Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 125 of 211
Found at i:39549179 original size:11 final size:11
Alignment explanation
Indices: 39549111--39549231 Score: 84
Period size: 11 Copynumber: 10.3 Consensus size: 11
39549101 TATATTTCTA
*
39549111 TATTATTTATTT
1 TATTA-TTATAT
*
39549123 TATTATTCTAT
1 TATTATTATAT
*
39549134 CTATTATTGTAT
1 -TATTATTATAT
39549146 TATCTATTATTAT
1 TAT-TATTA-TAT
39549159 CTATTATTATAT
1 -TATTATTATAT
* *
39549171 TATTCTTATAA
1 TATTATTATAT
39549182 TATTATTATAT
1 TATTATTATAT
*
39549193 ATATTATTTCTATT
1 -TATTA-TTATA-T
39549207 TAGTTATTAT-T
1 TA-TTATTATAT
39549218 TAGTTATTAT-T
1 TA-TTATTATAT
39549229 TAT
1 TAT
39549232 ATTTAGTCTA
Statistics
Matches: 91, Mismatches: 10, Indels: 18
0.76 0.08 0.15
Matches are distributed among these distances:
10 1 0.01
11 39 0.43
12 27 0.30
13 17 0.19
14 7 0.08
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (11 bp):
TATTATTATAT
Found at i:39549234 original size:17 final size:17
Alignment explanation
Indices: 39549214--39549277 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
39549204 ATTTAGTTAT
39549214 TATTTAGTTATTATTTA
1 TATTTAGTTATTATTTA
*
39549231 TATTTAG-T-CTATTTA
1 TATTTAGTTATTATTTA
* *
39549246 GAATTT-TTTATTATTTA
1 -TATTTAGTTATTATTTA
39549263 -ATTTAAGTTATTATT
1 TATTT-AGTTATTATT
39549278 ATTTAATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
15 10 0.27
16 6 0.16
17 21 0.57
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (17 bp):
TATTTAGTTATTATTTA
Found at i:39549278 original size:20 final size:20
Alignment explanation
Indices: 39549253--39549292 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39549243 TTAGAATTTT
39549253 TTATTATTTAATTTAAGTTA
1 TTATTATTTAATTTAAGTTA
39549273 TTATTATTTAATTTAAGTTA
1 TTATTATTTAATTTAAGTTA
39549293 AAGTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTATTATTTAATTTAAGTTA
Found at i:39558089 original size:12 final size:12
Alignment explanation
Indices: 39558072--39558096 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39558062 CAGAGGCTAT
39558072 TAACAATATTTA
1 TAACAATATTTA
39558084 TAACAATATTTA
1 TAACAATATTTA
39558096 T
1 T
39558097 GTTATAAAAT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:39560643 original size:21 final size:20
Alignment explanation
Indices: 39560614--39560652 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
39560604 ACGCCTACGA
39560614 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGGATTTAAG
39560634 AAAGAGTCGCTTGGATTTA
1 AAAGA-TCGCTTGGATTTA
39560653 TCCATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGGATTTAAG
Found at i:39560807 original size:16 final size:15
Alignment explanation
Indices: 39560782--39560820 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
39560772 AGGATTTGGT
39560782 TTGTTTATTTTATTA
1 TTGTTTATTTTATTA
39560797 TTGTATTATTTTATTA
1 TTGT-TTATTTTATTA
*
39560813 TTATTTAT
1 TTGTTTAT
39560821 CATTTCAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (15 bp):
TTGTTTATTTTATTA
Found at i:39560847 original size:14 final size:14
Alignment explanation
Indices: 39560828--39560865 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
39560818 TATCATTTCA
39560828 ATATATAATTAAAT
1 ATATATAATTAAAT
39560842 ATATATAAATTTAAAT
1 ATATAT-AA-TTAAAT
39560858 ATAT-TAAT
1 ATATATAAT
39560866 AATATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 8 0.36
15 3 0.14
16 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATATAATTAAAT
Found at i:39560883 original size:18 final size:17
Alignment explanation
Indices: 39560836--39560884 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
39560826 CAATATATAA
*
39560836 TTAAATATAT-ATAAAT
1 TTAAATAAATAATAAAT
*
39560852 TTAAATATATTAATAATAT
1 TTAAATA-AATAATAA-AT
39560871 TTAAATAAATAATA
1 TTAAATAAATAATA
39560885 TTAATAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.26
17 1 0.04
18 10 0.37
19 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAATAAATAATAAAT
Found at i:39568392 original size:3 final size:3
Alignment explanation
Indices: 39568384--39568430 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
39568374 ATACATAGTT
* *
39568384 ATA ATA ATA ATA ATT ATA ATA ATA ATA A-A ATA CTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39568431 GTATAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:39568440 original size:26 final size:26
Alignment explanation
Indices: 39568386--39568438 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
39568376 ACATAGTTAT
*
39568386 AATAATAATAATTATAATAATAATAA
1 AATAATAATAATAATAATAATAATAA
* *
39568412 AATACTAATAATAATAATAGT-ATAA
1 AATAATAATAATAATAATAATAATAA
39568437 AA
1 AA
39568439 ATGACAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
AATAATAATAATAATAATAATAATAA
Found at i:39577551 original size:23 final size:23
Alignment explanation
Indices: 39577520--39577571 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
39577510 TGATTTTTAA
* *
39577520 ATTTTGAATTATCTAGTGATAAT
1 ATTTAGAATTATCTAGCGATAAT
* *
39577543 ATTTAGAATTATTTGGCGATAAT
1 ATTTAGAATTATCTAGCGATAAT
39577566 ATTTAG
1 ATTTAG
39577572 TGATAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (23 bp):
ATTTAGAATTATCTAGCGATAAT
Found at i:39577576 original size:13 final size:13
Alignment explanation
Indices: 39577533--39577584 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
39577523 TTGAATTATC
39577533 TAGTGATAATATT
1 TAGTGATAATATT
*
39577546 TA--GA-ATTATT
1 TAGTGATAATATT
* *
39577556 TGGCGATAATATT
1 TAGTGATAATATT
39577569 TAGTGATAATATT
1 TAGTGATAATATT
39577582 TAG
1 TAG
39577585 GAAAAATCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
10 6 0.19
11 2 0.06
12 2 0.06
13 21 0.68
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (13 bp):
TAGTGATAATATT
Found at i:39584216 original size:20 final size:18
Alignment explanation
Indices: 39584191--39584249 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 18
39584181 ATTAACATGT
39584191 TTAATCATAATTAATTAA
1 TTAATCATAATTAATTAA
*
39584209 TCTTAATCATGATTTAACTTAA
1 --TTAATCAT-AATTAA-TTAA
39584231 TTAATCTATATATTAATTA
1 TTAATC-ATA-ATTAATTA
39584250 GTCTAATGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
20 18 0.55
21 11 0.33
22 4 0.12
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATCATAATTAATTAA
Found at i:39586017 original size:20 final size:20
Alignment explanation
Indices: 39585992--39586029 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39585982 CCGAGTAAAA
*
39585992 AATGAATGTAAAATAATAAT
1 AATGAATATAAAATAATAAT
39586012 AATGAATATAAAATAATA
1 AATGAATATAAAATAATA
39586030 CAAGAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
AATGAATATAAAATAATAAT
Found at i:39586095 original size:18 final size:19
Alignment explanation
Indices: 39586072--39586119 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
39586062 TGGCAAATAT
*
39586072 ATAAAAAG-AAATCAACAA
1 ATAAAAAGTAAATAAACAA
39586090 AT-AAAAGTAAATAAACAA
1 ATAAAAAGTAAATAAACAA
*
39586108 ATAAAAACTAAA
1 ATAAAAAGTAAA
39586120 GCACTTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 5 0.19
18 13 0.50
19 8 0.31
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.15
Consensus pattern (19 bp):
ATAAAAAGTAAATAAACAA
Found at i:39586319 original size:23 final size:21
Alignment explanation
Indices: 39586291--39586364 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 21
39586281 TGTAAGCATG
39586291 TATATATGAAAATTAAAAATA
1 TATATATGAAAATTAAAAATA
* *
39586312 TGCATATAT-AACATTATTAAATA
1 T--ATATATGAAAATTA-AAAATA
39586335 TATATATGAAAATTAAAAACGTA
1 TATATATGAAAATTAAAAA--TA
39586358 TATATAT
1 TATATAT
39586365 AGGACATACA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 10 0.23
22 12 0.28
23 21 0.49
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.36
Consensus pattern (21 bp):
TATATATGAAAATTAAAAATA
Found at i:39586512 original size:24 final size:24
Alignment explanation
Indices: 39586466--39586512 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
39586456 AATGTATGCT
*
39586466 TATATATATATATCGTAAAATATG
1 TATATATATATATAGTAAAATATG
* * *
39586490 TATATATGTATATATTAATATAT
1 TATATATATATATAGTAAAATAT
39586513 ATATGTTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (24 bp):
TATATATATATATAGTAAAATATG
Found at i:39591145 original size:47 final size:47
Alignment explanation
Indices: 39591076--39591169 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
39591066 ACAGAACACG
39591076 CACCGATACAAGTTCGTAAGAATTTAGTGAGGAAAACATCATTTACA
1 CACCGATACAAGTTCGTAAGAATTTAGTGAGGAAAACATCATTTACA
39591123 CACCGATACAAGTTCGTAAGAATTTAGTGAGGAAAACATCATTTACA
1 CACCGATACAAGTTCGTAAGAATTTAGTGAGGAAAACATCATTTACA
39591170 TGTGTCATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (47 bp):
CACCGATACAAGTTCGTAAGAATTTAGTGAGGAAAACATCATTTACA
Found at i:39594375 original size:11 final size:11
Alignment explanation
Indices: 39594361--39594392 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
39594351 ACCAAAACCA
39594361 AAATTCAATAT
1 AAATTCAATAT
*
39594372 AAATTAAATAT
1 AAATTCAATAT
39594383 AAATTCAATA
1 AAATTCAATA
39594393 AATTTACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (11 bp):
AAATTCAATAT
Found at i:39601237 original size:2 final size:2
Alignment explanation
Indices: 39601230--39601258 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39601220 TAACATAAAT
39601230 AG AG 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 AG AG A
39601259 ATTTTGTTTA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39601431 original size:5 final size:5
