Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 26 of 64
Found at i:3912383 original size:58 final size:58
Alignment explanation
Indices: 3912293--3912471 Score: 268
Period size: 58 Copynumber: 3.1 Consensus size: 58
3912283 GTTATTAATA
* * * *
3912293 CCTAAGCATTCTATGCACAATTCTTGTAATGGGAAGTATGGCATTACTTACAGTTTCT
1 CCTAAGCATTTTATGTACAATTCTTGTAATGGGAAGTATAGCATTACTTATAGTTTCT
**
3912351 CCTAAGCATTTTATGTACAATTCGCGTAATGGGAAGTATAGCATTACTTATAGTTTCT
1 CCTAAGCATTTTATGTACAATTCTTGTAATGGGAAGTATAGCATTACTTATAGTTTCT
* * * *
3912409 CTTAACCATTTTATGTACAATTCTTGTAATGGGAAGTATAACATTGCTTATAGTTTCT
1 CCTAAGCATTTTATGTACAATTCTTGTAATGGGAAGTATAGCATTACTTATAGTTTCT
3912467 CCTAA
1 CCTAA
3912472 CTATTCATGA
Statistics
Matches: 108, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 108 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (58 bp):
CCTAAGCATTTTATGTACAATTCTTGTAATGGGAAGTATAGCATTACTTATAGTTTCT
Found at i:3925726 original size:22 final size:22
Alignment explanation
Indices: 3925683--3925755 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
3925673 TGATGATTGC
* *
3925683 TTACTA-TA-ATTATCAATGAT
1 TTACTATTACATTATTATTGAT
**
3925703 TTACTATTATGTTATTATAT-AT
1 TTACTATTACATTATTAT-TGAT
3925725 TTACTATTACATTATTATTGAT
1 TTACTATTACATTATTATTGAT
*
3925747 TTAGTATTA
1 TTACTATTA
3925756 AGTTTTCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.14
21 3 0.07
22 33 0.77
23 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.53
Consensus pattern (22 bp):
TTACTATTACATTATTATTGAT
Found at i:3926121 original size:17 final size:17
Alignment explanation
Indices: 3926099--3926132 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3926089 TTTATCAATT
3926099 AATTAATATTAA-ATTAA
1 AATTAAT-TTAATATTAA
3926116 AATTAATTTAATATTAA
1 AATTAATTTAATATTAA
3926133 GTTATTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTAATTTAATATTAA
Found at i:3926154 original size:22 final size:22
Alignment explanation
Indices: 3926127--3926219 Score: 82
Period size: 22 Copynumber: 4.3 Consensus size: 22
3926117 ATTAATTTAA
* *
3926127 TATTAAGTTATTACTAATTTGT
1 TATTAAATTATCACTAATTTGT
* *
3926149 TGTTAAATTATCATTAATTTGT
1 TATTAAATTATCACTAATTTGT
* **
3926171 TATTAAATTATCAATAATTAAT
1 TATTAAATTATCACTAATTTGT
* *
3926193 TATT-AATTAGT-ACTTATTTTT
1 TATTAAATTA-TCACTAATTTGT
3926214 TATTAA
1 TATTAA
3926220 GTTACCTAGC
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
21 15 0.26
22 42 0.74
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (22 bp):
TATTAAATTATCACTAATTTGT
Found at i:3926175 original size:11 final size:11
Alignment explanation
Indices: 3926086--3926200 Score: 61
Period size: 11 Copynumber: 10.5 Consensus size: 11
3926076 TGCTATTAAA
*
3926086 TAATTTATCAAT
1 TAATTTAT-TAT
*
3926098 TAA-TTAATAT
1 TAATTTATTAT
* **
3926108 TAAATTAAAAT
1 TAATTTATTAT
*
3926119 TAATTTAATAT
1 TAATTTATTAT
* *
3926130 TAAGTTATTAC
1 TAATTTATTAT
* *
3926141 TAATTTGTTGT
1 TAATTTATTAT
* *
3926152 TAAATTATCAT
1 TAATTTATTAT
*
3926163 TAATTTGTTAT
1 TAATTTATTAT
* * *
3926174 TAAATTATCAA
1 TAATTTATTAT
*
3926185 TAATTAATTAT
1 TAATTTATTAT
3926196 TAATT
1 TAATT
3926201 AGTACTTATT
Statistics
Matches: 75, Mismatches: 27, Indels: 3
0.71 0.26 0.03
Matches are distributed among these distances:
10 5 0.07
11 67 0.89
12 3 0.04
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TAATTTATTAT
Found at i:3928974 original size:20 final size:20
Alignment explanation
Indices: 3928948--3928992 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
3928938 AAAAAATATT
*
3928948 ATTTTTTTAAAATTATTTA-
1 ATTTTTTTAAAATTAATTAG
3928967 ATTTTTTTAAAATTAATTAG
1 ATTTTTTTAAAATTAATTAG
3928987 ATTTTT
1 ATTTTT
3928993 CAATATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTTTTAAAATTAATTAG
Found at i:3939838 original size:31 final size:31
Alignment explanation
Indices: 3939800--3939872 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
3939790 AGCTATTTGG
*
3939800 CCTAACAAGTGGTATTAAAGCTGTGGTGATC
1 CCTAACAAGTGGTATTAAAGCTGTCGTGATC
* *
3939831 CCTAACAAGTGGTATTAGAGCTGTCGTGATT
1 CCTAACAAGTGGTATTAAAGCTGTCGTGATC
3939862 CCTAACAAGTG
1 CCTAACAAGTG
3939873 ATATCACAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (31 bp):
CCTAACAAGTGGTATTAAAGCTGTCGTGATC
Found at i:3942803 original size:52 final size:52
Alignment explanation
Indices: 3942688--3942843 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
3942678 TATAACCATA
* * * *
3942688 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAA-TCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
*
3942739 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
* * * *
3942791 CAAACTTACCTATTAAGAATCATCTTT-CTCTTGGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATC-CCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
3942843 C
1 C
3942844 TTCTTGTCCA
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
51 33 0.35
52 56 0.60
53 4 0.04
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:3942884 original size:11 final size:11
Alignment explanation
Indices: 3942868--3942909 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
3942858 GCAATATCTG
*
3942868 ACAAATCCCAA
1 ACAAATCTCAA
*
3942879 ACAAATCTCTA
1 ACAAATCTCAA
3942890 ACAAATCTCAA
1 ACAAATCTCAA
*
3942901 ACGAATCTC
1 ACAAATCTC
3942910 TTATGGGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:3942893 original size:22 final size:22
Alignment explanation
Indices: 3942868--3942910 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3942858 GCAATATCTG
3942868 ACAAATCCCAAACAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
* *
3942890 ACAAATCTCAAACGAATCTCT
1 ACAAATCCCAAACAAATCTCT
3942911 TATGGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:3947985 original size:25 final size:26
Alignment explanation
Indices: 3947928--3947986 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
3947918 CTCGAGCTAG
* *
3947928 AATATTATTTTTTAATAAAAATATTT
1 AATATTAATTTTTAATAAAAATATGT
* *
3947954 TAT-TTAATTTTTATTAAAAAT-TGT
1 AATATTAATTTTTAATAAAAATATGT
3947978 AATATTAAT
1 AATATTAAT
3947987 ATTAAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 4 0.15
25 21 0.78
26 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
AATATTAATTTTTAATAAAAATATGT
Found at i:3948017 original size:23 final size:25
Alignment explanation
Indices: 3947977--3948036 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
3947967 TTAAAAATTG
* **
3947977 TAATATTAATATTAAAATTTTTTTAA
1 TAATGTTAAT-TTAAAATTGCTTTAA
*
3948003 T-ATTTTAATTT-AAATTGCTTTAA
1 TAATGTTAATTTAAAATTGCTTTAA
3948026 TAATGTTAATT
1 TAATGTTAATT
3948037 AAGATAAACT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 11 0.38
24 10 0.34
25 7 0.24
26 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (25 bp):
TAATGTTAATTTAAAATTGCTTTAA
Found at i:3948328 original size:40 final size:42
Alignment explanation
Indices: 3948265--3948345 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 42
3948255 TAATATTATA
3948265 TTATTATTTTAATAATAAATAATAAATATTT-ATATAGTAATTT
1 TTATTATTTT-ATAATAAATAAT-AATATTTAATATAGTAATTT
* * *
3948308 TTATTATTTT-T-ATAATTAATATTGTTTAATATAGTAAT
1 TTATTATTTTATAATAAATAATAATATTTAATATAGTAAT
3948346 ATTATTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
39 5 0.15
40 18 0.53
41 1 0.03
43 10 0.29
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (42 bp):
TTATTATTTTATAATAAATAATAATATTTAATATAGTAATTT
Found at i:3948330 original size:18 final size:19
Alignment explanation
Indices: 3948309--3948357 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
3948299 TAGTAATTTT
* *
3948309 TATTATTTTTATA-ATTAA
1 TATTATTTTAATATAGTAA
*
3948327 TATT-GTTTAATATAGTAA
1 TATTATTTTAATATAGTAA
3948345 TATTATTTTAATA
1 TATTATTTTAATA
3948358 CGATGACTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 6 0.24
18 12 0.48
19 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
TATTATTTTAATATAGTAA
Found at i:3948512 original size:22 final size:26
Alignment explanation
Indices: 3948455--3948512 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 26
3948445 TTTAATAATA
3948455 AATATAAATAAATAATACATTTGTTAC
1 AATATAAAT-AATAATACATTTGTTAC
*
3948482 AAT-TTAATAATAA-ACA-TT-TT-C
1 AATATAAATAATAATACATTTGTTAC
3948503 AATATAAATA
1 AATATAAATA
3948513 TTTTAATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
21 4 0.14
22 7 0.25
23 2 0.07
24 3 0.11
25 5 0.18
26 4 0.14
27 3 0.11
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (26 bp):
AATATAAATAATAATACATTTGTTAC
Found at i:3948515 original size:15 final size:14
Alignment explanation
Indices: 3948484--3948531 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 14
3948474 TTTGTTACAA
*
3948484 TTTAATAATAAACAT
1 TTTAAT-ATAAATAT
3948499 TTTCAATATAAATAT
1 TTT-AATATAAATAT
3948514 TTTAATAGTAAATAT
1 TTTAATA-TAAATAT
3948529 TTT
1 TTT
3948532 TAAAATTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 4 0.13
15 23 0.77
16 3 0.10
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (14 bp):
TTTAATATAAATAT
Found at i:3948544 original size:24 final size:23
Alignment explanation
Indices: 3948507--3948577 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 23
3948497 ATTTTCAATA
* *
3948507 TAAATATTTTAATAGTAAATATTTT
1 TAAA-ATTTAAATA-TAAATATATT
3948532 TAAAATTTAAATAATAAATAATATT
1 TAAAATTTAAAT-ATAAAT-ATATT
*
3948557 AAAAATATTATAATATAAATA
1 TAAAAT-TTA-AATATAAATA
3948578 GAATAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 12 0.31
25 15 0.38
26 9 0.23
27 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
TAAAATTTAAATATAAATATATT
Found at i:3948558 original size:17 final size:18
Alignment explanation
Indices: 3948538--3948577 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
3948528 TTTTTAAAAT
3948538 TTAAATAATA-AATAATA
1 TTAAATAATATAATAATA
*
3948555 TTAAA-AATATTATAATA
1 TTAAATAATATAATAATA
3948572 -TAAATA
1 TTAAATA
3948578 GAATAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAATAATATAATAATA
Found at i:3948571 original size:27 final size:27
Alignment explanation
Indices: 3948508--3948577 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
3948498 TTTTCAATAT
* * * *
3948508 AAATATTTTAATAGTAAAT-ATTTTTA
1 AAATATTATAATAATAAATAATATTAA
3948534 AAAT-TTA-AATAATAAATAATATTAA
1 AAATATTATAATAATAAATAATATTAA
3948559 AAATATTATAAT-ATAAATA
1 AAATATTATAATAATAAATA
3948578 GAATAATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
24 9 0.24
25 11 0.30
26 14 0.38
27 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
AAATATTATAATAATAAATAATATTAA
Found at i:3952486 original size:64 final size:64
Alignment explanation
Indices: 3952385--3952542 Score: 246
Period size: 64 Copynumber: 2.5 Consensus size: 64
3952375 ATTTTTCACC
* *
3952385 AAAAATATCTTCAATAGTGCACC-CAAAAAATTTTATTGAAGGAATTATTGAAAGTGTTTGTGGC
1 AAAAATATCTTAAATAAT-C-CCTCAAAAAATTTTATTGAAGGAATTATTGAAAGTGTTTGTGGC
3952449 A
64 A
*
3952450 AAAAATATCTTAAATAATCCCTCAAAAAATTTTATTGAAGGAATTATTGAAGGTGTTTGTGGCA
1 AAAAATATCTTAAATAATCCCTCAAAAAATTTTATTGAAGGAATTATTGAAAGTGTTTGTGGCA
* *
3952514 AAAAATGTCTTAAATAATCCCTTAAAAAA
1 AAAAATATCTTAAATAATCCCTCAAAAAA
3952543 CCCTCAAAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
63 2 0.02
64 69 0.79
65 16 0.18
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (64 bp):
AAAAATATCTTAAATAATCCCTCAAAAAATTTTATTGAAGGAATTATTGAAAGTGTTTGTGGCA
Found at i:3954122 original size:2 final size:2
Alignment explanation
Indices: 3954115--3954143 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3954105 TGTGCTTAAG
3954115 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3954144 CTTTGATTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3962372 original size:31 final size:31
Alignment explanation
Indices: 3962320--3962385 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
3962310 TTCTTGCCAG
*
3962320 AAAATTCAACCGACGTCGAAAAGTTCA-TCGA
1 AAAATTCAACCGACGTCGAAAAATTCACT-GA
*
3962351 AAAATTCAACC-AGCGTTGAAAAATTCACTGA
1 AAAATTCAACCGA-CGTCGAAAAATTCACTGA
3962382 AAAA
1 AAAA
3962386 CTAGAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 1 0.03
31 29 0.94
32 1 0.03
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.20
Consensus pattern (31 bp):
AAAATTCAACCGACGTCGAAAAATTCACTGA
Found at i:3963640 original size:22 final size:22
Alignment explanation
Indices: 3963590--3963788 Score: 213
Period size: 22 Copynumber: 8.9 Consensus size: 22
3963580 AGTTTCACAT
*
3963590 CTCAATGATTCTCATTTG-AAA
1 CTCAAAGATTCTCATTTGAAAA
*
3963611 CTCAAAGATTTTCATTTGAAAA
1 CTCAAAGATTCTCATTTGAAAA
*
3963633 TTCAAAGATTCTCATTTGAAAA
1 CTCAAAGATTCTCATTTGAAAA
* * *
3963655 CTCAAAAATTTTTATTTGAAAA
1 CTCAAAGATTCTCATTTGAAAA
* *
3963677 TTTAAAGATTCTCATTTGAAACTTAAAA
1 CTCAAAGATTCTCATTTG------AAAA
*
3963705 CTCAAAGATTTTCATTTGAAAA
1 CTCAAAGATTCTCATTTGAAAA
*
3963727 CTCAAATATTCTCATTTG-AAA
1 CTCAAAGATTCTCATTTGAAAA
* *
3963748 CTCAAATACTCTCATTTGAAAA
1 CTCAAAGATTCTCATTTGAAAA
*
3963770 TTCAAAGATTCTCATTTGA
1 CTCAAAGATTCTCATTTGA
3963789 GGATTCACAA
Statistics
Matches: 148, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
21 36 0.24
22 93 0.63
28 19 0.13
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (22 bp):
CTCAAAGATTCTCATTTGAAAA
Found at i:3963763 original size:43 final size:43
Alignment explanation
Indices: 3963702--3963788 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
3963692 TTGAAACTTA
* * *
3963702 AAACTCAAAGATTTTCATTTGAAAACTCAAATATTCTCATTTG
1 AAACTCAAAGACTCTCATTTGAAAACTCAAAGATTCTCATTTG
* *
3963745 AAACTCAAATACTCTCATTTGAAAATTCAAAGATTCTCATTTG
1 AAACTCAAAGACTCTCATTTGAAAACTCAAAGATTCTCATTTG
3963788 A
1 A
3963789 GGATTCACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (43 bp):
AAACTCAAAGACTCTCATTTGAAAACTCAAAGATTCTCATTTG
Found at i:3964278 original size:71 final size:71
Alignment explanation
Indices: 3964203--3964338 Score: 166
Period size: 71 Copynumber: 1.9 Consensus size: 71
3964193 TGACCATAAT
* * * *
3964203 TCATAGGCTTTTTAGCACTTAACAATTTAAGAACAAATTTTGTCCAT-TGATCAATACTATTTTC
1 TCATAGGCTTGTCAACACTTAACAATTTAAGAACAAATTCTGTCC-TCTGATCAATACTATTTTC
3964267 ACCACAA
65 ACCACAA
* * * * * *
3964274 TCATAGGCTTGTCAACACTTTACCATTTCAGAATAAATTCTGTCCTCTGATCCATATTATTTTCA
1 TCATAGGCTTGTCAACACTTAACAATTTAAGAACAAATTCTGTCCTCTGATCAATACTATTTTCA
3964339 TCATTTAATC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
70 1 0.02
71 53 0.98
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (71 bp):
TCATAGGCTTGTCAACACTTAACAATTTAAGAACAAATTCTGTCCTCTGATCAATACTATTTTCA
CCACAA
Found at i:3965004 original size:38 final size:37
Alignment explanation
Indices: 3964953--3965033 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
3964943 CTCTTTTTCA
*
3964953 TTTTTTCCCTTTTTTTTC-TATTTTTTTATCTTT-TTATT
1 TTTTTTCCC-TTTTTGTCATA-TTTTTTATCTTTCTT-TT
* *
3964991 TTTTTTCTCTTTTTGTCATATTTTTTCTCTTTCTTTT
1 TTTTTTCCCTTTTTGTCATATTTTTTATCTTTCTTTT
3965028 TTTTTT
1 TTTTTT
3965034 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
37 26 0.68
38 12 0.32
ACGTcount: A:0.06, C:0.14, G:0.01, T:0.79
Consensus pattern (37 bp):
TTTTTTCCCTTTTTGTCATATTTTTTATCTTTCTTTT
Found at i:3965014 original size:27 final size:27
Alignment explanation
Indices: 3964962--3965031 Score: 63
Period size: 27 Copynumber: 2.6 Consensus size: 27
3964952 ATTTTTTCCC
* *
3964962 TTTTTTTTCTATTTTTTTATCTTTTTA
1 TTTTTTTTCTATTTTTTCATCATTTTA
*
3964989 TTTTTTTTCTCTTTTTGTCAT-ATTTT-
1 TTTTTTTTCTATTTTT-TCATCATTTTA
* * *
3965015 TTCTCTTTCTTTTTTTT
1 TTTTTTTTCTATTTTTT
3965032 TTAAATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 1 0.03
26 13 0.36
27 19 0.53
28 3 0.08
ACGTcount: A:0.07, C:0.11, G:0.01, T:0.80
Consensus pattern (27 bp):
TTTTTTTTCTATTTTTTCATCATTTTA
Found at i:3969517 original size:7 final size:8
Alignment explanation
Indices: 3969498--3969527 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3969488 AAAAAATATT
3969498 TTTTTTCA
1 TTTTTTCA
3969506 TTTTTTCA
1 TTTTTTCA
*
3969514 TTTTTTTA
1 TTTTTTCA
3969522 TTTTTT
1 TTTTTT
3969528 AAAATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTCA
Found at i:3979022 original size:19 final size:20
Alignment explanation
Indices: 3978974--3979024 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3978964 TAATATCATA
*
3978974 AATAAATTTTGTTACTTATT
1 AATAAATTTTATTACTTATT
*
3978994 AATAAATTTTATTATTTATT
1 AATAAATTTTATTACTTATT
*
3979014 AGT-AATTTTAT
1 AATAAATTTTAT
3979025 ATAAGAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
AATAAATTTTATTACTTATT
Found at i:3979435 original size:20 final size:19
Alignment explanation
Indices: 3979410--3979460 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
3979400 TAAATAATAA
3979410 TTTTATAATTTTATAAGCTT
1 TTTTATAATTTT-TAAGCTT
*
3979430 TTTTATAATTATTTAAGTTT
1 TTTTATAATT-TTTAAGCTT
3979450 TTTTAT-ATTTT
1 TTTTATAATTTT
3979461 GTTATAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 2 0.07
19 3 0.10
20 22 0.76
21 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTATAATTTTTAAGCTT
Found at i:3982211 original size:19 final size:19
Alignment explanation
Indices: 3982189--3982231 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3982179 CTTTAAATTA
*
3982189 AAAAATCTT-GAAAATTTTT
1 AAAAAT-TTAGAAAAATTTT
3982208 AAAAATTTAGAAAAATTTT
1 AAAAATTTAGAAAAATTTT
3982227 AAAAA
1 AAAAA
3982232 AGTAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (19 bp):
AAAAATTTAGAAAAATTTT
Found at i:3982351 original size:25 final size:25
Alignment explanation
Indices: 3982323--3982379 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
3982313 TCAAAAAAAA
3982323 AATCATGTTTCCT-AAATTTTTTAAC
1 AATCAT-TTTCCTAAAATTTTTTAAC
* *
3982348 AATCAATTTTCTTGAAAATTTTTTAGC
1 AATC-ATTTTCCT-AAAATTTTTTAAC
3982375 AATCA
1 AATCA
3982380 CATTTCAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 9 0.33
26 3 0.11
27 15 0.56
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (25 bp):
AATCATTTTCCTAAAATTTTTTAAC
Found at i:3982515 original size:17 final size:18
Alignment explanation
Indices: 3982495--3982530 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3982485 TTATTAAAAC
*
3982495 ATAATTTTT-AATTTTTT
1 ATAATTTTTCAAATTTTT
3982512 ATAATTTTTCAAATTTTT
1 ATAATTTTTCAAATTTTT
3982530 A
1 A
3982531 GAAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
ATAATTTTTCAAATTTTT
Found at i:3983015 original size:21 final size:21
Alignment explanation
Indices: 3982990--3983065 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
3982980 CAAAAAATTG
3982990 TAAAAATTGAAAATTATTTTT
1 TAAAAATTGAAAATTATTTTT
*
3983011 TAAAAAATTG-AAATCAAATTTTT
1 T-AAAAATTGAAAAT--TATTTTT
**
3983034 T-AAAATAAAAAATT-TCTTTT
1 TAAAAATTGAAAATTAT-TTTT
*
3983054 TGAAAATTGAAA
1 TAAAAATTGAAA
3983066 TATTTGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 1 0.02
20 5 0.12
21 18 0.42
22 12 0.28
23 7 0.16
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (21 bp):
TAAAAATTGAAAATTATTTTT
Found at i:3983572 original size:20 final size:20
Alignment explanation
Indices: 3983549--3983588 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3983539 AATCAATGAC
3983549 ACATTAGCAAAG-TCAATATT
1 ACATTAG-AAAGATCAATATT
*
3983569 ACATTAGTAAGATCAATATT
1 ACATTAGAAAGATCAATATT
3983589 TATATCATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (20 bp):
ACATTAGAAAGATCAATATT
Found at i:3990283 original size:10 final size:10
Alignment explanation
Indices: 3990237--3990276 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
3990227 ATTAAAAATT
* *
3990237 ATCAAGATTG
1 ATCAAGAATA
3990247 ATCAAGAATA
1 ATCAAGAATA
3990257 ATCAAGAATA
1 ATCAAGAATA
3990267 ATCAAGAATA
1 ATCAAGAATA
3990277 TTTAAGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (10 bp):
ATCAAGAATA
Found at i:3996742 original size:93 final size:94
Alignment explanation
Indices: 3996542--3996742 Score: 214
Period size: 93 Copynumber: 2.1 Consensus size: 94
