1 0.03
21 12 0.39
22 15 0.48
23 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAAAATTAATATTATAAATATA
Found at i:23474714 original size:22 final size:22
Alignment explanation
Indices: 23474655--23474715 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
23474645 CTTATAAATT
** *
23474655 AAAAATAATTATGCTTATTTAA
1 AAAAATAATTAAACTTATATAA
* *
23474677 AAAAATTAAATCAACTTATATAA
1 AAAAA-TAATTAAACTTATATAA
23474700 AAAAATAATTAAACTT
1 AAAAATAATTAAACTT
23474716 CTTTATGATC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAATAATTAAACTTATATAA
Found at i:23478231 original size:18 final size:17
Alignment explanation
Indices: 23478205--23478238 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23478195 TTTGTTTGAT
23478205 ATATGATAAAATAAAATA
1 ATATGAT-AAATAAAATA
*
23478223 ATATTATAAATAAAAT
1 ATATGATAAATAAAAT
23478239 TAAATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
ATATGATAAATAAAATA
Found at i:23483534 original size:23 final size:23
Alignment explanation
Indices: 23483489--23483548 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
23483479 TCTTATGTCC
23483489 TAAAATTTTTTTTTTGAACA-TT
1 TAAAATTTTTTTTTTGAACATTT
** *
23483511 TAAAATTTTTATTTTTTTATATTT
1 TAAAATTTTT-TTTTTGAACATTT
*
23483535 TAAAATTATTTTTT
1 TAAAATTTTTTTTT
23483549 ATGATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 10 0.31
23 11 0.34
24 11 0.34
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
TAAAATTTTTTTTTTGAACATTT
Found at i:23483567 original size:21 final size:19
Alignment explanation
Indices: 23483522--23483573 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
23483512 AAAATTTTTA
*
23483522 TTTTTTTATATTTTAAAAT
1 TTTTTTTATATTTTAAAAC
*
23483541 TATTTTTTATGATTTTTTAAAC
1 T-TTTTTTAT-A-TTTTAAAAC
23483563 -TTTTTTATATT
1 TTTTTTTATATT
23483574 AAAAATTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 2 0.07
19 2 0.07
20 16 0.57
21 1 0.04
22 7 0.25
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTTTTATATTTTAAAAC
Found at i:23483629 original size:25 final size:27
Alignment explanation
Indices: 23483567--23483629 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 27
23483557 TTAAACTTTT
* * *
23483567 TTATATTAAAAATTATGAAAATTTAATT
1 TTATAATAAAAATTA-GAAAATGTAATA
23483595 TTATAA-AAAAATTA-AAAATGTAATA
1 TTATAATAAAAATTAGAAAATGTAATA
23483620 TTA-AATAAAA
1 TTATAATAAAA
23483630 TAAAATCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 2 0.06
25 16 0.52
27 8 0.26
28 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (27 bp):
TTATAATAAAAATTAGAAAATGTAATA
Found at i:23485642 original size:11 final size:11
Alignment explanation
Indices: 23485626--23485654 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
23485616 TAAAAATATC
23485626 TATATAAAATA
1 TATATAAAATA
23485637 TATATAAAATA
1 TATATAAAATA
23485648 TAT-TAAA
1 TATATAAA
23485655 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATATAAAATA
Found at i:23486329 original size:25 final size:24
Alignment explanation
Indices: 23486301--23486356 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
23486291 AAATTAAAAA
* *
23486301 TAAAAAAAGTTATTGTAGTTACGAT
1 TAAAAAAA-TAATTGTAATTACGAT
* *
23486326 TAAAAAAATAATTTTAATTATGAT
1 TAAAAAAATAATTGTAATTACGAT
23486350 TAAAAAA
1 TAAAAAA
23486357 TTTATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.36
Consensus pattern (24 bp):
TAAAAAAATAATTGTAATTACGAT
Found at i:23486615 original size:23 final size:21
Alignment explanation
Indices: 23486588--23486629 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
23486578 AAATTGAAGA
23486588 AAATTATTTAATATATTATTAGT
1 AAATTATTTAAT-T-TTATTAGT
*
23486611 AAATTTTTTAATTTTATTA
1 AAATTATTTAATTTTATTA
23486630 ACAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
AAATTATTTAATTTTATTAGT
Found at i:23487169 original size:30 final size:30
Alignment explanation
Indices: 23487090--23487218 Score: 93
Period size: 30 Copynumber: 4.3 Consensus size: 30
23487080 TTAAATGTTT
* *
23487090 ATTTATATATAATAGAAATTAAAAGTTAAAA
1 ATTTATTTA-AATACAAATTAAAAGTTAAAA
* ** *
23487121 TTTTATTTGGATACAAATTAAATGTTAAAA
1 ATTTATTTAAATACAAATTAAAAGTTAAAA
** * **
23487151 ATTTATTTAAATGTAAATT-AAAGATCAATG
1 ATTTATTTAAATACAAATTAAAAG-TTAAAA
* * *
23487181 ACTTATTTAAATAC-AA-TAAAAATAAAAA
1 ATTTATTTAAATACAAATTAAAAGTTAAAA
