Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 132 of 318
Found at i:40804964 original size:15 final size:15
Alignment explanation
Indices: 40804944--40804972 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40804934 GTTCTGTTCA
40804944 CTCATTTCTTTTTCT
1 CTCATTTCTTTTTCT
40804959 CTCATTTCTTTTTC
1 CTCATTTCTTTTTC
40804973 AAACTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.66
Consensus pattern (15 bp):
CTCATTTCTTTTTCT
Found at i:40805119 original size:23 final size:23
Alignment explanation
Indices: 40805093--40805138 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
40805083 TCTCTTCACA
40805093 CTCTTTTTCTTTT-TCAATTTCTT
1 CTCTTTTT-TTTTCTCAATTTCTT
*
40805116 CTCTTTTTTTTTCTCGATTTCTT
1 CTCTTTTTTTTTCTCAATTTCTT
40805139 TCAAAATCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.07, C:0.22, G:0.02, T:0.70
Consensus pattern (23 bp):
CTCTTTTTTTTTCTCAATTTCTT
Found at i:40807414 original size:24 final size:24
Alignment explanation
Indices: 40807382--40807436 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
40807372 GTTGGGACAT
* *
40807382 ATTAAATTCGTCCACCAGCAGCTC
1 ATTAAATTCGTCAACCAACAGCTC
40807406 ATTAAATTCGTCAACCAACAGCTC
1 ATTAAATTCGTCAACCAACAGCTC
40807430 ATTAAAT
1 ATTAAAT
40807437 CTGTCCAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (24 bp):
ATTAAATTCGTCAACCAACAGCTC
Found at i:40808963 original size:126 final size:126
Alignment explanation
Indices: 40808738--40809112 Score: 502
Period size: 126 Copynumber: 3.0 Consensus size: 126
40808728 GGCCAAGTAT
* * *
40808738 GAACTACTGTAGAAAAAGAGCATCCATGTGAGAGCTTTTTTT-AGAAATTTTGATAACATTGA-A
1 GAACTACTGTAGAAAAAGAGCGTCCATGTGGGAG-TTTTTTTCAGAAATTTTGATGACATT-ACA
* *
40808801 TCCTACTTGAAGCGTTTTTGACACTATATGTTCAAAAACGTCTTCTTAAAATTATTTTTTCAA
64 TCCTACTTGAAGCGTTTTTGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAA
* * *
40808864 GAACTACTGTAGTAAAAGAGCGTCTATGTGGGAGTTTTTTTCAGAAATTTTAATGACATTACATC
1 GAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGTTTTTTTCAGAAATTTTGATGACATTACATC
* * * *
40808929 CTGCTTGAAGTGTTTTTGATACTATTTGTTCAAAAACGTCTTCTCAAAATTACTTTTTCAA
66 CTACTTGAAGCGTTTTTGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAA
* * * * * * * * * *
40808990 GAACTATTATAGCAAAAGAGTGTCCACGTGGGAGCTTTTTGCAAAAAATTTGATGACATTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGTTTTTTTCAGAAATTTTGATGACATTACATC
* *
40809055 CTACTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTT
66 CTACTTGAAGCGTTTTTGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTT
40809113 AGGGTAAAAA
Statistics
Matches: 217, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
125 8 0.04
126 209 0.96
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGTTTTTTTCAGAAATTTTGATGACATTACATC
CTACTTGAAGCGTTTTTGACACTATTTGTTCAAAAACGTCTTCTCAAAATTATTTTTTCAA
Found at i:40809144 original size:23 final size:25
Alignment explanation
Indices: 40809118--40809170 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 25
40809108 TTTTTAGGGT
40809118 AAAAATAATCA-AAT-TT-TGTTAAA
1 AAAAATAA-CACAATGTTATGTTAAA
* *
40809141 AAAATTAACACAATGTTATTTTAAA
1 AAAAATAACACAATGTTATGTTAAA
40809166 AAAAA
1 AAAAA
40809171 CTAAACCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 2 0.08
23 10 0.42
24 2 0.08
25 10 0.42
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (25 bp):
AAAAATAACACAATGTTATGTTAAA
Found at i:40809205 original size:28 final size:30
Alignment explanation
Indices: 40809173--40809252 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
40809163 AAAAAAAACT
**
40809173 AAACCCTAATTTAATTAAT-TTTAACCC-A
1 AAACCCTAATTTAATTAATCTAAAACCCTA
*
40809201 AAACCCTAATTTAATTTATCTAAAACCCTA
1 AAACCCTAATTTAATTAATCTAAAACCCTA
* *
40809231 GAACCCTAATTTACTTAATCTA
1 AAACCCTAATTTAATTAATCTA
40809253 TTTAAAAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
28 18 0.41
29 6 0.14
30 20 0.45
ACGTcount: A:0.41, C:0.23, G:0.01, T:0.35
Consensus pattern (30 bp):
AAACCCTAATTTAATTAATCTAAAACCCTA
Found at i:40809228 original size:22 final size:22
Alignment explanation
Indices: 40809200--40809453 Score: 80
Period size: 22 Copynumber: 11.5 Consensus size: 22
40809190 ATTTTAACCC
40809200 AAAACCCTAATTTAATTTATCT
1 AAAACCCTAATTTAATTTATCT
**
40809222 AAAACCCTAGAACCCTAATTTA-CT
1 AAAACCCT--AA-TTTAATTTATCT
* * **
40809246 -TAA-TCT-ATTTAA-AAATCAT
1 AAAACCCTAATTTAATTTATC-T
* * *
40809265 AA-ACCTTAATTTAATTTGTTT
1 AAAACCCTAATTTAATTTATCT
* *
40809286 TAAATCCTAATTTAATTTATCT
1 AAAACCCTAATTTAATTTATCT
* *
40809308 AAAACCCTAATTTAATTAATTTTAACCC
1 AAAACCCTAA--T--TTAA-TTT-ATCT
40809336 AAAACCCTAATTTAATTTATCT
1 AAAACCCTAATTTAATTTATCT
* **
40809358 AAAATCCTAGAACCCTAATTTA-CT
1 AAAACCCT--AA-TTTAATTTATCT
* * ** **
40809382 -TAA-TCT-ATTTAA-AAATAA
1 AAAACCCTAATTTAATTTATCT
*
40809400 AAAACCCTAATTTAATTTATTT
1 AAAACCCTAATTTAATTTATCT
* *
40809422 TAAACCCCAATTTAATTTATCT
1 AAAACCCTAATTTAATTTATCT
*
40809444 AAAATCCTAA
1 AAAACCCTAA
40809454 ACCCTAATTT
Statistics
Matches: 159, Mismatches: 49, Indels: 48
0.62 0.19 0.19
Matches are distributed among these distances:
17 2 0.01
18 7 0.04
19 6 0.04
20 3 0.02
21 14 0.09
22 73 0.46
23 7 0.04
24 13 0.08
25 14 0.09
26 5 0.03
27 3 0.02
28 12 0.08
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.39
Consensus pattern (22 bp):
AAAACCCTAATTTAATTTATCT
Found at i:40809278 original size:64 final size:63
Alignment explanation
Indices: 40809199--40809428 Score: 187
Period size: 64 Copynumber: 3.5 Consensus size: 63
40809189 AATTTTAACC
40809199 CAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAT
1 CAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAT
* * * * * ** * *
40809262 CATAAACCTTAATTTAATTTGTTTTAAATCCT--AA-TTTAATTTATCTAAAACCCTAATTTAAT
1 CA-AAACCCTAATTTAATTTATCTAAAACCCTAGAACCCTAATTTA-CT-TAA-TCT-ATTT-A-
*
40809324 TAATTTTAACC
59 -AA----AA-T
*
40809335 CAAAACCCTAATTTAATTTATCTAAAATCCTAGAACCCTAATTTACTTAATCTATTTAAAAAT
1 CAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAT
* * *
40809398 AAAAAACCCTAATTTAATTTATTTTAAACCC
1 -CAAAACCCTAATTTAATTTATCTAAAACCC
40809429 CAATTTAATT
Statistics
Matches: 127, Mismatches: 23, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
61 7 0.06
62 4 0.03
63 4 0.03
64 54 0.43
65 4 0.03
66 1 0.01
68 4 0.03
70 1 0.01
71 4 0.03
72 29 0.23
73 4 0.03
74 4 0.03
75 7 0.06
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.39
Consensus pattern (63 bp):
CAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCTAATTTACTTAATCTATTTAAAAAT
Found at i:40809374 original size:30 final size:28
Alignment explanation
Indices: 40809304--40809473 Score: 91
Period size: 29 Copynumber: 5.9 Consensus size: 28
40809294 AATTTAATTT
* * *
40809304 ATCTAAAACCCTAATTTAATTAATTTTAA
1 ATCT-AAACCCTAATTTAATTTATCTAAA
** *
40809333 CCCAAAACCCTAATTTAATTTATCTAAA
1 ATCTAAACCCTAATTTAATTTATCTAAA
* *
40809361 ATCCTAGAACCCTAATTTACTTAATCTATTTAAAA
1 AT-CTA-AACCCTAA--T--TTAATTTATCT-AAA
**
40809396 ATAAAAAACCCTAATTTAATTTAT-T---
1 AT-CTAAACCCTAATTTAATTTATCTAAA
*
40809421 -T-TAAACCCCAATTTAATTTATCTAAA
1 ATCTAAACCCTAATTTAATTTATCTAAA
* *
40809447 ATCCTAAACCCTAATTTACTTAATCTA
1 AT-CTAAACCCTAATTTAATTTATCTA
40809474 TTTAAAAATC
Statistics
Matches: 107, Mismatches: 20, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
22 18 0.17
23 1 0.01
24 1 0.01
27 1 0.01
28 21 0.20
29 24 0.22
30 16 0.15
32 2 0.02
34 17 0.16
35 6 0.06
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (28 bp):
ATCTAAACCCTAATTTAATTTATCTAAA
Found at i:40809405 original size:136 final size:136
Alignment explanation
Indices: 40809173--40809453 Score: 490
Period size: 136 Copynumber: 2.1 Consensus size: 136
40809163 AAAAAAAACT
40809173 AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCT
1 AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCT
* * * * * *
40809238 AATTTACTTAATCTATTTAAAAATCATAAACCTTAATTTAATTTGTTTTAAATCCTAATTTAATT
66 AATTTACTTAATCTATTTAAAAATAAAAAACCCTAATTTAATTTATTTTAAACCCCAATTTAATT
40809303 TATCTA
131 TATCTA
*
40809309 AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAATCCTAGAACCCT
1 AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCT
40809374 AATTTACTTAATCTATTTAAAAATAAAAAACCCTAATTTAATTTATTTTAAACCCCAATTTAATT
66 AATTTACTTAATCTATTTAAAAATAAAAAACCCTAATTTAATTTATTTTAAACCCCAATTTAATT
40809439 TATCTA
131 TATCTA
*
40809445 AAATCCTAA
1 AAACCCTAA
40809454 ACCCTAATTT
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
136 137 1.00
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.39
Consensus pattern (136 bp):
AAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTATCTAAAACCCTAGAACCCT
AATTTACTTAATCTATTTAAAAATAAAAAACCCTAATTTAATTTATTTTAAACCCCAATTTAATT
TATCTA
Found at i:40809480 original size:33 final size:34
Alignment explanation
Indices: 40809433--40809498 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
40809423 AAACCCCAAT
* *
40809433 TTAATTTATCT-AAAATCCTAAACCCTAATTTAC
1 TTAATCTATCTAAAAATCATAAACCCTAATTTAC
*
40809466 TTAATCTATTTAAAAATCATAAACCCTAATTTA
1 TTAATCTATCTAAAAATCATAAACCCTAATTTA
40809499 AATAATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 9 0.31
34 20 0.69
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (34 bp):
TTAATCTATCTAAAAATCATAAACCCTAATTTAC
Found at i:40809481 original size:85 final size:86
Alignment explanation
Indices: 40809337--40809499 Score: 292
Period size: 85 Copynumber: 1.9 Consensus size: 86
40809327 TTTTAACCCA
*
40809337 AAACCCTAATTTAATTTATCTAAAATCCTAGAACCCTAATTTACTTAATCTATTTAAAAATAAAA
