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 27 of 64
Found at i:4090950 original size:22 final size:23
Alignment explanation
Indices: 4090808--4091022 Score: 123
Period size: 23 Copynumber: 8.8 Consensus size: 23
4090798 TACTTATAAA
4090808 TAATATTATATTAATAAATAATAT
1 TAATATTA-ATTAATAAATAATAT
* * *
4090832 T-ATATGAATAAATAATATACTAT
1 TAATATTAATTAATAA-ATAATAT
*
4090855 TAATATAATATTAATAAATAATAT
1 TAATATTA-ATTAATAAATAATAT
*
4090879 T-ATAATATATTAATAAATAATAT
1 TAATATTA-ATTAATAAATAATAT
* *
4090902 T-ATATTAATAAATAATTTAATAATAAA
1 TAATATTAAT---TAA-TAAATAAT-AT
* *
4090929 TATTATTAATTTAATTAATAAATAAT
1 TAATATTAA-TTAATAAAT-AAT-AT
* **
4090955 ATAATAATAATGTATAAATAATA-
1 -TAATATTAATTAATAAATAATAT
* *
4090978 TAATATTAATAAATAATATACTAT
1 TAATATTAATTAATAA-ATAATAT
4091002 TAAAATATTATATTAATAAAT
1 T--AATATTA-ATTAATAAAT
4091023 CTTGTTAATA
Statistics
Matches: 151, Mismatches: 23, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
22 22 0.15
23 43 0.28
24 15 0.10
25 18 0.12
26 30 0.20
27 16 0.11
28 6 0.04
29 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (23 bp):
TAATATTAATTAATAAATAATAT
Found at i:4091167 original size:16 final size:15
Alignment explanation
Indices: 4091093--4091190 Score: 52
Period size: 17 Copynumber: 5.7 Consensus size: 15
4091083 TATTTTAGGT
*
4091093 ATTTTTATATTAACATA
1 ATTTTAATATT-A-ATA
4091110 ATATTTAATATTAAATA
1 AT-TTTAATATT-AATA
*
4091127 TTATTATTAAAATATAATTA
1 --ATT-TTAATAT-TAA-TA
*
4091147 TTTTTGAATATTAATA
1 ATTTT-AATATTAATA
*
4091163 ATTTTAATAATCAATA
1 ATTTTAAT-ATTAATA
4091179 ATTTTTAATATT
1 A-TTTTAATATT
4091191 TTAATAATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
15 3 0.05
16 15 0.23
17 17 0.26
18 17 0.26
19 10 0.15
20 3 0.05
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (15 bp):
ATTTTAATATTAATA
Found at i:4096258 original size:129 final size:126
Alignment explanation
Indices: 4096107--4096351 Score: 445
Period size: 129 Copynumber: 1.9 Consensus size: 126
4096097 TAACTGCACC
4096107 ACTTTTTGATCCGATCTAGGCTTCTATTTTGTCTATATCTCTTATGATTGTTAGCAATACTAAGT
1 ACTTTTTGATCCGATCTAGGCTTCTATTTTGTCTATATCTCTTATGATTGTTAGCAATACTAAGT
* *
4096172 GTTGTTCCCTTGTTAACTTTGCCTTTTTGTTTTTTGTTTATTTTGTTTTTTTTTTTCTCTTACA
66 GTTGTTCCCCTGTTAACTTTGCCTTTCTGTTTTTT-TTT-TTTT-TTTTTTTTTTTCTCTTACA
4096236 ACTTTTTGATCCGATCTAGGCTTCTATTTTGTCTATATCTCTTATGATTGTTAGCAATACTAAGT
1 ACTTTTTGATCCGATCTAGGCTTCTATTTTGTCTATATCTCTTATGATTGTTAGCAATACTAAGT
4096301 GTTGTTCCCCTGTTAACTTTGCCTTTCTGTTTTTTTTTTTTTTTTTTTTTT
66 GTTGTTCCCCTGTTAACTTTGCCTTTCTGTTTTTTTTTTTTTTTTTTTTTT
4096352 CTTTTAGATA
Statistics
Matches: 114, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
126 9 0.08
127 4 0.04
128 3 0.03
129 98 0.86
ACGTcount: A:0.15, C:0.16, G:0.12, T:0.57
Consensus pattern (126 bp):
ACTTTTTGATCCGATCTAGGCTTCTATTTTGTCTATATCTCTTATGATTGTTAGCAATACTAAGT
GTTGTTCCCCTGTTAACTTTGCCTTTCTGTTTTTTTTTTTTTTTTTTTTTTTTCTCTTACA
Found at i:4098475 original size:21 final size:21
Alignment explanation
Indices: 4098451--4098494 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
4098441 AGGTCTTATA
*
4098451 TTTTACTTTTTACAATTTTTTT
1 TTTTA-TTTTTAAAATTTTTTT
4098473 TTTTATTTTTAAAATTTTTTT
1 TTTTATTTTTAAAATTTTTTT
4098494 T
1 T
4098495 GACTTGAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTATTTTTAAAATTTTTTT
Found at i:4104836 original size:94 final size:95
Alignment explanation
Indices: 4104691--4104870 Score: 263
Period size: 94 Copynumber: 1.9 Consensus size: 95
4104681 ATAATGACGG
* * * ** *
4104691 TTATTATTATAATCATCAATATAAGTTCCAAAAAAATGTTAATTCCTAATTT-TTTTTAAAAAAA
1 TTATTATTATAACCATCAATATAAGCTACAAAAAAACATCAATTCCTAATTTCTTTTTAAAAAAA
4104755 TATTAATTCACAATATTTCCCCATTGATGT
66 TATTAATTCACAATATTTCCCCATTGATGT
* * *
4104785 TTATTATTATAACCATCAATATAAGCTATAAAAAAACATCAATTCCTAATTTCTTTTTTAAAAAG
1 TTATTATTATAACCATCAATATAAGCTACAAAAAAACATCAATTCCTAATTTCTTTTTAAAAAAA
*
4104850 TATTAATTCATAATATTTCCC
66 TATTAATTCACAATATTTCCC
4104871 TCTAAAAATT
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
94 45 0.60
95 30 0.40
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.42
Consensus pattern (95 bp):
TTATTATTATAACCATCAATATAAGCTACAAAAAAACATCAATTCCTAATTTCTTTTTAAAAAAA
TATTAATTCACAATATTTCCCCATTGATGT
Found at i:4105097 original size:16 final size:17
Alignment explanation
Indices: 4105076--4105117 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
4105066 CTGCCAGTCT
4105076 CCCTAATTCCCAAA-AA
1 CCCTAATTCCCAAATAA
*
4105092 CCCTAA-ACCCAAATAA
1 CCCTAATTCCCAAATAA
4105108 CCCTACATTC
1 CCCTA-ATTC
4105118 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:4109245 original size:24 final size:24
Alignment explanation
Indices: 4109205--4109251 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4109195 AAAACATATC
4109205 ATATTATAATTATAAATA-AATTA
1 ATATTATAATTATAAATATAATTA
4109228 ATATTAATAATTGA-AAATATAATT
1 ATATT-ATAATT-ATAAATATAATT
4109252 TAAAAAAAAA
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:4112741 original size:32 final size:32
Alignment explanation
Indices: 4112691--4112751 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
4112681 CATCACCATT
* *
4112691 CATTGTGTTGTATATAAGATAAAAAGGATATC
1 CATTGTCTCGTATATAAGATAAAAAGGATATC
*
4112723 CATTGTCTCGTATTTAAGATAAAAAGGAT
1 CATTGTCTCGTATATAAGATAAAAAGGAT
4112752 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:4113047 original size:13 final size:14
Alignment explanation
Indices: 4113022--4113049 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4113012 TTATTTCGTG
4113022 AAAATTGATTTTTA
1 AAAATTGATTTTTA
4113036 AAAATTGATTTTTA
1 AAAATTGATTTTTA
4113050 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:4113319 original size:67 final size:68
Alignment explanation
Indices: 4113240--4113514 Score: 256
Period size: 67 Copynumber: 4.0 Consensus size: 68
4113230 TACTTATAAA
* *
4113240 TAATATTATATTAATAAATAAATAATATTATATTAATAAATAATATTATATGAAT-AATAATATA
1 TAATATAATATTAATAAATAAATAATATTATATTAATAAATAATATTATATTAATAAATAATATA
4113304 TAT
66 TAT
* *
4113307 TAATATAATATTAATAAAT-AATATATAATATATTAATAAATAATA-TATATTAATAAATAATTT
1 TAATATAATATTAATAAATAAATA-ATATTATATTAATAAATAATATTATATTAATAAATAATAT
4113370 AATAAT
65 -AT-AT
* * * * *
4113376 AAATATTATTAATTTAATTAATAAATAATATAATAATAATGAATAAATAATATAATATTAATAAA
1 TAATA-TAAT-A-TTAATAAATAAATAATAT--T-AT-ATTAATAAATAATATTATATTAATAAA
4113441 TAATATACTAT
59 TAATATA-TAT
* * ** * * *
4113452 TAAAATAATA-T-ATTAATAAATCTTATTA-ATAAATAATATTATAATATATTAATAAATAATAT
1 TAATATAATATTAATAAATAAATAATATTATATTAATAA-ATAATATTATATTAATAAATAATAT
4113514 A
65 A
4113515 AAGAATAATA
Statistics
Matches: 173, Mismatches: 20, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
66 19 0.11
67 68 0.39
68 3 0.02
69 7 0.04
70 3 0.02
71 14 0.08
72 12 0.07
73 4 0.02
74 2 0.01
75 5 0.03
76 19 0.11
77 17 0.10
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (68 bp):
TAATATAATATTAATAAATAAATAATATTATATTAATAAATAATATTATATTAATAAATAATATA
TAT
Found at i:4113470 original size:121 final size:122
Alignment explanation
Indices: 4113235--4113513 Score: 308
Period size: 121 Copynumber: 2.3 Consensus size: 122
4113225 AATTTTACTT
4113235 ATAAATAATATTATATTAATAAATAAATAATATTATATTAATAAATAATATTATATGAATAATAA
1 ATAAATAATATTA-A-TAATAAATAAATAATATTATATTAATAAATAATATTATATGAATAATAA
* *
4113300 TATATATTAATATAATATTAATAAATAATATATAATATATTAATAAATAATAT-ATATTA
64 TATATATTAATATAATATTAATAAATAATATATAAAATAATAATAAATAA-ATCATATTA
*
4113359 ATAAATAAT-TTAATAATAAATATTATTAAT-TTA-ATTAATAAATAATA-TA-AT-AATAATGA
1 ATAAATAATATTAATAATAAATA--AATAATATTATATTAATAAATAATATTATATGAATAAT-A
* *
4113418 ATA-A-A-TAATATAATATTAATAAATAATATACTATTAAAATAATATATTAATAAATCTTATTA
63 ATATATATTAATATAATATTAATAAAT-A-ATA-TA-TAAAATAATA-ATAAATAAATCATATTA
*
4113480 ATAAATAATATTATAATATATTAATAAATAATAT
1 ATAAATAATA-T-TAATA-ATAAATAAATAATAT
4113514 AAAGAATAAT
Statistics
Matches: 134, Mismatches: 7, Indels: 28
0.79 0.04 0.17
Matches are distributed among these distances:
116 19 0.14
117 2 0.01
118 10 0.07
119 8 0.06
120 12 0.09
121 44 0.33
122 4 0.03
123 14 0.10
124 15 0.11
125 6 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (122 bp):
ATAAATAATATTAATAATAAATAAATAATATTATATTAATAAATAATATTATATGAATAATAATA
TATATTAATATAATATTAATAAATAATATATAAAATAATAATAAATAAATCATATTA
Found at i:4113528 original size:23 final size:23
Alignment explanation
Indices: 4113479--4113528 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
4113469 AAATCTTATT
* * *
4113479 AATAAATAATATTATAATATATT
1 AATAAATAATATAAGAATATATA
4113502 AATAAATAATATAAAGAATA-ATA
1 AATAAATAATAT-AAGAATATATA
4113525 AATA
1 AATA
4113529 GTTTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
AATAAATAATATAAGAATATATA
Found at i:4113617 original size:16 final size:15
Alignment explanation
Indices: 4113558--4113640 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 15
4113548 TATATTAACA
4113558 TAAT-ATTTTAATAT
1 TAATAATTTTAATAT
*
4113572 TAAATATATTATTAAAAT
1 T-AATA-ATT-TTAATAT
*
4113590 ATAATTATTTTTGAATAT
1 -TAA-TAATTTT-AATAT
4113608 TAATAATTTTAATAAT
1 TAATAATTTTAAT-AT
*
4113624 CAATAATTTTTAATAT
1 TAATAA-TTTTAATAT
4113640 T
1 T
4113641 TTAATAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
14 1 0.02
15 6 0.11
16 15 0.28
17 15 0.28
18 14 0.26
19 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (15 bp):
TAATAATTTTAATAT
Found at i:4113646 original size:34 final size:33
Alignment explanation
Indices: 4113518--4113658 Score: 103
Period size: 34 Copynumber: 4.2 Consensus size: 33
4113508 TAATATAAAG
* *
4113518 AATAATAAAT-AGTTTT-AT-TTTAATTATTTT
1 AATAATAAATAATTTTTAATATTTAATAATTTT
* * *
4113548 TATATTAACATAATATTTTAATATTAAATATATTATT
1 AATAATAA-ATAAT-TTTTAATATTTAATA-ATT-TT
*
4113585 AA-AATATAATTATTTTTGAATA-TTAATAATTTT
1 AATAATA-AATAATTTTT-AATATTTAATAATTTT
* *
4113618 AATAATCAATAATTTTTAATATTTTAATAATTAT
1 AATAATAAATAATTTTTAATA-TTTAATAATTTT
*
4113652 ATTAATA
1 AATAATA
4113659 TTATTTAAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
30 6 0.07
31 2 0.02
32 5 0.06
33 17 0.20
34 23 0.27
35 14 0.16
36 14 0.16
37 4 0.05
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (33 bp):
AATAATAAATAATTTTTAATATTTAATAATTTT
Found at i:4118719 original size:130 final size:127
Alignment explanation
Indices: 4118561--4118811 Score: 448
Period size: 130 Copynumber: 2.0 Consensus size: 127
4118551 GCATAACTGC
4118561 ACCACTTTTTGATCCGATCTAGGCTTCTATTTTGTCTATATCTCTTATGATTGTTAGCAATACTA