23487209 ATTTATTTAA
1 ATTTATTTAA
23487219 TCAAAATAAT
Statistics
Matches: 73, Mismatches: 23, Indels: 7
0.71 0.22 0.07
Matches are distributed among these distances:
28 13 0.18
29 8 0.11
30 46 0.63
31 6 0.08
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
ATTTATTTAAATACAAATTAAAAGTTAAAA
Found at i:23487588 original size:12 final size:12
Alignment explanation
Indices: 23487573--23487600 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
23487563 AAAATATTAA
23487573 ATATTATATTTT
1 ATATTATATTTT
23487585 ATATTATATTTT
1 ATATTATATTTT
23487597 ATAT
1 ATAT
23487601 AAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:23487613 original size:32 final size:31
Alignment explanation
Indices: 23487571--23487638 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
23487561 ATAAAATATT
* * *
23487571 AAATATTATATTTTATATT-ATATTTTATATAA
1 AAATAATATATTATA-ATTCATA-TTGATATAA
23487603 AAATAATATATTATAATTCATATTGATATAA
1 AAATAATATATTATAATTCATATTGATATAA
23487634 AAATA
1 AAATA
23487639 TTAAATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 16 0.50
32 16 0.50
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (31 bp):
AAATAATATATTATAATTCATATTGATATAA
Found at i:23488796 original size:17 final size:18
Alignment explanation
Indices: 23488771--23488808 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
23488761 AAAAATAGTT
*
23488771 CAATTTTTTATTATT-AA
1 CAATATTTTATTATTCAA
23488788 CAATATTTTATTATTCAA
1 CAATATTTTATTATTCAA
23488806 CAA
1 CAA
23488809 CAATAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
CAATATTTTATTATTCAA
Found at i:23489047 original size:18 final size:19
Alignment explanation
Indices: 23489012--23489053 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
23489002 TAAATTGAAT
23489012 TATATATTTTTATTAATTTG
1 TATATATTTTTA-TAATTTG
*
23489032 TATATATTTTTA-AATTTT
1 TATATATTTTTATAATTTG
23489050 TATA
1 TATA
23489054 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
20 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TATATATTTTTATAATTTG
Found at i:23490946 original size:25 final size:25
Alignment explanation
Indices: 23490912--23490961 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
23490902 TGTTGATAAG
23490912 TGTGTTCCATTAATGAACATGACTT
1 TGTGTTCCATTAATGAACATGACTT
23490937 TGTGTTCCATTAATGAACATGACTT
1 TGTGTTCCATTAATGAACATGACTT
23490962 GCATTCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (25 bp):
TGTGTTCCATTAATGAACATGACTT
Found at i:23491210 original size:3 final size:3
Alignment explanation
Indices: 23491202--23491226 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23491192 GCGAACCAAC
23491202 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
23491227 TTCTCTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:23497208 original size:35 final size:35
Alignment explanation
Indices: 23497169--23497236 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
23497159 TGACTTTGTT
* *
23497169 AAACCCTTTCCATTTCCCTATCTTGTTCTGACTGA
1 AAACCCTTTCCATTTCCCAATCTTGTCCTGACTGA
* *
23497204 AAACCTTTTCCATTTCTCAATCTTGTCCTGACT
1 AAACCCTTTCCATTTCCCAATCTTGTCCTGACT
23497237 TTGACCATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.21, C:0.31, G:0.07, T:0.41
Consensus pattern (35 bp):
AAACCCTTTCCATTTCCCAATCTTGTCCTGACTGA
Found at i:23501205 original size:18 final size:18
Alignment explanation
Indices: 23501181--23501219 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
23501171 TCACAACTAA
*
23501181 ATTTTTTTAATTAATTC-
1 ATTTTTTTAAGTAATTCT
23501198 ATTTTTTTAAGTAATTCT
1 ATTTTTTTAAGTAATTCT
23501216 ATTT
1 ATTT
23501220 CTGTGTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTTTTTAAGTAATTCT
Found at i:23519986 original size:2 final size:2
Alignment explanation
Indices: 23519981--23520008 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23519971 TTTAGAGATA
23519981 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
23520009 TTTTTATTTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:23537105 original size:2 final size:2
Alignment explanation
Indices: 23537098--23537122 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23537088 TACTTAAGAT
23537098 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