Alignment explanation
Indices: 39601421--39601473 Score: 106
Period size: 5 Copynumber: 10.6 Consensus size: 5
39601411 TTTTTATGTA
39601421 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
39601471 ATT
1 ATT
39601474 TTGATATTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:39604549 original size:40 final size:40
Alignment explanation
Indices: 39604505--39604593 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
39604495 AGCACTCATG
*
39604505 TGCATTCAGGGGTACCGAAGTACAAACAGTGGCACGTATA
1 TGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATA
* * * *
39604545 TGCATTTAGGGGTACTGAAGTACAAACAGGGGCATGTATG
1 TGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATA
*
39604585 TGCACTCAG
1 TGCATTCAG
39604594 TAACATTTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.22
Consensus pattern (40 bp):
TGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATA
Found at i:39605271 original size:26 final size:26
Alignment explanation
Indices: 39605242--39605298 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
39605232 AAATTACAAC
*
39605242 CAAGACCTTAAATTCATCATTAACAT
1 CAAGACCTTAAACTCATCATTAACAT
39605268 CAAGACCTTAAACTCATCATTAACAT
1 CAAGACCTTAAACTCATCATTAACAT
39605294 CAAGA
1 CAAGA
39605299 ACAATCAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.05, T:0.26
Consensus pattern (26 bp):
CAAGACCTTAAACTCATCATTAACAT
Found at i:39611385 original size:27 final size:27
Alignment explanation
Indices: 39611345--39611858 Score: 561
Period size: 27 Copynumber: 19.1 Consensus size: 27
39611335 TTACACTACT
* * * *
39611345 ATGATCGAAATACCTCTATAGGATAGA
1 ATGACCGAAATACCCCTATAGGGTAAA
*
39611372 ATGACCGAATTA-CCCTCATAGGGTAAA
1 ATGACCGAAATACCCCT-ATAGGGTAAA
* * * * *
39611399 ATGATCAAAATACCTCAATAGGGTAGA
1 ATGACCGAAATACCCCTATAGGGTAAA
*
39611426 ATGATCGAAATACCCCTATAGGGTAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
*
39611453 ATGACTGAAATA-CCCTCATAGGGTAAA
1 ATGACCGAAATACCCCT-ATAGGGTAAA
* *
39611480 ATGACTGAATTACCCCTATAGGGTAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* * * *
39611507 ATGACCAAAATACCCCCATAGAGTAGA
1 ATGACCGAAATACCCCTATAGGGTAAA
*
39611534 ATGACCGAAATACCCCTATAGGGTAGA
1 ATGACCGAAATACCCCTATAGGGTAAA
* * * *
39611561 ATGATCGTAATACCCCCATAAGGTAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* *
39611588 ATGACTGAAATACCTCTATAGGGTAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* * * *
39611615 ATAACCGAAATACCCCCATAGGATAGA
1 ATGACCGAAATACCCCTATAGGGTAAA
*
39611642 ATAACCGAAATACCCCTATAGGGTAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* *
39611669 ATGACTGAAATACCCCTATAGGATAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* * *
39611696 ATGACCGAAATACCCCTATCGGATAGA
1 ATGACCGAAATACCCCTATAGGGTAAA
* *
39611723 ATGACCCAAATACCCCCATAGGG-AAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* * * *
39611749 ATGACTGAAATACCCCCATAGGATAGA
1 ATGACCGAAATACCCCTATAGGGTAAA
*
39611776 ATGAACC-AAATACCCCCATAGGGTAAA
1 ATG-ACCGAAATACCCCTATAGGGTAAA
39611803 ATGACCGAAATACTCCC-ATAGGGTAAA
1 ATGACCGAAATAC-CCCTATAGGGTAAA
* *
39611830 ATGATCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
39611857 AT
1 AT
39611859 AACTGTTATA
Statistics
Matches: 412, Mismatches: 66, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
26 35 0.08
27 366 0.89
28 11 0.03
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (27 bp):
ATGACCGAAATACCCCTATAGGGTAAA
Found at i:39612138 original size:26 final size:26
Alignment explanation
Indices: 39612095--39612145 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
39612085 TTTGCCACAT
**
39612095 ATACTATTACTGGTAGCTTTGCTGCG
1 ATACTATTACTGACAGCTTTGCTGCG
*
39612121 ATACTATTATTGACAGCTTTGCTGC
1 ATACTATTACTGACAGCTTTGCTGC
39612146 AATATTAGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (26 bp):
ATACTATTACTGACAGCTTTGCTGCG
Found at i:39612282 original size:28 final size:28
Alignment explanation
Indices: 39612245--39612411 Score: 201
Period size: 28 Copynumber: 6.0 Consensus size: 28
39612235 CATTGTACTG
* *
39612245 ATTACTGTATCGGACTAAGGCCCACATT
1 ATTACTGTATTGGGCTAAGGCCCACATT
*
39612273 ATTATTGTATTGGGCTAAGGCCCACATT
1 ATTACTGTATTGGGCTAAGGCCCACATT
* *
39612301 GTTACT-TATTAGGCTAAGGCCCACATT
1 ATTACTGTATTGGGCTAAGGCCCACATT
* *
39612328 GTTACTGTATTGGGCTAAGGCCCATATT
1 ATTACTGTATTGGGCTAAGGCCCACATT
* *
39612356 ATTACTGTAATGGGCTAAGGCCCACACT
1 ATTACTGTATTGGGCTAAGGCCCACATT
* ** * *
39612384 GTTACTAAAATAGGCTAAGGCCCACATT
1 ATTACTGTATTGGGCTAAGGCCCACATT
39612412 GTACTATTAC
Statistics
Matches: 121, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
27 26 0.21
28 95 0.79
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (28 bp):
ATTACTGTATTGGGCTAAGGCCCACATT
Found at i:39612337 original size:55 final size:55
Alignment explanation
Indices: 39612259--39612420 Score: 202
Period size: 55 Copynumber: 3.0 Consensus size: 55
39612249 CTGTATCGGA
* *
39612259 CTAAGGCCCACATTATTATTGTATTGGGCTAAGGCCCACATTGTTACTTATTAGG
1 CTAAGGCCCACATTGTTACTGTATTGGGCTAAGGCCCACATTGTTACTTATTAGG
* * * *
39612314 CTAAGGCCCACATTGTTACTGTATTGGGCTAAGGCCCATATTATTACTGTAATGGG
1 CTAAGGCCCACATTGTTACTGTATTGGGCTAAGGCCCACATTGTTACT-TATTAGG
* ** * *
39612370 CTAAGGCCCACACTGTTACTAAAATAGGCTAAGGCCCACATTG-TAC-TATTA
1 CTAAGGCCCACATTGTTACTGTATTGGGCTAAGGCCCACATTGTTACTTATTA
39612421 CTGTATAGGG
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
53 3 0.03
55 47 0.52
56 41 0.45
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (55 bp):
CTAAGGCCCACATTGTTACTGTATTGGGCTAAGGCCCACATTGTTACTTATTAGG
Found at i:39612349 original size:83 final size:84
Alignment explanation
Indices: 39612246--39612413 Score: 257
Period size: 83 Copynumber: 2.0 Consensus size: 84
39612236 ATTGTACTGA
* * * * *
39612246 TTACTGTATCGGACTAAGGCCCACATTATTATTGTATTGGGCTAAGGCCCACATTGTTACT-TAT
1 TTACTGTATCGGACTAAGGCCCACATTATTACTGTAATGGGCTAAGGCCCACACTGTTACTAAAA
39612310 TAGGCTAAGGCCCACATTG
66 TAGGCTAAGGCCCACATTG
* * *
39612329 TTACTGTATTGGGCTAAGGCCCATATTATTACTGTAATGGGCTAAGGCCCACACTGTTACTAAAA
1 TTACTGTATCGGACTAAGGCCCACATTATTACTGTAATGGGCTAAGGCCCACACTGTTACTAAAA
39612394 TAGGCTAAGGCCCACATTG
66 TAGGCTAAGGCCCACATTG
39612413 T
1 T
39612414 ACTATTACTG
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
83 55 0.72
84 21 0.28
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (84 bp):
TTACTGTATCGGACTAAGGCCCACATTATTACTGTAATGGGCTAAGGCCCACACTGTTACTAAAA
TAGGCTAAGGCCCACATTG
Found at i:39614502 original size:26 final size:26
Alignment explanation
Indices: 39614473--39614627 Score: 161
Period size: 26 Copynumber: 6.0 Consensus size: 26
39614463 ACCTGAATAG
*
39614473 CAGGCCTTAAGCCGATGATTATTTAA
1 CAGGCCTTGAGCCGATGATTATTTAA
** * *
39614499 CAGGCCTTGAGCAAATGATTACTTAG
1 CAGGCCTTGAGCCGATGATTATTTAA
* *
39614525 CAGG-CTATGAGCCGGTGATTATTTAG
1 CAGGCCT-TGAGCCGATGATTATTTAA
* * *
39614551 TAGGCCTTGAGCAGGTGATTATTTAA
1 CAGGCCTTGAGCCGATGATTATTTAA
*
39614577 TAGGCCTTGAGCCGATGATTATTTAA
1 CAGGCCTTGAGCCGATGATTATTTAA
* *
39614603 TAGGCCTTGAGTC-AGTGATTATTTA
1 CAGGCCTTGAGCCGA-TGATTATTTA
39614628 GCAAGTACTA
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
25 3 0.03
26 106 0.95
27 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (26 bp):
CAGGCCTTGAGCCGATGATTATTTAA
Found at i:39614548 original size:52 final size:52
Alignment explanation
Indices: 39614470--39614630 Score: 209
Period size: 52 Copynumber: 3.1 Consensus size: 52
39614460 TGTACCTGAA
* * * *
39614470 TAGCAGGCCTTAAGCCGATGATTATTTAACAGGCCTTGAGCAAATGATTACT
1 TAGCAGGCCTTGAGCCGATGATTATTTAATAGGCCTTGAGCAAGTGATTATT
* * *
39614522 TAGCAGG-CTATGAGCCGGTGATTATTTAGTAGGCCTTGAGCAGGTGATTATT
1 TAGCAGGCCT-TGAGCCGATGATTATTTAATAGGCCTTGAGCAAGTGATTATT
**
39614574 TAATAGGCCTTGAGCCGATGATTATTTAATAGGCCTTGAGTC-AGTGATTATT
1 TAGCAGGCCTTGAGCCGATGATTATTTAATAGGCCTTGAG-CAAGTGATTATT
39614626 TAGCA
1 TAGCA
39614631 AGTACTATGT
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
51 2 0.02
52 87 0.95
53 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (52 bp):
TAGCAGGCCTTGAGCCGATGATTATTTAATAGGCCTTGAGCAAGTGATTATT
Found at i:39614621 original size:78 final size:78
Alignment explanation
Indices: 39614474--39614628 Score: 195
Period size: 78 Copynumber: 2.0 Consensus size: 78
39614464 CCTGAATAGC
* * *
39614474 AGGCCTTAAGCCGATGATTATTTAACAGGCCTTGAGCAAATGATTACTTAGCAGGCTATGAGCCG
1 AGGCCTTAAGCAGATGATTATTTAACAGGCCTTGAGCAAATGATTACTTAACAGGCTATGAGCCA
39614539 GTGATTATTTAGT
66 GTGATTATTTAGT
* * * ** * * *
39614552 AGGCCTTGAGCAGGTGATTATTTAATAGGCCTTGAGCCGATGATTATTTAATAGGCCT-TGAGTC
1 AGGCCTTAAGCAGATGATTATTTAACAGGCCTTGAGCAAATGATTACTTAACAGG-CTATGAGCC
39614616 AGTGATTATTTAG
65 AGTGATTATTTAG
39614629 CAAGTACTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
78 63 0.97
79 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (78 bp):
AGGCCTTAAGCAGATGATTATTTAACAGGCCTTGAGCAAATGATTACTTAACAGGCTATGAGCCA
GTGATTATTTAGT
Found at i:39616636 original size:23 final size:23
Alignment explanation
Indices: 39616610--39616662 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
39616600 AATCAAAAAA
*
39616610 AGAAAAAGCGGTCC-AAAGTCAAT
1 AGAAAAAGCAGTCCAAAAG-CAAT
*
39616633 AGAAAAAAGTAGTCCAAAAGCAAT
1 AG-AAAAAGCAGTCCAAAAGCAAT
39616657 AGAAAA
1 AGAAAA
39616663 GTATGACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 6 0.23
24 16 0.62
25 4 0.15
ACGTcount: A:0.57, C:0.13, G:0.19, T:0.11
Consensus pattern (23 bp):
AGAAAAAGCAGTCCAAAAGCAAT
Found at i:39617696 original size:7 final size:7
