Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 164 of 208
Found at i:50064373 original size:17 final size:17
Alignment explanation
Indices: 50064351--50064404 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
50064341 ACACGGGTTG
50064351 GCCACACGCCCGTGTGA
1 GCCACACGCCCGTGTGA
* **
50064368 GCCACATGGGC-TG-GA
1 GCCACACGCCCGTGTGA
50064383 --CACACGCCCGTGTGA
1 GCCACACGCCCGTGTGA
50064398 GCCACAC
1 GCCACAC
50064405 AGACTAGACA
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
13 6 0.22
14 2 0.07
15 4 0.15
16 2 0.07
17 13 0.48
ACGTcount: A:0.20, C:0.39, G:0.30, T:0.11
Consensus pattern (17 bp):
GCCACACGCCCGTGTGA
Found at i:50064387 original size:30 final size:30
Alignment explanation
Indices: 50064339--50064456 Score: 146
Period size: 30 Copynumber: 3.9 Consensus size: 30
50064329 CTGGGCATTT
* * *
50064339 CCACACGGGTTGGCCACACGCCCGTGTGAG
1 CCACACGGGCTAGACACACGCCCGTGTGAG
* *
50064369 CCACATGGGCTGGACACACGCCCGTGTGAG
1 CCACACGGGCTAGACACACGCCCGTGTGAG
* * *
50064399 CCACACAGACTAGACACACACCCGTGTGAG
1 CCACACGGGCTAGACACACGCCCGTGTGAG
* *
50064429 CCACACGGGCTAGCCACACGCCCATGTG
1 CCACACGGGCTAGACACACGCCCGTGTG
50064457 CTAGCCTGTG
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.23, C:0.37, G:0.28, T:0.12
Consensus pattern (30 bp):
CCACACGGGCTAGACACACGCCCGTGTGAG
Found at i:50066345 original size:7 final size:7
Alignment explanation
Indices: 50066333--50066361 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
50066323 TTAAAACACT
50066333 GTGAAAG
1 GTGAAAG
50066340 GTGAAAG
1 GTGAAAG
50066347 GTGAAAG
1 GTGAAAG
50066354 GTGAAAG
1 GTGAAAG
50066361 G
1 G
50066362 ACCTGTTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.45, T:0.14
Consensus pattern (7 bp):
GTGAAAG
Found at i:50072316 original size:3 final size:3
Alignment explanation
Indices: 50072308--50072333 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
50072298 TAATACAAAA
50072308 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
50072334 AAGTAGAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:50074472 original size:26 final size:26
Alignment explanation
Indices: 50074441--50074492 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
50074431 GTCTAGGGAA
50074441 CTCAAATTTTTTATTATTATCTGATT
1 CTCAAATTTTTTATTATTATCTGATT
50074467 CTCAAATTTTTTATTATTATCTGATT
1 CTCAAATTTTTTATTATTATCTGATT
50074493 TAGATCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.04, T:0.58
Consensus pattern (26 bp):
CTCAAATTTTTTATTATTATCTGATT
Found at i:50077104 original size:13 final size:13
Alignment explanation
Indices: 50077086--50077110 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50077076 TTAAAAATAA
50077086 AATTAACTAAATT
1 AATTAACTAAATT
50077099 AATTAACTAAAT
1 AATTAACTAAAT
50077111 AACACGACAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAACTAAATT
Found at i:50078937 original size:50 final size:50
Alignment explanation
Indices: 50078822--50079045 Score: 358
Period size: 50 Copynumber: 4.5 Consensus size: 50
50078812 GATAATAACA
* ** *
50078822 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
50078873 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
50078923 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
50078973 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
50079023 TGCCAATGCCATATCCCAGACAT
1 TGCCAATGCCATGTCCCAGACAT
50079046 NNNNNNNNNN
Statistics
Matches: 160, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 127 0.79
51 33 0.21
ACGTcount: A:0.21, C:0.32, G:0.22, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:50080508 original size:17 final size:17
Alignment explanation
Indices: 50080486--50080519 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
50080476 CACAGTCTGG
50080486 CATATGGCCATGTGGCA
1 CATATGGCCATGTGGCA
50080503 CATATGGCCATGTGGCA
1 CATATGGCCATGTGGCA
50080520 GCCCATGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (17 bp):
CATATGGCCATGTGGCA
Found at i:50080528 original size:29 final size:30
Alignment explanation
Indices: 50080493--50080559 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
50080483 TGGCATATGG
* * *
50080493 CCATGTGGCACATATGGCCATGTGGC-AGC
1 CCATGTGGCACACACGACCATGTGGCTAGC
* *
50080522 CCATGTGGCTCACACGACCATGTGTCTAGC
1 CCATGTGGCACACACGACCATGTGGCTAGC
50080552 CCATGTGG
1 CCATGTGG
50080560 AATGACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.22
Consensus pattern (30 bp):
CCATGTGGCACACACGACCATGTGGCTAGC
Found at i:50084720 original size:104 final size:104
Alignment explanation
Indices: 50084540--50084745 Score: 367
Period size: 104 Copynumber: 2.0 Consensus size: 104
50084530 CTATCCAACA
50084540 GCTCCCGAATATTGGTTTCAGAACTCTGCCCTCTTTCCCATGTAAACTAGGGTCATTTGAAGCCC
1 GCTCCCGAATATTGGTTTCAGAACTCTGCCCTCTTTCCCATGTAAACTAGGGTCATTTGAAGCCC
*
50084605 AGATTAGCTAACGAGCAATCATCCAAATCCTGACGAATT
66 AGATTAGCTAACGAGCAATCATCCAAAGCCTGACGAATT
* * *
50084644 GCTCCTGAATATTGGTTTCAGAGCTCTGCCCTCTTTCCCATGTATACTAGGGTCATTTGAAGCCC
1 GCTCCCGAATATTGGTTTCAGAACTCTGCCCTCTTTCCCATGTAAACTAGGGTCATTTGAAGCCC
*
50084709 AGATTAGCTAACGAGCAGTCATCCAAAGCCTGACGAA
66 AGATTAGCTAACGAGCAATCATCCAAAGCCTGACGAA
50084746 ATTATTCTAT
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 97 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (104 bp):
GCTCCCGAATATTGGTTTCAGAACTCTGCCCTCTTTCCCATGTAAACTAGGGTCATTTGAAGCCC
AGATTAGCTAACGAGCAATCATCCAAAGCCTGACGAATT
Found at i:50088965 original size:17 final size:17
Alignment explanation
Indices: 50088932--50088965 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
50088922 CATATAAGTT
*
50088932 ACTGAATTATTTAAAAA
1 ACTGAATTATTCAAAAA
50088949 ACTGAATTATTCGAAAA
1 ACTGAATTATTC-AAAA
50088966 TTTTTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (17 bp):
ACTGAATTATTCAAAAA
Found at i:50092287 original size:13 final size:13
Alignment explanation
Indices: 50092269--50092300 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
50092259 TTTCCAGCAA
50092269 TTATGAATTTATT
1 TTATGAATTTATT
50092282 TTATGAATTTATT
1 TTATGAATTTATT
*
50092295 TGATGA
1 TTATGA
50092301 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:50092502 original size:50 final size:50
Alignment explanation
Indices: 50092395--50092643 Score: 327
Period size: 50 Copynumber: 4.8 Consensus size: 50
50092385 GTTTGGGTAA
*
50092395 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GA-CATG
*
50092451 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* *
50092501 AGAGGTCCCATGTAAGACCATGTCTGGGTCATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* * * * *
50092551 AGAGGTCCCCTATAAGACCATATCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
** *
50092601 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
50092644 TGTTATTATC
Statistics
Matches: 175, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
50 97 0.55
51 35 0.20
55 2 0.01
56 41 0.23
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
Found at i:50094209 original size:15 final size:16
Alignment explanation
Indices: 50094186--50094219 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
50094176 TAATAATAAT
50094186 AAATAAAATGAAA-AG
1 AAATAAAATGAAATAG
*
50094201 AAATTAAATGAAATAG
1 AAATAAAATGAAATAG
50094217 AAA
1 AAA
50094220 GAAAGTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (16 bp):
AAATAAAATGAAATAG
Found at i:50094214 original size:20 final size:20
Alignment explanation
Indices: 50094185--50094223 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
50094175 GTAATAATAA
50094185 TAAATAAAAT-GAAAAGAAAT
1 TAAATAAAATAG-AAAGAAAT
*
50094205 TAAATGAAATAGAAAGAAA
1 TAAATAAAATAGAAAGAAA
50094224 GTGGAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (20 bp):
TAAATAAAATAGAAAGAAAT
Found at i:50104473 original size:2 final size:2
Alignment explanation
Indices: 50104466--50104492 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
50104456 AATTTACGTT
50104466 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
50104493 TAATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50104721 original size:27 final size:28
Alignment explanation
Indices: 50104686--50104754 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
50104676 AAATAATTAT
* **
50104686 AAAATTATAAAATA-TTCAGAAAATTTA
1 AAAAATATAAAATAGTTCAGAAAAACTA
* *
50104713 AAAAATAT-AAATAGTTTATAAAAACTA
1 AAAAATATAAAATAGTTCAGAAAAACTA
50104740 AAAAATCATAAAATA
1 AAAAAT-ATAAAATA
50104755 CATACGGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
26 5 0.15
27 22 0.65
28 2 0.06
29 5 0.15
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (28 bp):
AAAAATATAAAATAGTTCAGAAAAACTA
Found at i:50119909 original size:2 final size:2
Alignment explanation
Indices: 50119902--50119931 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
50119892 CATATTAAGA
*
50119902 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50119932 CTCAAAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:50120302 original size:3 final size:3
Alignment explanation
Indices: 50120294--50120321 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
50120284 ACTTCATAAG
50120294 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
50120322 GATGCTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:50126750 original size:16 final size:16
Alignment explanation
Indices: 50126729--50126759 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50126719 CGCGTCCTAA
50126729 CCCAGGCTCGACCCGG
1 CCCAGGCTCGACCCGG
*
50126745 CCCAGGCTCGGCCCG
1 CCCAGGCTCGACCCG
50126760 ACCCGAAATA
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:0.10, C:0.52, G:0.32, T:0.06