23537123 CATAGAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:23538656 original size:14 final size:14
Alignment explanation
Indices: 23538637--23538663 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23538627 TGGCTCAAAA
23538637 AAAAAAAAAAAACG
1 AAAAAAAAAAAACG
23538651 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
23538664 ATTTGGGGAT
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:0.89, C:0.07, G:0.04, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAACG
Found at i:23539112 original size:12 final size:12
Alignment explanation
Indices: 23539095--23539119 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23539085 TTTTAAACAA
23539095 ATTTAATAAAAT
1 ATTTAATAAAAT
23539107 ATTTAATAAAAT
1 ATTTAATAAAAT
23539119 A
1 A
23539120 ATAAATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTTAATAAAAT
Found at i:23539742 original size:2 final size:2
Alignment explanation
Indices: 23539735--23539764 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23539725 AACTCGAAGG
23539735 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
23539765 GTGTCTGACC
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):
CT
Found at i:23544685 original size:25 final size:25
Alignment explanation
Indices: 23544639--23544686 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
23544629 TTATATTTTG
** *
23544639 ATTTTAATATAATTTATGATATATA
1 ATTTTAATATAAAATATAATATATA
*
23544664 ATTTTTATATAAAATATAATATA
1 ATTTTAATATAAAATATAATATA
23544687 AATATAATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
ATTTTAATATAAAATATAATATATA
Found at i:23544689 original size:11 final size:11
Alignment explanation
Indices: 23544670--23544709 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
23544660 TATAATTTTT
23544670 ATATAAAATATA
1 ATAT-AAATATA
23544682 ATATAAATATA
1 ATATAAATATA
**
23544693 ATATTTATATA
1 ATATAAATATA
23544704 ATATAA
1 ATATAA
23544710 TAATACAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATATAAATATA
Found at i:23544699 original size:29 final size:30
Alignment explanation
Indices: 23544659--23544719 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
23544649 AATTTATGAT
* *
23544659 ATATAATTTTTATATAAAAT-ATAATATAA
1 ATATAATATTTATATAAAATAATAATACAA
*
23544688 ATATAATATTTATATAATATAATAATACAA
1 ATATAATATTTATATAAAATAATAATACAA
23544718 AT
1 AT
23544720 TATCATATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATAATATTTATATAAAATAATAATACAA
Found at i:23544706 original size:16 final size:16
Alignment explanation
Indices: 23544650--23544711 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
23544640 TTTTAATATA
23544650 ATTTATGAT-ATATAAT
1 ATTTAT-ATAATATAAT
* *
23544666 TTTTATATAAAAT-AT
1 ATTTATATAATATAAT
*
23544681 A-ATATA-AATATAAT
1 ATTTATATAATATAAT
23544695 ATTTATATAATATAAT
1 ATTTATATAATATAAT
23544711 A
1 A
23544712 ATACAAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
13 4 0.11
14 7 0.19
15 8 0.22
16 17 0.47
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTTATATAATATAAT
Found at i:23545740 original size:93 final size:94
Alignment explanation
Indices: 23545571--23545743 Score: 210
Period size: 93 Copynumber: 1.9 Consensus size: 94
23545561 AATTGATTAA
* *
23545571 AAATTTATTTTTTCAACATTATATAATTTCAAGAAAAATTACTTTTTTTAGATAAAAACATAGTT
1 AAATTTATTTTTTCAAAATTATATAATTTCAAGAAAAATTACTTTTTTTAAATAAAAACATAGTT
* *
23545636 TATCTTTAAAATATAGAATTTTGAAAAAT
66 TATATTGAAAATATAGAATTTTGAAAAAT
* * **
23545665 AAATTTA-TTTTTCAAAATTTTATAGTTTCAA-ATAAAATTAC-TTTTTTAAATTTTAAACATTA
1 AAATTTATTTTTTCAAAATTATATAATTTCAAGA-AAAATTACTTTTTTTAAA-TAAAAACA-TA
*
23545727 -TTTTTATTGAAAATATA
63 GTTTATATTGAAAATATA
23545744 TTGTAAAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
92 9 0.13
93 49 0.73
94 9 0.13
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (94 bp):
AAATTTATTTTTTCAAAATTATATAATTTCAAGAAAAATTACTTTTTTTAAATAAAAACATAGTT
TATATTGAAAATATAGAATTTTGAAAAAT
Found at i:23545931 original size:21 final size:22
Alignment explanation
Indices: 23545895--23545941 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
23545885 TTTTAAAATT
23545895 AAAAGATAATTTTTATC-T-TA
1 AAAAGATAATTTTTATCGTATA
*
23545915 AAAATATAATCTTTTATCGTATA
1 AAAAGATAAT-TTTTATCGTATA
23545938 AAAA
1 AAAA
23545942 CTACGTGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 7 0.30
22 1 0.04