3996532 TAAGATTTAA
* * * *
3996542 TTATAAATATTTTATTAAGCCTTCCAATAGTTTGATAAGATTTAATTTTAAAATGTAAATTCTCT
1 TTATAAAT-TTTTATTAAACCTTCCAATAGTTTGATAAAATTTAATTTTAAAATGTAAATCCTCC
* *
3996607 AATAATTTGGTAGGATTATTTCAAAAATTAT
65 AATAATTTAGTAGAATTATTT-AAAAATTAT
* * * *
3996638 TTTTTAA--TTTATTAAACCTTCCAATAGTTTGATAAAATTTAATTTTAAGACT-TAGATCCTCC
1 TTATAAATTTTTATTAAACCTTCCAATAGTTTGATAAAATTTAATTTTAA-AATGTAAATCCTCC
* * *
3996700 AATAGTTTATTAGAATTAATTT-AAAA-TGT
65 AATAATTTAGTAGAATT-ATTTAAAAATTAT
3996729 TTATAAATTTTTAT
1 TTATAAATTTTTAT
3996743 GTACTCCTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
91 7 0.08
92 4 0.05
93 64 0.74
94 6 0.07
96 5 0.06
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (94 bp):
TTATAAATTTTTATTAAACCTTCCAATAGTTTGATAAAATTTAATTTTAAAATGTAAATCCTCCA
ATAATTTAGTAGAATTATTTAAAAATTAT
Found at i:3996836 original size:21 final size:20
Alignment explanation
Indices: 3996812--3996852 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3996802 TTAAAAATTC
3996812 AAATCCAAATAAAATAAATAA
1 AAATCCAAAT-AAATAAATAA
* *
3996833 AAATGCAAGTAAATAAATAA
1 AAATCCAAATAAATAAATAA
3996853 CAAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (20 bp):
AAATCCAAATAAATAAATAA
Found at i:3997345 original size:2 final size:2
Alignment explanation
Indices: 3997338--3997362 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3997328 ATATTTATTA
3997338 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3997363 CACACAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3999476 original size:19 final size:19
Alignment explanation
Indices: 3999454--3999514 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
3999444 TGCAAAAGGG
*
3999454 TCAAAGATTCACAAAACAT
1 TCAAAGATTCACAAAAAAT
* **
3999473 TCAAA-ATTCTCAAATGAT
1 TCAAAGATTCACAAAAAAT
* **
3999491 TTAAAGATTTGCAAAAAAT
1 TCAAAGATTCACAAAAAAT
3999510 TCAAA
1 TCAAA
3999515 AGCCTACAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 14 0.44
19 18 0.56
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.28
Consensus pattern (19 bp):
TCAAAGATTCACAAAAAAT
Found at i:3999755 original size:23 final size:23
Alignment explanation
Indices: 3999724--3999772 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3999714 ATTTAAACCC
* *
3999724 AAAATTTTAAATATTCACATCGA
1 AAAAATTTAAAGATTCACATCGA
* *
3999747 AAAAATTTAGAGATTTACATCGA
1 AAAAATTTAAAGATTCACATCGA
3999770 AAA
1 AAA
3999773 TTTTGAAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (23 bp):
AAAAATTTAAAGATTCACATCGA
Found at i:3999782 original size:22 final size:22
Alignment explanation
Indices: 3999703--3999782 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
3999693 CACATTTGAG
* * *
3999703 AAATTTTAAAGATTTAAACCCA
1 AAATTTTAAAGATTTACATCGA
* *
3999725 AAATTTTAAATATTCACATCGAA
1 AAATTTTAAAGATTTACATCG-A
* *
3999748 AAAATTTAGAGATTTACATCGA
1 AAATTTTAAAGATTTACATCGA
*
3999770 AAATTTTGAAGAT
1 AAATTTTAAAGAT
3999783 ACACATTTGA
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
22 27 0.60
23 18 0.40
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (22 bp):
AAATTTTAAAGATTTACATCGA
Found at i:3999807 original size:91 final size:90
Alignment explanation
Indices: 3999679--3999879 Score: 226
Period size: 90 Copynumber: 2.2 Consensus size: 90
3999669 TTTCCAATAT
* * *
3999679 AAAA-TTCCAAGATTCACATTTGAGAAATTTTAAAGATTTAAACCCAAAATTTTAAATATTCACA
1 AAAATTTCAAAGATTCACATTTGAGAAATTTTAAAGATTTAAACCCAAAA-TTCAAAAATTCACA
* *
3999743 TCGAAAAAA-TTTAGAGATTTACATCG
65 TCAAAAAAATTTTAGAGA-TCACATCG
** * * * * ** *
3999769 AAAATTTTGAAGATACACATTTGAGAATTTTTAGAGATTTACATTCAAAATTCAAAAATTCGCAT
1 AAAATTTCAAAGATTCACATTTGAGAAATTTTAAAGATTTAAACCCAAAATTCAAAAATTCACAT
* *
3999834 TAAAAAAATTTTAGTGATCACATCG
66 CAAAAAAATTTTAGAGATCACATCG
3999859 AAAATTTCAAAGATTCACATT
1 AAAATTTCAAAGATTCACATT
3999880 AAAAAAAATT
Statistics
Matches: 91, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
90 47 0.52
91 44 0.48
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (90 bp):
AAAATTTCAAAGATTCACATTTGAGAAATTTTAAAGATTTAAACCCAAAATTCAAAAATTCACAT
CAAAAAAATTTTAGAGATCACATCG
Found at i:3999810 original size:46 final size:45
Alignment explanation
Indices: 3999687--3999879 Score: 158
Period size: 45 Copynumber: 4.3 Consensus size: 45
3999677 ATAAAATTCC
* * *
3999687 AAGATTCACATTTGAGAAATTTTAAAGATTTAAACCCAAAATTTTA
1 AAGATTCACATTTGAGAAATTTTAGAGATTTACA-TCAAAATTTTA
* * * * *
3999733 AATATTCACA-TCGAAAAAATTTAGAGATTTACATCGAAAATTTTG
1 AAGATTCACATTTGAGAAATTTTAGAGATTTACATC-AAAATTTTA
* * *
3999778 AAGATACACATTTGAGAATTTTTAGAGATTTACATTCAAAA-TTCA
1 AAGATTCACATTTGAGAAATTTTAGAGATTTACA-TCAAAATTTTA
* * ** * * * *
3999823 AAAATTCGCATTAAAAAAATTTTAGTGA-TCACATCGAAAATTTCA
1 AAGATTCACATTTGAGAAATTTTAGAGATTTACATC-AAAATTTTA
3999868 AAGATTCACATT
1 AAGATTCACATT
3999880 AAAAAAAATT
Statistics
Matches: 115, Mismatches: 27, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
43 2 0.02
44 9 0.08
45 70 0.61
46 32 0.28
47 2 0.02
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.34
Consensus pattern (45 bp):
AAGATTCACATTTGAGAAATTTTAGAGATTTACATCAAAATTTTA
Found at i:3999893 original size:25 final size:25
Alignment explanation
Indices: 3999859--3999935 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 25
3999849 GATCACATCG
3999859 AAAATTTCAAAGATTCACATTAAAA
1 AAAATTTCAAAGATTCACATTAAAA
** *
3999884 AAAATTTCAAAGATTTTCATTTGAAA
1 AAAATTTCAAAGATTCACA-TTAAAA
* * *
3999910 AGAATTTTAGAGATTCACATCTAAAA
1 AAAATTTCAAAGATTCACAT-TAAAA
3999936 TTTTAAAGAT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
25 18 0.44
26 23 0.56
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.32
Consensus pattern (25 bp):
AAAATTTCAAAGATTCACATTAAAA
Found at i:3999966 original size:46 final size:46
Alignment explanation
Indices: 3999884--4000081 Score: 176
Period size: 46 Copynumber: 4.3 Consensus size: 46
3999874 CACATTAAAA
* * *
3999884 AAAATTTCAAAGATT-TTCATTTGAAAAGAATTTTAGAGATTCACATCT
1 AAAATTTCAAAGATTCAT-ATTTG-AAA-AATTTTAGAGATTCAAATCC
* * *
3999932 AAAATTTTAAAGATTCATATTTGAAAAATTTTAGAGATTTATATCC
1 AAAATTTCAAAGATTCATATTTGAAAAATTTTAGAGATTCAAATCC
*
3999978 AAAA-TTCAAAGATTTCA-ATTTGAAAAA-TTTAGAGATTCAGAT-C
1 AAAATTTCAAAGA-TTCATATTTGAAAAATTTTAGAGATTCAAATCC
* * ***
4000021 TAAA-TTCAAAAGTTTACAT-TCAAAAAAATTTTAGAGATTCAAATCC
1 AAAATTTC-AAAGATT-CATATTTGAAAAATTTTAGAGATTCAAATCC
*
4000067 ATAATTTCAAAGATT
1 AAAATTTCAAAGATT
4000082 TGCATTGGAA
Statistics
Matches: 125, Mismatches: 17, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
43 9 0.07
44 25 0.20
45 31 0.25
46 34 0.27
47 6 0.05
48 19 0.15
49 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (46 bp):
AAAATTTCAAAGATTCATATTTGAAAAATTTTAGAGATTCAAATCC
Found at i:3999975 original size:24 final size:24
Alignment explanation
Indices: 3999859--4000016 Score: 80
Period size: 22 Copynumber: 6.7 Consensus size: 24
3999849 GATCACATCG
* * **
3999859 AAAATTTCAAAGATTCACATTAAAA
1 AAAATTTTAAAGATTCATATT-TGA
* *
3999884 AAAATTTCAAAGATT-TTCATTTGAA
1 AAAATTTTAAAGATTCAT-ATTTG-A
* * *
3999909 AAGAATTTTAGAGATTCACATCT--
1 AA-AATTTTAAAGATTCATATTTGA
3999932 AAAATTTTAAAGATTCATATTTGA
1 AAAATTTTAAAGATTCATATTTGA
* * **
3999956 AAAATTTTAGAGATT--TATATCC
1 AAAATTTTAAAGATTCATATTTGA
*
3999978 AAAA-TTCAAAGATTTCA-ATTTGA
1 AAAATTTTAAAGA-TTCATATTTGA
*
4000001 AAAA-TTTAGAGATTCA
1 AAAATTTTAAAGATTCA
4000017 GATCTAAATT
Statistics
Matches: 101, Mismatches: 23, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
21 6 0.06
22 31 0.31
23 15 0.15
24 14 0.14
25 21 0.21
26 14 0.14
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (24 bp):
AAAATTTTAAAGATTCATATTTGA
Found at i:4000016 original size:22 final size:23
Alignment explanation
Indices: 3999747--4000016 Score: 76
Period size: 22 Copynumber: 11.7 Consensus size: 23
3999737 TTCACATCGA
* *
3999747 AAAAATTTAGAGATTTACA-TCG
1 AAAAATTTAGAGATTCACATTTG
* *
3999769 -AAAATTTTGAAGATACACATTTG
1 AAAAATTTAG-AGATTCACATTTG
** *
3999792 AGAATTTTTAGAGATTTACA-TT-
1 A-AAAATTTAGAGATTCACATTTG
* * * * * **
3999814 CAAAATTCAAAAATTCGCATTAA
1 AAAAATTTAGAGATTCACATTTG
* *
3999837 AAAAATTTTAGTGA-TCACA-TCG
1 AAAAA-TTTAGAGATTCACATTTG
* **
3999859 -AAAATTTCAAAGATTCACATTAAA
1 AAAAATTT-AGAGATTCACATT-TG
* **
3999883 AAAAATTTCAAAGATTTTCATTTG
1 AAAAATTT-AGAGATTCACATTTG
*
3999907 AAAAGAATTTTAGAGATTCACATCT-
1 -AAA-AA-TTTAGAGATTCACATTTG
* * *
3999932 AAAATTTTAAAGATTCATATTTG
1 AAAAATTTAGAGATTCACATTTG
* * *
3999955 AAAAATTTTAGAGATT--TATATC
1 AAAAA-TTTAGAGATTCACATTTG
* * *
3999977 CAAAATTCAAAGATTTCA-ATTTG
1 AAAAATTTAGAGA-TTCACATTTG
4000000 AAAAATTTAGAGATTCA
1 AAAAATTTAGAGATTCA
4000017 GATCTAAATT
Statistics
Matches: 174, Mismatches: 54, Indels: 40
0.65 0.20 0.15
Matches are distributed among these distances:
20 3 0.02
21 32 0.18
22 42 0.24
23 31 0.18
24 23 0.13
25 28 0.16
26 12 0.07
27 3 0.02
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (23 bp):
AAAAATTTAGAGATTCACATTTG
Found at i:4000116 original size:24 final size:24
Alignment explanation
Indices: 4000095--4000143 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
4000085 ATTGGAAATT
* * *
4000095 TTTTAGAAATTTTTATTTGAAAAA
1 TTTTAAAAATTCTCATTTGAAAAA
4000119 TTTTAAAAATTCTCATTTGAAAAA
1 TTTTAAAAATTCTCATTTGAAAAA
4000143 T
1 T
4000144 ATTAGAGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (24 bp):
TTTTAAAAATTCTCATTTGAAAAA
Found at i:4000703 original size:38 final size:39
Alignment explanation
Indices: 4000566--4000708 Score: 153
Period size: 39 Copynumber: 3.6 Consensus size: 39
4000556 TCTTGTCCAA
** ** ** *
4000566 AAAATCTCATAATGAAAAGTTTTCCTCATTCCATAATTC
1 AAAATCTCATCTTGAAAAGTTTTCCTCATTTAAGGAGTC
*
4000605 AAAATCTCATCCTGAAAAAAGTTTTCCTCATTTAAGGAGTC
1 AAAATCTCATCTTG--AAAAGTTTTCCTCATTTAAGGAGTC
* *
4000646 AAAATCTCATCTTGAAAAGTTTTTCTCATTTAAGGATTC
1 AAAATCTCATCTTGAAAAGTTTTCCTCATTTAAGGAGTC
* *
4000685 -AAATCTTATCTTGGAAAGTTTTCC
1 AAAATCTCATCTTGAAAAGTTTTCC
4000709 CTATTCAAGG