Consensus pattern (16 bp):
CCCAGGCTCGACCCGG
Found at i:50126924 original size:29 final size:28
Alignment explanation
Indices: 50126861--50126914 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
50126851 ACCAAAAACT
50126861 TATTTTAAAAATAAAAAATAAAAAAAAG
1 TATTTTAAAAATAAAAAATAAAAAAAAG
50126889 TATTTTAAAAATAAAAAATAAAAAAA
1 TATTTTAAAAATAAAAAATAAAAAAA
50126915 TATATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (28 bp):
TATTTTAAAAATAAAAAATAAAAAAAAG
Found at i:50145807 original size:22 final size:22
Alignment explanation
Indices: 50145782--50145834 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
50145772 TAATTAAAAT
* * *
50145782 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAAGTAATTGTTAA
*
50145804 TAAAATTAAAAGTAATTGTTAT
1 TAAAATTAAAAGTAATTGTTAA
50145826 TAAAATTAA
1 TAAAATTAA
50145835 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAAGTAATTGTTAA
Found at i:50145827 original size:16 final size:16
Alignment explanation
Indices: 50145808--50145849 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
50145798 TTTTAATAAA
50145808 ATTAAAAGTAATTGTT
1 ATTAAAAGTAATTGTT
*
50145824 ATTAAAATTAATTGTT
1 ATTAAAAGTAATTGTT
*
50145840 AGTAAAAGTA
1 ATTAAAAGTA
50145850 TCAAATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (16 bp):
ATTAAAAGTAATTGTT
Found at i:50145909 original size:66 final size:66
Alignment explanation
Indices: 50145838--50146046 Score: 364
Period size: 66 Copynumber: 3.1 Consensus size: 66
50145828 AAATTAATTG
*
50145838 TTAGTAAAAGTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTG
1 TTAGTAAAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTG
50145903 A
66 A
*
50145904 TTAGTAAATTTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTG
1 TTAGTAAAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTG
50145969 A
66 A
* *
50145970 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
50146035 TGA
64 TGA
50146038 TTAGTAAAA
1 TTAGTAAAA
50146047 CAAACTTGAT
Statistics
Matches: 137, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
66 91 0.66
68 46 0.34
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.45
Consensus pattern (66 bp):
TTAGTAAAATTATCAAATTATTAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTG
A
Found at i:50146000 original size:9 final size:9
Alignment explanation
Indices: 50145988--50146015 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
50145978 TTTATCAAAT
50145988 TATTAATTG
1 TATTAATTG
50145997 TATTAATTG
1 TATTAATTG
50146006 TATTAATTG
1 TATTAATTG
50146015 T
1 T
50146016 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:50146159 original size:23 final size:24
Alignment explanation
Indices: 50146112--50146157 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
50146102 AAATAAACTT
50146112 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
50146136 AAAATAAAAAA-TATATATATTT
1 AAAATAAAAAACTAT-TATATTT
50146158 AATATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:50147875 original size:13 final size:14
Alignment explanation
Indices: 50147857--50147889 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
50147847 TTGTTCGCTT
50147857 TTTTTCTT-TTCTC
1 TTTTTCTTCTTCTC
*
50147870 TTTTTCTTCTTCTT
1 TTTTTCTTCTTCTC
50147884 TTTTTC
1 TTTTTC
50147890 CCACTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTCTTCTTCTC
Found at i:50149863 original size:29 final size:30
Alignment explanation
Indices: 50149804--50149861 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
50149794 TCCGAGCCTT
*
50149804 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
50149834 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
50149862 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:50150092 original size:13 final size:13
Alignment explanation
Indices: 50150074--50150104 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
50150064 TTCCAGCAAC
50150074 TATGAATTTATTT
1 TATGAATTTATTT
50150087 TATGAATTTATTT
1 TATGAATTTATTT
*
50150100 GATGA
1 TATGA
50150105 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:50150274 original size:50 final size:50
Alignment explanation
Indices: 50150199--50150351 Score: 288
Period size: 50 Copynumber: 3.1 Consensus size: 50
50150189 ATTTGGGTAA
50150199 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
50150249 AGAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
50150299 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
50150349 AGA
1 AGA
50150352 TTTTTTCTTA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 100 1.00
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:50150485 original size:22 final size:22
Alignment explanation
Indices: 50150423--50150508 Score: 118
Period size: 22 Copynumber: 3.9 Consensus size: 22
50150413 ATTGTTCAAA
* **
50150423 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
50150445 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
50150467 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * *
50150489 CATGAGGGTTTAGTTCGTTA
1 CATGAGAGCTTAGTACGTTA
50150509 AACAAAGTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:50157673 original size:13 final size:13
Alignment explanation
Indices: 50157655--50157685 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
50157645 TTCCAGCAAC
50157655 TATGAATTTATTT
1 TATGAATTTATTT
50157668 TATGAATTTATTT
1 TATGAATTTATTT
*
50157681 GATGA
1 TATGA
50157686 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:50157843 original size:18 final size:18
Alignment explanation
Indices: 50157820--50157857 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
50157810 ATGGCATTGG
*
50157820 CACCGAGATGAGAGGTCC
1 CACCGAGACGAGAGGTCC
50157838 CACCGAGACGAGAGGTCC
1 CACCGAGACGAGAGGTCC
50157856 CA
1 CA
50157858 TGTAAGACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.32, G:0.32, T:0.08
Consensus pattern (18 bp):
CACCGAGACGAGAGGTCC
Found at i:50157889 original size:68 final size:68
Alignment explanation
Indices: 50157780--50157906 Score: 245
Period size: 68 Copynumber: 1.9 Consensus size: 68
50157770 ATTTGGGTAA
50157780 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCACCGAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCACCGAG
50157845 ACG
66 ACG
*
50157848 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGATGTCCC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCC
50157907 CTATAAGACC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.18
Consensus pattern (68 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCACCGAG
ACG
Found at i:50157914 original size:50 final size:50
Alignment explanation
Indices: 50157838--50157990 Score: 198
Period size: 50 Copynumber: 3.0 Consensus size: 50
50157828 TGAGAGGTCC
* *
50157838 CACCGAGACGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
1 CACCGAGATGAGACGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
* * * * *
50157888 CACCGAGATGAGATGTCCCCTATAAGACCGTGTCTGGGACATGGCATGGG
1 CACCGAGATGAGACGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
* * * *
50157938 CACCAACATGAGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGG
1 CACCGAGATGAG-ACGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
50157989 CA
1 CA
50157991 TGTTATTATC
Statistics
Matches: 87, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 54 0.62
51 33 0.38
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.20
Consensus pattern (50 bp):
CACCGAGATGAGACGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
Found at i:50162799 original size:24 final size:24
Alignment explanation
Indices: 50162766--50162816 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
50162756 TTCTAGAAGT
* * *
50162766 TTTAGTATTTATGAGTATAATATA
1 TTTAGCATTTATAAGCATAATATA
50162790 TTTAGCATTTATAAGCATAATATA
1 TTTAGCATTTATAAGCATAATATA
50162814 TTT
1 TTT
50162817 GACTTTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTAGCATTTATAAGCATAATATA
Found at i:50167254 original size:24 final size:24
Alignment explanation
Indices: 50167189--50167242 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
50167179 TATTTCTAGA
** * *
50167189 ATATTTAGTATTTATGAGTATAAT
1 ATATTTAACATTTATTAGCATAAT
50167213 ATATTTAACATTTATTAGCATAAT
1 ATATTTAACATTTATTAGCATAAT
50167237 ATATTT
1 ATATTT
50167243 GACTTTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (24 bp):
ATATTTAACATTTATTAGCATAAT
Found at i:50169125 original size:20 final size:20
Alignment explanation
Indices: 50169100--50169141 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
50169090 TTATAATTAA
50169100 AAGTTAAAACCCTAAAATGT
1 AAGTTAAAACCCTAAAATGT
*
50169120 AAGTTAAACCCCTAAAATGT
1 AAGTTAAAACCCTAAAATGT
50169140 AA
1 AA
50169142 AACCTAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.24
Consensus pattern (20 bp):
AAGTTAAAACCCTAAAATGT
Found at i:50169178 original size:21 final size:21
Alignment explanation
Indices: 50169154--50169206 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
50169144 CCTAAACTAG
50169154 AGACCCTAAATCTTAAACCCA
1 AGACCCTAAATCTTAAACCCA
* *
50169175 AGACTCTAAACCCTTAAACCCA
1 AGACCCTAAA-TCTTAAACCCA
50169197 A-ACCCTAAAT
1 AGACCCTAAAT
50169207 ATGAGAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.43, C:0.34, G:0.04, T:0.19
Consensus pattern (21 bp):
AGACCCTAAATCTTAAACCCA
Found at i:50169443 original size:18 final size:18
Alignment explanation
Indices: 50169420--50169455 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
50169410 CCTTAGGTGA
50169420 TTTCTTGGGTTCAAATGC
1 TTTCTTGGGTTCAAATGC
50169438 TTTCTTGGGTTCAAATGC
1 TTTCTTGGGTTCAAATGC