1 ACCACTTTTTGATCCGATCTAGGCTTCTATTTTGTCTATATCTCTTATGATTGTTAGCAATACTA
* *
4118626 AGTGTTGTTCCCTTGTTAACTTTGCCTTTTGGTTTTTTGTTTATTTTGTTTTTTTTTTTTCTCTT
66 AGTGTTGTTCCCCTGTTAACTTTGCCTTTTGGTTTTTT-TTT-TTTT-TTTTTTCTTTTTCTCTT
4118691 ACCACTTTTTGATCCGATCTAGGCTTCTATTTTGTCTATATCTCTTATGATTGTTAGCAATACTA
1 ACCACTTTTTGATCCGATCTAGGCTTCTATTTTGTCTATATCTCTTATGATTGTTAGCAATACTA
*
4118756 AGTGTTGTTCCCCTGTTAACTTTGCCTTTTTGTTTTTTTTTTTTTTTTTTTCTTTT
66 AGTGTTGTTCCCCTGTTAACTTTGCCTTTTGGTTTTTTTTTTTTTTTTTTTCTTTT
4118812 AGATAGACAG
Statistics
Matches: 118, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
127 10 0.08
128 4 0.03
129 3 0.03
130 101 0.86
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.56
Consensus pattern (127 bp):
ACCACTTTTTGATCCGATCTAGGCTTCTATTTTGTCTATATCTCTTATGATTGTTAGCAATACTA
AGTGTTGTTCCCCTGTTAACTTTGCCTTTTGGTTTTTTTTTTTTTTTTTTTCTTTTTCTCTT
Found at i:4128944 original size:28 final size:28
Alignment explanation
Indices: 4128912--4128968 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
4128902 AATGATTGAG
4128912 GTATCACATTGAAATAGCTTTTATCATA
1 GTATCACATTGAAATAGCTTTTATCATA
4128940 GTATCACATTGAAATAGCTTTTATCATA
1 GTATCACATTGAAATAGCTTTTATCATA
4128968 G
1 G
4128969 GGTTGCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (28 bp):
GTATCACATTGAAATAGCTTTTATCATA
Found at i:4129721 original size:21 final size:21
Alignment explanation
Indices: 4129678--4129727 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
4129668 GGAAAAAAAT
*
4129678 AAAAAAAAAAGTGAGGAAGAG
1 AAAAAGAAAAGTGAGGAAGAG
* *
4129699 AAGAAGAAAAGTGAGGGTA-AG
1 AAAAAGAAAAGTGA-GGAAGAG
4129720 AAAAAGAA
1 AAAAAGAA
4129728 CAGTCAGTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAGTGAGGAAGAG
Found at i:4132153 original size:128 final size:130
Alignment explanation
Indices: 4131921--4132169 Score: 421
Period size: 128 Copynumber: 1.9 Consensus size: 130
4131911 CTAAATACAT
*
4131921 ACTTTTTGATATTTTTTCACCTTAGTTTGATCAAATAAGATTATATGATAATTTGAATTTTTTGT
1 ACTTTTTGATATTTTTTCACCTTAGTTTGATCAAATAAGATTATATGATAATTTAAATTTTTTGT
* * *
4131986 TTAAATTCTTAGATTTAGATTATTTTTGATAGCATGATATAAAGATT-TTTTTTTTGAAGTTATC
66 TTAAATTCTAAGATTTAGATTAATTTTGATAGCACGATATAAAGATTATTTTTTTTGAAGTTATC
* * *
4132050 ACTTTTTTATA-TTTTTCATCTTAGTTTGATCAAATAAGTTTATATGATAATTTAAATTTTTTGT
1 ACTTTTTGATATTTTTTCACCTTAGTTTGATCAAATAAGATTATATGATAATTTAAATTTTTTGT
4132114 TTAAATTCTAAGATTTAGATTAATTTTGATAGCACGATATAAAGATTATTTTTTTT
66 TTAAATTCTAAGATTTAGATTAATTTTGATAGCACGATATAAAGATTATTTTTTTT
4132170 TTGAAGTCAT
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
128 94 0.84
129 18 0.16
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.52
Consensus pattern (130 bp):
ACTTTTTGATATTTTTTCACCTTAGTTTGATCAAATAAGATTATATGATAATTTAAATTTTTTGT
TTAAATTCTAAGATTTAGATTAATTTTGATAGCACGATATAAAGATTATTTTTTTTGAAGTTATC
Found at i:4133921 original size:15 final size:16
Alignment explanation
Indices: 4133883--4133923 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
4133873 GTTAGGGGCA
4133883 AATATATTTTTTAATC
1 AATATATTTTTTAATC
* *
4133899 AA-AAATTTTTTTAT-
1 AATATATTTTTTAATC
4133913 AATATATTTTT
1 AATATATTTTT
4133924 CACAAAGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 2 0.10
15 17 0.81
16 2 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
AATATATTTTTTAATC
Found at i:4135416 original size:23 final size:23
Alignment explanation
Indices: 4135382--4135425 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
4135372 GCTAAAATAC
4135382 AAAAAAATTCTTT-TACATTTTGT
1 AAAAAAATTCTTTATAC-TTTTGT
4135405 AAAATAAA-TCTTTATACTTTT
1 AAAA-AAATTCTTTATACTTTT
4135426 ATTATACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (23 bp):
AAAAAAATTCTTTATACTTTTGT
Found at i:4135490 original size:22 final size:22
Alignment explanation
Indices: 4135465--4135506 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4135455 ATTTGTATTC
4135465 AAATAAGTCATTATCTTAAATA
1 AAATAAGTCATTATCTTAAATA
* * *
4135487 AAATAATTTATTATTTTAAA
1 AAATAAGTCATTATCTTAAA
4135507 AGCTTATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATAAGTCATTATCTTAAATA
Found at i:4135809 original size:21 final size:21
Alignment explanation
Indices: 4135771--4135810 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4135761 CTGACATAAA
*
4135771 AGTTGACTTTTTTGATGTGAT
1 AGTTGACTTTTATGATGTGAT
4135792 AGTTGACTTTATAT-ATGTG
1 AGTTGACTTT-TATGATGTG
4135811 GTGAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.50
Consensus pattern (21 bp):
AGTTGACTTTTATGATGTGAT
Found at i:4136486 original size:12 final size:11
Alignment explanation
Indices: 4136468--4136494 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4136458 CCATTAAAAC
4136468 ATTTTTTTGTA
1 ATTTTTTTGTA
4136479 ATTTTTTTGTA
1 ATTTTTTTGTA
4136490 ATTTT
1 ATTTT
4136495 GTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (11 bp):
ATTTTTTTGTA
Found at i:4139995 original size:19 final size:19
Alignment explanation
Indices: 4139967--4140005 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
4139957 TTGTTATTAG
*
4139967 TAATGGTAATGGAATTTTT
1 TAATGATAATGGAATTTTT
4139986 TAATGATAATGGAATTTTT
1 TAATGATAATGGAATTTTT
4140005 T
1 T
4140006 GTATGTAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (19 bp):
TAATGATAATGGAATTTTT
Found at i:4140677 original size:21 final size:22
Alignment explanation
Indices: 4140643--4140734 Score: 152
Period size: 21 Copynumber: 4.3 Consensus size: 22
4140633 TAAGATAATA
4140643 CTTTGAGTTTTCAAATAAGAAT
1 CTTTGAGTTTTCAAATAAGAAT
4140665 CTTTGAG-TTTCAAATAAGAAT
1 CTTTGAGTTTTCAAATAAGAAT
*
4140686 CTTTGAGTTTTCAAATGAGAAT
1 CTTTGAGTTTTCAAATAAGAAT
*
4140708 CTTTGAG-TTTCAAATGAGAAT
1 CTTTGAGTTTTCAAATAAGAAT
4140729 CTTTGA
1 CTTTGA
4140735 TATGTGAAAC
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
21 41 0.60
22 27 0.40
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (22 bp):
CTTTGAGTTTTCAAATAAGAAT
Found at i:4140697 original size:43 final size:43
Alignment explanation
Indices: 4140643--4140734 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
4140633 TAAGATAATA
4140643 CTTTGAGTTTTCAAATAAGAATCTTTGAGTTTCAAATAAGAAT
1 CTTTGAGTTTTCAAATAAGAATCTTTGAGTTTCAAATAAGAAT
* *
4140686 CTTTGAGTTTTCAAATGAGAATCTTTGAGTTTCAAATGAGAAT
1 CTTTGAGTTTTCAAATAAGAATCTTTGAGTTTCAAATAAGAAT
4140729 CTTTGA
1 CTTTGA
4140735 TATGTGAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (43 bp):
CTTTGAGTTTTCAAATAAGAATCTTTGAGTTTCAAATAAGAAT
Found at i:4141299 original size:18 final size:18
Alignment explanation
Indices: 4141232--4141301 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
4141222 AATTTTGGTT
* * *
4141232 AATTCTTGTGAAGCTAAA
1 AATTCTTGCGAATCTGAA
*
4141250 AAGTTCATGCGAATCTGAA
1 AA-TTCTTGCGAATCTGAA
** *
4141269 AATTCTAACGAATTTGAA
1 AATTCTTGCGAATCTGAA
*
4141287 AATTCTTGTGAATCT
1 AATTCTTGCGAATCT
4141302 TTGAATTGCG
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
18 25 0.64
19 14 0.36
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (18 bp):
AATTCTTGCGAATCTGAA
Found at i:4141502 original size:44 final size:43
Alignment explanation
Indices: 4141392--4141645 Score: 214
Period size: 44 Copynumber: 5.8 Consensus size: 43
4141382 GATTATCGAT
* * * *
4141392 GAGCTTTATTTACTTTTCCAAAGTCATTGAGCCT-TTGATTA-AA
1 GAGCATTATTTATTTTTCCAAAGTCGTTGAGCCTCTT--TTAGAG
4141435 GAG-ATTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAGAG
1 GAGCA-TTATTTATTTTTCCAAAGTCGTTGAGCCTCT-TTTAGAG
* * * * *
4141479 GAACATTATTTA-TTTTCATAAAGTTGTTGAACTTCTTATTAGAG
1 GAGCATTATTTATTTTTC-CAAAGTCGTTGAGCCTCTT-TTAGAG
* * *
4141523 GAGCATTGTTTATTTTTCCAAAGTCGTTAAGCCTCTAATTAGAG
1 GAGCATTATTTATTTTTCCAAAGTCGTTGAGCCTCT-TTTAGAG
* * * * *
4141567 GAGCATTATTTATTTTTCCAAAATAGTTGAACCTCTATGTAGAT
1 GAGCATTATTTATTTTTCCAAAGTCGTTGAGCCTCT-TTTAGAG
* *
4141611 GAGCCA-TATTTATTTTTCAAAAGTTG-TGAGCCTCT
1 GAG-CATTATTTATTTTTCCAAAGTCGTTGAGCCTCT
4141646 ACATAGGGGA
Statistics
Matches: 172, Mismatches: 29, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
43 47 0.27
44 116 0.67
45 9 0.05
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (43 bp):
GAGCATTATTTATTTTTCCAAAGTCGTTGAGCCTCTTTTAGAG
Found at i:4141545 original size:88 final size:88
Alignment explanation
Indices: 4141441--4141646 Score: 251
Period size: 88 Copynumber: 2.4 Consensus size: 88
4141431 TAAAGAGATT
** *
4141441 TATTTATTTTTCCAAAGTCGTTGAGCCTCTGTTTAGAGGAACATTATTTA-TTTT-CATAAAGTT
1 TATTTATTTTTCCAAAGTCGTTGAGCCTCTAATTAGAGGAACATTATTTATTTTTCCA-AAA-TA
*
4141504 GTTGAACTTCTTAT-TAGAGGAG-CA
64 GTTGAACCTC-TATGTAGAGGAGCCA
* * *
4141528 TTGTTTATTTTTCCAAAGTCGTTAAGCCTCTAATTAGAGGAGCATTATTTATTTTTCCAAAATAG
1 -TATTTATTTTTCCAAAGTCGTTGAGCCTCTAATTAGAGGAACATTATTTATTTTTCCAAAATAG
*
4141593 TTGAACCTCTATGTAGATGAGCCA
65 TTGAACCTCTATGTAGAGGAGCCA
* *
4141617 TATTTATTTTTCAAAAGTTG-TGAGCCTCTA
1 TATTTATTTTTCCAAAGTCGTTGAGCCTCTA
4141647 CATAGGGGAG
Statistics
Matches: 102, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
87 12 0.12
88 79 0.77
89 9 0.09
90 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (88 bp):
TATTTATTTTTCCAAAGTCGTTGAGCCTCTAATTAGAGGAACATTATTTATTTTTCCAAAATAGT
TGAACCTCTATGTAGAGGAGCCA
Found at i:4142600 original size:12 final size:12
Alignment explanation
Indices: 4142569--4142607 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
4142559 ATCCATTTTA
4142569 GAAAGAGAAAGAG
1 GAAA-AGAAAGAG
4142582 AGAAAAGAAAGAG
1 -GAAAAGAAAGAG
*
4142595 GAAAAGAGAGAG
1 GAAAAGAAAGAG
4142607 G
1 G
4142608 GGGAAAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.50
13 8 0.33
14 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (12 bp):
GAAAAGAAAGAG
Found at i:4142920 original size:17 final size:17
Alignment explanation
Indices: 4142898--4142933 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4142888 TTTTTAGTAT
* *
4142898 TTTTATTTATTTGTTTA
1 TTTTATTTAGTTATTTA
4142915 TTTTATTTAGTTATTTA
1 TTTTATTTAGTTATTTA
4142932 TT
1 TT
4142934 AATGTGTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTATTTAGTTATTTA
Found at i:4149934 original size:16 final size:18
Alignment explanation
Indices: 4149908--4149950 Score: 63
Period size: 16 Copynumber: 2.4 Consensus size: 18
4149898 ACTTTTTCTT
4149908 TAAACTTTTTTAATTTA-A
1 TAAA-TTTTTTAATTTAGA
4149926 -AAATTTTTTAATTTAGA
1 TAAATTTTTTAATTTAGA
4149943 TAAATTTT
1 TAAATTTT
4149951 GTGAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 12 0.52
17 4 0.17
18 7 0.30