23 6 0.26
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (22 bp):
AAAAGATAATTTTTATCGTATA
Found at i:23546514 original size:33 final size:32
Alignment explanation
Indices: 23546458--23546522 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
23546448 TCATGAATAT
*
23546458 TAAATAAATAATTTACATGTTAAA-AAAGTAAA
1 TAAATAAATAATTAACATGTTAAATAAA-TAAA
23546490 TAAATAAATAATTAAACATGTTAAATAAATAAA
1 TAAATAAATAATT-AACATGTTAAATAAATAAA
23546523 AAAAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.43
33 14 0.47
34 3 0.10
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (32 bp):
TAAATAAATAATTAACATGTTAAATAAATAAA
Found at i:23548961 original size:19 final size:18
Alignment explanation
Indices: 23548911--23548963 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
23548901 ATATTATTTT
23548911 AATAA-TATTTTTAATAA
1 AATAATTATTTTTAATAA
*
23548928 ATTTATATATATTTTTATATAA
1 A-ATA-AT-TATTTTTA-ATAA
23548950 AATAATTATTTTTA
1 AATAATTATTTTTA
23548964 CTTTATAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 1 0.03
18 2 0.07
19 9 0.31
20 2 0.07
21 10 0.34
22 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATAATTATTTTTAATAA
Found at i:23556592 original size:29 final size:30
Alignment explanation
Indices: 23556525--23556675 Score: 135
Period size: 30 Copynumber: 5.0 Consensus size: 30
23556515 AAAAAAGTTC
* * *
23556525 TTAAACTTTATAATTT-TACTTAAATAAACTC
1 TTAAA-TTT-TAATTTATATTTAAATAAAATT
* *
23556556 TTATATTTTTA-TTATATTTAAATAAAATT
1 TTAAATTTTAATTTATATTTAAATAAAATT
* * *
23556585 TTAAATTTTAATTTACACTTAAATAAATTT
1 TTAAATTTTAATTTATATTTAAATAAAATT
* * * * *
23556615 TTCATTTTTCATTTATATATAAATAAATTT
1 TTAAATTTTAATTTATATTTAAATAAAATT
* *
23556645 TTAAATTTTAATTTGTATCTAAATAAAATT
1 TTAAATTTTAATTTATATTTAAATAAAATT
23556675 T
1 T
23556676 AACAAAAATT
Statistics
Matches: 96, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
28 2 0.02
29 23 0.24
30 67 0.70
31 4 0.04
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (30 bp):
TTAAATTTTAATTTATATTTAAATAAAATT
Found at i:23556671 original size:60 final size:58
Alignment explanation
Indices: 23556525--23556658 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 58
23556515 AAAAAAGTTC
* * *
23556525 TTAAACTTTATAATTT-TACTTAAATAAACTCTTAT-ATTTTTATTATATTTAAATAAAATT
1 TTAAA-TTT-TAATTTACACTTAAATAAA-T-TTTTCATTTTTATTATATATAAATAAAATT
*
23556585 TTAAATTTTAATTTACACTTAAATAAATTTTTCATTTTTCATTTATATATAAATAAATTT
1 TTAAATTTTAATTTACACTTAAATAAATTTTTCATTTTT-A-TTATATATAAATAAAATT
23556645 TTAAATTTTAATTT
1 TTAAATTTTAATTT
23556659 GTATCTAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
57 3 0.05
58 13 0.20
59 15 0.23
60 35 0.53
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (58 bp):
TTAAATTTTAATTTACACTTAAATAAATTTTTCATTTTTATTATATATAAATAAAATT
Found at i:23556724 original size:16 final size:16
Alignment explanation
Indices: 23556691--23556721 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
23556681 AAATTATTCT
23556691 TTTATTTAAAATAAAA
1 TTTATTTAAAATAAAA
23556707 TTTATTT-AAATAAAA
1 TTTATTTAAAATAAAA
23556722 ATTAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTATTTAAAATAAAA
Found at i:23558720 original size:62 final size:61
Alignment explanation
Indices: 23558530--23559007 Score: 276
Period size: 62 Copynumber: 7.7 Consensus size: 61
23558520 ATAAAAAGAT
* * * * ** **
23558530 TTATTGAAGGTATTTTTTATCAAAAATACCTTTAATAATC-CTCCACAATTTTTTAAGAGAA
1 TTATTGAAGGTATTTTTTGTCAAAAATACCTTCAATAATCTCTCTAAAAAATTGAAAG-GAA
* * * * * *** * * *
23558591 TTATTAAAGGTATTTTTTGGTAAAAAATATCTTCAATAGTCGTATCT--ATTTTTTATGAGCAGA
1 TTATTGAAGGTATTTTTT-GTCAAAAATACCTTCAATAATC-TCTCTAAAAAATTGA-AAGGA-A
* * **
23558654 TTATTTAAGGTATTTTTTGTCCAAAACGCCTTCAATAATCTCTCATAAAAAATTGAAAGGAA
1 TTATTGAAGGTATTTTTTGTCAAAAATACCTTCAATAATCTCTC-TAAAAAATTGAAAGGAA
** * * *
23558716 TTATTGAAGGCGTTTTCT-ACACAAAATACCTTCAATAAT-TCTCTAAAAAAGATG-AAGGAAA
1 TTATTGAAGGTATTTTTTGTCA-AAAATACCTTCAATAATCTCTCTAAAAAA-TTGAAAGG-AA
** * * * *
23558777 TTATTGAAGGTAGTTTTTT-TACAAAAAATTTCTTCAATAATCCTTTTTAAAAAATTG-GATGAG
1 TTATTGAAGGTA-TTTTTTGT-C-AAAAATACCTTCAATAAT-CTCTCTAAAAAATTGAAAGGA-
23558840 A
61 A
* * * * *
23558841 TTATTGAATGTATTTTTTGTTAAAAAATGCCATCAATAATCTTCTCTAAAAAATTGAAAGGGA
1 TTATTGAAGGTATTTTTTG-TCAAAAATACCTTCAATAATC-TCTCTAAAAAATTGAAAGGAA
* * * *