1 AAACCCCAATTTAATTTATCTAAAATCCTAGAACCCTAATTTACTTAATCTATTTAAAAATAAAA
40809402 AACCCTAATTTAATTTATTTT
66 AACCCTAATTTAATTTATTTT
* *
40809423 AAACCCCAATTTAATTTATCTAAAATCCTA-AACCCTAATTTACTTAATCTATTTAAAAATCATA
1 AAACCCCAATTTAATTTATCTAAAATCCTAGAACCCTAATTTACTTAATCTATTTAAAAATAAAA
40809487 AACCCTAATTTAA
66 AACCCTAATTTAA
40809500 ATAATTTTTA
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
85 45 0.61
86 29 0.39
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.37
Consensus pattern (86 bp):
AAACCCCAATTTAATTTATCTAAAATCCTAGAACCCTAATTTACTTAATCTATTTAAAAATAAAA
AACCCTAATTTAATTTATTTT
Found at i:40809514 original size:119 final size:114
Alignment explanation
Indices: 40809291--40809504 Score: 250
Period size: 114 Copynumber: 1.8 Consensus size: 114
40809281 TGTTTTAAAT
* ** *
40809291 CCTAATTTAATTTATCTAAAACCCTAATTTAATTAATTTTAACCCAAAACCCTAATTTAATTTAT
1 CCTAATTTAATTTATCTAAAACCCCAATTTAATTAATTAAAACCCAAAACCCTAATTTAATCTAT
* **
40809356 CTAAAATCCTAGAACCCTAATTTACTTAATCTATTTAAAAATAAAAAAC
66 CTAAAATCATAGAACCCTAATTTAAATAATCTATTTAAAAATAAAAAAC
* * * * *
40809405 CCTAATTTAATTTATTTTAAACCCCAATTTAATTTATCTAAAATCCTAAACCCTAATTTACTTAA
1 CCTAATTTAATTTATCTAAAACCCCAATTTAATTAAT-TAAAACCCAAAACCCTAA--T--TTAA
*
40809470 TCTATTTAAAAATCATA-AACCCTAATTTAAATAAT
61 TCTATCT-AAAATCATAGAACCCTAATTTAAATAAT
40809505 TTTTATAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
114 33 0.41
115 14 0.17
117 1 0.01
119 25 0.31
120 8 0.10
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.38
Consensus pattern (114 bp):
CCTAATTTAATTTATCTAAAACCCCAATTTAATTAATTAAAACCCAAAACCCTAATTTAATCTAT
CTAAAATCATAGAACCCTAATTTAAATAATCTATTTAAAAATAAAAAAC
Found at i:40810255 original size:19 final size:19
Alignment explanation
Indices: 40810227--40810278 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
40810217 ATTTGACTTC
40810227 TTCATATTTAATTTTT-AA
1 TTCATATTTAATTTTTCAA
40810245 TTCAGTATTTAATTTTTCAA
1 TTCA-TATTTAATTTTTCAA
*
40810265 TTTATCATTTAATT
1 TTCAT-ATTTAATT
40810279 AACGATTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 4 0.13
19 13 0.43
20 13 0.43
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (19 bp):
TTCATATTTAATTTTTCAA
Found at i:40815693 original size:44 final size:46
Alignment explanation
Indices: 40815620--40815749 Score: 106
Period size: 49 Copynumber: 2.8 Consensus size: 46
40815610 TACAAAAATA
* * * *
40815620 ATTTAATACAAA-TAAT-TTTTTTTCCGTCATGCACATGTCA-TAAAC
1 ATTTAATACAAAGAAATCTATTTTT--GTCATGCACATGTAACCAAAC
* *
40815665 -TTTAATACAAAGAAATCTATTTTTGTCATGTACAATAATAACCAAAC
1 ATTTAATACAAAGAAATCTATTTTTGTCATGCAC-AT-GTAACCAAAC
* * *
40815712 AATTTAATACAAATAAATCTATTTTTGTCCTACACATG
1 -ATTTAATACAAAGAAATCTATTTTTGTCATGCACATG
40815750 ACTGACAATA
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
44 19 0.28
45 5 0.07
46 8 0.12
47 4 0.06
48 2 0.03
49 29 0.43
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (46 bp):
ATTTAATACAAAGAAATCTATTTTTGTCATGCACATGTAACCAAAC
Found at i:40815748 original size:93 final size:88
Alignment explanation
Indices: 40815619--40815818 Score: 201
Period size: 93 Copynumber: 2.2 Consensus size: 88
40815609 TTACAAAAAT
* * * **
40815619 AATTTAATACAAATAATTTTTTTTCCGTCATGCACATGTCAT-A-AACTTTAATACAAAGAAA-T
1 AATTTAATACAAATAATTATTTTT-CGTCATACACATGAC-TGACAA-TAAAATACAAAGAAATT
* *
40815681 CTATTTTTGTCATGTACAATAATAACCAAAC
63 C-ATTTCTATCATGT---ATAATAA-CAAAC
*
40815712 AATTTAATACAAATAAATCTATTTTT-GTCCTACACATGACTGACAATAAAATACAAAGAAATTC
1 AATTTAATACAAAT-AAT-TATTTTTCGTCATACACATGACTGACAATAAAATACAAAGAAATTC
40815776 ATTTCTATCATGTATAATAACAAAC
64 ATTTCTATCATGTATAATAACAAAC
*
40815801 AATTTAATACAAACAATT
1 AATTTAATACAAATAATT
40815819 CAAATATGAT
Statistics
Matches: 93, Mismatches: 9, Indels: 16
0.79 0.08 0.14
Matches are distributed among these distances:
87 1 0.01
88 3 0.03
89 18 0.19
90 7 0.08
92 1 0.01
93 50 0.54
94 7 0.08
95 6 0.06
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (88 bp):
AATTTAATACAAATAATTATTTTTCGTCATACACATGACTGACAATAAAATACAAAGAAATTCAT
TTCTATCATGTATAATAACAAAC
Found at i:40815814 original size:14 final size:15
Alignment explanation
Indices: 40815790--40815818 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40815780 CTATCATGTA
40815790 TAATAACAAACAATT
1 TAATAACAAACAATT
40815805 TAAT-ACAAACAATT
1 TAATAACAAACAATT
40815819 CAAATATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (15 bp):
TAATAACAAACAATT
Found at i:40816442 original size:19 final size:21
Alignment explanation
Indices: 40816396--40816443 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
40816386 ATAATAAATT
40816396 AAATAAAT-TTAAAAACATAA
1 AAATAAATATTAAAAACATAA
*
40816416 AAACAAATATT-AAAACA-AA
1 AAATAAATATTAAAAACATAA
40816435 AAATAAATA
1 AAATAAATA
40816444 AAAAATGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 13 0.52
21 2 0.08
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (21 bp):
AAATAAATATTAAAAACATAA
Found at i:40819896 original size:2 final size:2
Alignment explanation
Indices: 40819883--40819916 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
40819873 GATGCCCTTT
* *
40819883 GA GA GA GT GA GA GA GA GA GA GG GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
40819917 ACGGAATCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.53, T:0.03
Consensus pattern (2 bp):
GA
Found at i:40822617 original size:23 final size:23
Alignment explanation
Indices: 40822590--40822643 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
40822580 CCAATTTAAT
*
40822590 AATTTTAAAATCAAATTAAATCA
1 AATTTTAAAAACAAATTAAATCA
40822613 AATTTTAAAAACAAATTAAATCA
1 AATTTTAAAAACAAATTAAATCA
40822636 AATTTTAA
1 AATTTTAA
40822644 CAAATTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (23 bp):
AATTTTAAAAACAAATTAAATCA
Found at i:40822629 original size:13 final size:13
Alignment explanation
Indices: 40822590--40822643 Score: 57
Period size: 10 Copynumber: 4.6 Consensus size: 13
40822580 CCAATTTAAT
40822590 AATTTTAAAATCA
1 AATTTTAAAATCA
40822603 AA--TT-AAATCA
1 AATTTTAAAATCA
*
40822613 AATTTTAAAAACA
1 AATTTTAAAATCA
40822626 AA--TT-AAATCA
1 AATTTTAAAATCA
40822636 AATTTTAA
1 AATTTTAA
40822644 CAAATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
10 15 0.45
11 4 0.12
12 4 0.12
13 10 0.30
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTTTAAAATCA
Found at i:40823362 original size:20 final size:20
Alignment explanation
Indices: 40823337--40823402 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
40823327 TATTTTTTAG
40823337 TTAATTATTAAGTTATAATT
1 TTAATTATTAAGTTATAATT
*
40823357 TTAATTAGGTAA-TTATAATT
1 TTAATTA-TTAAGTTATAATT
* * * *
40823377 TTAA-AATTTAGATAAAATT
1 TTAATTATTAAGTTATAATT
40823396 TTAATTA
1 TTAATTA
40823403 AATAAAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.31
20 20 0.56
21 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (20 bp):
TTAATTATTAAGTTATAATT
Found at i:40829647 original size:354 final size:355
Alignment explanation
Indices: 40828979--40829687 Score: 1177
Period size: 354 Copynumber: 2.0 Consensus size: 355
40828969 TTCAAATTGT
* *
40828979 CCAAATCCTTTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTTCAGCTTCTAGTTTTTGGACATCGA
1 CCAAATCCTCTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTTCAGCTTCTAGTTTCTGGACATCGA
*
40829044 CATCTAGCCCCAACTGCATCTTTTCTCCCTCCAATTGCTCGATCCATTTTTCTAGCTCCAAACTT
66 CATCTAGCCCCAACTGCATCTTTTCTCCCTCCAATTGCTCGATCCATTTTTCTAGCTCCAAACTC
*
40829109 TTTCTCTCAAAATCTTATTTAATGATCTCTAACTCAGATGGGATCACCTTCAAGTGTTCTTCCAT
131 TTTCTCTCAAAATCTTATTTAATGATCTCTAACTCAAATGGGATCACCTTCAAGTGTTCTTCCAT
* *
40829174 TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTGTCGCTGATCCTCTAACCCCACCATTAGT
196 TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTGTCACTGATCCTCTAACCCCACCATCAGT
* *
40829239 CATACTCAGGGGTAGTCATTGGATTAGCAGCAAACCTTTTCATTTTACGAGTTTGGTTCCAGGCA
261 CATACTCAGGGGTAGTCATTAGATTAGCAGCAAACCTTTTCATTTTACGAGTTTGGTTCCAGACA
40829304 TTCGATATCTCACGAACTTTCTTTTTGTAA
326 TTCGATATCTCACGAACTTTCTTTTTGTAA
*
40829334 CCAAATCCTCTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTT-AGCTTCTAGTTTCTGGACATTGA
1 CCAAATCCTCTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTTCAGCTTCTAGTTTCTGGACATCGA
* * * ** * * *
40829398 CATCTAGCCCCAGCTGTATTTTTTCTCCCTTTAATTGCTGGATCCTTTTTTCTAGCTCCGAACTC
66 CATCTAGCCCCAACTGCATCTTTTCTCCCTCCAATTGCTCGATCCATTTTTCTAGCTCCAAACTC
* *
40829463 TTTCTCTCAAAATCTTGTTTGATGATCTCTAACTCAAATGGGATCACCTTCAAGTGTTCTTCCAT
131 TTTCTCTCAAAATCTTATTTAATGATCTCTAACTCAAATGGGATCACCTTCAAGTGTTCTTCCAT
* * *
40829528 TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTGTCATTGATCTTCTGACCCCACCATCAGT
196 TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTGTCACTGATCCTCTAACCCCACCATCAGT
* * *
40829593 CATACTCAGGGGTGGTCATTAGATTAGCAGCAAACCTTTTCATTTTATGAGTTTGGTTCTAGACA
261 CATACTCAGGGGTAGTCATTAGATTAGCAGCAAACCTTTTCATTTTACGAGTTTGGTTCCAGACA
*
40829658 TTTGATATCTCACGAACTTTCTTTTTGTAA
326 TTCGATATCTCACGAACTTTCTTTTTGTAA
40829688 TTATCTCCCT
Statistics
Matches: 328, Mismatches: 26, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
354 288 0.88
355 40 0.12
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.40
Consensus pattern (355 bp):
CCAAATCCTCTTCAGCCTTTTTTTTCCTTTTCTCAGCTTTTCAGCTTCTAGTTTCTGGACATCGA
CATCTAGCCCCAACTGCATCTTTTCTCCCTCCAATTGCTCGATCCATTTTTCTAGCTCCAAACTC
TTTCTCTCAAAATCTTATTTAATGATCTCTAACTCAAATGGGATCACCTTCAAGTGTTCTTCCAT
TGATCGGGTGTTTTCTTGATCTGACGTAGGGATGTTGTCACTGATCCTCTAACCCCACCATCAGT
