Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 178 of 189
Found at i:52925320 original size:13 final size:14
Alignment explanation
Indices: 52925287--52925324 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
52925277 TGAAACAGGG
52925287 GAGAAAGAAAGAAA
1 GAGAAAGAAAGAAA
*
52925301 GAAAAAGAAA-AAA
1 GAGAAAGAAAGAAA
52925314 GAGAAAGAAAG
1 GAGAAAGAAAG
52925325 GAAAAACTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
GAGAAAGAAAGAAA
Found at i:52929480 original size:6 final size:6
Alignment explanation
Indices: 52929432--52929480 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
52929422 TTCTAAAATC
* * *
52929432 AATTAAT AATTAC AATTAC AATTAC AATTAT AATTAT AATTAT AATTAT
1 AATT-AT AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT
52929481 TTTATTGGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
6 36 0.90
7 4 0.10
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (6 bp):
AATTAT
Found at i:52929480 original size:12 final size:12
Alignment explanation
Indices: 52929431--52929479 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
52929421 TTTCTAAAAT
52929431 CAATTAATAATTA
1 CAATT-ATAATTA
*
52929444 CAATTACAATTA
1 CAATTATAATTA
52929456 CAATTATAATTA
1 CAATTATAATTA
*
52929468 TAATTATAATTA
1 CAATTATAATTA
52929480 TTTTATTGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
12 28 0.85
13 5 0.15
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (12 bp):
CAATTATAATTA
Found at i:52932784 original size:105 final size:104
Alignment explanation
Indices: 52932610--52932803 Score: 255
Period size: 105 Copynumber: 1.9 Consensus size: 104
52932600 GTGTCTAAGC
* * * * *
52932610 CGTGTAACTCACTGTTTATGACTTAGGACCGCATAGCCAGGGACATGGGTGTGTGCCCAGGTCGT
1 CGTGTAACTCACTGTTTATGACTTAGAACCACACAGCCAGGGACATAGGTGTGTGCCCAGCTCGT
* *
52932675 GTGAGTCATACGGGCAAAGACATGTGCGTTTGTCTAGAT
66 GTGAGCCACACGGGCAAAGACATGTGCGTTTGTCTAGAT
** * *
52932714 CGTGTAACTCACTGTTTATGTTTTAGAACCACACGGGCAGAGGACATAGGTGTGTGCCCAAGCT-
1 CGTGTAACTCACTGTTTATGACTTAGAACCACACAGCCAG-GGACATAGGTGTGTGCCC-AGCTC
*
52932778 GTGTGAGCCACACGGGCAAGGACATG
64 GTGTGAGCCACACGGGCAAAGACATG
52932804 GGCCTGTGCC
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
104 33 0.43
105 40 0.53
106 3 0.04
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (104 bp):
CGTGTAACTCACTGTTTATGACTTAGAACCACACAGCCAGGGACATAGGTGTGTGCCCAGCTCGT
GTGAGCCACACGGGCAAAGACATGTGCGTTTGTCTAGAT
Found at i:52932812 original size:42 final size:42
Alignment explanation
Indices: 52932742--52932848 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
52932732 TGTTTTAGAA
* ** *
52932742 CCACACGGGCAGAGGACATAGGTGTGTGCCCAAGCTGTGTGAG
1 CCACACGGGCA-AGGACATGGGCCTGTGCCCAAGCCGTGTGAG
*
52932785 CCACACGGGCAAGGACATGGGCCTGTGCCCAGGCCGTGTGAG
1 CCACACGGGCAAGGACATGGGCCTGTGCCCAAGCCGTGTGAG
* *
52932827 CCACATGGACAAGGACATGGGC
1 CCACACGGGCAAGGACATGGGC
52932849 GTATGTCCAG
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
42 46 0.81
43 11 0.19
ACGTcount: A:0.23, C:0.27, G:0.36, T:0.13
Consensus pattern (42 bp):
CCACACGGGCAAGGACATGGGCCTGTGCCCAAGCCGTGTGAG
Found at i:52932823 original size:105 final size:104
Alignment explanation
Indices: 52932608--52932823 Score: 236
Period size: 105 Copynumber: 2.1 Consensus size: 104
52932598 GTGTGTCTAA
* * * * *
52932608 GCCGTGTAACTCACTGTTTATGACTTAGGACCGCATAGCCAGGGACATGGGTGTGTGCCCAGGTC
1 GCCGTGTAACTCACTGTTTATGACTTAGAACCACACAGCCAGGGACATAGGTGTGTGCCCAGCTC
* * * * * * *
52932673 GTGTGAGTCATACGGGCAAAGACATGTGCGTTTGTCTAG
66 GTGTGAGCCACACGGGCAAAGACATGGGCCTGTGCCCAG
** ** * *
52932712 ATCGTGTAACTCACTGTTTATGTTTTAGAACCACACGGGCAGAGGACATAGGTGTGTGCCCAAGC
1 GCCGTGTAACTCACTGTTTATGACTTAGAACCACACAGCCAG-GGACATAGGTGTGTGCCC-AGC
*
52932777 T-GTGTGAGCCACACGGGCAAGGACATGGGCCTGTGCCCAG
64 TCGTGTGAGCCACACGGGCAAAGACATGGGCCTGTGCCCAG
52932817 GCCGTGT
1 GCCGTGT
52932824 GAGCCACATG
Statistics
Matches: 89, Mismatches: 21, Indels: 3
0.79 0.19 0.03
Matches are distributed among these distances:
104 33 0.37
105 53 0.60
106 3 0.03
ACGTcount: A:0.22, C:0.23, G:0.31, T:0.24
Consensus pattern (104 bp):
GCCGTGTAACTCACTGTTTATGACTTAGAACCACACAGCCAGGGACATAGGTGTGTGCCCAGCTC
GTGTGAGCCACACGGGCAAAGACATGGGCCTGTGCCCAG
Found at i:52932859 original size:42 final size:42
Alignment explanation
Indices: 52932768--52932865 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 42
52932758 CATAGGTGTG
* * * *
52932768 TGCCCAAGCTGTGTGAGCCACACGGGCAAGGACATGGGCCTG
1 TGCCCAGGCCGTGTGAGCCACACGGACAAGGACATGGGCCTA
* *
52932810 TGCCCAGGCCGTGTGAGCCACATGGACAAGGACATGGGCGTA
1 TGCCCAGGCCGTGTGAGCCACACGGACAAGGACATGGGCCTA
*
52932852 TGTCCAGGCC-TGTG
1 TGCCCAGGCCGTGTG
52932866 GCTATGAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 4 0.08
42 45 0.92
ACGTcount: A:0.20, C:0.28, G:0.36, T:0.16
Consensus pattern (42 bp):
TGCCCAGGCCGTGTGAGCCACACGGACAAGGACATGGGCCTA
Found at i:52940819 original size:36 final size:36
Alignment explanation
Indices: 52940778--52940963 Score: 255
Period size: 36 Copynumber: 4.9 Consensus size: 36
52940768 CTTTGGCTAC
52940778 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
* * *
52940814 ACTTATCTGATCAAGAGACAAAGCGATAAGTGGTAGCTTTAGCT
1 ACTTATCTGATCAAGTGAAAAAGTGATAA---GT-G--TTA--T
52940858 ACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
1 --ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
52940896 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
52940932 ACTTATCTGATCAAGTGAAAAAGTGATAAGTG
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTG
52940964 GTAGCTTAGC
Statistics
Matches: 134, Mismatches: 6, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
36 94 0.70
38 1 0.01
39 2 0.01
40 4 0.03
42 4 0.03
43 2 0.01
44 1 0.01
46 26 0.19
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (36 bp):
ACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTAT
Found at i:52940842 original size:82 final size:82
Alignment explanation
Indices: 52940737--52940963 Score: 339
Period size: 82 Copynumber: 2.9 Consensus size: 82
52940727 TTTGAGTACT
* *
52940737 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTGGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
52940802 GATAAGTGTTATACTTA
66 GATAAGTGTTATACTTA
* *
52940819 TCTGATCAAGAGACAAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
52940884 GATAAGTGTTATACTTA
66 GATAAGTGTTATACTTA
*
52940901 TCTGATCAAGTGAAAAAGTGATAA---GT-G--TTA--T--ACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
52940956 GATAAGTG
66 GATAAGTG
52940964 GTAGCTTAGC
Statistics
Matches: 139, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
72 32 0.23
74 1 0.01
76 3 0.02
78 1 0.01
79 2 0.01
82 100 0.72
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (82 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGTTATACTTA
Found at i:52940911 original size:21 final size:20
Alignment explanation
Indices: 52940883--52940948 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
52940873 AGTGAAAAAG
52940883 TGATAAGTGTTATACTTATC
1 TGATAAGTGTTATACTTATC
* **
52940903 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGTTATACTTATC
52940919 TGATAAGTGTTATACTTATC
1 TGATAAGTGTTATACTTATC
52940939 TGATCAAGTG
1 TGAT-AAGTG
52940949 AAAAAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (20 bp):
TGATAAGTGTTATACTTATC
Found at i:52948916 original size:11 final size:11
Alignment explanation
Indices: 52948900--52948939 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
52948890 CCATAAAATA
52948900 TTTTTTATTTT
1 TTTTTTATTTT
52948911 TTTTTTATTTT
1 TTTTTTATTTT
**
52948922 TTTCGTATTTT
1 TTTTTTATTTT
52948933 GTTTTTT
1 -TTTTTT
52948940 TGTACTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.07, C:0.03, G:0.05, T:0.85
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:52950071 original size:20 final size:20
Alignment explanation
Indices: 52950031--52950072 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
52950021 TAATTCATCA
* *
52950031 TTACTCCAGAATTTATCGTC
1 TTACTCCAGAAATCATCGTC
*
52950051 TTACTCCAGAAATCATTGTC
1 TTACTCCAGAAATCATCGTC
52950071 TT
1 TT
52950073 GAAACTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (20 bp):
TTACTCCAGAAATCATCGTC
Found at i:52954265 original size:30 final size:30
Alignment explanation
Indices: 52954220--52954375 Score: 172
Period size: 30 Copynumber: 5.2 Consensus size: 30
52954210 ATTATTTTTG
* * * *
52954220 CATTTTGACCCCTAAACTTTTTTAAAATTT
1 CATTTTCACCCCTAAACTTTCTCAAAATTA
*
52954250 CATTTTCACCACTAAACTTTCTCAAAATTA
1 CATTTTCACCCCTAAACTTTCTCAAAATTA
* *
52954280 CA-ATTCAACCCCTAAACTTT-TTAAAATTA
1 CATTTTC-ACCCCTAAACTTTCTCAAAATTA
* * * *
52954309 CATTTTGATCTCTAAACTTTCTAAAAATTA
1 CATTTTCACCCCTAAACTTTCTCAAAATTA
*
52954339 CATTTTAACCCCTAAACTTTCTCAAAATTA
1 CATTTTCACCCCTAAACTTTCTCAAAATTA
52954369 CACTTTT
1 CA-TTTT
52954376 GCCATAAAAT
Statistics
Matches: 105, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
29 24 0.23
30 77 0.73
31 4 0.04
ACGTcount: A:0.35, C:0.23, G:0.01, T:0.40
Consensus pattern (30 bp):
CATTTTCACCCCTAAACTTTCTCAAAATTA
Found at i:52954306 original size:59 final size:59
Alignment explanation
Indices: 52954227--52954375 Score: 199
Period size: 59 Copynumber: 2.5 Consensus size: 59
52954217 TTGCATTTTG
* *
52954227 ACCCCTAAACTTTTTTAAAATTTCATTTTCACCACTAAACTTTCTCAAAATTACAATTCA
1 ACCCCTAAAC-TTTTTAAAATTACATTTTCACCACTAAACTTTCTAAAAATTACAATTCA
* * * * *
52954287 ACCCCTAAACTTTTTAAAATTACATTTTGATCTCTAAACTTTCTAAAAATTACATTTTA
1 ACCCCTAAACTTTTTAAAATTACATTTTCACCACTAAACTTTCTAAAAATTACAATTCA
*
52954346 ACCCCTAAACTTTCTCAAAATTACACTTTT
1 ACCCCTAAACTTT-TTAAAATTACA-TTTT
52954376 GCCATAAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
59 55 0.70
60 20 0.25
61 4 0.05
ACGTcount: A:0.36, C:0.23, G:0.01, T:0.40
Consensus pattern (59 bp):
ACCCCTAAACTTTTTAAAATTACATTTTCACCACTAAACTTTCTAAAAATTACAATTCA
Found at i:52954620 original size:30 final size:31
Alignment explanation
Indices: 52954553--52954623 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
52954543 GAAGGGAGTA
*
52954553 AGCAATAAAAAAAAGAAAAAAAAACAAATTTTG
1 AGCAA-AAAAAAAAGAAAAAAAAACAAA-TTAG
*
52954586 AGCAAAAAAAAAAGAAAGAAAAA-AAA-TAG
1 AGCAAAAAAAAAAGAAAAAAAAACAAATTAG
52954615 CAGCAAAAA
1 -AGCAAAAA
52954624 CACTAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 2 0.06
30 8 0.23
31 3 0.09
32 17 0.49
33 5 0.14
ACGTcount: A:0.73, C:0.07, G:0.11, T:0.08
Consensus pattern (31 bp):
AGCAAAAAAAAAAGAAAAAAAAACAAATTAG
Found at i:52954890 original size:6 final size:7
Alignment explanation
Indices: 52954870--52954916 Score: 58
Period size: 7 Copynumber: 6.3 Consensus size: 7
52954860 TTGAACGAAG
52954870 AAGAAAA
1 AAGAAAA
52954877 AAGAAAA
1 AAGAAAA
52954884 AAGAAAA
1 AAGAAAA
*
52954891 AAGAGGAAG
1 AAGA--AAA
52954900 AAGAAAGA
