Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 21 of 160
Found at i:5769476 original size:14 final size:14
Alignment explanation
Indices: 5769457--5769483 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5769447 AACTTAAACT
5769457 TTAACAATTCTTAG
1 TTAACAATTCTTAG
5769471 TTAACAATTCTTA
1 TTAACAATTCTTA
5769484 AAGTTTCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (14 bp):
TTAACAATTCTTAG
Found at i:5771206 original size:27 final size:25
Alignment explanation
Indices: 5771169--5771229 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 25
5771159 GATATAAAAA
* * *
5771169 TAATTTAATAAATTTTTAATAAATTAT
1 TAATTTTATAAATATTAAAT-AATT-T
5771196 TAATTTTATAAATATTAAATAATTT
1 TAATTTTATAAATATTAAATAATTT
*
5771221 AAATTTTAT
1 TAATTTTAT
5771230 TACATATAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 9 0.30
26 4 0.13
27 17 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TAATTTTATAAATATTAAATAATTT
Found at i:5771213 original size:15 final size:17
Alignment explanation
Indices: 5771182--5771213 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5771172 TTTAATAAAT
5771182 TTTTAATAAATTATTAA
1 TTTTAATAAATTATTAA
5771199 TTTT-ATAAA-TATTAA
1 TTTTAATAAATTATTAA
5771214 ATAATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTAATAAATTATTAA
Found at i:5772636 original size:21 final size:21
Alignment explanation
Indices: 5772598--5772646 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
5772588 CACTATAATA
*
5772598 AAATATTTAAAATGATATT-T
1 AAATTTTTAAAATGATATTAT
*
5772618 AAATTTTTAAAATTTATATTAT
1 AAATTTTTAAAA-TGATATTAT
5772640 AATATTT
1 AA-ATTT
5772647 GAATTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.46
21 6 0.25
22 3 0.12
23 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AAATTTTTAAAATGATATTAT
Found at i:5777640 original size:2 final size:2
Alignment explanation
Indices: 5777633--5777665 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5777623 GTATGAAAGT
*
5777633 TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
5777666 ATGTAGATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:5778818 original size:17 final size:17
Alignment explanation
Indices: 5778792--5778826 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5778782 CAACCGTAGG
5778792 GTTTTCTTTTTGTTTTT
1 GTTTTCTTTTTGTTTTT
* *
5778809 GTTTTTTTTTTTTTTTT
1 GTTTTCTTTTTGTTTTT
5778826 G
1 G
5778827 ACATGGGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (17 bp):
GTTTTCTTTTTGTTTTT
Found at i:5778872 original size:2 final size:2
Alignment explanation
Indices: 5778867--5778894 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5778857 GGGGGGGGGG
5778867 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5778895 TAAGTTTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5780839 original size:2 final size:2
Alignment explanation
Indices: 5780832--5780856 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5780822 ATGTTTATAC
5780832 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
5780857 CGCGTGCATA
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:5790850 original size:69 final size:69
Alignment explanation
Indices: 5790715--5790852 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 69
5790705 AACCGTTACA
*** * *
5790715 TATTTTTTAATAATTAAATATTTATTACAGATTTTTTTTTAATATATTTCATTTATGATGAGGAT
1 TATTTTTTAATAATTAAATATTTATTACAGATTTTTTAAAAATATATTTAATTTATGATGAAGAT
5790780 TTAT
66 TTAT
5790784 TATTTTTTAATAATTAAATATTTATTACAGATTTTTTAAAAATATATTTAATTTATGA-GAAAGA
1 TATTTTTTAATAATTAAATATTTATTACAGATTTTTTAAAAATATATTTAATTTATGATG-AAGA
5790848 TTTAT
65 TTTAT
5790853 GTAGCAGAAC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 1 0.02
69 62 0.98
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.54
Consensus pattern (69 bp):
TATTTTTTAATAATTAAATATTTATTACAGATTTTTTAAAAATATATTTAATTTATGATGAAGAT
TTAT
Found at i:5792552 original size:17 final size:18
Alignment explanation
Indices: 5792509--5792556 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
5792499 GAAGTAAATA
*
5792509 AAATATTATTAATATTTT
1 AAATAATATTAATATTTT
* *
5792527 ATATAAATATTTAT-TTTT
1 AAAT-AATATTAATATTTT
5792545 AAATAATATTAA
1 AAATAATATTAA
5792557 AATTATTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 7 0.29
18 10 0.42
19 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AAATAATATTAATATTTT
Found at i:5793068 original size:16 final size:16
Alignment explanation
Indices: 5793031--5793070 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
5793021 GAAAGACTTC
*
5793031 AAATA-TAATTTTATA
1 AAATATTAATTTAATA
5793046 AAA-ATTAATTTAATA
1 AAATATTAATTTAATA
5793061 AAATATTAAT
1 AAATATTAAT
5793071 GATCAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 15 0.68
16 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATTAATTTAATA
Found at i:5793657 original size:16 final size:17
Alignment explanation
Indices: 5793633--5793666 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5793623 TTGATTATAA
5793633 TAAAATATTA-TAAATT
1 TAAAATATTATTAAATT
*
5793649 TAAATTATTATTAAATT
1 TAAAATATTATTAAATT
5793666 T
1 T
5793667 TTATGGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAAATATTATTAAATT
Found at i:5793658 original size:29 final size:26
Alignment explanation
Indices: 5793603--5793659 Score: 62
Period size: 29 Copynumber: 2.1 Consensus size: 26
5793593 ATGACCTGAA
*
5793603 ATAAAAAATTTAAAATTTGATTGATT
1 ATAAAAAATTTAAAATTTAATTGATT
5793629 ATAATAAAATATTATAAATTTAAATT-ATT
1 ATAA-AAAAT-TTA-AAATTT-AATTGATT
5793658 AT
1 AT
5793660 TAAATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.15
27 5 0.19
28 3 0.12
29 11 0.42
30 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
ATAAAAAATTTAAAATTTAATTGATT
Found at i:5795235 original size:2 final size:2
Alignment explanation
Indices: 5795228--5795266 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5795218 CCTTGAAAGA
5795228 AT AT AT AT AT 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 AT AT AT AT AT A
5795267 AAGACCCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5795990 original size:2 final size:2
Alignment explanation
Indices: 5795983--5796020 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5795973 ATTCCTCTCA
5795983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5796021 TGGAACATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5814354 original size:27 final size:27
Alignment explanation
Indices: 5814316--5814367 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
5814306 CTTTTCATTT
* *
5814316 TGTTCTTTTCAAGTTGGTGAGAATCAA
1 TGTTATTTTCAAGTTGGTAAGAATCAA
5814343 TGTTATTTTCAAGTTGGTAAGAATC
1 TGTTATTTTCAAGTTGGTAAGAATC
5814368 TCTAGTGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (27 bp):
TGTTATTTTCAAGTTGGTAAGAATCAA
Found at i:5822229 original size:6 final size:6
Alignment explanation
Indices: 5822220--5822279 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
5822210 CTCAATAGGA
* * * **
5822220 AATTTT AATTTT AATTTT AATTTT GATTTG ATTTTT TTTGTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AAT-TTT AATTTT
*
5822269 ACTTTT -ATTTT
1 AATTTT AATTTT
5822280 TTGAAAAGTC
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
5 4 0.09
6 35 0.81
7 4 0.09
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (6 bp):
AATTTT
Found at i:5822785 original size:15 final size:16
Alignment explanation
Indices: 5822767--5822798 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5822757 GATTTCTGGG
5822767 TTTTTTTTTTC-TTTT
1 TTTTTTTTTTCGTTTT
5822782 TTTTTTTTTTCGTTTT
1 TTTTTTTTTTCGTTTT
5822798 T
1 T
5822799 CAAGGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (16 bp):
TTTTTTTTTTCGTTTT
Found at i:5823221 original size:15 final size:14
Alignment explanation
Indices: 5823198--5823270 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 14