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TAAATTTTTTAATTTAGA
Found at i:4150150 original size:8 final size:8
Alignment explanation
Indices: 4150137--4150206 Score: 72
Period size: 8 Copynumber: 8.8 Consensus size: 8
4150127 TTCTCTTTTT
4150137 TTTTTTCC
1 TTTTTTCC
4150145 TTTTTTCC
1 TTTTTTCC
* *
4150153 TTTTTAACT
1 TTTTT-TCC
*
4150162 TTTTTTTC
1 TTTTTTCC
4150170 TTTCTTT-C
1 TTT-TTTCC
*
4150178 TTTTTT-G
1 TTTTTTCC
4150185 TTTTTTCC
1 TTTTTTCC
4150193 TTTTTTCC
1 TTTTTTCC
4150201 TTTTTT
1 TTTTTT
4150207 TTGTCATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
7 9 0.17
8 34 0.65
9 9 0.17
ACGTcount: A:0.03, C:0.17, G:0.01, T:0.79
Consensus pattern (8 bp):
TTTTTTCC
Found at i:4150170 original size:40 final size:40
Alignment explanation
Indices: 4150130--4150208 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
4150120 ATGAGCTTTC
*
4150130 TCTTT-TTT-TTTTTCCTTTTTTCCTTTTTAACTTTTTTT
1 TCTTTCTTTCTTTTTTCTTTTTTCCTTTTTAACTTTTTTT
* **
4150168 TCTTTCTTTCTTTTTTGTTTTTTCCTTTTTTCCTTTTTTT
1 TCTTTCTTTCTTTTTTCTTTTTTCCTTTTTAACTTTTTTT
4150208 T
1 T
4150209 GTCATTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 5 0.14
39 3 0.09
40 27 0.77
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (40 bp):
TCTTTCTTTCTTTTTTCTTTTTTCCTTTTTAACTTTTTTT
Found at i:4150532 original size:12 final size:12
Alignment explanation
Indices: 4150514--4150554 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
4150504 TTTCAAGGTG
4150514 TATATAAATATA
1 TATATAAATATA
*
4150526 AATATAAATATA
1 TATATAAATATA
*
4150538 TATATATATATA
1 TATATAAATATA
4150550 TATAT
1 TATAT
4150555 TGTTATTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATAAATATA
Found at i:4150538 original size:2 final size:2
Alignment explanation
Indices: 4150514--4150554 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
4150504 TTTCAAGGTG
* * *
4150514 TA TA TA AA TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4150555 TGTTATTTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:4152633 original size:122 final size:120
Alignment explanation
Indices: 4152425--4153215 Score: 700
Period size: 122 Copynumber: 6.5 Consensus size: 120
4152415 CGGCATTCTA
* * ** **
4152425 GTCATTATAAATGCAATGTTTGAAT-ATCCTAAAACCAATTAACTAAATAAAACATAATATTTAA
1 GTCATTATAAATGCAATGTTTGAATAATACT-AAACCAATTAATTAAATAAAATGTTCTATTTAA
* * ** * **
4152489 CAAGCACGACATTTTTCTTTTTATAA-GCTCCCTACTATTGAACACGTC-TGACATTTTG
65 CAAGCATGACATTTTT-ATTTTATAATG-T-TGTACTATTGAACAAG-CATGATGTTTTG
* ** * *
4152547 ATCATTATAAACACAGTGTTTGAATAATACTAAACCAATTAATTAAACAAAATGTTCTATTTAAC
1 GTCATTATAAATGCAATGTTTGAATAATACTAAACCAATTAATTAAATAAAATGTTCTATTTAAC
* *
4152612 AAGCATTACATTTTATGTTTTATAAATGTTGTACTATTGAACAAGCATGATGTTTTG
66 AAGCATGACATTTT-TATTTTAT-AATGTTGTACTATTGAACAAGCATGATGTTTTG
* * * * * * *
4152669 GTCATTATAAATGTAATGTTTAAATAATACTAAACTAGTTAATTATATAAAATGTTCTACTTAGC
1 GTCATTATAAATGCAATGTTTGAATAATACTAAACCAATTAATTAAATAAAATGTTCTATTTAAC
* * * *
4152734 AAGAATGACATTTTTATTTTATAAATGTTG-AATATT-AAAAAGGCATAATGTTTTG
66 AAGCATGACATTTTTATTTTAT-AATGTTGTACTATTGAACAA-GCATGATGTTTTG
* * * * *
4152789 GTCATTATAAATGCTATGTTTGACTAATCATCAAAACCAATTAATTAAAATAAAATATTTTATTT
1 GTCATTATAAATGCAATGTTTGAATAAT-A-CTAAACCAATTAATT-AAATAAAATGTTCTATTT
* * *
4152854 AACAAGCATTACGTTTTATGTTTTATAAATGTTGTACTATTGAACAAGCATGATGTTTTG
63 AACAAGCATGACATTTT-TATTTTAT-AATGTTGTACTATTGAACAAGCATGATGTTTTG
* * * * * *
4152914 GTCATTATAAATGTAATGTTTAAATAATACTAAACTAGTTAATTATATAAAATGTTCTACTTAAC
1 GTCATTATAAATGCAATGTTTGAATAATACTAAACCAATTAATTAAATAAAATGTTCTATTTAAC
* * * *
4152979 AAGAATGACATTTTTATTTTATAAATGTTG-AATATT-AAAAAGGCATAATGTTTTG
66 AAGCATGACATTTTTATTTTAT-AATGTTGTACTATTGAACAA-GCATGATGTTTTG
* * * * *
4153034 GTCATTATAAATGCTATGTTTGACTAATCATCAAAACCAATTAATTAAAATAAAATATTTTATTT
1 GTCATTATAAATGCAATGTTTGAATAAT-A-CTAAACCAATTAATT-AAATAAAATGTTCTATTT
* * * * ** **
4153099 AACAAGCATGATATTTTTTTGTTTTATAAATGTTGTAATATTAAACAAGCACAACATTTTG
63 AACAAGCATGACA--TTTTTATTTTAT-AATGTTGTACTATTGAACAAGCATGATGTTTTG
** * *
4153160 GTCATTATAAACACAAAGCTTT-AATAAT-CATAAAACCAATTAAATAAATAAAATGT
1 GTCATTATAAATGCAATG-TTTGAATAATAC-T-AAACCAATTAATTAAATAAAATGT
4153216 AATATTTTAT
Statistics
Matches: 546, Mismatches: 100, Indels: 44
0.79 0.14 0.06
Matches are distributed among these distances:
119 8 0.01
120 82 0.15
121 33 0.06
122 205 0.38
123 73 0.13
124 27 0.05
125 72 0.13
126 39 0.07
127 7 0.01
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.39
Consensus pattern (120 bp):
GTCATTATAAATGCAATGTTTGAATAATACTAAACCAATTAATTAAATAAAATGTTCTATTTAAC
AAGCATGACATTTTTATTTTATAATGTTGTACTATTGAACAAGCATGATGTTTTG
Found at i:4152901 original size:245 final size:245
Alignment explanation
Indices: 4152578--4153170 Score: 1044
Period size: 245 Copynumber: 2.4 Consensus size: 245
4152568 GAATAATACT
* * *
4152578 AAACCAATTAATT-AAACAAAATGTTCTATTTAACAAGCATTACATTTTATGTTTTATAAATGTT
1 AAACCAATTAATTAAAATAAAATATTTTATTTAACAAGCATTACATTTTATGTTTTATAAATGTT
4152642 GTACTATTGAACAAGCATGATGTTTTGGTCATTATAAATGTAATGTTTAAATAATACTAAACTAG
66 GTACTATTGAACAAGCATGATGTTTTGGTCATTATAAATGTAATGTTTAAATAATACTAAACTAG
*
4152707 TTAATTATATAAAATGTTCTACTTAGCAAGAATGACATTTTTATTTTATAAATGTTGAATATTAA
131 TTAATTATATAAAATGTTCTACTTAACAAGAATGACATTTTTATTTTATAAATGTTGAATATTAA
4152772 AAAGGCATAATGTTTTGGTCATTATAAATGCTATGTTTGACTAATCATCA
196 AAAGGCATAATGTTTTGGTCATTATAAATGCTATGTTTGACTAATCATCA
*
4152822 AAACCAATTAATTAAAATAAAATATTTTATTTAACAAGCATTACGTTTTATGTTTTATAAATGTT
1 AAACCAATTAATTAAAATAAAATATTTTATTTAACAAGCATTACATTTTATGTTTTATAAATGTT
4152887 GTACTATTGAACAAGCATGATGTTTTGGTCATTATAAATGTAATGTTTAAATAATACTAAACTAG
66 GTACTATTGAACAAGCATGATGTTTTGGTCATTATAAATGTAATGTTTAAATAATACTAAACTAG
4152952 TTAATTATATAAAATGTTCTACTTAACAAGAATGACATTTTTATTTTATAAATGTTGAATATTAA
131 TTAATTATATAAAATGTTCTACTTAACAAGAATGACATTTTTATTTTATAAATGTTGAATATTAA
4153017 AAAGGCATAATGTTTTGGTCATTATAAATGCTATGTTTGACTAATCATCA
196 AAAGGCATAATGTTTTGGTCATTATAAATGCTATGTTTGACTAATCATCA
* * *
4153067 AAACCAATTAATTAAAATAAAATATTTTATTTAACAAGCATGATATTTTTTTGTTTTATAAATGT
1 AAACCAATTAATTAAAATAAAATATTTTATTTAACAAGCATTACA-TTTTATGTTTTATAAATGT
* * ** **
4153132 TGTAATATTAAACAAGCACAACATTTTGGTCATTATAAA
65 TGTACTATTGAACAAGCATGATGTTTTGGTCATTATAAA
4153171 CACAAAGCTT
Statistics
Matches: 332, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
244 13 0.04
245 268 0.81
246 51 0.15
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (245 bp):
AAACCAATTAATTAAAATAAAATATTTTATTTAACAAGCATTACATTTTATGTTTTATAAATGTT
GTACTATTGAACAAGCATGATGTTTTGGTCATTATAAATGTAATGTTTAAATAATACTAAACTAG
TTAATTATATAAAATGTTCTACTTAACAAGAATGACATTTTTATTTTATAAATGTTGAATATTAA
AAAGGCATAATGTTTTGGTCATTATAAATGCTATGTTTGACTAATCATCA
Found at i:4152980 original size:367 final size:368
Alignment explanation
Indices: 4152425--4153222 Score: 895
Period size: 367 Copynumber: 2.2 Consensus size: 368
4152415 CGGCATTCTA
* * *
4152425 GTCATTATAAATGCAATGTTTGAAT-ATCCTAAAACCAATTAACTAAATAAAACATAATATTTAA
1 GTCATTATAAATGCAATGTTTGAATAATCATAAAACCAATTAAATAAATAAAATATAATATTTAA
*
4152489 CAAGCACGACATTTTTCTTTTTATAAGCTCCCTACTATTGAACACGTCTGACATTTTGATCATTA
66 CAAGCACGACATTTTTCTTTTTATAAGCTCCCTACTATTGAACAAGTCTGACATTTTGATCATTA
* * * * *
4152554 TAAACACAGTGTTTGAATAATACTAAACCAATTAATTAAACAAAATGTTCTATTTAACAAGCATT
131 TAAACACAATGTTTAAATAATACTAAACCAATTAATTAAACAAAATGTTCTACTTAACAAGAATG
* * * *
4152619 ACATTTTATGTTTTATAAATGTTGTACTATTGAACAA-GCATGATGTTTTGGTCATTATAAATG-
196 ACATTTT-TATTTTATAAATGTTG-AATATT-AAAAAGGCATAATGTTTTGGTCATTATAAATGC
* * * * * *
4152682 TAATGTTTAAATAAT-A-CTAAACTAGTTAATT-ATATAAAATGTTCTACTTAGCAAGAATGACA
258 T-ATGTTTAAATAATCATCAAAACCAATTAATTAAAATAAAATATTCTACTTAACAAGAATGACA
* **
4152744 -TTTTTATTTTATAAATGTTG-AATATTAAA-AAGGCATAATGTTTTG
322 TTTTTTATTTTATAAATGTTGTAATATTAAACAA-GCACAACATTTTG
* * * **
4152789 GTCATTATAAATGCTATGTTTGACTAATCATCAAAACCAATTAATTAAAATAAAATATTTTATTT
1 GTCATTATAAATGCAATGTTTGAATAATCAT-AAAACCAATTAAAT-AAATAAAATATAATATTT
** * * ** ** *
4152854 AACAAGCATTACGTTTTAT-GTTTTATAAATG-T-TGTACTATTGAACAAG-CATGATGTTTTGG
64 AACAAGCACGACATTTT-TCTTTTTAT-AA-GCTCCCTACTATTGAACAAGTC-TGACATTTTGA
*** * * * *
4152915 TCATTATAAATGTAATGTTTAAATAATACTAAACTAGTTAATTATATAAAATGTTCTACTTAACA
125 TCATTATAAACACAATGTTTAAATAATACTAAACCAATTAATTAAACAAAATGTTCTACTTAACA
4152980 AGAATGACATTTTTATTTTATAAATGTTGAATATTAAAAAGGCATAATGTTTTGGTCATTATAAA
190 AGAATGACATTTTTATTTTATAAATGTTGAATATTAAAAAGGCATAATGTTTTGGTCATTATAAA
* * * * *
4153045 TGCTATGTTTGACTAATCATCAAAACCAATTAATTAAAATAAAATATTTTATTTAACAAGCATGA
255 TGCTATGTTTAAATAATCATCAAAACCAATTAATTAAAATAAAATATTCTACTTAACAAGAATGA
* *
4153110 TATTTTTTTGTTTTATAAATGTTGTAATATTAAACAAGCACAACATTTTG
320 CA-TTTTTTATTTTATAAATGTTGTAATATTAAACAAGCACAACATTTTG
** * *
4153160 GTCATTATAAACACAAAGCTTT-AATAATCATAAAACCAATTAAATAAATAAAATGTAATATTT
1 GTCATTATAAATGCAATG-TTTGAATAATCATAAAACCAATTAAATAAATAAAATATAATATTT
4153223 TATAATCACA
Statistics
Matches: 359, Mismatches: 58, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
364 27 0.08
365 45 0.13
366 31 0.09
367 134 0.37
368 28 0.08
369 16 0.04
370 32 0.09
371 41 0.11
372 5 0.01
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.39
Consensus pattern (368 bp):
GTCATTATAAATGCAATGTTTGAATAATCATAAAACCAATTAAATAAATAAAATATAATATTTAA
CAAGCACGACATTTTTCTTTTTATAAGCTCCCTACTATTGAACAAGTCTGACATTTTGATCATTA
TAAACACAATGTTTAAATAATACTAAACCAATTAATTAAACAAAATGTTCTACTTAACAAGAATG
ACATTTTTATTTTATAAATGTTGAATATTAAAAAGGCATAATGTTTTGGTCATTATAAATGCTAT
GTTTAAATAATCATCAAAACCAATTAATTAAAATAAAATATTCTACTTAACAAGAATGACATTTT
TTATTTTATAAATGTTGTAATATTAAACAAGCACAACATTTTG
Found at i:4153053 original size:120 final size:120
Alignment explanation
Indices: 4152563--4153215 Score: 706
Period size: 122 Copynumber: 5.3 Consensus size: 120
4152553 ATAAACACAG
* *
4152563 TGTTTGAATAATACTAAACCAATTAATTAAACAAAATGTTCTATTTAACAAGCATTACATTTTAT
1 TGTTTGAATAATACTAAACCAATTAATTAAATAAAATGTTCTATTTAACAAGCATGACATTTT-T
* * *
4152628 GTTTTATAAATGTTGTACTATTGAACAAGCATGATGTTTTGGTCATTATAAATGTAA
65 GTTTTATAAATGTTGTAATATT-AAAAAGCATAATGTTTTGGTCATTATAAATGTAA
* * * * * * * *
4152685 TGTTTAAATAATACTAAACTAGTTAATTATATAAAATGTTCTACTTAGCAAGAATGACATTTTTA
1 TGTTTGAATAATACTAAACCAATTAATTAAATAAAATGTTCTATTTAACAAGCATGACATTTTTG
4152750 TTTTATAAATGTTG-AATATTAAAAAGGCATAATGTTTTGGTCATTATAAATGCT-A
66 TTTTATAAATGTTGTAATATTAAAAA-GCATAATGTTTTGGTCATTATAAATG-TAA
* * * * * *
4152805 TGTTTGACTAATCATCAAAACCAATTAATTAAAATAAAATATTTTATTTAACAAGCATTACGTTT