1 AAGAAA-A
52954908 AAGAAAA
1 AAGAAAA
52954915 AA
1 AA
52954917 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 23 0.66
8 6 0.17
9 6 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:52955213 original size:25 final size:25
Alignment explanation
Indices: 52955154--52955212 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
52955144 CCAGCCCAGC
*
52955154 AGAGAGAAAACAAAAAGAAAAAAAG
1 AGAGAAAAAACAAAAAGAAAAAAAG
*
52955179 AGAGAAAAAAGAAAAAGAAAAAAAG
1 AGAGAAAAAACAAAAAGAAAAAAAG
52955204 AG-GAAAAAA
1 AGAGAAAAAA
52955213 AATAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 7 0.22
25 25 0.78
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (25 bp):
AGAGAAAAAACAAAAAGAAAAAAAG
Found at i:52955219 original size:25 final size:25
Alignment explanation
Indices: 52955154--52955229 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 25
52955144 CCAGCCCAGC
* *
52955154 AGAGAGAAAACAAAAAGAAAAAAAG
1 AGAGAAAAAAAAAAAAGAAAAAAAG
*
52955179 AGAGAAAAAAGAAAAAGAAAAAAAG
1 AGAGAAAAAAAAAAAAGAAAAAAAG
*
52955204 AG-GAAAAAAAATAAAAAATAAAAAAG
1 AGAGAAAAAAAA-AAAAGA-AAAAAAG
52955230 GAGTTCAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
24 8 0.18
25 30 0.67
26 7 0.16
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (25 bp):
AGAGAAAAAAAAAAAAGAAAAAAAG
Found at i:52955231 original size:24 final size:25
Alignment explanation
Indices: 52955160--52955231 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 25
52955150 CAGCAGAGAG
* *
52955160 AAAACAAAAAG-AAAAAAAGAGAGAA
1 AAAAGAAAAAGAAAAAAAAG-GAAAA
52955185 AAAAGAAAAAGAAAAAAAGAGGAAAA
1 AAAAGAAAAAGAAAAAAA-AGGAAAA
* *
52955211 AAAATAAAAA-ATAAAAAAGGA
1 AAAAGAAAAAGAAAAAAAAGGA
52955232 GTTCAATTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 4 0.10
25 16 0.39
26 19 0.46
27 2 0.05
ACGTcount: A:0.81, C:0.01, G:0.15, T:0.03
Consensus pattern (25 bp):
AAAAGAAAAAGAAAAAAAAGGAAAA
Found at i:52955399 original size:16 final size:16
Alignment explanation
Indices: 52955378--52955415 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
52955368 GCATTTATAT
52955378 TTTTAATTTAATTTAA
1 TTTTAATTTAATTTAA
* *
52955394 TTTTAATTTTATTTTA
1 TTTTAATTTAATTTAA
52955410 TTTTAA
1 TTTTAA
52955416 ATACTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTAATTTAATTTAA
Found at i:52955599 original size:19 final size:18
Alignment explanation
Indices: 52955575--52955636 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
52955565 TATATTTTTT
52955575 AAAATTTTTCGTGTCTTCA
1 AAAATTTTTCGTGT-TTCA
52955594 AAAATTTTTCTCGTGTTTCA
1 AAAA-TTTT-TCGTGTTTCA
* * *
52955614 AAAAATATTCGCGTTTTCA
1 AAAATTTTTCGTG-TTTCA
52955633 AAAA
1 AAAA
52955637 AATAAGGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.11
19 15 0.41
20 12 0.32
21 6 0.16
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (18 bp):
AAAATTTTTCGTGTTTCA
Found at i:52955613 original size:20 final size:19
Alignment explanation
Indices: 52955575--52955636 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
52955565 TATATTTTTT
52955575 AAAATTTT-TCGTGTCTTCA
1 AAAATTTTCTCGTGT-TTCA
52955594 AAAATTTTTCTCGTGTTTCAA
1 AAAA-TTTTCTCGTGTTTC-A
* *
52955615 AAAATATTCGCGT-TTTCA
1 AAAATTTTCTCGTGTTTCA
52955633 AAAA
1 AAAA
52955637 AATAAGGCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.13
19 8 0.21
20 14 0.37
21 11 0.29
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (19 bp):
AAAATTTTCTCGTGTTTCA
Found at i:52955881 original size:18 final size:18
Alignment explanation
Indices: 52955860--52956185 Score: 228
Period size: 18 Copynumber: 18.4 Consensus size: 18
52955850 AAAAATCTAT
* *
52955860 TTTTCAAAAGTTTTCATG
1 TTTTCAAAAATTTTCGTG
**
52955878 TTTTCAAAAAATTCCCGTG
1 TTTTC-AAAAATTTTCGTG
* **
52955897 TTTT-AAAAATTTCCACG
1 TTTTCAAAAATTTTCGTG
*
52955914 TTTTCAAAAATCTTTTGTG
1 TTTTCAAAAAT-TTTCGTG
**
52955933 TTTTCAAAAATCCTCGTG
1 TTTTCAAAAATTTTCGTG
52955951 TTTTCAAAAATTTT-GATG
1 TTTTCAAAAATTTTCG-TG
*
52955969 -TTTCAAAAATTTCCGTG
1 TTTTCAAAAATTTTCGTG
52955986 TTTT-AAAAA-TTTCTGTG
1 TTTTCAAAAATTTTC-GTG
*
52956003 TTTTCAAAAATTTTCGTA
1 TTTTCAAAAATTTTCGTG
** *
52956021 TTTAAAAAAAAATTT-GTG
1 TTT-TCAAAAATTTTCGTG
* * **
52956039 CTGT-AAAAATCCTCGTG
1 TTTTCAAAAATTTTCGTG
*
52956056 TTTTCAAAAA-TTCCGATG
1 TTTTCAAAAATTTTCG-TG
*
52956074 -TTTCAAAAATTTTCATG
1 TTTTCAAAAATTTTCGTG
* *
52956091 TTTTCAAAAA-TTCCAGAG
1 TTTTCAAAAATTTTC-GTG
* *
52956109 --ATCCAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
52956125 TTTTCTAAAAATTTCCGTG
1 TTTTC-AAAAATTTTCGTG
*
52956144 -TTTCAAAAATTTTCGTT
1 TTTTCAAAAATTTTCGTG
* *
52956161 TTTTCACAAATTTCCGTG
1 TTTTCAAAAATTTTCGTG
52956179 TTTTCAA
1 TTTTCAA
52956186 CGACTCTAGT
Statistics
Matches: 235, Mismatches: 52, Indels: 42
0.71 0.16 0.13
Matches are distributed among these distances:
16 17 0.07
17 76 0.32
18 92 0.39
19 50 0.21
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (18 bp):
TTTTCAAAAATTTTCGTG
Found at i:52955973 original size:35 final size:35
Alignment explanation
Indices: 52955860--52956185 Score: 177
Period size: 35 Copynumber: 9.2 Consensus size: 35
52955850 AAAAATCTAT
* * * **
52955860 TTTTCAAAAGTTTTCATGTTTTCAAAAAATTCCCGTG
1 TTTTCAAAAATCTTCGTGTTTTC-AAAAATT-TTGTG
**
52955897 TTTT-AAAAAT-TTCCACGTTTTCAAAAATCTTTTGTG
1 TTTTCAAAAATCTT-CGTGTTTTCAAAAA--TTTTGTG
*
52955933 TTTTCAAAAATCCTCGTGTTTTCAAAAATTTTGATG
1 TTTTCAAAAATCTTCGTGTTTTCAAAAATTTTG-TG
52955969 -TTTCAAAAAT-TTCCGTGTTTT-AAAAATTTCTGTG
1 TTTTCAAAAATCTT-CGTGTTTTCAAAAATTT-TGTG
* * ** *
52956003 TTTTCAAAAATTTTCGTATTTAAAAAAAAATTTGTG
1 TTTTCAAAAATCTTCGTGTTT-TCAAAAATTTTGTG
* * * **
52956039 CTGT-AAAAATCCTCGTGTTTTCAAAAATTCCGATG
1 TTTTCAAAAATCTTCGTGTTTTCAAAAATTTTG-TG
* * ** *
52956074 -TTTCAAAAATTTTCATGTTTTCAAAAATTCCAGAG
1 TTTTCAAAAATCTTCGTGTTTTCAAAAATT-TTGTG
* * * *
52956109 --ATCCAAAATTTTCGTGTTTTCTAAAAATTTCCGTG
1 TTTTCAAAAATCTTCGTGTTTTC-AAAAATTT-TGTG
* * * *
52956144 -TTTCAAAAATTTTCGTTTTTTCACAAATTTCCGTG
1 TTTTCAAAAATCTTCGTGTTTTCAAAAATTT-TGTG
52956179 TTTTCAA
1 TTTTCAA
52956186 CGACTCTAGT
Statistics
Matches: 233, Mismatches: 37, Indels: 39
0.75 0.12 0.13
Matches are distributed among these distances:
34 38 0.16
35 107 0.46
36 56 0.24
37 31 0.13
38 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (35 bp):
TTTTCAAAAATCTTCGTGTTTTCAAAAATTTTGTG
Found at i:52956077 original size:17 final size:17
Alignment explanation
Indices: 52956057--52956154 Score: 69
Period size: 17 Copynumber: 5.6 Consensus size: 17
52956047 ATCCTCGTGT
52956057 TTTCAAAAATTCCGATG
1 TTTCAAAAATTCCGATG
*
52956074 TTTCAAAAATTTTC-ATG
1 TTTCAAAAA-TTCCGATG
52956091 TTTTCAAAAATTCCAGA-G
1 -TTTCAAAAATTCC-GATG
* * * *
52956109 ATCCAAAATTTTCG-TG
1 TTTCAAAAATTCCGATG
52956125 TTTTCTAAAAATTTCCG-TG
1 -TTTC-AAAAA-TTCCGATG
52956144 TTTCAAAAATT
1 TTTCAAAAATT
52956155 TTCGTTTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
16 4 0.06
17 31 0.49
18 21 0.33
19 7 0.11
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (17 bp):
TTTCAAAAATTCCGATG
Found at i:52956258 original size:18 final size:18
Alignment explanation
Indices: 52956232--52956293 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
52956222 TTAATTTGTA
*
52956232 TTTCGAAAAATTCTCGTG
1 TTTCAAAAAATTCTCGTG
* *
52956250 TTTC-AAAAATTGTCATG
1 TTTCAAAAAATTCTCGTG
** *
52956267 TTAAAAAAAATTTTCGTG
1 TTTCAAAAAATTCTCGTG
52956285 TTTCAAAAA
1 TTTCAAAAA
52956294 TTTCGTTTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
17 13 0.37
18 22 0.63
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (18 bp):
TTTCAAAAAATTCTCGTG
Found at i:52956337 original size:32 final size:33
Alignment explanation
Indices: 52956274--52956338 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
52956264 ATGTTAAAAA
* *
52956274 AAATTTTCGTGTTTCAAAAATTTCGTTTTTTTT
1 AAATTTTCGTGCTTCAAAAATTTCGTGTTTTTT
52956307 AAATTTT-GTGCTTC-AAAATTCTCGTGTTTTTT
1 AAATTTTCGTGCTTCAAAAATT-TCGTGTTTTTT
52956339 TTAATTCTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 6 0.21
32 16 0.55
33 7 0.24
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (33 bp):
AAATTTTCGTGCTTCAAAAATTTCGTGTTTTTT
Found at i:52956337 original size:33 final size:33
Alignment explanation
Indices: 52956274--52956344 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
52956264 ATGTTAAAAA
*
52956274 AAATTTTCGTGTTTCAAAAATTTCGTTTTTTTT
1 AAATTTTCGTGCTTCAAAAATTTCGTTTTTTTT
52956307 AAATTTT-GTGCTTC-AAAATTCTCGTGTTTTTTT
1 AAATTTTCGTGCTTCAAAAATT-TCGT-TTTTTTT
*
52956340 TAATT
1 AAATT
52956345 CTCATATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 6 0.18
32 10 0.29
33 18 0.53
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.56
Consensus pattern (33 bp):
AAATTTTCGTGCTTCAAAAATTTCGTTTTTTTT
Found at i:52965355 original size:41 final size:41
Alignment explanation
Indices: 52965306--52965414 Score: 164
Period size: 41 Copynumber: 2.6 Consensus size: 41
52965296 GACTTTAAGT
* *
52965306 CTAGCAGGCTACGTGCCGGTGATTTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
*
52965347 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
* *
52965388 CTAGCAGGCTAAGTGCCGTTGAATCTG
1 CTAGCAGGCTACGTGCCGGTG-ATCTG
52965415 TTTAAATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
41 57 0.92
42 5 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
Found at i:52966665 original size:79 final size:76
Alignment explanation
Indices: 52966576--52967445 Score: 943
Period size: 79 Copynumber: 11.3 Consensus size: 76
52966566 TCAAGAAATA
** * *
52966576 TTTTTCAATTTCTGTTTTTTTAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAT
1 TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
52966641 GCCGAGGTATTTTT
66 GCCGAGGTA---TT
* *
52966655 TTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
1 TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
52966720 ATGCCGAGGTATT
66 --GCCGAGGTATT
*
52966733 TCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 T-TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--
52966798 CACGCCGAGGTATT
63 CACGCCGAGGTATT
*
52966812 TTTTT-AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACAC
1 TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* *
52966875 ATGTCAAGGTATT
66 --GCCGAGGTATT
* *
52966888 TCTTTTAAATTTTTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 T-TTTTCAATTTCTGTTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* *
52966953 TCATGCTGAGGTA--
62 TCACGCCGAGGTATT
* * **
52966966 TTTTTCAATTTTTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCCC
1 TTTTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
52967031 ACATGCCGAGGTA--
64 AC--GCCGAGGTATT
* * * *
52967044 CTTTTCAATTTCTGTTTTTTTTTTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGACTCGA
1 TTTTTCAATTTCTG-----TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