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
38 21 0.24
39 35 0.39
41 33 0.37
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (39 bp):
AAAATCTCATCTTGAAAAGTTTTCCTCATTTAAGGAGTC
Found at i:4002121 original size:10 final size:11
Alignment explanation
Indices: 4002100--4002133 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
4002090 GCTTTTAATC
4002100 TTTTTCATTTT
1 TTTTTCATTTT
4002111 TTTTTCATTTT
1 TTTTTCATTTT
4002122 TCATTTTCATTT
1 T--TTTTCATTT
4002134 CTACCTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
13 9 0.43
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTCATTTT
Found at i:4002134 original size:18 final size:18
Alignment explanation
Indices: 4002100--4002134 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4002090 GCTTTTAATC
**
4002100 TTTTTCATTTTTTTTTCA
1 TTTTTCATTTTCATTTCA
4002118 TTTTTCATTTTCATTTC
1 TTTTTCATTTTCATTTC
4002135 TACCTTTGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTCATTTTCATTTCA
Found at i:4007108 original size:13 final size:13
Alignment explanation
Indices: 4007090--4007142 Score: 72
Period size: 13 Copynumber: 4.2 Consensus size: 13
4007080 GTCAATTTTA
*
4007090 AGGGTTAAGGTTT
1 AGGGTTTAGGTTT
*
4007103 AGGG-TTAGGGTT
1 AGGGTTTAGGTTT
4007115 AGGGTTTAGGTTT
1 AGGGTTTAGGTTT
*
4007128 AAGGTTTAGGTTT
1 AGGGTTTAGGTTT
4007141 AG
1 AG
4007143 TGATAGCACT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
12 10 0.29
13 24 0.71
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (13 bp):
AGGGTTTAGGTTT
Found at i:4007114 original size:19 final size:19
Alignment explanation
Indices: 4007090--4007142 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
4007080 GTCAATTTTA
4007090 AGGGTTAAGGTTTAGGGTT
1 AGGGTTAAGGTTTAGGGTT
* *
4007109 AGGGTTAGGGTTTAGGTTT
1 AGGGTTAAGGTTTAGGGTT
* *
4007128 AAGGTTTAGGTTTAG
1 AGGGTTAAGGTTTAG
4007143 TGATAGCACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (19 bp):
AGGGTTAAGGTTTAGGGTT
Found at i:4007126 original size:6 final size:6
Alignment explanation
Indices: 4007092--4007142 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
4007082 CAATTTTAAG
* * *
4007092 GGTTAA GGTTTA GGGTTA GGGTTA GGGTTTA GGTTTAA GGTTTA GGTTTA
1 GGTTTA GGTTTA GGTTTA GGTTTA -GGTTTA GGTTT-A GGTTTA GGTTTA
4007142 G
1 G
4007143 TGATAGCACT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
6 29 0.73
7 11 0.28
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (6 bp):
GGTTTA
Found at i:4010654 original size:18 final size:18
Alignment explanation
Indices: 4010615--4010660 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
4010605 ATTAGTTTAT
* * *
4010615 GGTTTGGATTTGTTTTTG
1 GGTTTGGATTTGCTTCTA
4010633 GGTTTGGATTTGCTTCTA
1 GGTTTGGATTTGCTTCTA
*
4010651 GGTTTTGATT
1 GGTTTGGATT
4010661 GAGAATTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.09, C:0.04, G:0.30, T:0.57
Consensus pattern (18 bp):
GGTTTGGATTTGCTTCTA
Found at i:4017968 original size:25 final size:25
Alignment explanation
Indices: 4017918--4017991 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
4017908 TTAAAAGTGC
*
4017918 AAAATAAAAAAGCAAAAAAAATTTAA-
1 AAAAAAAAAAAG-AAAAAAAA-TTAAT
* *
4017944 AAAAAAAAGAAAGAGAAAGAATTAAT
1 AAAAAAAA-AAAGAAAAAAAATTAAT
*
4017970 AAAGAAAAAAAGAAAAAAAATT
1 AAAAAAAAAAAGAAAAAAAATT
4017992 GATGCAGCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 16 0.40
26 20 0.50
27 4 0.10
ACGTcount: A:0.77, C:0.01, G:0.09, T:0.12
Consensus pattern (25 bp):
AAAAAAAAAAAGAAAAAAAATTAAT
Found at i:4019832 original size:18 final size:17
Alignment explanation
Indices: 4019808--4019856 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
4019798 ACAAATCTGA
4019808 AAATTCTTATGAATTTG
1 AAATTCTTATGAATTTG
*
4019825 AAAGTTC-TAGTGAAATTG
1 AAA-TTCTTA-TGAATTTG
*
4019843 AAATTCTTGTGAAT
1 AAATTCTTATGAAT
4019857 CTATAAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (17 bp):
AAATTCTTATGAATTTG
Found at i:4019864 original size:18 final size:17
Alignment explanation
Indices: 4019801--4020057 Score: 119
Period size: 17 Copynumber: 14.9 Consensus size: 17
4019791 AGTTTTTACA
*
4019801 AATCTGAAAATTCTTATG
1 AATCT-AAAATTCTTGTG
* * *
4019819 AATTTGAAAGTTCTAGTG
1 AATCT-AAAATTCTTGTG
*
4019837 AAAT-TGAAATTCTTGTG
1 -AATCTAAAATTCTTGTG
4019854 AATCTATAAATTCTTGTG
1 AATCTA-AAATTCTTGTG
* * *
4019872 AAACT-AATTTCTTGTA
1 AATCTAAAATTCTTGTG
* *
4019888 AATTTGAAAATTATTGTG
1 AATCT-AAAATTCTTGTG
* * **
4019906 AACCTAAAATTTTTACG
1 AATCTAAAATTCTTGTG
*
4019923 AATCTAAAATTTTTGTG
1 AATCTAAAATTCTTGTG
* *
4019940 AACCTAAAATTCTTGCG
1 AATCTAAAATTCTTGTG
* * * *
4019957 AATTTGAAGTTCTTG-C
1 AATCTAAAATTCTTGTG
* *
4019973 AAACTTAAAATTAC-AGTG
1 AATC-TAAAATT-CTTGTG
* * * *
4019991 AACCTGAAGTT-TTGCG
1 AATCTAAAATTCTTGTG
*
4020007 AACCTAAAATTCTTGTG
1 AATCTAAAATTCTTGTG
* * *
4020024 AATGTGAAAATTTTTGCG
1 AATCT-AAAATTCTTGTG
*
4020042 AATCTAAAAATCTTGT
1 AATCTAAAATTCTTGT
4020058 AAATATTTCA
Statistics
Matches: 174, Mismatches: 54, Indels: 23
0.69 0.22 0.09
Matches are distributed among these distances:
16 28 0.16
17 84 0.48
18 59 0.34
19 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (17 bp):
AATCTAAAATTCTTGTG
Found at i:4020219 original size:34 final size:34
Alignment explanation
Indices: 4020181--4020310 Score: 120
Period size: 34 Copynumber: 3.8 Consensus size: 34
4020171 CAAATTTGAG
* *
4020181 TTCTTATGAATCTGAAAACCTTACGAATCTTCCA
1 TTCTTGTGAATCTGAAAATCTTACGAATCTTCCA
* * *****
4020215 TTCTTGTGATTCT-AAATTCTTACGAATAAGAAA
1 TTCTTGTGAATCTGAAAATCTTACGAATCTTCCA
* *
4020248 ATCTTGTGAATCTAAAAATCTTACGAATCTTCCA
1 TTCTTGTGAATCTGAAAATCTTACGAATCTTCCA
*
4020282 TTCTT-TCAAATCTGAAAAGTCTTACGAAT
1 TTCTTGT-GAATCTGAAAA-TCTTACGAAT
4020311 TTTTGTGTCT
Statistics
Matches: 73, Mismatches: 20, Indels: 5
0.74 0.20 0.05
Matches are distributed among these distances:
33 25 0.34
34 38 0.52
35 10 0.14
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (34 bp):
TTCTTGTGAATCTGAAAATCTTACGAATCTTCCA
Found at i:4020275 original size:17 final size:18
Alignment explanation
Indices: 4020232--4020277 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
4020222 GATTCTAAAT
*
4020232 TCTTACGAAT-AAGAAAA
1 TCTTACGAATCTAGAAAA
**
4020249 TCTTGTGAATCTA-AAAA
1 TCTTACGAATCTAGAAAA
4020266 TCTTACGAATCT
1 TCTTACGAATCT
4020278 TCCATTCTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (18 bp):
TCTTACGAATCTAGAAAA
Found at i:4020864 original size:24 final size:24
Alignment explanation
Indices: 4020835--4020887 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
4020825 AAGGGAAACT
*
4020835 CAAAAAATGAAATCAAACCAAATCA
1 CAAAAAAT-AAATCAAACAAAATCA
* *
4020860 CAAAAAATTAATCAAATAAAATCA
1 CAAAAAATAAATCAAACAAAATCA
4020884 CAAA
1 CAAA
4020888 TTTGGGGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.66, C:0.17, G:0.02, T:0.15
Consensus pattern (24 bp):
CAAAAAATAAATCAAACAAAATCA
Found at i:4021129 original size:18 final size:18
Alignment explanation
Indices: 4021108--4021153 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4021098 TTAGTTTCCA
4021108 GGTTTGGATTTG-TTTCTG
1 GGTTTGGATTTGCTTT-TG
*
4021126 GGTTTGAATTTGCTTTTG
1 GGTTTGGATTTGCTTTTG
*
4021144 GGTTTTGATT
1 GGTTTGGATT
4021154 GGGAATTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.09, C:0.04, G:0.30, T:0.57
Consensus pattern (18 bp):
GGTTTGGATTTGCTTTTG
Found at i:4021916 original size:14 final size:15
Alignment explanation
Indices: 4021895--4021931 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
4021885 ATATGTATAT
4021895 TATATTATTGCATAA
1 TATATTATTGCATAA
*
4021910 T-TATTATTGCATGA
1 TATATTATTGCATAA
4021924 TATATTAT
1 TATATTAT
4021932 ATTATTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.51
Consensus pattern (15 bp):
TATATTATTGCATAA
Found at i:4023473 original size:105 final size:104
Alignment explanation
Indices: 4023292--4023493 Score: 359
Period size: 105 Copynumber: 1.9 Consensus size: 104
4023282 AATCAAATTG
4023292 ACTTGCTAAACTTCATTATGATATTCACTTGTTGAAAATTATATATATTCTCTTGAATAACTAAA
1 ACTTGCTAAACTTCATTATGATATTCACTTGTTGAAAATTATATATATTCTCTTGAATAACTAAA
4023357 GTATGATATGAAGTTTAAGGATATAATTAGTAAGATCTA
66 GTATGATATGAAGTTTAAGGATATAATTAGTAAGATCTA
* * *
4023396 ACTTGCTAAACTTCATTATGATATTCATTTAGTTGAAAATTATATATATTCTTTTGAATGACTAA
1 ACTTGCTAAACTTCATTATGATATTCACTT-GTTGAAAATTATATATATTCTCTTGAATAACTAA
*
4023461 AGTATGATATGAAGTTTAAGGATGTAATTAGTA
65 AGTATGATATGAAGTTTAAGGATATAATTAGTA
4023494 GGAACTTGAA
Statistics
Matches: 93, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
104 29 0.31
105 64 0.69
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (104 bp):
ACTTGCTAAACTTCATTATGATATTCACTTGTTGAAAATTATATATATTCTCTTGAATAACTAAA
GTATGATATGAAGTTTAAGGATATAATTAGTAAGATCTA
Found at i:4026031 original size:7 final size:7
Alignment explanation
Indices: 4026002--4026175 Score: 76
Period size: 7 Copynumber: 25.0 Consensus size: 7
4025992 TTGGGGTTTA
4026002 GTTTAGG
1 GTTTAGG
*
4026009 GTTT-TG
1 GTTTAGG
* *
4026015 GCTTAAG
1 GTTTAGG
4026022 GTTTAGG
1 GTTTAGG
*
4026029 GTTTTGG
1 GTTTAGG
* *
4026036 TTTTAGA
1 GTTTAGG
4026043 G-TTAGG
1 GTTTAGG
*
4026049 TTTTAGG
1 GTTTAGG
*
4026056 GTTTAAG
1 GTTTAGG
4026063 GTTT--G
1 GTTTAGG
4026068 GTTTAGG
1 GTTTAGG
*
4026075 ATTTTGCATGGTG
1 -GTTT--A--G-G
4026088 GTTTGAGG
1 GTTT-AGG
4026096 GTTTAGG
1 GTTTAGG
*
4026103 ATTTA--
1 GTTTAGG
4026108 GTTTAGG
1 GTTTAGG
*
4026115 GTTT-TG
1 GTTTAGG
* *
4026121 ATTT-TG
1 GTTTAGG
*
4026127 GTTTAGA
1 GTTTAGG
* *
4026134 TTTTCGG
1 GTTTAGG
4026141 GTTTAGG
1 GTTTAGG
4026148 GTTTAGG
1 GTTTAGG
*
4026155 ATTTAGG
1 GTTTAGG
4026162 GTTTAGG
1 GTTTAGG
4026169 GTTTAGG
1 GTTTAGG
4026176 CTTTTTAAAG
Statistics
Matches: 123, Mismatches: 31, Indels: 26
0.68 0.17 0.14
Matches are distributed among these distances:
5 9 0.07
6 17 0.14
7 81 0.66
8 8 0.07
9 1 0.01
10 1 0.01
11 1 0.01
12 4 0.03
13 1 0.01
ACGTcount: A:0.16, C:0.02, G:0.35, T:0.48
