Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 64 of 66
Found at i:24960497 original size:35 final size:35
Alignment explanation
Indices: 24960458--24960589 Score: 138
Period size: 35 Copynumber: 3.8 Consensus size: 35
24960448 TTCCATATGG
* * * *
24960458 AGTAGTGCTTTACTTATTCTAGTTGTTTTACTTTA
1 AGTAGTGCTTCACTTGTTCTAGTTGTTTTACGTGA
* * * *
24960493 AGTAGTACTGCACTTGTTCTAATTGTTTTGCGTGA
1 AGTAGTGCTTCACTTGTTCTAGTTGTTTTACGTGA
* * *
24960528 AGTAGTGCTTCACTTGTTCTAGTTATTCTGCGTGA
1 AGTAGTGCTTCACTTGTTCTAGTTGTTTTACGTGA
** *
24960563 AGTAGCACTTCACTTGTTCAAGTTGTT
1 AGTAGTGCTTCACTTGTTCTAGTTGTT
24960590 CTTTGTACAA
Statistics
Matches: 80, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 80 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (35 bp):
AGTAGTGCTTCACTTGTTCTAGTTGTTTTACGTGA
Found at i:24960566 original size:70 final size:70
Alignment explanation
Indices: 24960458--24960589 Score: 167
Period size: 70 Copynumber: 1.9 Consensus size: 70
24960448 TTCCATATGG
* * * * * *
24960458 AGTAGTGCTTTACTTATTCTAGTTGTTTTACTTTAAGTAGTACTGCACTTGTTCTAA-TTGTTTT
1 AGTAGTGCTTCACTTATTCTAGTTATTCTACGTGAAGTAGCACTGCACTTGTTC-AAGTTGTTTT
24960522 GCGTGA
65 GCGTGA
* * *
24960528 AGTAGTGCTTCACTTGTTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTGTTCAAGTTGTT
1 AGTAGTGCTTCACTTATTCTAGTTATTCTACGTGAAGTAGCACTGCACTTGTTCAAGTTGTT
24960590 CTTTGTACAA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
69 2 0.04
70 50 0.96
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (70 bp):
AGTAGTGCTTCACTTATTCTAGTTATTCTACGTGAAGTAGCACTGCACTTGTTCAAGTTGTTTTG
CGTGA
Found at i:24976519 original size:2 final size:2
Alignment explanation
Indices: 24976512--24976537 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24976502 CATCTTTCAA
24976512 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
24976538 GGCTTTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24980573 original size:15 final size:17
Alignment explanation
Indices: 24980543--24980574 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
24980533 AAAATGAAAG
24980543 AAGTATTAATTATAATT
1 AAGTATTAATTATAATT
24980560 AAGTA-TAA-TATAATT
1 AAGTATTAATTATAATT
24980575 TATATAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
AAGTATTAATTATAATT
Found at i:24986899 original size:28 final size:28
Alignment explanation
Indices: 24986850--24986913 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
24986840 AAAATAAATT
* *
24986850 ATTTTATAAAATTTAAATAAATATTTAT
1 ATTTTATTAAATTTAAATAAATATTTAC
* * *
24986878 TTTTTATTATATTT-AATCAAATTTTTAC
1 ATTTTATTAAATTTAAAT-AAATATTTAC
24986906 ATTTTATT
1 ATTTTATT
24986914 TCAAATCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 3 0.10
28 26 0.90
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTTTATTAAATTTAAATAAATATTTAC
Found at i:25016285 original size:29 final size:29
Alignment explanation
Indices: 25016234--25016289 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
25016224 GTGAATTTTG
* *
25016234 ATTATGACGTATATTTTTTATATTAGTTA
1 ATTATGACGTATATCTTTAATATTAGTTA
*
25016263 ATTATGACGTGTATCTTTAATATTAGT
1 ATTATGACGTATATCTTTAATATTAGT
25016290 AGACATCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.52
Consensus pattern (29 bp):
ATTATGACGTATATCTTTAATATTAGTTA
Found at i:25032945 original size:51 final size:51
Alignment explanation
Indices: 25032863--25032966 Score: 174