50169456 GCCTAAGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (18 bp):
TTTCTTGGGTTCAAATGC
Found at i:50172263 original size:27 final size:26
Alignment explanation
Indices: 50172233--50172285 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
50172223 ATTTAATATT
* *
50172233 TTAATTTAATACTTAAAAAATATTAAA
1 TTAATATAATA-TTAAAAAATAATAAA
*
50172260 TTAATATAATATTAAATAATAATAAA
1 TTAATATAATATTAAAAAATAATAAA
50172286 AGCAAGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
TTAATATAATATTAAAAAATAATAAA
Found at i:50172284 original size:16 final size:16
Alignment explanation
Indices: 50172251--50172280 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50172241 ATACTTAAAA
50172251 AATATTAAATTAATAT
1 AATATTAAATTAATAT
50172267 AATATTAAA-TAATA
1 AATATTAAATTAATA
50172281 ATAAAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATTAAATTAATAT
Found at i:50180494 original size:46 final size:46
Alignment explanation
Indices: 50180394--50180555 Score: 258
Period size: 46 Copynumber: 3.6 Consensus size: 46
50180384 TACGTATGAT
* * *
50180394 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAG-TTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
50180437 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
50180483 CACTTATCACTTTGTCACATGATCAAATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
50180529 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
50180556 AGCACTTAAA
Statistics
Matches: 109, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
43 10 0.09
44 5 0.05
45 18 0.17
46 76 0.70
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:50186980 original size:104 final size:104
Alignment explanation
Indices: 50186789--50186994 Score: 335
Period size: 104 Copynumber: 2.0 Consensus size: 104
50186779 TGTATATAAA
** *
50186789 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
*
50186854 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
50186893 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATC
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATC
50186957 TTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCC
64 TTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCC
50186995 GATTTCATTG
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
104 53 0.56
105 41 0.43
106 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.32
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:50187021 original size:77 final size:77
Alignment explanation
Indices: 50186894--50187071 Score: 347
Period size: 77 Copynumber: 2.3 Consensus size: 77
50186884 ATTCCCCCGA
*
50186894 GGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 GGGGTTGCTATGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
50186959 TGAAATGAAAAG
66 TGAAATGAAAAG
50186971 GGGGTTGCTATGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 GGGGTTGCTATGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
50187036 TGAAATGAAAAG
66 TGAAATGAAAAG
50187048 GGGGTTGCTATGTGCTGATTCCCC
1 GGGGTTGCTATGTGCTGATTCCCC
50187072 CGAGGGGTTG
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 100 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (77 bp):
GGGGTTGCTATGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAG
Found at i:50187094 original size:181 final size:179
Alignment explanation
Indices: 50186786--50187132 Score: 581
Period size: 181 Copynumber: 1.9 Consensus size: 179
50186776 TGTTGTATAT
* *
50186786 AAAAGGGGTTGCTGTGTGCTGATTCCCCGATTCATGGGTGGTGCTATGTGCGTGATCCACCATAT
1 AAAAGGGGTTGCTATGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATAT
*
50186851 CTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCC
66 CTTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCC
* *
50186916 CCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTTTGAAATG
131 CCGA-TTCAGTGGTGGTGCTAAGTGCGAGATCCACCATATCTTTGAAATG
*
50186966 AAAAGGGGGTTGCTATGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCA
1 AAAA-GGGGTTGCTATGTGCTGATTCCCCGA-TTCATGGGTGGTGCTAAGTGCG-TGATCCACCA
50187030 TATCTTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGAT
63 TATCTTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGAT
*
50187094 TCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
128 TCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
50187133 ATAACGGTTA
Statistics
Matches: 157, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
180 33 0.21
181 82 0.52
182 41 0.26
183 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.30
Consensus pattern (179 bp):
AAAAGGGGTTGCTATGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATAT
CTTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCC
CCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCATATCTTTGAAATG
Found at i:50189180 original size:25 final size:25
Alignment explanation
Indices: 50189152--50189320 Score: 137
Period size: 25 Copynumber: 6.8 Consensus size: 25
50189142 TAGCTCGCAA
* * *
50189152 GAGCGTCCCGTTATTTAGCTCTTAT
1 GAGCTTCCCGTTATTTGGCTCTCAT
* * * *
50189177 GAGCATCCCATTATATGGCTCTCAC
1 GAGCTTCCCGTTATTTGGCTCTCAT
*
50189202 GAGCTTCCCGATATTTGGCTCTCAT
1 GAGCTTCCCGTTATTTGGCTCTCAT
* *
50189227 GAGCTTCCCGATTA-ATGGCTCTCTT
1 GAGCTTCCCG-TTATTTGGCTCTCAT
* *
50189252 AAGCTTCCCGTT-TATGGCTCGT-AT
1 GAGCTTCCCGTTATTTGGCTC-TCAT
* * * *
50189276 GAGCTTTCCGATATTTGGCTCGCAA
1 GAGCTTCCCGTTATTTGGCTCTCAT
* *
50189301 GAGCTTCCCTTTATATGGCT
1 GAGCTTCCCGTTATTTGGCT
50189321 TGGAAGAGCT
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
24 19 0.17
25 92 0.81
26 2 0.02
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.36
Consensus pattern (25 bp):
GAGCTTCCCGTTATTTGGCTCTCAT
Found at i:50189245 original size:50 final size:49
Alignment explanation
Indices: 50189144--50189309 Score: 153
Period size: 50 Copynumber: 3.3 Consensus size: 49
50189134 ACACACCATA
* * * *
50189144 GCTCGCAAGAGCGTCCCGTTATTTAGCTCTTATGAGCATCCC-ATTATATG
1 GCTCTCAAGAGCTTCCCG-TATTTGGCTC-TATGAGCTTCCCGATTATATG
*
50189194 GCTCTCACGAGCTTCCCGATATTTGGCTCTCATGAGCTTCCCGATTA-ATG
1 GCTCTCAAGAGCTTCCCG-TATTTGGCTCT-ATGAGCTTCCCGATTATATG
* * *
50189244 GCTCTCTTA-AGCTTCCCGT-TTATGGCTCGTATGAGCTTTCCGA-TATTTG
1 GCTCTC-AAGAGCTTCCCGTATT-TGGCTC-TATGAGCTTCCCGATTATATG
*
50189293 GCTCGCAAGAGCTTCCC
1 GCTCTCAAGAGCTTCCC
50189310 TTTATATGGC
Statistics
Matches: 97, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
48 5 0.05
49 35 0.36
50 53 0.55
51 4 0.04
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.33
Consensus pattern (49 bp):
GCTCTCAAGAGCTTCCCGTATTTGGCTCTATGAGCTTCCCGATTATATG
Found at i:50189319 original size:74 final size:75
Alignment explanation
Indices: 50189144--50189320 Score: 191
Period size: 74 Copynumber: 2.4 Consensus size: 75
50189134 ACACACCATA
* * * * *
50189144 GCTCGCAAGAGCGTCCCGTTATTTAGCTCTTATGAGCATCCCATTATATGGCTCTCACGAGCTTC
1 GCTCGCAAGAGCTTCCCATTATATGGCTCTTATAAGCATCCCATTATATGGCTCTCACGAGCTTC
50189209 CCGATATTTG
66 CCGATATTTG
* * * * *
50189219 GCTCTCATGAGCTTCCCGATTA-ATGGCTCTCT-TAAGCTTCCCGTT-TATGGCTCGT-ATGAGC
1 GCTCGCAAGAGCTTCCC-ATTATATGGCTCT-TATAAGCATCCCATTATATGGCTC-TCACGAGC
*
50189280 TTTCCGATATTTG
63 TTCCCGATATTTG
*
50189293 GCTCGCAAGAGCTTCCCTTTATATGGCT
1 GCTCGCAAGAGCTTCCCATTATATGGCT
50189321 TGGAAGAGCT
Statistics
Matches: 84, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
73 3 0.04
74 46 0.55
75 31 0.37
76 4 0.05
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.34
Consensus pattern (75 bp):
GCTCGCAAGAGCTTCCCATTATATGGCTCTTATAAGCATCCCATTATATGGCTCTCACGAGCTTC
CCGATATTTG
Found at i:50190650 original size:18 final size:17
Alignment explanation
Indices: 50190610--50190783 Score: 145
Period size: 17 Copynumber: 9.8 Consensus size: 17
50190600 AAATTTTTTG
50190610 TTTTGAAA-ACGCAAGAA-
1 TTTTGAAACACG-AA-AAT
*
50190627 TTTTGAAACACAATAAAT
1 TTTTGAAACACGA-AAAT
*
50190645 TTTTGAGAACACGGAAAT
1 TTTTGA-AACACGAAAAT
*
50190663 TTTTGAAATACGAAAAT
1 TTTTGAAACACGAAAAT
*
50190680 TTTAGAAACACGAAAAT
1 TTTTGAAACACGAAAAT
* *
50190697 TTCTAAAACACGAAAAT
1 TTTTGAAACACGAAAAT
**
50190714 TTTTGAAAACACGAGATTT
1 TTTTG-AAACACGA-AAAT
* *
50190733 TTTTTAAACACGAAATTTT
1 TTTTGAAACACGAAA--AT
* *
50190752 TTTTAAAAACACGGAAAT
1 TTTT-GAAACACGAAAAT
50190770 TTTTGAAACACGAA
1 TTTTGAAACACGAA
50190784 GTTTTTAAAA
Statistics
Matches: 127, Mismatches: 21, Indels: 18
0.77 0.13 0.11
Matches are distributed among these distances:
17 61 0.48
18 40 0.31
19 17 0.13
20 9 0.07
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.31
Consensus pattern (17 bp):
TTTTGAAACACGAAAAT
Found at i:50190732 original size:17 final size:17
Alignment explanation
Indices: 50190627--50190794 Score: 112
Period size: 18 Copynumber: 9.6 Consensus size: 17
50190617 AACGCAAGAA
**
50190627 TTTTGAAACACAATAAAT
1 TTTTGAAA-ACACGAAAT
*
50190645 TTTTGAGAACACGGAAAT
1 TTTTGAAAACAC-GAAAT
* *
50190663 TTTTG-AAATACGAAAA
1 TTTTGAAAACACGAAAT
50190679 TTTT-AGAAACACGAAAAT
1 TTTTGA-AAACACG-AAAT
*
50190697 TTCT-AAAACACGAAAAT
1 TTTTGAAAACACG-AAAT
*
50190714 TTTTGAAAACACGAGATT
1 TTTTGAAAACACGA-AAT
**
50190732 TTTTTTAAACACGAAATTTT
1 TTTTGAAAACACGAAA---T
*
50190752 TTTTAAAAACACGGAAAT
1 TTTTGAAAACAC-GAAAT
*
50190770 TTTTG-AAACACGAAGT
1 TTTTGAAAACACGAAAT
50190786 TTTT-AAAAC
1 TTTTGAAAAC
50190795 GTACAGTATT
Statistics
Matches: 121, Mismatches: 18, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
16 20 0.17
17 36 0.30
18 50 0.41
20 11 0.09
21 4 0.03
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (17 bp):
TTTTGAAAACACGAAAT
Found at i:50191609 original size:28 final size:26
Alignment explanation