Consensus pattern (7 bp):
GTTTAGG
Found at i:4026070 original size:20 final size:18
Alignment explanation
Indices: 4026008--4026071 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 18
4025998 TTTAGTTTAG
*
4026008 GGTTTTGGCTTAAGGTTT
1 GGTTTTGGTTTAAGGTTT
* *
4026026 AGGGTTTTGGTTTTAGAGTTA
1 --GGTTTTGGTTTAAG-GTTT
4026047 GGTTTTAGGGTTTAAGGTTT
1 GGTTTT--GGTTTAAGGTTT
4026067 GGTTT
1 GGTTT
4026072 AGGATTTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 6 0.17
20 20 0.56
21 10 0.28
ACGTcount: A:0.14, C:0.02, G:0.34, T:0.50
Consensus pattern (18 bp):
GGTTTTGGTTTAAGGTTT
Found at i:4026113 original size:59 final size:54
Alignment explanation
Indices: 4026027--4026173 Score: 140
Period size: 59 Copynumber: 2.6 Consensus size: 54
4026017 TTAAGGTTTA
* * *
4026027 GGGTTTTGGTTTTA-GAGTTAGGTTTTAGGGTTTAAG-GTTTGGTTTAGGATTTTGC
1 GGGTTTAGGGTTTAGGATTTAGG-TTTAGGGTTTAAGAGTTTGGTTTA-GATTTT-C
* *
4026082 ATGGTGGTTTGAGGGTTTAGGATTTA-GTTTAGGGTTT-TGATTTTGGTTTAGATTTTC
1 ---G-GGTTT-AGGGTTTAGGATTTAGGTTTAGGGTTTAAGAGTTTGGTTTAGATTTTC
4026139 GGGTTTAGGGTTTAGGATTTAGGGTTTAGGGTTTA
1 GGGTTTAGGGTTTAGGATTTA-GGTTTAGGGTTTA
4026174 GGCTTTTTAA
Statistics
Matches: 77, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
52 15 0.19
53 5 0.06
54 12 0.16
57 1 0.01
58 8 0.10
59 24 0.31
60 7 0.09
61 5 0.06
ACGTcount: A:0.16, C:0.01, G:0.35, T:0.48
Consensus pattern (54 bp):
GGGTTTAGGGTTTAGGATTTAGGTTTAGGGTTTAAGAGTTTGGTTTAGATTTTC
Found at i:4027139 original size:12 final size:12
Alignment explanation
Indices: 4027107--4027142 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4027097 TCTCCTTAAA
4027107 AAAAATAATATG
1 AAAAATAATATG
4027119 -AAAAT--TATG
1 AAAAATAATATG
4027128 AAAAATAATATG
1 AAAAATAATATG
4027140 AAA
1 AAA
4027143 TGTAATAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
9 4 0.19
10 5 0.24
11 5 0.24
12 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (12 bp):
AAAAATAATATG
Found at i:4035393 original size:15 final size:15
Alignment explanation
Indices: 4035373--4035403 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4035363 TTTTCTTTCT
4035373 ATATATAATACATAA
1 ATATATAATACATAA
*
4035388 ATATATAATATATAA
1 ATATATAATACATAA
4035403 A
1 A
4035404 CTGATCATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATATAATACATAA
Found at i:4035734 original size:16 final size:16
Alignment explanation
Indices: 4035695--4035806 Score: 60
Period size: 16 Copynumber: 7.2 Consensus size: 16
4035685 GCTGTCCTTA
*
4035695 TTTTATATATTTTTAT
1 TTTTATTTATTTTTAT
*
4035711 GTTGTATTTATTTTTAT
1 -TTTTATTTATTTTTAT
4035728 TTTTATTT-TATTTTA-
1 TTTTATTTAT-TTTTAT
* **
4035743 TGTTGCTTATCTTTT-T
1 TTTTATTTAT-TTTTAT
*
4035759 CTTTATTTA-TTTTAT
1 TTTTATTTATTTTTAT
*
4035774 TTATCA-TTA-TTTTA-
1 TT-TTATTTATTTTTAT
4035788 -TTTATTTATATTTTAT
1 TTTTATTTAT-TTTTAT
4035804 TTT
1 TTT
4035807 ACTTCTCATT
Statistics
Matches: 71, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
12 2 0.03
13 4 0.06
14 4 0.06
15 21 0.30
16 24 0.34
17 16 0.23
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (16 bp):
TTTTATTTATTTTTAT
Found at i:4035736 original size:5 final size:5
Alignment explanation
Indices: 4035717--4035838 Score: 56
Period size: 6 Copynumber: 23.2 Consensus size: 5
4035707 TTATGTTGTA
* * * *
4035717 TTTATT TTTATT TTTAT TTTAT TTTAT GTT-G CTTAT CTTTTT CTTTA-
1 TTTA-T TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT -TTTAT
*
4035764 TTTAT TTTA- TTTAT CATTAT TTTA- TTTAT TTATAT TTTAT TTTACT
1 TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT TT-TAT TTTAT TTTA-T
*
4035810 TCTCA- TTTAT CTTTAT CTTTAT CTTTAT T
1 T-TTAT TTTAT -TTTAT -TTTAT -TTTAT T
4035839 ATTTTACCTT
Statistics
Matches: 94, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
4 16 0.17
5 31 0.33
6 45 0.48
7 2 0.02
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (5 bp):
TTTAT
Found at i:4035785 original size:15 final size:14
Alignment explanation
Indices: 4035755--4035805 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
4035745 TTGCTTATCT
*
4035755 TTTTCTTTAT-TTA
1 TTTTATTTATATTA
4035768 TTTTATTTATCATTA
1 TTTTATTTAT-ATTA
*
4035783 TTTTATTTATTTATA
1 TTTTATTTATAT-TA
4035798 TTTTATTT
1 TTTTATTT
4035806 TACTTCTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 9 0.27
14 1 0.03
15 23 0.70
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTATATTA
Found at i:4035785 original size:19 final size:18
Alignment explanation
Indices: 4035717--4035807 Score: 59
Period size: 19 Copynumber: 5.2 Consensus size: 18
4035707 TTATGTTGTA
*
4035717 TTTATTTTTATT-TTTAT
1 TTTATTTATATTATTTAT
* **
4035734 TTTATTTTATGTTGCTTAT
1 TTTA-TTTATATTATTTAT
* *
4035753 CTT-TTTCT-TTATTTAT
1 TTTATTTATATTATTTAT
4035769 TTTATTTATCATTATTT-T
1 TTTATTTAT-ATTATTTAT
4035787 ATTTATTTATA-T-TTTAT
1 -TTTATTTATATTATTTAT
4035804 TTTA
1 TTTA
4035808 CTTCTCATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
16 15 0.26
17 14 0.24
18 8 0.14
19 21 0.36
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTATTTATATTATTTAT
Found at i:4036946 original size:58 final size:60
Alignment explanation
Indices: 4036818--4036948 Score: 144
Period size: 58 Copynumber: 2.2 Consensus size: 60
4036808 AAACTAAATC
* ** * *
4036818 TTATTAAATTATTGGAAGGTTTAATTATATTTTTCTTAAAATATATTTTTGAAGTCAATC
1 TTATCAAATTATTGGAAGGTTTAATTATATTTTTCAGAAAATATATTTTTGAAATCAATA
* * *
4036878 TTACCAAATTATTGGAAGGTTTAA-T-T-TTTTTCAAGAAAATGA-ATTTTTTAAATTAATA
1 TTATCAAATTATTGGAAGGTTTAATTATATTTTTC-AGAAAAT-ATATTTTTGAAATCAATA
4036936 TTATCAAATTATT
1 TTATCAAATTATT
4036949 AGAGGATATA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
57 6 0.10
58 30 0.50
59 2 0.03
60 22 0.37
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.48
Consensus pattern (60 bp):
TTATCAAATTATTGGAAGGTTTAATTATATTTTTCAGAAAATATATTTTTGAAATCAATA
Found at i:4038403 original size:13 final size:12
Alignment explanation
Indices: 4038364--4038392 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4038354 AAAAATTCAA
4038364 TTAAAT-ATAAT
1 TTAAATCATAAT
4038375 TTAAATCATAAT
1 TTAAATCATAAT
4038387 TTAAAT
1 TTAAAT
4038393 TTCAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
TTAAATCATAAT
Found at i:4040911 original size:16 final size:18
Alignment explanation
Indices: 4040890--4040952 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
4040880 ATAAATAATA
4040890 AATAAATCATAC-A-AAT
1 AATAAATCATACAACAAT
4040906 AATAAATCA-AGCAACAAT
1 AATAAATCATA-CAACAAT
* *
4040924 AAATAAATCATGCAATAAT
1 -AATAAATCATACAACAAT
*
4040943 ATTAAATCAT
1 AATAAATCAT
4040953 GCAAATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 1 0.03
16 10 0.26
17 1 0.03
18 12 0.31
19 15 0.38
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.25
Consensus pattern (18 bp):
AATAAATCATACAACAAT
Found at i:4040950 original size:18 final size:17
Alignment explanation
Indices: 4040890--4040967 Score: 77
Period size: 18 Copynumber: 4.4 Consensus size: 17
4040880 ATAAATAATA
*
4040890 AATAAATCATAC-AAAT
1 AATAAATCATGCAAAAT
*
4040906 AATAAATCAAGCAACAAT
1 AATAAATCATGCAA-AAT
4040924 AAATAAATCATGCAATAAT
1 -AATAAATCATGCAA-AAT
*
4040943 ATTAAATCATGCAAATAT
1 AATAAATCATGCAAA-AT
*
4040961 ATTAAAT
1 AATAAAT
4040968 ATCTTACCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
16 10 0.19
17 2 0.04
18 25 0.47
19 16 0.30
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.27
Consensus pattern (17 bp):
AATAAATCATGCAAAAT
Found at i:4041028 original size:7 final size:7
Alignment explanation
Indices: 4041016--4041053 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
4041006 ATTACACAGA
4041016 AAATAAT
1 AAATAAT
4041023 AAATAAAT
1 AAAT-AAT
4041031 AAATAAT
1 AAATAAT
*
4041038 AAAAAAT
1 AAATAAT
4041045 AAA-AAT
1 AAATAAT
4041051 AAA
1 AAA
4041054 AACTTAAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
AAATAAT
Found at i:4041081 original size:12 final size:12
Alignment explanation
Indices: 4041020--4041091 Score: 54
Period size: 12 Copynumber: 5.6 Consensus size: 12
4041010 CACAGAAAAT
4041020 AATAAATAAATAAA
1 AATAAA-AAAT-AA
4041034 TAATAAAAAATAAA
1 -AATAAAAAAT-AA
*
4041048 AATAAAAACTTAA
1 AATAAAAA-ATAA
* *
4041061 ACTAGAAAATAA
1 AATAAAAAATAA
*
4041073 AATAAAAAAGAA
1 AATAAAAAATAA
*
4041085 AAGAAAA
1 AATAAAA
4041092 GCAAAAACTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
12 18 0.38
13 16 0.33
14 8 0.17
15 6 0.12
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.17
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:4042139 original size:12 final size:12
Alignment explanation
Indices: 4042109--4042159 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
4042099 CTTTTGACTA
4042109 AAAAT-AAAAAT
1 AAAATCAAAAAT
*
4042120 -AAACCAAAAAT
1 AAAATCAAAAAT
4042131 AAAATC-AAAAT
1 AAAATCAAAAAT
*
4042142 CAAAATCAAAATT
1 -AAAATCAAAAAT
4042155 AAAAT
1 AAAAT
4042160 TAAACCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 3 0.09
11 11 0.33
12 15 0.45
13 4 0.12
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAATCAAAAAT
Found at i:4042163 original size:6 final size:6
Alignment explanation
Indices: 4042126--4042159 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
4042116 AAATAAACCA
*
4042126 AAAAT- AAAATC AAAATC AAAATC AAAATT AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
4042160 TAAACCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAATC
Found at i:4044332 original size:8 final size:8
Alignment explanation
Indices: 4044319--4044347 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4044309 CAATTTTTTA
4044319 AAATAATT
1 AAATAATT
4044327 AAATAATT
1 AAATAATT
4044335 AAATAATT
1 AAATAATT
4044343 AAATA
1 AAATA
4044348 GCTAATCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAATAATT
Found at i:4044881 original size:12 final size:12
Alignment explanation
Indices: 4044866--4044949 Score: 69
Period size: 12 Copynumber: 6.6 Consensus size: 12