Period size: 51 Copynumber: 2.0 Consensus size: 51
25032853 TGACTCTGCT
* *
25032863 GAAACTAGTCTGGTTAGCTTAACTTTCGGTTTAGTGGATATGGCTTGGTTG
1 GAAACTAGTCTGATTAGCTTAACTTTCGGTTTAGTGGATATGGCTTGGCTG
25032914 GAAACTAGTCTGATTAGCTTAACTTAT-GGTTTAGTGGATATGGCTTGGCTG
1 GAAACTAGTCTGATTAGCTTAACTT-TCGGTTTAGTGGATATGGCTTGGCTG
25032965 GA
1 GA
25032967 GATATAGTGG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
51 49 0.98
52 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.38
Consensus pattern (51 bp):
GAAACTAGTCTGATTAGCTTAACTTTCGGTTTAGTGGATATGGCTTGGCTG
Found at i:25036437 original size:16 final size:16
Alignment explanation
Indices: 25036388--25036439 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
25036378 ATTTGGGGTA
25036388 TTTTTAAAAATAACTC
1 TTTTTAAAAATAACTC
* * * *
25036404 --TTAAAAAAAAATTA
1 TTTTTAAAAATAACTC
25036418 TTTTTAAAAATAACTC
1 TTTTTAAAAATAACTC
25036434 TTTTTA
1 TTTTTA
25036440 TAATTTTAAC
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 10 0.38
16 16 0.62
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTTTAAAAATAACTC
Found at i:25054558 original size:228 final size:228
Alignment explanation
Indices: 25053876--25054559 Score: 708
Period size: 228 Copynumber: 3.0 Consensus size: 228
25053866 ACGCAAACAA
* * * * * * * * * * *
25053876 GATGCAGATCTTCGTTAAGACACTCACCGGCAAGACAATCACCCTCGAAGTCGAGAGTTCCGACA
1 GATGCAGATCTTCGTCAAGACCCTGACGGGTAAAACCATAACCCTGGAAGTCGAAAGCTCCGACA
* * *
25053941 CGATCGACAACGTGAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCGGACCAACAAAGGCTT
66 CCATCGACAACGTGAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTT
* * *
25054006 ATCTTTGCTGGGAAGCAGCTCGAGGACGGCCGAAC-CTTGGCCGATTACAACATCCAGAAGGAGT
131 ATCTTTGCTGGGAAGCAGCTCGAGGACGGACGAACTC-TGGCTGATTACAACATTCAGAAGGAGT
* * * * * *
25054070 CGACTCTCCACCTCGTCCTCCGTCTACGTGGTGG
195 CGACACTTCACCTGGTCTTGCGCCTACGTGGTGG
* *
25054104 GATGCAGATCTTCGTCAAGACCCTGACGGGTAAGACGATAACCCTGGAAGTCGAAAGCTCCGACA
1 GATGCAGATCTTCGTCAAGACCCTGACGGGTAAAACCATAACCCTGGAAGTCGAAAGCTCCGACA
* *
25054169 CCATCGACAACGTGAAGGCCAAGATCCAGGACAAGGAAGGAATCCCGCCAGACCAGCAAAGGCTT
66 CCATCGACAACGTGAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTT
* * * *
25054234 ATCTTTGCTGGGAAGCAGCTCGAGGACGGTCGAACTTTGGCTGATTATAACATTCAGAAAGAGTC
131 ATCTTTGCTGGGAAGCAGCTCGAGGACGGACGAACTCTGGCTGATTACAACATTCAGAAGGAGTC
** * * * *
25054299 GACACTTCATTTGGTTTTGAGGCTCCGTGGTGG
196 GACACTTCACCTGGTCTTGCGCCTACGTGGTGG
* * * * ** * * * * *
25054332 GATGCAGATTTTCGTTAAGACTCTGACAGGG-AAAACCATTACTTTGGAGGTGGAGAGCTCGGAT
1 GATGCAGATCTTCGTCAAGACCCTGAC-GGGTAAAACCATAACCCTGGAAGTCGAAAGCTCCGAC
* * * * * * * *
25054396 ACCATTGATAATGTTAAGGCAAAGATTCAGGACAAGGAAGGGATTCCACCAGATCAGCAAAGG-T
65 ACCATCGACAACGTGAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCT
* ** * * * * * *
25054460 TGATATTTGCTGGGAAGCAATTGGAAGATGGAAGGACTCTGGCTGATTACAATATTCAGAAGGAG
130 T-ATCTTTGCTGGGAAGCAGCTCGAGGACGGACGAACTCTGGCTGATTACAACATTCAGAAGGAG
* * *
25054525 TCCACCCTTCACCTGGTCTTGCGCCTTCGTGGTGG
194 TCGACACTTCACCTGGTCTTGCGCCTACGTGGTGG
25054560 TTTCTAAGCT
Statistics
Matches: 377, Mismatches: 76, Indels: 6
0.82 0.17 0.01
Matches are distributed among these distances:
227 2 0.01
228 372 0.99
229 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (228 bp):
GATGCAGATCTTCGTCAAGACCCTGACGGGTAAAACCATAACCCTGGAAGTCGAAAGCTCCGACA