23558904 TTATTGAAGGTA-TTTTTGATCAAAAATACTTTCAATAATCTCT-TCATCAAAATTTAAAGGGA
1 TTATTGAAGGTATTTTTTG-TCAAAAATACCTTCAATAATCTCTCT-A-AAAAATTGAAAGGAA
** * *
23558966 TTATTGAAGGCGCTTTTTTGT-AAAAAAATCTTCAATAATCTC
1 TTATTGAAGG-TATTTTTTGTCAAAAATACCTTCAATAATCTC
23559008 CTTAAATTTT
Statistics
Matches: 323, Mismatches: 69, Indels: 49
0.73 0.16 0.11
Matches are distributed among these distances:
60 12 0.04
61 43 0.13
62 141 0.44
63 86 0.27
64 31 0.10
65 10 0.03
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (61 bp):
TTATTGAAGGTATTTTTTGTCAAAAATACCTTCAATAATCTCTCTAAAAAATTGAAAGGAA
Found at i:23566771 original size:20 final size:21
Alignment explanation
Indices: 23566735--23566786 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
23566725 TCCGAAATTA
23566735 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
23566757 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
23566778 AT-AAATATT
1 ATAAAATATT
23566787 TAAATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:23566777 original size:21 final size:22
Alignment explanation
Indices: 23566735--23566786 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
23566725 TCCGAAATTA
23566735 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
23566757 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
23566778 AT-AAATATT
1 ATAAAATATT
23566787 TAAATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:23566779 original size:14 final size:14
Alignment explanation
Indices: 23566771--23566810 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
23566761 AATATTATTT
23566771 TTTAAATATAAATA
1 TTTAAATATAAATA
23566785 TTTAAATATATAATTA
1 TTTAAATATA-AA-TA
*
23566801 TATAAATATA
1 TTTAAATATA
23566811 TATAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 2 0.09
16 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAATATAAATA
Found at i:23566792 original size:8 final size:8
Alignment explanation
Indices: 23566776--23566812 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
23566766 TATTTTTTAA
23566776 ATATAAAT
1 ATATAAAT
*
23566784 ATTTAAAT
1 ATATAAAT
*
23566792 ATATAATT
1 ATATAAAT
23566800 ATATAAAT
1 ATATAAAT
23566808 ATATA
1 ATATA
23566813 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATAAAT
Found at i:23566819 original size:14 final size:14
Alignment explanation
Indices: 23566773--23566820 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
23566763 TATTATTTTT
* *
23566773 TAAATATAAATATT
1 TAAATATATATATA
23566787 TAAATATATAATTATA
1 TAAATATAT-A-TATA
*
23566803 TAAATATATATAAA
1 TAAATATATATATA
23566817 TAAA
1 TAAA
23566821 AAATTAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 15 0.52
15 2 0.07
16 12 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATATATATATA
Found at i:23566825 original size:26 final size:24
Alignment explanation
Indices: 23566776--23566826 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
23566766 TATTTTTTAA
* *
23566776 ATATAAATATTTAAATATATAATT
1 ATATAAATATTTAAATAAAAAATT
23566800 ATATAAATATATATAAATAAAAAATT
1 ATATAAATAT-T-TAAATAAAAAATT
23566826 A
1 A
23566827 ATTTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 1 0.04
26 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATAAATATTTAAATAAAAAATT
Found at i:23569557 original size:24 final size:25
Alignment explanation
Indices: 23569530--23569606 Score: 70
Period size: 24 Copynumber: 3.1 Consensus size: 25
23569520 TATATTATAA
23569530 TTTATT-AATATTAAATATAA-ATTT
1 TTTATTAAAT-TTAAATATAATATTT
*
23569554 TTTATTAAATTTATATATAATA-TT
1 TTTATTAAATTTAAATATAATATTT
* * *
23569578 TTAATAAAATTTTAAAATATATTATTT
1 TTTATTAAA-TTT-AAATATAATATTT
23569605 TT
1 TT
23569607 ATATGGTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
24 24 0.56
25 7 0.16
26 8 0.19
27 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTATTAAATTTAAATATAATATTT
Found at i:23570707 original size:12 final size:12
Alignment explanation
Indices: 23570673--23570710 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
23570663 TTAAAGAGAA
23570673 TTAAA-AATAA-
1 TTAAATAATAAT
23570683 TTAAATAATTAAT
1 TTAAATAA-TAAT
23570696 TTAAATAATAAT
1 TTAAATAATAAT
23570708 TTA
1 TTA
23570711 TTTAGATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.20
11 2 0.08
12 10 0.40