Alignment explanation
Indices: 39617680--39617710 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
39617670 AAAAAAGAAA
39617680 GGGG-TT
1 GGGGCTT
39617686 GGGGCTT
1 GGGGCTT
39617693 GGGGCTT
1 GGGGCTT
39617700 GGGGCTT
1 GGGGCTT
39617707 GGGG
1 GGGG
39617711 GATTTGGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.00, C:0.10, G:0.65, T:0.26
Consensus pattern (7 bp):
GGGGCTT
Found at i:39619623 original size:14 final size:13
Alignment explanation
Indices: 39619597--39619621 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39619587 AAAAAAAATT
39619597 ATTTTGGGAAAAG
1 ATTTTGGGAAAAG
39619610 ATTTTGGGAAAA
1 ATTTTGGGAAAA
39619622 AGTCAATGGC
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:0.00, G:0.28, T:0.32
Consensus pattern (13 bp):
ATTTTGGGAAAAG
Found at i:39620958 original size:21 final size:21
Alignment explanation
Indices: 39620932--39620974 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
39620922 TTTTGCCTAA
*
39620932 AATATGAATTGGATTAAATTG
1 AATATGAAATGGATTAAATTG
*
39620953 AATATGAAATGTATTAAATTG
1 AATATGAAATGGATTAAATTG
39620974 A
1 A
39620975 TGTTAAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (21 bp):
AATATGAAATGGATTAAATTG
Found at i:39621447 original size:25 final size:25
Alignment explanation
Indices: 39621413--39621515 Score: 115
Period size: 25 Copynumber: 4.2 Consensus size: 25
39621403 ACACACCGCA
* *
39621413 GCTCTTTTGAGCATCCCGA-TATATG
1 GCTCTTTTGAGCTTCCTGATTA-ATG
*
39621438 GCTCTTTTGAGCTTCCTGATTAAAG
1 GCTCTTTTGAGCTTCCTGATTAATG
39621463 GCTCTTTGTGAGCTTCCTGATTAATG
1 GCTCTTT-TGAGCTTCCTGATTAATG
*
39621489 GCTC-TTCGCAGCTTCCTGA-T-ATG
1 GCTCTTTTG-AGCTTCCTGATTAATG
39621512 GCTC
1 GCTC
39621516 ACTTGAACTT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.10
24 2 0.03
25 38 0.54
26 23 0.33
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (25 bp):
GCTCTTTTGAGCTTCCTGATTAATG
Found at i:39621478 original size:26 final size:26
Alignment explanation
Indices: 39621437--39621508 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
39621427 CCCGATATAT
39621437 GGCTCTTT-TGAGCTTCCTGATTAAA
1 GGCTCTTTGTGAGCTTCCTGATTAAA
*
39621462 GGCTCTTTGTGAGCTTCCTGATTAAT
1 GGCTCTTTGTGAGCTTCCTGATTAAA
* *
39621488 GGCTCTTCG-CAGCTTCCTGAT
1 GGCTCTTTGTGAGCTTCCTGAT
39621509 ATGGCTCACT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 19 0.44
26 24 0.56
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCCTGATTAAA
Found at i:39621490 original size:51 final size:50
Alignment explanation
Indices: 39621413--39621539 Score: 127
Period size: 51 Copynumber: 2.6 Consensus size: 50
39621403 ACACACCGCA
*
39621413 GCTCTTTTGAGCATCCCGATATATGGCTCTTTTG-AGCTTCCTGATTAAAG
1 GCTCTTTTGAGCATCCCGATATATGGCTC-TTCGCAGCTTCCTGATTAAAG
* * *
39621463 GCTCTTTGTGAGCTTCCTGAT-TAATGGCTCTTCGCAGCTTCCTGA-T-ATG
1 GCTCTTT-TGAGCATCCCGATAT-ATGGCTCTTCGCAGCTTCCTGATTAAAG
** * *
39621512 GCTCACTTGAACTTCCCGATATATGGCT
1 GCTCTTTTGAGCATCCCGATATATGGCT
39621540 ATCCGTAGCT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
48 17 0.26
49 8 0.12
50 12 0.18
51 28 0.43
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.37
Consensus pattern (50 bp):
GCTCTTTTGAGCATCCCGATATATGGCTCTTCGCAGCTTCCTGATTAAAG
Found at i:39621618 original size:24 final size:24
Alignment explanation
Indices: 39621413--39621619 Score: 95
Period size: 25 Copynumber: 8.5 Consensus size: 24
39621403 ACACACCGCA
* *
39621413 GCTCTTTTGAGCATCCCGATATATG
1 GCTCTTATGAGCTTCCCGAT-TATG
* * *
39621438 GCTCTTTTGAGCTTCCTGATTAAAG
1 GCTCTTATGAGCTTCCCGATT-ATG
* *
39621463 GCTCTTTGTGAGCTTCCTGATTAATG
1 GCTC-TTATGAGCTTCCCGATT-ATG
* *
39621489 GCTCTT-CGCAGCTTCCTGA-TATG
1 GCTCTTATG-AGCTTCCCGATTATG
* *
39621512 GCTCACT-TGAACTTCCCGATATATG
1 GCTC-TTATGAGCTTCCCGAT-TATG
* ** *
39621537 GCT-ATCCGTAGCTTCCCG-TTAAG
1 GCTCTTATG-AGCTTCCCGATTATG
* *
39621560 TGCTCTTCA-AAGCTACCCG-TTATTG
1 -GCTCTT-ATGAGCTTCCCGATTA-TG
**
39621585 GCTCGCATGAGCTTCCCGATTATG
1 GCTCTTATGAGCTTCCCGATTATG
39621609 GCTCTTATGAG
1 GCTCTTATGAG
39621620 GTTCTCGTTA
Statistics
Matches: 143, Mismatches: 25, Indels: 29
0.73 0.13 0.15
Matches are distributed among these distances:
23 20 0.14
24 44 0.31
25 56 0.39
26 23 0.16
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (24 bp):
GCTCTTATGAGCTTCCCGATTATG
Found at i:39623478 original size:14 final size:14
Alignment explanation
Indices: 39623445--39623495 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
39623435 TGAATTTGGG
39623445 TAAA-TATTTAA-T
1 TAAATTATTTAATT
39623457 TAAATTATTTAATT
1 TAAATTATTTAATT
*
39623471 TAATTTATATT-ATT
1 TAAATTAT-TTAATT
39623485 TAAATATATTT
1 TAAAT-TATTT
39623496 TACATTTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 4 0.12
13 7 0.21
14 17 0.52
15 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAAATTATTTAATT
Found at i:39623484 original size:19 final size:18
Alignment explanation
Indices: 39623450--39623487 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
39623440 TTGGGTAAAT
39623450 ATTTAATTAAATTATTTA
1 ATTTAATTAAATTATTTA
*
39623468 ATTTAATTTATATTATTTA
1 ATTTAA-TTAAATTATTTA
39623487 A
1 A
39623488 ATATATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTAATTAAATTATTTA
Found at i:39627312 original size:28 final size:30
Alignment explanation
Indices: 39627275--39627342 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
39627265 AAATTAAAAT
* *
39627275 TTCATGTATA-AATTGTACA-AAATCAAAG
1 TTCATGTATACAATTGCACATAAACCAAAG
* *
39627303 TTCATGTATACAATTGCACATTAACCATAG
1 TTCATGTATACAATTGCACATAAACCAAAG
39627333 TTCATGTATA
1 TTCATGTATA
39627343 GTTTTGAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 10 0.29
29 8 0.24
30 16 0.47
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (30 bp):
TTCATGTATACAATTGCACATAAACCAAAG
Found at i:39627940 original size:19 final size:20
Alignment explanation
Indices: 39627902--39627947 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
39627892 CGACCAGTTT
39627902 AATTAAATGAAATATAAAAA
1 AATTAAATGAAATATAAAAA
* *
39627922 AATTAAAT-ATATATTAAAA
1 AATTAAATGAAATATAAAAA
39627941 AATTAAA
1 AATTAAA
39627948 AAAAATTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
AATTAAATGAAATATAAAAA
Found at i:39628086 original size:19 final size:19
Alignment explanation
Indices: 39628065--39628257 Score: 72
Period size: 19 Copynumber: 10.4 Consensus size: 19
39628055 CCAGTTCAAG
*
39628065 TTTTTATGATTTTTATAAG
1 TTTTTATGATTTTTATAAA
* * *
39628084 TTTATATCAATTTTA-AAA
1 TTTTTATGATTTTTATAAA
*
39628102 CTTTTAAT-ACTTTTT-TACAA
1 -TTTTTATGA-TTTTTATA-AA
39628122 TTTTTATGATTTTTATAGAA
1 TTTTTATGATTTTTATA-AA
39628142 TTTTAATATG-TTTTTATAAA
1 TTTT--TATGATTTTTATAAA
* * *
39628162 ATTTTA-AATATTT-T-AA
1 TTTTTATGATTTTTATAAA
*
39628178 ---TTAT-A-TTTTATTAA
1 TTTTTATGATTTTTATAAA
*
39628192 TTTTTATAGTTTTTTTATAAA
1 TTTTTAT-G-ATTTTTATAAA
* *
39628213 TTATTAT-ATTTTGGATAATA
1 TTTTTATGATTTT-TATAA-A
**
39628233 TTTTTATTTTTTTTAT-AA
1 TTTTTATGATTTTTATAAA
39628251 TTTTTAT
1 TTTTTAT
39628258 AAGTTTATAT
Statistics
Matches: 131, Mismatches: 21, Indels: 45
0.66 0.11 0.23
Matches are distributed among these distances:
12 3 0.02
13 5 0.04
14 2 0.02
16 2 0.02
17 5 0.04
18 21 0.16
19 38 0.29
20 25 0.19
21 26 0.20
22 4 0.03
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTTTATGATTTTTATAAA
Found at i:39628157 original size:21 final size:21
Alignment explanation
Indices: 39628097--39628168 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
39628087 ATATCAATTT
*
39628097 TAAAACTTTTAATA-CTTTTT-
1 TAAAA-TTTTAATATGTTTTTA
*
39628117 TACAATTTT--TATGATTTTTA
1 TAAAATTTTAATATG-TTTTTA
*
39628137 TAGAATTTTAATATGTTTTTA
1 TAAAATTTTAATATGTTTTTA
39628158 TAAAATTTTAA
1 TAAAATTTTAA
39628169 ATATTTTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 2 0.05
19 9 0.21
20 12 0.28
21 16 0.37
22 4 0.09
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (21 bp):
TAAAATTTTAATATGTTTTTA
Found at i:39628171 original size:22 final size:22
Alignment explanation
Indices: 39628126--39628175 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
39628116 TTACAATTTT
*
39628126 TATGATTTTTATAGAATTTTAA
1 TATGATTTTTATAAAATTTTAA
39628148 TATG-TTTTTATAAAATTTTAA
1 TATGATTTTTATAAAATTTTAA
39628169 -AT-ATTTT
1 TATGATTTT
39628176 AATTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 16 0.62
22 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (22 bp):
TATGATTTTTATAAAATTTTAA
Found at i:39628206 original size:20 final size:20
Alignment explanation
Indices: 39628183--39628263 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 20
39628173 TTTAATTATA
*
39628183 TTTTATTAATTTTTATAGTTT
1 TTTTATAAATTTTTATAG-TT
*
39628204 TTTTATAAATTATTATA-TT
1 TTTTATAAATTTTTATAGTT
** *
39628223 TTGGATAATATTTTTAT-TTT
1 TTTTATAA-ATTTTTATAGTT
39628243 TTTTAT-AATTTTTATAAGTT
1 TTTTATAAATTTTTAT-AGTT
39628263 T
1 T
39628264 ATATCAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
18 8 0.17
19 9 0.19
20 16 0.33
21 15 0.31
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTTATAAATTTTTATAGTT
Found at i:39628243 original size:38 final size:38
Alignment explanation
Indices: 39628177--39628258 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
39628167 AAATATTTTA
39628177 ATTATATTTTATTAATTTTTATAG-TTTTTTTATAAATT
1 ATTATATTTTATTAATTTTTATAGTTTTTTTTAT-AATT
39628215 ATTATATTTTGGA-TAATATTTT-TA-TTTTTTTTATAATT
1 ATTATATTTT--ATTAAT-TTTTATAGTTTTTTTTATAATT
*
39628253 TTTATA
1 ATTATA
39628259 AGTTTATATC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