Indices: 50191578--50191630 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
50191568 TATTTTTTTA
* *
50191578 TTTTTTCTTTCTTTTTCTCTCATTTTCC
1 TTTTTCCTTTCTTCTTCT-TC-TTTTCC
50191606 TTTTTCCTTTCTTCTTCTTCTTTTC
1 TTTTTCCTTTCTTCTTCTTCTTTTC
50191631 TTAACTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 2 0.09
28 16 0.70
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTTTCCTTTCTTCTTCTTCTTTTCC
Found at i:50192495 original size:30 final size:30
Alignment explanation
Indices: 50192363--50192496 Score: 96
Period size: 30 Copynumber: 4.5 Consensus size: 30
50192353 AACATGGGGC
* **
50192363 CAAATTATAATTTTTAG-AAATTTAAGGGGT
1 CAAAATATAATTTAAAGAAAATTTAA-GGGT
** * *
50192393 CAAAATGA-AATTTTGAGAAAGTTAAAGGGT
1 CAAAAT-ATAATTTAAAGAAAATTTAAGGGT
* *
50192423 CAAAATATAA-ATATAAGAAAGTTT-AGGGT
1 CAAAATATAATTTA-AAGAAAATTTAAGGGT
*
50192452 CCAAAATACAATTTAAAGAAAATTTAAGGGT
1 -CAAAATATAATTTAAAGAAAATTTAAGGGT
* *
50192483 CTAAATGTAATTTA
1 CAAAATATAATTTA
50192497 TATTTTTTGT
Statistics
Matches: 83, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
29 7 0.08
30 62 0.75
31 14 0.17
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.31
Consensus pattern (30 bp):
CAAAATATAATTTAAAGAAAATTTAAGGGT
Found at i:50200486 original size:24 final size:24
Alignment explanation
Indices: 50200448--50200496 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
50200438 TGCCTTTGTA
**
50200448 AGTAGTTGTAGATATGGGAATTCT
1 AGTAGTTGTAGATATGAAAATTCT
50200472 AGTAGTTGT-GTATATGAAAATTCT
1 AGTAGTTGTAG-ATATGAAAATTCT
50200496 A
1 A
50200497 CTGTTCAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (24 bp):
AGTAGTTGTAGATATGAAAATTCT
Found at i:50203826 original size:58 final size:58
Alignment explanation
Indices: 50203736--50203852 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
50203726 TATAGAACAC
*
50203736 TGTTATGAAGTTTATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
1 TGTTATGAAGTTCATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
50203794 TGTTATGAAGTTCATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
1 TGTTATGAAGTTCATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
50203852 T
1 T
50203853 TAATGAATGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (58 bp):
TGTTATGAAGTTCATTTTAAAGATGCATCTAGGTTTTGTATTACTTTTCAATGCTTCA
Found at i:50208283 original size:28 final size:28
Alignment explanation
Indices: 50208235--50208297 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
50208225 TAATATTAGG
50208235 CTTTATTTATTATTATTATTTGAAAGTTA
1 CTTT-TTTATTATTATTATTTGAAAGTTA
*
50208264 CTTTTTTATT-TTTTTCATTTGAAAGTTA
1 CTTTTTTATTATTATT-ATTTGAAAGTTA
50208292 -TTTTTT
1 CTTTTTT
50208298 GATAACATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 10 0.31
28 18 0.56
29 4 0.12
ACGTcount: A:0.24, C:0.05, G:0.06, T:0.65
Consensus pattern (28 bp):
CTTTTTTATTATTATTATTTGAAAGTTA
Found at i:50217005 original size:16 final size:15
Alignment explanation
Indices: 50216984--50217018 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
50216974 ATATATATTT
*
50216984 AAAAATTTTAAAAATA
1 AAAAATTGTAAAAA-A
50217000 AAAAATTGTAAAAAA
1 AAAAATTGTAAAAAA
50217015 AAAA
1 AAAA
50217019 CTATACGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAAATTGTAAAAAA
Found at i:50217652 original size:241 final size:239
Alignment explanation
Indices: 50217233--50217705 Score: 684
Period size: 241 Copynumber: 2.0 Consensus size: 239
50217223 TTTCAACAAT
* * *
50217233 TTTTTTCATGTCATTGATGCATAATTTTGGTAATTTTTTTACCCTGAACTCCGAACATAAAACCA
1 TTTTTTCATGTCATTGATACATAATTTTGGTAATTTTTTTACCCTGAACTCCAAACACAAAACCA
* * *
50217298 TGATCCTTGAACCCTAAATCTTGACCTTAGACCCTAAATTCAAACCTTAAATCTTGAATCTCAAA
66 TGATCCTTGAACCCTAAATCTTGACCTTAGACCCCAAACTCAAACCTTAAATCTTAAATCTCAAA
* * * *
50217363 CCCTAAACTCATACCTAAACTTGAATCCTAGACCTTGAACCCTAAACTTGAGATTTGGGTTTGGT
131 CCCTAAACTCAGACCTAAACTCGAATCCTAAACCTTGAACCCTAAACTTGAGATTTGGGTTTGGC
50217428 ATTTTGGGTCTAAGGTTTGAGTTC-GAGGTTCAAGATTTTGGTAA
196 ATTTTGGGTCTAAGGTTTGAGTTCGGA-GTTCAAGATTTTGGTAA
*
50217472 TTTTTTCATGTCATTGATACATAATTTTGGTAACTTTTTTTTACCTTGAACTCCAAACACAAAAC
1 TTTTTTCATGTCATTGATACATAATTTTGGTAA--TTTTTTTACCCTGAACTCCAAACACAAAAC
* * * * *
50217537 CATGATCCTT-ATATCCTGAGTCTTGACCTTATACCCCAAACTCAAA-CTTGAA-CATTAAATCT
64 CATGATCCTTGA-ACCCTAAATCTTGACCTTAGACCCCAAACTCAAACCTTAAATC-TTAAATCT
* *
50217599 CAAACCCTAAACTTCAGACCTAAACTCGAATTCTAAATCTTGAACCCTAAACTTGAGATTTGGGT
127 CAAACCCTAAAC-TCAGACCTAAACTCGAATCCTAAACCTTGAACCCTAAACTTGAGATTTGGGT
* *
50217664 TTGGCATTTTGGGTTTAGGGTTTGAGTTCGGAGTTCAAGATT
191 TTGGCATTTTGGGTCTAAGGTTTGAGTTCGGAGTTCAAGATT
50217706 CAGGGCTCGA
Statistics
Matches: 208, Mismatches: 20, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
239 33 0.16
240 25 0.12
241 148 0.71
242 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (239 bp):
TTTTTTCATGTCATTGATACATAATTTTGGTAATTTTTTTACCCTGAACTCCAAACACAAAACCA
TGATCCTTGAACCCTAAATCTTGACCTTAGACCCCAAACTCAAACCTTAAATCTTAAATCTCAAA
CCCTAAACTCAGACCTAAACTCGAATCCTAAACCTTGAACCCTAAACTTGAGATTTGGGTTTGGC
ATTTTGGGTCTAAGGTTTGAGTTCGGAGTTCAAGATTTTGGTAA
Found at i:50225847 original size:2 final size:2
Alignment explanation
Indices: 50225840--50225870 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
50225830 ATAATGTGTA
50225840 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
50225871 TTTGATTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50228493 original size:24 final size:24
Alignment explanation
Indices: 50228466--50228522 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
50228456 CCTGTCTAGG
50228466 TTATTTATTTTTATGTATTAATTT
1 TTATTTATTTTTATGTATTAATTT
* *
50228490 TTATTTCA-TTTTATTTATTTATTT
1 TTATTT-ATTTTTATGTATTAATTT
*
50228514 AT-TTTATTT
1 TTATTTATTT
50228523 ACTCATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 1 0.04
23 5 0.18
24 21 0.75
25 1 0.04
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (24 bp):
TTATTTATTTTTATGTATTAATTT
Found at i:50228519 original size:9 final size:9
Alignment explanation
Indices: 50228488--50228523 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
50228478 ATGTATTAAT
50228488 TTTTATTTCA
1 TTTTATTT-A
50228498 TTTTATTTA
1 TTTTATTTA
50228507 -TTTATTTA
1 TTTTATTTA
50228515 TTTTATTTA
1 TTTTATTTA
50228524 CTCATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.32
9 9 0.36
10 8 0.32
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:50228604 original size:16 final size:18
Alignment explanation
Indices: 50228574--50228612 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
50228564 ATTTATTGTG
*
50228574 CATTTTTATTTTTTATTT
1 CATTTTTATTCTTTATTT
50228592 -ATTTTTA-TCTTTATTT
1 CATTTTTATTCTTTATTT
50228608 CATTT
1 CATTT
50228613 ACCTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (18 bp):
CATTTTTATTCTTTATTT
Found at i:50243790 original size:30 final size:30
Alignment explanation
Indices: 50243750--50243843 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 30
50243740 AAGTTCTTAA
50243750 AGAAAGAGATCATATGTCGGTATGGCATGCC
1 AGAAA-AGATCATATGTCGGTATGGCATGCC
*
50243781 AGAAAAGATCATA--TCGG-A---CA---A
1 AGAAAAGATCATATGTCGGTATGGCATGCC
*
50243802 AGAAGGAGATCATATGTCGGTATGGCATGCC
1 AGAA-AAGATCATATGTCGGTATGGCATGCC
50243833 AGAAAAGATCA
1 AGAAAAGATCA
50243844 ATTTGAACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 21
0.66 0.05 0.28
Matches are distributed among these distances:
21 4 0.08
22 8 0.16
24 6 0.12
25 1 0.02
27 1 0.02
28 6 0.12
30 14 0.29
31 9 0.18
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (30 bp):
AGAAAAGATCATATGTCGGTATGGCATGCC
Found at i:50245464 original size:44 final size:44
Alignment explanation
Indices: 50245376--50246181 Score: 504
Period size: 44 Copynumber: 17.6 Consensus size: 44
50245366 CATTATGGCG
* * * **
50245376 AATCTTATCAT-CCTGAAGTTGCAGTGGAACAGGTTGAATTTACA
1 AATCTTATC-TCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * *
50245420 AGTCTTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTACAAATTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG------A-TACA
** * * * * * * *
50245471 AATCTTATCTTTCTGAAGTTGTAATGGGGTAGATTGAAGTTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * ** * *
50245515 GATCTTATCTCCCTGAAGTTACAGTGGATTAGATCAGAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA-CA
* * * *
50245560 AATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * * * *
50245604 AACCTTATCTCCTTGAAGTTGTAGTGAAGTA-AGTTAAAAATAAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGAT--ACA
* * * * * *
50245650 AATCTTCTCCCCCTGAAATTGTAGTGGAGTAGATTGAAGACAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT----A-AAGATACA
** **
50245699 AATCTTATCTCTTTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* **
50245743 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * **
50245787 AATTTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAATATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA-CA
** * * * * * * *
50245832 AATCTTATCTATCTGAAATTGTAGTAGAGTAGATTGAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * *
50245876 AATTTTATCTCCCTGAAGTTGCAGTGAAGCAGATTGAAGATA-A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* *
50245919 TGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACC
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * *
50245965 AATCTTATTTCTCTGAAGTTGCAGTGGAACATATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-----A--TACA
* * * *
50246016 AA-CATTATCACCCTGAAGTTGCAGTGGAGTAGATTAAATATACG
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * * * *
50246060 AATTTTATTTCCCTGAAGTTGTAGTGAAACAGATTAAGGTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T----TA-AAGATACA
* * * * * *
50246110 AATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGATGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
*
50246154 AATCTTATTTCCCTGAAGTTGCAGTGGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGA
50246182 ACGGATCTTA
Statistics
Matches: 585, Mismatches: 140, Indels: 74
0.73 0.18 0.09
Matches are distributed among these distances:
43 3 0.01
44 305 0.52
45 110 0.19
46 30 0.05
47 1 0.00
49 35 0.06
50 32 0.05
51 69 0.12
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
Found at i:50245611 original size:89 final size:88
Alignment explanation
Indices: 50245468--50246181 Score: 444
Period size: 89 Copynumber: 7.9 Consensus size: 88
50245458 GCTACAAATT
** * * * * * * *
50245468 ACAAATCTTATCTTTCTGAAGTTGTAATGGGGTAGATTGAAGTTATAGATCTTATCTCCCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTCCCTGAAG
* **
50245533 TTACAGTGGATTAGATCAGAGATA
66 TTGCAGTGGAGCAGAT-AGAGATA
* * * * * * *
50245557 GCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCTTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTCCCTGAAG
* * * * * *
50245622 TTGTAGTGAAGTAAGTTAAAAATAA
66 TTGCAGTGGAG-CAGATAGAGAT-A
* * * * **
50245647 ACAAATCTTCTCCCCCTGAAATTGTAGTGGAGTAGATTGAAGACAAGCTACAAATCTTATCTCTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT----A-AAGCTACAAATCTTATCTCCC
* **
50245712 TGAAGTTGCAGTGGAGCAGATTAAAG-CC
61 TGAAGTTGCAGTGGAGCAGA-TAGAGATA
* *
50245740 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCACAAATTTTATCTCCCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTCCCTGAAG
*
50245805 TTGCAGTGGAGCAGATTGA-ATA
66 TTGCAGTGGAGCAGATAGAGATA
** ** * * * * * *
50245827 TAGTGAATCTTATCTATCTGAAATTGTAGTAGAGTAGATTGAAGCTATAAATTTTATCTCCCTGA
1 -A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTCCCTGA
* *
50245892 AGTTGCAGTGAAGCAGATTGAAGATA
64 AGTTGCAGTGGAGCAGATAG-AGATA
** * * * * * *
50245918 ATGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACCAATCTTATTTCTCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTCCCTGAAG
* * * *
50245983 TTGCAGTGGAACATATTAAAGCTACAAGTT
66 TTGCAGTGGAGCAGA-T--AG--A-GA-TA
* ** * * *
50246013 ACAAA-CATTATCACCCTGAAGTTGCAGTGGAGTAGATTAAATATACGAATTTTATTTCCCTGAA
1 ACAAATC-TTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTCCCTGAA
* * * * *
50246077 GTTGTAGTGAAACAGATTAAGGTACAAGTT
65 GTTGCAGTGGAGCAGA-T-A-G-A-GA-TA
* * * * * * * * *
50246107 ACAAATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGATGCGAATCTTATTTCCCTGAAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTCCCTGAAG
50246172 TTGCAGTGGA
66 TTGCAGTGGA
50246182 ACGGATCTTA
Statistics
Matches: 500, Mismatches: 103, Indels: 39
0.78 0.16 0.06
Matches are distributed among these distances:
87 2 0.00
88 38 0.08
89 200 0.40
90 37 0.07
91 3 0.01
92 1 0.00
93 35 0.07
94 77 0.15
95 107 0.21
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (88 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATCTCCCTGAAG
TTGCAGTGGAGCAGATAGAGATA
Found at i:50246263 original size:44 final size:44
Alignment explanation
Indices: 50246198--50246299 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
50246188 CTTATCTCCT
50246198 TGAAGTTGT-AGTGGAGCAGATTGAAGCAACAAACCCTATACCTC
1 TGAAGTT-TCAGTGGAGCAGATTGAAGCAACAAACCCTATACCTC
* * *
50246242 TGAAGTTTCAGTGGAGTAGATTGAAGCAACAAATCTTATACCTC
1 TGAAGTTTCAGTGGAGCAGATTGAAGCAACAAACCCTATACCTC
** *
50246286 AAAAGTTGCAGTGG
1 TGAAGTTTCAGTGG
50246300 GTTAGAATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
43 1 0.02
44 50 0.98
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (44 bp):
TGAAGTTTCAGTGGAGCAGATTGAAGCAACAAACCCTATACCTC
Found at i:50246311 original size:44 final size:44
Alignment explanation
Indices: 50246200--50246311 Score: 127
Period size: 44 Copynumber: 2.5 Consensus size: 44
50246190 TATCTCCTTG
* * * **
50246200 AAGTTGTAGTGGAGCAGATTGAAGCAACAAACCCTATACCTCTG
1 AAGTTGCAGTGGAGTAGAATGAAGCAACAAACCCTATACCTCAA
* * * *
50246244 AAGTTTCAGTGGAGTAGATTGAAGCAACAAATCTTATACCTCAA
1 AAGTTGCAGTGGAGTAGAATGAAGCAACAAACCCTATACCTCAA
50246288 AAGTTGCAGTGG-GTTAGAATGAAG
1 AAGTTGCAGTGGAG-TAGAATGAAG
50246312 TTACTTGAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 1 0.02
44 57 0.98
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (44 bp):
AAGTTGCAGTGGAGTAGAATGAAGCAACAAACCCTATACCTCAA
Found at i:50247750 original size:24 final size:23
Alignment explanation
Indices: 50247723--50247779 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
50247713 CCTGTCTAGG
50247723 TTATTTATTTTTATGTA-TTACTTT
1 TTATTTATTTTTATGTATTTA--TT
*
50247747 TTATTTCA-TTTTATTTATTTATT
1 TTATTT-ATTTTTATGTATTTATT
50247770 TTATTTATTT
1 TTATTTATTT
50247780 ACTAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 1 0.03
23 10 0.34
24 14 0.48
25 4 0.14
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (23 bp):
TTATTTATTTTTATGTATTTATT
Found at i:50247770 original size:38 final size:39
Alignment explanation
Indices: 50247723--50247802 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 39
50247713 CCTGTCTAGG
**
50247723 TTATTTATTTTTATGTA-TTACTTTTTATTT-CATTTTAT
1 TTATTTA-TTTTATGTATTTACTAATTATTTCCATTTTAT
* *
50247761 TTATTTATTTTATTTATTTACTAATTATTTCCTTTTTAT
1 TTATTTATTTTATGTATTTACTAATTATTTCCATTTTAT
50247800 TTA
1 TTA
50247803 AAAATGGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 8 0.22
38 18 0.50
39 10 0.28
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (39 bp):
TTATTTATTTTATGTATTTACTAATTATTTCCATTTTAT
Found at i:50247772 original size:13 final size:13
Alignment explanation
Indices: 50247746--50247780 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
50247736 TGTATTACTT
50247746 TTTATTTCATTTTA
1 TTTATTT-ATTTTA
50247760 TTTATTTATTTTA
1 TTTATTTATTTTA
50247773 TTTATTTA
1 TTTATTTA
50247781 CTAATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:50247911 original size:19 final size:20
Alignment explanation
Indices: 50247871--50247912 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
50247861 TTCATTTGCC
*
50247871 TTTATTATCGTTATTATTTA
1 TTTATTATCGTTATTATATA
*
50247891 TTTATTAT-GTTCTTATATA
1 TTTATTATCGTTATTATATA
50247910 TTT
1 TTT
50247913 TCAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTATTATCGTTATTATATA
Found at i:50255314 original size:19 final size:20
Alignment explanation
Indices: 50255275--50255314 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
50255265 TTCTCTTATA
*
50255275 TAAAATGTATTTCAATGTTT
1 TAAAATGTATTTCAATATTT
*
50255295 TAAAAT-TATTTGAATATTT
1 TAAAATGTATTTCAATATTT
50255314 T
1 T
50255315 GGTAGGTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (20 bp):
TAAAATGTATTTCAATATTT
Found at i:50261246 original size:11 final size:11
Alignment explanation
Indices: 50261230--50261304 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
50261220 TTTAATCATT
50261230 TTAATATTAAA
1 TTAATATTAAA
50261241 TTAATA--AAA
1 TTAATATTAAA
50261250 -TAATATT-AA
1 TTAATATTAAA
50261259 TTAAGTATTAAA
1 TTAA-TATTAAA
50261271 TTAA-ATTTAATA
1 TTAATA-TTAA-A
50261283 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
50261296 ATAATATTA
1 TTAATATTA
50261305 TTTTTATAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 20
0.72 0.01 0.27
Matches are distributed among these distances:
8 5 0.09
9 5 0.09
10 4 0.08
11 19 0.36
12 11 0.21
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:50261259 original size:25 final size:25
Alignment explanation
Indices: 50261230--50261304 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
50261220 TTTAATCATT
* *
50261230 TTAATATTAAATTAATAAAATAATA
1 TTAATATTAAACTATTAAAATAATA
* *
50261255 TT-A-ATT-AAGTATTAAATTAA-A
1 TTAATATTAAACTATTAAAATAATA
50261276 TTTAATATTAAACTATTAAAATAATA
1 -TTAATATTAAACTATTAAAATAATA
50261302 TTA
1 TTA
50261305 TTTTTATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
21 1 0.03
22 13 0.32
23 4 0.10
24 4 0.10
25 17 0.43
26 1 0.03
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (25 bp):
TTAATATTAAACTATTAAAATAATA
Found at i:50269245 original size:11 final size:11
Alignment explanation
Indices: 50269223--50269256 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
50269213 AATGCTAACT
*
50269223 ACAAAAGAAAC
1 ACAAATGAAAC
*
50269234 ATAAATGAAAC
1 ACAAATGAAAC
50269245 ACAAATGAAAC
1 ACAAATGAAAC
50269256 A
1 A
50269257 AATAAACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.68, C:0.15, G:0.09, T:0.09
Consensus pattern (11 bp):
ACAAATGAAAC
Found at i:50270684 original size:41 final size:39
Alignment explanation
Indices: 50270569--50270702 Score: 128
Period size: 41 Copynumber: 3.4 Consensus size: 39
50270559 AACAGTTTGG
* * *
50270569 CACCCAGTGCCGCATCGAATAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAATAA-TCCAAGTAGTAAATTGA
* ** ** * *
50270609 CACTCAGTATCTCATCGGCTAAACCAA--AGTAAATTGG
1 CACCCAGTGCCTCATCGAATAATCCAAGTAGTAAATTGA
50270646 CACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCC-AAGTAGTAAATTGA
*
50270687 CACCCAGTGTCTCATC
1 CACCCAGTGCCTCATC
50270703 AACTCGAAGT
Statistics
Matches: 72, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
37 22 0.31
38 5 0.07
39 5 0.07
40 16 0.22
41 24 0.33
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGAATAATCCAAGTAGTAAATTGA
Found at i:50270882 original size:15 final size:15
Alignment explanation
Indices: 50270835--50270884 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
50270825 CAATTCAAAT
*
50270835 AATCAATATATATTC
1 AATCAATATAAATTC
50270850 AAT-ATATATACCAATTC
1 AATCA-ATATA--AATTC