13 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTAAATAATAAT
Found at i:23583405 original size:45 final size:45
Alignment explanation
Indices: 23583356--23583642 Score: 179
Period size: 45 Copynumber: 6.5 Consensus size: 45
23583346 CATTCAAAAA
*
23583356 ATTCATCA-CCAAAATTTCAAAAATCTCATTCGAAAAATTTTAGAG
1 ATTCA-CATCCAAAATTTCAAAAATTTCATTCGAAAAATTTTAGAG
* * * *
23583401 ATTCATATCCAAAA-GT-AAAAGATTTTTC-TTTGAAAAA-CTTAGAG
1 ATTCACATCCAAAATTTCAAAA-A--TTTCATTCGAAAAATTTTAGAG
* * * *
23583445 ATTCACAAT-GAAAAATTCAAAAA--T--TT--AAAAACTTTA-AT
1 ATTCAC-ATCCAAAATTTCAAAAATTTCATTCGAAAAATTTTAGAG
* * *
23583483 ATTTCACAACCAAAATTTCAAAGATTCTCATTCGAAAAAATTTTAGGG
1 A-TTCACATCCAAAATTTCAAAAATT-TCATTCG-AAAAATTTTAGAG
* * * * *
23583531 TTTCACATCCAAAATTTCAAAGATTTCCATTC-AAAAAATTCAAAG
1 ATTCACATCCAAAATTTCAAAAATTT-CATTCGAAAAATTTTAGAG
* * * *
23583576 TTTCACATCCAAATTTTCAAATATTTACATTCGAAAAATTTTAAAG
1 ATTCACATCCAAAATTTCAAAAATTT-CATTCGAAAAATTTTAGAG
* *
23583622 ATTTACATCCAAAGTTTCAAA
1 ATTCACATCCAAAATTTCAAA
23583643 GGTTCTTTTT
Statistics
Matches: 190, Mismatches: 31, Indels: 41
0.73 0.12 0.16
Matches are distributed among these distances:
38 8 0.04
39 19 0.10
40 2 0.01
41 1 0.01
42 1 0.01
43 4 0.02
44 20 0.11
45 61 0.32
46 37 0.19
47 37 0.19
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.33
Consensus pattern (45 bp):
ATTCACATCCAAAATTTCAAAAATTTCATTCGAAAAATTTTAGAG
Found at i:23583557 original size:23 final size:23
Alignment explanation
Indices: 23583483--23583643 Score: 109
Period size: 22 Copynumber: 7.0 Consensus size: 23
23583473 AAACTTTAAT
*
23583483 ATTTCACAACCAAAATTTCAAAG
1 ATTTCACATCCAAAATTTCAAAG
* * * *
23583506 ATTCTCA-TTCGAAAAAATTT-TAGG
1 ATT-TCACATC--CAAAATTTCAAAG
*
23583530 GTTTCACATCCAAAATTTCAAAG
1 ATTTCACATCCAAAATTTCAAAG
* *
23583553 ATTTC-CATTCAAAAAATTCAAAG
1 ATTTCACA-TCCAAAATTTCAAAG
* *
23583576 -TTTCACATCCAAATTTTCAAAT
1 ATTTCACATCCAAAATTTCAAAG
* *
23583598 ATTT-ACATTCGAAAAATTTTAAAG
1 ATTTCACA-TC-CAAAATTTCAAAG
*
23583622 ATTT-ACATCCAAAGTTTCAAAG
1 ATTTCACATCCAAAATTTCAAAG
23583644 GTTCTTTTTC
Statistics
Matches: 104, Mismatches: 24, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
22 37 0.36
23 35 0.34
24 25 0.24
25 7 0.07
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (23 bp):
ATTTCACATCCAAAATTTCAAAG
Found at i:23587539 original size:22 final size:23
Alignment explanation
Indices: 23587509--23587562 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
23587499 TGTAAAATGC
23587509 ATGAATGTAATAAGAAGGATTTA
1 ATGAATGTAATAAGAAGGATTTA
23587532 A-GAATGTAATAAGAAGGATTTA
1 ATGAATGTAATAAGAAGGATTTA
23587554 ATG-ATGTAA
1 ATGAATGTAA
23587563 ATGCATGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (23 bp):
ATGAATGTAATAAGAAGGATTTA
Found at i:23588073 original size:21 final size:20
Alignment explanation
Indices: 23588032--23588076 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
23588022 ATACATGTGC
*
23588032 AAATGAATAACAAATATATA
1 AAATGAATAACAAATAAATA
*
23588052 AAATGAATAAATAAATAAATA
1 AAATGAAT-AACAAATAAATA
23588073 AAAT
1 AAAT
23588077 ACAAACAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
AAATGAATAACAAATAAATA
Found at i:23589079 original size:17 final size:15
Alignment explanation
Indices: 23589057--23589105 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 15
23589047 TAATTCAAAC
23589057 AAATATAACAAAAACAT
1 AAATATAA-AAAAA-AT
*
23589074 AAATATAAAAATAAT
1 AAATATAAAAAAAAT
*
23589089 ATATAT-AAAAAAAT
1 AAATATAAAAAAAAT
23589103 AAA
1 AAA
23589106 ACAAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 9 0.32
15 7 0.25
16 4 0.14
17 8 0.29
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (15 bp):
AAATATAAAAAAAAT
Found at i:23589084 original size:15 final size:14
Alignment explanation
Indices: 23589066--23589105 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
23589056 CAAATATAAC
*
23589066 AAAAACATAAATAT
1 AAAAAAATAAATAT
*
23589080 AAAAATAATATATAT
1 AAAAA-AATAAATAT
23589095 AAAAAAATAAA
1 AAAAAAATAAA
23589106 ACAAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAAAATAAATAT
Found at i:23589111 original size:28 final size:28
Alignment explanation
Indices: 23589058--23589113 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
23589048 AATTCAAACA
* *
23589058 AATATAACAAAAACATAAATATAAAAAT