38 19 0.49
39 15 0.38
40 5 0.13
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (38 bp):
ATTATATTTTATTAATTTTTATAGTTTTTTTTATAATT
Found at i:39628253 original size:18 final size:19
Alignment explanation
Indices: 39628183--39628257 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 19
39628173 TTTAATTATA
*
39628183 TTTTATTAATTTTTATAGTTT
1 TTTTATAAATTTTTAT--TTT
* *
39628204 TTTTATAAATTATTATATT
1 TTTTATAAATTTTTATTTT
**
39628223 TTGGATAATATTTTTATTTT
1 TTTTATAA-ATTTTTATTTT
39628243 TTTTAT-AATTTTTAT
1 TTTTATAAATTTTTAT
39628258 AAGTTTATAT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
18 8 0.18
19 9 0.20
20 13 0.30
21 14 0.32
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (19 bp):
TTTTATAAATTTTTATTTT
Found at i:39628254 original size:9 final size:9
Alignment explanation
Indices: 39628065--39628274 Score: 66
Period size: 9 Copynumber: 21.4 Consensus size: 9
39628055 CCAGTTCAAG
*
39628065 TTTTTATGA
1 TTTTTATAA
39628074 TTTTTATAA
1 TTTTTATAA
*
39628083 GTTTATATCAA
1 -TTTTTAT-AA
*
39628094 -TTTTAAAA
1 TTTTTATAA
* *
39628102 CTTTTAATACT
1 -TTTTTATA-A
*
39628113 TTTTTACAA
1 TTTTTATAA
*
39628122 TTTTTATGA
1 TTTTTATAA
39628131 TTTTTATAGAA
1 TTTTTAT--AA
* *
39628142 TTTTAATATG
1 TTTTTATA-A
39628152 TTTTTATAAA
1 TTTTTAT-AA
*
39628162 ATTTTA-AA
1 TTTTTATAA
*
39628170 TATTTTAATTA
1 T-TTTT-ATAA
39628181 TATTTTATTAA
1 T-TTTTA-TAA
*
39628192 TTTTTATAGTT
1 TTTTTATA--A
39628203 TTTTTATAAA
1 TTTTTAT-AA
*
39628213 TTATTAT-A
1 TTTTTATAA
*
39628221 TTTTGGATAATA
1 TTTT-TAT-A-A
**
39628233 TTTTTATTT
1 TTTTTATAA
39628242 TTTTTATAA
1 TTTTTATAA
39628251 TTTTTATAA
1 TTTTTATAA
*
39628260 GTTTATATCAA
1 -TTTTTAT-AA
39628271 TTTT
1 TTTT
39628275 CAATTTTTTT
Statistics
Matches: 146, Mismatches: 33, Indels: 43
0.66 0.15 0.19
Matches are distributed among these distances:
8 8 0.05
9 51 0.35
10 50 0.34
11 31 0.21
12 6 0.04
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:39628304 original size:37 final size:37
Alignment explanation
Indices: 39628240--39628310 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
39628230 ATATTTTTAT
* *
39628240 TTTTTTTATAATTTTTATAAGTTTATATCAATTTTCAA
1 TTTTTTTATAATTTTAATAAGTGTATAT-AATTTTCAA
39628278 TTTTTTTA-AATATTTAATAA-TGTATATAATTTT
1 TTTTTTTATAAT-TTTAATAAGTGTATATAATTTT
39628311 TTATCCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 6 0.20
37 9 0.30
38 15 0.50
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (37 bp):
TTTTTTTATAATTTTAATAAGTGTATATAATTTTCAA
Found at i:39632132 original size:12 final size:12
Alignment explanation
Indices: 39632111--39632156 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
39632101 AACTATTTTC
39632111 TGAAAATGAAAA
1 TGAAAATGAAAA
*
39632123 TGAAACTGAAAA
1 TGAAAATGAAAA
39632135 TTGAAAATTGAAAA
1 -TGAAAA-TGAAAA
39632149 TAGAAAAT
1 T-GAAAAT
39632157 AGTTTTAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 11 0.38
ACGTcount: A:0.61, C:0.02, G:0.15, T:0.22
Consensus pattern (12 bp):
TGAAAATGAAAA
Found at i:39632158 original size:7 final size:6
Alignment explanation
Indices: 39632111--39632156 Score: 56
Period size: 7 Copynumber: 7.2 Consensus size: 6
39632101 AACTATTTTC
*
39632111 TGAAAA TGAAAA TGAAAC TGAAAA TTGAAAA TTGAAAA TAGAAAA T
1 TGAAAA TGAAAA TGAAAA TGAAAA -TGAAAA -TGAAAA T-GAAAA T
39632157 AGTTTTAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
6 17 0.47
7 19 0.53
ACGTcount: A:0.61, C:0.02, G:0.15, T:0.22
Consensus pattern (6 bp):
TGAAAA
Found at i:39632457 original size:3 final size:3
Alignment explanation
Indices: 39632449--39632480 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
39632439 GCCCCCTGAA
39632449 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
39632481 AGGAGAAGTC
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:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (3 bp):
GGT
Found at i:39632729 original size:43 final size:43
Alignment explanation
Indices: 39632668--39632750 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
39632658 ATATCATATA
* * *
39632668 ATAATATCCTATAATATCCCATTAGGAATTAAATTTCTAAGAG
1 ATAATATCCTATAATATCCCATTAGAAATCAAATTGCTAAGAG
*
39632711 ATAATATCCTATAATATCCCTTTAGAAATCAAATTGCTAA
1 ATAATATCCTATAATATCCCATTAGAAATCAAATTGCTAA
39632751 AATATACTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (43 bp):
ATAATATCCTATAATATCCCATTAGAAATCAAATTGCTAAGAG
Found at i:39634631 original size:16 final size:16
Alignment explanation
Indices: 39634574--39634638 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 16
39634564 CTAATGCAAC
* *
39634574 AACTCTTGTTTAAAAT
1 AACTATTGTTCAAAAT
** * **
39634590 AGTTATTGTTCAGAGC
1 AACTATTGTTCAAAAT
39634606 AACTATTGTTCGAAAAT
1 AACTATTGTTC-AAAAT
39634623 AACTA-TGTTCAAAAT
1 AACTATTGTTCAAAAT
39634638 A
1 A
39634639 GGGCTTCAGT
Statistics
Matches: 36, Mismatches: 12, Indels: 3
0.71 0.24 0.06
Matches are distributed among these distances:
15 6 0.17
16 23 0.64
17 7 0.19
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (16 bp):
AACTATTGTTCAAAAT
Found at i:39634638 original size:15 final size:17
Alignment explanation
Indices: 39634606--39634638 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
39634596 TGTTCAGAGC
39634606 AACTATTGTTCGAAAAT
1 AACTATTGTTCGAAAAT
39634623 AACTA-TGTTC-AAAAT
1 AACTATTGTTCGAAAAT
39634638 A
1 A
39634639 GGGCTTCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (17 bp):
AACTATTGTTCGAAAAT
Found at i:39637040 original size:24 final size:25
Alignment explanation
Indices: 39637011--39637065 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
39637001 GAGTTACCTG
*
39637011 TTAAGCTCACATGAGCTTTCTGTT-
1 TTAAGCTCACATGAGCTTCCTGTTA
**
39637035 TTAAGCTCTTATGAGCTTCCTGTTA
1 TTAAGCTCACATGAGCTTCCTGTTA
39637060 TTAAGC
1 TTAAGC
39637066 CCGGAAAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (25 bp):
TTAAGCTCACATGAGCTTCCTGTTA
Found at i:39644192 original size:24 final size:25
Alignment explanation
Indices: 39644162--39644219 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
39644152 CAGAGTTACC
*
39644162 TATTAAGCTCACATGAGCTTTCTAT
1 TATTAAGCTCACATGAGCTTCCTAT
* ** *
39644187 T-TTAAGATCTTATGAGCTTCCTGT
1 TATTAAGCTCACATGAGCTTCCTAT
39644211 TATTAAGCT
1 TATTAAGCT
39644220 TGGATAAGCT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (25 bp):
TATTAAGCTCACATGAGCTTCCTAT
Found at i:39651576 original size:21 final size:22
Alignment explanation
Indices: 39651550--39651596 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
39651540 CTCTGCTCAA
*
39651550 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
*
39651571 ACTCCACCTGTTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
39651593 ACTC
1 ACTC
39651597 ACTCCTTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.23
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:39657215 original size:21 final size:21
Alignment explanation
Indices: 39657189--39657231 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
39657179 AGTATAATTT
39657189 TTTTAAAA-ACTGTAAAAGTTG
1 TTTTAAAATA-TGTAAAAGTTG
*
39657210 TTTTAAAATATTTAAAAGTTG
1 TTTTAAAATATGTAAAAGTTG
39657231 T
1 T
39657232 AAAAATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (21 bp):
TTTTAAAATATGTAAAAGTTG
Found at i:39657252 original size:28 final size:28
Alignment explanation
Indices: 39657221--39657279 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
39657211 TTTAAAATAT
*
39657221 TTAAAAGTTGTAAAAAT-TATTAAAAACA
1 TTAAAAGTTGTAAAAATATA-TAAAAAAA
** *
39657249 TTAAATTTTGTAAATATATATAAAAAAA
1 TTAAAAGTTGTAAAAATATATAAAAAAA
39657277 TTA
1 TTA
39657280 TAATTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (28 bp):
TTAAAAGTTGTAAAAATATATAAAAAAA
Found at i:39657284 original size:29 final size:28
Alignment explanation
Indices: 39657228--39657334 Score: 91
Period size: 28 Copynumber: 3.9 Consensus size: 28
39657218 TATTTAAAAG
*
39657228 TTGTAAAAATTATTAAAAACATTAAATT
1 TTGTAAAAATTATTAAAAAAATTAAATT
*
39657256 TTGTAAATA-TATATAAAAAAATTATAATT
1 TTGTAAAAATTAT-TAAAAAAATTA-AATT
* * *
39657285 TT-TTAAAATGA--AAAAAATTTAAATT
1 TTGTAAAAATTATTAAAAAAATTAAATT
*
39657310 AT-TAAAAATTA-TAAAAAATATTAAA
1 TTGTAAAAATTATTAAAAAA-ATTAAA
39657335 AAGTATTTTC
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
25 12 0.19
26 15 0.23
27 8 0.12
28 22 0.34
29 7 0.11
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (28 bp):
TTGTAAAAATTATTAAAAAAATTAAATT
Found at i:39657302 original size:25 final size:24
Alignment explanation
Indices: 39657270--39657334 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 24
39657260 AAATATATAT
* *
39657270 AAAAAAATTATAATTTTTTAAAATG
1 AAAAAAATT-TAAATTATTAAAATG
*
39657295 AAAAAAATTTAAATTATTAAAAATT
1 AAAAAAATTTAAATTATT-AAAATG
39657320 ATAAAAAATATTAAA
1 A-AAAAAAT-TTAAA
39657335 AAGTATTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.21
25 15 0.44
26 7 0.21
27 5 0.15
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAAAAATTTAAATTATTAAAATG
Found at i:39657644 original size:66 final size:64
Alignment explanation
Indices: 39657527--39657651 Score: 146
Period size: 65 Copynumber: 1.9 Consensus size: 64
39657517 TTTCACAAAT
* * * *
39657527 TTTTTTACTTTTTAAATATTTTTTGCAATTTTTATAAAATTTTAATGATTTTATTAATTATCAA
1 TTTTTTAATTTTTAAATATTTTTTACAATTTTTATAAAATTTTAATAATTTTAATAATTATCAA
**
39657591 TTTTTTAATATTTTAAAT-TATTTTTACAGATTTTTAT-AGTTTTTAATAAATTTTAATAATT
1 TTTTTTAAT-TTTTAAATAT-TTTTTACA-ATTTTTATAAAATTTTAAT-AATTTTAATAATT