CCATCGACAACGTGAAGGCCAAGATCCAGGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTT
ATCTTTGCTGGGAAGCAGCTCGAGGACGGACGAACTCTGGCTGATTACAACATTCAGAAGGAGTC
GACACTTCACCTGGTCTTGCGCCTACGTGGTGG
Found at i:25093799 original size:16 final size:17
Alignment explanation
Indices: 25093778--25093822 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
25093768 TATACATATG
25093778 TATATATAATAT-TTAT
1 TATATATAATATCTTAT
*
25093794 TATATATATTATCTTAT
1 TATATATAATATCTTAT
*
25093811 GATATA-AATATC
1 TATATATAATATC
25093823 AATTATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (17 bp):
TATATATAATATCTTAT
Found at i:25094215 original size:18 final size:16
Alignment explanation
Indices: 25094176--25094219 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
25094166 TGGCCTTCTC
*
25094176 TTTCTCTCTTTCTATT
1 TTTCTCTCTTTCTATA
25094192 TCTTCTTCTCTTTCTATAA
1 T-TTC-TCTCTTTCTAT-A
25094211 TTTCTCTCT
1 TTTCTCTCT
25094220 CGCAATTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 8 0.33
18 14 0.58
19 1 0.04
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTCTCTCTTTCTATA
Found at i:25100023 original size:2 final size:2
Alignment explanation
Indices: 25100016--25100041 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25100006 TCAGGTCTAA
25100016 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
25100042 GTTGGGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25103315 original size:31 final size:31
Alignment explanation
Indices: 25103280--25103343 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
25103270 TGAACCCAAC
25103280 GCAGAATTCTGTTGGGGCCAGTCTTTTGCAG
1 GCAGAATTCTGTTGGGGCCAGTCTTTTGCAG
25103311 GCAGAATTCTGTTGGGGCCAGTCTTTTGCAG
1 GCAGAATTCTGTTGGGGCCAGTCTTTTGCAG
25103342 GC
1 GC
25103344 GTGGAAGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.16, C:0.20, G:0.33, T:0.31
Consensus pattern (31 bp):
GCAGAATTCTGTTGGGGCCAGTCTTTTGCAG
Found at i:25105365 original size:24 final size:25
Alignment explanation
Indices: 25105327--25105373 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
25105317 AATGTGTTAA
*
25105327 ATATAATTAAATATTTATATTTTCG
1 ATATAAATAAATATTTATATTTTCG
25105352 ATATAAAT-AATATTTATATTTT
1 ATATAAATAAATATTTATATTTT
25105374 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
ATATAAATAAATATTTATATTTTCG
Found at i:25105382 original size:24 final size:24
Alignment explanation
Indices: 25105323--25105382 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
25105313 TTTAAATGTG
*
25105323 TTAAATATAATTAAATATTTATATT
1 TTAAATATAAAT-AATATTTATATT
**
25105348 TTCGATATAAATAATATTTATATT
1 TTAAATATAAATAATATTTATATT
*
25105372 TTAAATTTAAA
1 TTAAATATAAA
25105383 ATATGTGTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TTAAATATAAATAATATTTATATT
Found at i:25105555 original size:13 final size:14
Alignment explanation
Indices: 25105537--25105566 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
25105527 AATTAAAAAT
25105537 AAATATTTATAA-A
1 AAATATTTATAACA
25105550 AAATATTTATAACA
1 AAATATTTATAACA
25105564 AAA
1 AAA
25105567 CAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATTTATAACA
Found at i:25105895 original size:18 final size:18
Alignment explanation
Indices: 25105858--25105895 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25105848 ATGCATGTTA
*
25105858 AAATATGATAACACGTTT
1 AAATATGATAACACGATT
*