1 AATATAACAAAAAAATAAATACAAAAAT
*
23589086 AATATATATAAAAAAATAAA-ACAAAAAT
1 AATATA-ACAAAAAAATAAATACAAAAAT
23589114 TTTTTGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.21
Consensus pattern (28 bp):
AATATAACAAAAAAATAAATACAAAAAT
Found at i:23589586 original size:17 final size:15
Alignment explanation
Indices: 23589564--23589612 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 15
23589554 TAATTCAAAC
23589564 AAATATAACAAAAACAT
1 AAATATAA-AAAAA-AT
*
23589581 AAATATAAAAATAAT
1 AAATATAAAAAAAAT
*
23589596 ATATAT-AAAAAAAT
1 AAATATAAAAAAAAT
23589610 AAA
1 AAA
23589613 ACAAAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 9 0.32
15 7 0.25
16 4 0.14
17 8 0.29
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (15 bp):
AAATATAAAAAAAAT
Found at i:23589591 original size:15 final size:14
Alignment explanation
Indices: 23589573--23589612 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
23589563 CAAATATAAC
*
23589573 AAAAACATAAATAT
1 AAAAAAATAAATAT
*
23589587 AAAAATAATATATAT
1 AAAAA-AATAAATAT
23589602 AAAAAAATAAA
1 AAAAAAATAAA
23589613 ACAAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAAAATAAATAT
Found at i:23589622 original size:508 final size:509
Alignment explanation
Indices: 23588600--23589624 Score: 1876
Period size: 507 Copynumber: 2.0 Consensus size: 509
23588590 AAGATTTATT
23588600 AAAATTTTTTGTAAAAAATTTTTATTTGTGAAAACAATTTATTCTAAAAAACATCTTTCAATCTG
1 AAAATTTTTTGTAAAAAATTTTTATTTGTGAAAACAATTTATTCTAAAAAACATCTTTCAATCTG
* *
23588665 TTGATAAGATTTTTTGTCAAAAATTATCCTCTAATCTATTAGTATGATTTTTTTTAAAACATATA
66 TTGATAAGATTTTCTGTCAAAAATTATCCTCTAATCTATTAGTAAGATTTTTTTTAAAACATATA
* *
23588730 TTTTTAAGAAATTCATTAAGCTTTCCACTAATTTGTGAAGACTTAATTCAAAATTTAAATCTTAC
131 TTTTAAAGAAATTCATTAAGCTTTCCACTAATTTGGGAAGACTTAATTCAAAATTTAAATCTTAC
* * *
23588795 AATAGTTTGGTAGAATTAAAAAATATTTTTTTTTTAATTTTTTGTAAAATTTGAAAGAAAAAAAG
196 AATAGTTTGGTAGAATTAAAAAACATTATTTTTTTAATTTTTTGTAAAACTTGAAAGAAAAAAAG
23588860 AAATTAAAATAAACAAAAATTATCATGCAAAGCAATTATGCAATATATTTAATAAATCATGCAAT
261 AAATTAAAATAAACAAAAATTATCATGCAAAGCAATTATGCAATATATTTAATAAATCATGCAAT
23588925 AAGTATAAAAACATGCAATTAGATATTTAAAAAAATCATGTAAATATATTAAACTCATGTTAAGA
326 AAGTATAAAAACATGCAATTAGATATTTAAAAAAATCATGTAAATATATTAAACTCATGTTAAGA
*
23588990 TAAATACTAAAAAAATTCATGCAAAGATAAACTAATTTTCCTATTTTCTCATCTCATTAATTCAA
391 TAAATACTAAAAAAATTCATGCAAAGATAAACTAATTTTCCTATTTTCTCATCACATTAATTCAA
23589055 ACAAATATAACAAAAACATAAATATAAAAATAATATATATAAAAAAATAAAACA
456 ACAAATATAACAAAAACATAAATATAAAAATAATATATATAAAAAAATAAAACA
* *
23589109 AAAATTTTTTGT-AAAAATTTTTATTTGTGAAAACAATTTATTTTCAAAAACATCTTTCAATCTG
1 AAAATTTTTTGTAAAAAATTTTTATTTGTGAAAACAATTTATTCTAAAAAACATCTTTCAATCTG
* *
23589173 TTGATAAGATTTTCTGTCAAGAATTATCCTCTATTCTATTAGTAAGATTTTTTTTAAAACATATA
66 TTGATAAGATTTTCTGTCAAAAATTATCCTCTAATCTATTAGTAAGATTTTTTTTAAAACATATA
23589238 TTTTAAAGAAATTCATTAAG-TCTTCCACTAATTTGGGAAGACTTAATTCAAAATTTAAATCTTA
131 TTTTAAAGAAATTCATTAAGCT-TTCCACTAATTTGGGAAGACTTAATTCAAAATTTAAATCTTA
*
23589302 CAATGGTTTGGTAGAATTAAAAAACA-TATTTTTTTAATTTTTTGTAAAACTTGAAAGAAAAAAA
195 CAATAGTTTGGTAGAATTAAAAAACATTATTTTTTTAATTTTTTGTAAAACTTGAAAGAAAAAAA
23589366 GAAATTAAAATAAACAAAAATTATCATGCAAAGCAATTATGCAATATATTTAATAAATCATGCAA
260 GAAATTAAAATAAACAAAAATTATCATGCAAAGCAATTATGCAATATATTTAATAAATCATGCAA
* *
23589431 TAAGTATAAAAATATGCAATTAGATATTTAAAAAAATCATGTAAATATATTAAACTCCTGTTAAG
325 TAAGTATAAAAACATGCAATTAGATATTTAAAAAAATCATGTAAATATATTAAACTCATGTTAAG
23589496 ATAAATACTAAAAAAATTCATGCAAAGATAAACTAATTTTCCTATTTTCTCATCACATTAATTCA
390 ATAAATACTAAAAAAATTCATGCAAAGATAAACTAATTTTCCTATTTTCTCATCACATTAATTCA
23589561 AACAAATATAACAAAAACATAAATATAAAAATAATATATATAAAAAAATAAAACA
455 AACAAATATAACAAAAACATAAATATAAAAATAATATATATAAAAAAATAAAACA
*
23589616 AAAAATTTT
1 AAAATTTTT
23589625 AAAAAATAAA
Statistics
Matches: 499, Mismatches: 16, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
507 292 0.59
508 195 0.39
509 12 0.02
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (509 bp):
AAAATTTTTTGTAAAAAATTTTTATTTGTGAAAACAATTTATTCTAAAAAACATCTTTCAATCTG
TTGATAAGATTTTCTGTCAAAAATTATCCTCTAATCTATTAGTAAGATTTTTTTTAAAACATATA
TTTTAAAGAAATTCATTAAGCTTTCCACTAATTTGGGAAGACTTAATTCAAAATTTAAATCTTAC
AATAGTTTGGTAGAATTAAAAAACATTATTTTTTTAATTTTTTGTAAAACTTGAAAGAAAAAAAG
AAATTAAAATAAACAAAAATTATCATGCAAAGCAATTATGCAATATATTTAATAAATCATGCAAT