39657652 TTGTACAACT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
64 9 0.18
65 23 0.45
66 19 0.37
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (64 bp):
TTTTTTAATTTTTAAATATTTTTTACAATTTTTATAAAATTTTAATAATTTTAATAATTATCAA
Found at i:39657652 original size:95 final size:96
Alignment explanation
Indices: 39657493--39657672 Score: 215
Period size: 95 Copynumber: 1.9 Consensus size: 96
39657483 AATCGTATAC
* * *
39657493 ATTTTTTAATATTTTTAAAATAATTTTCACAAATTTTTTTACTTTTTAAATATTTTTTGCAATTT
1 ATTTTTTAATATTTTTAAAATAATTTTCACAAATTTTTATACTTTTTAAAAATTTTAT-CAATTT
39657558 T-TATAAAATTTTAATGATTTTATTAATTATCA
65 TGTA-AAAATTTTAATGATTTTATTAATTATCA
* * * *
39657590 ATTTTTTAATA-TTTT-AAATTATTTTTACAGATTTTTATAGTTTTTAATAAATTTTAAT-AATT
1 ATTTTTTAATATTTTTAAAATAATTTTCACAAATTTTTATACTTTTTAA-AAATTTT-ATCAATT
* *
39657652 TTGTACAACTTTTAATGATTT
64 TTGTAAAAATTTTAATGATTT
39657673 GTCCTATCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
95 47 0.66
96 12 0.17
97 12 0.17
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.58
Consensus pattern (96 bp):
ATTTTTTAATATTTTTAAAATAATTTTCACAAATTTTTATACTTTTTAAAAATTTTATCAATTTT
GTAAAAATTTTAATGATTTTATTAATTATCA
Found at i:39657756 original size:20 final size:20
Alignment explanation
Indices: 39657699--39657742 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
39657689 ATCAACACAA
*
39657699 TCAACATAG-CACGTCATCAG
1 TCAACAT-GCCACATCATCAG
39657719 TCAACATGCCACATCATCAG
1 TCAACATGCCACATCATCAG
39657739 TCAA
1 TCAA
39657743 TGTGCCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.36, C:0.32, G:0.11, T:0.20
Consensus pattern (20 bp):
TCAACATGCCACATCATCAG
Found at i:39663813 original size:16 final size:16
Alignment explanation
Indices: 39663773--39663819 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
39663763 ACACGAATAT
39663773 ATTAATTA--ATTATAA
1 ATTAATTATTATT-TAA
39663788 A-TAATGTATTATTTAA
1 ATTAAT-TATTATTTAA
39663804 ATTAATTATTATTTAA
1 ATTAATTATTATTTAA
39663820 TTAGTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 4 0.14
15 3 0.11
16 14 0.50
17 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTAATTATTATTTAA
Found at i:39666155 original size:6 final size:6
Alignment explanation
Indices: 39666144--39666172 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
39666134 AACCTCATCC
39666144 TGCCAG TGCCAG TGCCAG TGCCAG TGCCA
1 TGCCAG TGCCAG TGCCAG TGCCAG TGCCA
39666173 CATTGTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (6 bp):
TGCCAG
Found at i:39676064 original size:5 final size:5
Alignment explanation
Indices: 39676054--39676080 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39676044 CAATACATAT
39676054 AGAAA AGAAA AGAAA AGAAA AGAAA AG
1 AGAAA AGAAA AGAAA AGAAA AGAAA AG
39676081 GGTGAGTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:39681825 original size:16 final size:15
Alignment explanation
Indices: 39681804--39681844 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
39681794 TGCAACCATA
*
39681804 ATTTTGTTTTTATTTT
1 ATTTTGTTTTT-GTTT
39681820 ATTTTGTTTTTGTTT
1 ATTTTGTTTTTGTTT
*
39681835 ATTTTATTTT
1 ATTTTGTTTT
39681845 CTTTATCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (15 bp):
ATTTTGTTTTTGTTT
Found at i:39683136 original size:116 final size:116
Alignment explanation
Indices: 39682929--39683165 Score: 429
Period size: 116 Copynumber: 2.0 Consensus size: 116
39682919 AATCCTTGAG
* *
39682929 GCTAATCTACATAGATCTCTTTCTTCAGATAATCATTCAAAAAAGTTGATTAAACATGCATTTGA
1 GCTAATCTACATAGATCTCTTTCTTCAAATAACCATTCAAAAAAGTTGATTAAACATGCATTTGA
*
39682994 TGTATTTTCCAACCCTTTTGAGCTGCAAGTGTTAATAGCAGCCTTATGGTA
66 TGTATTTTCCAACCCTTTTGAACTGCAAGTGTTAATAGCAGCCTTATGGTA
*
39683045 GCTAATCTACATAGATCTCTTTGTTCAAATAACCATTCAAAAAAGTTGATTAAACATGCATTTGA
1 GCTAATCTACATAGATCTCTTTCTTCAAATAACCATTCAAAAAAGTTGATTAAACATGCATTTGA
39683110 TGTATTTTCCAACCCTTTTGAACTGCAAGTGTTAATAGCAGCCTTATGGTA
66 TGTATTTTCCAACCCTTTTGAACTGCAAGTGTTAATAGCAGCCTTATGGTA
*
39683161 TCTAA
1 GCTAA
39683166 CCTTTCTACA
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (116 bp):
GCTAATCTACATAGATCTCTTTCTTCAAATAACCATTCAAAAAAGTTGATTAAACATGCATTTGA
TGTATTTTCCAACCCTTTTGAACTGCAAGTGTTAATAGCAGCCTTATGGTA
Found at i:39683695 original size:288 final size:288
Alignment explanation
Indices: 39683179--39683754 Score: 967
Period size: 288 Copynumber: 2.0 Consensus size: 288
39683169 TTCTACAGGG
* * * *
39683179 GCAAAGGTCTCAGTAAAATCCACACTAAATTGCTGACTATACCCCTTGATAACCAATCTGGCCTT
1 GCAAAGGTCTCAGTAAAATCAACACCAAATTGCTGACTATACCCCTTGATAACCAATCTAGCCAT
*
39683244 GTACTTATTGATAGAACCATCAAGTTTCATTTTGGTTCTAAACACCTATTTGACCCCAATAACTT
66 GTACTTATTGATAGAACCATCAAGATTCATTTTGGTTCTAAACACCTATTTGACCCCAATAACTT
* *
39683309 TCTTATGAATCAGTCTATCTACCAACTCCCAAGTCTTATTCTTGTTGATCATACTAATATCTTCC
131 TCTTATGAATCAGTCTATCTAACAACTCCCAAGTCTCATTCTTGTTGATCATACTAATATCTTCC
39683374 TTCATAGCATCTCTCTATTCAAGATTTTGTGCTACCTCTTTAAACGTAACTGGTTCCAACACTGC
196 TTCATAGCATCTCTCTATTCAAGATTTTGTGCTACCTCTTTAAACGTAACTGGTTCCAACACTGC
*
39683439 CAGATTACATATCTGATAAACTTTAGTA
261 CAGATTACATATCTGATAAACTTCAGTA
*
39683467 GCAAAGGTCTCAGTAAAATCAACACCAAATTGCTGACTATACCTCTTGATAACCAATCTAGCCAT
1 GCAAAGGTCTCAGTAAAATCAACACCAAATTGCTGACTATACCCCTTGATAACCAATCTAGCCAT
* *
39683532 GTACTTGTTGATAGAACCATCAAGATTCATTTTGGTTCTGAACACCTATTTGACCCCAATAACTT
66 GTACTTATTGATAGAACCATCAAGATTCATTTTGGTTCTAAACACCTATTTGACCCCAATAACTT
* *
39683597 TCTTATGAA-CTGGTCTATCTAACAACTCCCAAGTCTCATTCTTGTTGATCATACTAATCTCTTC
131 TCTTATGAATC-AGTCTATCTAACAACTCCCAAGTCTCATTCTTGTTGATCATACTAATATCTTC
* * *
39683661 CTTCATAGCATCTCTTTATTCAAG-TTCTTGTGCTACCTCTTTAAAGGTAATTGGTTCCAACACT
195 CTTCATAGCATCTCTCTATTCAAGATT-TTGTGCTACCTCTTTAAACGTAACTGGTTCCAACACT
*
39683725 GCCAGATTACATATTTGATAAACTTCAGTA
259 GCCAGATTACATATCTGATAAACTTCAGTA
39683755 ATTGGTCTTG
Statistics
Matches: 269, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
287 3 0.01
288 266 0.99
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.35
Consensus pattern (288 bp):
GCAAAGGTCTCAGTAAAATCAACACCAAATTGCTGACTATACCCCTTGATAACCAATCTAGCCAT
GTACTTATTGATAGAACCATCAAGATTCATTTTGGTTCTAAACACCTATTTGACCCCAATAACTT
TCTTATGAATCAGTCTATCTAACAACTCCCAAGTCTCATTCTTGTTGATCATACTAATATCTTCC
TTCATAGCATCTCTCTATTCAAGATTTTGTGCTACCTCTTTAAACGTAACTGGTTCCAACACTGC
CAGATTACATATCTGATAAACTTCAGTA
Found at i:39688668 original size:164 final size:164
Alignment explanation
Indices: 39688390--39688884 Score: 884
Period size: 164 Copynumber: 3.0 Consensus size: 164
39688380 TTTTCTGTGT
39688390 AGGAATCTTGCATGTTAGAAGCATGACATTTTTCAAGTTAACAACGAAAAATGGAATGGAGCACA
1 AGGAATCTTGCATGTTAGAAGCATGACATTTTTCAAGTTAACAACGAAAAATGGAATGGAGCAC-
*
39688455 T-ACCATTAGATTACAGAACTATCACGATCAATCGGGTAACTTATTTCCTTATCTTTTTAGGGCT
65 TCACCATTAGATTACAGAACTATCACGATCAATCGGGTAACTTCTTTCCTTATCTTTTTAGGGCT
39688519 ACACATTGAGGACAATGTGTTATCTAAAGTGTGGG
130 ACACATTGAGGACAATGTGTTATCTAAAGTGTGGG
*
39688554 AGGAATCTTGCATGTTAGAAGCATGTCATTTTTCAAGTTAACAACGAAAAATGGAATGGAGCACT
1 AGGAATCTTGCATGTTAGAAGCATGACATTTTTCAAGTTAACAACGAAAAATGGAATGGAGCACT
39688619 CACCATTAGATTACAGAACTATCACGATCAATCGGGTAACTTCTTTCCTTATCTTTTTAGGGCTA
66 CACCATTAGATTACAGAACTATCACGATCAATCGGGTAACTTCTTTCCTTATCTTTTTAGGGCTA
* *
39688684 CACATTAAGGACAATGTGTTATCTAAAGTGTGAG
131 CACATTGAGGACAATGTGTTATCTAAAGTGTGGG
* * *
39688718 AGGAATCTTTCATGTTAGAAGCATGACATTTTTCAAGTTAACAACAAAAAATGGAATGGAGGACT
1 AGGAATCTTGCATGTTAGAAGCATGACATTTTTCAAGTTAACAACGAAAAATGGAATGGAGCACT
*
39688783 CACCATTAGATTACAGAACTATCACGATCAATCGGGTAACTTCTTTTCTTATCTTTTTAGGGCTA
66 CACCATTAGATTACAGAACTATCACGATCAATCGGGTAACTTCTTTCCTTATCTTTTTAGGGCTA
**
39688848 CATGTTGAGGACAATGTGTTATCTAAAGTGTGGG
131 CACATTGAGGACAATGTGTTATCTAAAGTGTGGG
39688882 AGG
1 AGG
39688885 GTAACATAGG
Statistics
Matches: 317, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
163 1 0.00
164 316 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (164 bp):
AGGAATCTTGCATGTTAGAAGCATGACATTTTTCAAGTTAACAACGAAAAATGGAATGGAGCACT
CACCATTAGATTACAGAACTATCACGATCAATCGGGTAACTTCTTTCCTTATCTTTTTAGGGCTA
CACATTGAGGACAATGTGTTATCTAAAGTGTGGG
Found at i:39696580 original size:16 final size:16
Alignment explanation
Indices: 39696559--39696589 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39696549 AACTGGACTA
*
39696559 TTCGCCATTTGTGTTG
1 TTCGCCATGTGTGTTG
39696575 TTCGCCATGTGTGTT
1 TTCGCCATGTGTGTT
39696590 CGCCAATGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.19, G:0.26, T:0.48
Consensus pattern (16 bp):
TTCGCCATGTGTGTTG
Found at i:39709725 original size:17 final size:17
Alignment explanation
Indices: 39709697--39709741 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
39709687 CTATTAAGTC
*
39709697 TATATAAGATATTAGTTT
1 TATATAAAATATTA-TTT
39709715 T-TATAAAATATTATTT
1 TATATAAAATATTATTT
39709731 TAATATAAAAT
1 T-ATATAAAAT
39709742 GAACTTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.17
17 11 0.46
18 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
TATATAAAATATTATTT
Found at i:39715163 original size:158 final size:158
Alignment explanation
Indices: 39714870--39715156 Score: 416
Period size: 158 Copynumber: 1.8 Consensus size: 158
39714860 CTTCTTCTTC
* * * * * **
39714870 TTCTTAGACTTTTTTGTTGTCTTCACTTTGGTTGCAGGGGAAAGATTTGATGGGACATCGTTGTT
1 TTCTTACACTTCTGTGTTGTCTTCACTTTGGTTACAAGGGAAAGATTTGATGGGACATCGTCATT
* *
39714935 ATTGTTGTTGTTTCAACGACAGCGATGGAGGGGGTTATCATCGTTGATTGTGGAGACTAAATTAA
66 ATTGTTGTTGTTTCAACGACAACAATGGAGGGGGTTATCATCGTTGATTGTGGAGACTAAATTAA
39715000 AGCATCGTCATTGTTGTTATTGTTGTTG
131 AGCATCGTCATTGTTGTTATTGTTGTTG
* * *