CATACTCAGGGGTAGTCATTAGATTAGCAGCAAACCTTTTCATTTTACGAGTTTGGTTCCAGACA
TTCGATATCTCACGAACTTTCTTTTTGTAA
Found at i:40832557 original size:3 final size:3
Alignment explanation
Indices: 40832551--40832603 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
40832541 TAATAGTAAG
40832551 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
40832599 AAC AA
1 AAC AA
40832604 TAATAATAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:40833816 original size:21 final size:21
Alignment explanation
Indices: 40833786--40833838 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
40833776 TAATTTTTGG
*
40833786 GTTTTAGGTTTAGGTTGGTTT
1 GTTTTGGGTTTAGGTTGGTTT
** *
40833807 -TTATTGGGTTGGGGTTTGTTT
1 GTT-TTGGGTTTAGGTTGGTTT
40833828 GTTTTGGGTTT
1 GTTTTGGGTTT
40833839 GATGGTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.06, C:0.00, G:0.36, T:0.58
Consensus pattern (21 bp):
GTTTTGGGTTTAGGTTGGTTT
Found at i:40835486 original size:20 final size:20
Alignment explanation
Indices: 40835463--40835503 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40835453 ATTTCTGGTG
*
40835463 GCTTGTCCACAATGCTGGCA
1 GCTTGTCCACAATACTGGCA
*
40835483 GCTTGTCTACAATACTGGCA
1 GCTTGTCCACAATACTGGCA
40835503 G
1 G
40835504 TTTATCTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (20 bp):
GCTTGTCCACAATACTGGCA
Found at i:40835511 original size:20 final size:20
Alignment explanation
Indices: 40835471--40835520 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
40835461 TGGCTTGTCC
* *
40835471 ACAATGCTGGCAGCTTGTCT
1 ACAATACTGGCAGCTTATCT
*
40835491 ACAATACTGGCAGTTTATCT
1 ACAATACTGGCAGCTTATCT
*
40835511 ACATTACTGG
1 ACAATACTGG
40835521 TGGTTTGTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (20 bp):
ACAATACTGGCAGCTTATCT
Found at i:40835526 original size:20 final size:20
Alignment explanation
Indices: 40835488--40835601 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
40835478 TGGCAGCTTG
* *
40835488 TCTACAATACTGGCAGTTTA
1 TCTACATTACTGGTAGTTTA
* *
40835508 TCTACATTACTGGTGGTTTG
1 TCTACATTACTGGTAGTTTA
* * *
40835528 TCTACATTATTGGTAGCTTG
1 TCTACATTACTGGTAGTTTA
* *
40835548 TCTGCATTACTGGTGGCTTGT-
1 TCTACATTACTGGTAG-TT-TA
40835569 TC-ACATTTA-TGGTAGTTTA
1 TCTACA-TTACTGGTAGTTTA
**
40835588 TCTGTATTACTGGT
1 TCTACATTACTGGT
40835602 GGCTTGTCCA
Statistics
Matches: 73, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.01
19 7 0.10
20 58 0.79
21 6 0.08
22 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (20 bp):
TCTACATTACTGGTAGTTTA
Found at i:40835546 original size:60 final size:60
Alignment explanation
Indices: 40835442--40835560 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
40835432 AAGTACTGAT
* * *
40835442 AGTTTATCTGCATTTCTGGTGGCTTGTCCACAATGCTGGCAGCTTGTCTACAATACTGGC
1 AGTTTATCTACATTACTGGTGGCTTGTCCACAATACTGGCAGCTTGTCTACAATACTGGC
* * * * * * *
40835502 AGTTTATCTACATTACTGGTGGTTTGTCTACATTATTGGTAGCTTGTCTGCATTACTGG
1 AGTTTATCTACATTACTGGTGGCTTGTCCACAATACTGGCAGCTTGTCTACAATACTGG
40835561 TGGCTTGTTC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.39
Consensus pattern (60 bp):
AGTTTATCTACATTACTGGTGGCTTGTCCACAATACTGGCAGCTTGTCTACAATACTGGC
Found at i:40835556 original size:40 final size:40
Alignment explanation
Indices: 40835483--40835609 Score: 150
Period size: 40 Copynumber: 3.2 Consensus size: 40
40835473 AATGCTGGCA
* * * *
40835483 GCTTGTCTACAATACTGGCAGTTTATCTACATTACTGGTG
1 GCTTGTCTACATTATTGGTAGTTTATCTGCATTACTGGTG
* * *
40835523 GTTTGTCTACATTATTGGTAGCTTGTCTGCATTACTGGTG
1 GCTTGTCTACATTATTGGTAGTTTATCTGCATTACTGGTG
*
40835563 GCTTGT-TCACATT-TATGGTAGTTTATCTGTATTACTGGTG
1 GCTTGTCT-ACATTAT-TGGTAGTTTATCTGCATTACTGGTG
40835603 GCTTGTC
1 GCTTGTC
40835610 CACAAAATGG
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.03
40 71 0.97
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (40 bp):
GCTTGTCTACATTATTGGTAGTTTATCTGCATTACTGGTG
Found at i:40838242 original size:10 final size:10
Alignment explanation
Indices: 40838221--40838255 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
40838211 AATTAAATTC
40838221 TAAAAGATAAA
1 TAAAA-ATAAA
40838232 TAAAAATAAA
1 TAAAAATAAA
*
40838242 TAAAGATAAA
1 TAAAAATAAA
40838252 TAAA
1 TAAA
40838256 TATTAAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:40839503 original size:26 final size:26
Alignment explanation
Indices: 40839472--40839524 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
40839462 AACCACCAAG
40839472 TATATCCCATTGTGATTGAAATAATT
1 TATATCCCATTGTGATTGAAATAATT
*
40839498 TATATCTCATTGTGATTGAAATAATT
1 TATATCCCATTGTGATTGAAATAATT
40839524 T
1 T
40839525 TGCAAGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (26 bp):
TATATCCCATTGTGATTGAAATAATT
Found at i:40843601 original size:21 final size:21
Alignment explanation
Indices: 40843577--40843617 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40843567 ATTTGCTCAA
*
40843577 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGTTGTGGAGTAC
40843598 ACTCCACCTGTTGTGGAGTA
1 ACTCCACCTGTTGTGGAGTA
40843618 TCGCTCGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGTTGTGGAGTAC
Found at i:40846386 original size:16 final size:16
Alignment explanation
Indices: 40846361--40846391 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40846351 CACCACTTGG
*
40846361 ATTGTTTGCCATTAAA
1 ATTGTCTGCCATTAAA
40846377 ATTGTCTGCCATTAA
1 ATTGTCTGCCATTAA
40846392 TCATAATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (16 bp):
ATTGTCTGCCATTAAA
Found at i:40849487 original size:31 final size:31
Alignment explanation
Indices: 40849451--40849516 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
40849441 TTTTTTAGCT
*
40849451 AAATTTGACCATAAATCTTTTAAAAACAGTC
1 AAATTTGACCATAAACCTTTTAAAAACAGTC
* **
40849482 AAATTTGACTATAAACCTTTTAAAAGGAGTC
1 AAATTTGACCATAAACCTTTTAAAAACAGTC
40849513 AAAT
1 AAAT
40849517 AGTTGCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (31 bp):
AAATTTGACCATAAACCTTTTAAAAACAGTC
Found at i:40849632 original size:16 final size:17
Alignment explanation
Indices: 40849607--40849645 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
40849597 TTTTATACTT
*
40849607 TTTTTTAATTTTT-ATA
1 TTTTTAAATTTTTAATA
40849623 TTTTTAAATTTTTGAATA
1 TTTTTAAATTTTT-AATA
40849641 TTTTT
1 TTTTT
40849646 TTATCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
18 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTTAAATTTTTAATA
Found at i:40851609 original size:12 final size:12
Alignment explanation
Indices: 40851592--40851621 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40851582 GGAAAAGCTT
40851592 AAATAATGACAA
1 AAATAATGACAA
*
40851604 AAATAATTACAA
1 AAATAATGACAA
40851616 AAATAA
1 AAATAA
40851622 AAATAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (12 bp):
AAATAATGACAA
Found at i:40859685 original size:46 final size:45
Alignment explanation
Indices: 40859581--40859810 Score: 178
Period size: 46 Copynumber: 4.9 Consensus size: 45
40859571 ACATATCAAT
* * * *
40859581 GCCGATGCTATATCCCAGATATGGTCTTACACTGGCTCTTACATATCCG
1 GCCGATGC-ATGTCCCAGACAT-GTCTTACACTGG--CTTACATCTCAG
** *
40859630 TGTTGATGCATGTCCCAAACATGTCTTACACTGGCTTACATCTCGAG
1 -GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTC-AG
* * *
40859677 GCCGATGCATGTCCCAGACATGTCTTACACTAG--TACTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTA--CATCTC-AG
* * *
40859723 GCCGATGCCATGTCCCAGGCATGGTCTTACACTGGCTTTCATAAT-ATG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACAT-CTCA-G
* * *
40859771 GCCGATGCATGTCCTAGACATGTCTTGCACTGGCTCACAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACAT
40859811 AATAGCAGTG
Statistics
Matches: 146, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
44 2 0.01
46 67 0.46
47 27 0.18
48 32 0.22
49 11 0.08
50 7 0.05
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCAG
Found at i:40866260 original size:46 final size:46
Alignment explanation
Indices: 40866101--40866384 Score: 240
Period size: 46 Copynumber: 6.1 Consensus size: 46
40866091 GAAATCTTAC
* * * *
40866101 ACATATCGATGCCAATGCCATATCCCAGATATGGTCTTACACTGGCTCTT
1 ACATCTCGATGCCGATG-CATGTCCCAGACAT-GTCTTACACTGG--CTT
* * * * *
40866151 ACATATCCATGCCGATGCATGTTCCAAACATGTCTTACACTAGC--
1 ACATCTCGATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
40866195 ACATCTCG-TAGCCGATGCATGTCCC-GAACATGTCTTACACTGGCTT
1 ACATCTCGAT-GCCGATGCATGTCCCAG-ACATGTCTTACACTGGCTT
* * * *
40866241 ACATCTCGAGGCTGATGCATGTCCCAGACATGTCTTACACCGGCACT
1 ACATCTCGATGCCGATGCATGTCCCAGACATGTCTTACACTGGC-TT
* *
40866288 -CATCTCAATGCCGATGCCATGTCCCAGACATGGTCTTCCACTGGCTT
1 ACATCTCGATGCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTT
* * * * *
40866335 TCATAAT--ATGGCCGGTGCATGTCCCAGACATGTCTTGCACTGGCTC
1 ACAT-CTCGAT-GCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
40866381 ACAT
1 ACAT
40866385 AACAGCAGTG
Statistics
Matches: 195, Mismatches: 27, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 36 0.18
46 68 0.35
47 33 0.17
48 31 0.16
49 11 0.06
50 15 0.08
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (46 bp):
ACATCTCGATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
Found at i:40866354 original size:94 final size:91
Alignment explanation
Indices: 40866100--40866370 Score: 275
Period size: 94 Copynumber: 2.9 Consensus size: 91
40866090 GGAAATCTTA
* * * *
40866100 CACATATCGATGCCAATGCCATATCCCAGATATGGTCTTACACTGGCTCTTACATATCCAT-GCC
1 CACATCTC-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TT-CATAT-CATGGCC