50270867 AATCAATATAAATTC
1 AATCAATATAAATTC
50270882 AAT
1 AAT
50270885 AAATTTATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
17 12 0.40
18 1 0.03
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (15 bp):
AATCAATATAAATTC
Found at i:50271666 original size:5 final size:5
Alignment explanation
Indices: 50271658--50271715 Score: 109
Period size: 5 Copynumber: 11.8 Consensus size: 5
50271648 TTTGTTTTGT
50271658 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
50271708 TAT-A TATA
1 TATAA TATA
50271716 CTTAATACTT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.08
5 48 0.92
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:50271728 original size:22 final size:24
Alignment explanation
Indices: 50271703--50271746 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
50271693 TATAATATAA
50271703 TATAATATATA-T-ACTTAATACT
1 TATAATATATATTAACTTAATACT
50271725 TATAATATATATTAACTTAATA
1 TATAATATATATTAACTTAATA
50271747 TAGTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
23 1 0.05
24 8 0.40
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (24 bp):
TATAATATATATTAACTTAATACT
Found at i:50271748 original size:20 final size:20
Alignment explanation
Indices: 50271660--50271764 Score: 87
Period size: 20 Copynumber: 5.2 Consensus size: 20
50271650 TGTTTTGTTA
50271660 TAATATAATATA-ATATAA-T
1 TAATATAATATATAT-TAACT
50271679 ATAATATAATATA-ATATAA-T
1 -TAATATAATATATAT-TAACT
50271699 ATAATATAATATATA-T-ACT
1 -TAATATAATATATATTAACT
50271718 TAATACTTATAATATATATTAACT
1 T-A-A--TATAATATATATTAACT
*
50271742 TAATATAGTATATATTAACT
1 TAATATAATATATATTAACT
50271762 TAA
1 TAA
50271765 AGTTTTATGA
Statistics
Matches: 76, Mismatches: 1, Indels: 16
0.82 0.01 0.17
Matches are distributed among these distances:
18 2 0.03
19 3 0.04
20 52 0.68
21 1 0.01
22 12 0.16
23 2 0.03
24 4 0.05
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (20 bp):
TAATATAATATATATTAACT
Found at i:50278027 original size:25 final size:25
Alignment explanation
Indices: 50277999--50278048 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
50277989 ACCAAGCATG
50277999 CTATAATGCCCTCTAATTTGTTATT
1 CTATAATGCCCTCTAATTTGTTATT
50278024 CTATAATGCCCTCTAATTTGTTATT
1 CTATAATGCCCTCTAATTTGTTATT
50278049 GAATACTTAT
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:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (25 bp):
CTATAATGCCCTCTAATTTGTTATT
Found at i:50278888 original size:18 final size:19
Alignment explanation
Indices: 50278846--50278890 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
50278836 TCAAGATCTT
50278846 AAATTAATGTGGTCCAAAG
1 AAATTAATGTGGTCCAAAG
50278865 AAATTAATGTGGTCCAAA-
1 AAATTAATGTGGTCCAAAG
50278883 AAATTAAT
1 AAATTAAT
50278891 TAGTACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.29
Consensus pattern (19 bp):
AAATTAATGTGGTCCAAAG
Found at i:50282313 original size:11 final size:11
Alignment explanation
Indices: 50282297--50282348 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
50282287 TTATATCTTT
50282297 AATAATAATAC
1 AATAATAATAC
50282308 AATAATAATAC
1 AATAATAATAC
* **
50282319 TTATAAT-ATTT
1 -AATAATAATAC
50282330 AATAATAATAC
1 AATAATAATAC
50282341 AATAATAA
1 AATAATAA
50282349 AAAAATGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 5 0.15
11 23 0.70
12 5 0.15
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAATAATAC
Found at i:50282336 original size:33 final size:32
Alignment explanation
Indices: 50282276--50282348 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 32
50282266 TATGTTGAAT
*
50282276 AATAATAATACTTATATCTTTAATAATAATAC
1 AATAATAATACTTATATATTTAATAATAATAC
50282308 AATAATAATACTTATAATATTTAATAATAATAC
1 AATAATAATACTTAT-ATATTTAATAATAATAC
50282341 AATAATAA
1 AATAATAA
50282349 AAAAATGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 15 0.38
33 24 0.62
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (32 bp):
AATAATAATACTTATATATTTAATAATAATAC
Found at i:50285442 original size:55 final size:57
Alignment explanation
Indices: 50285338--50285444 Score: 130
Period size: 55 Copynumber: 1.9 Consensus size: 57
50285328 AATCTATTAT
* * * * * *
50285338 TATTTTTATTATTTATTTTTAACATAAATATGATTTTATTTATTATTTAATATTCAA
1 TATTTTTAATATATATTATTAACATAAATATGAATATATTAATTATTTAATATTCAA
50285395 TATTTTTAATATATATTATT-A-ATAAATATGAATATATATAATT-TTTAATA
1 TATTTTTAATATATATTATTAACATAAATATGAATATAT-TAATTATTTAATA
50285445 ATTTATTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
55 21 0.49
56 5 0.12
57 17 0.40
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (57 bp):
TATTTTTAATATATATTATTAACATAAATATGAATATATTAATTATTTAATATTCAA
Found at i:50285764 original size:40 final size:40
Alignment explanation
Indices: 50285696--50285771 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
50285686 GACGAGCCAG
* *
50285696 CAAATCGCGTCCACATCAGAGCGCTTTGCTGATGTGGCAA
1 CAAATCGCGTCCACATAAGAGCGATTTGCTGATGTGGCAA
* * *
50285736 CAAATCGCGTCCACGTAAGCGTGATTTGCTGATGTG
1 CAAATCGCGTCCACATAAGAGCGATTTGCTGATGTG
50285772 TAGCGCGCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (40 bp):
CAAATCGCGTCCACATAAGAGCGATTTGCTGATGTGGCAA
Found at i:50285932 original size:23 final size:23
Alignment explanation
Indices: 50285905--50285957 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
50285895 ACTAATCATT
50285905 TCTCAAATTTCC-TCTC-AATTTCC
1 TCTCAAATTTCCTTC-CAAATTT-C
50285928 TCTCAAA-TTCCTTCCAAATTTC
1 TCTCAAATTTCCTTCCAAATTTC
50285950 TCTCAAAT
1 TCTCAAAT
50285958 CCATATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (23 bp):
TCTCAAATTTCCTTCCAAATTTC
Found at i:50285956 original size:11 final size:12
Alignment explanation
Indices: 50285905--50285957 Score: 69
Period size: 11 Copynumber: 4.7 Consensus size: 12
50285895 ACTAATCATT
50285905 TCTCAAATTTCC
1 TCTCAAATTTCC
50285917 TCTC-AATTTCC
1 TCTCAAATTTCC
50285928 TCTCAAA-TTCC
1 TCTCAAATTTCC
50285939 T-TCCAAATTT-C
1 TCT-CAAATTTCC
50285950 TCTCAAAT
1 TCTCAAAT
50285958 CCATATTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.03
11 27 0.73
12 9 0.24
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (12 bp):
TCTCAAATTTCC
Found at i:50288156 original size:21 final size:21
Alignment explanation
Indices: 50288116--50288162 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
50288106 ATGCCATACT
*
50288116 GGAAGAACCAGAATCCCTGCC
1 GGAAGAACCACAATCCCTGCC
*
50288137 TGAAGAACCACAA-CCGCTGCC
1 GGAAGAACCACAATCC-CTGCC
50288158 GGAAG
1 GGAAG
50288163 CTGGACAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.34, C:0.32, G:0.26, T:0.09
Consensus pattern (21 bp):
GGAAGAACCACAATCCCTGCC
Found at i:50288444 original size:21 final size:21
Alignment explanation
Indices: 50288409--50288720 Score: 182
Period size: 21 Copynumber: 14.7 Consensus size: 21
50288399 ACAAACCTTA
50288409 AACCCTTAA-TCT-AAAACCCT
1 AACCCTTAACT-TAAAAACCCT
* * *
50288429 AACCCATAACTTTAAAACCTT
1 AACCCTTAACTTAAAAACCCT
*
50288450 AACCCTTAAATTAAAAACCCT
1 AACCCTTAACTTAAAAACCCT
50288471 AAACCCTTAACTTAAAAACCCT
1 -AACCCTTAACTTAAAAACCCT
*
50288493 AAACCCTAAACCTT--AAACCCT
1 -AACCCTTAA-CTTAAAAACCCT
*
50288514 AAGCCCTTAACCTAAAAACCCTT
1 AA-CCCTTAACTTAAAAACCC-T
*
50288537 AA-CCTAAAAACCTT--AAACCCTT
1 AACCCT--TAA-CTTAAAAACCC-T
* *
50288559 AA--ATTAA---AAACCCTAACCTT
1 AACCCTTAACTTAAA----AACCCT
* ******
50288579 AA-CCTAAAAACCCTAACCCT
1 AACCCTTAACTTAAAAACCCT
*
50288599 AACCCTTAACTTAAAAACCTT
1 AACCCTTAACTTAAAAACCCT
*
50288620 AACCCTTAAATTAAAAACCCT
1 AACCCTTAACTTAAAAACCCT
* *
50288641 AAACCCTTAACTTTAAAACCGT
1 -AACCCTTAACTTAAAAACCCT
* *
50288663 AACCCTTAAATAAAAAAACCCT
1 AACCCTTAACT-TAAAAACCCT
*
50288685 AACACTTAACTTAAAAACCCT
1 AACCCTTAACTTAAAAACCCT
50288706 AACCCTTAACTTAAA
1 AACCCTTAACTTAAA
50288721 TATAATTTGA
Statistics
Matches: 226, Mismatches: 42, Indels: 47
0.72 0.13 0.15
Matches are distributed among these distances:
17 1 0.00
19 2 0.01
20 23 0.10
21 111 0.49
22 79 0.35
23 8 0.04
24 2 0.01
ACGTcount: A:0.45, C:0.31, G:0.01, T:0.23
Consensus pattern (21 bp):
AACCCTTAACTTAAAAACCCT
Found at i:50288474 original size:7 final size:7
Alignment explanation
Indices: 50288464--50288529 Score: 55
Period size: 7 Copynumber: 9.4 Consensus size: 7
50288454 CTTAAATTAA
50288464 AAACCCT
1 AAACCCT
50288471 AAACCCT
1 AAACCCT
* *
50288478 TAA-CTT
1 AAACCCT
50288484 AAAAACCCT
1 --AAACCCT
50288493 AAACCCT
1 AAACCCT
*
50288500 AAACCTT
1 AAACCCT
50288507 AAACCCT
1 AAACCCT
*
50288514 AAGCCCT
1 AAACCCT
*
50288521 TAA-CCT
1 AAACCCT
50288527 AAA
1 AAA
50288530 AACCCTTAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
6 7 0.15
7 35 0.76
8 2 0.04
9 2 0.04
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:50288490 original size:43 final size:43
Alignment explanation
Indices: 50288401--50288720 Score: 283
Period size: 43 Copynumber: 7.5 Consensus size: 43
50288391 TTTAGTTGAC
* *
50288401 AAACCTTAAACCCTT-AATCT-AAAACCCT-AACCCATAACTTTA
1 AAACCTT-AACCCTTAAAT-TAAAAACCCTAAACCCTTAACTTAA
50288443 AAACCTTAACCCTTAAATTAAAAACCCTAAACCCTTAACTTAA
1 AAACCTTAACCCTTAAATTAAAAACCCTAAACCCTTAACTTAA
* * *
50288486 AAACCCTAAACCC-TAAACCTT--AAACCCTAAGCCCTTAACCTAA
1 AAA-CCTTAACCCTTAAA--TTAAAAACCCTAAACCCTTAACTTAA
* *
50288529 AAACCCTTAA-CC------TAAAAACCTTAAACCCTTAAATTAA
1 AAA-CCTTAACCCTTAAATTAAAAACCCTAAACCCTTAACTTAA
* **
50288566 AAACCCTAA-CCTTAACCTAAAAACCCTAACCCTAACCCTTAACTTAA
1 AAACCTTAACCCTTAAATTAAAAACCCT-A----AACCCTTAACTTAA
*
50288613 AAACCTTAACCCTTAAATTAAAAACCCTAAACCCTTAACTTTA
1 AAACCTTAACCCTTAAATTAAAAACCCTAAACCCTTAACTTAA
* * *
50288656 AAACCGTAACCCTTAAATAAAAAAACCCT-AACACTTAACTTAA