*
52967109 GTCACGTCGAGGTA--
61 GTCACGCCGAGGTATT
* * *
52967123 TTTTTCAATTTTTGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCG
1 TTTTTCAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--
*
52967188 CACGCTGAGGTA--
63 CACGCCGAGGTATT
* * *
52967200 -TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCGAGTCAC
1 TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
52967264 GTCGAGGTA--
66 GCCGAGGTATT
* * * *
52967273 TTTTTCAATTTCTATTTTTCCAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGAGTCAC
1 TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
52967338 GTCGAGGTA--
66 GCCGAGGTATT
* * *
52967347 TTTTTCAA-TTCTTGCTTTTCAAAAAAATCAACTCATATTGCTAGAGGTGAGTTG-GGCTCGGGT
1 TTTTTCAATTTC-TGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-
*
52967410 TGCACGCCGAGCTA--
62 T-CACGCCGAGGTATT
* *
52967424 -TTCTCGATTTCTGTTTTTCAAA
1 TTTTTCAATTTCTGTTTTTCAAA
52967446 TAAAAAATTT
Statistics
Matches: 696, Mismatches: 65, Indels: 65
0.84 0.08 0.08
Matches are distributed among these distances:
73 13 0.02
74 93 0.13
75 83 0.12
76 114 0.16
77 96 0.14
78 40 0.06
79 151 0.22
80 6 0.01
81 90 0.13
82 4 0.01
83 6 0.01
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (76 bp):
TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
GCCGAGGTATT
Found at i:52966868 original size:156 final size:151
Alignment explanation
Indices: 52966577--52967445 Score: 1020
Period size: 150 Copynumber: 5.6 Consensus size: 151
52966567 CAAGAAATAT
* ** * *
52966577 TTTTCAATTTCTGTTTTTTTAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCATG
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACG
*
52966642 CCGAGGTATTTTTTTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
66 CCGAGGTA-----TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
52966707 AGCCTCGGGACACATGCCGAGGTATTTC
126 AGCCTCGGGACACATGCCGAGGTA--TC
52966735 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--CA
*
52966800 CGCCGAGGTATTTTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
64 CGCCGAGGTA-TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* *
52966865 CCTC-GGACACATGTCAAGGTATTTC
128 CCTCGGGACACATGCCGAGGTA--TC
*
52966890 TTTTAAATTTTTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTAAATTTCTGTTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
* * * *
52966955 ATGCTGAGGTATTTTTCAATTTTTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
63 ACGCCGAGGTATTTTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTG
**
52967020 AGCCTCGGCCCACATGCCGAGGTA-C
126 AGCCTCGGGACACATGCCGAGGTATC
* * * *
52967045 TTTTCAATTTCTGTTTTTTTTTTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGACTCGAG
1 TTTTAAATTTCTG-----TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* * *
52967110 TCACGTCGAGGTATTTTTCAATTTTTGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTT
61 TCACGCCGAGGTATTTTTCAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTT
* * * * *
52967175 AAGCCTCGGGTCGCACGCTGAGGTA--
125 GAGCCTCGGGACACATGCCGAGGTATC
* *
52967200 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCGAGTCACG
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACG
* * * *
52967265 TCGAGGTATTTTTCAATTTCTATTTTTCCAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCT
66 CCGAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* * *
52967330 CGAGTCAC--GTCGAGGTAT-
131 CGGGACACATGCCGAGGTATC
* * * *
52967348 TTTTCAA-TTCTTGCTTTTCAAAAAAATCAACTCATATTGCTAGAGGTGAGTTG-GGCTCGGGTT
1 TTTTAAATTTC-TGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-T
* * *
52967411 GCACGCCGAGCTA-TTCTCGATTTCTGTTTTTCAAA
62 -CACGCCGAGGTATTTTTCAATTTCTGTTTTTCAAA
52967446 TAAAAAATTT
Statistics
Matches: 632, Mismatches: 60, Indels: 46
0.86 0.08 0.06
Matches are distributed among these distances:
147 10 0.02
148 13 0.02
149 46 0.07
150 123 0.19
151 10 0.02
155 78 0.12
156 119 0.19
157 104 0.16
158 112 0.18
160 17 0.03
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (151 bp):
TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACG
CCGAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
CGGGACACATGCCGAGGTATC
Found at i:52967089 original size:157 final size:151
Alignment explanation
Indices: 52966577--52967445 Score: 940
Period size: 156 Copynumber: 5.6 Consensus size: 151
52966567 CAAGAAATAT
*
52966577 TTTTCAATTTCTGTTTTTTT--AAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* * *
52966640 TGCCGAGGTATTTTTTTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
66 CGCTGAGGTA-----TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
52966705 TGAGCCTCGGGACACATGCCGAGGTA
126 TGAGCCTCGGGACACATGCCGAGGTA
*
52966731 TTTCTTTTAAATTTCTG--TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 ----TTTTCAATTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
* *
52966794 GTCACACGCCGAGGTATTTTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGA
62 GT--CACGCTGAGGTA-TTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGA
* *
52966859 GTTGAGCCTC-GGACACATGTCAAGGTA
124 GTTGAGCCTCGGGACACATGCCGAGGTA
* * ***
52966886 TTTCTTTTAAATTTTTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
1 ----TTTTCAATTTCTGTTTTT-TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
* * *
52966951 GGTCATGCTGAGGTATTTTTCAATTTTTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGA
61 GGTCACGCTGAGGTATTTTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGA
**
52967016 GTTGAGCCTCGGCCCACATGCCGAGGTA
124 GTTGAGCCTCGGGACACATGCCGAGGTA
* * *
52967044 CTTTTCAATTTCTGTTTTTTTTTTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGACTCGA
1 -TTTTCAATTTCTG---TTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
* *
52967109 GTCACG-TCGAGGTATTTTTCAATTTTTGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAG
62 GTCACGCT-GAGGTATTTTTCAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAG
* * * * *
52967173 TTAAGCCTCGGGTCGCACGCTGAGGTA
125 TTGAGCCTCGGGACACATGCCGAGGTA
* * *
52967200 TTTTAAATTTCTG--TTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCGAGTCA
1 TTTTCAATTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* * *
52967263 CG-TCGAGGTATTTTTCAATTTCTATTTTTCCAAAATCAACTCATATTGTGAGAGGTGAGTTGAG
66 CGCT-GAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* * *
52967327 CCTCGAGTCAC--GTCGAGGTA
130 CCTCGGGACACATGCCGAGGTA
** * *
52967347 TTTTTCAA-TTCT-TGCTTTTCAAAAAAATCAACTCATATTGCTAGAGGTGAGTTG-GGCTCGGG
1 -TTTTCAATTTCTGTTTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* * * *
52967409 TTGCACGCCGAGCTA-TTCTCGATTTCTGTTTTTCAAA
63 -T-CACGCTGAGGTATTTTTCAATTTCTGTTTTTCAAA
52967446 TAAAAAATTT
Statistics
Matches: 627, Mismatches: 62, Indels: 52
0.85 0.08 0.07
Matches are distributed among these distances:
147 11 0.02
148 11 0.02
149 46 0.07
150 123 0.20
151 9 0.01
155 72 0.11
156 125 0.20
157 107 0.17
158 112 0.18
160 11 0.02
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (151 bp):
TTTTCAATTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
CGCTGAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
CTCGGGACACATGCCGAGGTA
Found at i:52967645 original size:30 final size:30
Alignment explanation
Indices: 52967614--52967769 Score: 217
Period size: 30 Copynumber: 5.2 Consensus size: 30
52967604 TTATTTTTTG
* *
52967614 CATTTTGACCCCTAAACTTT-TCTAAAATTG
1 CATTTTAACCCCTAAACTTTCTC-AAAATTA
*
52967644 CATTTTAACCACTAAACTTTCTCAAAATTA
1 CATTTTAACCCCTAAACTTTCTCAAAATTA
* * *
52967674 CATTTCAACCCCTAAAATTT-TTAAAATTA
1 CATTTTAACCCCTAAACTTTCTCAAAATTA
*
52967703 CATTTTAACCTCTAAACTTTCTCAAAATTA
1 CATTTTAACCCCTAAACTTTCTCAAAATTA
52967733 CATTTTAACCCCTAAACTTTCTCAAAATTA
1 CATTTTAACCCCTAAACTTTCTCAAAATTA
52967763 CACTTTT
1 CA-TTTT
52967770 GCCCCAAAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
29 25 0.23
30 80 0.72
31 6 0.05
ACGTcount: A:0.36, C:0.24, G:0.01, T:0.39
Consensus pattern (30 bp):
CATTTTAACCCCTAAACTTTCTCAAAATTA
Found at i:52967707 original size:59 final size:59
Alignment explanation
Indices: 52967621--52967769 Score: 226
Period size: 59 Copynumber: 2.5 Consensus size: 59
52967611 TTGCATTTTG
*
52967621 ACCCCTAAACTTTTCTAAAATTGCATTTTAACCACTAAACTTTCTCAAAATTACATTTCA
1 ACCCCTAAACTTTT-TAAAATTACATTTTAACCACTAAACTTTCTCAAAATTACATTTCA
* * *
52967681 ACCCCTAAAATTTTTAAAATTACATTTTAACCTCTAAACTTTCTCAAAATTACATTTTA
1 ACCCCTAAACTTTTTAAAATTACATTTTAACCACTAAACTTTCTCAAAATTACATTTCA
*
52967740 ACCCCTAAACTTTCTCAAAATTACACTTTT
1 ACCCCTAAACTTT-TTAAAATTACA-TTTT
52967770 GCCCCAAAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
59 54 0.67
60 23 0.28
61 4 0.05
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (59 bp):
ACCCCTAAACTTTTTAAAATTACATTTTAACCACTAAACTTTCTCAAAATTACATTTCA
Found at i:52967780 original size:89 final size:89
Alignment explanation
Indices: 52967614--52967783 Score: 245
Period size: 89 Copynumber: 1.9 Consensus size: 89
52967604 TTATTTTTTG
* *
52967614 CATTTTGACCCCTAAACTTTTCTAAAATTGCATTTTAACCACTAAACTTTCTCAAAATTACATTT
1 CATTTTAACCCCTAAACTTTTCTAAAATTACATTTTAACCACTAAACTTTCTCAAAATTACATTT
*
52967679 CAACCCCTAAAATTTTTAAAATTA
66 CAACCCCAAAAATTTTTAAAATTA
* *
52967703 CATTTTAACCTCTAAAC-TTTCTCAAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACACT
1 CATTTTAACCCCTAAACTTTTCT-AAAATTACATTTTAACCACTAAACTTTCTCAAAATTACA-T
**
52967767 TT-TGCCCCAAAAATTTT
64 TTCAACCCCAAAAATTTT
52967784 GCTGAGTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
88 5 0.07
89 64 0.89
90 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (89 bp):
CATTTTAACCCCTAAACTTTTCTAAAATTACATTTTAACCACTAAACTTTCTCAAAATTACATTT
CAACCCCAAAAATTTTTAAAATTA
Found at i:52968597 original size:25 final size:25
Alignment explanation
Indices: 52968538--52968596 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
52968528 CCAGCCCAGC
*
52968538 AGAGAGAAAACAAAAAGAAAAAAAG
1 AGAGAAAAAACAAAAAGAAAAAAAG
*
52968563 AGAGAAAAAAGAAAAAGAAAAAAAG
1 AGAGAAAAAACAAAAAGAAAAAAAG
52968588 AG-GAAAAAA
1 AGAGAAAAAA
52968597 AATAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 7 0.22
25 25 0.78
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (25 bp):
AGAGAAAAAACAAAAAGAAAAAAAG
Found at i:52968603 original size:25 final size:25
Alignment explanation
Indices: 52968538--52968607 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
52968528 CCAGCCCAGC
* *
52968538 AGAGAGAAAACAAAAAGAAAAAAAG
1 AGAGAAAAAAAAAAAAGAAAAAAAG
*
52968563 AGAGAAAAAAGAAAAAGAAAAAAAG
1 AGAGAAAAAAAAAAAAGAAAAAAAG
*
52968588 AG-GAAAAAAAATAAA-AAAAA
1 AGAGAAAAAAAAAAAAGAAAAA
52968608 TAAAAAGGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.12
24 11 0.27
25 25 0.61
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (25 bp):
AGAGAAAAAAAAAAAAGAAAAAAAG
Found at i:52968786 original size:16 final size:16