* * *
40866164 GATGCATGTTCCAAACATGTCTTACACTAG
62 GATGCATGTCCCAGACATGTCTTACACCAG
* * * *
40866194 CACATCTCGTAGCCGATG-CATGTCCC-GAACAT-GTCTTACACTGGCTTACATCTCGA-GGCTG
1 CACATCTCAT-GCCGATGCCATGTCCCAG-ACATGGTCTTACACTGGCTTTCATATC-ATGGCCG
*
40866255 ATGCATGTCCCAGACATGTCTTACACCGG
63 ATGCATGTCCCAGACATGTCTTACACCAG
*
40866284 CACTCATCTCAATGCCGATGCCATGTCCCAGACATGGTCTTCCACTGGCTTTCATAAT-ATGGCC
1 CA--CATCTC-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCAT-ATCATGGCC
*
40866348 GGTGCATGTCCCAGACATGTCTT
62 GATGCATGTCCCAGACATGTCTT
40866371 GCACTGGCTC
Statistics
Matches: 147, Mismatches: 18, Indels: 24
0.78 0.10 0.13
Matches are distributed among these distances:
89 1 0.01
90 35 0.24
91 1 0.01
92 28 0.19
93 25 0.17
94 56 0.38
95 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (91 bp):
CACATCTCATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATCATGGCCGATG
CATGTCCCAGACATGTCTTACACCAG
Found at i:40879608 original size:22 final size:21
Alignment explanation
Indices: 40879589--40879629 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40879579 AATATGTTCT
*
40879589 GCATCTGTATCTGAACTGTTTA
1 GCATCT-TACCTGAACTGTTTA
*
40879611 GCGTCTTACCTGAACTGTT
1 GCATCTTACCTGAACTGTT
40879630 ACGATAGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (21 bp):
GCATCTTACCTGAACTGTTTA
Found at i:40898856 original size:24 final size:23
Alignment explanation
Indices: 40898800--40898915 Score: 101
Period size: 23 Copynumber: 4.9 Consensus size: 23
40898790 AACTCACCGT
*
40898800 AGCTCGTATGAGCTTACTGATATATC
1 AGCTCGTAAGAGCTTACTG-T-T-TC
40898826 AGCTCGTAAGAGCTTACTGTTCTC
1 AGCTCGTAAGAGCTTACTGTT-TC
* **
40898850 AGCTCGTATGAGCTTACTAATTC
1 AGCTCGTAAGAGCTTACTGTTTC
* * *
40898873 AGCTCGTTAGAGCTTATTGTTTT
1 AGCTCGTAAGAGCTTACTGTTTC
40898896 AGCT--TAATAGAGCTTACTGT
1 AGCTCGT-A-AGAGCTTACTGT
40898916 CCATTAGCTT
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.01
23 34 0.45
24 21 0.28
25 1 0.01
26 18 0.24
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (23 bp):
AGCTCGTAAGAGCTTACTGTTTC
Found at i:40899638 original size:15 final size:15
Alignment explanation
Indices: 40899618--40899647 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40899608 GTTGATGAAA
40899618 TGGAGATGTGCAAAT
1 TGGAGATGTGCAAAT
*
40899633 TGGAGATGTTCAAAT
1 TGGAGATGTGCAAAT
40899648 GTGTTTGTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (15 bp):
TGGAGATGTGCAAAT
Found at i:40899906 original size:30 final size:30
Alignment explanation
Indices: 40899863--40899926 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
40899853 ACGGGAAGAG
* *
40899863 ACACCGGCGTGTGTCTCAG-CAGTGTGTGAC
1 ACACCGGCCTGTGTCTCAGCCA-TGTGCGAC
*
40899893 ACACGGGCCTGTGTCTCAGCCATGTGCGAC
1 ACACCGGCCTGTGTCTCAGCCATGTGCGAC
40899923 ACAC
1 ACAC
40899927 AGTTATGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.20
Consensus pattern (30 bp):
ACACCGGCCTGTGTCTCAGCCATGTGCGAC
Found at i:40907460 original size:54 final size:54
Alignment explanation
Indices: 40907265--40907681 Score: 362
Period size: 55 Copynumber: 7.9 Consensus size: 54
40907255 TTTCCTTTTT
* * * *
40907265 GAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* * * ** *
40907318 GAACTCACCAATGCCATGCCTTGGCATGATCTTACATGGGA-CCTTTGTCTTATA
1 GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATA
* * * * *
40907372 GTAACTCT-TCAATGTCATGTCTTGACATGGTCTTACATGATTTCCTAGCCTTATA
1 G-AACT-TACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* *
40907427 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATA----T-CCTTAT-
1 GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
** * *
40907475 ---CTTACCATATGCCATGTTCC-AAACATGGTCTTAAATGGTATCCTTGCCTTAT-
1 GAACTTACCA-ATGCCATG--CCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* **
40907527 GAACTCACCAATGCCATGCCTTCG-CATGGTCTTACATGGGA-CCTTTGCCTTATA
1 GAACTTACCAATGCCATGCCTT-GACATGGTCTTACATGATATCC-TTGCCTTATA
* * * * *
40907581 GTAACTCATCAATGCCATGTCTTGACATAGTCTTACATGATTTCCTTGCCTTATA
1 G-AACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* *
40907636 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTT
40907682 ATCTTACCAA
Statistics
Matches: 294, Mismatches: 46, Indels: 47
0.76 0.12 0.12
Matches are distributed among these distances:
45 6 0.02
46 8 0.03
47 15 0.05
48 2 0.01
49 6 0.02
51 1 0.00
52 12 0.04
53 67 0.23
54 85 0.29
55 88 0.30
56 4 0.01
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (54 bp):
GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
Found at i:40907463 original size:109 final size:108
Alignment explanation
Indices: 40907276--40907673 Score: 499
Period size: 109 Copynumber: 3.7 Consensus size: 108
40907266 AACTTACCAT
* *
40907276 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
* * *
40907341 GCATGATCTTACATGGGACCTTTGTCTTATAGTAACTCTTCAA
66 GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
* * * * *
40907384 TGTCATGTCTTGACATGGTCTTACATGATTTCCTAGCCTTATAGAACTTATCAATGCCATGCCTT
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAT-GAACTCACCAATGCCATGCCTT
* * *
40907449 GGCATGGTCTTACAT--GA--TAT-CCTTAT-CTTAC-CAT--A
65 GGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
*** * *
40907484 TGCCATGTTCCAAACATGGTCTTAAATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTT
1 TGCCATG-TCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATGCCATGCCTT
*
40907549 CGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
65 GGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
* * * *
40907593 TGCCATGTCTTGACATAGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTT
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAT-GAACTCACCAATGCCATGCCTT
40907658 GGCATGGTCTTACATG
65 GGCATGGTCTTACATG
40907674 ATATCCTTAT
Statistics
Matches: 241, Mismatches: 37, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
100 41 0.17
101 28 0.12
102 4 0.02
103 3 0.01
104 7 0.03
105 8 0.03
106 3 0.01
107 5 0.02
108 65 0.27
109 77 0.32
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (108 bp):
TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
Found at i:40907648 original size:209 final size:209
Alignment explanation
Indices: 40907288--40907734 Score: 786
Period size: 209 Copynumber: 2.1 Consensus size: 209
40907278 CCATGTCTTG
* *
40907288 ACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTGGCATGATCTTAC
1 ACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTCGCATGATCTTAC
* * * *
40907353 ATGGGACCTTTGTCTTATAGTAACTCTTCAATGTCATGTCTTGACATGGTCTTACATGATTTCCT
66 ATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATAGTCTTACATGATTTCCT
*
40907418 AGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAT
131 AGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAA
40907483 ATGCCATGTTCCAA
196 ATGCCATGTTCCAA
* *
40907497 ACATGGTCTTAAATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTCGCATGGTCTTAC
1 ACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTCGCATGATCTTAC
40907562 ATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATAGTCTTACATGATTTCCT
66 ATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATAGTCTTACATGATTTCCT
*
40907627 TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAA
131 AGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAA
*
40907692 ATGTCATGTTCCAA
196 ATGCCATGTTCCAA
*
40907706 ACATGGTCTTACATGGTATCCTTGTCTTA
1 ACATGGTCTTACATGGTATCCTTGCCTTA
40907735 GTGCCAATGC
Statistics
Matches: 225, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
209 225 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (209 bp):
ACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTCGCATGATCTTAC
ATGGGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATAGTCTTACATGATTTCCT
AGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAA
ATGCCATGTTCCAA
Found at i:40909429 original size:20 final size:21
Alignment explanation
Indices: 40909401--40909440 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40909391 GCTTTAGTTT
*
40909401 AGCTTTTTCAAG-TTCTGTTC
1 AGCTCTTTCAAGCTTCTGTTC
*
40909421 AGCTCTTTCGAGCTTCTGTT
1 AGCTCTTTCAAGCTTCTGTT
40909441 AAACTCTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.47
Consensus pattern (21 bp):
AGCTCTTTCAAGCTTCTGTTC
Found at i:40909439 original size:21 final size:21
Alignment explanation
Indices: 40909380--40909479 Score: 84
Period size: 21 Copynumber: 4.9 Consensus size: 21
40909370 CTTTCTATTT
* *
40909380 AGCTCTTTCGTGCTT-TAGTTT
1 AGCTCTTTCGAGCTTCT-GTTA
* * *
40909401 AGCTTTTTCAAG-TTCTGTTC
1 AGCTCTTTCGAGCTTCTGTTA
40909421 AGCTCTTTCGAGCTTCTGTTA
1 AGCTCTTTCGAGCTTCTGTTA
* *
40909442 AACTCTTAT-GAGTTTCTGTTA
1 AGCTCTT-TCGAGCTTCTGTTA
40909463 AG--CTTTCGAGCTTCTGT
1 AGCTCTTTCGAGCTTCTGT
40909480 CAGTGTATCT
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
18 1 0.02
19 12 0.19
20 15 0.23
21 35 0.55
22 1 0.02
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
AGCTCTTTCGAGCTTCTGTTA
Found at i:40917412 original size:20 final size:20
Alignment explanation
Indices: 40917387--40917440 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
40917377 GGGATTGCAC
40917387 TTTGGTGTCTCTATTAGCAT
1 TTTGGTGTCTCTATTAGCAT
40917407 TTTGGTGTCTCTATTAGCAT
1 TTTGGTGTCTCTATTAGCAT
*
40917427 TTTGATGCTCTCTA
1 TTTGGTG-TCTCTA
40917441 GTGTGTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 26 0.81
21 6 0.19
ACGTcount: A:0.15, C:0.17, G:0.19, T:0.50
Consensus pattern (20 bp):
TTTGGTGTCTCTATTAGCAT