4044856 TTTCACTTAA
4044866 GGTTTTATTTAG
1 GGTTTTATTTAG
* **
4044878 GGTTTCACCTAG
1 GGTTTTATTTAG
*
4044890 GGTTTTGTTTTAG
1 GGTTTT-ATTTAG
4044903 GGTTTTATTTAG
1 GGTTTTATTTAG
4044915 GGTTTTAATTTTAG
1 GGTTTT-A-TTTAG
**
4044929 AATTTTAATTTTAG
1 GGTTTT-A-TTTAG
4044943 GGTTTTA
1 GGTTTTA
4044950 GGAATTTACA
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
12 25 0.44
13 11 0.19
14 21 0.37
ACGTcount: A:0.19, C:0.04, G:0.23, T:0.55
Consensus pattern (12 bp):
GGTTTTATTTAG
Found at i:4044882 original size:24 final size:24
Alignment explanation
Indices: 4044849--4044921 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
4044839 CACATAGGGT
* *
4044849 TTTAGAGTTTCACTTAAGGTTTTA
1 TTTAGGGTTTCACTTAGGGTTTTA
* *
4044873 TTTAGGGTTTCACCTAGGGTTTTGT
1 TTTAGGGTTTCACTTAGGGTTTT-A
* *
4044898 TTTAGGGTTTTATTTAGGGTTTTA
1 TTTAGGGTTTCACTTAGGGTTTTA
4044922 ATTTTAGAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 20 0.50
25 20 0.50
ACGTcount: A:0.18, C:0.07, G:0.23, T:0.52
Consensus pattern (24 bp):
TTTAGGGTTTCACTTAGGGTTTTA
Found at i:4044915 original size:25 final size:25
Alignment explanation
Indices: 4044847--4044929 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 25
4044837 TACACATAGG
*
4044847 GTTTTAGAGTTTCACTTAAGGTTTT
1 GTTTTAGAGTTTCACTTAGGGTTTT
* * *
4044872 -ATTTAGGGTTTCACCTAGGGTTTT
1 GTTTTAGAGTTTCACTTAGGGTTTT
* * *
4044896 GTTTTAGGGTTTTATTTAGGGTTTT
1 GTTTTAGAGTTTCACTTAGGGTTTT
*
4044921 AATTTTAGA
1 -GTTTTAGA
4044930 ATTTTAATTT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
24 20 0.43
25 20 0.43
26 6 0.13
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (25 bp):
GTTTTAGAGTTTCACTTAGGGTTTT
Found at i:4044948 original size:14 final size:14
Alignment explanation
Indices: 4044887--4044949 Score: 78
Period size: 14 Copynumber: 4.7 Consensus size: 14
4044877 GGGTTTCACC
*
4044887 TAGGGTTTT-GTTT
1 TAGGGTTTTAATTT
4044900 TAGGGTTTT-A-TT
1 TAGGGTTTTAATTT
4044912 TAGGGTTTTAATTT
1 TAGGGTTTTAATTT
**
4044926 TAGAATTTTAATTT
1 TAGGGTTTTAATTT
4044940 TAGGGTTTTA
1 TAGGGTTTTA
4044950 GGAATTTACA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
12 11 0.26
13 10 0.23
14 22 0.51
ACGTcount: A:0.21, C:0.00, G:0.22, T:0.57
Consensus pattern (14 bp):
TAGGGTTTTAATTT
Found at i:4045017 original size:103 final size:103
Alignment explanation
Indices: 4044907--4045102 Score: 277
Period size: 103 Copynumber: 1.9 Consensus size: 103
4044897 TTTTAGGGTT
4044907 TTATTTAGGGTTTTAATTTTAGAATTTTAATTTTAG-GGTTTTAGGAATTTACAAACCTCTCTAA
1 TTATTTAGGGTTTTAATTTTAGAATTTTAATTTTAGAGG-TTTAGGAATTTACAAACCTCTCTAA
* * *
4044971 AAATCTTTAATATCTAGGCAGATTTTTTGGAGTAAGTTG
65 AAATCTCTAACATCTAGACAGATTTTTTGGAGTAAGTTG
* * ** ** *
4045010 TTATTTAGGGTTTTAATTTTAGAGTTTTAGTTTTAGAGGTTTAGGAATTTATGAATTTCTTTAAA
1 TTATTTAGGGTTTTAATTTTAGAATTTTAATTTTAGAGGTTTAGGAATTTACAAACCTCTCTAAA
*
4045075 AATCTCTAACATCTAGATAGATTTTTTG
66 AATCTCTAACATCTAGACAGATTTTTTG
4045103 AAACAAGTTC
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
103 79 0.98
104 2 0.02
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (103 bp):
TTATTTAGGGTTTTAATTTTAGAATTTTAATTTTAGAGGTTTAGGAATTTACAAACCTCTCTAAA
AATCTCTAACATCTAGACAGATTTTTTGGAGTAAGTTG
Found at i:4045036 original size:14 final size:14
Alignment explanation
Indices: 4045013--4045052 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
4045003 TAAGTTGTTA
*
4045013 TTTAGGGTTTTAAT
1 TTTAGAGTTTTAAT
*
4045027 TTTAGAGTTTTAGT
1 TTTAGAGTTTTAAT
*
4045041 TTTAGAGGTTTA
1 TTTAGAGTTTTA
4045053 GGAATTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (14 bp):
TTTAGAGTTTTAAT
Found at i:4045188 original size:28 final size:28
Alignment explanation
Indices: 4045157--4045210 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
4045147 CTTTTGTATT
4045157 TTTTATTAA-AAATTATTTATTATTTATC
1 TTTTATTAATAAATT-TTTATTATTTATC
**
4045185 TTTTATTAATTTATTTTTATTATTTA
1 TTTTATTAATAAATTTTTATTATTTA
4045211 ATAATTCTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTATTAATAAATTTTTATTATTTATC
Found at i:4045189 original size:14 final size:13
Alignment explanation
Indices: 4045172--4045210 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 13
4045162 TTAAAAATTA
4045172 TTTATTATTTATCT
1 TTTATTATTTAT-T
4045186 TTTATTAATTTATT
1 TTTATT-ATTTATT
4045200 TTTATTATTTA
1 TTTATTATTTA
4045211 ATAATTCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.21
14 13 0.54
15 6 0.25
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTATTTATT
Found at i:4045199 original size:8 final size:7
Alignment explanation
Indices: 4045168--4045210 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
4045158 TTTATTAAAA
4045168 ATTATTT
1 ATTATTT
4045175 ATTATTT
1 ATTATTT
4045182 ATCT-TTT
1 AT-TATTT
4045189 ATTAATTT
1 ATT-ATTT
4045197 ATT-TTT
1 ATTATTT
4045203 ATTATTT
1 ATTATTT
4045210 A
1 A
4045211 ATAATTCTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 7 0.22
7 18 0.56
8 7 0.22
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTATTT
Found at i:4045460 original size:15 final size:15
Alignment explanation
Indices: 4045436--4045494 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
4045426 AAATAAACAT
*
4045436 ATAATCACAATAATC
1 ATAATAACAATAATC
*
4045451 ATAATAACAATATTC
1 ATAATAACAATAATC
*
4045466 ATAATAACAATAATA
1 ATAATAACAATAATC
* *
4045481 ATTATAATAATAAT
1 ATAATAACAATAAT
4045495 AGTGGTAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAATAACAATAATC
Found at i:4045472 original size:3 final size:3
Alignment explanation
Indices: 4045444--4045620 Score: 133
Period size: 3 Copynumber: 59.0 Consensus size: 3
4045434 ATATAATCAC
* * * * * *
4045444 AAT AAT CAT AAT AAC AAT ATT CAT AAT AAC AAT AAT AAT TAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** * ** * * **
4045492 AAT AGT GGT AAT AAT AAT AAT TAT TTT AAT TAT AAT AAT AGT GGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
4045540 AAT AAT GAT AAT GAT AAT GAT AAT AAAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
* *
4045585 AA- AAT ATAT TAT AAT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4045621 GTAAAAGCTA
Statistics
Matches: 134, Mismatches: 36, Indels: 8
0.75 0.20 0.04
Matches are distributed among these distances:
2 4 0.03
3 125 0.93
4 5 0.04
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:4050572 original size:30 final size:30
Alignment explanation
Indices: 4050538--4050697 Score: 115
Period size: 30 Copynumber: 5.1 Consensus size: 30
4050528 AACACAAATA
4050538 AAGTTTTGTTCAAACTTTGAAAATCATATT
1 AAGTTTTGTTCAAACTTTGAAAATCATATT
* * ** *
4050568 AAGTTTTGATTTAAGAAATAAGAAAA-CACAATT
1 AAGTTTTG--TTCA-AACTTTGAAAATCA-TATT
4050601 AAAGTTTTGTTCAAACTTTGAAAATCATATT
1 -AAGTTTTGTTCAAACTTTGAAAATCATATT
* * ** * * *
4050632 AAGTTTTGATTTAAGAAATAAGAAAACACAAATA
1 AAGTTTTG--TTCA-AACTTTGAAAA-TCATATT
*
4050666 AAGGTTTGTTCAAACTTTGAAAATCATATT
1 AAGTTTTGTTCAAACTTTGAAAATCATATT
4050696 AA
1 AA
4050698 TTATTTAATA
Statistics
Matches: 95, Mismatches: 25, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
30 22 0.23
31 19 0.20
32 16 0.17
33 19 0.20
34 19 0.20
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (30 bp):
AAGTTTTGTTCAAACTTTGAAAATCATATT
Found at i:4050722 original size:64 final size:64
Alignment explanation
Indices: 4050505--4050697 Score: 368
Period size: 64 Copynumber: 3.0 Consensus size: 64
4050495 ATTTAAAGAT
4050505 AGTTTTGATTTAAGAAATAAGAAAACACAAATAAAGTTTTGTTCAAACTTTGAAAATCATATTA
1 AGTTTTGATTTAAGAAATAAGAAAACACAAATAAAGTTTTGTTCAAACTTTGAAAATCATATTA
*
4050569 AGTTTTGATTTAAGAAATAAGAAAACACAATTAAAGTTTTGTTCAAACTTTGAAAATCATATTA
1 AGTTTTGATTTAAGAAATAAGAAAACACAAATAAAGTTTTGTTCAAACTTTGAAAATCATATTA
*
4050633 AGTTTTGATTTAAGAAATAAGAAAACACAAATAAAGGTTTGTTCAAACTTTGAAAATCATATTA
1 AGTTTTGATTTAAGAAATAAGAAAACACAAATAAAGTTTTGTTCAAACTTTGAAAATCATATTA
4050697 A
1 A
4050698 TTATTTAATA
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 126 1.00
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (64 bp):
AGTTTTGATTTAAGAAATAAGAAAACACAAATAAAGTTTTGTTCAAACTTTGAAAATCATATTA
Found at i:4058968 original size:32 final size:32
Alignment explanation
Indices: 4058925--4058992 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
4058915 GACAATATTT
* *
4058925 TTGGTTATGGGCCTTTGGCCATTTGAG-CTATA
1 TTGGTTATGGGCCTGTCGCCATTTGAGTC-ATA
*
4058957 TTGGTTGTGGGCCTGTCGCCATTTGAGTCATA
1 TTGGTTATGGGCCTGTCGCCATTTGAGTCATA
4058989 TTGG
1 TTGG
4058993 CTTTAAACTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.13, C:0.16, G:0.31, T:0.40
Consensus pattern (32 bp):
TTGGTTATGGGCCTGTCGCCATTTGAGTCATA
Found at i:4059041 original size:14 final size:14
Alignment explanation
Indices: 4059019--4059142 Score: 76
Period size: 14 Copynumber: 8.4 Consensus size: 14
4059009 TCATTCATTC
*
4059019 TTTTCATTTTTATT
1 TTTTTATTTTTATT
4059033 TTTTTATTTTTATT
1 TTTTTATTTTTATT
*
4059047 TTTTTATAAATTATAATT
1 TTTTTAT---TT-TTATT
*
4059065 TCTTTACTATTTTATT
1 TTTTTA-T-TTTTATT
* * *
4059081 ATTACATTTACTATTATA
1 -TT---TTTATTTTTATT
4059099 TTTTTATTTTTA-T
1 TTTTTATTTTTATT
4059112 TTTTTATTTTTA--
1 TTTTTATTTTTATT
4059124 -TTTTATTTTTATT
1 TTTTTATTTTTATT
4059137 TTTTTA
1 TTTTTA
4059143 ATAGCCAACA
Statistics
Matches: 87, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
11 11 0.13
13 12 0.14
14 33 0.38
16 4 0.05
17 8 0.09
18 14 0.16
19 1 0.01
20 4 0.05
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:4059106 original size:6 final size:6
Alignment explanation
Indices: 4059097--4059139 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
4059087 TTTACTATTA
4059097 TATTTT TATTTT TATTTTT TATTTT TA-TTT TATTTT TATTTT T
1 TATTTT TATTTT TA-TTTT TATTTT TATTTT TATTTT TATTTT T
4059140 TTAATAGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.14
6 24 0.69
7 6 0.17
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:4059110 original size:20 final size:20
Alignment explanation