5823188 ATCGTAGGTA
*
5823198 TTTTTT-TTTCTAT
1 TTTTTTATTTTTAT
5823211 TTTTTTATTTTTAT
1 TTTTTTATTTTTAT
*
5823225 TTATTTTATTTTTAG
1 TT-TTTTATTTTTAT
* *
5823240 ATTTTTCTTTATTAT
1 TTTTTTATTT-TTAT
* *
5823255 TATTATTATTATTAT
1 T-TTTTTATTTTTAT
5823270 T
1 T
5823271 ATTATTATTA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
13 6 0.13
14 15 0.32
15 20 0.43
16 6 0.13
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (14 bp):
TTTTTTATTTTTAT
Found at i:5823243 original size:23 final size:24
Alignment explanation
Indices: 5823208--5823279 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 24
5823198 TTTTTTTTTC
**
5823208 TATTTTTTTATTTTTATTTATT-T
1 TATTTTTAGATTTTTATTTATTAT
*
5823231 TATTTTTAGATTTTTCTTTATTAT
1 TATTTTTAGATTTTTATTTATTAT
* *
5823255 TATTATT--ATTATTA-TTATTAT
1 TATTTTTAGATTTTTATTTATTAT
5823276 TATT
1 TATT
5823280 AATTGAACAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
21 11 0.26
22 5 0.12
23 19 0.45
24 7 0.17
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.74
Consensus pattern (24 bp):
TATTTTTAGATTTTTATTTATTAT
Found at i:5823256 original size:3 final size:3
Alignment explanation
Indices: 5823248--5823280 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5823238 AGATTTTTCT
5823248 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5823281 ATTGAACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5827280 original size:8 final size:9
Alignment explanation
Indices: 5827263--5827331 Score: 72
Period size: 9 Copynumber: 7.8 Consensus size: 9
5827253 ATTGTTTAAG
5827263 ATGAAAAAA
1 ATGAAAAAA
5827272 ATGAAAAAA
1 ATGAAAAAA
5827281 ATGAAAAAA
1 ATGAAAAAA
*
5827290 ATAAAAAAGA
1 ATGAAAAA-A
*
5827300 AAGAAAAAGA
1 ATGAAAAA-A
5827310 A--AAAAAA
1 ATGAAAAAA
*
5827317 AAGAAAAAA
1 ATGAAAAAA
5827326 A-GAAAA
1 ATGAAAA
5827332 CTTAAATTGA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
7 2 0.04
8 10 0.19
9 32 0.59
10 10 0.19
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.06
Consensus pattern (9 bp):
ATGAAAAAA
Found at i:5827306 original size:25 final size:24
Alignment explanation
Indices: 5827266--5827331 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 24
5827256 GTTTAAGATG
* *
5827266 AAAAAAATGAAA-AAAATGAAAAA
1 AAAAAAAAGAAAGAAAAAGAAAAA
5827289 AATAAAAAAGAAAGAAAAAGAAAAA
1 AA-AAAAAAGAAAGAAAAAGAAAAA
*
5827314 AAAAAGAAAAAAAGAAAA
1 AAAAA-AAAGAAAGAAAA
5827332 CTTAAATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 2 0.05
24 12 0.32
25 23 0.62
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.05
Consensus pattern (24 bp):
AAAAAAAAGAAAGAAAAAGAAAAA
Found at i:5827319 original size:17 final size:18
Alignment explanation
Indices: 5827265--5827331 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
5827255 TGTTTAAGAT
* *
5827265 GAAAAAAATGAAAAAAAT
1 GAAAAAAATAAAAAAAAA
5827283 GAAAAAAATAAAAAAGAAA
1 GAAAAAAATAAAAAA-AAA
*
5827302 GAAAAAGA-AAAAAAAAA
1 GAAAAAAATAAAAAAAAA
*
5827319 GAAAAAAAGAAAA
1 GAAAAAAATAAAA
5827332 CTTAAATTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
17 10 0.23
18 24 0.56
19 9 0.21
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (18 bp):
GAAAAAAATAAAAAAAAA
Found at i:5828062 original size:24 final size:24
Alignment explanation
Indices: 5828035--5828097 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
5828025 TTGATAATTA
*
5828035 CATTTGCATCATAGTTGGGGTATG
1 CATTTGCATCATAGTTGGGGCATG
*
5828059 CATTTGCATCATGGTTGGGGCATG
1 CATTTGCATCATAGTTGGGGCATG
*
5828083 CATTTGAATCATAGT
1 CATTTGCATCATAGT
5828098 ATAACATTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (24 bp):
CATTTGCATCATAGTTGGGGCATG
Found at i:5828418 original size:29 final size:29
Alignment explanation
Indices: 5828385--5828444 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
5828375 AACCCAAAAT
*
5828385 TTTTTAGATGAGAATCTTTGAAATGTTGG
1 TTTTTAAATGAGAATCTTTGAAATGTTGG
* *
5828414 TTTTTAAATGTGAATCTTTGAAATTTTGG
1 TTTTTAAATGAGAATCTTTGAAATGTTGG
5828443 TT
1 TT
5828445 CTAAACTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.27, C:0.03, G:0.20, T:0.50
Consensus pattern (29 bp):
TTTTTAAATGAGAATCTTTGAAATGTTGG
Found at i:5828912 original size:67 final size:67
Alignment explanation
Indices: 5828838--5828979 Score: 275
Period size: 67 Copynumber: 2.1 Consensus size: 67
5828828 TACAAAGCTA
5828838 AATTCTTGTGAATCTTTCATTCTTATGAGTATTTGAGTTCTTGCAAACTTGAAACCTTGCAAATC
1 AATTCTTGTGAATCTTTCATTCTTATGAGTATTTGAGTTCTTGCAAACTTGAAACCTTGCAAATC
5828903 TG
66 TG
*
5828905 AATTCTTGTGAATCTTTCATTCTTATGAGTTTTTGAGTTCTTGCAAACTTGAAACCTTGCAAATC
1 AATTCTTGTGAATCTTTCATTCTTATGAGTATTTGAGTTCTTGCAAACTTGAAACCTTGCAAATC
5828970 TG
66 TG
5828972 AATTCTTG
1 AATTCTTG
5828980 CAAACCTAAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 74 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (67 bp):
AATTCTTGTGAATCTTTCATTCTTATGAGTATTTGAGTTCTTGCAAACTTGAAACCTTGCAAATC
TG
Found at i:5828979 original size:16 final size:16
Alignment explanation
Indices: 5828942--5829002 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
5828932 AGTTTTTGAG
5828942 TTCTTGCAAA-CTTGAA
1 TTCTTGCAAATC-TGAA
**
5828958 ACCTTGCAAATCTGAA
1 TTCTTGCAAATCTGAA
* *
5828974 TTCTTGCAAACCTAAA
1 TTCTTGCAAATCTGAA
*
5828990 TTCTTGCGAATCT
1 TTCTTGCAAATCT
5829003 AAAAGTCCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
16 35 0.97
17 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (16 bp):
TTCTTGCAAATCTGAA
Found at i:5829004 original size:16 final size:16
Alignment explanation
Indices: 5828960--5829005 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
5828950 AACTTGAAAC
*
5828960 CTTGCAAATCTGAATT
1 CTTGCAAATCTAAATT
*
5828976 CTTGCAAACCTAAATT
1 CTTGCAAATCTAAATT
*
5828992 CTTGCGAATCTAAA
1 CTTGCAAATCTAAA
5829006 AGTCCTTGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (16 bp):
CTTGCAAATCTAAATT
Found at i:5830444 original size:12 final size:12
Alignment explanation
Indices: 5830424--5830494 Score: 72
Period size: 12 Copynumber: 5.8 Consensus size: 12
5830414 GTATTTCTTT
*
5830424 TTTTTTTTTTAA
1 TTTTATTTTTAA
5830436 TTTTATTTTTAA
1 TTTTATTTTTAA
*
5830448 TTTTATTTTTTTA
1 TTTTA-TTTTTAA
*
5830461 TTATTATTATT-A
1 TT-TTATTTTTAA
*
5830473 TTTTATCTTTAA
1 TTTTATTTTTAA
5830485 TTATTATTTT
1 TT-TTATTTT
5830495 ACTTATTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
11 6 0.12
12 22 0.45
13 18 0.37
14 3 0.06
ACGTcount: A:0.23, C:0.01, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTTTTAA
Found at i:5830451 original size:18 final size:18
Alignment explanation
Indices: 5830435--5830495 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
5830425 TTTTTTTTTA
5830435 ATTTTATTTTTAATT-TT
1 ATTTTATTTTTAATTATT
5830452 ATTTT-TTTATTATTATTATT
1 ATTTTATTT-TTA--ATTATT
*
5830472 ATTTTATCTTTAATTATT
1 ATTTTATTTTTAATTATT
5830490 ATTTTA
1 ATTTTA
5830496 CTTATTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
16 3 0.08
17 8 0.21
18 12 0.32
19 3 0.08
20 10 0.26
21 2 0.05
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTATTTTTAATTATT
Found at i:5833442 original size:21 final size:21
Alignment explanation
Indices: 5833412--5833451 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5833402 TTAATTTTGG
5833412 AGAGAAAGAGAATAAATTTTT
1 AGAGAAAGAGAATAAATTTTT
* *
5833433 AGAGAGAGAGTATAAATTT
1 AGAGAAAGAGAATAAATTT
5833452 AGATGAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.28
Consensus pattern (21 bp):
AGAGAAAGAGAATAAATTTTT
Found at i:5833783 original size:36 final size:36
Alignment explanation
Indices: 5833682--5833787 Score: 94
Period size: 36 Copynumber: 3.0 Consensus size: 36
5833672 AAAAATACCA
* *
5833682 AATATACAATAAATTTTATTATATAAAAAATTTAAT
1 AATATACTATAAATTTTATTATATAAAAATTTTAAT
* ** * **
5833718 -TTGATA-TATAAAAATAATT-T-TAGTAATTTTAAT