39715028 TTCTTACACTTCTGTGTTGTCTTTACTTTGGTTACAAGGGAAGGATTTGATGGGACATTGTCATT
1 TTCTTACACTTCTGTGTTGTCTTCACTTTGGTTACAAGGGAAAGATTTGATGGGACATCGTCATT
* *
39715093 ATTGTTGTTGTTTTCGAC-AGCAACAATGGA-GGGGTTATCATCGTTGATTGTGGAGACTGAATT
66 ATTGTTGTTG-TTTCAACGA-CAACAATGGAGGGGGTTATCATCGTTGATTGTGGAGACTAAATT
39715156 A
129 A
39715157 GGGCATCACT
Statistics
Matches: 113, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
158 99 0.88
159 14 0.12
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.40
Consensus pattern (158 bp):
TTCTTACACTTCTGTGTTGTCTTCACTTTGGTTACAAGGGAAAGATTTGATGGGACATCGTCATT
ATTGTTGTTGTTTCAACGACAACAATGGAGGGGGTTATCATCGTTGATTGTGGAGACTAAATTAA
AGCATCGTCATTGTTGTTATTGTTGTTG
Found at i:39715190 original size:158 final size:158
Alignment explanation
Indices: 39714858--39715190 Score: 411
Period size: 158 Copynumber: 2.1 Consensus size: 158
39714848 CCAAACATTC
* * * * *
39714858 TTCTTCTTCTTCTTCTTAGACTTTTTTGTTGTCTTCACTTTGGTTGCAGGGGAAAGATTTGATGG
1 TTCTTCTTCTTCTTCTTACACTTCTGTGTTGTCTTCACTTTGGTTACAAGGGAAAGATTTGATGG
** * *
39714923 GACATCGTTGTTATTGTTGTTGTTTCAACGACAGCGATGGAGGGGGTTATCATCGTTGATTGTGG
66 GACATCGTCATTATTGTTGTTGTTTCAACGACAACAATGGAGGGGGTTATCATCGTTGATTGTGG
* *
39714988 AGACTAAATTAAAGCATCGTCATTGTTG
131 AGACTAAATTAAAGCATCCTCATTATTG
* * * * * *
39715016 TTATTGTTGTTGTTCTTACACTTCTGTGTTGTCTTTACTTTGGTTACAAGGGAAGGATTTGATGG
1 TTCTTCTTCTTCTTCTTACACTTCTGTGTTGTCTTCACTTTGGTTACAAGGGAAAGATTTGATGG
* *
39715081 GACATTGTCATTATTGTTGTTGTTTTCGAC-AGCAACAATGGA-GGGGTTATCATCGTTGATTGT
66 GACATCGTCATTATTGTTGTTG-TTTCAACGA-CAACAATGGAGGGGGTTATCATCGTTGATTGT
* ** *
39715144 GGAGACTGAATTAGGGCATCACTGA-TATTG
129 GGAGACTAAATTAAAGCATC-CTCATTATTG
39715174 TTCTTCTTCTTCTTCTT
1 TTCTTCTTCTTCTTCTT
39715191 CAATTAGAAT
Statistics
Matches: 145, Mismatches: 27, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
158 129 0.89
159 16 0.11
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (158 bp):
TTCTTCTTCTTCTTCTTACACTTCTGTGTTGTCTTCACTTTGGTTACAAGGGAAAGATTTGATGG
GACATCGTCATTATTGTTGTTGTTTCAACGACAACAATGGAGGGGGTTATCATCGTTGATTGTGG
AGACTAAATTAAAGCATCCTCATTATTG
Found at i:39715751 original size:12 final size:12
Alignment explanation
Indices: 39715733--39715764 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39715723 AGAATTAACC
39715733 AATATTTTTAAA
1 AATATTTTTAAA
*
39715745 TATATTTTTAAA
1 AATATTTTTAAA
39715757 AATATTTT
1 AATATTTT
39715765 ATTGATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATATTTTTAAA
Found at i:39719713 original size:35 final size:35
Alignment explanation
Indices: 39719672--39719741 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
39719662 CACGATGTGG
39719672 AACTAAGCCACTCAATAACCATATGCAAGTGAACT
1 AACTAAGCCACTCAATAACCATATGCAAGTGAACT
39719707 AACTAAGCCACTCAATAACCATATGCAAGTGAACT
1 AACTAAGCCACTCAATAACCATATGCAAGTGAACT
39719742 GACATATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (35 bp):
AACTAAGCCACTCAATAACCATATGCAAGTGAACT
Found at i:39721009 original size:16 final size:16
Alignment explanation
Indices: 39720988--39721021 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
39720978 ATTCTCTTAT
39720988 AAAATAATT-TTCAAAA
1 AAAATAATTATT-AAAA
39721004 AAAATAATTATTAAAA
1 AAAATAATTATTAAAA
39721020 AA
1 AA
39721022 TTTATCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAATTATTAAAA
Found at i:39728960 original size:42 final size:42
Alignment explanation
Indices: 39728906--39729014 Score: 146
Period size: 42 Copynumber: 2.6 Consensus size: 42
39728896 AAAGCTAATT
* *
39728906 AGAAGCTCATAAAAGCTGAACAGAAATTAATAAGAGTTGAAC
1 AGAAGCTCATAAAAGCTGAACAGAAACTAATAAGACTTGAAC
* * *
39728948 AGAAGCTCATAAAAGCTTAACAGAAACTCATAAGACTTGAAT
1 AGAAGCTCATAAAAGCTGAACAGAAACTAATAAGACTTGAAC
* * *
39728990 AAAAGCTCGTAAGAGCTGAACAGAA
1 AGAAGCTCATAAAAGCTGAACAGAA
39729015 GCTCGAAAGA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (42 bp):
AGAAGCTCATAAAAGCTGAACAGAAACTAATAAGACTTGAAC
Found at i:39729019 original size:21 final size:21
Alignment explanation
Indices: 39728846--39729027 Score: 128
Period size: 21 Copynumber: 9.0 Consensus size: 21
39728836 CAGATACGCC
39728846 AACAGAAGCTCG-AA-AGCTG
1 AACAGAAGCTCGTAAGAGCTG
*
39728865 AACAGAAGCTCG-AA-AGCTA
1 AACAGAAGCTCGTAAGAGCTG
*
39728884 AACAGAAGCTTG-AA-AGCT-
1 AACAGAAGCTCGTAAGAGCTG
* * *
39728902 AATTAGAAGCTCATAAAAGCTG
1 AA-CAGAAGCTCGTAAGAGCTG
** ** *
39728924 AACAGAAATTAATAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTG
* * *
39728945 AACAGAAGCTCATAAAAGCTT
1 AACAGAAGCTCGTAAGAGCTG
* *
39728966 AACAGAAACTCATAAGA-CTTG
1 AACAGAAGCTCGTAAGAGC-TG
* *
39728987 AATAAAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
*
39729008 AACAGAAGCTCGAAAGAGCT
1 AACAGAAGCTCGTAAGAGCT
39729028 AAATAGAAAG
Statistics
Matches: 130, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
18 2 0.02
19 42 0.32
20 3 0.02
21 80 0.62
22 3 0.02
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:39729035 original size:21 final size:21
Alignment explanation
Indices: 39728987--39729035 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
39728977 ATAAGACTTG
* * *
39728987 AATAAAAGCTCGTAAGAGCTG
1 AATAGAAGCTCGAAAGAGCTA
*
39729008 AACAGAAGCTCGAAAGAGCTA
1 AATAGAAGCTCGAAAGAGCTA
39729029 AATAGAA
1 AATAGAA
39729036 AGTAAAACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.49, C:0.14, G:0.22, T:0.14
Consensus pattern (21 bp):
AATAGAAGCTCGAAAGAGCTA
Found at i:39730313 original size:33 final size:33
Alignment explanation
Indices: 39730266--39730331 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
39730256 CTCCTAAGAG
39730266 ATGAAAACACACGCGCCGATGCTTTGTCAAAGT
1 ATGAAAACACACGCGCCGATGCTTTGTCAAAGT
*
39730299 ATGACAACACACGCGCCGATGCTTTGTCAAAGT
1 ATGAAAACACACGCGCCGATGCTTTGTCAAAGT
39730332 TAGCATCTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (33 bp):
ATGAAAACACACGCGCCGATGCTTTGTCAAAGT
Found at i:39731971 original size:69 final size:69
Alignment explanation
Indices: 39731830--39732170 Score: 285
Period size: 69 Copynumber: 5.0 Consensus size: 69
39731820 CAATAGCATT
** * * * ** * * * ** * *
39731830 TCCCAGCTGTTGTGCTAAGCCTCGTAGGTGAAGAGCCGCAAGCTCTAATACAGTTAGCAAAAGCG
1 TCCCAGCTGTCATGCTAAGGCTCGCAGGCGAAGAGTTGCAACCTCCAACACAGTTAGTGAGAGCA
*
39731895 AAGC
66 AAAC
* *** *
39731899 TCCCAGCTGTCATGCTAAGGCTCGTAGGCGAAGAGTTGCAACCTCTTGCACAGATAGTGAGAGCA
1 TCCCAGCTGTCATGCTAAGGCTCGCAGGCGAAGAGTTGCAACCTCCAACACAGTTAGTGAGAGCA
*
39731964 AACC
66 AAAC
* * * * *
39731968 TCCCAACTGT--TGTTAAGGCTCGCAAGCGAAGAGTCGCAGCCTCCAACACAGTTAGTGAGAGCA
1 TCCCAGCTGTCATGCTAAGGCTCGCAGGCGAAGAGTTGCAACCTCCAACACAGTTAGTGAGAGCA
*
39732031 AAGC
66 AAAC
* * * * * * * *
39732035 TCCCAGCTGTCGTCCTCAGGTTCGCAGGCGAAAAG--CCAAAGCCTCCAACACATTTAGCGAGAG
1 TCCCAGCTGTCATGCTAAGGCTCGCAGGCGAAGAGTTGC-AA-CCTCCAACACAGTTAGTGAGAG
39732098 CAAAAC
64 CAAAAC
* * **
39732104 TCCCAGCTGTCATGCTAAGGCTCGCAGGCAAAGAGTTGCAACCTCCAACACAATTAGCAAGAGCA
1 TCCCAGCTGTCATGCTAAGGCTCGCAGGCGAAGAGTTGCAACCTCCAACACAGTTAGTGAGAGCA
39732169 AA
66 AA
39732171 GCTACCAATT
Statistics
Matches: 218, Mismatches: 48, Indels: 12
0.78 0.17 0.04
Matches are distributed among these distances:
67 57 0.26
68 1 0.00
69 157 0.72
70 2 0.01
71 1 0.00
ACGTcount: A:0.30, C:0.28, G:0.24, T:0.18
Consensus pattern (69 bp):
TCCCAGCTGTCATGCTAAGGCTCGCAGGCGAAGAGTTGCAACCTCCAACACAGTTAGTGAGAGCA
AAAC
Found at i:39731997 original size:67 final size:67
Alignment explanation
Indices: 39731914--39732220 Score: 206
Period size: 69 Copynumber: 4.5 Consensus size: 67
39731904 GCTGTCATGC
* * * ***
39731914 TAAGGCTCGTAGGCGAAGAGTTGCAACCTCTTGCACAGATAGTGAGAGCAAACCTCCCAACTGTT
1 TAAGGCTCGCAAGCGAAGAGTCGCAACCTCCAACACAGATAGTGAGAGCAAACCTCCCAACTGTT
39731979 GT
66 GT
* * * * *
39731981 TAAGGCTCGCAAGCGAAGAGTCGCAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCCCAGCTGTC
1 TAAGGCTCGCAAGCGAAGAGTCGCAACCTCCAACACAGATAGTGAGAGCAAACCTCCCAACTGTT
39732046 GT
66 GT
* * * * ** * * *
39732048 CCTCAGGTTCGCAGGCGAAAAG-C-CAAAGCCTCCAACACATTTAGCGAGAGCAAAACTCCCAGC
1 --TAAGGCTCGCAAGCGAAGAGTCGC-AA-CCTCCAACACAGATAGTGAGAGCAAACCTCCCAAC
*
39732111 TGTCATGC
62 TGT--TGT
* * * ** * * *
39732119 TAAGGCTCGCAGGCAAAGAGTTGCAACCTCCAACACA-ATTAGCAAGAGCAAAGCTACCAATTGT
1 TAAGGCTCGCAAGCGAAGAGTCGCAACCTCCAACACAGA-TAGTGAGAGCAAACCTCCCAACTG-
39732183 TGTGT
64 T-TGT
* * * * *
39732188 TAAGACTTGCAAGTGAAAAGTCACAACCTCCAA
1 TAAGGCTCGCAAGCGAAGAGTCGCAACCTCCAA
39732221 AAAATTTAGC
Statistics
Matches: 188, Mismatches: 42, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
67 57 0.30
68 2 0.01
69 124 0.66
70 3 0.02
71 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.19
Consensus pattern (67 bp):
TAAGGCTCGCAAGCGAAGAGTCGCAACCTCCAACACAGATAGTGAGAGCAAACCTCCCAACTGTT
GT
Found at i:39732206 original size:138 final size:137
Alignment explanation
Indices: 39731957--39732269 Score: 319
Period size: 138 Copynumber: 2.3 Consensus size: 137
39731947 CACAGATAGT
* * * * * * *
39731957 GAGAGCAAACCTCCCAACTGT-TGTTAAGGCTCGCAAGCGAAGAGTCGCAGCCTCCAACACAGTT
1 GAGAGCAAAACTCCCAGCTGTCTGCTAAGGCTCGCAGGCAAAGAGTCGCAACCTCCAACACAATT
** * * * * * *
39732021 AGTGAGAGCAAAGCTCCCAGCTGTCGTCCTCAGGTTCGCAGGCGAAAAGCCA-AAGCCTCCAACA
66 AGCAAGAGCAAAGCTACCAACTGTCGTCCTAAGCTTCGCAAGCGAAAAGCCACAA-CCTCCAAAA
*
39732085 CATTTAGC
130 AATTTAGC
*
39732093 GAGAGCAAAACTCCCAGCTGTCATGCTAAGGCTCGCAGGCAAAGAGTTGCAACCTCCAACACAAT
1 GAGAGCAAAACTCCCAGCTGTC-TGCTAAGGCTCGCAGGCAAAGAGTCGCAACCTCCAACACAAT
* * ** * *
39732158 TAGCAAGAGCAAAGCTACCAATTGTTGTGTTAAGACTT-GCAAGTGAAAAGTCACAACCTCCAAA
65 TAGCAAGAGCAAAGCTACCAACTGTCGTCCTAAG-CTTCGCAAGCGAAAAGCCACAACCTCCAAA