Found at i:40919230 original size:20 final size:20
Alignment explanation
Indices: 40919183--40919233 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 20
40919173 TGCTCTATAT
*
40919183 ATTATTT-TATT-TTTTTGA
1 ATTATTTATATTATTTTTAA
40919201 A-TA-TTA-ATTATTTTTAA
1 ATTATTTATATTATTTTTAA
40919218 ATTATTTATATTATTT
1 ATTATTTATATTATTT
40919234 ACTTTAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
16 5 0.19
17 9 0.33
18 3 0.11
19 3 0.11
20 7 0.26
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTATTTATATTATTTTTAA
Found at i:40919252 original size:25 final size:24
Alignment explanation
Indices: 40919219--40919290 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 24
40919209 TATTTTTAAA
40919219 TTATTTATATTATTTACTTTAAA-C
1 TTATTTATATTATTTA-TTTAAACC
* * *
40919243 TGTTTTTATAGTATCTATTTTAAACC
1 T-TATTTATATTATTTA-TTTAAACC
*
40919269 TTATATATATTATTTATTTAAA
1 TTATTTATATTATTTATTTAAA
40919291 ATTATCTTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
24 7 0.18
25 29 0.76
26 2 0.05
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (24 bp):
TTATTTATATTATTTATTTAAACC
Found at i:40921636 original size:22 final size:23
Alignment explanation
Indices: 40921611--40921674 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 23
40921601 GATTATCTTT
40921611 TTTAATA-ATATTATTTTAAAAA
1 TTTAATATATATTATTTTAAAAA
*
40921633 TTTAAATCATATATTTCTTTTAAAAA
1 TTT-AAT-ATATA-TTATTTTAAAAA
* *
40921659 TATAATATATCTTATT
1 TTTAATATATATTATT
40921675 ATTACATCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
22 3 0.09
23 7 0.21
24 5 0.15
25 6 0.18
26 13 0.38
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAATATATATTATTTTAAAAA
Found at i:40922497 original size:16 final size:16
Alignment explanation
Indices: 40922476--40922525 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
40922466 AGTTAATTAT
40922476 TAAATTTATATAAATA
1 TAAATTTATATAAATA
*
40922492 TAAA-TTAT-TAATTTA
1 TAAATTTATATAA-ATA
40922507 TTAAATTTTATATAAATA
1 -TAAA-TTTATATAAATA
40922525 T
1 T
40922526 TTTATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.11
15 6 0.22
16 8 0.30
17 1 0.04
18 6 0.22
19 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATTTATATAAATA
Found at i:40927363 original size:20 final size:20
Alignment explanation
Indices: 40927338--40927378 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40927328 ACACTTTAAT
40927338 TACATAGTATTTTCAACCAA
1 TACATAGTATTTTCAACCAA
40927358 TACATAGTATTTTCAACCAA
1 TACATAGTATTTTCAACCAA
40927378 T
1 T
40927379 TTCAAACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.37
Consensus pattern (20 bp):
TACATAGTATTTTCAACCAA
Found at i:40928306 original size:42 final size:42
Alignment explanation
Indices: 40928206--40928367 Score: 184
Period size: 43 Copynumber: 3.8 Consensus size: 42
40928196 AGCCTGTACA
* * * *
40928206 ATGCCAACGTCCTAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATA-CG
* *
40928249 ATGTCACTGTCCCAGACAG-GGTCTTACACGAAATCAAATACG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGAAATCAAATACG
*
40928291 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCATAAGT-CG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-AAATCA-AA-TACG
* *
40928335 TTGCCAAAGTCCCAGACGTGGTCTTACACGAAA
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAA
40928368 CACATATCGG
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
42 28 0.27
43 41 0.40
44 32 0.31
45 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATACG
Found at i:40933942 original size:29 final size:29
Alignment explanation
Indices: 40933909--40933965 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
40933899 GGACAAAGAG
40933909 GTTCCCTACGTCTCCAAGGGTACTTTATA
1 GTTCCCTACGTCTCCAAGGGTACTTTATA
*
40933938 GTTCCTTACGTCTCCAAGGGTACTTTAT
1 GTTCCCTACGTCTCCAAGGGTACTTTAT
40933966 GGTGTATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (29 bp):
GTTCCCTACGTCTCCAAGGGTACTTTATA
Found at i:40935698 original size:13 final size:14
Alignment explanation
Indices: 40935656--40935700 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
40935646 TAATAATGAT
40935656 TAAAGTATATTATAA
1 TAAAGTA-ATTATAA
40935671 TAATA-TAA-TATAA
1 TAA-AGTAATTATAA
40935684 TAAAGTAATTA-AA
1 TAAAGTAATTATAA
40935697 TAAA
1 TAAA
40935701 AAAATAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.04
13 17 0.63
14 3 0.11
15 5 0.19
16 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
TAAAGTAATTATAA
Found at i:40935793 original size:16 final size:19
Alignment explanation
Indices: 40935752--40935794 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
40935742 GAAACAGAGC
40935752 AAGGAAAGAAAGAAAGAAA
1 AAGGAAAGAAAGAAAGAAA
40935771 AAGGGAAAG-AA-AAAG-AA
1 AA-GGAAAGAAAGAAAGAAA
40935788 AAGGAAA
1 AAGGAAA
40935795 ATTTAGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 4 0.17
18 4 0.17
19 4 0.17
20 6 0.26
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (19 bp):
AAGGAAAGAAAGAAAGAAA
Found at i:40937551 original size:20 final size:20
Alignment explanation
Indices: 40937522--40937568 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
40937512 GGTCTGGCCC
*
40937522 CACGGCCATGTCCCAAGCCA
1 CACGGGCATGTCCCAAGCCA
*
40937542 CACGGGCATGTCCCAGGCCA
1 CACGGGCATGTCCCAAGCCA
40937562 CACGGGC
1 CACGGGC
40937569 GTGTGCTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.43, G:0.28, T:0.09
Consensus pattern (20 bp):
CACGGGCATGTCCCAAGCCA
Found at i:40940912 original size:38 final size:38
Alignment explanation
Indices: 40940861--40940937 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
40940851 AATGGGATTA
**
40940861 TACAAATTTTGCTGAGTTGGAGATTGCTTCCTGGATGT
1 TACAAATTTTGCTGAGTTGGAGATCACTTCCTGGATGT
*
40940899 TACAAATTTTGCTGAGTTGGAGATCATTTCCTGGATGT
1 TACAAATTTTGCTGAGTTGGAGATCACTTCCTGGATGT
40940937 T
1 T
40940938 GGATCTACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.22, C:0.13, G:0.25, T:0.40
Consensus pattern (38 bp):
TACAAATTTTGCTGAGTTGGAGATCACTTCCTGGATGT
Found at i:40947275 original size:20 final size:21
Alignment explanation
Indices: 40947232--40947277 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
40947222 ACTGTTTTGT
40947232 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
40947252 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
40947271 TATGGGC
1 TATGGGC
40947278 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:40947344 original size:60 final size:60
Alignment explanation
Indices: 40947270--40947404 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 60
40947260 AACTGTGTTA
* * *
40947270 ATATGGGCAAGGCCCAATATA-TCTCA-ACTTGTAATAGGGCTACGGCCTAGATTGATACTG
1 ATATGGGCTAGGCCCAATATACTCTCATAC-TGTAA-AGGGCTACGGCCCAGATTAATACTG
* * * *
40947330 ATATGGGCTAGGCCCAATATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAATATACTCTCATACTGTAAAGGGCTACGGCCCAGATTAATACTG
40947390 ATATGGGCTAAGGCC
1 ATATGGGCT-AGGCC
40947405 AGTTAACTCT
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
60 49 0.75
61 14 0.22
62 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (60 bp):
ATATGGGCTAGGCCCAATATACTCTCATACTGTAAAGGGCTACGGCCCAGATTAATACTG
Found at i:40948099 original size:16 final size:16
Alignment explanation
Indices: 40948078--40948116 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
40948068 GTTTTCAATG
*
40948078 AAAACATAGTTTTCGA
1 AAAACACAGTTTTCGA
*
40948094 AAAACACGGTTTTCGA
1 AAAACACAGTTTTCGA
40948110 AAAACAC
1 AAAACAC
40948117 TTTAATGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (16 bp):
AAAACACAGTTTTCGA
Found at i:40955325 original size:47 final size:47
Alignment explanation
Indices: 40955268--40955397 Score: 163
Period size: 47 Copynumber: 2.8 Consensus size: 47
40955258 ACAATCGATA
* *
40955268 AGTACCTATACCATCACCCGTAGCCAAATCAAGGTAACTTATCTCGG
1 AGTACCTATACCATGACCCGTAGCCAAATCAAGGTAACTCATCTCGG
* * * * * *
40955315 AGTACTTATACCATGGCCTGTAGTCAAATCAAGGTAACTCCTCTCTG
1 AGTACCTATACCATGACCCGTAGCCAAATCAAGGTAACTCATCTCGG
*
40955362 AATACCTATACCATGGA-CCGTAGCCAAATCAAGGTA
1 AGTACCTATACCAT-GACCCGTAGCCAAATCAAGGTA
40955398 TTATTCACAC
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
47 68 0.99
48 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (47 bp):
AGTACCTATACCATGACCCGTAGCCAAATCAAGGTAACTCATCTCGG
Found at i:40961320 original size:13 final size:13
Alignment explanation
Indices: 40961302--40961330 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40961292 TTTAGTTTAA
40961302 TTAGTTAATTAGT
1 TTAGTTAATTAGT
40961315 TTAGTTAATTAGT
1 TTAGTTAATTAGT
40961328 TTA
1 TTA
40961331 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:40966782 original size:6 final size:6
Alignment explanation
Indices: 40966771--40966832 Score: 117
Period size: 6 Copynumber: 10.5 Consensus size: 6
40966761 TCCTCCTATC
40966771 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
40966818 TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTT
40966833 CAATTTAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.09
6 50 0.91
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:40968664 original size:21 final size:22
Alignment explanation
Indices: 40968624--40968664 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40968614 TATTTAGCAT
*
40968624 ATTTATGGATGTTTATTACTAG
1 ATTTATGGATGTTTAGTACTAG
*
40968646 ATTTGTGGAT-TTTAGTACT
1 ATTTATGGATGTTTAGTACT
40968665 CTTAATCCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.24, C:0.05, G:0.20, T:0.51
Consensus pattern (22 bp):
ATTTATGGATGTTTAGTACTAG