1 TGTTTGAATAAT-A-CTAAACCAATTAATT-AAATAAAATGTTCTATTTAACAAGCATGACATTT
* * *
4152870 TATGTTTTATAAATGTTGTACTATTGAACAAGCATGATGTTTTGGTCATTATAAATGTAA
63 T-TGTTTTATAAATGTTGTAATATT-AAAAAGCATAATGTTTTGGTCATTATAAATGTAA
* * * * * * *
4152930 TGTTTAAATAATACTAAACTAGTTAATTATATAAAATGTTCTACTTAACAAGAATGACATTTTTA
1 TGTTTGAATAATACTAAACCAATTAATTAAATAAAATGTTCTATTTAACAAGCATGACATTTTTG
4152995 TTTTATAAATGTTG-AATATTAAAAAGGCATAATGTTTTGGTCATTATAAATGCT-A
66 TTTTATAAATGTTGTAATATTAAAAA-GCATAATGTTTTGGTCATTATAAATG-TAA
* * * * *
4153050 TGTTTGACTAATCATCAAAACCAATTAATTAAAATAAAATATTTTATTTAACAAGCATGATATTT
1 TGTTTGAATAAT-A-CTAAACCAATTAATT-AAATAAAATGTTCTATTTAACAAGCATGACA--T
* ** ***
4153115 TTTTGTTTTATAAATGTTGTAATATTAAACAAGCACAACATTTTGGTCATTATAAACACAA
61 TTTTGTTTTATAAATGTTGTAATATTAAA-AAGCATAATGTTTTGGTCATTATAAATGTAA
* *
4153176 AGCTTT-AATAAT-CATAAAACCAATTAAATAAATAAAATGT
1 TG-TTTGAATAATAC-T-AAACCAATTAATTAAATAAAATGT
4153216 AATATTTTAT
Statistics
Matches: 440, Mismatches: 69, Indels: 42
0.80 0.13 0.08
Matches are distributed among these distances:
119 8 0.02
120 82 0.19
121 34 0.08
122 106 0.24
123 65 0.15
124 27 0.06
125 72 0.16
126 41 0.09
127 5 0.01
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (120 bp):
TGTTTGAATAATACTAAACCAATTAATTAAATAAAATGTTCTATTTAACAAGCATGACATTTTTG
TTTTATAAATGTTGTAATATTAAAAAGCATAATGTTTTGGTCATTATAAATGTAA
Found at i:4157202 original size:53 final size:53
Alignment explanation
Indices: 4157124--4157253 Score: 152
Period size: 53 Copynumber: 2.5 Consensus size: 53
4157114 AAATTTTATG
* * * * *
4157124 TTAAATTGATAAACATGATATTTTCATTAAGTTAAACATAGTATTTATCTAAT
1 TTAACTTGACAAAAATGATATTTTCATCAAGCTAAACATAGTATTTATCTAAT
* * ** *
4157177 TTAGCTTGACAAAAATGATGTTTTCATCAAGCTAAATGTAGTATTTGTCTAAT
1 TTAACTTGACAAAAATGATATTTTCATCAAGCTAAACATAGTATTTATCTAAT
* *
4157230 TTAACTTGACAAAGATAATATTTT
1 TTAACTTGACAAAAATGATATTTT
4157254 ATATTAAAAC
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 63 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (53 bp):
TTAACTTGACAAAAATGATATTTTCATCAAGCTAAACATAGTATTTATCTAAT
Found at i:4157389 original size:22 final size:22
Alignment explanation
Indices: 4157361--4157402 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4157351 GATACTTTCT
*
4157361 TAAATTAAAAAAATTAATTACA
1 TAAATTAAAAAAAGTAATTACA
4157383 TAAATTAAAAAAAGTAATTA
1 TAAATTAAAAAAAGTAATTA
4157403 TAACATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAATTAAAAAAAGTAATTACA
Found at i:4168555 original size:18 final size:19
Alignment explanation
Indices: 4168528--4168565 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4168518 CCTTTCGTGC
*
4168528 TTTTTCATTGTTTTT-TAT
1 TTTTTAATTGTTTTTCTAT
4168546 TTTTTAATTGTTTTTCTAT
1 TTTTTAATTGTTTTTCTAT
4168565 T
1 T
4168566 GTTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTTAATTGTTTTTCTAT
Found at i:4168570 original size:18 final size:17
Alignment explanation
Indices: 4168529--4168589 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
4168519 CTTTCGTGCT
*
4168529 TTTTCATTGTTTTT-TA
1 TTTTAATTGTTTTTCTA
4168545 TTTTTTAATTGTTTTTCTA
1 --TTTTAATTGTTTTTCTA
*
4168564 TTGTTAATTATTTTGTCT-
1 TT-TTAATTGTTTT-TCTA
4168582 TTTTAATT
1 TTTTAATT
4168590 AGATAACTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 8 0.21
18 25 0.66
19 5 0.13
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (17 bp):
TTTTAATTGTTTTTCTA
Found at i:4169813 original size:17 final size:17
Alignment explanation
Indices: 4169793--4169830 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4169783 TTTTAAACTT
4169793 TTTTAAATTTTAAA-AAA
1 TTTTAAA-TTTAAATAAA
*
4169810 TTTTTAATTTAAATAAA
1 TTTTAAATTTAAATAAA
4169827 TTTT
1 TTTT
4169831 GTGAAACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAAATTTAAATAAA
Found at i:4170045 original size:18 final size:18
Alignment explanation
Indices: 4170006--4170046 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
4169996 ATGAGTTTTT
*
4170006 TTTTTTCCTTTTTGAATT
1 TTTTTTCCTTTTTGAATC
**
4170024 TTTTTTCCTTTTTTTATC
1 TTTTTTCCTTTTTGAATC
4170042 TTTTT
1 TTTTT
4170047 AATAAATGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTTCCTTTTTGAATC
Found at i:4171290 original size:7 final size:7
Alignment explanation
Indices: 4171265--4171360 Score: 58
Period size: 7 Copynumber: 13.7 Consensus size: 7
4171255 GGTTTGGATT
4171265 GGTTTAG
1 GGTTTAG
*
4171272 GGTCTA-
1 GGTTTAG
4171278 GG-TTAG
1 GGTTTAG
4171284 GGTTTAG
1 GGTTTAG
*
4171291 CGTTTAG
1 GGTTTAG
*
4171298 CGTTTTAG
1 -GGTTTAG
*
4171306 GATTTAAG
1 GGTTT-AG
4171314 AGGTTTTAG
1 -GG-TTTAG
4171323 GG-TTAG
1 GGTTTAG
*
4171329 AGTTTA-
1 GGTTTAG
*
4171335 GATTTAG
1 GGTTTAG
4171342 GGTTT-G
1 GGTTTAG
4171348 AGGTTTAG
1 -GGTTTAG
4171356 GGTTT
1 GGTTT
4171361 TGATTTAGGA
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
5 2 0.03
6 14 0.21
7 36 0.53
8 10 0.15
9 3 0.04
10 3 0.04
ACGTcount: A:0.19, C:0.03, G:0.35, T:0.43
Consensus pattern (7 bp):
GGTTTAG
Found at i:4171341 original size:13 final size:13
Alignment explanation
Indices: 4171267--4171369 Score: 55
Period size: 13 Copynumber: 7.5 Consensus size: 13
4171257 TTTGGATTGG
*
4171267 TTTAGGGTCTAG-
1 TTTAGGGTTTAGA
* *
4171279 GTTAGGGTTTAGCG
1 TTTAGGGTTTAG-A
*
4171293 TTTAGCGTTTTAGGA
1 TTTAG-GGTTTA-GA
*
4171308 TTTAAGAGGTTTTAGG
1 TTT-AG-GG-TTTAGA
* *
4171324 GTTAGAGTTTAGA
1 TTTAGGGTTTAGA
*
4171337 TTTAGGGTTTGAGG
1 TTTAGGGTTT-AGA
*
4171351 TTTAGGGTTTTGA
1 TTTAGGGTTTAGA
4171364 TTTAGG
1 TTTAGG
4171370 ATTTGTGGTT
Statistics
Matches: 68, Mismatches: 16, Indels: 13
0.70 0.16 0.13
Matches are distributed among these distances:
12 10 0.15
13 20 0.29
14 17 0.25
15 10 0.15
16 7 0.10
17 4 0.06
ACGTcount: A:0.19, C:0.03, G:0.34, T:0.44
Consensus pattern (13 bp):
TTTAGGGTTTAGA
Found at i:4171342 original size:19 final size:20
Alignment explanation
Indices: 4171318--4171355 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4171308 TTTAAGAGGT
4171318 TTTAGGGTTAGA-GTTTAGA
1 TTTAGGGTTAGAGGTTTAGA
*
4171337 TTTAGGGTTTGAGGTTTAG
1 TTTAGGGTTAGAGGTTTAG
4171356 GGTTTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (20 bp):
TTTAGGGTTAGAGGTTTAGA
Found at i:4171355 original size:27 final size:27
Alignment explanation
Indices: 4171280--4171381 Score: 89
Period size: 27 Copynumber: 3.6 Consensus size: 27
4171270 AGGGTCTAGG
*
4171280 TTAGGGTTT-AGCGTTTAGCGTTTTAGGAT
1 TTAGGGTTTGAG-GTTTAGAG-TTTA-GAT
* *
4171309 TTAAGAGGTTTTAGGGTTAGAGTTTAGAT
1 TT-AG-GGTTTGAGGTTTAGAGTTTAGAT
* *
4171338 TTAGGGTTTGAGGTTTAGGGTTTTGAT
1 TTAGGGTTTGAGGTTTAGAGTTTAGAT
* *
4171365 TTAGGATTTGTGGTTTA
1 TTAGGGTTTGAGGTTTA
4171382 AGGTTTGGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
27 34 0.55
28 2 0.03
29 7 0.11
30 6 0.10
31 11 0.18
32 2 0.03
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (27 bp):
TTAGGGTTTGAGGTTTAGAGTTTAGAT
Found at i:4171373 original size:34 final size:33
Alignment explanation
Indices: 4171313--4171387 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 33
4171303 TAGGATTTAA
4171313 GAGGTTTTAGGGTTAGAGTTTAGATTTAG-GGTTT
1 GAGG-TTTAGGGTTAGAGTTTAGATTT-GTGGTTT
*
4171347 GAGGTTTAGGGTTTTGA-TTTAGGATTTGTGGTTT
1 GAGGTTTAGGG-TTAGAGTTTA-GATTTGTGGTTT
*
4171381 AAGGTTT
1 GAGGTTT
4171388 GGATTGAGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
33 12 0.33
34 24 0.67
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.47
Consensus pattern (33 bp):
GAGGTTTAGGGTTAGAGTTTAGATTTGTGGTTT
Found at i:4171386 original size:27 final size:27
Alignment explanation
Indices: 4171330--4171392 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
4171320 TAGGGTTAGA
* *
4171330 GTTTAGATTTAGGGTTTGAGGTTTAGG
1 GTTTAGATTTAGGATTTGAGGTTTAAG
* *
4171357 GTTTTGATTTAGGATTTGTGGTTTAAG
1 GTTTAGATTTAGGATTTGAGGTTTAAG
*
4171384 GTTTGGATT
1 GTTTAGATT
4171393 GAGATGTCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.49
Consensus pattern (27 bp):
GTTTAGATTTAGGATTTGAGGTTTAAG
Found at i:4173748 original size:13 final size:13
Alignment explanation
Indices: 4173730--4173774 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
4173720 TGTTAGAGGA
*
4173730 TTTTTTTTGTGTG
1 TTTTTTTTGTTTG
*
4173743 TTTTTTTTTTTTG
1 TTTTTTTTGTTTG
* *
4173756 CTTTTTTGGTTTG
1 TTTTTTTTGTTTG
4173769 TTTTTT
1 TTTTTT
4173775 GTTTTTTCTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (13 bp):
TTTTTTTTGTTTG
Found at i:4173760 original size:26 final size:27
Alignment explanation
Indices: 4173731--4173781 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
4173721 GTTAGAGGAT
*
4173731 TTTTTTTGTGTGTTTTTT-TTTTTTGC
1 TTTTTTGGTGTGTTTTTTGTTTTTTGC
*
4173757 TTTTTTGGTTTGTTTTTTGTTTTTT
1 TTTTTTGGTGTGTTTTTTGTTTTTT
4173782 CTAGAACAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (27 bp):
TTTTTTGGTGTGTTTTTTGTTTTTTGC
Found at i:4174715 original size:21 final size:22
Alignment explanation
Indices: 4174689--4174729 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
4174679 GGAAAATAAA
4174689 AAGTTTACTA-TAGATTTCAAC
1 AAGTTTACTATTAGATTTCAAC
4174710 AAGTTTACTATTAGATTTCA
1 AAGTTTACTATTAGATTTCA
4174730 CAACAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (22 bp):
AAGTTTACTATTAGATTTCAAC
Found at i:4180528 original size:22 final size:21
Alignment explanation
Indices: 4180490--4180550 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 21
4180480 CTTTCCTTTT
* *
4180490 TTTTTTTTTTTGC-ATTTT-G
1 TTTTTATTTTTCCTATTTTAG
*
4180509 TTGTTTCTTTTATCCTATTTTAG
1 TT-TTTATTTT-TCCTATTTTAG
*
4180532 TTTTTATTTTTCTTATTTT
1 TTTTTATTTTTCCTATTTT
4180551 TTATATGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.06
20 7 0.21
21 10 0.29
22 12 0.35
23 3 0.09
ACGTcount: A:0.10, C:0.08, G:0.07, T:0.75
Consensus pattern (21 bp):
TTTTTATTTTTCCTATTTTAG
Found at i:4181754 original size:16 final size:18
Alignment explanation
Indices: 4181733--4181768 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
4181723 CTTTAAACTG
4181733 TTTTAATTTA-A-AAATT
1 TTTTAATTTAGATAAATT
4181749 TTTTAATTTAGATAAATT
1 TTTTAATTTAGATAAATT
4181767 TT
1 TT
4181769 GTGAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTAATTTAGATAAATT
Found at i:4181972 original size:7 final size:8
Alignment explanation
Indices: 4181953--4182021 Score: 79
Period size: 8 Copynumber: 8.8 Consensus size: 8
4181943 TTTCTCTTCT
4181953 TTTTTTCC
1 TTTTTTCC
4181961 TTTTTTCC
1 TTTTTTCC
4181969 TTTTTTCC
1 TTTTTTCC
**
4181977 TTTTTAAC
1 TTTTTTCC
*
4181985 TTTTTTTC
1 TTTTTTCC
4181993 TTTCTTT-C