AAGTATAAAAACATGCAATTAGATATTTAAAAAAATCATGTAAATATATTAAACTCATGTTAAGA
TAAATACTAAAAAAATTCATGCAAAGATAAACTAATTTTCCTATTTTCTCATCACATTAATTCAA
ACAAATATAACAAAAACATAAATATAAAAATAATATATATAAAAAAATAAAACA
Found at i:23589650 original size:22 final size:22
Alignment explanation
Indices: 23589602--23589650 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
23589592 TAATATATAT
**
23589602 AAAAAAATAAAACAAAAAATTT
1 AAAAAAATAAAACAAAAAATAA
* *
23589624 TAAAAAATAAACCAAAAAATAA
1 AAAAAAATAAAACAAAAAATAA
23589646 AAAAA
1 AAAAA
23589651 TGGATAAACC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (22 bp):
AAAAAAATAAAACAAAAAATAA
Found at i:23590335 original size:3 final size:3
Alignment explanation
Indices: 23590327--23590364 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
23590317 CATAATCATC
23590327 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
23590365 TTATTATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:23590369 original size:3 final size:3
Alignment explanation
Indices: 23590363--23590394 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
23590353 ATAATAATAA
23590363 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
23590395 AATACTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:23596367 original size:2 final size:2
Alignment explanation
Indices: 23596355--23596386 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
23596345 TAGTTTTTAA
*
23596355 CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
23596387 TTTCTCCATC
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:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:23600215 original size:13 final size:13
Alignment explanation
Indices: 23600199--23600231 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
23600189 CGATTAATCA
23600199 AATTAAATAATTT
1 AATTAAATAATTT
*
23600212 AATTAATTAATTT
1 AATTAAATAATTT
23600225 AATTAAA
1 AATTAAA
23600232 ATCGAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTAAATAATTT
Found at i:23601810 original size:56 final size:58
Alignment explanation
Indices: 23601740--23601951 Score: 204
Period size: 58 Copynumber: 3.7 Consensus size: 58
23601730 TTATACAAGG
*
23601740 AAAATTAATACTTTCAACTTTTTCTT-AAA-GTATTTTAA-AGTTTTATTTTTC-AAGAA
1 AAAATTAATACTTTCAACTTTTTCTTAAAATGTATTTTAATAATTTTA-TTTTCAAAG-A
* *
23601796 AAAATTAATACTTTCAACTTTTCCTTAAAATGTTTTTTAATAATTTTATTTTCAAAGA
1 AAAATTAATACTTTCAACTTTTTCTTAAAATGTATTTTAATAATTTTATTTTCAAAGA
* * * * * *
23601854 AAAATTGATATTTTCAACTTTTTCCTCAAAAATATTTTTTTTGAA-AATTTTATTTTC-AAGG
1 AAAATTAATACTTTCAACTTTTT-CT--TAAA-ATGTATTTT-AATAATTTTATTTTCAAAGA
* * *
23601915 AAAGTTAATACTTTTAACTTTTCCTTAAAA-GTATTTT
1 AAAATTAATACTTTCAACTTTTTCTTAAAATGTATTTT
23601952 TTTATATTTT
Statistics
Matches: 130, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
56 30 0.23
57 4 0.03
58 37 0.28
59 11 0.08
60 2 0.02
61 24 0.18
62 20 0.15
63 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (58 bp):
AAAATTAATACTTTCAACTTTTTCTTAAAATGTATTTTAATAATTTTATTTTCAAAGA
Found at i:23601974 original size:67 final size:64
Alignment explanation
Indices: 23601828--23602090 Score: 258
Period size: 61 Copynumber: 4.1 Consensus size: 64
23601818 CCTTAAAATG
* *
23601828 TTTTTT-AATAATTTTATTTTCAAAGAAAAATTGATA-TTTTCAACTTTTTCCTCAAAA-A---T
1 TTTTTTGAA-AATTTTATTTTC-AAGGAAAATTGATACTTTT-AAC-TTTTCCTTAAAATATTTT
*
23601887 ATT
62 TTT
* *
23601890 TTTTTTGAAAATTTTATTTTCAAGGAAAGTTAATACTTTTAACTTTTCCTTAAAAGTATTTTTTT
1 TTTTTTGAAAATTTTATTTTCAAGGAAAATTGATACTTTTAACTTTTCCTTAAAA-TATTTTTTT
* * *
23601955 ATATTTTTGAAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAA-A--TATT
1 -T-TTTTTGAAAATTTTATTTTCAAGGAAAATTGATACTTTTAACTTTTCCTTAAAATATTTTTT
23602017 T
64 T
* * *
23602018 TTTTTTGAAAATTTTATAGTT-AAGAAAAAATGATACTTTTAACTTTTCCTTAAAAATAATTTTT
1 TTTTTTGAAAATTTTAT-TTTCAAGGAAAATTGATACTTTTAACTTTTCCTT-AAAAT-ATTTTT
23602082 TT
63 TT
23602084 GTTTTTT
1 -TTTTTT
23602091 TTATTTTTGA
Statistics
Matches: 169, Mismatches: 16, Indels: 27
0.80 0.08 0.13
Matches are distributed among these distances:
60 11 0.07
61 56 0.33
62 30 0.18
63 6 0.04
64 1 0.01
65 4 0.02
66 5 0.03
67 56 0.33
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (64 bp):
TTTTTTGAAAATTTTATTTTCAAGGAAAATTGATACTTTTAACTTTTCCTTAAAATATTTTTTT
Done.