Indices: 4059067--4059139 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 20
4059057 TTATAATTTC
* **
4059067 TTTACTATTTTATTATTACA
1 TTTACTATTTTATTTTTATT
*
4059087 TTTACTATTATATTTTTATT
1 TTTACTATTTTATTTTTATT
*
4059107 TTTA-TTTTTTATTTTTA-T
1 TTTACTATTTTATTTTTATT
4059125 TTTA-T-TTTTATTTTT
1 TTTACTATTTTATTTTT
4059140 TTAATAGCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 10 0.21
18 6 0.13
19 11 0.23
20 20 0.43
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTACTATTTTATTTTTATT
Found at i:4059114 original size:11 final size:11
Alignment explanation
Indices: 4059100--4059138 Score: 60
Period size: 11 Copynumber: 3.4 Consensus size: 11
4059090 ACTATTATAT
4059100 TTTTATTTTTA
1 TTTTATTTTTA
4059111 TTTTTTATTTTTA
1 --TTTTATTTTTA
4059124 TTTTATTTTTA
1 TTTTATTTTTA
4059135 TTTT
1 TTTT
4059139 TTTAATAGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 15 0.58
13 11 0.42
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:4059140 original size:19 final size:20
Alignment explanation
Indices: 4059094--4059142 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
4059084 ACATTTACTA
4059094 TTATATTTTTATTTTTATTT
1 TTATATTTTTATTTTTATTT
4059114 TT-TATTTTTA-TTTTATTT
1 TTATATTTTTATTTTTATTT
*
4059132 TTATTTTTTTA
1 TTATATTTTTA
4059143 ATAGCCAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 10 0.37
19 15 0.56
20 2 0.07
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (20 bp):
TTATATTTTTATTTTTATTT
Found at i:4059469 original size:11 final size:11
Alignment explanation
Indices: 4059449--4059485 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
4059439 CTTGAGGAAA
4059449 GTTTTTTTTTT
1 GTTTTTTTTTT
* *
4059460 GTTTTGTTTTA
1 GTTTTTTTTTT
4059471 GTTTTTTTTTT
1 GTTTTTTTTTT
4059482 GTTT
1 GTTT
4059486 GAGCTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.14, T:0.84
Consensus pattern (11 bp):
GTTTTTTTTTT
Found at i:4059766 original size:35 final size:35
Alignment explanation
Indices: 4059696--4059781 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 35
4059686 AGGATGTTCG
* ** *
4059696 AGACTAAGCCACAAGTCAAAAAAGAATGATGACCA
1 AGACTAAGTCACAAGTCAAAAAAGAAAAATAACCA
* *
4059731 AGA-TAGGATCACAAGTCAAAAAATAAAAATAACCA
1 AGACTAAG-TCACAAGTCAAAAAAGAAAAATAACCA
4059766 AGACTAAGTCACAAGT
1 AGACTAAGTCACAAGT
4059782 TAGGATATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
34 3 0.07
35 36 0.86
36 3 0.07
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.14
Consensus pattern (35 bp):
AGACTAAGTCACAAGTCAAAAAAGAAAAATAACCA
Found at i:4062484 original size:84 final size:84
Alignment explanation
Indices: 4062343--4062512 Score: 340
Period size: 84 Copynumber: 2.0 Consensus size: 84
4062333 ATGGCCAAAG
4062343 TAGTCAATGCATAAGCAATCTGATTTTCTTTTCAAGGAACAAGTTAAAACTAGACCTTTTTGAAC
1 TAGTCAATGCATAAGCAATCTGATTTTCTTTTCAAGGAACAAGTTAAAACTAGACCTTTTTGAAC
4062408 TACTTAATCAAATAAGCCA
66 TACTTAATCAAATAAGCCA
4062427 TAGTCAATGCATAAGCAATCTGATTTTCTTTTCAAGGAACAAGTTAAAACTAGACCTTTTTGAAC
1 TAGTCAATGCATAAGCAATCTGATTTTCTTTTCAAGGAACAAGTTAAAACTAGACCTTTTTGAAC
4062492 TACTTAATCAAATAAGCCA
66 TACTTAATCAAATAAGCCA
4062511 TA
1 TA
4062513 TGCTTTTAGT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (84 bp):
TAGTCAATGCATAAGCAATCTGATTTTCTTTTCAAGGAACAAGTTAAAACTAGACCTTTTTGAAC
TACTTAATCAAATAAGCCA
Found at i:4063837 original size:157 final size:157
Alignment explanation
Indices: 4063551--4063870 Score: 498
Period size: 157 Copynumber: 2.0 Consensus size: 157
4063541 ATTCTCATAT
* *
4063551 ATAAAAACATATGTTATTTGATATGATACATATAAACTGTAACTTATTCATGCATATCAAGCCTG
1 ATAAAAACATATGTTATTTGATAGGATACATATAAACCGTAACTTATTCATGCATATCAAGCCTG
* * ** * * **
4063616 TGAATCAAGTATTAAAATTTTGAATAATTTTAATATCATGTATTTATAATTTGGCTCTGTAACAA
66 TCAATCAAGTATTAAAATATCAAATAATTTTAATATCATGTATATATAATTTGGCCCAATAACAA
4063681 CAAAATAGTCTTAAACATACACAAACA
131 CAAAATAGTCTTAAACATACACAAACA
* *
4063708 ATAAAAACATATGTTATTTGATAGGATACATATCAACCGTAACTTGTTCATGCATATCAAGCCTG
1 ATAAAAACATATGTTATTTGATAGGATACATATAAACCGTAACTTATTCATGCATATCAAGCCTG
4063773 TCAATCAAGTATTAAAATATCAAATAATTTTAATATCATGTATATA-AATTTTGGCCCAATAACA
66 TCAATCAAGTATTAAAATATCAAATAATTTTAATATCATGTATATATAA-TTTGGCCCAATAACA
* *
4063837 ACACAATAGTCTTAAACATACTCAAACA
130 ACAAAATAGTCTTAAACATACACAAACA
4063865 ATAAAA
1 ATAAAA
4063871 GCTTTCGATA
Statistics
Matches: 148, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
156 2 0.01
157 146 0.99
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.33
Consensus pattern (157 bp):
ATAAAAACATATGTTATTTGATAGGATACATATAAACCGTAACTTATTCATGCATATCAAGCCTG
TCAATCAAGTATTAAAATATCAAATAATTTTAATATCATGTATATATAATTTGGCCCAATAACAA
CAAAATAGTCTTAAACATACACAAACA
Found at i:4070611 original size:170 final size:169
Alignment explanation
Indices: 4070382--4071128 Score: 959
Period size: 170 Copynumber: 4.4 Consensus size: 169
4070372 AGATGTGTAA
*
4070382 GCATTTATTCCAAGAAAATGCCTTTAATAATTCATTTTTAA-CTTAGTACATAATTACTAAAGGC
1 GCATTTATTCAAAGAAAATGCCTTTAATAATTCA-TTTTAAGCTTAGTACATAATTACTAAAGGC
* * *
4070446 GTTTGTTAATAACAAACGCCTACACATCTTTCCCTCTAAAAAATTTTAGGGTTATTAAAGGCATC
65 GTTTGTTAATAACAAACGCCTACACATCTTTCCCTCTAAAAAATTTTAGGATTATTAAAAGCGTC
* * *
4070511 TTCTACTAGAAAATGCCTTCAATATACTACGGTTATAGAAG
130 TTCTACTA-AAAATACCTTCAATATACTACAGTTATAAAAG
* * * *
4070552 GCATTTATTCAAAAAAAATGCCTTTAATAATTCATTTTAAGCTTAGTACGTAGTTACTAAAGGCA
1 GCATTTATTCAAAGAAAATGCCTTTAATAATTCATTTTAAGCTTAGTACATAATTACTAAAGGCG
** * * * *
4070617 TTTGTTAATAGTAAACACCTACACATCTTTCCCTCTAAAAACTTTTGGGATTATTAAAAGCGTTT
66 TTTGTTAATAACAAACGCCTACACATCTTTCCCTCTAAAAAATTTTAGGATTATTAAAAGCGTCT
* * * * *
4070682 TCTACTAAAAA-ACACTTAAATATAGTATAGATATAGAAG
131 TCTACTAAAAATAC-CTTCAATATACTACAGTTATAAAAG
* * *
4070721 GTATTTATTCTAAGAAAATGCCTTTAATAATTC-TTTTAAGCTTAGTACATAATTACTAAAGGCA
1 GCATTTATTCAAAGAAAATGCCTTTAATAATTCATTTTAAGCTTAGTACATAATTACTAAAGGCG
* *
4070785 TTTATTAATAACAAACGCCTACA-ATCTTTTCCTCTAAAAAATTTTA-GATTATTAAAAGCGTCT
66 TTTGTTAATAACAAACGCCTACACATCTTTCCCTCTAAAAAATTTTAGGATTATTAAAAGCGTCT
* *
4070848 T-TACTAAAAATATCTTCAATATACTATAGTTATAAAAG
131 TCTACTAAAAATACCTTCAATATACTACAGTTATAAAAG
* * * * * * * *
4070886 GCGTTTATTCTAGGAAAACGCCTTTAATAATACCTTTTAAGCTTAATACATAATTATTGAAA-GC
1 GCATTTATTCAAAGAAAATGCCTTTAATAATTCATTTTAAGCTTAGTACATAATTACT-AAAGGC
* * *
4070950 GTTTGTTAATAACAAACGCCTACACATATTTTCCTCTAAAAAATTTTAGGATTATTAAAGGCGTC
65 GTTTGTTAATAACAAACGCCTACACATCTTTCCCTCTAAAAAATTTTAGGATTATTAAAAGCGTC
*
4071015 TTCTACTAGAAAATGCCTTCAATATACTACAGTTATAAAAG
130 TTCTACTA-AAAATACCTTCAATATACTACAGTTATAAAAG
* * * * * * *
4071056 GCATTTATTCAAGGAAAATGCCTTTAATAGTTCCTTTTTAAGCTCAGAACATAATTACTGAAGGT
1 GCATTTATTCAAAGAAAATGCCTTTAATAATT-CATTTTAAGCTTAGTACATAATTACTAAAGGC
4071121 GTTTGTTA
65 GTTTGTTA
4071129 TTAAAGGCAT
Statistics
Matches: 502, Mismatches: 64, Indels: 21
0.86 0.11 0.04
Matches are distributed among these distances:
165 58 0.12
166 64 0.13
167 45 0.09
168 66 0.13
169 65 0.13
170 174 0.35
171 30 0.06
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (169 bp):
GCATTTATTCAAAGAAAATGCCTTTAATAATTCATTTTAAGCTTAGTACATAATTACTAAAGGCG
TTTGTTAATAACAAACGCCTACACATCTTTCCCTCTAAAAAATTTTAGGATTATTAAAAGCGTCT
TCTACTAAAAATACCTTCAATATACTACAGTTATAAAAG
Found at i:4071004 original size:334 final size:339
Alignment explanation
Indices: 4070256--4071119 Score: 971
Period size: 334 Copynumber: 2.5 Consensus size: 339
4070246 TTTCATAATG
* * * * * * *
4070256 TACATAATTATTAAAGGCATTTCTT-ATAACAACCATCTTCA-ATAATTT-TCTCTTTAAAAATT
1 TACATAATTACTAAAGGCATTTGTTAATAACAAACACCTACACAT-ATTTCCCTC-TAAAAAATT
* * * ** * * * * **
4070318 TTAGGATTATTAAAGGCGTCTTCTATTGGAAAACGCCTTCAACAAACTACAAAAAGATGTGTAA-
64 TTAGGATTATTAAAAGCGTCTTCTACTAGAAAATACCTT-AA-ATA-TAC-TACAGATATAAAAG
4070382 GCATTTATTCCAAGAAAATGCCTTTAATAATTCATTTTTAA-CTTAGTACATAATTACTAAAGGC
125 GCATTTATT-CAAGAAAATGCCTTTAATAATTC-TTTTTAAGCTTAGTACATAATTACTAAAGGC
* * * *
4070446 GTTTGTTAATAACAAACGCCTACACATCTTTCCCTCTAAAAAATTTTAGGGTTATTAAAGGCATC
188 ATTTATTAATAACAAACGCCTACACATCTTTCCCTCTAAAAAATTTTAGGATTATTAAAAGCATC
* * * *
4070511 TTCTACTAGAAAATGCCTTCAATATACTACGGTTATAGAAGGCATTTATTCAAAAAAAATGCCTT
253 TTCTACTAGAAAATACCTTCAATATACTACAGTTATAAAAGGCATTTATTCAAAAAAAACGCCTT
* *
4070576 TAATAATTCATTTTAAGCTTAG
318 TAATAATACATTTTAAGCTTAA
* * ** * *
4070598 TACGTAGTTACTAAAGGCATTTGTTAATAGTAAACACCTACACATCTTTCCCTCTAAAAACTTTT
1 TACATAATTACTAAAGGCATTTGTTAATAACAAACACCTACACATATTTCCCTCTAAAAAATTTT
* * * * * *
4070663 GGGATTATTAAAAGCGTTTTCTACTA-AAAA-ACACTTAAATATAGTATAGATATAGAAGGTATT
66 AGGATTATTAAAAGCGTCTTCTACTAGAAAATAC-CTTAAATATACTACAGATATAAAAGGCATT
4070726 TATTCTAAGAAAATGCCTTTAATAATTC-TTTTAAGCTTAGTACATAATTACTAAAGGCATTTAT
130 TATTC-AAGAAAATGCCTTTAATAATTCTTTTTAAGCTTAGTACATAATTACTAAAGGCATTTAT
* *
4070790 TAATAACAAACGCCTACA-ATCTTTTCCTCTAAAAAATTTTA-GATTATTAAAAGCGTCTT-TAC
194 TAATAACAAACGCCTACACATCTTTCCCTCTAAAAAATTTTAGGATTATTAAAAGCATCTTCTAC
* * * * **
4070852 TA-AAAATATCTTCAATATACTATAGTTATAAAAGGCGTTTATTCTAGGAAAACGCCTTTAATAA
259 TAGAAAATACCTTCAATATACTACAGTTATAAAAGGCATTTATTCAAAAAAAACGCCTTTAATAA
*
4070916 TACCTTTTAAGCTTAA
324 TACATTTTAAGCTTAA
* * * *
4070932 TACATAATTATTGAAA-GCGTTTGTTAATAACAAACGCCTACACATATTTTCCTCTAAAAAATTT
1 TACATAATTACT-AAAGGCATTTGTTAATAACAAACACCTACACATATTTCCCTCTAAAAAATTT
* * * *
4070996 TAGGATTATTAAAGGCGTCTTCTACTAGAAAATGCCTTCAATATACTACAGTTATAAAAGGCATT
65 TAGGATTATTAAAAGCGTCTTCTACTAGAAAATACCTTAAATATACTACAGATATAAAAGGCATT
* * * *
4071061 TATTCAAGGAAAATGCCTTTAATAGTTCCTTTTTAAGCTCAGAACATAATTACTGAAGG
130 TATTCAA-GAAAATGCCTTTAATAATT-CTTTTTAAGCTTAGTACATAATTACTAAAGG
4071120 TGTTTGTTAT
Statistics
Matches: 439, Mismatches: 70, Indels: 31
0.81 0.13 0.06
Matches are distributed among these distances:
334 141 0.32
335 59 0.13
336 17 0.04
337 54 0.12
338 54 0.12
339 32 0.07
340 2 0.00
341 3 0.01
342 28 0.06
343 44 0.10
344 5 0.01
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (339 bp):
TACATAATTACTAAAGGCATTTGTTAATAACAAACACCTACACATATTTCCCTCTAAAAAATTTT