1 TTT-TTTCC
*
4182001 TTTTTT-G
1 TTTTTTCC
4182008 TTTTTTCC
1 TTTTTTCC
4182016 TTTTTT
1 TTTTTT
4182022 TTGTCATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
7 9 0.17
8 41 0.77
9 3 0.06
ACGTcount: A:0.03, C:0.17, G:0.01, T:0.78
Consensus pattern (8 bp):
TTTTTTCC
Found at i:4184518 original size:122 final size:120
Alignment explanation
Indices: 4184211--4184750 Score: 445
Period size: 121 Copynumber: 4.4 Consensus size: 120
4184201 TATTCTAGTT
* * * ** **
4184211 ATTATAAATGCAATGTTTGAAT-ATCCTAAAACCAATTAACTAAATAAAACATAATATTTAACAA
1 ATTATAAATGCTATGTTTGAATAATACT-AAACCAATTAATTAAATAAAATGTTCTATTTAACAA
* * ** * * ** *
4184275 GCACGACATTTTTCTTTT-TATAA-GCTCCCTAATATTGAACACGTC-TGACATTTTGATC
65 GCATGACATTTTTGTTTTATA-AATG-T-TGTAATATT-AACAAG-CATAATGTTTTGGTC
* *
4184333 ATTATAACA--CAATGTTTGAATAATACTAAACCAATTAATTAAACAAAATGTTCTATTTAACAA
1 ATTATAA-ATGCTATGTTTGAATAATACTAAACCAATTAATTAAATAAAATGTTCTATTTAACAA
* * * *
4184396 GCATTACGTTTTATGTTTTATAAATGTTGTACTATTGAACAAGCATGATGTTTTGGTC
65 GCATGACATTTT-TGTTTTATAAATGTTGTAATATT-AACAAGCATAATGTTTTGGTC
* * * * *
4184454 ATTATAAATG-TAGTGTTTAAATAATACTAAACTAGTTAATTATATAAAATGTTCTACTTAACAA
1 ATTATAAATGCTA-TGTTTGAATAATACTAAACCAATTAATTAAATAAAATGTTCTATTTAACAA
* * *
4184518 GAATGACATTTTTATTTTATAAATGTTG-AATATTAAAAAGGCATAATGTTTTGGTC
65 GCATGACATTTTTGTTTTATAAATGTTGTAATATTAACAA-GCATAATGTTTTGGTC
* * * *
4184574 ATTATAAATGCTATGTTTGACTAATCATCAAAACCAATTAATTAAAATAAAATATTTTATTTAAC
1 ATTATAAATGCTATGTTTGAATAAT-A-CTAAACCAATTAATT-AAATAAAATGTTCTATTTAAC
* * **
4184639 AAGCATGATATTTTTTGTTTTAT-AATGTTGTAATATTAAACAAGCACAACATTTTGGTC
63 AAGCATGACA-TTTTTGTTTTATAAATGTTGTAATATT-AACAAGCATAATGTTTTGGTC
** * * *
4184698 ATTATAAACACAAAGCTTT-AATAAT-CATAAAACCAATTAAATAAATAAAATGT
1 ATTATAAATGCTATG-TTTGAATAATAC-T-AAACCAATTAATTAAATAAAATGT
4184751 AATATTTGAC
Statistics
Matches: 342, Mismatches: 56, Indels: 40
0.78 0.13 0.09
Matches are distributed among these distances:
119 4 0.01
120 42 0.12
121 100 0.29
122 95 0.28
123 48 0.14
124 46 0.13
125 7 0.02
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.38
Consensus pattern (120 bp):
ATTATAAATGCTATGTTTGAATAATACTAAACCAATTAATTAAATAAAATGTTCTATTTAACAAG
CATGACATTTTTGTTTTATAAATGTTGTAATATTAACAAGCATAATGTTTTGGTC
Found at i:4184652 original size:123 final size:120
Alignment explanation
Indices: 4184344--4184750 Score: 435
Period size: 122 Copynumber: 3.3 Consensus size: 120
4184334 TTATAACACA
* * * *
4184344 ATGTTTGAATAATACTAAACCAATTAATTAAACAAAATGTTCTATTTAACAAGCATTACGTTTTA
1 ATGTTTGAATAATACAAAACCAATTAATTAAATAAAATGTTCTATTTAACAAGCATGACATTTT-
* * *
4184409 TGTTTTATAAATGTTGTACTATTGAACAAGCATGATGTTTTGGTCATTATAAATG-T
65 TGTTTTATAAATGTTGTAATATT-AAAAAGCATAATGTTTTGGTCATTATAAATGCT
* * * * * * *
4184465 AGTGTTTAAATAATACTAAACTAGTTAATTATATAAAATGTTCTACTTAACAAGAATGACATTTT
1 A-TGTTTGAATAATACAAAACCAATTAATTAAATAAAATGTTCTATTTAACAAGCATGACATTTT
*
4184530 TATTTTATAAATGTTG-AATATTAAAAAGGCATAATGTTTTGGTCATTATAAATGCT
65 TGTTTTATAAATGTTGTAATATTAAAAA-GCATAATGTTTTGGTCATTATAAATGCT
* * * *
4184586 ATGTTTGACTAATCATCAAAACCAATTAATTAAAATAAAATATTTTATTTAACAAGCATGATATT
1 ATGTTTGAATAAT-A-CAAAACCAATTAATT-AAATAAAATGTTCTATTTAACAAGCATGACA-T
* ** ** *
4184651 TTTTGTTTTAT-AATGTTGTAATATTAAACAAGCACAACATTTTGGTCATTATAAACACA
62 TTTTGTTTTATAAATGTTGTAATATTAAA-AAGCATAATGTTTTGGTCATTATAAATGCT
* * *
4184710 AAGCTTT-AATAATCATAAAACCAATTAAATAAATAAAATGT
1 ATG-TTTGAATAAT-ACAAAACCAATTAATTAAATAAAATGT
4184751 AATATTTGAC
Statistics
Matches: 240, Mismatches: 36, Indels: 19
0.81 0.12 0.06
Matches are distributed among these distances:
119 4 0.02
120 40 0.17
121 19 0.08
122 76 0.32
123 45 0.19
124 51 0.21
125 5 0.02
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (120 bp):
ATGTTTGAATAATACAAAACCAATTAATTAAATAAAATGTTCTATTTAACAAGCATGACATTTTT
GTTTTATAAATGTTGTAATATTAAAAAGCATAATGTTTTGGTCATTATAAATGCT
Found at i:4187993 original size:23 final size:25
Alignment explanation
Indices: 4187943--4187993 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
4187933 TTCTATATTT
* *
4187943 TATATATATTTATGTAAATTCAACA
1 TATATATATTTATATAAATCCAACA
*
4187968 TATA-ATATTTATATAAGTCCAA-A
1 TATATATATTTATATAAATCCAACA
4187991 TAT
1 TAT
4187994 TTTCTCTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 4 0.17
24 15 0.65
25 4 0.17
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (25 bp):
TATATATATTTATATAAATCCAACA
Found at i:4188755 original size:52 final size:53
Alignment explanation
Indices: 4188677--4188806 Score: 145
Period size: 52 Copynumber: 2.5 Consensus size: 53
4188667 CAAATTTTAT
* * * *
4188677 GTTAAATTGATAAACATGATATTTTCATTAAGTTAAACATAGTATTTATCTAA
1 GTTAACTTGACAAACATGATATTTTCATCAAGCTAAACATAGTATTTATCTAA
* * * ** *
4188730 TTTAGCTTGACAAA-ATGATGTTTTCATCAAGCTAAATGTAGTATTTGTCTAA
1 GTTAACTTGACAAACATGATATTTTCATCAAGCTAAACATAGTATTTATCTAA
* *
4188782 GTTAACTTGACAAAGATAATATTTT
1 GTTAACTTGACAAACATGATATTTT
4188807 ATATTAAAAC
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
52 44 0.71
53 18 0.29
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (53 bp):
GTTAACTTGACAAACATGATATTTTCATCAAGCTAAACATAGTATTTATCTAA
Found at i:4188942 original size:22 final size:22
Alignment explanation
Indices: 4188914--4188957 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4188904 GATACTTTCT
*
4188914 TAAATTAAAAAAATTAATTATA
1 TAAATTAAAAAAAGTAATTATA
4188936 TAAATTAAAAAAAGTAATTATA
1 TAAATTAAAAAAAGTAATTATA
4188958 ACATTCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
TAAATTAAAAAAAGTAATTATA
Found at i:4198834 original size:7 final size:7
Alignment explanation
Indices: 4198773--4198854 Score: 69
Period size: 7 Copynumber: 11.4 Consensus size: 7
4198763 CCAACTAAAC
4198773 TTTCTTT
1 TTTCTTT
4198780 CTTTCTTT
1 -TTTCTTT
*
4198788 TTTTTTT
1 TTTCTTT
*
4198795 TTTATTT
1 TTTCTTT
4198802 TTT-TTGCT
1 TTTCTT--T
*
4198810 TTTCGTTG
1 TTTC-TTT
4198818 TTTCTTT
1 TTTCTTT
4198825 TTTCTTT
1 TTTCTTT
**
4198832 TTTCAGT
1 TTTCTTT
4198839 TTTC-TT
1 TTTCTTT
4198845 TTTCTTT
1 TTTCTTT
4198852 TTT
1 TTT
4198855 ATATTTAATA
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
6 7 0.11
7 38 0.61
8 15 0.24
10 2 0.03
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.80
Consensus pattern (7 bp):
TTTCTTT
Found at i:4198840 original size:20 final size:18
Alignment explanation
Indices: 4198785--4198855 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 18
4198775 TCTTTCTTTC
4198785 TTTTTTT-TTTTTTA-TT
1 TTTTTTTCTTTTTTAGTT
*
4198801 TTTTTTGCTTTTCGTT-GTT
1 TTTTTTTCTTTT--TTAGTT
4198820 TCTTTTTTCTTTTTTCAGTT
1 T-TTTTTTCTTTTTT-AGTT
4198840 TTCTTTTTCTTTTTTA
1 TT-TTTTTCTTTTTTA
4198856 TATTTAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
16 6 0.13
17 4 0.09
18 2 0.04
19 7 0.16
20 26 0.58
ACGTcount: A:0.04, C:0.10, G:0.06, T:0.80
Consensus pattern (18 bp):
TTTTTTTCTTTTTTAGTT
Found at i:4199202 original size:18 final size:19
Alignment explanation
Indices: 4199175--4199212 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4199165 CCTTTCTTGC
*
4199175 TTTTTCATTGTTTTT-TAT
1 TTTTTAATTGTTTTTCTAT
4199193 TTTTTAATTGTTTTTCTAT
1 TTTTTAATTGTTTTTCTAT
4199212 T
1 T
4199213 GTTAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTTAATTGTTTTTCTAT
Found at i:4199217 original size:18 final size:17
Alignment explanation
Indices: 4199176--4199236 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
4199166 CTTTCTTGCT
*
4199176 TTTTCATTGTTTTT-TA
1 TTTTAATTGTTTTTCTA
4199192 TTTTTTAATTGTTTTTCTA
1 --TTTTAATTGTTTTTCTA
*
4199211 TTGTTAATTATTTTGTCT-
1 TT-TTAATTGTTTT-TCTA
4199229 TTTTAATT
1 TTTTAATT
4199237 AGATAACTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 8 0.21
18 25 0.66
19 5 0.13
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (17 bp):
TTTTAATTGTTTTTCTA
Found at i:4200663 original size:17 final size:16
Alignment explanation
Indices: 4200622--4200653 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
4200612 CCGAATGAGT
4200622 TTTTTTTTCCTTTTTGA
1 TTTTTTTTCCTTTTT-A
4200639 TTTTTTTTCCTTTTT
1 TTTTTTTTCCTTTTT
4200654 TTATCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTTTTCCTTTTTA
Found at i:4201907 original size:7 final size:7
Alignment explanation
Indices: 4201882--4201979 Score: 53
Period size: 7 Copynumber: 14.0 Consensus size: 7
4201872 GGTTTGGATT
4201882 GGTTTAG
1 GGTTTAG
*
4201889 GGTCTA-
1 GGTTTAG
4201895 GG-TTAG
1 GGTTTAG
4201901 GGTTTAG
1 GGTTTAG
*
4201908 CGTTTTAG
1 -GGTTTAG
*
4201916 GATTTAAG
1 GGTTT-AG
4201924 AGGTTTTAG
1 -GG-TTTAG
4201933 GG-TTAG
1 GGTTTAG
*
4201939 GATTTA-
1 GGTTTAG
*
4201945 GATTTAG
1 GGTTTAG
4201952 GGTTTTAG
1 GG-TTTAG
*
4201960 GTTTTAG
1 GGTTTAG
4201967 GG-TTAG
1 GGTTTAG
*
4201973 GATTTAG
1 GGTTTAG
4201980 ATTTAAAATC
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
5 2 0.03
6 20 0.28
7 27 0.38
8 16 0.23
9 3 0.04
10 3 0.04
ACGTcount: A:0.20, C:0.02, G:0.35, T:0.43
Consensus pattern (7 bp):
GGTTTAG
Found at i:4204094 original size:11 final size:12
Alignment explanation
Indices: 4204065--4204114 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 12
4204055 GTTAAAGGAT
*
4204065 TTTTTTTTGTGTGT
1 TTTTTTTT-T-TGC
4204079 TTTTTTTTTTGC
1 TTTTTTTTTTGC
4204091 TTTTTTTGTTTGC
1 TTTTTTT-TTTGC
4204104 TTTTTGTTTTT
1 TTTTT-TTTTT
4204115 TCTAGAACAG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 9 0.27
13 14 0.42
14 10 0.30
ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTTGC
Found at i:4204095 original size:14 final size:14
Alignment explanation
Indices: 4204064--4204115 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
4204054 TGTTAAAGGA
*
4204064 TTTTTTTTTGTG-T
1 TTTTTTTTTTTGCT
4204077 GTTTTTTTTTTTGC-
1 -TTTTTTTTTTTGCT
*
4204091 TTTTTTTGTTTGCT
1 TTTTTTTTTTTGCT
4204105 TTTTGTTTTTT
1 TTTT-TTTTTT
4204116 CTAGAACAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 12 0.38
14 15 0.47
15 5 0.16
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTTTGCT
Found at i:4204098 original size:25 final size:27
Alignment explanation
Indices: 4204066--4204115 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
4204056 TTAAAGGATT
4204066 TTTTTTTGTGTG-TTTTT-TTTTTTGC
1 TTTTTTTGTGTGCTTTTTGTTTTTTGC
*
4204091 TTTTTTTGTTTGCTTTTTGTTTTTT
1 TTTTTTTGTGTGCTTTTTGTTTTTT
4204116 CTAGAACAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 5 0.23
27 6 0.27
ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82
Consensus pattern (27 bp):