1 AAT-ATACTATAAATTTTATTATATAAAAATTTTAAT
*
5833751 AATATACTATAAATTTTATTATATACAAATTTTAAT
1 AATATACTATAAATTTTATTATATAAAAATTTTAAT
5833787 A
1 A
5833788 TAATGTTCTT
Statistics
Matches: 51, Mismatches: 14, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
33 13 0.25
34 12 0.24
35 11 0.22
36 15 0.29
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (36 bp):
AATATACTATAAATTTTATTATATAAAAATTTTAAT
Found at i:5837414 original size:57 final size:55
Alignment explanation
Indices: 5837223--5837435 Score: 201
Period size: 55 Copynumber: 3.8 Consensus size: 55
5837213 ATAAACAAAG
* * * * **
5837223 TAATGTAATAAATCAATGCAAATAAATAAAAGCAAAAACTTCATATTAAATTAAAA
1 TAATCTAATAAATCAATGTAAACAAATAAAA-AAAAAACAACATATTAAATTAAAA
* ** *
5837279 TAATCTAATAAACCAACATAAACAAATAAAAAACAAACAACATATTAAATTAAAA
1 TAATCTAATAAATCAATGTAAACAAATAAAAAAAAAACAACATATTAAATTAAAA
* * * * * ***
5837334 TAATATAATAGATTAATGAAAACATATAAAAAAAATAAGGTGCATATTAAATTAAAA
1 TAATCTAATAAATCAATGTAAACAAATAAAAAAAA-AA-CAACATATTAAATTAAAA
* * *
5837391 CAATCTAACAAATCAATGTAAACAAATAAAAAATAAAACAGCATA
1 TAATCTAATAAATCAATGTAAACAAATAAAAAA-AAAACAACATA
5837436 ATTTACTATT
Statistics
Matches: 123, Mismatches: 31, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
55 46 0.37
56 32 0.26
57 43 0.35
58 2 0.02
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (55 bp):
TAATCTAATAAATCAATGTAAACAAATAAAAAAAAAACAACATATTAAATTAAAA
Found at i:5838126 original size:50 final size:50
Alignment explanation
Indices: 5838038--5838136 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
5838028 ATAAAAATAT
* *
5838038 CATATTAAATTAAAATAATCTAATAAATGAATGTAAACAGACAAAAAAAA
1 CATATTAAATTAAAATAATATAATAAATGAATGCAAACAGACAAAAAAAA
* * * * *
5838088 CATATTAAATTAAAATAATATGATAGATTAATGCAAACATATAAAAAAA
1 CATATTAAATTAAAATAATATAATAAATGAATGCAAACAGACAAAAAAA
5838137 TAGGACTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.61, C:0.07, G:0.06, T:0.26
Consensus pattern (50 bp):
CATATTAAATTAAAATAATATAATAAATGAATGCAAACAGACAAAAAAAA
Found at i:5840262 original size:23 final size:23
Alignment explanation
Indices: 5840236--5840282 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5840226 ATAAACTAAA
5840236 ATAACAATTTAAAAATATTTAGG
1 ATAACAATTTAAAAATATTTAGG
** **
5840259 ATAATTATTTTCAAATATTTAGG
1 ATAACAATTTAAAAATATTTAGG
5840282 A
1 A
5840283 ATGAAAACAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (23 bp):
ATAACAATTTAAAAATATTTAGG
Found at i:5842390 original size:13 final size:13
Alignment explanation
Indices: 5842372--5842397 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5842362 TAAGTTTTTC
5842372 TATTATTATTATT
1 TATTATTATTATT
5842385 TATTATTATTATT
1 TATTATTATTATT
5842398 AAAAAGTGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:5842877 original size:16 final size:18
Alignment explanation
Indices: 5842843--5842879 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
5842833 TACTTAATAT
5842843 TAAAATTTAAAATTTTTA
1 TAAAATTTAAAATTTTTA
5842861 TAAAA-TTAAAA-TTTTA
1 TAAAATTTAAAATTTTTA
5842877 TAA
1 TAA
5842880 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAATTTAAAATTTTTA
Found at i:5842886 original size:17 final size:16
Alignment explanation
Indices: 5842845--5842879 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5842835 CTTAATATTA
5842845 AAATTTAAAATTTTTAT
1 AAATTTAAAA-TTTTAT
*
5842862 AAAATTAAAATTTTAT
1 AAATTTAAAATTTTAT
5842878 AA
1 AA
5842880 TTTTTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTTAAAATTTTAT
Found at i:5842893 original size:24 final size:22
Alignment explanation
Indices: 5842836--5842895 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
5842826 TTTAATGTAC
5842836 TTAATATTAAAATTTAAAATTTT
1 TTAATATTAAAATTTAAAA-TTT
* *
5842859 TATAAAATTAAAATTTTATAATTT
1 T-TAATATTAAAA-TTTAAAATTT
5842883 TTAATATTTAAAA
1 TTAATA-TTAAAA
5842896 GTAAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 5 0.16
24 20 0.65
25 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAATATTAAAATTTAAAATTT
Found at i:5843035 original size:29 final size:30
Alignment explanation
Indices: 5842983--5843044 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
5842973 GAAATAAAAT
5842983 AAAAATTTTATATTTTAATATATTTTT-TA
1 AAAAATTTTATATTTTAATATATTTTTGTA
*
5843012 AAAAATTTTATTTTATTAAT-TATTTTTGTA
1 AAAAATTTTATATT-TTAATATATTTTTGTA
5843042 AAA
1 AAA
5843045 TTTAAAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
AAAAATTTTATATTTTAATATATTTTTGTA
Found at i:5843127 original size:3 final size:3
Alignment explanation
Indices: 5843121--5843146 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5843111 TTGGTGGTGG
5843121 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
5843147 GCCATGATCA
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:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:5843281 original size:15 final size:15
Alignment explanation
Indices: 5843261--5843290 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5843251 TAGCAATAAG
5843261 TAACAAGGGTTTTGT
1 TAACAAGGGTTTTGT
*
5843276 TAACAAGTGTTTTGT
1 TAACAAGGGTTTTGT
5843291 CACCTTTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (15 bp):
TAACAAGGGTTTTGT
Found at i:5844112 original size:32 final size:31
Alignment explanation
Indices: 5844070--5844165 Score: 95
Period size: 32 Copynumber: 3.0 Consensus size: 31
5844060 AATAAAATAT
* * *
5844070 TTAATGTAATATTTTAATTATAAATTTATTAA
1 TTAATATAATATTTAAAATAT-AATTTATTAA
*
5844102 TTAATATAATATTTAAAATATTATTTATTAA
1 TTAATATAATATTTAAAATATAATTTATTAA
* *
5844133 TTATTTATCATTATTTAAAAT-TAATTATATTAA
1 TTA-ATAT-AATATTTAAAATATAATT-TATTAA
5844166 AATAAAATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
31 12 0.22
32 25 0.46
33 17 0.31
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (31 bp):
TTAATATAATATTTAAAATATAATTTATTAA
Found at i:5844214 original size:28 final size:28
Alignment explanation
Indices: 5844183--5844260 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 28
5844173 TATTATATTT
5844183 ATTAACATATTTATA-ATTTAAATATCAC
1 ATTAA-ATATTTATATATTTAAATATCAC
* * *
5844211 ATTAAAATATTTATATATTTATATATTAT
1 ATT-AAATATTTATATATTTAAATATCAC
5844240 ATTAAATATTTCATTATATTT
1 ATTAAATATTT-A-TATATTT
5844261 CAAAATCTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
28 20 0.47
29 16 0.37
30 7 0.16
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTAAATATTTATATATTTAAATATCAC
Found at i:5850100 original size:3 final size:3
Alignment explanation
Indices: 5850092--5850128 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5850082 ATGCTTAAAG
5850092 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5850129 GACTAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5850237 original size:3 final size:3
Alignment explanation
Indices: 5850231--5850263 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5850221 ATTTGACAGG
5850231 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5850264 ATTTTCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5850446 original size:30 final size:30
Alignment explanation
Indices: 5850396--5850452 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5850386 TAAAAAATCT
*
5850396 AAACCTTAAAACCCTTAAACCCCAAAATTG
1 AAACCTTAAAACCCTCAAACCCCAAAATTG
*
5850426 AAACCTT-AAACCCTCCAAACCCTAAAA
1 AAACCTTAAAACCCT-CAAACCCCAAAA
5850453 CTATATCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.18
Consensus pattern (30 bp):
AAACCTTAAAACCCTCAAACCCCAAAATTG
Found at i:5850567 original size:15 final size:15
Alignment explanation
Indices: 5850528--5850575 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
5850518 CTCGAATCGT
5850528 AAAA-TTTAAAATCC
1 AAAACTTTAAAATCC
* **
5850542 TAAACCCTAAAATCC
1 AAAACTTTAAAATCC
*
5850557 AAAACTTTAAAACCC
1 AAAACTTTAAAATCC
5850572 AAAA
1 AAAA
5850576 TTTTGAGAAC