39732222 AAATTTAGC
129 AAATTTAGC
* * *
39732231 GAAAG-AAAAGCTCCTAGCTGTCGTACTAAGGCTCGCAGG
1 GAGAGCAAAA-CTCCCAGCTGTC-TGCTAAGGCTCGCAGG
39732270 TGAAAAATCA
Statistics
Matches: 145, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
136 19 0.13
137 4 0.03
138 118 0.81
139 4 0.03
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (137 bp):
GAGAGCAAAACTCCCAGCTGTCTGCTAAGGCTCGCAGGCAAAGAGTCGCAACCTCCAACACAATT
AGCAAGAGCAAAGCTACCAACTGTCGTCCTAAGCTTCGCAAGCGAAAAGCCACAACCTCCAAAAA
ATTTAGC
Found at i:39732273 original size:69 final size:69
Alignment explanation
Indices: 39732030--39732282 Score: 201
Period size: 69 Copynumber: 3.7 Consensus size: 69
39732020 TAGTGAGAGC
* * * * * * *
39732030 AAAGCTCCCAGCTGTCGTCCTCAGGTTCGCAGGCGAAAAGCCA-AAGCCTCCAACACATTTAGCG
1 AAAGCTCCCAGCTGTCGTGCTAAGGCTCGCAGGTGAAAAGTCACAA-CCTCCAAAAAATTTAGCG
*
39732094 AGAGCA
65 AAAG-A
* * ** *
39732100 AAA-CTCCCAGCTGTCATGCTAAGGCTCGCAGG-CAAAGAGTTGCAACCTCCAACACAA-TTAGC
1 AAAGCTCCCAGCTGTCGTGCTAAGGCTCGCAGGTGAAA-AGTCACAACCTCCAA-AAAATTTAGC
*
39732162 -AAGAGC
64 GAA-AGA
* ** * * * * *
39732168 AAAGCTACCAATTGTTGTGTTAAGACTTGCAAGTGAAAAGTCACAACCTCCAAAAAATTTAGCGA
1 AAAGCTCCCAGCTGTCGTGCTAAGGCTCGCAGGTGAAAAGTCACAACCTCCAAAAAATTTAGCGA
39732233 AAGA
66 AAGA
* * *
39732237 AAAGCTCCTAGCTGTCGTACTAAGGCTCGCAGGTGAAAAATCACAA
1 AAAGCTCCCAGCTGTCGTGCTAAGGCTCGCAGGTGAAAAGTCACAA
39732283 TCACCAAAGT
Statistics
Matches: 137, Mismatches: 38, Indels: 17
0.71 0.20 0.09
Matches are distributed among these distances:
68 10 0.07
69 116 0.85
70 11 0.08
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (69 bp):
AAAGCTCCCAGCTGTCGTGCTAAGGCTCGCAGGTGAAAAGTCACAACCTCCAAAAAATTTAGCGA
AAGA
Found at i:39732325 original size:14 final size:14
Alignment explanation
Indices: 39732306--39732338 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
39732296 AATCTCCTAG
39732306 CTACCACATTGAAA
1 CTACCACATTGAAA
39732320 CTACCACATTGAAA
1 CTACCACATTGAAA
39732334 CTACC
1 CTACC
39732339 GAATGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.06, T:0.21
Consensus pattern (14 bp):
CTACCACATTGAAA
Found at i:39740307 original size:25 final size:25
Alignment explanation
Indices: 39740278--39740328 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
39740268 AAGAATTTAA
39740278 AATTTTATTTTTAAATTTTAAGAAT
1 AATTTTATTTTTAAATTTTAAGAAT
**
39740303 AATTTTATTTTTATTTTTTAAGAAT
1 AATTTTATTTTTAAATTTTAAGAAT
39740328 A
1 A
39740329 CTAACAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
AATTTTATTTTTAAATTTTAAGAAT
Found at i:39740547 original size:23 final size:22
Alignment explanation
Indices: 39740487--39740552 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
39740477 CGCGAATCAA
*
39740487 TTTTTTATATTAAAAAATATTTT
1 TTTTTTTTATT-AAAAATATTTT
* * *
39740510 TTTGTTTAAAT-AAAATATTTT
1 TTTTTTTTATTAAAAATATTTT
39740531 TTTATTTTTATTAAAAATATTT
1 TTT-TTTTTATTAAAAATATTT
39740553 AAATATATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 13 0.38
22 5 0.15
23 16 0.47
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTTTTTATTAAAAATATTTT
Found at i:39740773 original size:9 final size:10
Alignment explanation
Indices: 39740749--39740854 Score: 76
Period size: 12 Copynumber: 10.0 Consensus size: 10
39740739 CCACCGGAAG
39740749 AGAGAAAGAAA
1 AGAG-AAGAAA
39740760 AGAG-AGAAA
1 AGAGAAGAAA
*
39740769 GGAGAAGAAAA
1 AGAGAAG-AAA
*
39740780 AAAGAAGAAGA
1 AGAGAAGAA-A
39740791 AGAGAAGAAGA
1 AGAGAAGAA-A
39740802 AGAAGAAGAAGA
1 AG-AGAAGAA-A
39740814 AGAAGAAGAAGA
1 AG-AGAAGAA-A
39740826 AGAAGAAGAAGA
1 AG-AGAAGAA-A
39740838 AGA-AAG-AA
1 AGAGAAGAAA
39740846 AGA-AAGAAA
1 AGAGAAGAAA
39740855 GAAAAAAAGG
Statistics
Matches: 86, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
8 7 0.08
9 11 0.13
10 7 0.08
11 26 0.30
12 35 0.41
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
AGAGAAGAAA
Found at i:39740787 original size:3 final size:3
Alignment explanation
Indices: 39740771--39740841 Score: 119
Period size: 3 Copynumber: 24.3 Consensus size: 3
39740761 GAGAGAAAGG
*
39740771 AGA AGA A-A AAA AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
39740817 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
39740842 AGAAAGAAAG
Statistics
Matches: 65, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
2 4 0.06
3 61 0.94
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:39741053 original size:61 final size:59
Alignment explanation
Indices: 39741013--39741145 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 59
39741003 ATGTAATTTT
* * * *
39741013 TTTTTGTTTTTTATAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAA
1 TTTTTG-TGTTTATAATTATTTTAAAATTAATTTATTAGT-ATTTAGGATAATGTAATAAA
* *
39741074 TTTTTGTGTTTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAA-GTTATAAA
1 TTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGT-ATTTAGGA-TAATGTAATAAA
**
39741134 TGGTTGTGTTTA
1 TTTTTGTGTTTA
39741146 GTTTAGTATT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
60 56 0.88
61 8 0.12
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (59 bp):
TTTTTGTGTTTATAATTATTTTAAAATTAATTTATTAGTATTTAGGATAATGTAATAAA
Found at i:39741098 original size:60 final size:60
Alignment explanation
Indices: 39741026--39741144 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
39741016 TTGTTTTTTA
* * **
39741026 TAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATGGTTGTGTTTG
39741086 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATGGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATGGTTGTGTTT
39741145 AGTTTAGTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATGGTTGTGTTTG
Found at i:39743363 original size:33 final size:33
Alignment explanation
Indices: 39743326--39743424 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
39743316 GTCATCTTAA
39743326 CTCGTATCCACCTCAGTACTCCGCTCCTTCCGG
1 CTCGTATCCACCTCAGTACTCCGCTCCTTCCGG
* * * *
39743359 CTCGTATCTACCTTAGTACTTCGCTCCTTCTGG
1 CTCGTATCCACCTCAGTACTCCGCTCCTTCCGG
* * * *
39743392 CCCGTATCCACCGCCGTACTCCACTCCTTCCGG
1 CTCGTATCCACCTCAGTACTCCGCTCCTTCCGG
39743425 TTCAAGTTCA
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.12, C:0.43, G:0.15, T:0.29
Consensus pattern (33 bp):
CTCGTATCCACCTCAGTACTCCGCTCCTTCCGG
Found at i:39743753 original size:27 final size:27
Alignment explanation
Indices: 39743715--39743810 Score: 156
Period size: 27 Copynumber: 3.6 Consensus size: 27
39743705 ACCTCTGAGT
* *
39743715 TAGGCACAACTAGTTGCGCCTGTCAGA
1 TAGGCTCAACTAGTCGCGCCTGTCAGA
*
39743742 TAGGCTCAACTAGTCGTGCCTGTCAGA
1 TAGGCTCAACTAGTCGCGCCTGTCAGA
*
39743769 TAGGCTCAACTAGTCGCGCCTCTCAGA
1 TAGGCTCAACTAGTCGCGCCTGTCAGA
39743796 TAGGCTCAACTAGTC
1 TAGGCTCAACTAGTC
39743811 CCTGTATTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (27 bp):
TAGGCTCAACTAGTCGCGCCTGTCAGA
Found at i:39751143 original size:27 final size:27
Alignment explanation
Indices: 39751104--39751156 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
39751094 GGGGGAATGA
39751104 GTCTAATGAACCAAGTGTATTACCTCG
1 GTCTAATGAACCAAGTGTATTACCTCG
* * *
39751131 GTCTGATGCACCAAGTGTGTTACCTC
1 GTCTAATGAACCAAGTGTATTACCTC
39751157 CTTCAATCTC
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:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (27 bp):
GTCTAATGAACCAAGTGTATTACCTCG
Found at i:39756921 original size:28 final size:28
Alignment explanation
Indices: 39756873--39756960 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
39756863 ATGTAAGATG
* *
39756873 AATATATAAAAAATTTCAATAAATAAAA
1 AATATATAAAATATTTAAATAAATAAAA
*
39756901 AATATATAAAAT-TATTAAAT-ATTAAAA
1 AATATATAAAATAT-TTAAATAAATAAAA
* *
39756928 TAATA-ATATAAATATTTAAAAAAATTAAA
1 -AATATATA-AAATATTTAAATAAATAAAA
39756957 AATA
1 AATA
39756961 GTATGAGTGG
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
27 10 0.20
28 33 0.67
29 6 0.12
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (28 bp):
AATATATAAAATATTTAAATAAATAAAA
Found at i:39776009 original size:23 final size:22
Alignment explanation
Indices: 39775964--39776009 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
39775954 AATTTCAAGT
39775964 AAATATTCAATTCAATTCCACAC
1 AAATATTCAATTCAATT-CACAC
39775987 AAATATTCATTATTCAATT-ACAC
1 AAATATTCA--ATTCAATTCACAC
39776010 TTAATCGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 13 0.62
25 8 0.38
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATATTCAATTCAATTCACAC
Found at i:39776296 original size:51 final size:51
Alignment explanation
Indices: 39776177--39776275 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
39776167 GTGACCATCA
* * *
39776177 CTATCCGATACACGTAGTAGCCTGCACATAATACTACACACGTGATCAAAG
1 CTATCCGGTACACATAGTAGCCTGCACATAATACTACACACGTGACCAAAG
*
39776228 CTATCCGGTACGCATAGTAGCCTGCACATAATACTACACACGTGACCA
1 CTATCCGGTACACATAGTAGCCTGCACATAATACTACACACGTGACCA
39776276 TCACTTTCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.21
Consensus pattern (51 bp):
CTATCCGGTACACATAGTAGCCTGCACATAATACTACACACGTGACCAAAG
Found at i:39781934 original size:18 final size:17
Alignment explanation
Indices: 39781913--39781946 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39781903 GATTTTGTTT
*
39781913 TATTTAGTTTTTTTTATA
1 TATTTA-TTTATTTTATA
39781931 TATTTATTTATTTTAT
1 TATTTATTTATTTTAT
39781947 TTTTTGTGAT
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:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TATTTATTTATTTTATA
Found at i:39785234 original size:16 final size:16