25105876 AAATATGATAATACGATT
1 AAATATGATAACACGATT
25105894 AA
1 AA
25105896 TTAAACGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (18 bp):
AAATATGATAACACGATT
Found at i:25107792 original size:20 final size:20
Alignment explanation
Indices: 25107767--25107804 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
25107757 ATCTATAATT
*
25107767 ATAAAAATAATTATAATAAA
1 ATAAAAATAATAATAATAAA
25107787 ATAAAAATAATAATAATA
1 ATAAAAATAATAATAATA
25107805 TCAAATAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAAAATAATAATAATAAA
Found at i:25108229 original size:23 final size:20
Alignment explanation
Indices: 25108188--25108233 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
25108178 AATAAAAAAC
*
25108188 TTAAAATATTTTTTATTAAT
1 TTAAAAAATTTTTTATTAAT
*
25108208 TTAAAAAA-TTATTATT-AT
1 TTAAAAAATTTTTTATTAAT
25108226 TTAAAAAA
1 TTAAAAAA
25108234 AATAAAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.42
19 7 0.29
20 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAAAAATTTTTTATTAAT
Found at i:25110971 original size:68 final size:68
Alignment explanation
Indices: 25110899--25111027 Score: 222
Period size: 68 Copynumber: 1.9 Consensus size: 68
25110889 TTTTAATAAA
*
25110899 TTTTTATAATTAATAATTAATCAATTTTTATTAATAAAAATATTATTTATGATTATATGTCCTAT
1 TTTTTATAATCAATAATTAATCAATTTTTATTAATAAAAATATTATTTATGATTATATGTCCTAT
25110964 GAG
66 GAG
* * *
25110967 TTTTTATAATCGATGATTAATCAATTTTTATTAATAAAAATATTATTTGTGATTATATGTC
1 TTTTTATAATCAATAATTAATCAATTTTTATTAATAAAAATATTATTTATGATTATATGTC
25111028 ACGTGATATA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 57 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (68 bp):
TTTTTATAATCAATAATTAATCAATTTTTATTAATAAAAATATTATTTATGATTATATGTCCTAT
GAG
Found at i:25118082 original size:13 final size:13
Alignment explanation
Indices: 25118064--25118089 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25118054 GTTAAATGAA
25118064 TAATATTAATATT
1 TAATATTAATATT
25118077 TAATATTAATATT
1 TAATATTAATATT
25118090 AAATGTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAATATTAATATT
Found at i:25118111 original size:18 final size:18
Alignment explanation
Indices: 25118084--25118119 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25118074 ATTTAATATT
* *
25118084 AATATTAAATGTTTTTAA
1 AATATAAAATATTTTTAA
25118102 AATATAAAATATTTTTAA
1 AATATAAAATATTTTTAA
25118120 TATTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AATATAAAATATTTTTAA
Found at i:25120944 original size:26 final size:24
Alignment explanation
Indices: 25120915--25120962 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
25120905 TTTATATAAT
25120915 TTATATTAAATATTATATTATTTTTG
1 TTATATT-AATATT-TATTATTTTTG
*
25120941 TTATATTATTATTTATTATTTT
1 TTATATTAATATTTATTATTTT
25120963 AAGAATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 5 0.24
26 7 0.33
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTATATTAATATTTATTATTTTTG
Found at i:25121209 original size:15 final size:15
Alignment explanation
Indices: 25121167--25121214 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
25121157 CACGGTAAAG
25121167 TTATATTTTCAATAA
1 TTATATTTTCAATAA
* ***
25121182 TCATATACCCAATAA
1 TTATATTTTCAATAA
25121197 TTATATTTTCAATAA
1 TTATATTTTCAATAA
25121212 TTA
1 TTA
25121215 CATTCTCAGT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (15 bp):