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 3 0.12
15 23 0.88
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAACTTTAAAATCC
Found at i:5858471 original size:23 final size:22
Alignment explanation
Indices: 5858431--5858492 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
5858421 ACCTTCGAGT
5858431 ATGATTTTTAAGACCTCCAAGC
1 ATGATTTTTAAGACCTCCAAGC
* *
5858453 ATGATTTTCTAAGATCTCCAGGC
1 ATGATTTT-TAAGACCTCCAAGC
* * *
5858476 ATAATCTTTAAAACCTC
1 ATGATTTTTAAGACCTC
5858493 TAGGCATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (22 bp):
ATGATTTTTAAGACCTCCAAGC
Found at i:5858608 original size:154 final size:154
Alignment explanation
Indices: 5858323--5858614 Score: 345
Period size: 154 Copynumber: 1.9 Consensus size: 154
5858313 AAAGATTTCG
* * * * * **
5858323 TAATCTTTAAGACTTCCAGGCATGATTTTGATTTGTGATATTATCCCGATCGATTCTTTAATTTT
1 TAATCTTTAAAACCTCCAGGCATAATTTCGATTTGCGATATTATCCCGATCGATTCTCCAATTTT
* * * * *
5858388 GACTTACAGTGTTGTCTCGATCAATTCTGTAAAACCTTCGAGTATGATTTTTAAGACCTCCAAGC
66 GACTTACAGTATTGTCTCGATCAATTCTGTAAAACCTCCGAGCATAATCTTTAAGACCTCCAAGC
*
5858453 ATGATTTTCTAAGATCTCCAGGCA
131 ATAATTTTCTAAGATCTCCAGGCA
* * **
5858477 TAATCTTTAAAACCTCTAGGCATAATTTCGATTTGCGATGTTATCTTGATCGATTCTCCAATTTT
1 TAATCTTTAAAACCTCCAGGCATAATTTCGATTTGCGATATTATCCCGATCGATTCTCCAATTTT
* * * * **
5858542 GACTTGC-GATATTTTTTCGATCAATTCTGTAAGACCTCCG-GACATAATCTTTAAGACCTCTGA
66 GACTTACAG-TATTGTCTCGATCAATTCTGTAAAACCTCCGAG-CATAATCTTTAAGACCTCCAA
5858605 GCATAATTTT
129 GCATAATTTT
5858615 GATCTACGAT
Statistics
Matches: 113, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
153 2 0.02
154 111 0.98
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (154 bp):
TAATCTTTAAAACCTCCAGGCATAATTTCGATTTGCGATATTATCCCGATCGATTCTCCAATTTT
GACTTACAGTATTGTCTCGATCAATTCTGTAAAACCTCCGAGCATAATCTTTAAGACCTCCAAGC
ATAATTTTCTAAGATCTCCAGGCA
Found at i:5858773 original size:36 final size:36
Alignment explanation
Indices: 5858717--5858787 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
5858707 CCTCCAGACA
* *
5858717 TAATTTTGATTTGTAGTGTTGTCTTGATCGATTCTT
1 TAATTTTGACTTGTAGTGTTGTCTCGATCGATTCTT
*
5858753 TAATTTTGACTTGT-GATGTTGTCTCGATTGATTCT
1 TAATTTTGACTTGTAG-TGTTGTCTCGATCGATTCT
5858788 GTTGTCTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.17, C:0.10, G:0.20, T:0.54
Consensus pattern (36 bp):
TAATTTTGACTTGTAGTGTTGTCTCGATCGATTCTT
Found at i:5858782 original size:109 final size:109
Alignment explanation
Indices: 5858462--5858789 Score: 321
Period size: 109 Copynumber: 3.0 Consensus size: 109
5858452 CATGATTTTC
* * * * * *
5858462 TAAGATCTCCAGG-CATAATCTTTAAAACCTCTAGGCATAATTTCGATTTG-CGATGTTATCTTG
1 TAAGACCTCC-GGACATAATCTTTAAAACCTCCAGACATAATTTTGATTTGTAGATGTTGTCTTG
** **
5858525 ATCGATTCTCCAATTTTGACTTGCGATATTTTTTCGATCAATTCTG
65 ATCGATTCTTTAATTTTGACTTGCGATA-TTTTTCGATTGATTCTG
* * * **
5858571 TAAGACCTCCGGACATAATCTTTAAGACCT-CTGAGCATAATTTTGA--TCTACGATGTTGTCCC
1 TAAGACCTCCGGACATAATCTTTAAAACCTCCAGA-CATAATTTTGATTTGTA-GATGTTGTCTT
* * * *
5858633 GATCGATTCTTTATTTTTTAACTTACGATATTTTTTGATTGATTCTG
64 GATCGATTCTTTA-ATTTTGACTTGCGATATTTTTCGATTGATTCTG
*
5858680 TAAGACCTCC-GAGCATGAT-TTCTAAAACCTCCAGACATAATTTTGATTTGTAG-TGTTGTCTT
1 TAAGACCTCCGGA-CATAATCTT-TAAAACCTCCAGACATAATTTTGATTTGTAGATGTTGTCTT
* * *
5858742 GATCGATTCTTTAATTTTGACTTGTGATGTTGTCTCGATTGATTCTG
64 GATCGATTCTTTAATTTTGACTTGCGATATT-TTTCGATTGATTCTG
5858789 T
1 T
5858790 TGTCTCGATC
Statistics
Matches: 176, Mismatches: 32, Indels: 22
0.77 0.14 0.10
Matches are distributed among these distances:
107 1 0.01
108 20 0.11
109 135 0.77
110 17 0.10
111 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (109 bp):
TAAGACCTCCGGACATAATCTTTAAAACCTCCAGACATAATTTTGATTTGTAGATGTTGTCTTGA
TCGATTCTTTAATTTTGACTTGCGATATTTTTCGATTGATTCTG
Found at i:5858792 original size:18 final size:18
Alignment explanation
Indices: 5858769--5858807 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5858759 TGACTTGTGA
*
5858769 TGTTGTCTCGATTGATTC
1 TGTTGTCTCGATCGATTC
5858787 TGTTGTCTCGATCGATTC
1 TGTTGTCTCGATCGATTC
5858805 TGT
1 TGT
5858808 AAGACTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.49
Consensus pattern (18 bp):
TGTTGTCTCGATCGATTC
Found at i:5859089 original size:110 final size:110
Alignment explanation
Indices: 5858829--5859089 Score: 301
Period size: 110 Copynumber: 2.4 Consensus size: 110
5858819 GCATGATTTT
* * **
5858829 TAAGACCTCTGGGCATAATCTT-TAAGATCTTCAAGCATAATTTCAATTTATGGTGTTGTCCCGA
1 TAAGACCTCTGGGCATGAT-TTCTAAGACCTTCAAGCATAATTTCAATTTACAGTGTTGTCCCGA
* * *
5858893 TCGATTCTTTATTTTTTGACTTACAGTGTTATCTCGATCGATTCTG
65 TCGATTCTTTATTTTTTAACTTACAGTGTTATCTCGATCAATTCTC
* * * ** *
5858939 TAAGACCTTTGGACATGATTTCTAAGACCTTC-AGATATAATTTTGATTTACATTGTTGTCCCGA
1 TAAGACCTCTGGGCATGATTTCTAAGACCTTCAAG-CATAATTTCAATTTACAGTGTTGTCCCGA
* * * * *
5859003 TCGATTCTTTATTTTTTAACTTGCGGTGTTGTCTTGGTCAATTCTC
65 TCGATTCTTTATTTTTTAACTTACAGTGTTATCTCGATCAATTCTC
* * *
5859049 TAAGACCTCCGGGTATGATTTCTAAGACCTCCAAGCATAAT
1 TAAGACCTCTGGGCATGATTTCTAAGACCTTCAAGCATAAT
5859090 CTTTAAAAAT
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
109 4 0.03
110 118 0.95
111 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (110 bp):
TAAGACCTCTGGGCATGATTTCTAAGACCTTCAAGCATAATTTCAATTTACAGTGTTGTCCCGAT
CGATTCTTTATTTTTTAACTTACAGTGTTATCTCGATCAATTCTC
Found at i:5859234 original size:23 final size:23
Alignment explanation
Indices: 5859208--5859273 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
5859198 ATTTTATAAG
5859208 ACCTCCAAGCATAATCTTTAAAA
1 ACCTCCAAGCATAATCTTTAAAA
* * * *
5859231 ACCTTCAGGCATAATCTCT-AAG
1 ACCTCCAAGCATAATCTTTAAAA
** *
5859253 ACCTCTGAGAATAATCTTTAA
1 ACCTCCAAGCATAATCTTTAA
5859274 GACCTCCGGG
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (23 bp):
ACCTCCAAGCATAATCTTTAAAA
Found at i:5859267 original size:155 final size:155
Alignment explanation
Indices: 5858975--5859296 Score: 335
Period size: 155 Copynumber: 2.1 Consensus size: 155
5858965 ACCTTCAGAT
* * * * * *
5858975 ATAATTTTGATTTACATTGTTGTCCCGATCGATTCTTTATTTTTTAACTTGCGGTGTTGTCTTGG
1 ATAATTTTGATTTACATTATTGTCCCGATCGATTCTTTATTTTTTAACTTACAGTATTATCTTAG
* ** * * * * *
5859040 TCAATTCTCTAAGACCTCCGGGTATGATTTCTAAGACCTCCAAGCATAATCTTTAAAAATCTCCA
66 TCAATTCTATAAGACCTCCAAGCATAATTTCTAAAACCTCCAAGCATAATCTCTAAAAACCTCCA
* * **
5859105 AGCATAATCTCTAAGCCCTTTGGGC
131 AGAATAATCTCTAAGACCTCCGGGC
* * *
5859130 ATAATTTTGATTTACGA-TATTGTCTCGATCGATTTTTTATTTTTTGACTTACAGTATTATCTTA
1 ATAATTTTGATTTAC-ATTATTGTCCCGATCGATTCTTTATTTTTTAACTTACAGTATTATCTTA
* * * *
5859194 GTCAATTTTATAAGACCTCCAAGCATAATCTT-TAAAAACCTTCAGGCATAATCTCT-AAGACCT
65 GTCAATTCTATAAGACCTCCAAGCATAAT-TTCT-AAAACCTCCAAGCATAATCTCTAAAAACCT
** * *
5859257 CTGAGAATAATCTTTAAGACCTCCGGGT
128 CCAAGAATAATCTCTAAGACCTCCGGGC
5859285 ATAATTTTGATT
1 ATAATTTTGATT
5859297 CACGGTGTTA
Statistics
Matches: 135, Mismatches: 29, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
155 114 0.84
156 21 0.16
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (155 bp):
ATAATTTTGATTTACATTATTGTCCCGATCGATTCTTTATTTTTTAACTTACAGTATTATCTTAG
TCAATTCTATAAGACCTCCAAGCATAATTTCTAAAACCTCCAAGCATAATCTCTAAAAACCTCCA
AGAATAATCTCTAAGACCTCCGGGC
Found at i:5859289 original size:22 final size:22
Alignment explanation
Indices: 5859204--5859280 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
5859194 GTCAATTTTA
5859204 TAAGACCTCCAAGCATAATCTT
1 TAAGACCTCCAAGCATAATCTT
* * * *
5859226 TAAAAACCTTCAGGCATAATCTC
1 T-AAGACCTCCAAGCATAATCTT
** *
5859249 TAAGACCTCTGAGAATAATCTT
1 TAAGACCTCCAAGCATAATCTT
5859271 TAAGACCTCC
1 TAAGACCTCC
5859281 GGGTATAATT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
22 24 0.57
23 18 0.43
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.27
Consensus pattern (22 bp):
TAAGACCTCCAAGCATAATCTT