AGGATTATTAAAAGCGTCTTCTACTAGAAAATACCTTAAATATACTACAGATATAAAAGGCATTT
ATTCAAGAAAATGCCTTTAATAATTCTTTTTAAGCTTAGTACATAATTACTAAAGGCATTTATTA
ATAACAAACGCCTACACATCTTTCCCTCTAAAAAATTTTAGGATTATTAAAAGCATCTTCTACTA
GAAAATACCTTCAATATACTACAGTTATAAAAGGCATTTATTCAAAAAAAACGCCTTTAATAATA
CATTTTAAGCTTAA
Found at i:4071390 original size:62 final size:64
Alignment explanation
Indices: 4071319--4071437 Score: 147
Period size: 62 Copynumber: 1.9 Consensus size: 64
4071309 GGTATGAGAT
* *
4071319 TATTAAAGGCATCTT-CT-ACTGACAAATACCTTTAATAA-TTCCTTTT-AAATTTTTTACATAA
1 TATTAAAGGCAT-TTACTGA-TAACAAACACCTTTAATAATTTCCTTTTAAAATTTTTTACATAA
4071380 G
64 G
* * *
4071381 TATTGAAGGCATTTATTGATAACAAACGCCTTTAATAATTTCCTTTTAAAATTTTTT
1 TATTAAAGGCATTTACTGATAACAAACACCTTTAATAATTTCCTTTTAAAATTTTTT
4071438 GGCATTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
61 2 0.04
62 28 0.58
63 9 0.19
64 9 0.19
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (64 bp):
TATTAAAGGCATTTACTGATAACAAACACCTTTAATAATTTCCTTTTAAAATTTTTTACATAAG
Found at i:4072544 original size:79 final size:80
Alignment explanation
Indices: 4072335--4072578 Score: 332
Period size: 80 Copynumber: 3.1 Consensus size: 80
4072325 CTTAAATATT
* * * * * * * *
4072335 ATGGTTTGTTGAAGCTTGTTGTCTAATATTGTTTTACTGAATGGTACTGAATGATATTGAGGGGT
1 ATGGTTTGCTAAACCTTGTTGTCTGATATTGTTTTGCTGAATGGTATTGTATGATATTGAGGGGC
4072400 TGAATCATATGCTGA
66 TGAATCATATGCTGA
4072415 ATGGTTTGCTAAACCTTGTTGTCTGATATTGTTTTG-TCGAATGGTATTGTATGATATT-AGGGG
1 ATGGTTTGCTAAACCTTGTTGTCTGATATTGTTTTGCT-GAATGGTATTGTATGATATTGA-GGG
*
4072478 GCTAAATCATATGCTGA
64 GCTGAATCATATGCTGA
* * * *
4072495 ATGGTTTGCTAAA-CTTTTTGTTTGATATTGTTTTGCTGAATGGTTTTGTATAATATTGAGGGGC
1 ATGGTTTGCTAAACCTTGTTGTCTGATATTGTTTTGCTGAATGGTATTGTATGATATTGAGGGGC
4072559 TGAATCATATGCTGA
66 TGAATCATATGCTGA
4072574 ATGGT
1 ATGGT
4072579 GTTTTTGAAT
Statistics
Matches: 146, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
79 64 0.44
80 82 0.56
ACGTcount: A:0.24, C:0.08, G:0.25, T:0.43
Consensus pattern (80 bp):
ATGGTTTGCTAAACCTTGTTGTCTGATATTGTTTTGCTGAATGGTATTGTATGATATTGAGGGGC
TGAATCATATGCTGA
Found at i:4082365 original size:94 final size:95
Alignment explanation
Indices: 4082263--4082442 Score: 274
Period size: 94 Copynumber: 1.9 Consensus size: 95
4082253 ATAATGACGG
* * ** *
4082263 TTATTATTATAATCATCAATATAAGTTCCAAAAAAATGTTAATTCCTAATTT-TTTTTATAAAAA
1 TTATTATTATAACCATCAATATAAGCTCCAAAAAAACATCAATTCCTAATTTCTTTTT-TAAAAA
4082327 -TATTAATTCACAATATTTCCCCATTGATGT
65 GTATTAATTCACAATATTTCCCCATTGATGT
*
4082357 TTATTATTATAACCATCAATATAAGCTCTAAAAAAACATCAATTCCTAATTTCTTTTTTAAAAAG
1 TTATTATTATAACCATCAATATAAGCTCCAAAAAAACATCAATTCCTAATTTCTTTTTTAAAAAG
*
4082422 TATTAATTCATAATATTTCCC
66 TATTAATTCACAATATTTCCC
4082443 TCTAAAAATT
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
94 52 0.68
95 25 0.32
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.42
Consensus pattern (95 bp):
TTATTATTATAACCATCAATATAAGCTCCAAAAAAACATCAATTCCTAATTTCTTTTTTAAAAAG
TATTAATTCACAATATTTCCCCATTGATGT
Found at i:4082669 original size:16 final size:17
Alignment explanation
Indices: 4082648--4082689 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
4082638 CTGCCAGTCT
4082648 CCCTAATTCCCAAA-AA
1 CCCTAATTCCCAAATAA
*
4082664 CCCTAA-ACCCAAATAA
1 CCCTAATTCCCAAATAA
4082680 CCCTACATTC
1 CCCTA-ATTC
4082690 GTAAATCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 6 0.29
16 13 0.62
17 1 0.05
18 1 0.05
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.19
Consensus pattern (17 bp):
CCCTAATTCCCAAATAA
Found at i:4086819 original size:24 final size:24
Alignment explanation
Indices: 4086779--4086825 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4086769 AAAACATATC
4086779 ATATTATAATTATAAATA-AATTA
1 ATATTATAATTATAAATATAATTA
4086802 ATATTAATAATTGA-AAATATAATT
1 ATATT-ATAATT-ATAAATATAATT
4086826 TAAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATTATAATTATAAATATAATTA
Found at i:4090155 original size:30 final size:30
Alignment explanation
Indices: 4090106--4090162 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
4090096 ATTGGGTTCT
* *
4090106 TATTTACCTGAAATCATTAAATACAACAAA
1 TATTAACCTAAAATCATTAAATACAACAAA
* *
4090136 TATTAACCTAAAATTATTAAATTCAAC
1 TATTAACCTAAAATCATTAAATACAAC
4090163 TCACATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (30 bp):
TATTAACCTAAAATCATTAAATACAACAAA
Found at i:4090310 original size:32 final size:32
Alignment explanation
Indices: 4090260--4090320 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
4090250 CATCACCATT
* *
4090260 CATTGTGTTGTATATAAGATAAAAAGGATATC
1 CATTGTCTCGTATATAAGATAAAAAGGATATC
*
4090292 CATTGTCTCGTATTTAAGATAAAAAGGAT
1 CATTGTCTCGTATATAAGATAAAAAGGAT
4090321 GTTTAGATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (32 bp):
CATTGTCTCGTATATAAGATAAAAAGGATATC
Found at i:4090616 original size:13 final size:14
Alignment explanation
Indices: 4090591--4090618 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4090581 TTATTTTGTG
4090591 AAAATTGATTTTTA
1 AAAATTGATTTTTA
4090605 AAAATTGATTTTTA
1 AAAATTGATTTTTA
4090619 TATTTTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AAAATTGATTTTTA
Found at i:4090826 original size:18 final size:18
Alignment explanation
Indices: 4090803--4091063 Score: 192
Period size: 18 Copynumber: 14.6 Consensus size: 18
4090793 AATTTTACTT
4090803 ATAAATAATATTATATTA
1 ATAAATAATATTATATTA
*
4090821 ATAAATAATATTATATGA
1 ATAAATAATATTATATTA
4090839 ATAAATAATA-TACTATTA
1 ATAAATAATATTA-TATTA
*
4090857 AT--ATAATATTA-ATAA
1 ATAAATAATATTATATTA
* *
4090872 ATAATATTATAATATATTA
1 ATAA-ATAATATTATATTA
4090891 ATAAATAATATTATATTA
1 ATAAATAATATTATATTA
4090909 ATAAATAAT-TTA-A-TA
1 ATAAATAATATTATATTA
*
4090924 ATAAATATTATTAATTTAATTA
1 ATAAATAATATT-A--T-ATTA
4090946 ATAAATAATATAATAATAATGT-
1 ATAAATAATAT--T-AT-AT-TA
*
4090968 ATAAATAATATAATATTA
1 ATAAATAATATTATATTA
4090986 ATAAATAATA-TACTA-T-
1 ATAAATAATATTA-TATTA
4091002 -T-AA-AATATTATATTA
1 ATAAATAATATTATATTA
** * *
4091017 ATAAATCTTGTTA-ATAA
1 ATAAATAATATTATATTA
* *
4091034 ATAATATTATAATATATTA
1 ATAA-ATAATATTATATTA
4091053 ATAAATAATAT
1 ATAAATAATAT
4091064 AAAGAATAAT
Statistics
Matches: 194, Mismatches: 23, Indels: 52
0.72 0.09 0.19
Matches are distributed among these distances:
13 6 0.03
14 5 0.03
15 16 0.08
16 10 0.05
17 20 0.10
18 89 0.46
19 16 0.08
21 1 0.01
22 27 0.14
23 1 0.01
24 3 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (18 bp):
ATAAATAATATTATATTA
Found at i:4090858 original size:11 final size:11
Alignment explanation
Indices: 4090808--4090992 Score: 90
Period size: 11 Copynumber: 16.9 Consensus size: 11
4090798 TACTTATAAA
*
4090808 TAATATTATAT
1 TAATATAATAT
4090819 TAATAAATAATAT
1 TAAT--ATAATAT
*
4090832 T-ATATGAATAAA
1 TAATAT-AAT-AT
*
4090844 TAATATACTAT
1 TAATATAATAT
4090855 TAATATAATAT
1 TAATATAATAT
*
4090866 TAATA-AATAA
1 TAATATAATAT
*
4090876 TATTATAATA-
1 TAATATAATAT
*
4090886 T-AT-TAATAAA
1 TAATATAAT-AT
*
4090896 TAATATTATAT
1 TAATATAATAT
4090907 TAATA-AATAATT
1 TAATATAAT-A-T
4090919 TAATAATAAATAT
1 TAAT-AT-AATAT
4090932 T-AT-TAAT-T
1 TAATATAATAT
*
4090940 TAAT-TAATAAA
1 TAATATAAT-AT
*
4090951 TAATATAATAA
1 TAATATAATAT
4090962 TAATGTATAA-A-
1 TAA--TATAATAT
4090973 TAATATAATAT
1 TAATATAATAT
4090984 TAATA-AATA
1 TAATATAATA
4090993 ATATACTATT
Statistics
Matches: 139, Mismatches: 12, Indels: 47
0.70 0.06 0.24
Matches are distributed among these distances:
8 6 0.04
9 16 0.12
10 20 0.14
11 53 0.38
12 21 0.15
13 19 0.14
14 1 0.01
15 3 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TAATATAATAT
Found at i:4090858 original size:29 final size:28
Alignment explanation
Indices: 4090826--4091064 Score: 133
Period size: 29 Copynumber: 8.9 Consensus size: 28
4090816 TATTAATAAA
*
4090826 TAATATTATATGAATAAATAATATACTAT
1 TAATATTATATTAATAAATAATATA-TAT
*
4090855 TAATATAATATTAATAAATAATAT-TA-
1 TAATATTATATTAATAAATAATATATAT
4090881 T-A-A-TATATTAATAAATAATATTATAT
1 TAATATTATATTAATAAATAATA-TATAT
*
4090907 TAATA-AATAATTTAAT-AATAA-ATATTAT
1 TAATATTAT-A-TTAATAAATAATATA-TAT
4090935 TAAT-TTA-ATTAATAAATAATATA-A-
1 TAATATTATATTAATAAATAATATATAT
* * *
4090959 TAATAATGTATAAATAATATAATAT-TAAT
1 TAATATTATATTAATAA-ATAATATAT-AT
* * * *
4090988 AAATAATATACT-ATTAA-AATATTATAT
1 TAATATTATATTAATAAATAATA-TATAT
*
4091015 TAATAAATCT-TGTTAATAAATAATAT-TA-
1 TAAT--AT-TATATTAATAAATAATATATAT
4091043 T-A-A-TATATTAATAAATAATATA
1 TAATATTATATTAATAAATAATATA
4091065 AAGAATAATA
Statistics
Matches: 165, Mismatches: 19, Indels: 57
0.68 0.08 0.24
Matches are distributed among these distances:
22 1 0.01
23 31 0.19
24 7 0.04
25 10 0.06
26 19 0.12
27 23 0.14
28 18 0.11
29 41 0.25
30 11 0.07
31 4 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
TAATATTATATTAATAAATAATATATAT
Found at i:4090898 original size:70 final size:70
Alignment explanation
Indices: 4090803--4091022 Score: 248
Period size: 70 Copynumber: 3.0 Consensus size: 70
4090793 AATTTTACTT
* *
4090803 ATAA-ATAATATTATATTAATAAATAATATTATATGAATAAATAATATACTATTAATATAATATT
1 ATAATATAATAATATATTAATAAATAATATTATATTAATAAATAATATACTATTAATATAATATT
4090867 AATAA
66 AATAA
* * * *
4090872 ATAATATTATAATATATTAATAAATAATATTATATTAATAAATAATTTAATAATAAATATTATTA
1 ATAATATAATAATATATTAATAAATAATATTATATTAATAAATAA--T-ATACT-ATTAATA-TA
4090937 ATTTAATTAATAA
61 A--T-ATTAATAA
* *
4090950 ATAATATAATAATA-ATGT-ATAAATAATATAATATTAATAAATAATATACTATTAAAATATTAT
1 ATAATATAATAATATAT-TAATAAATAATATTATATTAATAAATAATATACTATT--AATATAAT
4091013 ATTAATAA
63 ATTAATAA
4091021 AT
1 AT
4091023 CTTGTTAATA
Statistics
Matches: 127, Mismatches: 12, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
69 4 0.03
70 37 0.29
71 10 0.08
72 2 0.02
73 6 0.05
74 11 0.09
75 7 0.06
77 28 0.22
78 22 0.17
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (70 bp):
ATAATATAATAATATATTAATAAATAATATTATATTAATAAATAATATACTATTAATATAATATT
AATAA
Done.