TTTTTTTGTGTGCTTTTTGTTTTTTGC
Found at i:4204102 original size:13 final size:13
Alignment explanation
Indices: 4204066--4204108 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
4204056 TTAAAGGATT
*
4204066 TTTTTTTGTGTG-
1 TTTTTTTGTTTGC
*
4204078 TTTTTTTTTTTGC
1 TTTTTTTGTTTGC
4204091 TTTTTTTGTTTGC
1 TTTTTTTGTTTGC
4204104 TTTTT
1 TTTTT
4204109 GTTTTTTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.00, C:0.05, G:0.14, T:0.81
Consensus pattern (13 bp):
TTTTTTTGTTTGC
Found at i:4204228 original size:48 final size:48
Alignment explanation
Indices: 4204169--4204512 Score: 167
Period size: 49 Copynumber: 7.1 Consensus size: 48
4204159 AAATCATTCT
* * *
4204169 GGAAAATGGCTCCTATTAACATTGACAAGGAACTTTAAAAATCTATATA
1 GGAAAAGGGCTCCTATTAACATAGACAAGAAACTTTAAAAATCTAT-TA
** * *
4204218 GGAAAA-GGCTCCTATTAACATAGGTAATAAACTTTAAAAATCTATTT
1 GGAAAAGGGCTCCTATTAACATAGACAAGAAACTTTAAAAATCTATTA
** *
4204265 GGAAAAAGGGCTCCTATTAACATAGGTAATG-AACGTTAAAAAATCTATCT-
1 GG-AAAAGGGCTCCTATTAACATAGACAA-GAAAC-TTTAAAAATCTAT-TA
* * * ** *
4204315 TGAAAAGAGCTCCTA-TAAAATATG-CATCAAACTTTAAAAAAAAT-TTTCTA
1 GGAAAAGGGCTCCTATTAACATA-GACAAGAAACTTT---AAAAATCTAT-TA
* * * ** * **
4204365 -CAAAAAGGCTCATATGCA-ATGGACATCAAACTTTAAAAATCTATCT-
1 GGAAAAGGGCTCCTATTAACATAGACAAGAAACTTTAAAAATCTAT-TA
** * * **
4204411 GG-AAAGGGCTTATACTAA-ATAGGCATCAAACTTTAAAAATCTATTTA
1 GGAAAAGGGCTCCTATTAACATAGACAAGAAACTTTAAAAATCTA-TTA
* *
4204458 -GAAAAGGGCTCCTATTAACATA-AGCAACAAACATTAAAATATCTATCTA
1 GGAAAAGGGCTCCTATTAACATAGA-CAAGAAACTTTAAAA-ATCTAT-TA
4204507 -GAAAAG
1 GGAAAAG
4204513 TGATTCGAAA
Statistics
Matches: 235, Mismatches: 38, Indels: 44
0.74 0.12 0.14
Matches are distributed among these distances:
46 42 0.18
47 23 0.10
48 66 0.28
49 83 0.35
50 20 0.09
51 1 0.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (48 bp):
GGAAAAGGGCTCCTATTAACATAGACAAGAAACTTTAAAAATCTATTA
Found at i:4204347 original size:97 final size:94
Alignment explanation
Indices: 4204157--4204512 Score: 267
Period size: 97 Copynumber: 3.7 Consensus size: 94
4204147 ACTTCAAAAA
* * * ** * * *
4204157 AAAAATC-ATTCTGGAAAATGGCTCCTATTAACATTGACAAGGAACTTTAAAAATCTATATAGGA
1 AAAAATCTATT-TGGAAAAGGGCTCCTATTAACATAGGCAATAAACTTAAAAAATCTATCT-TGA
* *
4204221 AAAGGCTCCTATTAACATAGGTAAT-AAACTTT
64 AAAGGCTCCTA-TAAAATAGG-CATCAAACTTT
* *
4204253 AAAAATCTATTTGGAAAAAGGGCTCCTATTAACATAGGTAATGAACGTTAAAAAATCTATCTTGA
1 AAAAATCTATTTGG-AAAAGGGCTCCTATTAACATAGGCAATAAAC-TTAAAAAATCTATCTTGA
*
4204318 AAAGAGCTCCTATAAAATATGCATCAAACTTT
64 AAAG-GCTCCTATAAAATAGGCATCAAACTTT
** * ** * * ** * *
4204350 AAAAAAAATTTTCTACAAAAAGGCTCATATGCA-AT-GG-ACATCAAACTTTAAAAATCTATCTG
1 -AAAAATCTATT-TGGAAAAGGGCTCCTATTAACATAGGCA-AT-AAACTTAAAAAATCTATCTT
*
4204412 GAAAGGGCT--TATACTAAATAGGCATCAAACTTT
62 GAAAAGGCTCCTATA--AAATAGGCATCAAACTTT
* * * * *
4204445 AAAAATCTATTTAGAAAAGGGCTCCTATTAACATAAGCAACAAACATTAAAATATCTATCTAGAA
1 AAAAATCTATTTGGAAAAGGGCTCCTATTAACATAGGCAATAAAC-TTAAAAAATCTATCTTGAA
4204510 AAG
65 AAG
4204513 TGATTCGAAA
Statistics
Matches: 206, Mismatches: 39, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
93 19 0.09
94 14 0.07
95 41 0.20
96 36 0.17
97 54 0.26
98 41 0.20
99 1 0.00
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.28
Consensus pattern (94 bp):
AAAAATCTATTTGGAAAAGGGCTCCTATTAACATAGGCAATAAACTTAAAAAATCTATCTTGAAA
AGGCTCCTATAAAATAGGCATCAAACTTT
Found at i:4204440 original size:46 final size:47
Alignment explanation
Indices: 4204388--4204510 Score: 140
Period size: 46 Copynumber: 2.6 Consensus size: 47
4204378 ATGCAATGGA
* *
4204388 CATCAAACTTTAAAAATCTATCTGGAAAGGGCTTATACTAA-ATAGG
1 CATCAAACTTTAAAAATCTATCTGGAAAGGGCTCATACTAACATAAG
* * * *
4204434 CATCAAACTTTAAAAATCTATTTAGAAAAGGGCTCCTATTAACATAAG
1 CATCAAACTTTAAAAATCTATCT-GGAAAGGGCTCATACTAACATAAG
* * *
4204482 CAACAAACATTAAAATATCTATCTAGAAA
1 CATCAAACTTTAAAA-ATCTATCTGGAAA
4204511 AGTGATTCGA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
46 22 0.35
47 14 0.22
48 20 0.32
49 7 0.11
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.28
Consensus pattern (47 bp):
CATCAAACTTTAAAAATCTATCTGGAAAGGGCTCATACTAACATAAG
Found at i:4205039 original size:21 final size:21
Alignment explanation
Indices: 4205013--4205056 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
4205003 AGAAAATAAA
4205013 AAGTTTACTATAGATTTCAAC
1 AAGTTTACTATAGATTTCAAC
4205034 AAGTTTACTATAGATTTCAAC
1 AAGTTTACTATAGATTTCAAC
4205055 AA
1 AA
4205057 CAAATTCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (21 bp):
AAGTTTACTATAGATTTCAAC
Found at i:4207041 original size:25 final size:26
Alignment explanation
Indices: 4206981--4207043 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
4206971 CTCATTTTTC
* *
4206981 TTTCTTTTCTTTTCTTTTTCACCATTT
1 TTTCTTTT-TCTTCTTTTTCACAATTT
* *
4207008 TATTATTTTTCTT-TTTTTCATAATTT
1 T-TTCTTTTTCTTCTTTTTCACAATTT
4207034 TTTCTTTTTC
1 TTTCTTTTTC
4207044 AATTTTTCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 8 0.27
26 12 0.40
27 4 0.13
28 6 0.20
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTCTTTTTCTTCTTTTTCACAATTT
Found at i:4207057 original size:15 final size:16
Alignment explanation
Indices: 4207012--4207057 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
4207002 CCATTTTATT
4207012 ATTTTTCTTTTTTTCATA
1 ATTTTTC-TTTTTTCA-A
4207030 ATTTTT-TCTTTTTC-A
1 ATTTTTCT-TTTTTCAA
4207045 ATTTTTCTTTTTT
1 ATTTTTCTTTTTT
4207058 TTTCTTTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 12 0.46
16 2 0.08
17 6 0.23
18 6 0.23
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTCTTTTTTCAA
Found at i:4211855 original size:13 final size:13
Alignment explanation
Indices: 4211833--4211869 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
4211823 AATAATTCAC
*
4211833 AAATTAAAAATAT
1 AAATTTAAAATAT
4211846 AAATTTAAAATAT
1 AAATTTAAAATAT
4211859 AAATTTAAAAT
1 AAATTTAAAAT
4211870 TTTCTAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATTTAAAATAT
Found at i:4213634 original size:32 final size:30
Alignment explanation
Indices: 4213472--4213673 Score: 172
Period size: 31 Copynumber: 6.5 Consensus size: 30
4213462 AGCTAGTTTG
* * * *
4213472 GGCTTAATTTTCTTTGGTGCCAGTTAAACTA
1 GGCTTAATCTTCATAGGTGCCAGCT-AACTA
* * ** *
4213503 GGCTAAAATCTTC-TTGGTAACAACTATACTA
1 GGCT-TAATCTTCATAGGTGCCAGCTA-ACTA
*
4213534 GGCTTAATCTTTATAGGTGCCAGCTAAACTA
1 GGCTTAATCTTCATAGGTGCCAGCT-AACTA
* * *
4213565 GGCTTAATCTTTATAGATGCCAGTTAGACTA
1 GGCTTAATCTTCATAGGTGCCAGCTA-ACTA
* *
4213596 GGCTTAACTCTTCATAGGTTCTAGCTAATCTA
1 GGCTTAA-TCTTCATAGGTGCCAGCTAA-CTA
4213628 GGCTTAATTCTTCATAGGTGCCAGCTAACATA
1 GGCTTAA-TCTTCATAGGTGCCAGCTAAC-TA
*
4213660 GGCTTAATCCTCAT
1 GGCTTAATCTTCAT
4213674 CTCTTTCAAA
Statistics
Matches: 140, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
30 8 0.06
31 74 0.53
32 58 0.41
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (30 bp):
GGCTTAATCTTCATAGGTGCCAGCTAACTA
Found at i:4214741 original size:42 final size:42
Alignment explanation
Indices: 4214672--4214928 Score: 186
Period size: 42 Copynumber: 6.2 Consensus size: 42
4214662 AATTTACACC
* ** *
4214672 AGAGTAAATGATTCACTA-TTTAAAAGACTCTAGATTCATAAT
1 AGAGTAAATAATTCA-TAGTTTGGAAGACTCTGGATTCATAAT
* * * *
4214714 AGAGTAAATGATTCATAGTTTGGAAGACTTTGGATACATAAC
1 AGAGTAAATAATTCATAGTTTGGAAGACTCTGGATTCATAAT
* * * *
4214756 AAAATAAATGATTCATAG-TTGAGAAGACTCTGGATTCA-CAT
1 AGAGTAAATAATTCATAGTTTG-GAAGACTCTGGATTCATAAT
* * *
4214797 CAGAGT-AATAATTTATAG-TTGGAAGGACTTTGGATAT-ACAAT
1 -AGAGTAAATAATTCATAGTTTGGAA-GACTCTGGAT-TCATAAT
* * * * ***
4214839 AAAGTAAATAATTCACAGTTT-GAAGGCTCTGGGTTCATCGC
1 AGAGTAAATAATTCATAGTTTGGAAGACTCTGGATTCATAAT
* * * *
4214880 AGAGTAAACAATTCATAGTTTAGAAGACTCTAGATTCACAAT
1 AGAGTAAATAATTCATAGTTTGGAAGACTCTGGATTCATAAT
4214922 AGAGTAA
1 AGAGTAA
4214929 TAGTTTGAAA
Statistics
Matches: 167, Mismatches: 38, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
40 4 0.02
41 59 0.35
42 102 0.61
43 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (42 bp):
AGAGTAAATAATTCATAGTTTGGAAGACTCTGGATTCATAAT
Found at i:4214898 original size:83 final size:83
Alignment explanation
Indices: 4214695--4214908 Score: 209
Period size: 83 Copynumber: 2.6 Consensus size: 83
4214685 CACTATTTAA
* * ** * *
4214695 AAGACTCTAGATTCATAATAGAGTAAATGATTCATAGTTTGGAAGACTTTGGATACATAACAAAA
1 AAGACTCTGGATTCACAGCAGAGTAAATAATTCATAG-TTGGAAGACTTTGGATACACAACAAAA
* *
4214760 TAAATGATTCATAGTTGAG
65 TAAATAATTCACAGTTGAG
* * * * *
4214779 AAGACTCTGGATTCACATCAGAGT-AATAATTTATAGTTGGAAGGACTTTGGATATACAATAAAG
1 AAGACTCTGGATTCACAGCAGAGTAAATAATTCATAGTTGGAA-GACTTTGGATACACAACAAAA
*
4214843 TAAATAATTCACAGTT-TG
65 TAAATAATTCACAGTTGAG
* * * *
4214861 AAGGCTCTGGGTTCATC-GCAGAGTAAACAATTCATAGTTTAGAAGACT
1 AAGACTCTGGATTCA-CAGCAGAGTAAATAATTCATAG-TTGGAAGACT
4214909 CTAGATTCAC
Statistics
Matches: 107, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
82 26 0.24
83 56 0.52
84 25 0.23
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (83 bp):
AAGACTCTGGATTCACAGCAGAGTAAATAATTCATAGTTGGAAGACTTTGGATACACAACAAAAT
AAATAATTCACAGTTGAG
Found at i:4216076 original size:8 final size:7
Alignment explanation
Indices: 4216057--4216100 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
4216047 TAGAGCCACA
4216057 TTCTTTT
1 TTCTTTT
4216064 TTCTTTT
1 TTCTTTT
4216071 TCTCTTTT
1 T-TCTTTT
*
4216079 TTCCTTT
1 TTCTTTT
*
4216086 TT-TGTT
1 TTCTTTT
4216092 TTCTTTT
1 TTCTTTT
4216099 TT
1 TT
4216101 TTATTATTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 4 0.13
7 20 0.65
8 7 0.23
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (7 bp):
TTCTTTT
Found at i:4216078 original size:15 final size:14
Alignment explanation
Indices: 4216057--4216100 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
4216047 TAGAGCCACA
4216057 TTCTTTTTTCTTTT
1 TTCTTTTTTCTTTT
*
4216071 TCTCTTTTTTCCTTT
1 T-TCTTTTTTCTTTT
*
4216086 TT-TGTTTTCTTTT
1 TTCTTTTTTCTTTT
4216099 TT
1 TT
4216101 TTATTATTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 11 0.42
14 2 0.08
15 13 0.50
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (14 bp):
TTCTTTTTTCTTTT
Found at i:4216087 original size:22 final size:22
Alignment explanation
Indices: 4216059--4216102 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4216049 GAGCCACATT
*
4216059 CTTTTTTCTTTTTCTCTTTTTTC
1 CTTTTTT-GTTTTCTCTTTTTTC
*
4216082 CTTTTTTGTTTTCTTTTTTTT
1 CTTTTTTGTTTTCTCTTTTTT