Found at i:5859396 original size:22 final size:22
Alignment explanation
Indices: 5859371--5859420 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
5859361 AGATCTTTGG
5859371 GCATAAT-TTCTAAGACCTCCAA
1 GCATAATCTT-TAAGACCTCCAA
5859393 GCATAATCTTTAAGACCTCCAA
1 GCATAATCTTTAAGACCTCCAA
*
5859415 ACATAA
1 GCATAA
5859421 GTTTGATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (22 bp):
GCATAATCTTTAAGACCTCCAA
Found at i:5859475 original size:132 final size:132
Alignment explanation
Indices: 5859238--5859489 Score: 344
Period size: 132 Copynumber: 1.9 Consensus size: 132
5859228 AAAACCTTCA
** **** *
5859238 GGCATAATCTCTAAGACCTCTGAGAATAATCTTTAAGACCTCCGGGTATAATTTTGATTCACGGT
1 GGCATAATCTCTAAGACCTCCAAGAATAATCTTTAAGACCTCCAAACATAAGTTTGATTCACGGT
* * * *
5859303 GTTATCCTGATCAATTCTTTATTTATTGACTTGTGGTGTTGTCCCATTCGATTCTATAAGATCTT
66 GTTATCCTGATCAATTCTTCATTTATCGACTTGCGGTGTTGTCCCAATCGATTCTATAAGATCTT
5859368 TG
131 TG
* * *
5859370 GGCATAATTTCTAAGACCTCCAAGCATAATCTTTAAGACCTCCAAACATAAGTTTGATTTACGGT
1 GGCATAATCTCTAAGACCTCCAAGAATAATCTTTAAGACCTCCAAACATAAGTTTGATTCACGGT
* *
5859435 GTTAT-CTCGATCGATTCTTCATTTCTCGACTTGCGGTGTTGTCCCAATCGATTCT
66 GTTATCCT-GATCAATTCTTCATTTATCGACTTGCGGTGTTGTCCCAATCGATTCT
5859490 TTAATTTTGA
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
131 2 0.02
132 101 0.98
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (132 bp):
GGCATAATCTCTAAGACCTCCAAGAATAATCTTTAAGACCTCCAAACATAAGTTTGATTCACGGT
GTTATCCTGATCAATTCTTCATTTATCGACTTGCGGTGTTGTCCCAATCGATTCTATAAGATCTT
TG
Found at i:5859485 original size:37 final size:37
Alignment explanation
Indices: 5859444--5859622 Score: 134
Period size: 36 Copynumber: 4.9 Consensus size: 37
5859434 TGTTATCTCG
*
5859444 ATCGATTCTTCATTTCTCGACTTGCGGTGTTGTCCCA
1 ATCGATTCTTAATTTCTCGACTTGCGGTGTTGTCCCA
* * ** *
5859481 ATCGATTCTTTAATTT-T-GACTCGCAGTGTCATCCCG
1 ATCGATTC-TTAATTTCTCGACTTGCGGTGTTGTCCCA
* * *
5859517 ATCGATTCTTTATTTCTCGACTTGTGGTGTTGTCTCA
1 ATCGATTCTTAATTTCTCGACTTGCGGTGTTGTCCCA
* ** * *
5859554 GTCGATTCTTTAATTT-T-GACTTATGGTGTTGTCTCG
1 ATCGATTC-TTAATTTCTCGACTTGCGGTGTTGTCCCA
* * * *
5859590 GTCGATTCTCTACTTT-TTGACTTGCGATGTTGT
1 ATCGATTCT-TAATTTCTCGACTTGCGGTGTTGT
5859623 TTCAGTAGAT
Statistics
Matches: 114, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
35 7 0.06
36 54 0.47
37 41 0.36
38 12 0.11
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.45
Consensus pattern (37 bp):
ATCGATTCTTAATTTCTCGACTTGCGGTGTTGTCCCA
Found at i:5859582 original size:36 final size:36
Alignment explanation
Indices: 5859422--5859655 Score: 163
Period size: 37 Copynumber: 6.4 Consensus size: 36
5859412 CAAACATAAG
* * * *
5859422 TTTGATTTACGGTGTTATCTC-GATCGATTC-TTCAT
1 TTTGACTTGCGGTGTTGTCTCAG-TCGATTCTTTAAT
* *
5859457 TTCTCGACTTGCGGTGTTGTCCCAATCGATTCTTTAAT
1 TT-T-GACTTGCGGTGTTGTCTCAGTCGATTCTTTAAT
* * ** *
5859495 TTTGACTCGCAGTGTCATC-CCGATCGATTCTTT-AT
1 TTTGACTTGCGGTGTTGTCTCAG-TCGATTCTTTAAT
*
5859530 TTCTCGACTTGTGGTGTTGTCTCAGTCGATTCTTTAAT
1 TT-T-GACTTGCGGTGTTGTCTCAGTCGATTCTTTAAT
** * * *
5859568 TTTGACTTATGGTGTTGTCTCGGTCGATTCTCTACTT
1 TTTGACTTGCGGTGTTGTCTCAGTCGATTCTTTA-AT
* * * *
5859605 TTTGACTTGCGATGTTGTTTCAGTAGATT-TTTTAT
1 TTTGACTTGCGGTGTTGTCTCAGTCGATTCTTTAAT
*
5859640 TTTCGACTAGCGGTGT
1 TTT-GACTTGCGGTGT
5859656 GTCACGCCCC
Statistics
Matches: 155, Mismatches: 33, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
35 11 0.07
36 64 0.41
37 68 0.44
38 12 0.08
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.46
Consensus pattern (36 bp):
TTTGACTTGCGGTGTTGTCTCAGTCGATTCTTTAAT
Found at i:5859595 original size:73 final size:73
Alignment explanation
Indices: 5859422--5859655 Score: 249
Period size: 73 Copynumber: 3.2 Consensus size: 73
5859412 CAAACATAAG
* * * *
5859422 TTTGATTTACGGTGTTATCTCGATCGATTCTTCATTTCTCGACTTGCGGTGTTGTCCCAATCGAT
1 TTTGACTTACGGTGTTATCTCGATCGATTCTTTATTTCTCGACTTGCGGTGTTGTCTCAGTCGAT
5859487 TCTTTAAT
66 TCTTTAAT
** * * * *
5859495 TTTGACTCGCAGTGTCATCCCGATCGATTCTTTATTTCTCGACTTGTGGTGTTGTCTCAGTCGAT
1 TTTGACTTACGGTGTTATCTCGATCGATTCTTTATTTCTCGACTTGCGGTGTTGTCTCAGTCGAT
5859560 TCTTTAAT
66 TCTTTAAT
* * * * * * * *
5859568 TTTGACTTATGGTGTTGTCTCGGTCGATTCTCTACTTT-TTGACTTGCGATGTTGTTTCAGTAGA
1 TTTGACTTACGGTGTTATCTCGATCGATTCTTTA-TTTCTCGACTTGCGGTGTTGTCTCAGTCGA
*
5859632 TT-TTTTAT
65 TTCTTTAAT
5859640 TTTCGAC-TAGCGGTGT
1 TTT-GACTTA-CGGTGT
5859656 GTCACGCCCC
Statistics
Matches: 132, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
72 10 0.08
73 119 0.90
74 3 0.02
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.46
Consensus pattern (73 bp):
TTTGACTTACGGTGTTATCTCGATCGATTCTTTATTTCTCGACTTGCGGTGTTGTCTCAGTCGAT
TCTTTAAT
Found at i:5860233 original size:16 final size:16
Alignment explanation
Indices: 5860212--5860243 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5860202 AAAATCATCG
5860212 TAAATCATCATTATCA
1 TAAATCATCATTATCA
5860228 TAAATCATCATTATCA
1 TAAATCATCATTATCA
5860244 ATCAAATCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATCATCATTATCA
Found at i:5860258 original size:15 final size:15
Alignment explanation
Indices: 5860238--5860270 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5860228 TAAATCATCA
5860238 TTATCAATCAAATCG
1 TTATCAATCAAATCG
*
5860253 TTATCATTCAAATCG
1 TTATCAATCAAATCG
5860268 TTA
1 TTA
5860271 GCTACGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (15 bp):
TTATCAATCAAATCG
Found at i:5862218 original size:15 final size:15
Alignment explanation
Indices: 5862166--5862218 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
5862156 ATAATCAATA
**
5862166 AAAAAAATAAAAACA
1 AAAAAAATAAAAATG
5862181 AAAAAAATAAAAATG
1 AAAAAAATAAAAATG
*
5862196 AATAAAAACAAAAATG
1 AA-AAAAATAAAAATG
5862212 AAAAAAA
1 AAAAAAA
5862219 AATAAGACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 20 0.59
16 14 0.41
ACGTcount: A:0.83, C:0.04, G:0.04, T:0.09
Consensus pattern (15 bp):
AAAAAAATAAAAATG
Found at i:5862218 original size:25 final size:25
Alignment explanation
Indices: 5862162--5862209 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
5862152 TATCATAATC
*
5862162 AATAAAAA-AAATAAAAACAAAAAA
1 AATAAAAATGAATAAAAACAAAAAA
5862186 AATAAAAATGAATAAAAACAAAAA
1 AATAAAAATGAATAAAAACAAAAA
5862210 TGAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.10
Consensus pattern (25 bp):
AATAAAAATGAATAAAAACAAAAAA
Found at i:5862219 original size:16 final size:16
Alignment explanation
Indices: 5862165--5862219 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
5862155 CATAATCAAT
*
5862165 AAAAAAAATAAAAA-C
1 AAAAAAAATAAAAATG
5862180 AAAAAAAATAAAAATG
1 AAAAAAAATAAAAATG
* *
5862196 AATAAAAACAAAAATG
1 AAAAAAAATAAAAATG
5862212 AAAAAAAA
1 AAAAAAAA
5862220 ATAAGACAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
15 14 0.40
16 21 0.60
ACGTcount: A:0.84, C:0.04, G:0.04, T:0.09
Consensus pattern (16 bp):
AAAAAAAATAAAAATG
Found at i:5862615 original size:30 final size:31
Alignment explanation
Indices: 5862579--5862637 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
5862569 TCTCATCTAT
*
5862579 CAAAAAACAAAAAAC-CCAAAACA-AATCCAC
1 CAAAAAA-AAAAAACAACAAAACATAATCCAC
5862609 CAAAAAAAAAAAACAACAAAACATAATCC
1 CAAAAAAAAAAAACAACAAAACATAATCC
5862638 TCTTCATAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.27
30 14 0.54
31 5 0.19
ACGTcount: A:0.69, C:0.25, G:0.00, T:0.05
Consensus pattern (31 bp):
CAAAAAAAAAAAACAACAAAACATAATCCAC
Found at i:5863188 original size:15 final size:15
Alignment explanation
Indices: 5863155--5863194 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
5863145 TTTCTAATTT
*
5863155 TTTTA-TATTATTAG
1 TTTTATTATTTTTAG
5863169 TTTTATTATTTTTAG
1 TTTTATTATTTTTAG
5863184 TTTTATT-TTTT
1 TTTTATTATTTT
5863195 AATAATCATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (15 bp):