Alignment explanation
Indices: 52968765--52968796 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52968755 GCATTTATAT
52968765 TTTTAATTTAATTTAA
1 TTTTAATTTAATTTAA
*
52968781 TTTTAATTTATTTTAA
1 TTTTAATTTAATTTAA
52968797 ATACTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTAATTTAATTTAA
Found at i:52968994 original size:20 final size:18
Alignment explanation
Indices: 52968952--52969017 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 18
52968942 AAATTATATT
52968952 TTTC-AAAATTTTTCGTG
1 TTTCAAAAATTTTTCGTG
52968969 TCTTCAAAAATTTTTCTTGTG
1 T-TTCAAAAATTTTTC--GTG
* * *
52968990 TTTCAAAAAATCTTCGCG
1 TTTCAAAAATTTTTCGTG
52969008 TTTTCAAAAA
1 -TTTCAAAAA
52969018 AATAAGGCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.02
18 5 0.12
19 19 0.46
20 12 0.29
21 4 0.10
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.45
Consensus pattern (18 bp):
TTTCAAAAATTTTTCGTG
Found at i:52969267 original size:18 final size:18
Alignment explanation
Indices: 52969246--52969569 Score: 274
Period size: 17 Copynumber: 18.4 Consensus size: 18
52969236 AAAAATCTAT
* *
52969246 TTTTCAAAAGTTTTCATG
1 TTTTCAAAAATTTTCGTG
*
52969264 TTTTCAAAAAATTCTCGTG
1 TTTTC-AAAAATTTTCGTG
*
52969283 TTTT-AAAAATTTTCGCG
1 TTTTCAAAAATTTTCGTG
* ***
52969300 TTTTCAGAAATTTTTACG
1 TTTTCAAAAATTTTCGTG
**
52969318 TTTTCAAAAATCCTCGTG
1 TTTTCAAAAATTTTCGTG
52969336 TTTTCAAAAATTTT-GATG
1 TTTTCAAAAATTTTCG-TG
*
52969354 -TTTCAAAAATTTCCGTG
1 TTTTCAAAAATTTTCGTG
52969371 TTTT-AAAAA-TTTCTGTG
1 TTTTCAAAAATTTTC-GTG
52969388 TTTTCAAAAATTTTCGT-
1 TTTTCAAAAATTTTCGTG
* * **
52969405 ATTTAAAAAAAATTCGTG
1 TTTTCAAAAATTTTCGTG
* **
52969423 TTGT-AAAAATCCTCGTG
1 TTTTCAAAAATTTTCGTG
* *
52969440 TTTTCAAAAATTCTGGTG
1 TTTTCAAAAATTTTCGTG
52969458 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
52969475 TTTTCAAAAA-TTCCG-G
1 TTTTCAAAAATTTTCGTG
*** *
52969491 AGATCCAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
52969509 TTTTCTAAAAATTTCCGTG
1 TTTTC-AAAAATTTTCGTG
*
52969528 -TTTCAAAAATTTTCGTT
1 TTTTCAAAAATTTTCGTG
* *
52969545 TTTTCACAAATTTCCGTG
1 TTTTCAAAAATTTTCGTG
52969563 TTTTCAA
1 TTTTCAA
52969570 CGACTCTAGT
Statistics
Matches: 242, Mismatches: 49, Indels: 30
0.75 0.15 0.09
Matches are distributed among these distances:
16 10 0.04
17 102 0.42
18 101 0.42
19 29 0.12
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (18 bp):
TTTTCAAAAATTTTCGTG
Found at i:52969537 original size:17 final size:17
Alignment explanation
Indices: 52969265--52969565 Score: 163
Period size: 18 Copynumber: 17.2 Consensus size: 17
52969255 GTTTTCATGT
*
52969265 TTTCAAAAAATTCTCGTG
1 TTTCAAAAATTTC-CGTG
*
52969283 TTTTAAAAATTTTCGCGT-
1 TTTCAAAAA-TTTC-CGTG
* *
52969301 TTTCAGAAATTTTTACGT-
1 TTTCA-AAA-ATTTCCGTG
*
52969319 TTTCAAAAA-TCCTCGTG
1 TTTCAAAAATTTC-CGTG
*
52969336 TTTTCAAAAATTT-TGATG
1 -TTTCAAAAATTTCCG-TG
52969354 TTTCAAAAATTTCCGTG
1 TTTCAAAAATTTCCGTG
* *
52969371 TTTTAAAAATTTCTGTG
1 TTTCAAAAATTTCCGTG
* *
52969388 TTTTCAAAAATTTTCGTA
1 -TTTCAAAAATTTCCGTG
* *
52969406 TTTAAAAAAAATT-CGTG
1 TTT-CAAAAATTTCCGTG
*
52969423 TTGT-AAAAA-TCCTCGTG
1 TT-TCAAAAATTTC-CGTG
*
52969440 TTTTCAAAAA-TTCTGGTG
1 -TTTCAAAAATTTC-CGTG
*
52969458 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTTCCGTG
52969475 TTTTCAAAAA-TTCCG-G
1 -TTTCAAAAATTTCCGTG
** * *
52969491 AGATCCAAAATTTTCGTG
1 -TTTCAAAAATTTCCGTG
52969509 TTTTCTAAAAATTTCCGTG
1 -TTTC-AAAAATTTCCGTG
* *
52969528 TTTCAAAAATTTTCGTTT
1 TTTCAAAAATTTCCG-TG
*
52969546 TTTCACAAATTTCCGTG
1 TTTCAAAAATTTCCGTG
52969563 TTT
1 TTT
52969566 TCAACGACTC
Statistics
Matches: 219, Mismatches: 42, Indels: 45
0.72 0.14 0.15
Matches are distributed among these distances:
15 2 0.01
16 15 0.07
17 80 0.37
18 98 0.45
19 24 0.11
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (17 bp):
TTTCAAAAATTTCCGTG
Found at i:52969558 original size:35 final size:35
Alignment explanation
Indices: 52969247--52969565 Score: 285
Period size: 35 Copynumber: 9.1 Consensus size: 35
52969237 AAAATCTATT
* * *
52969247 TTTCAAAAGTTTTCATGTTTTCAAAAAATTCTCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTTC-CGTG
* * * *
52969283 TTTTAAAAATTTTCGCGTTTTCAGAAATTTTTACGT-
1 TTTCAAAAATTTTCGTGTTTTCA-AAA-ATTTCCGTG
** *
52969319 TTTCAAAAATCCTCGTGTTTTCAAAAATTT-TGATG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTTCCG-TG
* *
52969354 TTTCAAAAATTTCCGTGTTTT-AAAAATTTCTGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTTCCGTG
* ** *
52969388 TTTTCAAAAATTTTCGTATTTAAAAAAAATT-CGTG
1 -TTTCAAAAATTTTCGTGTTTTCAAAAATTTCCGTG
** *
52969423 TTGT-AAAAATCCTCGTGTTTTCAAAAA-TTCTGGTG
1 TT-TCAAAAATTTTCGTGTTTTCAAAAATTTC-CGTG
52969458 TTTCAAAAATTTTCGTGTTTTCAAAAA-TTCCG-G
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTTCCGTG
** *
52969491 AGATCCAAAATTTTCGTGTTTTCTAAAAATTTCCGTG
1 -TTTCAAAAATTTTCGTGTTTTC-AAAAATTTCCGTG
* *
52969528 TTTCAAAAATTTTCGTTTTTTCACAAATTTCCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTTCCGTG
52969563 TTT
1 TTT
52969566 TCAACGACTC
Statistics
Matches: 230, Mismatches: 38, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
33 4 0.02
34 55 0.24
35 94 0.41
36 68 0.30
37 7 0.03
38 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAATTTCCGTG
Found at i:52969642 original size:17 final size:17
Alignment explanation
Indices: 52969617--52969711 Score: 72
Period size: 17 Copynumber: 5.5 Consensus size: 17
52969607 AAAAATTGTA
*
52969617 TTTCGAAAAATTCTCGTG
1 TTTC-AAAAATTTTCGTG
*
52969635 TTTCAAAAATTGTCGTG
1 TTTCAAAAATTTTCGTG
*
52969652 -TT-AAAATTTTTTTTTCGTG
1 TTTCAAAA----ATTTTCGTG
*
52969671 TTTCTAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
52969688 TTTCAAAAA-TTTCGT-
1 TTTCAAAAATTTTCGTG
*
52969703 TTTTAAAAA
1 TTTCAAAAA
52969712 AAAAAATTTG
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
15 12 0.19
16 8 0.12
17 28 0.44
18 4 0.06
19 7 0.11
20 2 0.03
21 3 0.05
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (17 bp):
TTTCAAAAATTTTCGTG
Found at i:52969712 original size:16 final size:16
Alignment explanation
Indices: 52969664--52969712 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
52969654 AAAATTTTTT
* *
52969664 TTTCGTGTTTCTAAAAT
1 TTTCGTGTTT-AAAAAA
*
52969681 TTTCGTGTTTCAAAAA
1 TTTCGTGTTTAAAAAA
*
52969697 TTTCGTTTTTAAAAAA
1 TTTCGTGTTTAAAAAA
52969713 AAAAATTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 18 0.64
17 10 0.36
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (16 bp):
TTTCGTGTTTAAAAAA
Found at i:52970478 original size:14 final size:15
Alignment explanation
Indices: 52970456--52970532 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
52970446 CAATCAAACA
52970456 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
52970470 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
52970485 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
52970505 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
52970519 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
52970533 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:52970497 original size:20 final size:20
Alignment explanation
Indices: 52970472--52970511 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
52970462 AATATTTTCC
*
52970472 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
52970492 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
52970512 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:52970517 original size:34 final size:35
Alignment explanation
Indices: 52970460--52970526 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
52970450 CAAACACCAG
*
52970460 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
52970495 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
52970527 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:52970533 original size:14 final size:14
Alignment explanation
Indices: 52970495--52970534 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
52970485 ACAGAAAAGT
*
52970495 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
52970509 AAATCATTTTACGG
1 AAAACATTTTACAG
52970523 AAAACATTTTAC
1 AAAACATTTTAC
52970535 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:52970818 original size:26 final size:26
Alignment explanation
Indices: 52970784--52970849 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
52970774 TATATTCGAT
*
52970784 TCGATTCGATTCGAATTCCATCTCAC
1 TCGACTCGATTCGAATTCCATCTCAC
52970810 TCGACTCGATTCGAATTCCATCTCAC
1 TCGACTCGATTCGAATTCCATCTCAC
52970836 TCGACTCGATTCGA
1 TCGACTCGATTCGA
52970850 GAAAACTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.32
Consensus pattern (26 bp):
TCGACTCGATTCGAATTCCATCTCAC
Found at i:52973190 original size:17 final size:17
Alignment explanation
Indices: 52973164--52973525 Score: 170
Period size: 17 Copynumber: 20.7 Consensus size: 17
52973154 ATCCGAATTT
52973164 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAGAA
**
52973181 TTTTGGAAACAC---AA
1 TTTTTAAAACACGAGAA
** * *
52973195 TTTAAAAAAAACGAAAA
1 TTTTTAAAACACGAGAA
* * *
52973212 TTTATGAAACACGAGATTT
1 TTTTTAAAACACGAGA--A
*
52973231 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAGAA
52973249 TTTTTAAAACACCGA-AA
1 TTTTTAAAACA-CGAGAA
*
52973266 TTTTTAAAAACACGAGGA
1 TTTTT-AAAACACGAGAA
* * *
52973284 TTTTTAAGATACGAAAAA
1 TTTTTAAAACACG-AGAA
* *
52973302 TTTTGAAAACACGAAAA
1 TTTTTAAAACACGAGAA
*
52973319 TTTTTGAAAAC-CCAGAAA
1 TTTTT-AAAACACGAG-AA
52973337 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAGAA
*
52973354 TTTTTTGAAACACCG-GAA
1 -TTTTTAAAACA-CGAGAA
*
52973372 TTTTCAAAAACACGA-AGA
1 TTTT-TAAAACACGAGA-A
* *
52973390 TTTTTGAAACACGAAAAA
1 TTTTTAAAACACG-AGAA
*
52973408 TTTTGAAAACACG-GAAA
1 TTTTTAAAACACGAG-AA
* *
52973425 TTTTTGAAACATG-GAAA
1 TTTTTAAAACACGAG-AA
*
52973442 TTTTTAGAAAACACGAAAAA
1 TTTTT--AAAACACG-AGAA
* * *
52973462 TTTTGAAAA-ATTGA-AT
1 TTTTTAAAACA-CGAGAA
*
52973478 TTTTTGAAAACACGGGAA
1 TTTTT-AAAACACGAGAA
* *
52973496 TTTTTGAAAACATGAAAA
1 TTTTT-AAAACACGAGAA
*
52973514 TTTTTTAAACAC
1 TTTTTAAAACAC
52973526 CTGACTTTTT
Statistics
Matches: 263, Mismatches: 53, Indels: 58
0.70 0.14 0.16
Matches are distributed among these distances:
14 10 0.04
16 5 0.02
17 110 0.42
18 110 0.42
19 13 0.05
20 15 0.06
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (17 bp):
TTTTTAAAACACGAGAA
Found at i:52973264 original size:18 final size:17
Alignment explanation
Indices: 52973164--52973525 Score: 200
Period size: 18 Copynumber: 20.7 Consensus size: 17
52973154 ATCCGAATTT
*
52973164 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAAAA
**
52973181 TTTTGGAAACAC---AA
1 TTTTTAAAACACGAAAA
** *
52973195 TTTAAAAAAAACGAAAA
1 TTTTTAAAACACGAAAA
* * **
52973212 TTTATGAAACACGAGATTT
1 TTTTTAAAACACGA-A-AA