Found at i:40969794 original size:13 final size:13
Alignment explanation
Indices: 40969776--40969804 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40969766 TTTAGTTTAA
40969776 TTAGTTAATTAGT
1 TTAGTTAATTAGT
40969789 TTAGTTAATTAGT
1 TTAGTTAATTAGT
40969802 TTA
1 TTA
40969805 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:40981493 original size:13 final size:13
Alignment explanation
Indices: 40981455--40981493 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
40981445 TTTTTTCATT
40981455 TATTTATTTTTAA
1 TATTTATTTTTAA
* **
40981468 TAATTATAATTAA
1 TATTTATTTTTAA
40981481 TATTTATTTTTAA
1 TATTTATTTTTAA
40981494 AACAAATTTA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTATTTTTAA
Found at i:40982797 original size:22 final size:22
Alignment explanation
Indices: 40982772--40982814 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
40982762 TATCCAAACA
40982772 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
40982794 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
40982815 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:40983552 original size:17 final size:18
Alignment explanation
Indices: 40983522--40983567 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
40983512 ATTTAAATTG
40983522 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
40983540 CGGTCGC-GTCGCG-TTT
1 CGGTCGCGGTCGCGTTTT
40983556 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
40983568 GACATAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 3 0.11
17 6 0.22
18 7 0.26
ACGTcount: A:0.00, C:0.30, G:0.41, T:0.28
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:40985365 original size:14 final size:13
Alignment explanation
Indices: 40985339--40985376 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
40985329 TTTAAAATGT
40985339 ATAATATAATTAA
1 ATAATATAATTAA
40985352 ATAATATAAATTAA
1 ATAATAT-AATTAA
40985366 ATTAA-ATAATT
1 A-TAATATAATT
40985377 CAATTAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.48
14 9 0.39
15 3 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATATAATTAA
Found at i:40987867 original size:3 final size:3
Alignment explanation
Indices: 40987859--40987955 Score: 68
Period size: 3 Copynumber: 32.0 Consensus size: 3
40987849 GTAAAAAATT
* **
40987859 TAA TAA TAA TAA TAC TGG TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* * * * * * ** * *
40987905 TAA TCA TGA TGA TGA TGA TGA TGG TAT TAA TAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40987953 TAA
1 TAA
40987956 AAATCTTAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
3 77 0.96
4 3 0.04
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:40988012 original size:17 final size:17
Alignment explanation
Indices: 40987992--40988024 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40987982 AAGGATATAC
40987992 TATATAGAT-AAATAAAA
1 TATATA-ATAAAATAAAA
40988009 TATATAATAAAATAAA
1 TATATAATAAAATAAA
40988025 TGTATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
TATATAATAAAATAAAA
Found at i:40991598 original size:11 final size:11
Alignment explanation
Indices: 40991579--40991615 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
40991569 TGCAACCAAA
*
40991579 TTTTGTGCACT
1 TTTTGTGCAAT
*
40991590 TTTTATGCAAT
1 TTTTGTGCAAT
40991601 TTTTGTGCAAT
1 TTTTGTGCAAT
40991612 TTTT
1 TTTT
40991616 TTCATATTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (11 bp):
TTTTGTGCAAT
Found at i:40991724 original size:14 final size:14
Alignment explanation
Indices: 40991698--40991758 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
40991688 TCAATATTGG
40991698 GATTTAG-GATTTAA
1 GATTTAGAG-TTTAA
40991712 GATTTAGAGTTTAA
1 GATTTAGAGTTTAA
* * * *
40991726 AATTCAAAGTTCAA
1 GATTTAGAGTTTAA
*
40991740 TGATTTAGGGTTTAA
1 -GATTTAGAGTTTAA
40991755 GATT
1 GATT
40991759 CAATAGTTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
14 26 0.72
15 10 0.28
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (14 bp):
GATTTAGAGTTTAA
Found at i:40993779 original size:12 final size:12
Alignment explanation
Indices: 40993764--40993791 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
40993754 TTTTGTTTCC
40993764 TTTAGCATACAT
1 TTTAGCATACAT
40993776 TTTAGCATACAT
1 TTTAGCATACAT
40993788 TTTA
1 TTTA
40993792 ATTTTGCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (12 bp):
TTTAGCATACAT
Found at i:41000465 original size:42 final size:42
Alignment explanation
Indices: 41000406--41000500 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
41000396 TTTGATTGTT
*
41000406 ACATGGCCTGGGACATGGGCATGTGTCTCAGCCATGTCAGTC
1 ACATGGCCTGGGACATGGGCATGTGTCTCAACCATGTCAGTC
* * *
41000448 ACATGGCTTGAGG-CATGGGCATGTGTCTCAACCGTGTGAGTC
1 ACATGGCCTG-GGACATGGGCATGTGTCTCAACCATGTCAGTC
*
41000490 ACACGGCCTGG
1 ACATGGCCTGG
41000501 CCACATGGCC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.02
42 43 0.93
43 2 0.04
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.23
Consensus pattern (42 bp):
ACATGGCCTGGGACATGGGCATGTGTCTCAACCATGTCAGTC
Found at i:41010167 original size:26 final size:26
Alignment explanation
Indices: 41010136--41010185 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
41010126 TCCTGTACAT
* *
41010136 ATATGCTCACATGAGCTGTGAAATCA
1 ATATGCTCACACGAGATGTGAAATCA
41010162 ATATGCTCACACGAGATGTGAAAT
1 ATATGCTCACACGAGATGTGAAAT
41010186 GGGCTTGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (26 bp):
ATATGCTCACACGAGATGTGAAATCA
Found at i:41021528 original size:18 final size:18
Alignment explanation
Indices: 41021505--41021539 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41021495 GCTGATGAAA
41021505 ATCCCCAAATCAGTCATG
1 ATCCCCAAATCAGTCATG
41021523 ATCCCCAAATCAGTCAT
1 ATCCCCAAATCAGTCAT
41021540 ATCAAATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.34, G:0.09, T:0.23
Consensus pattern (18 bp):
ATCCCCAAATCAGTCATG
Found at i:41046643 original size:31 final size:31
Alignment explanation
Indices: 41046581--41046643 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
41046571 ACAACATTTC
**
41046581 AAAAAGAAAATCTAAAAAATGAAATCTTGAG
1 AAAAAGAAAATCTAAAAAATGAAATAATGAG
* *
41046612 AAAAAGAAAATTTAATAAATG-AATAAATGAG
1 AAAAAGAAAATCTAAAAAATGAAAT-AATGAG
41046643 A
1 A
41046644 CATTTATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.63, C:0.03, G:0.13, T:0.21
Consensus pattern (31 bp):
AAAAAGAAAATCTAAAAAATGAAATAATGAG
Found at i:41049838 original size:29 final size:29
Alignment explanation
Indices: 41049774--41049846 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
41049764 ATGAATTTTG
* *
41049774 GTGATGTTATATATAAATTTTGATTTTAT
1 GTGATTTTATAAATAAATTTTGATTTTAT
*
41049803 GTAATTTTATAAATAAATTTT-ATTTTAAT
1 GTGATTTTATAAATAAATTTTGATTTT-AT
*
41049832 TTGATTTTCATAAAT
1 GTGATTTT-ATAAAT
41049847 TTTTGATATC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.14
29 26 0.70
30 6 0.16
ACGTcount: A:0.36, C:0.01, G:0.08, T:0.55
Consensus pattern (29 bp):
GTGATTTTATAAATAAATTTTGATTTTAT
Found at i:41054915 original size:16 final size:15
Alignment explanation
Indices: 41054889--41054927 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
41054879 ATTGAATTAT
* *
41054889 TTATATTTTATATAA
1 TTATATATTATAAAA
41054904 TTGATATATTATAAAA
1 TT-ATATATTATAAAA
41054920 TTATATAT
1 TTATATAT
41054928 GATTTAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TTATATATTATAAAA
Found at i:41058032 original size:102 final size:104
Alignment explanation
Indices: 41057850--41058045 Score: 227
Period size: 103 Copynumber: 1.9 Consensus size: 104
41057840 TTGTAAGTTT
* * ** * * *
41057850 GTGAGAAATAGAATGCTATTTTGGTATCGATTTTAAGACGGGGTATCGATATTTCAAAAAATATT
1 GTGAAAAACAGAATGCTATTTTGGTATCGATTTTAAGACAAGGTATCAATAATTCAAAAAATATC
* * *
41057915 GATATTTTACCAAAAA-GTATTGATACTTAATTGGGTTC
66 GATACTTGACCAAAAAGGTATCGATACTTAATTGGGTTC
* * *
41057953 GTGAAAAACAGAATG-TCATTTTGGTATTGCTTTTAAGA-AAGGTATCAATAATTCATAAAATAT
1 GTGAAAAACAGAATGCT-ATTTTGGTATCGATTTTAAGACAAGGTATCAATAATTCAAAAAATAT
* *
41058016 CGATACTTGGCTAAAAAGGTATCGATACTT
65 CGATACTTGACCAAAAAGGTATCGATACTT
41058046 TTTGGCCTAG
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
102 33 0.43
103 43 0.57
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (104 bp):
GTGAAAAACAGAATGCTATTTTGGTATCGATTTTAAGACAAGGTATCAATAATTCAAAAAATATC
GATACTTGACCAAAAAGGTATCGATACTTAATTGGGTTC
Found at i:41060789 original size:20 final size:20
Alignment explanation
Indices: 41060747--41060794 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
41060737 GGGGTATCAA
*
41060747 AGTGCAAATAGCGGCACCAT
1 AGTGCAAATAGCGGAACCAT
* **
41060767 AGTGCAAATAGGGGAACTGT
1 AGTGCAAATAGCGGAACCAT
41060787 AGTGCAAA
1 AGTGCAAA
41060795 CAAGGGCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.29, T:0.17
Consensus pattern (20 bp):
AGTGCAAATAGCGGAACCAT
Found at i:41060805 original size:21 final size:20
Alignment explanation
Indices: 41060766--41060805 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
41060756 AGCGGCACCA
* *
41060766 TAGTGCAAATAGGGGAACTG
1 TAGTGCAAAAAGGGCAACTG
41060786 TAGTGCAAACAAGGGCAACT
1 TAGTGCAAA-AAGGGCAACT
41060806 AAGTGTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.15, G:0.30, T:0.17
Consensus pattern (20 bp):
TAGTGCAAAAAGGGCAACTG
Found at i:41067610 original size:178 final size:178
Alignment explanation
Indices: 41067311--41067669 Score: 682
Period size: 178 Copynumber: 2.0 Consensus size: 178
41067301 ACAAAATTAA