1 AAACCTTAACCCTTAAAT-TAAAAACCCTAAACCCTTAACTTAA
* *
50288699 AAACCCTAACCCTTAACTTAAA
1 AAACCTTAACCCTTAAATTAAA
50288721 TATAATTTGA
Statistics
Matches: 233, Mismatches: 24, Indels: 42
0.78 0.08 0.14
Matches are distributed among these distances:
35 1 0.00
36 7 0.03
37 21 0.09
41 8 0.03
42 32 0.14
43 107 0.46
44 17 0.07
45 2 0.01
47 22 0.09
48 16 0.07
ACGTcount: A:0.45, C:0.31, G:0.01, T:0.23
Consensus pattern (43 bp):
AAACCTTAACCCTTAAATTAAAAACCCTAAACCCTTAACTTAA
Found at i:50288550 original size:14 final size:15
Alignment explanation
Indices: 50288471--50288552 Score: 68
Period size: 15 Copynumber: 5.7 Consensus size: 15
50288461 TAAAAACCCT
*
50288471 AAACCCTTAACTTAA
1 AAACCCTTAACCTAA
*
50288486 AAACCCTAAACCCT--
1 AAACCCTTAA-CCTAA
50288500 AAA-CCTTAAACCCT--
1 AAACCCTT-AA-CCTAA
*
50288514 AAGCCCTTAACCTAA
1 AAACCCTTAACCTAA
50288529 AAACCCTTAACCTAA
1 AAACCCTTAACCTAA
50288544 AAA-CCTTAA
1 AAACCCTTAA
50288553 ACCCTTAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
13 6 0.11
14 19 0.33
15 30 0.53
16 2 0.04
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (15 bp):
AAACCCTTAACCTAA
Found at i:50288554 original size:7 final size:8
Alignment explanation
Indices: 50288486--50288561 Score: 51
Period size: 7 Copynumber: 10.4 Consensus size: 8
50288476 CTTAACTTAA
50288486 AAACCC-T
1 AAACCCTT
50288493 AAACCC-T
1 AAACCCTT
50288500 AAA-CCTT
1 AAACCCTT
50288507 AAACCC-T
1 AAACCCTT
*
50288514 AAGCCCTT
1 AAACCCTT
*
50288522 -AA-CCTAA
1 AAACCCT-T
50288529 AAACCCTT
1 AAACCCTT
*
50288537 -AA-CCTA
1 AAACCCTT
*
50288543 AAAACCTT
1 AAACCCTT
50288551 AAACCCTT
1 AAACCCTT
50288559 AAA
1 AAA
50288562 TTAAAAACCC
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
6 8 0.15
7 25 0.46
8 18 0.33
9 3 0.06
ACGTcount: A:0.45, C:0.34, G:0.01, T:0.20
Consensus pattern (8 bp):
AAACCCTT
Found at i:50288600 original size:57 final size:56
Alignment explanation
Indices: 50288471--50288596 Score: 168
Period size: 58 Copynumber: 2.2 Consensus size: 56
50288461 TAAAAACCCT
*
50288471 AAACCCTTAACTTAAAAACCCTAAACCCTAAACCTTAAACCCTAAGCCCTTAACCTAA
1 AAACCCTTAACCTAAAAACCCTAAACCCTAAA-CTTAAACCCTAA-CCCTTAACCTAA
*
50288529 AAACCCTTAACCTAAAAACCTTAAACCCTTAAA-TTAAAAACCCTAA-CCTTAACCTAA
1 AAACCCTTAACCTAAAAACCCTAAACCC-TAAACTT--AAACCCTAACCCTTAACCTAA
50288586 AAACCC-TAACC
1 AAACCCTTAACC
50288597 CTAACCCTTA
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
56 5 0.08
57 19 0.30
58 26 0.41
59 13 0.21
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (56 bp):
AAACCCTTAACCTAAAAACCCTAAACCCTAAACTTAAACCCTAACCCTTAACCTAA
Found at i:50290664 original size:126 final size:125
Alignment explanation
Indices: 50290412--50290979 Score: 818
Period size: 126 Copynumber: 4.5 Consensus size: 125
50290402 CCCAAACATG
*
50290412 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * *
50290477 TAGAAGCG-ATTTTATACTATTTTCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGAC
66 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * *
50290536 CTACTGTAGCAAAAGCGCGTCCATGAGGACGTGATATCACAAATTCTTCTCA-AATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* * *
50290600 CTTGCAGCGGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
65 CTTGAAGC-GTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
50290662 CTACTGTAGCAAAAGCGCGTCCAC-ATGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGA-GGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTG
* * * *
50290726 CTTAAAGTGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCAAGAC
65 CTTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGAC
* * *
50290788 CAACTGTAGCAAAAGTGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
*
50290853 TTGAAGCGTTGTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
66 TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * * * * * *
50290913 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCATGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
50290978 TT
66 TT
50290980 TGATTTTATC
Statistics
Matches: 396, Mismatches: 41, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
123 2 0.01
124 62 0.16
125 108 0.27
126 221 0.56
127 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:50290903 original size:251 final size:251
Alignment explanation
Indices: 50290412--50290979 Score: 847
Period size: 251 Copynumber: 2.3 Consensus size: 251
50290402 CCCAAACATG
50290412 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * * *
50290477 -TAGAAGCGATTTTATACTATTTTCTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCTACT
66 TTAGAAGCGATTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGACCAACT
* ** *
50290541 GTAGCAAAAGCGCGTCCATGAGGACGTGATATCACAAATTCTTCTCAAATAGCATCCTGCTTGCA
131 GTAGCAAAAGCGCGTCCACGAGGACACGATATCACAAATTCTTCTCAAATAGCATCCTGCTTGAA
* * *
50290606 GCGGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
196 GCGGTTGTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
*
50290662 CTACTGTAGCAAAAGCGCGTCCACATGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
50290727 TTA-AAGTGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCAAGACCAA
66 TTAGAAGCG-ATTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTT-TTCCAAGACCAA
* * *
50290791 CTGTAGCAAAAGTGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTT
129 CTGTAGCAAAAGCGCGTCCACGAGGACACGATATCACAAATTCTTCTCA-AATAGCATCCTGCTT
50290855 GAAGC-GTTGTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
193 GAAGCGGTTGTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * * * * *
50290913 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAAAAATCCTTCTGATAAATCATCATGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
50290978 TT
66 TT
50290980 TGATTTTATC
Statistics
Matches: 287, Mismatches: 27, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
250 68 0.24
251 148 0.52
252 69 0.24
253 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (251 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTAGAAGCGATTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGACCAACT
GTAGCAAAAGCGCGTCCACGAGGACACGATATCACAAATTCTTCTCAAATAGCATCCTGCTTGAA
GCGGTTGTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:50291115 original size:8 final size:9
Alignment explanation
Indices: 50291095--50291131 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
50291085 TTTTTTCTCC
*
50291095 AAAACCCTA
1 AAAATCCTA
50291104 AAAATCCTA
1 AAAATCCTA
*
50291113 AAAACCCTA
1 AAAATCCTA
50291122 AAAATCCTA
1 AAAATCCTA
50291131 A
1 A
50291132 CGTGGGAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAATCCTA
Found at i:50291118 original size:18 final size:18
Alignment explanation
Indices: 50291095--50291131 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
50291085 TTTTTTCTCC
50291095 AAAACCCTAAAAATCCTA
1 AAAACCCTAAAAATCCTA
50291113 AAAACCCTAAAAATCCTA
1 AAAACCCTAAAAATCCTA
50291131 A
1 A
50291132 CGTGGGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAACCCTAAAAATCCTA
Found at i:50300169 original size:24 final size:25
Alignment explanation
Indices: 50300142--50300196 Score: 58
Period size: 27 Copynumber: 2.2 Consensus size: 25
50300132 GAAAAGGGAA
50300142 AAAAATCATTTT-TTCTTTACTAAT
1 AAAAATCATTTTGTTCTTTACTAAT
* * *
50300166 AAAAGTTATTTTGGATTGTTTACTAAT
1 AAAAATCATTTT-G-TTCTTTACTAAT
50300193 AAAA
1 AAAA
50300197 TTTAAATCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 10 0.40
27 15 0.60
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (25 bp):
AAAAATCATTTTGTTCTTTACTAAT
Found at i:50312720 original size:6 final size:6
Alignment explanation
Indices: 50312709--50312736 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
50312699 TCGCTCCTGT
50312709 TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATT
50312737 AAGTCCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:50313091 original size:31 final size:32
Alignment explanation
Indices: 50313024--50313091 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
50313014 TGGGCACTAT
* * *
50313024 CATTACATACTTTTTATTATTTTAGTCAATGT
1 CATTACATACTATTTATCATTTTAGTCAATGC
*
50313056 CATTACATAC-ATTTATCATTTTA-TCACTTGC
1 CATTACATACTATTTATCATTTTAGTCA-ATGC
50313087 CATTA
1 CATTA
50313092 ATTTGTCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 3 0.10
31 18 0.58
32 10 0.32
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (32 bp):
CATTACATACTATTTATCATTTTAGTCAATGC
Found at i:50315120 original size:18 final size:19
Alignment explanation
Indices: 50315088--50315133 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
50315078 AATTTAATAC
50315088 TTTAAAAAATTATATAT-ATT
1 TTTAAAAAA-TATAT-TGATT
50315108 TTTAAAAAA-ATATTGATT
1 TTTAAAAAATATATTGATT
50315126 TTTAAAAA
1 TTTAAAAA
50315134 TTGTATAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.04
18 15 0.60
20 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTAAAAAATATATTGATT
Found at i:50321774 original size:21 final size:21
Alignment explanation
Indices: 50321748--50321795 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
50321738 AAAATCAATG
* *
50321748 TCACACGGTCATGTGGTTACT
1 TCACACGCTCATGTGGCTACT
**
50321769 TCACACGCTTGTGTGGCTACT
1 TCACACGCTCATGTGGCTACT
50321790 TCACAC
1 TCACAC
50321796 ACCCGTGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (21 bp):
TCACACGCTCATGTGGCTACT
Found at i:50321803 original size:21 final size:21
Alignment explanation
Indices: 50321759--50321803 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
50321749 CACACGGTCA
* * **
50321759 TGTGGTTACTTCACACGCTTG
1 TGTGGCTACTTCACACACCCG
50321780 TGTGGCTACTTCACACACCCG
1 TGTGGCTACTTCACACACCCG