TTTTATTATTTTTAG
Found at i:5863324 original size:3 final size:3
Alignment explanation
Indices: 5863316--5863362 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
5863306 ATTCTTAAAA
* *
5863316 AAT AAT AAT AAT -AT AA- AAT AAT AAT AAT AAT ACT AAT -AG AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5863361 AA
1 AA
5863363 ATTTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 5 0.14
3 32 0.86
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5863335 original size:16 final size:16
Alignment explanation
Indices: 5863314--5863344 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5863304 AAATTCTTAA
5863314 AAAATAATAATAATAT
1 AAAATAATAATAATAT
5863330 AAAATAATAATAATA
1 AAAATAATAATAATA
5863345 ATACTAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAATAATAATAT
Found at i:5863340 original size:19 final size:19
Alignment explanation
Indices: 5863311--5863362 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
5863301 TAAAAATTCT
5863311 TAAAAAATAATAATAATA-
1 TAAAAAATAATAATAATAC
5863329 TAAAATAATAATAATAATAC
1 TAAAA-AATAATAATAATAC
*
5863349 TAATAGAATAATAA
1 TAA-AAAATAATAA
5863363 ATTTTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 5 0.17
19 13 0.43
20 11 0.37
21 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
TAAAAAATAATAATAATAC
Found at i:5863461 original size:3 final size:3
Alignment explanation
Indices: 5863455--5863526 Score: 135
Period size: 3 Copynumber: 24.0 Consensus size: 3
5863445 AATTGAAAGG
*
5863455 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5863503 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
5863527 ATCTTCATAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5863729 original size:30 final size:30
Alignment explanation
Indices: 5863695--5863770 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 30
5863685 TAAAACCCTT
* * *
5863695 AAACCCCGAAATTGAAATCTTATACCCTCA
1 AAACCCTGAAATTGAAATCTTAAAACCTCA
* * * *
5863725 AAACCTTAAAACT-AAATCTTAAAACCTCT
1 AAACCCTGAAATTGAAATCTTAAAACCTCA
5863754 AAACCCTGAAATTGAAA
1 AAACCCTGAAATTGAAA
5863771 CCCCAAAACC
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.46, C:0.25, G:0.05, T:0.24
Consensus pattern (30 bp):
AAACCCTGAAATTGAAATCTTAAAACCTCA
Found at i:5867943 original size:3 final size:3
Alignment explanation
Indices: 5867937--5867983 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5867927 AAATTAAATA
5867937 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5867984 AATGGTGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5868303 original size:23 final size:23
Alignment explanation
Indices: 5868277--5868321 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
5868267 TCCTCTCAGC
5868277 AGAGGCTCAACAACTTTAAAATG
1 AGAGGCTCAACAACTTTAAAATG
5868300 AGAGGCTCAACAACTTTAAAAT
1 AGAGGCTCAACAACTTTAAAAT
5868322 CTGGTCTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (23 bp):
AGAGGCTCAACAACTTTAAAATG
Found at i:5868347 original size:71 final size:73
Alignment explanation
Indices: 5868226--5868369 Score: 238
Period size: 71 Copynumber: 2.0 Consensus size: 73
5868216 TCTTTTCAGT
*
5868226 AGAGGCTCAACAACTTTAAAAGTCTCATATCTTGAAAAAACTCCTCTCAGCAGAGGCTCAACAAC
1 AGAGGCTCAACAACTTTAAAAGTCT-AGATCTTGAAAAAACTCCTCTCAGCAGAGGCTCAACAAC
5868291 TTTAAAATG
65 TTTAAAATG
* *
5868300 AGAGGCTCAACAACTTTAAAA-TCT-GGTCTTGGAAAAACTCCTCTCAGCAGAGGCTCAACAACT
1 AGAGGCTCAACAACTTTAAAAGTCTAGATCTTGAAAAAACTCCTCTCAGCAGAGGCTCAACAACT
5868363 TTAAAAT
66 TTAAAAT
5868370 TTCATCTTGG
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
71 43 0.64
73 3 0.04
74 21 0.31
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (73 bp):
AGAGGCTCAACAACTTTAAAAGTCTAGATCTTGAAAAAACTCCTCTCAGCAGAGGCTCAACAACT
TTAAAATG
Found at i:5868378 original size:48 final size:48
Alignment explanation
Indices: 5868300--5868511 Score: 288
Period size: 48 Copynumber: 4.5 Consensus size: 48
5868290 CTTTAAAATG
* **
5868300 AGAGGCTCAACAACTTTAAAATCTGGTCTTGGAAAAACTCCTCTCAGC
1 AGAGGCTCAACAACTTTAAAATTTCATCTTGGAAAAACTCCTCTCAGC
* *
5868348 AGAGGCTCAACAACTTTAAAATTTCATCTTGGAAAAGCTCCTCTCAGT
1 AGAGGCTCAACAACTTTAAAATTTCATCTTGGAAAAACTCCTCTCAGC
* * *
5868396 TGAGGCTCAACAACTTTAAAA-TTC-CCTT-GAAAAAGTTCCTCTCAGC
1 AGAGGCTCAACAACTTTAAAATTTCATCTTGGAAAAA-CTCCTCTCAGC
* *
5868442 AGA-GCTCAACAACTTTAAAATCTCATCTTGGAAAAGCTCCTCTCAGC
1 AGAGGCTCAACAACTTTAAAATTTCATCTTGGAAAAACTCCTCTCAGC
*
5868489 AGAAGCTCAACAACTTTAAAATT
1 AGAGGCTCAACAACTTTAAAATT
5868512 CTCTTTTATT
Statistics
Matches: 143, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
45 22 0.15
46 16 0.11
47 19 0.13
48 86 0.60
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.27
Consensus pattern (48 bp):
AGAGGCTCAACAACTTTAAAATTTCATCTTGGAAAAACTCCTCTCAGC
Found at i:5868468 original size:93 final size:94
Alignment explanation
Indices: 5868300--5868512 Score: 322
Period size: 93 Copynumber: 2.3 Consensus size: 94
5868290 CTTTAAAATG
**
5868300 AGAGGCTCAACAACTTTAAAATCTGGTCTTGGAAAAACTCCTCTCAGCAGAGGCTCAACAACTTT
1 AGAGGCTCAACAACTTTAAAAT-T-CCCTTGGAAAAACTCCTCTCAGCAGAGGCTCAACAACTTT
* *
5868365 AAAATTTCATCTTGGAAAAGCTCCTCTCAGT
64 AAAATCTCATCTTGGAAAAGCTCCTCTCAGC
* *
5868396 TGAGGCTCAACAACTTTAAAATTCCCTT-GAAAAAGTTCCTCTCAGCAGA-GCTCAACAACTTTA
1 AGAGGCTCAACAACTTTAAAATTCCCTTGGAAAAA-CTCCTCTCAGCAGAGGCTCAACAACTTTA
5868459 AAATCTCATCTTGGAAAAGCTCCTCTCAGC
65 AAATCTCATCTTGGAAAAGCTCCTCTCAGC
*
5868489 AGAAGCTCAACAACTTTAAAATTC
1 AGAGGCTCAACAACTTTAAAATTC
5868513 TCTTTTATTT
Statistics
Matches: 108, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
93 70 0.65
94 16 0.15
95 1 0.01
96 21 0.19
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.27
Consensus pattern (94 bp):
AGAGGCTCAACAACTTTAAAATTCCCTTGGAAAAACTCCTCTCAGCAGAGGCTCAACAACTTTAA
AATCTCATCTTGGAAAAGCTCCTCTCAGC
Found at i:5872577 original size:14 final size:14
Alignment explanation
Indices: 5872558--5872588 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5872548 TCATCATCTC
5872558 TCAAATTTACTGAT
1 TCAAATTTACTGAT
5872572 TCAAATTTACTGAT
1 TCAAATTTACTGAT
5872586 TCA
1 TCA
5872589 GTAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (14 bp):
TCAAATTTACTGAT
Found at i:5880331 original size:3 final size:3
Alignment explanation
Indices: 5880325--5880356 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5880315 AAATTAAATA
5880325 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5880357 AAATGGTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5882402 original size:2 final size:2
Alignment explanation
Indices: 5882384--5882419 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5882374 AAACGTACAC
* *
5882384 TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5882420 AACAAACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:5884116 original size:15 final size:16
Alignment explanation
Indices: 5884069--5884119 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
5884059 ATGGTATATT
5884069 TTTATTATAAAATTAAA
1 TTTATTA-AAAATTAAA
**
5884086 -AGATTAAAAATTTAAA
1 TTTATTAAAAA-TTAAA
5884102 TTTATTAAAAA-TAAA
1 TTTATTAAAAATTAAA
5884117 TTT
1 TTT
5884120 TAAAAACGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 11 0.39
16 9 0.32
17 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TTTATTAAAAATTAAA
Found at i:5884840 original size:18 final size:17
Alignment explanation
Indices: 5884819--5884859 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
5884809 TTTTATTTGA
*
5884819 TTTATTTTTTAAATTATT
1 TTTATTTTTT-AATAATT
5884837 TTTATTTTTTAATAATT
1 TTTATTTTTTAATAATT
5884854 TTTATT
1 TTTATT
5884860 AACTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTTTTAATAATT
Found at i:5885136 original size:30 final size:30
Alignment explanation
Indices: 5885100--5885167 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
5885090 CTAAATTAAT