52973231 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
52973249 TTTTTAAAACACCG-AAA
1 TTTTTAAAACA-CGAAAA
**
52973266 TTTTTAAAAACACGAGGA
1 TTTTT-AAAACACGAAAA
* *
52973284 TTTTTAAGATACGAAAAA
1 TTTTTAAAACACG-AAAA
*
52973302 TTTTGAAAACACGAAAA
1 TTTTTAAAACACGAAAA
*
52973319 TTTTTGAAAAC-CCAGAAA
1 TTTTT-AAAACACGA-AAA
*
52973337 TTTTTAAAACACGAGAAT
1 TTTTTAAAACACGA-AAA
* *
52973355 TTTTTGAAACACCG-GAA
1 TTTTTAAAACA-CGAAAA
* *
52973372 TTTTCAAAAACACGAAGA
1 TTTT-TAAAACACGAAAA
*
52973390 TTTTTGAAACACGAAAAA
1 TTTTTAAAACACG-AAAA
* *
52973408 TTTTGAAAACACGGAAA
1 TTTTTAAAACACGAAAA
* * *
52973425 TTTTTGAAACATGGAAA
1 TTTTTAAAACACGAAAA
52973442 TTTTTAGAAAACACGAAAAA
1 TTTTT--AAAACACG-AAAA
* * *
52973462 TTTTGAAAA-ATTG-AAT
1 TTTTTAAAACA-CGAAAA
**
52973478 TTTTTGAAAACACGGGAA
1 TTTTT-AAAACACGAAAA
*
52973496 TTTTTGAAAACATGAAAA
1 TTTTT-AAAACACGAAAA
*
52973514 TTTTTTAAACAC
1 TTTTTAAAACAC
52973526 CTGACTTTTT
Statistics
Matches: 262, Mismatches: 59, Indels: 48
0.71 0.16 0.13
Matches are distributed among these distances:
14 10 0.04
16 6 0.02
17 107 0.41
18 111 0.42
19 13 0.05
20 15 0.06
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:52973270 original size:35 final size:35
Alignment explanation
Indices: 52973231--52973507 Score: 231
Period size: 35 Copynumber: 7.8 Consensus size: 35
52973221 CACGAGATTT
52973231 TTTTTGAAAACACGAAAATTTTTAAAACACCGAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACCGAAA
* ** * *
52973266 TTTTTAAAAACACGAGGATTTTTAAGATA-CGAAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACCG-AAA
*
52973301 ATTTTGAAAACACGAAAATTTTTGAAAAC-CCAGAAA
1 TTTTTGAAAACACGAAAATTTTT-AAAACACC-GAAA
* * *
52973337 TTTTT-AAAACACGAGAATTTTTTGAAACACCGGAA
1 TTTTTGAAAACACGA-AAATTTTTAAAACACCGAAA
** * *
52973372 TTTTCAAAAACACGAAGATTTTTGAAACA-CGAAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACCG-AAA
* * * **
52973407 ATTTTGAAAACACGGAAATTTTTGAAACATGGAAA
1 TTTTTGAAAACACGAAAATTTTTAAAACACCGAAA
* ** *
52973442 TTTTTAGAAAACACGAAAAATTTTGAAAA-ATTGAAT
1 TTTTT-GAAAACACG-AAAATTTTTAAAACACCGAAA
**
52973478 TTTTTGAAAACACGGGAATTTTTGAAAACA
1 TTTTTGAAAACACGAAAATTTTT-AAAACA
52973508 TGAAAATTTT
Statistics
Matches: 195, Mismatches: 34, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
34 10 0.05
35 124 0.64
36 50 0.26
37 11 0.06
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTAAAACACCGAAA
Found at i:52973311 original size:53 final size:52
Alignment explanation
Indices: 52973238--52973541 Score: 212
Period size: 53 Copynumber: 5.8 Consensus size: 52
52973228 TTTTTTTTGA
*
52973238 AAACACG-AAAATTTTTAAAACACCGAAATTTTTAAAAACACGAGGATTTTT
1 AAACACGAAAAATTTTGAAAACACCGAAATTTTTAAAAACACGAGGATTTTT
* * * *
52973289 AAGATACGAAAAATTTTGAAAACA-CGAAAATTTTTGAAAAC-CCAGAAATTTTT
1 AA-ACACGAAAAATTTTGAAAACACCG-AAATTTTTAAAAACACGAG-GATTTTT
** * * *
52973342 AAAACACGAGAATTTTTTG-AAACACCGGAATTTTCAAAAACACGAAGATTTTT
1 -AAACACGA-AAAATTTTGAAAACACCGAAATTTTTAAAAACACGAGGATTTTT
* * * *
52973395 GAAACACGAAAAATTTTGAAAACACGGAAATTTTT-GAAACATG-GAAATTTTT
1 -AAACACGAAAAATTTTGAAAACACCGAAATTTTTAAAAACACGAG-GATTTTT
** * *
52973447 AGAAAACACGAAAAATTTTGAAAA-ATTGAATTTTTTGAAAACACG-GGAATTTTT
1 ---AAACACGAAAAATTTTGAAAACACCGAAATTTTTAAAAACACGAGG-ATTTTT
* ** **
52973501 GAAAACATG-AAAATTTTTTAAACACCTGACTTTTTTAAAAA
1 --AAACACGAAAAATTTTGAAAACACC-GAAATTTTTAAAAA
52973542 GAAACAATTT
Statistics
Matches: 199, Mismatches: 38, Indels: 29
0.75 0.14 0.11
Matches are distributed among these distances:
51 2 0.01
52 39 0.20
53 99 0.50
54 59 0.30
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (52 bp):
AAACACGAAAAATTTTGAAAACACCGAAATTTTTAAAAACACGAGGATTTTT
Found at i:52973382 original size:71 final size:70
Alignment explanation
Indices: 52973232--52973504 Score: 242
Period size: 71 Copynumber: 3.9 Consensus size: 70
52973222 ACGAGATTTT
* * *
52973232 TTTTGAAAACACGAAAATTTTT-AAAACACC-GAAATTTTTAAAAACACGAGGATTTTT-AAGAT
1 TTTTAAAAACACGAAAATTTTTGAAAACACCAGAAATTTTTAAAAACACGAGAATTTTTGAA-AC
*
52973294 ACGAAAAA
65 ACG--GAA
*
52973302 TTTTGAAAACACGAAAATTTTTGAAAAC-CCAGAAATTTTT-AAAACACGAGAATTTTTTGAAAC
1 TTTTAAAAACACGAAAATTTTTGAAAACACCAGAAATTTTTAAAAACACGAGAA-TTTTTGAAAC
52973365 ACCGGAA
65 A-CGGAA
* * * *
52973372 TTTTCAAAAACACGAAGATTTTTG-AAACACGA-AAAATTTTGAAAACACG-GAAATTTTTGAAA
1 TTTT-AAAAACACGAAAATTTTTGAAAACACCAGAAATTTTTAAAAACACGAG-AATTTTTGAAA
*
52973434 CATGGAAA
64 CACGG-AA
* ** * * *
52973442 TTTTTAGAAAACACGAAAAATTTTGAAAA-A-TTGAATTTTTTGAAAACACGGGAATTTTTGAAA
1 -TTTTA-AAAACACGAAAATTTTTGAAAACACCAGAAATTTTTAAAAACACGAGAATTTTTGAAA
52973505 ACATGAAAAT
Statistics
Matches: 174, Mismatches: 14, Indels: 29
0.80 0.06 0.13
Matches are distributed among these distances:
69 2 0.01
70 67 0.39
71 97 0.56
72 8 0.05
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (70 bp):
TTTTAAAAACACGAAAATTTTTGAAAACACCAGAAATTTTTAAAAACACGAGAATTTTTGAAACA
CGGAA
Found at i:52973686 original size:21 final size:20
Alignment explanation
Indices: 52973660--52973700 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
52973650 GTTACCTTAA
52973660 TTTTGAAAACACGAGAAATTT
1 TTTTGAAAACACGA-AAATTT
*
52973681 TTTTGAAGACACGAAAATTT
1 TTTTGAAAACACGAAAATTT
52973701 CGAAACCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (20 bp):
TTTTGAAAACACGAAAATTT
Found at i:52973873 original size:5 final size:5
Alignment explanation
Indices: 52973863--52973887 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
52973853 TAAAATTATT
52973863 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
52973888 ATTGAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:52974090 original size:5 final size:5
Alignment explanation
Indices: 52974065--52974115 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
52974055 ACAAATTGCA
* * *
52974065 TTTTT TTTTC TCTTC TTTT- TTCTTT TTTTC TTTTC TTTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC -TTTTC TTTTC TTTTC
52974116 GGCTGGGCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 2 0.05
5 30 0.77
6 7 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:52974092 original size:19 final size:19
Alignment explanation
Indices: 52974068--52974109 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
52974058 AATTGCATTT
52974068 TTTTTTCTCTTCT-TTTTTC
1 TTTTTT-TCTTCTCTTTTTC
*
52974087 TTTTTTTCTTTTCTTTTTC
1 TTTTTTTCTTCTCTTTTTC
52974106 TTTT
1 TTTT
52974110 CTTTTCGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTTCTTCTCTTTTTC
Found at i:52974092 original size:20 final size:19
Alignment explanation
Indices: 52974067--52974109 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
52974057 AAATTGCATT
52974067 TTTTTTTCTCTTCTTTTTTC
1 TTTTTTTCTCTTC-TTTTTC
*
52974087 TTTTTTTCTTTTCTTTTTC
1 TTTTTTTCTCTTCTTTTTC
52974106 TTTT
1 TTTT
52974110 CTTTTCGGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTCTCTTCTTTTTC
Found at i:52974168 original size:26 final size:25
Alignment explanation
Indices: 52974117--52974173 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
52974107 TTTCTTTTCG
*
52974117 GCTGGGCTGCCTGCTGTGGGCTGCT
1 GCTGGGCTGCCTGCTGTGGGCCGCT
* * *
52974142 GTTGGGCTGCGCTGGTTTGGGCCGCT
1 GCTGGGCTGC-CTGCTGTGGGCCGCT
52974168 GCTGGG
1 GCTGGG
52974174 TAGGCTGGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.00, C:0.25, G:0.47, T:0.28
Consensus pattern (25 bp):
GCTGGGCTGCCTGCTGTGGGCCGCT
Found at i:52974260 original size:14 final size:13
Alignment explanation
Indices: 52974242--52974285 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
52974232 GCCTGCCCCT
52974242 TTTTTTTTGCTTA
1 TTTTTTTTGCTTA
52974255 TTTTTTTTGCTT-
1 TTTTTTTTGCTTA
*
52974267 TGTTTTTT-CTTTA
1 TTTTTTTTGC-TTA
52974280 TTTTTT
1 TTTTTT
52974286 GGGCAGCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 9 0.33
13 17 0.63
ACGTcount: A:0.05, C:0.07, G:0.07, T:0.82
Consensus pattern (13 bp):
TTTTTTTTGCTTA
Found at i:52974285 original size:11 final size:12
Alignment explanation
Indices: 52974240--52974286 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 12
52974230 TGGCCTGCCC
52974240 CTTT-TTTTTTG
1 CTTTATTTTTTG
*
52974251 CTTATTTTTTTTG
1 CTT-TATTTTTTG
*
52974264 CTTTGTTTTTT-
1 CTTTATTTTTTG
52974275 CTTTATTTTTTG
1 CTTTATTTTTTG
52974287 GGCAGCTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 13 0.42
12 8 0.26
13 10 0.32
ACGTcount: A:0.04, C:0.09, G:0.09, T:0.79
Consensus pattern (12 bp):
CTTTATTTTTTG
Found at i:52974353 original size:8 final size:8
Alignment explanation
Indices: 52974340--52974377 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
52974330 CTTTATTATT
*
52974340 TTTTTTTC
1 TTTTTCTC
52974348 TTTTT-TC
1 TTTTTCTC
52974355 TTTTTCTC
1 TTTTTCTC
52974363 TTTTTCTC
1 TTTTTCTC
52974371 TTTTTCT
1 TTTTTCT
52974378 TCCTTCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTCTC
Found at i:52974384 original size:15 final size:15
Alignment explanation
Indices: 52974342--52974417 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
52974332 TTATTATTTT
52974342 TTTTTCTT-TT-TTC
1 TTTTTCTTCTTCTTC
*
52974355 TTTTTC-TCTTTTTC
1 TTTTTCTTCTTCTTC
*
52974369 TCTTT-TTCTTCCTTC
1 TTTTTCTTCTT-CTTC
52974384 TTCTTTCTTCTTCTTC
1 TT-TTTCTTCTTCTTC
*
52974400 TTGTTCTTCTTCTTC
1 TTTTTCTTCTTCTTC
52974415 TTT
1 TTT
52974418 ACGCATTGGT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
12 1 0.02
13 8 0.15
14 11 0.21
15 18 0.35
16 9 0.17
17 5 0.10
ACGTcount: A:0.00, C:0.25, G:0.01, T:0.74
Consensus pattern (15 bp):
TTTTTCTTCTTCTTC
Found at i:52974388 original size:3 final size:3
Alignment explanation
Indices: 52974352--52974416 Score: 62
Period size: 3 Copynumber: 21.7 Consensus size: 3
52974342 TTTTTCTTTT
* * *
52974352 TTC TTT TTC -TC TTT TTC -TC TTT TTC TTCC TTC TTC TTTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC -TTC TTC TTC
*
52974397 TTC TTG TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TT
52974417 TACGCATTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:52974522 original size:16 final size:16
Alignment explanation
Indices: 52974501--52974532 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52974491 TCCTTTCTTC
*
52974501 CTCTCCTTTCTCTTTT
1 CTCTCCTATCTCTTTT
52974517 CTCTCCTATCTCTTTT
1 CTCTCCTATCTCTTTT
52974533 TTTCGAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (16 bp):
CTCTCCTATCTCTTTT
Found at i:52974837 original size:29 final size:29
Alignment explanation
Indices: 52974785--52974895 Score: 118
Period size: 29 Copynumber: 3.9 Consensus size: 29
52974775 AAATTTTGAG
**
52974785 AAAGTTTAGGGGTCAAAACATAATTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTCAA
* * * *
52974814 AAAGTTTATGGATCAAAATGTAATTTTATG
1 AAAGTTTAGGGGTCAAAATGTAATTTCA-A
* *
52974844 AAA-TTTAGGGGT-TAAATGCAATTTCAA
1 AAAGTTTAGGGGTCAAAATGTAATTTCAA
*