4216103 ATTATTACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (22 bp):
CTTTTTTGTTTTCTCTTTTTTC
Found at i:4216484 original size:19 final size:20
Alignment explanation
Indices: 4216441--4216484 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
4216431 TTAATCATTC
4216441 ATTTTT-TTCTTTTCTTTCT
1 ATTTTTCTTCTTTTCTTTCT
*
4216460 -TCTTTCTTCTTTTCTTT-T
1 ATTTTTCTTCTTTTCTTTCT
4216478 ATTTTTC
1 ATTTTTC
4216485 CCTTGCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (20 bp):
ATTTTTCTTCTTTTCTTTCT
Found at i:4217751 original size:12 final size:12
Alignment explanation
Indices: 4217727--4217763 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
4217717 AAAAAAAAAC
4217727 TTTCTCA-TTTT
1 TTTCTCATTTTT
4217738 TTTCTCATTTTT
1 TTTCTCATTTTT
*
4217750 TTTGTCATTTTT
1 TTTCTCATTTTT
4217762 TT
1 TT
4217764 CTTTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.08, C:0.14, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTCTCATTTTT
Found at i:4217761 original size:23 final size:20
Alignment explanation
Indices: 4217731--4217781 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 20
4217721 AAAAACTTTC
4217731 TCATTTTTTTCTCATTTTTTTT
1 TCATTTTTTTCT--TTTTTTTT
4217753 GTCATTTTTTTCTTTTTTTTT
1 -TCATTTTTTTCTTTTTTTTT
*
4217774 TAATTTTT
1 TCATTTTT
4217782 AGTTTCAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.26
21 8 0.30
23 12 0.44
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (20 bp):
TCATTTTTTTCTTTTTTTTT
Found at i:4217781 original size:11 final size:11
Alignment explanation
Indices: 4217727--4217765 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
4217717 AAAAAAAAAC
4217727 TTTCTCATTTT
1 TTTCTCATTTT
4217738 TTTCTCATTTTT
1 TTTCTCA-TTTT
*
4217750 TTTGTCATTTT
1 TTTCTCATTTT
4217761 TTTCT
1 TTTCT
4217766 TTTTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.08, C:0.15, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTCTCATTTT
Found at i:4220619 original size:37 final size:37
Alignment explanation
Indices: 4220563--4220682 Score: 118
Period size: 37 Copynumber: 3.2 Consensus size: 37
4220553 AAACATGCAT
* *
4220563 TATCTCATTATGATATGCATGAAATAGAATGCATGTAC
1 TATCT-ATTATAATATGCATGAAATAGAATGTATGTAC
* **
4220601 TATCTATTATAATGTGCATGGGAT-GAAATGTATGTAC
1 TATCTATTATAATATGCATGAAATAG-AATGTATGTAC
* * * *
4220638 CATCTGTTA-AGATATGCATGAAAAAGAATATATGTAC
1 TATCTATTATA-ATATGCATGAAATAGAATGTATGTAC
4220675 TATCTATT
1 TATCTATT
4220683 GATGTGGATG
Statistics
Matches: 65, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
36 2 0.03
37 57 0.88
38 6 0.09
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.36
Consensus pattern (37 bp):
TATCTATTATAATATGCATGAAATAGAATGTATGTAC
Found at i:4220948 original size:20 final size:21
Alignment explanation
Indices: 4220910--4220949 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4220900 ATTCAAAGAT
* *
4220910 TTTTTTTTTTGTTTCTTTTGA
1 TTTTTTTTTTCTATCTTTTGA
*
4220931 TTTTTTTTTTCTATTTTTT
1 TTTTTTTTTTCTATCTTTT
4220950 TCGTTTAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.85
Consensus pattern (21 bp):
TTTTTTTTTTCTATCTTTTGA
Found at i:4220950 original size:22 final size:22
Alignment explanation
Indices: 4220907--4220950 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4220897 AGGATTCAAA
*
4220907 GATTTTTTTTTTTGTTTCTTTT
1 GATTTTTTTTTTTATTTCTTTT
4220929 GATTTTTTTTTTCTATTT-TTTT
1 GATTTTTTTTTT-TATTTCTTTT
4220951 CGTTTAGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.82
Consensus pattern (22 bp):
GATTTTTTTTTTTATTTCTTTT
Found at i:4221803 original size:25 final size:25
Alignment explanation
Indices: 4221722--4221808 Score: 108
Period size: 25 Copynumber: 3.6 Consensus size: 25
4221712 TAACAACAAT
4221722 ATATA-AT-AAATGACATAATTAAA
1 ATATACATGAAATGACATAATTAAA
* * *
4221745 ATATCCAGGAAATGTA-AAAATTAAA
1 ATATACATGAAATG-ACATAATTAAA
*
4221770 ATATGCATGAAATGACATAATTAAA
1 ATATACATGAAATGACATAATTAAA
4221795 ATATACATGAAATG
1 ATATACATGAAATG
4221809 TAAAACACAC
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
23 4 0.08
24 2 0.04
25 46 0.87
26 1 0.02
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (25 bp):
ATATACATGAAATGACATAATTAAA
Found at i:4221906 original size:18 final size:18
Alignment explanation
Indices: 4221874--4221942 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
4221864 GCCAATAATA
4221874 TTTTAGATTTCTTTTCAATT
1 TTTTA-ATTT-TTTTCAATT
* *
4221894 TTTTGATTTTTTTTCAATG
1 TTTT-AATTTTTTTCAATT
* * *
4221913 CTTCAATTTTTTTCATTT
1 TTTTAATTTTTTTCAATT
4221931 TTTTAATTTTTT
1 TTTTAATTTTTT
4221943 AAATTTTCTC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 21 0.54
19 10 0.26
20 7 0.18
21 1 0.03
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTTAATTTTTTTCAATT
Found at i:4221941 original size:19 final size:19
Alignment explanation
Indices: 4221874--4221942 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
4221864 GCCAATAATA
*
4221874 TTTTAGATTTCTTTTCAATT
1 TTTTA-ATTTTTTTTCAATT
* *
4221894 TTTTGATTTTTTTTCAATG
1 TTTTAATTTTTTTTCAATT
* * *
4221913 CTTCAA-TTTTTTTCATTT
1 TTTTAATTTTTTTTCAATT
4221931 TTTTAATTTTTT
1 TTTTAATTTTTT
4221943 AAATTTTCTC
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
18 14 0.37
19 20 0.53
20 4 0.11
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTTAATTTTTTTTCAATT
Found at i:4223057 original size:7 final size:7
Alignment explanation
Indices: 4223039--4223085 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
4223029 TTGGATTACA
4223039 GGTTTA-
1 GGTTTAG
4223045 GGTTTAG
1 GGTTTAG
4223052 GGTTTAG
1 GGTTTAG
*
4223059 GATTTA-
1 GGTTTAG
4223065 GGTTTAG
1 GGTTTAG
4223072 GGTTTAG
1 GGTTTAG
*
4223079 GATTTAG
1 GGTTTAG
4223086 ATTTGGGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
6 11 0.31
7 25 0.69
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.45
Consensus pattern (7 bp):
GGTTTAG
Found at i:4223066 original size:20 final size:20
Alignment explanation
Indices: 4223041--4223096 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
4223031 GGATTACAGG
4223041 TTTAGGTTTAGGGTTTAGGA
1 TTTAGGTTTAGGGTTTAGGA
4223061 TTTAGGTTTAGGGTTTAGGA
1 TTTAGGTTTAGGGTTTAGGA
* *
4223081 TTTAGATTTGGGGTTT
1 TTTAGGTTTAGGGTTT
4223097 TGATTAGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (20 bp):
TTTAGGTTTAGGGTTTAGGA
Found at i:4224861 original size:19 final size:19
Alignment explanation
Indices: 4224809--4224865 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
4224799 CAGTTTTAAT
*
4224809 TTTATTTGATTAATTTTGAC
1 TTTATTT-ATTAAGTTTGAC
* ** *
4224829 TTTGTGGATCAAGTTTGAC
1 TTTATTTATTAAGTTTGAC
4224848 TTTATTTATTAAGTTTGA
1 TTTATTTATTAAGTTTGA
4224866 TTAAATTTGA
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (19 bp):
TTTATTTATTAAGTTTGAC
Found at i:4225127 original size:20 final size:20
Alignment explanation
Indices: 4225102--4225147 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
4225092 ATTAGCTTCT
4225102 ATTTTTATATTTTTTTACTC
1 ATTTTTATATTTTTTTACTC
* * **
4225122 ATTTTTTTTTTTTTTTTTTC
1 ATTTTTATATTTTTTTACTC
4225142 ATTTTT
1 ATTTTT
4225148 TTCATTTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (20 bp):
ATTTTTATATTTTTTTACTC
Found at i:4226295 original size:20 final size:19
Alignment explanation
Indices: 4226258--4226296 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
4226248 GATAATATAC
*
4226258 TTTATTTTTAATTAATTAT
1 TTTATTTTTAAATAATTAT
4226277 TTTATTTTTAAATATATTAT
1 TTTATTTTTAAATA-ATTAT
4226297 AAGAAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTTTTAAATAATTAT
Found at i:4234311 original size:109 final size:110
Alignment explanation
Indices: 4234180--4234390 Score: 307
Period size: 109 Copynumber: 1.9 Consensus size: 110
4234170 AAAGAGATCA
* * *
4234180 AAGTTAAGAAAGATAAATTAGAAGTGCTAGCTAATGGTCCGAAGCTCCCATGTCCACTACTTTTT
1 AAGTTAAGAAAGATAAATTAGAACTACTAGCTAATGGTCCGAAGCTCCCATATCCACTACTTTTT
*
4234245 T-GAATCAATATTCTTAATACACCAATTATCAATATTAGAGACCC
66 TAAAATCAATATTCTTAATACACCAATTATCAATATTAGAGACCC
* * * * * *
4234289 AAGTTCAGAAAGGTAAATTAGAACTACTAGCTAGTGGTCCTAAGCTCCCATATCCATTATTTTTT
1 AAGTTAAGAAAGATAAATTAGAACTACTAGCTAATGGTCCGAAGCTCCCATATCCACTACTTTTT
* *
4234354 TAAAATTAATATTCTTAATACATCAATTATCAATATT
66 TAAAATCAATATTCTTAATACACCAATTATCAATATT
4234391 TTCGTTTACG
Statistics
Matches: 89, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
109 57 0.64
110 32 0.36
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (110 bp):
AAGTTAAGAAAGATAAATTAGAACTACTAGCTAATGGTCCGAAGCTCCCATATCCACTACTTTTT
TAAAATCAATATTCTTAATACACCAATTATCAATATTAGAGACCC
Found at i:4234743 original size:26 final size:27
Alignment explanation
Indices: 4234706--4234760 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
4234696 TTTAAATTCG
4234706 TTTTAATCATTTT-ATAAATGTAATCA
1 TTTTAATCATTTTAATAAATGTAATCA
* *
4234732 TTTTAATTATTTTAATAAATGTAGTCA
1 TTTTAATCATTTTAATAAATGTAATCA
4234759 TT
1 TT
4234761 ATGTTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (27 bp):
TTTTAATCATTTTAATAAATGTAATCA
Found at i:4240939 original size:36 final size:35
Alignment explanation
Indices: 4240899--4240992 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 35
4240889 AAAACATCTT
4240899 CATTACTTATTCTACCATTTTTTAGAGAAACACTCA
1 CATTACTTATTCT-CCATTTTTTAGAGAAACACTCA
* * * *
4240935 CATTATTTATTCTCTTATTTTTTAGGGAAACACTCG
1 CATTACTTATTCTC-CATTTTTTAGAGAAACACTCA
* *
4240971 CATTACTTGTTCTCCAATTTTT
1 CATTACTTATTCTCCATTTTTT
4240993 CTTAAAGGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
35 7 0.14
36 42 0.86
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (35 bp):
CATTACTTATTCTCCATTTTTTAGAGAAACACTCA
Found at i:4241964 original size:17 final size:17
Alignment explanation
Indices: 4241942--4241975 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4241932 TTTAAAGTTA
*
4241942 TTAAAATTGAGGATAAG
1 TTAAAACTGAGGATAAG
*
4241959 TTAAAACTGATGATAAG
1 TTAAAACTGAGGATAAG
4241976 ACTATTTCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.21, T:0.29
Consensus pattern (17 bp):
TTAAAACTGAGGATAAG
Found at i:4247205 original size:17 final size:18
Alignment explanation
Indices: 4247173--4247211 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
4247163 TCTAGTACAT
4247173 GAAAATATTAAAGAAAAA
1 GAAAATATTAAAGAAAAA
*
4247191 GAAAATA-TCAAGAAAAA
1 GAAAATATTAAAGAAAAA
4247208 -AAAA
1 GAAAA
4247212 GAAAGAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 9 0.45
18 7 0.35