* * *
5885100 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATTATTATATAAATATAAATAATTA
* *
5885130 AAAATATCATTATATAAATATATATAATTA
1 AAAATATTATTATATAAATATAAATAATTA
5885160 AAAA-ATTA
1 AAAATATTA
5885168 ATTAAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (30 bp):
AAAATATTATTATATAAATATAAATAATTA
Found at i:5885169 original size:12 final size:12
Alignment explanation
Indices: 5885154--5885179 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5885144 TAAATATATA
5885154 TAATTAAAAAAT
1 TAATTAAAAAAT
5885166 TAATTAAAAAAT
1 TAATTAAAAAAT
5885178 TA
1 TA
5885180 TTTTTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAATTAAAAAAT
Found at i:5885557 original size:19 final size:19
Alignment explanation
Indices: 5885519--5885557 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5885509 ATTTTAATAT
*
5885519 TTATATTTTTTATATTAAA
1 TTATATTTTTTATATAAAA
5885538 TTATAATTTTTTATA-AAAA
1 TTAT-ATTTTTTATATAAAA
5885557 T
1 T
5885558 AAAATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATATTTTTTATATAAAA
Found at i:5887162 original size:13 final size:14
Alignment explanation
Indices: 5887144--5887181 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
5887134 AAAATAATAT
5887144 TTTTTTCA-ATTTA
1 TTTTTTCACATTTA
5887157 TTTTTTCACA--TA
1 TTTTTTCACATTTA
5887169 TTTTTTCACATTT
1 TTTTTTCACATTT
5887182 TTCATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.55
13 8 0.36
14 2 0.09
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTTCACATTTA
Found at i:5890807 original size:17 final size:19
Alignment explanation
Indices: 5890771--5890810 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
5890761 TTATTATTCA
*
5890771 TATTTGTTTAAATTATTTT
1 TATTTGTTTAAATGATTTT
5890790 TATTT-TTT-AATGATTTT
1 TATTTGTTTAAATGATTTT
5890807 TATT
1 TATT
5890811 AACTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
18 3 0.15
19 5 0.25
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TATTTGTTTAAATGATTTT
Found at i:5891048 original size:28 final size:28
Alignment explanation
Indices: 5890996--5891050 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
5890986 TGTTTAATTT
*
5890996 AATAAATTTATATAATTATATTTTAAAA
1 AATAAATTTATATAATTATAATTTAAAA
5891024 AATAATATTTA-ATAAATT-TAATTTAAA
1 AATAA-ATTTATAT-AATTATAATTTAAA
5891051 TTTTAATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AATAAATTTATATAATTATAATTTAAAA
Found at i:5892071 original size:9 final size:9
Alignment explanation
Indices: 5892059--5892088 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5892049 ACTAAATATA
*
5892059 TTAAAATTT
1 TTAAAAATT
5892068 TTAAAAATT
1 TTAAAAATT
5892077 TTAAAAATT
1 TTAAAAATT
5892086 TTA
1 TTA
5892089 TATGAATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TTAAAAATT
Found at i:5897341 original size:17 final size:17
Alignment explanation
Indices: 5897319--5897357 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
5897309 TTTTATAAAT
*
5897319 AAATAATTTATTTTTAG
1 AAATAATTTATTTTTAA
5897336 AAATAATTTATTTTTAA
1 AAATAATTTATTTTTAA
5897353 AAATA
1 AAATA
5897358 TCTTTCAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
AAATAATTTATTTTTAA
Found at i:5897601 original size:14 final size:14
Alignment explanation
Indices: 5897582--5897623 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
5897572 AAATAAATAT
* *
5897582 AAATTATCTTGTAA
1 AAATTATCATGCAA
5897596 AAATTATCATGCAA
1 AAATTATCATGCAA
*
5897610 AAAATATCATGCAA
1 AAATTATCATGCAA
5897624 TAATAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (14 bp):
AAATTATCATGCAA
Found at i:5897896 original size:7 final size:7
Alignment explanation
Indices: 5897841--5897899 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
5897831 ATCAACCTTT
5897841 TAAAATA
1 TAAAATA
5897848 -ATAAATA
1 TA-AAATA
5897855 TTAAAATA
1 -TAAAATA
5897863 T-AAATA
1 TAAAATA
5897869 TTAAAATA
1 -TAAAATA
5897877 T--AA-A
1 TAAAATA
5897881 TAAAATA
1 TAAAATA
5897888 TAAAATA
1 TAAAATA
5897895 TAAAA
1 TAAAA
5897900 AAATCAAAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
6 8 0.18
7 21 0.48
8 10 0.23
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TAAAATA
Found at i:5897899 original size:14 final size:14
Alignment explanation
Indices: 5897840--5897882 Score: 77
Period size: 14 Copynumber: 3.0 Consensus size: 14
5897830 AATCAACCTT
5897840 TTAAAATAATAAATA
1 TTAAAAT-ATAAATA
5897855 TTAAAATATAAATA
1 TTAAAATATAAATA
5897869 TTAAAATATAAATA
1 TTAAAATATAAATA
5897883 AAATATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 21 0.75
15 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAATATAAATA
Found at i:5898358 original size:20 final size:19
Alignment explanation
Indices: 5898329--5898388 Score: 79
Period size: 20 Copynumber: 3.2 Consensus size: 19
5898319 CCAAAAAAAA
5898329 AAATCTAAAAATTCAAATC
1 AAATCTAAAAATTCAAATC
*
5898348 AAATCCTAAAATTTCAAATC
1 AAAT-CTAAAAATTCAAATC
5898368 AAAT-TCAAAAATTCAAA-C
1 AAATCT-AAAAATTCAAATC
5898386 AAA
1 AAA
5898389 AAATTCTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.14
19 14 0.38
20 18 0.49
ACGTcount: A:0.58, C:0.17, G:0.00, T:0.25
Consensus pattern (19 bp):
AAATCTAAAAATTCAAATC
Found at i:5898958 original size:18 final size:17
Alignment explanation
Indices: 5898931--5898995 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 17
5898921 AATAAATCAC
5898931 AAAATTAAAATCAAACT
1 AAAATTAAAATCAAACT
* *
5898948 AAATTTAAAAATCTAAATT
1 AAAATT-AAAATC-AAACT
*
5898967 AAAATTAAAATCAAAAT
1 AAAATTAAAATCAAACT
*
5898984 CAAGATTAAAAT
1 -AAAATTAAAAT
5898996 AAAAATTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 9 0.22
18 22 0.55
19 9 0.22
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.28
Consensus pattern (17 bp):
AAAATTAAAATCAAACT
Found at i:5898976 original size:6 final size:6
Alignment explanation
Indices: 5898931--5899007 Score: 59
Period size: 6 Copynumber: 12.8 Consensus size: 6
5898921 AATAAATCAC
* * * *
5898931 AAAATT AAAA-T CAAACT AAATTT AAAAATCT -AAATT AAAATT AAAATC
1 AAAATT AAAATT AAAATT AAAATT -AAAAT-T AAAATT AAAATT AAAATT
* * *
5898979 AAAATC AAGATT AAAATA AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAAT
5899008 CAAATTTCAA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
5 5 0.09
6 46 0.82
7 4 0.07
8 1 0.02
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.27
Consensus pattern (6 bp):
AAAATT
Found at i:5898982 original size:24 final size:23
Alignment explanation
Indices: 5898955--5899023 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 23
5898945 ACTAAATTTA
5898955 AAAATCTAAATTAAAATTAAAATC
1 AAAATC-AAATTAAAATTAAAATC
* *
5898979 AAAATCAAGATTAAAATAAAAATT
1 AAAATCAA-ATTAAAATTAAAATC
**
5899003 AAAATCAAATTTCAATTAAAA
1 AAAATCAAATTAAAATTAAAA
5899024 ATTTTAAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 12 0.31
24 27 0.69
ACGTcount: A:0.64, C:0.07, G:0.01, T:0.28
Consensus pattern (23 bp):
AAAATCAAATTAAAATTAAAATC
Found at i:5898995 original size:36 final size:36
Alignment explanation
Indices: 5898931--5899007 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 36
5898921 AATAAATCAC
* **
5898931 AAAATTAAAATCAAACTAAATTTAAAAATCTAAATT
1 AAAATTAAAATCAAAATAAATTTAAAAATAAAAATT
5898967 AAAATTAAAATCAAAATCAAGA-TT-AAAATAAAAATT
1 AAAATTAAAATCAAAAT-AA-ATTTAAAAATAAAAATT
5899003 AAAAT
1 AAAAT
5899008 CAAATTTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 31 0.86
37 4 0.11
38 1 0.03
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.27
Consensus pattern (36 bp):
AAAATTAAAATCAAAATAAATTTAAAAATAAAAATT
Found at i:5899198 original size:2 final size:2
Alignment explanation
Indices: 5899191--5899222 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5899181 TCTCTTGTAA
5899191 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5899223 CAGTAGGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5901161 original size:2 final size:2