Alignment explanation
Indices: 39785213--39785267 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
39785203 GTTTGGTTTA
*
39785213 CTGTAATGGAATAAGG
1 CTGTAATAGAATAAGG
* *
39785229 CTGTAATTGAATAAAG
1 CTGTAATAGAATAAGG
*
39785245 TTGTAATAGAAT-AGAG
1 CTGTAATAGAATAAG-G
39785261 CTGTAAT
1 CTGTAAT
39785268 CAGTAATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 1 0.03
16 31 0.97
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (16 bp):
CTGTAATAGAATAAGG
Found at i:39785611 original size:61 final size:58
Alignment explanation
Indices: 39785476--39785612 Score: 143
Period size: 57 Copynumber: 2.3 Consensus size: 58
39785466 TAATGAAAAT
* * * * *
39785476 AAAAATAAAAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATACAATTTA
1 AAAAAT-ATAATATATAATTTAATAACATTTTAACAAAATTATTATTAAATACAATTTA
* * *
39785535 ATAAA-ATAATATATAATTTAATAACATTCTTAATAAAATTATTATTAAAATATGAA-TTA
1 AAAAATATAATATATAATTTAATAACATT-TTAACAAAATTATTATT-AAATA-CAATTTA
39785594 AAAAATCATAATATATAAT
1 AAAAAT-ATAATATATAAT
39785613 ATTATAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
57 19 0.30
58 15 0.23
59 16 0.25
60 2 0.03
61 12 0.19
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (58 bp):
AAAAATATAATATATAATTTAATAACATTTTAACAAAATTATTATTAAATACAATTTA
Found at i:39785621 original size:23 final size:21
Alignment explanation
Indices: 39785590--39785632 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39785580 TAAAATATGA
39785590 ATTAAAAAATCATAATATATAAT
1 ATTAAAAAA--ATAATATATAAT
*
39785613 ATTATAAAAATAATATATAA
1 ATTAAAAAAATAATATATAA
39785633 CCTATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAAAAAAATAATATATAAT
Found at i:39795678 original size:3 final size:3
Alignment explanation
Indices: 39795672--39795705 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
39795662 TGATGATGGC
* *
39795672 GGT GGT GAT GAT GGT GGT GGT GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
39795706 ATGCTCTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.06, C:0.00, G:0.62, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:39795679 original size:15 final size:15
Alignment explanation
Indices: 39795659--39795693 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
39795649 TTCCTCTCCA
39795659 TGGTGATGATGGCGG
1 TGGTGATGATGGCGG
*
39795674 TGGTGATGATGGTGG
1 TGGTGATGATGGCGG
39795689 TGGTG
1 TGGTG
39795694 GTGGTGGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.03, G:0.54, T:0.31
Consensus pattern (15 bp):
TGGTGATGATGGCGG
Found at i:39795680 original size:12 final size:12
Alignment explanation
Indices: 39795672--39795708 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
39795662 TGATGATGGC
*
39795672 GGTGGTGATGAT
1 GGTGGTGGTGAT
*
39795684 GGTGGTGGTGGT
1 GGTGGTGGTGAT
39795696 GGTGGTGGTGAT
1 GGTGGTGGTGAT
39795708 G
1 G
39795709 CTCTTCCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.08, C:0.00, G:0.59, T:0.32
Consensus pattern (12 bp):
GGTGGTGGTGAT
Found at i:39795757 original size:27 final size:27
Alignment explanation
Indices: 39795725--39795860 Score: 254
Period size: 27 Copynumber: 5.0 Consensus size: 27
39795715 CTCATGATCC
*
39795725 TCTTCATCATGGTGTTCGTGGTCATGG
1 TCTTCATCATGGTGCTCGTGGTCATGG
39795752 TCTTCATCATGGTGCTCGTGGTCATGG
1 TCTTCATCATGGTGCTCGTGGTCATGG
39795779 TCTTCATCATGGTGCTCGTGGTCATGG
1 TCTTCATCATGGTGCTCGTGGTCATGG
39795806 TCTTCATCATGGTGCTCGTGGTCATGG
1 TCTTCATCATGGTGCTCGTGGTCATGG
*
39795833 TCTTCATCATGGTGTTCGTGGTCATGG
1 TCTTCATCATGGTGCTCGTGGTCATGG
39795860 T
1 T
39795861 GGTCTGGCTT
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 107 1.00
ACGTcount: A:0.11, C:0.21, G:0.29, T:0.39
Consensus pattern (27 bp):
TCTTCATCATGGTGCTCGTGGTCATGG
Found at i:39795763 original size:12 final size:12
Alignment explanation
Indices: 39795746--39795845 Score: 65
Period size: 12 Copynumber: 7.6 Consensus size: 12
39795736 GTGTTCGTGG
39795746 TCATGGTCTTCA
1 TCATGGTCTTCA
**
39795758 TCATGGTGCTCGTGG
1 TCATGGT-CT--TCA
39795773 TCATGGTCTTCA
1 TCATGGTCTTCA
**
39795785 TCATGGTGCTCGTGG
1 TCATGGT-CT--TCA
39795800 TCATGGTCTTCA
1 TCATGGTCTTCA
**
39795812 TCATGGTGCTCGTGG
1 TCATGGT-CT--TCA
39795827 TCATGGTCTTCA
1 TCATGGTCTTCA
39795839 TCATGGT
1 TCATGGT
39795846 GTTCGTGGTC
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
12 31 0.46
13 6 0.09
14 6 0.09
15 24 0.36
ACGTcount: A:0.12, C:0.22, G:0.28, T:0.38
Consensus pattern (12 bp):
TCATGGTCTTCA
Found at i:39799423 original size:48 final size:48
Alignment explanation
Indices: 39799355--39799526 Score: 227
Period size: 48 Copynumber: 3.6 Consensus size: 48
39799345 AACAGATTTC
* * * * * ** * *
39799355 TCGGTGGCCTACACACAGTCCGTACCACCTTTGTGTAATAACAGACTC
1 TCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTTAACAGAATA
39799403 TCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTTAACAGAATA
1 TCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTTAACAGAATA
*
39799451 TTGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTTAACAGAATA
1 TCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTTAACAGAATA
* * *
39799499 TTGGTGGCCTGCACACAGTACGTGCCAC
1 TCGGTGGCCTGCACATAGTCCGTGCCAC
39799527 ATATGCGATC
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 112 1.00
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.26
Consensus pattern (48 bp):
TCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTTAACAGAATA
Found at i:39802011 original size:56 final size:57
Alignment explanation
Indices: 39801945--39802107 Score: 192
Period size: 56 Copynumber: 2.9 Consensus size: 57
39801935 AAATTTGAAT
* *
39801945 AATATTATTAAATATAATTTAATAAAAAATAATATATAATTTAATCATA-TTTTAAC
1 AATATTATTAAATATAATTTAATAAAAAATAATATATAATTTAATAAAATTTTTAAC
* * *
39802001 ATTATTATTAAATACAATTTAAT--AAAATAATATATAATTTAATAAAATTTTTAAT
1 AATATTATTAAATATAATTTAATAAAAAATAATATATAATTTAATAAAATTTTTAAC
*
39802056 AATATTATTAAA-ATACGAATTAATAAAAATCATAATATATAATATT-ATAAAA
1 AATATTATTAAATATA--ATTTAATAAAAA--ATAATATATAAT-TTAATAAAA
39802108 ATAATATATA
Statistics
Matches: 91, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
54 24 0.26
55 17 0.19
56 27 0.30
58 3 0.03
60 18 0.20
61 2 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (57 bp):
AATATTATTAAATATAATTTAATAAAAAATAATATATAATTTAATAAAATTTTTAAC
Found at i:39802058 original size:20 final size:21
Alignment explanation
Indices: 39802007--39802049 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
39801997 TAACATTATT
*
39802007 ATTAA-ATACAATTTAATAAA
1 ATTAATATATAATTTAATAAA
39802027 A-TAATATATAATTTAATAAA
1 ATTAATATATAATTTAATAAA
39802047 ATT
1 ATT
39802050 TTTAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 16 0.80
21 1 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTAATATATAATTTAATAAA
Found at i:39806294 original size:36 final size:32
Alignment explanation
Indices: 39806249--39806341 Score: 125
Period size: 36 Copynumber: 2.8 Consensus size: 32
39806239 TTATTCAATC
*
39806249 ATTTTAATAAGATAATATTAATCAATTAATCAA
1 ATTTTAATAAGATAATATTCATCAATTAAT-AA
39806282 TTTATTTTAATAAGATAATATTCATCAATTAATAA
1 ---ATTTTAATAAGATAATATTCATCAATTAATAA
*
39806317 A-TTGAATAAGATAATATTCATCAAT
1 ATTTTAATAAGATAATATTCATCAAT
39806342 CATTTTATCC
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 23 0.42
32 1 0.02
35 2 0.04
36 29 0.53
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.41
Consensus pattern (32 bp):
ATTTTAATAAGATAATATTCATCAATTAATAA
Found at i:39806751 original size:3 final size:3
Alignment explanation
Indices: 39806732--39806796 Score: 76
Period size: 3 Copynumber: 21.7 Consensus size: 3
39806722 GGGTTTTGGC
* * * **
39806732 TCA TTA TCA TTA TCA TCA TCA TCA TCA TCG TTG TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
*
39806780 TCA TCG TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TC
39806797 TTTATATCCA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.28, C:0.29, G:0.05, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:39808777 original size:7 final size:8
Alignment explanation
Indices: 39808763--39808788 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39808753 ATAATGAAAT
39808763 TAAAAAAA
1 TAAAAAAA
39808771 TAAAAAAA
1 TAAAAAAA
39808779 TAAAAAAA
1 TAAAAAAA
39808787 TA
1 TA
39808789 TTTTCTTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
TAAAAAAA
Found at i:39809271 original size:15 final size:15
Alignment explanation
Indices: 39809251--39809282 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39809241 AGTTGTTGGA
*
39809251 TTAATTTATTTTTTT
1 TTAATTGATTTTTTT
39809266 TTAATTGATTTTTTT
1 TTAATTGATTTTTTT
39809281 TT
1 TT
39809283 TGTAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (15 bp):
TTAATTGATTTTTTT
Found at i:39809282 original size:18 final size:19
Alignment explanation
Indices: 39809254--39809289 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39809244 TGTTGGATTA
*
39809254 ATTTATTTTTTTTTAATTG
1 ATTTATTTTTTTGTAATTG
39809273 ATTT-TTTTTTTGTAATT
1 ATTTATTTTTTTGTAATT
39809290 ATTGGTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (19 bp):
ATTTATTTTTTTGTAATTG
Found at i:39810502 original size:21 final size:21
Alignment explanation
Indices: 39810478--39810518 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39810468 TTTCATTCAC
39810478 CGTCATCATCACCATCATCAT
1 CGTCATCATCACCATCATCAT
* * *
39810499 CGTCGTCGTCATCATCATCA
1 CGTCATCATCACCATCATCA
39810519 CTTTCTCGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.29
Consensus pattern (21 bp):
CGTCATCATCACCATCATCAT
Done.