41067311 GCATACATGCATACAGATTTAGATACATAATCAAAAGCAGATATAGCTTTAGATTCAGAATCAGA
1 GCATACATGCATACAGATTTAGATACATAATCAAAAGCAGATATAGCTTTAGATTCAGAATCAGA
* *
41067376 TCCAGATTCATATTATAGATACAGATATGCATAAATCCTACCCCATCCTCTACACACCATCTTCG
66 TCCAGATCCATATTATAGATACAGATATGCATAAATCCTACCCCATCCTCTACACACCATCTCCG
41067441 TCCATCCCATCACACCATGTGAGGTTTAAAACACTCATCCATCCCTAC
131 TCCATCCCATCACACCATGTGAGGTTTAAAACACTCATCCATCCCTAC
*
41067489 GCATACATGCATACAGATTTAGATACATAATCAAAAGCAGATATAGCTTTAGATTCAGAATTAGA
1 GCATACATGCATACAGATTTAGATACATAATCAAAAGCAGATATAGCTTTAGATTCAGAATCAGA
41067554 TCCAGATCCATATTATAGATACAGATATGCATAAATCCTACCCCATCCTCTACACACCATCTCCG
66 TCCAGATCCATATTATAGATACAGATATGCATAAATCCTACCCCATCCTCTACACACCATCTCCG
*
41067619 TCCATCCCATCACACCCTGTGAGGTTTAAAACACTCATCCATCCCTAC
131 TCCATCCCATCACACCATGTGAGGTTTAAAACACTCATCCATCCCTAC
41067667 GCA
1 GCA
41067670 CCACATTGTG
Statistics
Matches: 177, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
178 177 1.00
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (178 bp):
GCATACATGCATACAGATTTAGATACATAATCAAAAGCAGATATAGCTTTAGATTCAGAATCAGA
TCCAGATCCATATTATAGATACAGATATGCATAAATCCTACCCCATCCTCTACACACCATCTCCG
TCCATCCCATCACACCATGTGAGGTTTAAAACACTCATCCATCCCTAC
Found at i:41077616 original size:16 final size:16
Alignment explanation
Indices: 41077592--41077633 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
41077582 AAATAATAAA
*
41077592 TAATTTAATTA-TATTT
1 TAATATAATTATTA-TT
41077608 TAATATAATTATTATT
1 TAATATAATTATTATT
*
41077624 AAATATAATT
1 TAATATAATT
41077634 TAATAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATATAATTATTATT
Found at i:41077625 original size:26 final size:25
Alignment explanation
Indices: 41077595--41077680 Score: 91
Period size: 26 Copynumber: 3.3 Consensus size: 25
41077585 TAATAAATAA
41077595 TTTAATTATATTTTAATATAATTAT
1 TTTAATTATATTTTAATATAATTAT
* * * * *
41077620 TATTAAATATAATTTAATAAAAATAA
1 T-TTAATTATATTTTAATATAATTAT
*
41077646 TTTAATAATATTTTTAATATAATTAT
1 TTTAATTATA-TTTTAATATAATTAT
41077672 TTTATATTA
1 TTTA-ATTA
41077681 AAATATTTTA
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
25 8 0.17
26 35 0.76
27 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTTAATTATATTTTAATATAATTAT
Found at i:41077645 original size:14 final size:14
Alignment explanation
Indices: 41077623--41077653 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41077613 TAATTATTAT
*
41077623 TAAATATAATTTAA
1 TAAAAATAATTTAA
41077637 TAAAAATAATTTAA
1 TAAAAATAATTTAA
41077651 TAA
1 TAA
41077654 TATTTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAAATAATTTAA
Found at i:41077667 original size:14 final size:15
Alignment explanation
Indices: 41077650--41077691 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
41077640 AAATAATTTA
41077650 ATAATATTTT-TAAT
1 ATAATATTTTATAAT
*
41077664 ATAATTATTTTATATT
1 ATAA-TATTTTATAAT
*
41077680 AAAATATTTTAT
1 ATAATATTTTAT
41077692 TTTTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATAATATTTTATAAT
Found at i:41082444 original size:29 final size:29
Alignment explanation
Indices: 41082412--41082467 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
41082402 AGAATTTGAC
*
41082412 CAAATTAAAATTTCATGTATAAAATTGTA
1 CAAAATAAAATTTCATGTATAAAATTGTA
* * *
41082441 CAAAATCAAATTTTATGTATAGAATTG
1 CAAAATAAAATTTCATGTATAAAATTG
41082468 CACATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (29 bp):
CAAAATAAAATTTCATGTATAAAATTGTA
Found at i:41082481 original size:31 final size:29
Alignment explanation
Indices: 41082419--41082493 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
41082409 GACCAAATTA
*
41082419 AAATTTCATGTATAAAATTGTACAAAATC
1 AAATTTCATGTATAAAATTGCACAAAATC
* *
41082448 AAATTTTATGTATAGAATTGCACATTAAATC
1 AAATTTCATGTATAAAATTGCACA--AAATC
* *
41082479 AAAGTTCATGAATAA
1 AAATTTCATGTATAA
41082494 TTTTGATATT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 21 0.57
31 16 0.43
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (29 bp):
AAATTTCATGTATAAAATTGCACAAAATC
Found at i:41083932 original size:18 final size:21
Alignment explanation
Indices: 41083911--41083955 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
41083901 AGGAGTAAAC
41083911 TATTGA-TGAGGA-AA-ATTT
1 TATTGACTGAGGAGAAGATTT
*
41083929 TATTTACTGAGGAGAAGGATTT
1 TATTGACTGAGGAGAA-GATTT
41083951 TATTG
1 TATTG
41083956 TTTATGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 2 0.10
22 8 0.38
ACGTcount: A:0.33, C:0.02, G:0.24, T:0.40
Consensus pattern (21 bp):
TATTGACTGAGGAGAAGATTT
Found at i:41084406 original size:19 final size:18
Alignment explanation
Indices: 41084374--41084409 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41084364 TTTTTTAAAA
41084374 ATAAAATTTGAAATTTTT
1 ATAAAATTTGAAATTTTT
*
41084392 ATAAATATTTTAAATTTT
1 ATAAA-ATTTGAAATTTT
41084410 AAAAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATAAAATTTGAAATTTTT
Found at i:41084409 original size:18 final size:19
Alignment explanation
Indices: 41084374--41084431 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
41084364 TTTTTTAAAA
41084374 ATAAA-ATTTGAAATTTTT
1 ATAAATATTTGAAATTTTT
*
41084392 ATAAATATTTTAAA-TTTT
1 ATAAATATTTGAAATTTTT
* *
41084410 AAAAATTATTATGAATTTTTT
1 ATAAA-TATT-TGAAATTTTT
41084431 A
1 A
41084432 GAATTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 13 0.41
19 11 0.34
20 3 0.09
21 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (19 bp):
ATAAATATTTGAAATTTTT
Found at i:41084450 original size:20 final size:20
Alignment explanation
Indices: 41084413--41084449 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41084403 AAATTTTAAA
41084413 AATTATTATGAATTTTTTAG
1 AATTATTATGAATTTTTTAG
*
41084433 AATTATTTTG-ATTTTTT
1 AATTATTATGAATTTTTT
41084450 TTAAAGAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
AATTATTATGAATTTTTTAG
Found at i:41086153 original size:44 final size:44
Alignment explanation
Indices: 41086085--41086240 Score: 172
Period size: 44 Copynumber: 3.5 Consensus size: 44
41086075 CAAAGCGAGC
*
41086085 CTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCTACGAAT
1 CTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAAT
* * ** *
41086129 CTTATCTACC-GTAAGTTGTGGTGGAGCAGATTGAATTTATAAAT
1 CTTATCTCCCTG-AAGTTGTAGTGGAGCAGATTGAAGCTACAAAT
* * * *
41086173 CTTATCTCCCTGAAGTTGCAGTAGAGCAAATTGAAGCTACAATT
1 CTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAAT
* *
41086217 CCTATAC-CCCTGAAGTTGTTGTGG
1 CTTAT-CTCCCTGAAGTTGTAGTGG
41086241 GTTAGAACGA
Statistics
Matches: 90, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
43 1 0.01
44 87 0.97
45 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAAT
Found at i:41087981 original size:22 final size:22
Alignment explanation
Indices: 41087956--41088005 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
41087946 CATTTACTTT
41087956 CATTTTTC-TTTATTGTT-TTTA
1 CATTTTTCATTT-TTGTTATTTA
41087977 GCA-TTTTCATTTTTGTTATTTA
1 -CATTTTTCATTTTTGTTATTTA
41087999 CATTTTT
1 CATTTTT
41088006 GCTCTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.68
Consensus pattern (22 bp):
CATTTTTCATTTTTGTTATTTA
Found at i:41087992 original size:21 final size:21
Alignment explanation
Indices: 41087959--41088004 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
41087949 TTACTTTCAT
41087959 TTTTCTTTATTGTT-TTTAGCA
1 TTTTCTTTATTGTTATTTA-CA
41087980 TTTTCATTT-TTGTTATTTACA
1 TTTTC-TTTATTGTTATTTACA
41088001 TTTT
1 TTTT
41088005 TGCTCTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.15, C:0.09, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTCTTTATTGTTATTTACA
Found at i:41090612 original size:142 final size:141
Alignment explanation
Indices: 41090361--41090702 Score: 303
Period size: 142 Copynumber: 2.5 Consensus size: 141
41090351 AGATAGGTAT
* * ** * * *
41090361 TTTTACTATTTAGTTTTTAATCCGAAAGCATAAAGTGAAAATTGC-TTTGAGATGAAAT--AATA
1 TTTTACTACTTAGTTTTAAATAAGGAAGCATAAAGTAAAAACTGCATTTGAGATGAAATCAAATA
* * * *
41090423 GATCTGAATATATGTCGAACACAGGTCTCATACACATAGGCTATAGGAGAAAGTGAAGAGATCT-
66 GATCTAAATATATGTCAAACACAGGTCTCATACACATAGGCTATAGGAAAAAAT-AA-AGAT-TG
41090487 AATAATATAGATTAA
128 AATAATATA-ATTAA
*
41090502 TTTTACTACTTAGTTTTAAATATGGAAGCATAAAGTAAAAACTGCATTTGAGATGAAATCAAAT-
1 TTTTACTACTTAGTTTTAAATAAGGAAGCATAAAGTAAAAACTGCATTTGAGATGAAATCAAATA
* * * * * * * *
41090566 G-TCTAAATCTATGTCAAACATAGGTCTTGAGTGCATAT-GTCT-TAGGAAAAAATAAAGGTTGG
66 GATCTAAATATATGTCAAACACAGGTC-TCA-TACACATAGGCTATAGGAAAAAATAAAGATTGA
*
41090628 ATAATATAATTGA
129 ATAATATAATTAA
* * * *
41090641 TTTT-C-ACTTAG-CTTAAA-AACGATAGCATGAAGTAAAAACTGCTATTGGAGATGAAATCAAA
1 TTTTACTACTTAGTTTTAAATAAGGA-AGCATAAAGTAAAAACTGC-ATTTGAGATGAAATCAAA
41090702 T
64 T
41090703 TGTTTTTAGA
Statistics
Matches: 168, Mismatches: 25, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
135 3 0.02
136 23 0.14
137 24 0.14
138 1 0.01
139 9 0.05
140 11 0.07
141 40 0.24
142 43 0.26
143 6 0.04
144 8 0.05
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (141 bp):
TTTTACTACTTAGTTTTAAATAAGGAAGCATAAAGTAAAAACTGCATTTGAGATGAAATCAAATA
GATCTAAATATATGTCAAACACAGGTCTCATACACATAGGCTATAGGAAAAAATAAAGATTGAAT
AATATAATTAA
Found at i:41103698 original size:30 final size:31
Alignment explanation
Indices: 41103650--41103708 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
41103640 TTTAATTTGA
*
41103650 TCAATTTTAGTTCTTATACTTTTAGAATTAG
1 TCAACTTTAGTTCTTATACTTTTAGAATTAG
*
41103681 TCAACTTTAGTTC-TATACTTTTTGAATT
1 TCAACTTTAGTTCTTATACTTTTAGAATT