Alignment explanation
Indices: 5901156--5901185 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5901146 CTATATACAA
*
5901156 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5901186 TCTTTCTCAC
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5905960 original size:17 final size:18
Alignment explanation
Indices: 5905933--5905968 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5905923 GTAAAGCATG
5905933 AAAGCTAAAAGAAACAAT
1 AAAGCTAAAAGAAACAAT
*
5905951 AAAG-TAAAAGAAGCAAT
1 AAAGCTAAAAGAAACAAT
5905968 A
1 A
5905969 GTTATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.67, C:0.08, G:0.14, T:0.11
Consensus pattern (18 bp):
AAAGCTAAAAGAAACAAT
Found at i:5910165 original size:30 final size:30
Alignment explanation
Indices: 5910131--5910208 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
5910121 ATATTCATTC
* * *
5910131 ATTTAAAAATTTTATTAAATAAAAATAAAT
1 ATTTAAAAATTTAATTAAACAAAAATAAAA
**
5910161 ATTTAAAAGCTTAATTAAACAAAAATAAAA
1 ATTTAAAAATTTAATTAAACAAAAATAAAA
*
5910191 ATTAAAAAATTTAATTAA
1 ATTTAAAAATTTAATTAA
5910209 TTATAATAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.35
Consensus pattern (30 bp):
ATTTAAAAATTTAATTAAACAAAAATAAAA
Found at i:5911717 original size:15 final size:15
Alignment explanation
Indices: 5911697--5911734 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5911687 TATTAAGAAT
5911697 ATTTTTTTTC-ATAGA
1 ATTTTTTTTCTATA-A
*
5911712 ATTTTTTTTCTGTAA
1 ATTTTTTTTCTATAA
5911727 ATTTTTTT
1 ATTTTTTT
5911735 ATTCATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (15 bp):
ATTTTTTTTCTATAA
Found at i:5911718 original size:17 final size:17
Alignment explanation
Indices: 5911692--5911741 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
5911682 CTTAATATTA
*
5911692 AGAATATTTTTTTTCAT
1 AGAATTTTTTTTTTCAT
* *
5911709 AGAATTTTTTTTCT-GT
1 AGAATTTTTTTTTTCAT
*
5911725 A-AATTTTTTTATTCAT
1 AGAATTTTTTTTTTCAT
5911741 A
1 A
5911742 AAATAATATC
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
15 10 0.38
16 4 0.15
17 12 0.46
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (17 bp):
AGAATTTTTTTTTTCAT
Found at i:5913518 original size:33 final size:33
Alignment explanation
Indices: 5913476--5913543 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
5913466 GTCAATTCGG
* *
5913476 ACACCAATATCACAAGTAGTCATTGCTCCGGTC
1 ACACCAATATCACAAGCAGTCATTGCTCCAGTC
*
5913509 ACACCAATATCACAAGCAGTTATTGCTCCAGTC
1 ACACCAATATCACAAGCAGTCATTGCTCCAGTC
5913542 AC
1 AC
5913544 TTGATCCTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.24
Consensus pattern (33 bp):
ACACCAATATCACAAGCAGTCATTGCTCCAGTC
Found at i:5915366 original size:14 final size:15
Alignment explanation
Indices: 5915345--5915380 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
5915335 CAAATACTTC
5915345 ATTATAAAGATACAA
1 ATTATAAAGATACAA
*
5915360 A-TATAAATATACAA
1 ATTATAAAGATACAA
5915374 ATTATAA
1 ATTATAA
5915381 TATTATAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (15 bp):
ATTATAAAGATACAA
Found at i:5916183 original size:14 final size:14
Alignment explanation
Indices: 5916156--5916212 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 14
5916146 TATATAAAAT
*
5916156 TTTTTTTA-AATTA
1 TTTTTTTATATTTA
5916169 TTTTTTTATATTTA
1 TTTTTTTATATTTA
* *
5916183 TATTTATATATTTA
1 TTTTTTTATATTTA
5916197 TTTAATTTTATATTTA
1 TTT--TTTTATATTTA
5916213 CATTAAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
13 8 0.22
14 18 0.50
16 10 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTTTATATTTA
Found at i:5916200 original size:18 final size:16
Alignment explanation
Indices: 5916177--5916212 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
5916167 TATTTTTTTA
5916177 TATTTATATTTATATATT
1 TATTTA-ATTT-TATATT
5916195 TATTTAATTTTATATT
1 TATTTAATTTTATATT
5916211 TA
1 TA
5916213 CATTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTAATTTTATATT
Found at i:5916232 original size:20 final size:20
Alignment explanation
Indices: 5916209--5916252 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5916199 TAATTTTATA
5916209 TTTACA-TTAAAAATTAATAT
1 TTTACATTTAAAAA-TAATAT
*
5916229 TTTATATTTAAAAATAATAT
1 TTTACATTTAAAAATAATAT
5916249 TTTA
1 TTTA
5916253 TTAATTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTACATTTAAAAATAATAT
Found at i:5916259 original size:22 final size:21
Alignment explanation
Indices: 5916215--5916253 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
5916205 TATATTTACA
5916215 TTAAAAATTAATATTTTATAT
1 TTAAAAATTAATATTTTATAT
5916236 TTAAAAA-TAATATTTTAT
1 TTAAAAATTAATATTTTAT
5916254 TAATTTCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAAAATTAATATTTTATAT
Found at i:5923877 original size:18 final size:17
Alignment explanation
Indices: 5923839--5923874 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5923829 ACAAAAAAAC
5923839 TTAAAAAAAAATAAATT
1 TTAAAAAAAAATAAATT
*
5923856 TTAAGAAAAAATAAATT
1 TTAAAAAAAAATAAATT
5923873 TT
1 TT
5923875 TAATAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAAAAAAAAATAAATT
Found at i:5924154 original size:13 final size:14
Alignment explanation
Indices: 5924136--5924164 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5924126 ATAAAAAAAT
5924136 TTATGAGTA-TTAA
1 TTATGAGTACTTAA
5924149 TTATGAGTACTTAA
1 TTATGAGTACTTAA
5924163 TT
1 TT
5924165 TTAATTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (14 bp):
TTATGAGTACTTAA
Found at i:5924459 original size:2 final size:2
Alignment explanation
Indices: 5924447--5924483 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5924437 TGGATGACCG
*
5924447 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5924484 TTACAGTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5925697 original size:26 final size:26
Alignment explanation
Indices: 5925660--5925712 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
5925650 GAAGAAAGAA
* *
5925660 AACTGAAGAAACTTTTAACTTTGCTT
1 AACTGAAAAAACTTATAACTTTGCTT
5925686 AACTGAAAAAACTTATAACTTTGCTT
1 AACTGAAAAAACTTATAACTTTGCTT
5925712 A
1 A
5925713 CTTCTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (26 bp):
AACTGAAAAAACTTATAACTTTGCTT
Found at i:5933718 original size:48 final size:48
Alignment explanation
Indices: 5933647--5933752 Score: 169
Period size: 48 Copynumber: 2.2 Consensus size: 48
5933637 TTATCAATGG
5933647 GTGAACTAAACTATTCAAAACATCATTGAAAGAGGAAATAATAATTAA
1 GTGAACTAAACTATTCAAAACATCATTGAAAGAGGAAATAATAATTAA
* * *
5933695 GTGAACTAAACTATTGAAAACATCATTGAAATAGGAAATAGTAATTAA
1 GTGAACTAAACTATTCAAAACATCATTGAAAGAGGAAATAATAATTAA
5933743 GTAGAA-TAAA
1 GT-GAACTAAA
5933753 ATGCAACCAT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 51 0.94
49 3 0.06
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.25
Consensus pattern (48 bp):
GTGAACTAAACTATTCAAAACATCATTGAAAGAGGAAATAATAATTAA
Found at i:5941823 original size:19 final size:20
Alignment explanation
Indices: 5941799--5941840 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
5941789 ATCTGAGTAG
5941799 AAAATTAAAAATAATTT-TA
1 AAAATTAAAAATAATTTATA
*
5941818 AAAATTAATAATAATTTATA
1 AAAATTAAAAATAATTTATA
5941838 AAA
1 AAA
5941841 CATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTAAAAATAATTTATA
Found at i:5941847 original size:19 final size:20
Alignment explanation
Indices: 5941799--5941852 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
5941789 ATCTGAGTAG
5941799 AAAATTAA-AAATAATTTTA
1 AAAATTAATAAATAATTTTA
5941818 AAAATTAAT-AATAATTTATA
1 AAAATTAATAAATAATTT-TA
5941838 AAACA-T-ATAAATAAT
1 AAA-ATTAATAAATAAT
5941853 CATAATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 18 0.58
20 12 0.39
21 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATTAATAAATAATTTTA
Done.