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (18 bp):
GAAAATATTAAAGAAAAA
Found at i:4248976 original size:24 final size:24
Alignment explanation
Indices: 4248949--4248997 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
4248939 ATAGCCAGGC
4248949 ATCGCATCAAAATTTGTTTACATA
1 ATCGCATCAAAATTTGTTTACATA
4248973 ATCGCATCAAAATTTGTTTACATA
1 ATCGCATCAAAATTTGTTTACATA
4248997 A
1 A
4248998 ATATCAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (24 bp):
ATCGCATCAAAATTTGTTTACATA
Found at i:4257637 original size:19 final size:19
Alignment explanation
Indices: 4257613--4257655 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
4257603 TGAGTTCTAG
4257613 GTAATACCCTTTAAACTCA
1 GTAATACCCTTTAAACTCA
4257632 GTAATACCCTTTAAACTCA
1 GTAATACCCTTTAAACTCA
*
4257651 CTAAT
1 GTAAT
4257656 GCACCTACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.33
Consensus pattern (19 bp):
GTAATACCCTTTAAACTCA
Found at i:4259062 original size:4 final size:4
Alignment explanation
Indices: 4259053--4259219 Score: 85
Period size: 4 Copynumber: 40.8 Consensus size: 4
4259043 TATATTTGTA
* *
4259053 TATT TATT TATT TATT TATT TATA TATCT TATG TATT TA-T TATT TATT
1 TATT TATT TATT TATT TATT TATT TAT-T TATT TATT TATT TATT TATT
* * *
4259101 TATT TA-T TATT ACTATT TATT AATATA TATT TTTT TA-T TATT TATC
1 TATT TATT TATT --TATT TATT --TATT TATT TATT TATT TATT TATT
* * * * * * *
4259147 TGTT AATATA TATG TACT TA-T TA-T TATT TATC TATT TATA TATT ATAATC
1 TATT --TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT -T-ATT
*
4259197 TATT TA-T TATT ATTTT TATT TAT
1 TATT TATT TATT -TATT TATT TAT
4259220 CTGTTTATAT
Statistics
Matches: 124, Mismatches: 24, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
3 18 0.15
4 87 0.70
5 8 0.06
6 11 0.09
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (4 bp):
TATT
Found at i:4259096 original size:32 final size:32
Alignment explanation
Indices: 4259036--4259145 Score: 106
Period size: 31 Copynumber: 3.5 Consensus size: 32
4259026 TTTTAAAATT
*
4259036 TTTATTT-TATATTTGTATATTTATTTATTTA
1 TTTATTTATATATTTATATATTTATTTATTTA
*
4259067 TTTATTTATATATCTTATGTATTTA-TTATTTA
1 TTTATTTATATAT-TTATATATTTATTTATTTA
* *
4259099 TTTATTTAT-TA-TTA-CTATTTATTAATATATA
1 TTTATTTATATATTTATATATTTATT--TATTTA
*
4259130 TTTTTTTAT-TATTTAT
1 TTTATTTATATATTTAT
4259146 CTGTTAATAT
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
28 6 0.09
29 4 0.06
31 24 0.36
32 24 0.36
33 9 0.13
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (32 bp):
TTTATTTATATATTTATATATTTATTTATTTA
Found at i:4259176 original size:32 final size:29
Alignment explanation
Indices: 4259103--4259189 Score: 95
Period size: 32 Copynumber: 2.9 Consensus size: 29
4259093 TATTTATTTA
* *
4259103 TTTATTATTA-CTATTTATTAATATATAT
1 TTTATTATTATTTATCTATTAATATATAT
* *
4259131 TTTTTTATTATTTATCTGTTAATATATAT
1 TTTATTATTATTTATCTATTAATATATAT
*
4259160 GTACTTATTATTATTTATCTATTTATATAT
1 -T--TTATTATTATTTATCTATTAATATAT
4259190 TATAATCTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 9 0.19
29 15 0.31
30 1 0.02
32 23 0.48
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTATTATTATTTATCTATTAATATATAT
Found at i:4260281 original size:71 final size:72
Alignment explanation
Indices: 4260198--4260343 Score: 231
Period size: 71 Copynumber: 2.0 Consensus size: 72
4260188 AAATATTTTT
*
4260198 AAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT-AAAAAATATTTTTGAGGAA
1 AAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCTAAAAAAATATTTTTAAGGAA
*
4260262 AGGTTGA
66 AAGTTGA
* * *
4260269 AAGGAAATGTTGAAAGTATCAATTTTCCTTTAAAATAAGTTTTCTAAAAAAATATTTTTAAGGAA
1 AAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCTAAAAAAATATTTTTAAGGAA
*
4260334 AATTTGA
66 AAGTTGA
4260341 AAG
1 AAG
4260344 TATCGATTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
71 42 0.62
72 26 0.38
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (72 bp):
AAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCTAAAAAAATATTTTTAAGGAA
AAGTTGA
Found at i:4260435 original size:58 final size:58
Alignment explanation
Indices: 4260271--4260529 Score: 317
Period size: 59 Copynumber: 4.4 Consensus size: 58
4260261 AAGGTTGAAA
* * * *
4260271 GGAAATGTTGAAAGTATCAATTTTCCTTTAAAATAAGTTTTCTAAAAAAATATTTTTAA
1 GGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTAAAAAAATATTTTT-G
* * * *
4260330 GGAAAATTTGAAAGTATCGATTTTTTTTGAAAATAAGCTTTCTAAAAAAATATTTTTG
1 GGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTAAAAAAATATTTTTG
* ***
4260388 GGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGTTTTC-AAAAATGGATTTTTG
1 GG-AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTAAAAAAATATTTTTG
* *
4260446 AGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTT-T-AAAAAATATTTTTG
1 -GGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT-AAGTTTTCTAAAAAAATATTTTTG
* *
4260504 GAAAAAATTGAAAGTATCAATTTTTC
1 GGAAAAGTTGAAAGTATCAATTTTTC
4260530 CTATACAAAA
Statistics
Matches: 172, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
57 24 0.14
58 54 0.31
59 94 0.55
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (58 bp):
GGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTCTAAAAAAATATTTTTG
Found at i:4270962 original size:8 final size:8
Alignment explanation
Indices: 4270949--4270987 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 8
4270939 AATGAAACGT
4270949 AAAAAATGA
1 AAAAAAT-A
4270958 AAAAAATGA
1 AAAAAAT-A
4270967 AAAAAAT-
1 AAAAAATA
4270974 AAAAAATA
1 AAAAAATA
4270982 AAAAAA
1 AAAAAA
4270988 AAACAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.24
8 6 0.21
9 16 0.55
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:4270977 original size:15 final size:15
Alignment explanation
Indices: 4270957--4271003 Score: 62
Period size: 14 Copynumber: 3.2 Consensus size: 15
4270947 GTAAAAAATG
4270957 AAAAAAATGAAAAAA
1 AAAAAAATGAAAAAA
4270972 ATAAAAAAT-AAAAAA
1 A-AAAAAATGAAAAAA
*
4270987 AAAACAA-GAAAAAA
1 AAAAAAATGAAAAAA
4271001 AAA
1 AAA
4271004 GTGAATGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 14 0.48
15 8 0.28
16 7 0.24
ACGTcount: A:0.87, C:0.02, G:0.04, T:0.06
Consensus pattern (15 bp):
AAAAAAATGAAAAAA
Found at i:4270977 original size:23 final size:23
Alignment explanation
Indices: 4270932--4271000 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 23
4270922 ATACTATGCT
**
4270932 TGAAAAAAATGAAACGTAAAAAA
1 TGAAAAAAATGAAACAAAAAAAA
*
4270955 TGAAAAAAATGAAAAAAATAAAAAA
1 TGAAAAAAATG-AAACAA-AAAAAA
4270980 T-AAAAAAA--AAACAAGAAAAAA
1 TGAAAAAAATGAAACAA-AAAAAA
4271001 AAAGTGAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 11 0.28
23 11 0.28
24 10 0.26
25 7 0.18
ACGTcount: A:0.78, C:0.03, G:0.09, T:0.10
Consensus pattern (23 bp):
TGAAAAAAATGAAACAAAAAAAA
Found at i:4270988 original size:9 final size:9
Alignment explanation
Indices: 4270949--4271000 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
4270939 AATGAAACGT
*
4270949 AAAAAATGA
1 AAAAAATAA
*
4270958 AAAAAATGA
1 AAAAAATAA
4270967 AAAAAATAA
1 AAAAAATAA
4270976 AAAATAA-AA
1 AAAA-AATAA
*
4270985 AAAAAACAA
1 AAAAAATAA
4270994 GAAAAAA
1 -AAAAAA
4271001 AAAGTGAATG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
8 2 0.05
9 29 0.74
10 8 0.21
ACGTcount: A:0.85, C:0.02, G:0.06, T:0.08
Consensus pattern (9 bp):
AAAAAATAA
Found at i:4270988 original size:16 final size:16
Alignment explanation
Indices: 4270958--4270988 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4270948 TAAAAAATGA
*
4270958 AAAAAATGAAAAAAAT
1 AAAAAATAAAAAAAAT
4270974 AAAAAATAAAAAAAA
1 AAAAAATAAAAAAAA
4270989 AACAAGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:4272050 original size:43 final size:43
Alignment explanation
Indices: 4272002--4272290 Score: 358
Period size: 42 Copynumber: 6.8 Consensus size: 43
4271992 GGGTGATATG
* *
4272002 TTTTTCAAAGTCGGTGAGCCTCTGTTTAGAGGAGCTTTATTTA
1 TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTA
*
4272045 TTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTATTTA
1 TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTA
* * *
4272088 TTTTTCAAAGTCGTAGAGCCTCTGATTAGATGAGC--AATTTA
1 TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTA
* ** * * *
4272129 CTTCCCAAAAGTCGTTGAGCCTCTAATTAGAGGAAC--CATTTA
1 TTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTA
*
4272171 -TTTTCAAACTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTA
1 TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTA
* *
4272213 -TTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTTTGTTTA
1 TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTA
4272255 TGTTTTTCAAAGTCGTTGAGCCTCT-ACTTAGAGGAG
1 --TTTTTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAG
4272291 TTTTGATCAA
Statistics
Matches: 214, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
40 26 0.12
41 11 0.05
42 74 0.35
43 72 0.34
44 1 0.00
45 30 0.14
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (43 bp):
TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTA
Found at i:4272222 original size:82 final size:85
Alignment explanation
Indices: 4272002--4272290 Score: 329
Period size: 82 Copynumber: 3.4 Consensus size: 85
4271992 GGGTGATATG
* * * *
4272002 TTTTTCAAAGTCGGTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTTGTTGAGCCTC
1 TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTACTTTTCAAAGTCGTTGAGCCTC
* *
4272067 TGATTAGAGGAGCTTTATTTA
66 TGATTAGAGGAAC-TCATTTA
* * * **
4272088 TTTTTCAAAGTCGTAGAGCCTCTGATTAGATGAGC--AATTTACTTCCCAAAAGTCGTTGAGCCT
1 TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTACTTTTC-AAAGTCGTTGAGCCT
*
4272151 CTAATTAGAGGAAC-CATTTA
65 CTGATTAGAGGAACTCATTTA
* *
4272171 -TTTTCAAACTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTA-TTTTCAAAGTCATTGAGCCTC
1 TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTACTTTTCAAAGTCGTTGAGCCTC
* **
4272234 TGATTAGAGGAGCTTTGTTTA
66 TGATTAGAGGAAC-TCATTTA
4272255 TGTTTTTCAAAGTCGTTGAGCCTCT-ACTTAGAGGAG
1 --TTTTTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAG
4272291 TTTTGATCAA
Statistics
Matches: 170, Mismatches: 24, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
82 57 0.34
83 8 0.05
84 17 0.10
85 26 0.15
86 32 0.19
87 30 0.18
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (85 bp):
TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTATTTACTTTTCAAAGTCGTTGAGCCTC
TGATTAGAGGAACTCATTTA
Done.