TTATATTTTCAATAA
Found at i:25145699 original size:2 final size:2
Alignment explanation
Indices: 25145692--25145718 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25145682 TATTAACATC
25145692 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
25145719 ATGCCTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:25150869 original size:2 final size:2
Alignment explanation
Indices: 25150862--25150887 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25150852 AATAATAATA
25150862 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
25150888 TCTACTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25213038 original size:3 final size:3
Alignment explanation
Indices: 25213030--25213057 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
25213020 ATCTGGGATA
25213030 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
25213058 CCAGGCAAAG
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:25236394 original size:24 final size:26
Alignment explanation
Indices: 25236366--25236413 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
25236356 CTTTTGTCGG
25236366 AAAGAAAGAAAAA-AAAA-AAAAGGA
1 AAAGAAAGAAAAATAAAACAAAAGGA
*
25236390 AAAGAGAGAAAAATAAAACAAAAG
1 AAAGAAAGAAAAATAAAACAAAAG
25236414 AGACAGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
25 4 0.19
26 5 0.24
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (26 bp):
AAAGAAAGAAAAATAAAACAAAAGGA
Found at i:25241000 original size:15 final size:15
Alignment explanation
Indices: 25240962--25241000 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
25240952 TGACAATGCT
*
25240962 ATATGATTACAAGTA
1 ATATGATTGCAAGTA
25240977 ATATGATTGCAAGTA
1 ATATGATTGCAAGTA
*
25240992 ATGTGATTG
1 ATATGATTG
25241001 TAAGAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (15 bp):
ATATGATTGCAAGTA
Found at i:25241234 original size:6 final size:6
Alignment explanation
Indices: 25241223--25241270 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
25241213 ATGTCATATA
* * *
25241223 TTTTAT TTTTAT TTTTAT TATAAT TTTATAT ATTTTAT TTTCAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT -TTTTAT TTTTAT TTTT
25241271 TAATATAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 26 0.76
7 5 0.15
8 3 0.09
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTAT
Found at i:25241278 original size:33 final size:33
Alignment explanation
Indices: 25241218--25241303 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
25241208 TTTTAATGTC
*
25241218 ATATATTTTATTTTTA-TTTTTATTATAATTTT
1 ATATATTTTATTTTTATTTTTTAATATAATTTT
*
25241250 ATATATTTTATTTTCATTTTTTAATATAATTTT
1 ATATATTTTATTTTTATTTTTTAATATAATTTT
* *
25241283 TTATATTATATCTTTTATTTT
1 ATATATTTTAT-TTTTATTTT
25241304 AATTTCTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 15 0.32
33 24 0.51
34 8 0.17
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTTTTAATATAATTTT
Found at i:25241401 original size:15 final size:15
Alignment explanation
Indices: 25241365--25241409 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
25241355 TTTTAATTTC
*
25241365 TAATTTTTATATTACA
1 TAATTTTTATTTTA-A
25241381 T-A-TTTTATTTTAA
1 TAATTTTTATTTTAA
25241394 TAATTTTTATTTTAA
1 TAATTTTTATTTTAA
25241409 T
1 T
25241410 TATAACATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 2 0.08
14 10 0.38
15 13 0.50
16 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATTTTTATTTTAA
Found at i:25245979 original size:5 final size:5
Alignment explanation
Indices: 25245969--25245995 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
25245959 ACCTCAGACT
25245969 AGGAA AGGAA AGGAA AGGAA AGGAA AG
1 AGGAA AGGAA AGGAA AGGAA AGGAA AG
25245996 AAAAACCATG
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:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
AGGAA
Found at i:25251644 original size:2 final size:2
Alignment explanation
Indices: 25251637--25251681 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
25251627 NNNNNNNNNN
25251637 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25251679 TA T
1 TA T
25251682 TTCATTCATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25258894 original size:45 final size:45
Alignment explanation
Indices: 25258834--25258927 Score: 107
Period size: 45 Copynumber: 2.1 Consensus size: 45
25258824 AATATATTAA
* * * *
25258834 TATTATTTCACTATAATAAATATTATAAAGCATATTACTTAATAT
1 TATTATTTCAATATAATAAATATAACAAAGAATATTACTTAATAT
* * * * *
25258879 TATTATTTGAATATAATCAATGTAACAAAGAATATTATTTAGTAT
1 TATTATTTCAATATAATAAATATAACAAAGAATATTACTTAATAT
25258924 TATT
1 TATT
25258928 TAAATTTAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (45 bp):
TATTATTTCAATATAATAAATATAACAAAGAATATTACTTAATAT
Found at i:25259008 original size:46 final size:43
Alignment explanation
Indices: 25258921--25259078 Score: 149
Period size: 46 Copynumber: 3.5 Consensus size: 43
25258911 TATTATTTAG
* *
25258921 TATTATTTAAATT-TAATGAAGAATATATTTTATCTTTTAATATTAAA
1 TATTATTT-AATTATAAT-AAAAATATA-ATTATCTTTTAATA--AAA
* *
25258968 TATTATTTAATTATAATAAAAAGTTTAATTATCTTCTAATACAAAA
1 TATTATTTAATTATAATAAAAA-TATAATTATCTTTTAAT--AAAA
* * *
25259014 TATT-TTTAAATTATAATAAAAATATATTTGTATTTTAATGAAAA
1 TATTATTT-AATTATAATAAAAATATAATTATCTTTTAAT-AAAA
25259058 TATTATTTAATTATAATAAAA
1 TATTATTTAATTATAATAAAA
25259079 GTTATTTTGA
Statistics
Matches: 95, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
44 21 0.22
45 18 0.19
46 40 0.42
47 15 0.16
48 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (43 bp):
TATTATTTAATTATAATAAAAATATAATTATCTTTTAATAAAA
Found at i:25259036 original size:22 final size:23
Alignment explanation
Indices: 25258921--25259078 Score: 105
Period size: 22 Copynumber: 7.0 Consensus size: 23
25258911 TATTATTTAG
*
25258921 TATTATTTAAATT-TAATGAAGAA
1 TATTATTTAAATTATAAT-AAAAA
** * *
25258944 TA-TATTTTATCTTTTAATATTAAA
1 TATTA-TTTAAATTATAATA-AAAA
25258968 TATTATTT-AATTATAATAAAAA
1 TATTATTTAAATTATAATAAAAA
* ** *
25258990 GT-TTAATTATCTTCTAATACAAAA
1 -TATTATTTAAATTATAATA-AAAA
25259014 TATT-TTTAAATTATAATAAAAA
1 TATTATTTAAATTATAATAAAAA
** * *
25259036 TA-TATTTGTATTTTAATGAAAA
1 TATTATTTAAATTATAATAAAAA
25259058 TATTATTT-AATTATAATAAAA
1 TATTATTTAAATTATAATAAAA
25259079 GTTATTTTGA
Statistics
Matches: 102, Mismatches: 23, Indels: 21
0.70 0.16 0.14
Matches are distributed among these distances:
21 1 0.01
22 42 0.41
23 40 0.39
24 17 0.17
25 2 0.02
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (23 bp):
TATTATTTAAATTATAATAAAAA
Found at i:25259094 original size:44 final size:47
Alignment explanation
Indices: 25258944--25259094 Score: 147
Period size: 44 Copynumber: 3.3 Consensus size: 47
25258934 TAATGAAGAA
* * **
25258944 TATATTTTATCTTTTAATATTAAATATTATTTAATTATAATAAAAAGT