41103709 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (31 bp):
TCAACTTTAGTTCTTATACTTTTAGAATTAG
Found at i:41106964 original size:25 final size:25
Alignment explanation
Indices: 41106935--41107001 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
41106925 TTAATATTAA
*
41106935 ATTAATATAATATTAAGATAATCACT
1 ATTAATATAATATTAAGAAAAT-ACT
*
41106961 -TTAATATTAA-ATTAATAAAATACT
1 ATTAATA-TAATATTAAGAAAATACT
*
41106985 ATTAAGATAAGTATTAA
1 ATTAATATAA-TATTAA
41107002 ATTTAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
24 6 0.18
25 20 0.59
26 8 0.24
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (25 bp):
ATTAATATAATATTAAGAAAATACT
Found at i:41106967 original size:20 final size:20
Alignment explanation
Indices: 41106916--41106976 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
41106906 AAACTAGCCC
41106916 TTAATCACTTTAATATTAAA
1 TTAATCACTTTAATATTAAA
41106936 TTAAT-A---TAATATTAAGA
1 TTAATCACTTTAATATTAA-A
41106953 -TAATCACTTTAATATTAAA
1 TTAATCACTTTAATATTAAA
41106972 TTAAT
1 TTAAT
41106977 AAAATACTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
16 13 0.37
17 2 0.06
19 2 0.06
20 18 0.51
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.44
Consensus pattern (20 bp):
TTAATCACTTTAATATTAAA
Found at i:41108531 original size:21 final size:21
Alignment explanation
Indices: 41108507--41108572 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
41108497 ATTTAATGAA
41108507 GTAAGTTGTCTTTCTGACAAT
1 GTAAGTTGTCTTTCTGACAAT
41108528 GTAAACG-T-TC-TT-T-ACAAT
1 GT-AA-GTTGTCTTTCTGACAAT
41108546 GCCTAAGTTGTCTTTCTGACAAT
1 G--TAAGTTGTCTTTCTGACAAT
41108569 GTAA
1 GTAA
41108573 ACATTCTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 18
0.67 0.00 0.33
Matches are distributed among these distances:
18 7 0.19
19 4 0.11
20 5 0.14
21 9 0.25
22 4 0.11
23 7 0.19
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (21 bp):
GTAAGTTGTCTTTCTGACAAT
Found at i:41108565 original size:41 final size:41
Alignment explanation
Indices: 41108508--41108589 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
41108498 TTTAATGAAG
*
41108508 TAAGTTGTCTTTCTGACAATGTAAACGTTCTTTACAATGCC
1 TAAGTTGTCTTTCTGACAATGTAAACATTCTTTACAATGCC
41108549 TAAGTTGTCTTTCTGACAATGTAAACATTCTTTACAATGCC
1 TAAGTTGTCTTTCTGACAATGTAAACATTCTTTACAATGCC
41108590 ACTGATCTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (41 bp):
TAAGTTGTCTTTCTGACAATGTAAACATTCTTTACAATGCC
Found at i:41115245 original size:21 final size:21
Alignment explanation
Indices: 41115211--41115262 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
41115201 TTTTTTGATT
* *
41115211 TATAACATTTATATTGAAAATA
1 TATAATATTAATATT-AAAATA
41115233 -ATAATATTAATATTAAAATA
1 TATAATATTAATATTAAAATA
41115253 TATATATATT
1 TATA-ATATT
41115263 TTCCTCCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 6 0.23
21 15 0.58
22 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TATAATATTAATATTAAAATA
Found at i:41115599 original size:4 final size:4
Alignment explanation
Indices: 41115586--41115614 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
41115576 TTCATAACAG
41115586 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
41115615 GAGGGGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:41119162 original size:62 final size:61
Alignment explanation
Indices: 41119033--41119150 Score: 209
Period size: 62 Copynumber: 1.9 Consensus size: 61
41119023 CAATGTACCT
* *
41119033 AATTTATATTAAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATTTGATTTATATAACAA
1 AATTTATATTAAAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTTAATTTATATAACAA
41119094 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTTAATTTATAT
1 AATTTATATTA-AAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTTAATTTATAT
41119151 TATAAAGTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
61 11 0.20
62 43 0.80
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (61 bp):
AATTTATATTAAAAGTTTGTTCCAAGTTTTAATATTGTAATGTATTTAATTTATATAACAA
Found at i:41120149 original size:28 final size:28
Alignment explanation
Indices: 41120117--41120181 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
41120107 GTATGTTTGT
41120117 ATTTATTTTATATTTTCATTCATTCATA
1 ATTTATTTTATATTTTCATTCATTCATA
41120145 ATTTATTTTATATTTTCATTCATTCATA
1 ATTTATTTTATATTTTCATTCATTCATA
41120173 ATTTATTTT
1 ATTTATTTT
41120182 TAATGTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (28 bp):
ATTTATTTTATATTTTCATTCATTCATA
Found at i:41123253 original size:14 final size:14
Alignment explanation
Indices: 41123234--41123262 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41123224 TGGAACAAAC
41123234 TTTGTAATATAAAT
1 TTTGTAATATAAAT
41123248 TTTGTAATATAAAT
1 TTTGTAATATAAAT
41123262 T
1 T
41123263 AAATACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGTAATATAAAT
Found at i:41123281 original size:62 final size:62
Alignment explanation
Indices: 41123205--41123372 Score: 300
Period size: 62 Copynumber: 2.7 Consensus size: 62
41123195 CAACATTACA
*
41123205 ACATTACTACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
* * *
41123267 ACATTACAATATTAAAACTTGCAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
41123329 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT
41123373 AGGTACATTC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 100 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (62 bp):
ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
Found at i:41125441 original size:46 final size:46
Alignment explanation
Indices: 41125370--41125462 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
41125360 TCAGCTAAGA
41125370 TGCGTCGCATCGGGGTCTTTAAGCTACATATGTGGCCTAGGATTAT
1 TGCGTCGCATCGGGGTCTTTAAGCTACATATGTGGCCTAGGATTAT
* *
41125416 TGCGTCGCGTCGGGGTCTTTGAGCTACATATGTGGCCTAGGATTAT
1 TGCGTCGCATCGGGGTCTTTAAGCTACATATGTGGCCTAGGATTAT
41125462 T
1 T
41125463 ATGTATCACA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.33
Consensus pattern (46 bp):
TGCGTCGCATCGGGGTCTTTAAGCTACATATGTGGCCTAGGATTAT
Found at i:41128821 original size:9 final size:9
Alignment explanation
Indices: 41128807--41128831 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41128797 TGGATTAAAT
41128807 TGAATGAAA
1 TGAATGAAA
41128816 TGAATGAAA
1 TGAATGAAA
41128825 TGAATGA
1 TGAATGA
41128832 TTGAATGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (9 bp):
TGAATGAAA
Found at i:41134717 original size:28 final size:28
Alignment explanation
Indices: 41134677--41134733 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
41134667 TTATGCGGAC
41134677 TTAAAACGAAAAGATATTGAATTTGAGA
1 TTAAAACGAAAAGATATTGAATTTGAGA
*
41134705 TTAAAATGAAAAGATATTGAATTTGAGA
1 TTAAAACGAAAAGATATTGAATTTGAGA
41134733 T
1 T
41134734 CGATGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.32
Consensus pattern (28 bp):
TTAAAACGAAAAGATATTGAATTTGAGA
Found at i:41139849 original size:26 final size:26
Alignment explanation
Indices: 41139820--41139926 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
41139810 TGGTACAAAT
41139820 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
41139846 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41139872 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41139898 TGATAATGGGTTAGGTAAATGTT-CA
1 TGATAATGGGTTAGGTAAATGTTCCA
41139923 TGAT
1 TGAT
41139927 GGGCATTTCA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
25 6 0.08
26 73 0.92
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:41142723 original size:26 final size:26
Alignment explanation
Indices: 41142694--41142801 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
41142684 TGATACAAAT
41142694 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
41142720 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41142746 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41142772 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41142798 TGAT
1 TGAT
41142802 GGGCATTTCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:41145921 original size:28 final size:28
Alignment explanation
Indices: 41145858--41146011 Score: 220
Period size: 28 Copynumber: 5.5 Consensus size: 28
41145848 ATATTAAGTC
*
41145858 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41145885 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
41145913 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
41145941 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41145969 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
41145998 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41146012 CAATCTCATG
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.19
28 76 0.66
29 18 0.16
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41153889 original size:27 final size:26
Alignment explanation
Indices: 41153872--41153994 Score: 142
Period size: 27 Copynumber: 4.6 Consensus size: 26
41153862 ATATTAAGTC
41153872 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
41153899 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
41153927 CGCACACTTAGTGCTA-ATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
41153954 CGCACACTTAGTGCTA-ATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
41153980 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
41153995 GTACAATTTA
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
26 19 0.20
27 55 0.59
28 20 0.21
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Done.