52974871 AAAGTTTAGGGGTTAAAATGTAATT
1 AAAGTTTAGGGGTCAAAATGTAATT
52974896 CTTTATTTTT
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
27 3 0.05
28 20 0.31
29 39 0.60
30 3 0.05
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.34
Consensus pattern (29 bp):
AAAGTTTAGGGGTCAAAATGTAATTTCAA
Found at i:52974867 original size:28 final size:28
Alignment explanation
Indices: 52974806--52974887 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
52974796 GTCAAAACAT
* * * *
52974806 AATTTCAAAAAGTTTATGGATCAAAATGT
1 AATTTCAAAAAGTTTAGGGGT-TAAATGC
* *
52974835 AATTTTATGAAA-TTTAGGGGTTAAATGC
1 AATTTCA-AAAAGTTTAGGGGTTAAATGC
52974863 AATTTCAAAAAGTTTAGGGGTTAAA
1 AATTTCAAAAAGTTTAGGGGTTAAA
52974888 ATGTAATTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
27 3 0.07
28 24 0.56
29 13 0.30
30 3 0.07
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.35
Consensus pattern (28 bp):
AATTTCAAAAAGTTTAGGGGTTAAATGC
Found at i:52977228 original size:9 final size:9
Alignment explanation
Indices: 52977184--52977289 Score: 56
Period size: 9 Copynumber: 11.3 Consensus size: 9
52977174 GTTTTTATTA
52977184 TTATAAA-T
1 TTATAAATT
*
52977192 TTATAAGTT
1 TTATAAATT
*
52977201 TATATCAATT
1 T-TATAAATT
*
52977211 ATA-ATAATT
1 TTATA-AATT
52977220 TTATAAATT
1 TTATAAATT
*
52977229 TTAAAAATT
1 TTATAAATT
* *
52977238 TTATGATTT
1 TTATAAATT
52977247 TTATAGAAATT
1 TTAT--AAATT
* *
52977258 TAATATATTT
1 TTATA-AATT
52977268 TTATAAAATT
1 TTAT-AAATT
52977278 TTA-AATATT
1 TTATAA-ATT
52977287 TTA
1 TTA
52977290 GATATGTTTT
Statistics
Matches: 73, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
8 8 0.11
9 39 0.53
10 19 0.26
11 7 0.10
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (9 bp):
TTATAAATT
Found at i:52977285 original size:20 final size:20
Alignment explanation
Indices: 52977209--52977288 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 20
52977199 TTTATATCAA
52977209 TTATAATAATTTTATAA-A-TT
1 TTATAA-AATTTTA-AATATTT
52977229 TTA-AAAATTTT--ATGATTT
1 TTATAAAATTTTAAAT-ATTT
52977247 TTATAGAAA-TTTAATATATTT
1 TTATA-AAATTTTAA-ATATTT
52977268 TTATAAAATTTTAAATATTT
1 TTATAAAATTTTAAATATTT
52977288 T
1 T
52977289 AGATATGTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
15 1 0.02
17 1 0.02
18 11 0.22
19 6 0.12
20 16 0.31
21 14 0.27
22 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTATAAAATTTTAAATATTT
Found at i:52977609 original size:22 final size:23
Alignment explanation
Indices: 52977566--52977609 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
52977556 ATCTAATTGA
*
52977566 TTATGTTAATTAACGACATAAAC
1 TTATGTTAATTAAAGACATAAAC
52977589 TTAT-TTAATATAAAGAC-TAAA
1 TTATGTTAAT-TAAAGACATAAA
52977610 TTAATTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (23 bp):
TTATGTTAATTAAAGACATAAAC
Found at i:52981251 original size:122 final size:122
Alignment explanation
Indices: 52981092--52981337 Score: 492
Period size: 122 Copynumber: 2.0 Consensus size: 122
52981082 TATATTGAAG
52981092 CCAAATTTAACCCATATTATAAACATATCTAGATTTTTTTGTTAAAATACATTTTTCGACCTTAA
1 CCAAATTTAACCCATATTATAAACATATCTAGATTTTTTTGTTAAAATACATTTTTCGACCTTAA
52981157 TATTCTAATCCAAACCGTCCCAAATATTTTTTTAAAAAATTTTTTGAGTTTGGATCA
66 TATTCTAATCCAAACCGTCCCAAATATTTTTTTAAAAAATTTTTTGAGTTTGGATCA
52981214 CCAAATTTAACCCATATTATAAACATATCTAGATTTTTTTGTTAAAATACATTTTTCGACCTTAA
1 CCAAATTTAACCCATATTATAAACATATCTAGATTTTTTTGTTAAAATACATTTTTCGACCTTAA
52981279 TATTCTAATCCAAACCGTCCCAAATATTTTTTTAAAAAATTTTTTGAGTTTGGATCA
66 TATTCTAATCCAAACCGTCCCAAATATTTTTTTAAAAAATTTTTTGAGTTTGGATCA
52981336 CC
1 CC
52981338 TTTGGATAAG
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 124 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (122 bp):
CCAAATTTAACCCATATTATAAACATATCTAGATTTTTTTGTTAAAATACATTTTTCGACCTTAA
TATTCTAATCCAAACCGTCCCAAATATTTTTTTAAAAAATTTTTTGAGTTTGGATCA
Found at i:52981977 original size:25 final size:24
Alignment explanation
Indices: 52981928--52981977 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
52981918 TGAAAATAAA
*
52981928 AAATTTAAATATATTATAAATTAT
1 AAATTTAAATATATTATAAAGTAT
*
52981952 AAATTATAAATATTGTTAT-AAGTAT
1 AAATT-TAAATA-TATTATAAAGTAT
52981977 A
1 A
52981978 TAATAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 5 0.23
25 12 0.55
26 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
AAATTTAAATATATTATAAAGTAT
Found at i:52987034 original size:4 final size:4
Alignment explanation
Indices: 52987027--52987064 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
52987017 ATATATATAC
52987027 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
52987065 CTATTGTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:52988346 original size:58 final size:58
Alignment explanation
Indices: 52988256--52988370 Score: 230
Period size: 58 Copynumber: 2.0 Consensus size: 58
52988246 GCAAAACTAC
52988256 GTTGTTTTGATAAATGTTTACTCATTAAGTTAAAAGCAAAACCATTATATTTGTTTAG
1 GTTGTTTTGATAAATGTTTACTCATTAAGTTAAAAGCAAAACCATTATATTTGTTTAG
52988314 GTTGTTTTGATAAATGTTTACTCATTAAGTTAAAAGCAAAACCATTATATTTGTTTA
1 GTTGTTTTGATAAATGTTTACTCATTAAGTTAAAAGCAAAACCATTATATTTGTTTA
52988371 TGTAATTAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (58 bp):
GTTGTTTTGATAAATGTTTACTCATTAAGTTAAAAGCAAAACCATTATATTTGTTTAG
Found at i:52988718 original size:28 final size:30
Alignment explanation
Indices: 52988687--52988746 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
52988677 TTTGGTATTT
* *
52988687 AAATATT-TT-TTACTCAATTTGATATCTA
1 AAATATTCTTGTTACCCAATTTGATACCTA
*
52988715 AAATATTCTTGTTTCCCAATTTGATACCTA
1 AAATATTCTTGTTACCCAATTTGATACCTA
52988745 AA
1 AA
52988747 GTGAGCATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 7 0.26
29 2 0.07
30 18 0.67
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (30 bp):
AAATATTCTTGTTACCCAATTTGATACCTA
Found at i:52988961 original size:23 final size:22
Alignment explanation
Indices: 52988909--52988972 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 22
52988899 ATAAATATAT
* *
52988909 AATAAAATTCAAAAAAATATTAT
1 AATAAAATT-AAAAAATTATTAA
* *
52988932 CACAAAATTATAAAAATTATTAA
1 AATAAAATTA-AAAAATTATTAA
52988955 AATAAAATTTAGAAAAAT
1 AATAAAA-TTA-AAAAAT
52988973 ATGGTAAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 1 0.03
23 22 0.69
24 9 0.28
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (22 bp):
AATAAAATTAAAAAATTATTAA
Found at i:52989103 original size:20 final size:21
Alignment explanation
Indices: 52989080--52989123 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
52989070 AATTTTTTTT
*
52989080 AAAATTGA-TTAAAATTTGT-A
1 AAAATT-ATTTAAAAATTGTGA
52989100 AAAATTATTTAAAAATTGTGA
1 AAAATTATTTAAAAATTGTGA
52989121 AAA
1 AAA
52989124 CTATAAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 16 0.76
21 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (21 bp):
AAAATTATTTAAAAATTGTGA
Found at i:52989164 original size:28 final size:28
Alignment explanation
Indices: 52989110--52989164 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
52989100 AAAATTATTT
* *
52989110 AAAAATTGTGAAAACTATAAGAGTTTTA
1 AAAAATTGTAAAAACTATAAGACTTTTA
* *
52989138 AAAAATTGTAAAAATTATAATACTTTT
1 AAAAATTGTAAAAACTATAAGACTTTT
52989165 GTACACATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (28 bp):
AAAAATTGTAAAAACTATAAGACTTTTA
Found at i:52990070 original size:3 final size:3
Alignment explanation
Indices: 52990064--52990146 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
52990054 CTTTTTTTCA
52990064 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
52990112 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
52990147 AATTAACATA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:52990975 original size:24 final size:24
Alignment explanation
Indices: 52990947--52991000 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
52990937 TCTTTCTAAA
** *
52990947 ATATTTATTATTTATTAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
52990971 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
*
52990995 TTATTT
1 ATATTT
52991001 GGCCTACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:52996190 original size:19 final size:20
Alignment explanation
Indices: 52996162--52996200 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
52996152 TAGATTTTTA
*
52996162 GAAAA-TTTTAGAATCTTAT
1 GAAAACTTTAAGAATCTTAT
*
52996181 GAAAACTTTAAGAATTTTAT
1 GAAAACTTTAAGAATCTTAT
52996201 TGGTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (20 bp):
GAAAACTTTAAGAATCTTAT
Found at i:52996200 original size:20 final size:19
Alignment explanation
Indices: 52996147--52996200 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
52996137 GTTTGTTTGG
* *
52996147 AATTTTAGATTTTTA-GAA
1 AATTTAAGAATTTTATGAA
* *
52996165 AATTTTAGAATCTTATGAA
1 AATTTAAGAATTTTATGAA
52996184 AACTTTAAGAATTTTAT
1 AA-TTTAAGAATTTTAT
52996201 TGGTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 13 0.43
19 5 0.17
20 12 0.40
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (19 bp):
AATTTAAGAATTTTATGAA
Found at i:53000561 original size:46 final size:47
Alignment explanation
Indices: 53000492--53000603 Score: 154
Period size: 46 Copynumber: 2.4 Consensus size: 47
53000482 ATTTTATTTG
* *
53000492 GCCTTTGTGGCGTATTCTGTATGTTGCGTTTGTGGCATACTCTGTTA
1 GCCTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCATACTCTGATA
* * **
53000539 GCCTTTGT-TCGTATTCTTTATGTTGCCTTTGTGGTGTACTCTGATA
1 GCCTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCATACTCTGATA
*
53000585 GCCTTTGTGGCGTACTCTG
1 GCCTTTGTGGCGTATTCTG
53000604 ATAACCTTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 40 0.73
47 15 0.27
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.46
Consensus pattern (47 bp):
GCCTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCATACTCTGATA
Found at i:53000591 original size:22 final size:22
Alignment explanation
Indices: 53000492--53000620 Score: 98
Period size: 22 Copynumber: 5.6 Consensus size: 22
53000482 ATTTTATTTG
* *
53000492 GCCTTTGTGGCGTATTCTGTATGTT
1 GCCTTTGTGGCGTACTCTG-A--TA
* * *
53000517 GCGTTTGTGGCATACTCTGTTA
1 GCCTTTGTGGCGTACTCTGATA
* * * *
53000539 GCCTTTGT-TCGTATTCTTTATGTT
1 GCCTTTGTGGCGTACTC-TGA--TA
*
53000563 GCCTTTGTGGTGTACTCTGATA
1 GCCTTTGTGGCGTACTCTGATA
53000585 GCCTTTGTGGCGTACTCTGATA
1 GCCTTTGTGGCGTACTCTGATA
*
53000607 ACCTTTGTGGCGTA
1 GCCTTTGTGGCGTA
53000621 TTTTGTCTGG
Statistics
Matches: 81, Mismatches: 19, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
21 5 0.06
22 44 0.54
24 11 0.14
25 21 0.26
ACGTcount: A:0.12, C:0.19, G:0.26, T:0.44
Consensus pattern (22 bp):
GCCTTTGTGGCGTACTCTGATA
Found at i:53004478 original size:29 final size:30
Alignment explanation
Indices: 53004432--53004499 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 30