50321801 TGT
1 TGT
50321804 ATGTTGACCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.29, G:0.22, T:0.33
Consensus pattern (21 bp):
TGTGGCTACTTCACACACCCG
Found at i:50326617 original size:16 final size:18
Alignment explanation
Indices: 50326585--50326617 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
50326575 ATTTCAAAAA
50326585 TTTTAATACATTACTATT
1 TTTTAATACATTACTATT
50326603 TTTTAA-ACATT-CTAT
1 TTTTAATACATTACTAT
50326618 GATATAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTAATACATTACTATT
Found at i:50328481 original size:17 final size:17
Alignment explanation
Indices: 50328455--50328490 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
50328445 TTCTATGATG
*
50328455 AAATGCCATGCAGTCAA
1 AAATGCCATGCAGCCAA
*
50328472 AAATGTCATGCAGCCAA
1 AAATGCCATGCAGCCAA
50328489 AA
1 AA
50328491 CAAAACACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (17 bp):
AAATGCCATGCAGCCAA
Found at i:50330224 original size:3 final size:3
Alignment explanation
Indices: 50330216--50330255 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
50330206 ATAGTAATTA
* *
50330216 AAT AAT AAT TA- AAT AAT AAT AAT AAT GAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
50330256 GGAGAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:50330224 original size:11 final size:11
Alignment explanation
Indices: 50330204--50330235 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
50330194 ATGTACATAA
*
50330204 AAATAGTAATT
1 AAATAATAATT
50330215 AAATAATAATT
1 AAATAATAATT
50330226 AAATAATAAT
1 AAATAATAAT
50330236 AATAATGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
AAATAATAATT
Found at i:50338563 original size:124 final size:123
Alignment explanation
Indices: 50338246--50338594 Score: 619
Period size: 123 Copynumber: 2.8 Consensus size: 123
50338236 TTATTTCGAG
*
50338246 TTGACGTTTCTG-GTCAAATAGTATAAAATCGGCTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGT
*
50338310 GAAATCGCACCCTCGTGGACGCGATTTTGCTACAGTAGGTCATATAAGAAATAATTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATATAAGAAATAATTTTT
*
50338369 TTGACGTTTCTAAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
50338434 AAATCGCGCCCTCGTGGACGTGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATATAAGAAAT-AATTTTT
*
50338493 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGGGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
50338558 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
50338595 CAAGTTTGGG
Statistics
Matches: 216, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
123 109 0.50
124 107 0.50
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATATAAGAAATAATTTTT
Found at i:50341715 original size:10 final size:10
Alignment explanation
Indices: 50341700--50341724 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
50341690 CAAGTCTAAC
50341700 ATTATGTAAA
1 ATTATGTAAA
50341710 ATTATGTAAA
1 ATTATGTAAA
50341720 ATTAT
1 ATTAT
50341725 TAAGTCTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:50341769 original size:55 final size:54
Alignment explanation
Indices: 50341708--50341864 Score: 194
Period size: 56 Copynumber: 2.8 Consensus size: 54
50341698 ACATTATGTA
*
50341708 AAATTATGTAAAATTATTAAGTCTCAAAGTTTTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTC-CAAAATTTTGTTAATGGTTAGTAAAATTATC
* *
50341763 AAATTATGTAAAATTATTAAG-CCAAAAAAATTTTAATTAA--ATTAGGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCC---AAAATTTT-GTTAATGGTTA-GTAAAATTATC
*
50341819 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGT
1 AAATTATGTAAAATTATTAAGTCC-AAAATTTTGTTAATGGTTAGT
50341865 CGGCGACAGT
Statistics
Matches: 88, Mismatches: 6, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
53 1 0.01
54 5 0.06
55 34 0.39
56 42 0.48
57 6 0.07
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (54 bp):
AAATTATGTAAAATTATTAAGTCCAAAATTTTGTTAATGGTTAGTAAAATTATC
Found at i:50341775 original size:18 final size:18
Alignment explanation
Indices: 50341752--50341835 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 18
50341742 TTAATGGTTA
50341752 GTAAAATTATCAAATTAT
1 GTAAAATTATCAAATTAT
* ***
50341770 GTAAAATTATTAAGCCA-
1 GTAAAATTATCAAATTAT
** * *
50341787 AAAAAATTTTAATTAAATTAG
1 GTAAAA--TT-ATCAAATTAT
50341808 GTAAAATTATCAAATTAT
1 GTAAAATTATCAAATTAT
50341826 GTAAAATTAT
1 GTAAAATTAT
50341836 TAAGTCCAAA
Statistics
Matches: 49, Mismatches: 13, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
17 4 0.08
18 31 0.63
19 4 0.08
20 6 0.12
21 4 0.08
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (18 bp):
GTAAAATTATCAAATTAT
Found at i:50342068 original size:55 final size:55
Alignment explanation
Indices: 50341984--50342093 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
50341974 NNNNNNNNNN
50341984 TTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGTAAAATTA
1 TTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGTAAAATTA
*
50342039 TTAAGTCCAACAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGTAAAATTA
1 TTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGTAAAATTA
50342094 GGTTAGGGTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (55 bp):
TTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGTAAAATTA
Found at i:50342124 original size:18 final size:18
Alignment explanation
Indices: 50342101--50342142 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
50342091 TTAGGTTAGG
50342101 GTTAGGATTTTTAATTAA
1 GTTAGGATTTTTAATTAA
*
50342119 GTTAGGGTTTTTAATTAA
1 GTTAGGATTTTTAATTAA
50342137 GTTAGG
1 GTTAGG
50342143 TTAGGGTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (18 bp):
GTTAGGATTTTTAATTAA
Found at i:50342151 original size:29 final size:26
Alignment explanation
Indices: 50342119--50342246 Score: 115
Period size: 29 Copynumber: 4.9 Consensus size: 26
50342109 TTTTAATTAA
50342119 GTTAGGGTTTTTAATTAAGTTAGGTT
1 GTTAGGGTTTTTAATTAAGTTAGGTT
50342145 AGGGTTAGGGTTTTTAATTAAGTTAGGTT
1 ---GTTAGGGTTTTTAATTAAGTTAGGTT
* * * *
50342174 TTTA----ATTAAATTAGGTTAGG--
1 GTTAGGGTTTTTAATTAAGTTAGGTT
*
50342194 GTTAGGGTTTTTAATTAAATTAGGTT
1 GTTAGGGTTTTTAATTAAGTTAGGTT
50342220 AGAGTTAGGGTTTTTAATTAAGTTAGG
1 ---GTTAGGGTTTTTAATTAAGTTAGG
50342247 GTTTTTAATT
Statistics
Matches: 80, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
20 3 0.04
22 13 0.16
24 12 0.15
26 3 0.04
29 49 0.61
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (26 bp):
GTTAGGGTTTTTAATTAAGTTAGGTT
Found at i:50342160 original size:47 final size:46
Alignment explanation
Indices: 50342091--50342281 Score: 235
Period size: 47 Copynumber: 4.1 Consensus size: 46
50342081 TTATGTAAAA
*
50342091 TTAGGTTAGGGTTAGGATTTTTAATTAAGTTAGGGTTTTTAATTAAG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTA-GGTTTTTAATTAAG
*
50342138 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTTTTAATTAAA
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTTTTAATTAAG
* ** * *
50342184 TTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG-TTAGAGTTAGGG
1 TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTTTTAATTA-AG
* *
50342230 TTTTTA-ATTA-AGTTAGGGTTTTTAATTAAGTTAGGTTTTTAATTAAG
1 ---TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTTTTAATTAAG
50342277 TTAGG
1 TTAGG
50342282 GTTTTTAATT
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
44 3 0.02
45 6 0.05
46 46 0.38
47 55 0.45
48 9 0.07
49 3 0.02
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (46 bp):
TTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTTTTAATTAAG
Found at i:50342171 original size:18 final size:18
Alignment explanation
Indices: 50342148--50342188 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
50342138 TTAGGTTAGG
50342148 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
50342166 GTTA-GGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
50342183 ATTAGG
1 GTTAGG
50342189 TTAGGGTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:50342187 original size:93 final size:91
Alignment explanation
Indices: 50342088--50342281 Score: 239
Period size: 93 Copynumber: 2.1 Consensus size: 91
50342078 AAATTATGTA
* ** * *
50342088 AAATTAGGTTAGGGTTAGGATTTTTAATTAAGTTAGGGTTTTTAATTA-AG-TTAGGTTAGGGTT
1 AAATTAGGTTAGGGTTAGGATTTTTAATTAAATTA-GG-TTAGAATTAGAGTTTA-ATTA-AGTT
50342151 AGGGTTTTTAATTAAGTTAGGTTTTTAATT
62 AGGGTTTTTAATTAAGTTAGGTTTTTAATT
* * *
50342181 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAGTTAG
1 AAATTAGGTTAGGGTTAGGATTTTTAATTAAATTAGGTTAGAATTAGAG--TTTAATTAAGTTAG
50342246 GGTTTTTAATTAAGTTAGGTTTTTAATT
64 GGTTTTTAATTAAGTTAGGTTTTTAATT
*
50342274 AAGTTAGG
1 AAATTAGG
50342282 GTTTTTAATT
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
91 6 0.07
92 3 0.03
93 73 0.83
94 3 0.03
95 3 0.03
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (91 bp):
AAATTAGGTTAGGGTTAGGATTTTTAATTAAATTAGGTTAGAATTAGAGTTTAATTAAGTTAGGG
TTTTTAATTAAGTTAGGTTTTTAATT
Found at i:50342191 original size:46 final size:46
Alignment explanation
Indices: 50342088--50342219 Score: 228
Period size: 46 Copynumber: 2.8 Consensus size: 46
50342078 AAATTATGTA
*
50342088 AAATTAGGTTAGGGTTAGGATTTTTAATTAAGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTA-GGTTTTTAATT
*
50342135 AAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTTTTAATT
*
50342181 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTT
50342220 AGAGTTAGGG
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
46 48 0.59
47 33 0.41
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (46 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTTTTAATT
Done.