53004422 AATAAACTTA
*
53004432 AAATTTT-AAAGTAAAAAAGTAAAAAGATT
1 AAATTTTCAAAGTAAAAAAATAAAAAGATT
* * *
53004461 AAATTTTCAAA-TATAAAAATATAAATATT
1 AAATTTTCAAAGTAAAAAAATAAAAAGATT
53004490 AAA-TTTCAAA
1 AAATTTTCAAA
53004500 CATAGAAGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.21
29 24 0.71
30 3 0.09
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.32
Consensus pattern (30 bp):
AAATTTTCAAAGTAAAAAAATAAAAAGATT
Found at i:53013624 original size:149 final size:152
Alignment explanation
Indices: 53013183--53013626 Score: 571
Period size: 149 Copynumber: 2.9 Consensus size: 152
53013173 AAACCAAAGT
* * * * * *
53013183 TTTCTTTAAAAAAAATCATTACTTTTCTTAAAAATCATAA-C-CTTATTTTGAAATAGTT-AAAA
1 TTTCTTTAAAAAAAAACACTATTTTTCTTAAAGATTA-AAGCTTTTATTTTGAAATAGTTGAAAA
* * *
53013245 AAATCAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACTTAAAAAACAAATTTTTAT
65 AAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATGACTAAAAAAACATATTTTTAT
*
53013310 TTTTCAAAATCTAAACTTTCTCC
130 TTTTCAAAATCTAAACGTTCTCC
* * * **
53013333 TTTTTTTAAAAAACAAACACTATTTTTCTTAAAGTTTAAAGATTTTATTTTGATGTAGTTGAAAA
1 TTTCTTTAAAAAA-AAACACTATTTTTCTTAAAGATTAAAGCTTTTATTTTGAAATAGTTG--AA
*
53013398 AAAAATTAAAACTTTG-TTTAAAAATTTTAAACTTTCCTTTAAAATGACTAAAAAAAACATATTT
63 AAAAATCAAAACTTTGTTTTAAAAA-TTTAAACTTTCCTTTAAAATGACT-AAAAAAACATATTT
53013462 TTATTTTTCAAAATCTAAA-GTT-T-C
126 TTATTTTTCAAAATCTAAACGTTCTCC
*
53013486 -TTCTTTAAAAAAAAACACTATTTTTCTTAAAGATTAAAGCTTTTACTTTGAAATAGTTGAAAAA
1 TTTCTTTAAAAAAAAACACTATTTTTCTTAAAGATTAAAGCTTTTATTTTGAAATAGTTGAAAAA
* * *
53013550 AATCAAAATTTTGTTTTAAAAATTTAAAATTTCCTTTAAAATAACTAAGAAAAACATATTTTTAT
66 AATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATGACTAA-AAAAACATATTTTTAT
**
53013615 TTTAGAAAATCT
130 TTTTCAAAATCT
53013627 CTTTTTTTTA
Statistics
Matches: 256, Mismatches: 28, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
148 2 0.01
149 64 0.25
150 22 0.09
151 60 0.23
152 25 0.10
153 1 0.00
154 8 0.03
155 43 0.17
156 31 0.12
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (152 bp):
TTTCTTTAAAAAAAAACACTATTTTTCTTAAAGATTAAAGCTTTTATTTTGAAATAGTTGAAAAA
AATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATGACTAAAAAAACATATTTTTATT
TTTCAAAATCTAAACGTTCTCC
Found at i:53016680 original size:26 final size:25
Alignment explanation
Indices: 53016636--53016684 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
53016626 TCTCATCCCA
53016636 ATTTTACTCAAGTAAAATTTTGACG
1 ATTTTACTCAAGTAAAATTTTGACG
*
53016661 ATTTTACTCCTAGTAAAATTTTGA
1 ATTTTACT-CAAGTAAAATTTTGA
53016685 GAAAATTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (25 bp):
ATTTTACTCAAGTAAAATTTTGACG
Found at i:53022951 original size:21 final size:21
Alignment explanation
Indices: 53022925--53022973 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
53022915 AGAATCCCAG
*
53022925 AACCCTAATAAACCC-AACTCT
1 AACCCTAAT-AACCCTAACCCT
*
53022946 AACCCTAATCACCCTAACCCT
1 AACCCTAATAACCCTAACCCT
53022967 AACCCTA
1 AACCCTA
53022974 TTAATTCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.39, C:0.43, G:0.00, T:0.18
Consensus pattern (21 bp):
AACCCTAATAACCCTAACCCT
Found at i:53049818 original size:349 final size:349
Alignment explanation
Indices: 53049179--53049883 Score: 1385
Period size: 349 Copynumber: 2.0 Consensus size: 349
53049169 TCCGGGTCCG
53049179 TCAATTCATATTCATGTGCGTACATTTCCATTTCAGAGAGCACACTCCCGCGAACCTCATCCTTA
1 TCAATTCATATTCATGTGCGTACATTTCCATTTCAGAGAGCACACTCCCGCGAACCTCATCCTTA
53049244 CAGCGGGATTACCAATCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCGGGATTA
66 CAGCGGGATTACCAATCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCGGGATTA
53049309 CCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCTGAATTACCAATC
131 CCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCTGAATTACCAATC
53049374 CAGGCTAAATTCAGACCCTAATTCAGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTT
196 CAGGCTAAATTCAGACCCTAATTCAGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTT
53049439 CGGGAGGGCTATATTAGGATAGGATCACCCGTCTGGGCTAGATCCTTTTTACCGTCAATTCATTT
261 CGGGAGGGCTATATTAGGATAGGATCACCCGTCTGGGCTAGATCCTTTTTACCGTCAATTCATTT
53049504 TTAGGGATCCATCGAATTTTCCTT
326 TTAGGGATCCATCGAATTTTCCTT
53049528 TCAATTCATATTCATGTGCGTACATTTCCATTTCAGAGAGCACACTCCCGCGAACCTCATCCTTA
1 TCAATTCATATTCATGTGCGTACATTTCCATTTCAGAGAGCACACTCCCGCGAACCTCATCCTTA
*
53049593 CAGCGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCGGGATTA
66 CAGCGGGATTACCAATCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCGGGATTA
53049658 CCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCTGAATTACCAATC
131 CCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCTGAATTACCAATC
*
53049723 CAGGCTAAATTCAGACCCTAATTCGGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTT
196 CAGGCTAAATTCAGACCCTAATTCAGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTT
53049788 CGGGAGGGCTATATTAGGATAGGATCACCCGTCTGGGCTAGATCCTTTTTACCGTCAATTCATTT
261 CGGGAGGGCTATATTAGGATAGGATCACCCGTCTGGGCTAGATCCTTTTTACCGTCAATTCATTT
53049853 TTAGGGATCCATCGAATTTTCCTT
326 TTAGGGATCCATCGAATTTTCCTT
53049877 TC-ATTCA
1 TCAATTCA
53049884 ACCGAGATTT
Statistics
Matches: 354, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
348 5 0.01
349 349 0.99
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (349 bp):
TCAATTCATATTCATGTGCGTACATTTCCATTTCAGAGAGCACACTCCCGCGAACCTCATCCTTA
CAGCGGGATTACCAATCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTCGGGATTA
CCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGCTTGGATCTGAATTACCAATC
CAGGCTAAATTCAGACCCTAATTCAGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTT
CGGGAGGGCTATATTAGGATAGGATCACCCGTCTGGGCTAGATCCTTTTTACCGTCAATTCATTT
TTAGGGATCCATCGAATTTTCCTT
Found at i:53057559 original size:20 final size:18
Alignment explanation
Indices: 53057512--53057560 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
53057502 TAAGATAAAC
53057512 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
53057529 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
53057549 ATTAAATTAATA
1 ATTAAATTAATA
53057561 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:53060153 original size:19 final size:17
Alignment explanation
Indices: 53060119--53060153 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
53060109 CTAAAATAGT
53060119 AACAAAGTTAACAATAA
1 AACAAAGTTAACAATAA
53060136 AACAAGAGTTATACAATA
1 AACAA-AGTTA-ACAATA
53060154 TCCAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.20
Consensus pattern (17 bp):
AACAAAGTTAACAATAA
Found at i:53060218 original size:22 final size:22
Alignment explanation
Indices: 53060161--53060220 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
53060151 ATATCCAAAC
* *
53060161 AATAATAACAAAATAGTAGTAA
1 AATAATAAAAAAATAGTAGCAA
* *** *
53060183 CATAATAGTGAAATATTAGCAA
1 AATAATAAAAAAATAGTAGCAA
53060205 AATAATAAAAAAATAG
1 AATAATAAAAAAATAG
53060221 CATTTTTTTA
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (22 bp):
AATAATAAAAAAATAGTAGCAA
Found at i:53067856 original size:12 final size:12
Alignment explanation
Indices: 53067839--53067871 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
53067829 CAGGCCGCCC
53067839 ATATTAATTTTT
1 ATATTAATTTTT
53067851 ATATT-ATTTTT
1 ATATTAATTTTT
53067862 ATA-TAATTTT
1 ATATTAATTTT
53067872 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:53068039 original size:30 final size:30
Alignment explanation
Indices: 53067995--53068057 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
53067985 ACTTAACTAG
* *
53067995 CAAATATTTCTAAAATAATAACAAAATTAA
1 CAAATATTTCTAAAAAAACAACAAAATTAA
* *
53068025 CAAATGTTTTTAAAAAAACAACAAAATTAA
1 CAAATATTTCTAAAAAAACAACAAAATTAA
53068055 CAA
1 CAA
53068058 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATATTTCTAAAAAAACAACAAAATTAA
Found at i:53076445 original size:53 final size:53
Alignment explanation
Indices: 53076378--53076484 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
53076368 TTGTACCATG
** *
53076378 AATTGCTTTGAGTGTGGACTTAACCAATTGAATCAAAATACAGAACTAGAAAA
1 AATTGCTTCAAGTGTGGACTTAACCAATTGAATCAAAACACAGAACTAGAAAA
53076431 AATTGCTTCAAGTGTGGACTTAACCAATTGAATCAAAACACAGAACTAGAAAA
1 AATTGCTTCAAGTGTGGACTTAACCAATTGAATCAAAACACAGAACTAGAAAA
53076484 A
1 A
53076485 GTTTTCTCTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (53 bp):
AATTGCTTCAAGTGTGGACTTAACCAATTGAATCAAAACACAGAACTAGAAAA
Found at i:53077187 original size:12 final size:12
Alignment explanation
Indices: 53077170--53077194 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53077160 TGCAAACGGA
53077170 TCATTTCCATTT
1 TCATTTCCATTT
53077182 TCATTTCCATTT
1 TCATTTCCATTT
53077194 T
1 T
53077195 TGAAAACCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:53086891 original size:3 final size:3
Alignment explanation
Indices: 53086883--53086910 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
53086873 TACACTATTT
53086883 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
53086911 ACTTATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:53093688 original size:27 final size:28
Alignment explanation
Indices: 53093658--53093722 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
53093648 ATGTTTAGAC
**
53093658 TAAATTTTAAAAAA-AAATTGTTTTTTT
1 TAAATTTTAAAAAAGAAATTAATTTTTT
*
53093685 TAAATATTAAAAAAGTAAATTAATTTTTT
1 TAAATTTTAAAAAAG-AAATTAATTTTTT
*
53093714 AAAATTTTA
1 TAAATTTTA
53093723 TGAGAATAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 13 0.42
29 18 0.58
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (28 bp):
TAAATTTTAAAAAAGAAATTAATTTTTT
Found at i:53093959 original size:22 final size:22
Alignment explanation
Indices: 53093934--53093976 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
53093924 ATTTTTTTAC
*
53093934 AAAATAAT-TTTTGTATAAAAAT
1 AAAA-AATGTTTTGTAAAAAAAT
*
53093956 AAAAATTGTTTTGTAAAAAAA
1 AAAAAATGTTTTGTAAAAAAA
53093977 ATATAAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
AAAAAATGTTTTGTAAAAAAAT
Found at i:53094918 original size:27 final size:27
Alignment explanation
Indices: 53094861--53094919 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
53094851 AGGGAGGGAG
* * *
53094861 AAAAAATTAATAATTGGTGATTAAATTA
1 AAAAAATTAATAATTAGTGACT-AATGA
53094889 AAAAAATTAATAATTAGTGACCT-ATGA
1 AAAAAATTAATAATTAGTGA-CTAATGA
53094916 AAAA
1 AAAA
53094920 GAGAAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.26
28 19 0.70
29 1 0.04
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (27 bp):
AAAAAATTAATAATTAGTGACTAATGA
Found at i:53111960 original size:21 final size:21
Alignment explanation
Indices: 53111935--53111991 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
53111925 TACCATATTT
*
53111935 AATACCCTCACCAACATTTTC
1 AATACCCTAACCAACATTTTC
* * *
53111956 CATACACTAACCAGCATTTTC
1 AATACCCTAACCAACATTTTC
*
53111977 AATACCCTTACCAAC
1 AATACCCTAACCAAC
53111992 CTTTACATGG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.26
Consensus pattern (21 bp):
AATACCCTAACCAACATTTTC
Found at i:53112525 original size:16 final size:16
Alignment explanation
Indices: 53112504--53112537 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
53112494 ATAACAGGTT
53112504 AATATAATATTCTTTC
1 AATATAATATTCTTTC
53112520 AATATAATATTCTTTC
1 AATATAATATTCTTTC
53112536 AA
1 AA
53112538 GAATAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATAATATTCTTTC
Found at i:53119325 original size:17 final size:16
Alignment explanation
Indices: 53119303--53119342 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
53119293 ATCTTCCTGA
*
53119303 ACAAAAAATTAGATATG
1 ACAAAAAATTA-AGATG
53119320 ACAAAAAAATTAAGATG
1 AC-AAAAAATTAAGATG
53119337 ACAAAA
1 ACAAAA
53119343 TGAGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 8 0.38
18 9 0.43
ACGTcount: A:0.65, C:0.07, G:0.10, T:0.17
Consensus pattern (16 bp):
ACAAAAAATTAAGATG
Found at i:53119328 original size:18 final size:17
Alignment explanation
Indices: 53119305--53119342 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
53119295 CTTCCTGAAC
*
53119305 AAAAAATTAGATATGACA
1 AAAAAATTA-AGATGACA
53119323 AAAAAATTAAGATGACA
1 AAAAAATTAAGATGACA
53119340 AAA
1 AAA
53119343 TGAGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (17 bp):
AAAAAATTAAGATGACA
Found at i:53141091 original size:10 final size:10
Alignment explanation
Indices: 53141078--53141102 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53141068 ATTTTTAAAA
53141078 TTTTATAATT
1 TTTTATAATT
53141088 TTTTATAATT
1 TTTTATAATT
53141098 TTTTA
1 TTTTA
53141103 AAAATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTATAATT
Found at i:53141140 original size:5 final size:5
Alignment explanation
Indices: 53141130--53141156 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
53141120 TTTTTGAAAA
53141130 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
53141157 TTGTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:53143219 original size:14 final size:14
Alignment explanation
Indices: 53143200--53143229 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53143190 TAAACTTTCA
*
53143200 TATATATATATATG
1 TATATATATACATG
53143214 TATATATATACATG
1 TATATATATACATG
53143228 TA
1 TA
53143230 CATTATTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (14 bp):
TATATATATACATG
Found at i:53153602 original size:9 final size:9
Alignment explanation
Indices: 53153588--53153662 Score: 55
Period size: 9 Copynumber: 8.2 Consensus size: 9
53153578 TTTTACATAC
53153588 TTTTTAATT
1 TTTTTAATT
**
53153597 TTTTTAAAA
1 TTTTTAATT
* *
53153606 TTTAT-ACT
1 TTTTTAATT
53153614 TTTTTAATT
1 TTTTTAATT
53153623 TTTTTAATT
1 TTTTTAATT
**
53153632 TTAAAATATATT
1 TT--TTTA-ATT
53153644 TTTTTAA-T
1 TTTTTAATT
53153652 TTTTTAATT
1 TTTTTAATT
53153661 TT
1 TT
53153663 AAAATATTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
8 13 0.26
9 28 0.56
10 2 0.04
11 2 0.04
12 5 0.10
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTTAATT
Found at i:53153673 original size:11 final size:11
Alignment explanation
Indices: 53153659--53153709 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
53153649 AATTTTTTAA
53153659 TTTTAAAATAT
1 TTTTAAAATAT
53153670 TTTTAAAATACT
1 TTTTAAAATA-T
*
53153682 TTTT-TAAT-T
1 TTTTAAAATAT
53153691 TTTT-AAA-AT
1 TTTTAAAATAT
53153700 TTTTAAAATA
1 TTTTAAAATA
53153710 AAAATGGGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
9 12 0.35
10 3 0.09
11 14 0.41
12 5 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:53153685 original size:30 final size:30
Alignment explanation
Indices: 53153622--53153710 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 30
53153612 CTTTTTTAAT
**
53153622 TTTTTTAATTTTAAAATATATTTT--TTTAA
1 TTTTTTAATTTTAAAATAT-TTTTAAAATAA
*
53153651 TTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTTAAAATATTTTTAAAATAA
*
53153681 TTTTTTAATTTTTTAAA-ATTTTTAAAATAA
1 TTTTTTAA-TTTTAAAATATTTTTAAAATAA
53153711 AAATGGGCCG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
28 4 0.08
29 19 0.37
30 22 0.42
31 7 0.13
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTTTAATTTTAAAATATTTTTAAAATAA
Found at i:53153701 original size:40 final size:40
Alignment explanation
Indices: 53153613--53153709 Score: 112
Period size: 38 Copynumber: 2.5 Consensus size: 40
53153603 AAATTTATAC
** *
53153613 TTTTTTAATTTTT-TTA-ATTTTAAAATATATTTTTTTAA
1 TTTTTTAATTTTTAAAATATTTTAAAATATACTTTTTTAA
*
53153651 TTTTTTAA-TTTTAAAATATTTTTAAA-ATACTTTTTTAA
1 TTTTTTAATTTTTAAAATATTTTAAAATATACTTTTTTAA
53153689 TTTTTTAAAATTTTTAAAATA
1 TTTTTT--AATTTTTAAAATA
53153710 AAAATGGGCC
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
37 4 0.08
38 26 0.52
39 8 0.16
40 2 0.04
41 10 0.20
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (40 bp):
TTTTTTAATTTTTAAAATATTTTAAAATATACTTTTTTAA
Found at i:53156444 original size:29 final size:29
Alignment explanation
Indices: 53156352--53156428 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
53156342 AAAATATTTT
* *
53156352 AAAATTAATATAAACTTATAACAATCATA
1 AAAAATAATAAAAACTTATAACAATCATA
53156381 AAAAATAATAAAAACTTATAACAATCATA
1 AAAAATAATAAAAACTTATAACAATCATA
53156410 AAAAATAATAAAAACTTAT
1 AAAAATAATAAAAACTTAT
53156429 TAATATTATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (29 bp):
AAAAATAATAAAAACTTATAACAATCATA
Found at i:53156548 original size:19 final size:19
Alignment explanation
Indices: 53156381--53156613 Score: 66
Period size: 19 Copynumber: 11.9 Consensus size: 19
53156371 AACAATCATA
*
53156381 AAAAATAATAAAAACTTAT
1 AAAAATCATAAAAACTTAT
* * *
53156400 AACAATCATAAAAAATAAT
1 AAAAATCATAAAAACTTAT
* * *
53156419 AAAAACTTATTAATA-TTAT
1 AAAAA-TCATAAAAACTTAT
*
53156438 AAAAAATC-TAATAAA-TTTT
1 -AAAAATCATAA-AAACTTAT
* ****
53156457 AATAAATTATAATTTTTTTAT
1 AA-AAATCATAA-AAACTTAT
* *
53156478 AAAATTAATGAAAATACTTA-
1 AAAAATCAT-AAAA-ACTTAT
* * *
53156498 AAATATTATAAAAACGTAT
1 AAAAATCATAAAAACTTAT
* *
53156517 ACAAATTCTTAAAAACTTAT
1 A-AAAATCATAAAAACTTAT
*
53156537 AAAAATCATAAAAAATTATT
1 AAAAATCATAAAAACTTA-T
* *
53156557 AAGAA-CATTAAAA-TTGAT
1 AAAAATCATAAAAACTT-AT
* *
53156575 ACAAACTTATAAAAA-TTATTT
1 A-AAAATCATAAAAACTTA--T
53156596 AAAAAATCATAAAAACTT
1 -AAAAATCATAAAAACTT
53156614 GATTTAGACT
Statistics
Matches: 152, Mismatches: 44, Indels: 33
0.66 0.19 0.14
Matches are distributed among these distances:
18 12 0.08
19 62 0.41
20 53 0.35
21 22 0.14
22 3 0.02
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAATCATAAAAACTTAT
Found at i:53156553 original size:30 final size:30
Alignment explanation
Indices: 53156488--53156558 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
53156478 AAAATTAATG
* *
53156488 AAAATACTTAAAATATTATAAAAACGTATA
1 AAAATTCTTAAAATATTATAAAAACATATA
*
53156518 CAAATTCTTAAAA-ACTTATAAAAATCATA-A
1 AAAATTCTTAAAATA-TTATAAAAA-CATATA
*
53156548 AAAATTATTAA
1 AAAATTCTTAA
53156559 GAACATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 1 0.03
30 30 0.88
31 3 0.09
ACGTcount: A:0.59, C:0.08, G:0.01, T:0.31
Consensus pattern (30 bp):
AAAATTCTTAAAATATTATAAAAACATATA
Found at i:53157138 original size:21 final size:19
Alignment explanation
Indices: 53157104--53157176 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
53157094 ATAGTTCATG
53157104 TTTTTATGATTTTTTAATA
1 TTTTTATGATTTTTTAATA
* *
53157123 ATTTTAT-ATCATTTTTATTTA
1 TTTTTATGAT--TTTTTA-ATA
*
53157144 TTTTTAT-ATTTTTCAATA
1 TTTTTATGATTTTTTAATA
53157162 TTTTTTATGATTTTT
1 -TTTTTATGATTTTT
53157177 ATATGTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
18 4 0.09
19 18 0.41
20 12 0.27
21 10 0.23
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTTTATGATTTTTTAATA
Found at i:53157181 original size:11 final size:10
Alignment explanation
Indices: 53157104--53157187 Score: 70
Period size: 10 Copynumber: 8.6 Consensus size: 10
53157094 ATAGTTCATG
53157104 TTTTTATGAT-
1 TTTTTAT-ATA
53157114 TTTTTA-ATA
1 TTTTTATATA
*
53157123 ATTTTATATCA
1 TTTTTATAT-A
*
53157134 TTTTTATTTA
1 TTTTTATATA
53157144 TTTTTATAT-
1 TTTTTATATA
*
53157153 TTTTCA-ATA
1 TTTTTATATA
53157162 TTTTT-TATGA
1 TTTTTATAT-A
*
53157172 TTTTTATATG
1 TTTTTATATA
53157182 TTTTTA
1 TTTTTA
53157188 AGAAATTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
8 4 0.07
9 16 0.27
10 29 0.48
11 11 0.18
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (10 bp):
TTTTTATATA
Found at i:53157185 original size:19 final size:19
Alignment explanation
Indices: 53157101--53157206 Score: 74
Period size: 20 Copynumber: 5.4 Consensus size: 19
53157091 GATATAGTTC
53157101 ATGTTTTTATGATTTTTTAAT
1 ATGTTTTTATGA-TTTTT-AT
* *
53157122 AAT-TTTATATCATTTTTAT
1 -ATGTTTTTATGATTTTTAT
* *
53157141 TTATTTTTAT-ATTTTTCAAT
1 ATGTTTTTATGATTTTT--AT
53157161 AT-TTTTTATGATTTTTAT
1 ATGTTTTTATGATTTTTAT
* *
53157179 ATGTTTTTAAGAAATTTTAT
1 ATGTTTTTATG-ATTTTTAT
*
53157199 AGGTTTTT
1 ATGTTTTT
53157207 TTTATAAAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
18 11 0.16
19 22 0.31
20 28 0.40
21 7 0.10
22 2 0.03
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (19 bp):
ATGTTTTTATGATTTTTAT
Found at i:53157308 original size:8 final size:9
Alignment explanation
Indices: 53157244--53157370 Score: 73
Period size: 9 Copynumber: 13.8 Consensus size: 9
53157234 TAATGTTACA
53157244 AATTGTTTAT
1 AATT-TTTAT
53157254 AATTGTTTAT
1 AATT-TTTAT
*
53157264 TATTTTTAT
1 AATTTTTAT
*
53157273 AA-TATTAT
1 AATTTTTAT
53157281 AAGTTTTTATT
1 AA-TTTTTA-T
53157292 AATTTTTAT
1 AATTTTTAT
*
53157301 AATTTTATGT
1 AATTTT-TAT
* *
53157311 AATCTTAAT
1 AATTTTTAT
*
53157320 -ATTCTT-T
1 AATTTTTAT
*
53157327 AATATTTAAT
1 AAT-TTTTAT
*
53157337 GATTTTTAT
1 AATTTTTAT
*
53157346 GATTTTTAT
1 AATTTTTAT
*
53157355 GATTTTT-T
1 AATTTTTAT
53157363 AATATTTT
1 AAT-TTTT
53157371 TATGGGAAAA
Statistics
Matches: 93, Mismatches: 16, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
7 1 0.01
8 15 0.16
9 41 0.44
10 33 0.35
11 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.62
Consensus pattern (9 bp):
AATTTTTAT
Found at i:53157308 original size:28 final size:27
Alignment explanation
Indices: 53157249--53157308 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
53157239 TTACAAATTG
53157249 TTTATAATTGTTTATTATTTTTATAAT
1 TTTATAATTGTTTATTATTTTTATAAT
*
53157276 ATTATAAGTT-TTTATTAATTTTTATAAT
1 TTTATAA-TTGTTTATT-ATTTTTATAAT
53157304 TTTAT
1 TTTAT
53157309 GTAATCTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (27 bp):
TTTATAATTGTTTATTATTTTTATAAT
Done.