1 TATATTTGATATTTTAATACAAAATATTATTTAATTATAAT-AAAAGT
* * * *
25258992 T-TAATT-ATCTTCTAATACAAAATATT-TTTAAATTATAATAAAA-A
1 TATATTTGATATTTTAATACAAAATATTATTT-AATTATAATAAAAGT
*
25259036 TATATTTG-TATTTTAAT-GAAAATATTATTTAATTATAATAAAAGT
1 TATATTTGATATTTTAATACAAAATATTATTTAATTATAATAAAAGT
25259081 TAT-TTTGAT-TTTTA
1 TATATTTGATATTTTA
25259095 TTGCTCAGAA
Statistics
Matches: 87, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
44 31 0.36
45 25 0.29
46 26 0.30
47 4 0.05
48 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (47 bp):
TATATTTGATATTTTAATACAAAATATTATTTAATTATAATAAAAGT
Found at i:25259399 original size:11 final size:12
Alignment explanation
Indices: 25259383--25259416 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
25259373 TACATAATAG
25259383 CTATTCT-TTCT
1 CTATTCTATTCT
25259394 CTATTCTATTCT
1 CTATTCTATTCT
25259406 -TATTCTATTCT
1 CTATTCTATTCT
25259417 TTCTAGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (12 bp):
CTATTCTATTCT
Found at i:25259404 original size:16 final size:16
Alignment explanation
Indices: 25259383--25259420 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
25259373 TACATAATAG
25259383 CTATTCTT-TCTCTATT
1 CTATTCTTAT-TCTATT
25259399 CTATTCTTATTCTATT
1 CTATTCTTATTCTATT
25259415 CT-TTCT
1 CTATTCT
25259421 AGTAAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 16 0.76
17 1 0.05
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.63
Consensus pattern (16 bp):
CTATTCTTATTCTATT
Found at i:25266061 original size:22 final size:23
Alignment explanation
Indices: 25266036--25266082 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
25266026 AAAATCTAGA
25266036 ATCTTTTAAAATAA-ATATTTAT
1 ATCTTTTAAAATAATATATTTAT
*
25266058 ATCTTTTATAATAATATATTTAT
1 ATCTTTTAAAATAATATATTTAT
25266081 AT
1 AT
25266083 ATAAATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
ATCTTTTAAAATAATATATTTAT
Found at i:25267252 original size:24 final size:26
Alignment explanation
Indices: 25267209--25267259 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
25267199 TAGAATAGAA
25267209 TTTTTTTTCATTTTCATTTTT-GGGG
1 TTTTTTTTCATTTTCATTTTTAGGGG
*
25267234 TTTTTTTTTATTTTC-TTTTTAGGGG
1 TTTTTTTTCATTTTCATTTTTAGGGG
25267259 T
1 T
25267260 GTTGAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.08, C:0.06, G:0.16, T:0.71
Consensus pattern (26 bp):
TTTTTTTTCATTTTCATTTTTAGGGG
Found at i:25282821 original size:138 final size:138
Alignment explanation
Indices: 25282572--25282831 Score: 466
Period size: 138 Copynumber: 1.9 Consensus size: 138
25282562 ATATATACCA
* *
25282572 GTGGCCACCTACCAAGAGATAAATTTTCATTGCGTTCATATGCTTAAAATCCATATTTCTTGACA
1 GTGGCCACCTACCAAGAGATAAATTTTCATTGCATTCATATGCTTAAAATCCATAGTTCTTGACA
* * *
25282637 TAATGGAAAATCTTTCTTTTATCATCCAAGATTCAACCTGTTTTAATATCCACTGTTGGCATTCA
66 TAATGGAAAATCTTTCTTTTAGCATCCAAGATTCAACCTATCTTAATATCCACTGTTGGCATTCA
25282702 CATCAGAT
131 CATCAGAT
*
25282710 GTGGCCACCTACCAAGAGATAAATTTTCATTGCATTCATATGCTTAAAATCTATAGTTCTTGACA
1 GTGGCCACCTACCAAGAGATAAATTTTCATTGCATTCATATGCTTAAAATCCATAGTTCTTGACA
25282775 TAATGGAAAATCTTTCTTTTAGCATCCAAGATTCAACCTATCTTAATATCCACTGTT
66 TAATGGAAAATCTTTCTTTTAGCATCCAAGATTCAACCTATCTTAATATCCACTGTT
25282832 AGCCAATCAT
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
138 116 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (138 bp):
GTGGCCACCTACCAAGAGATAAATTTTCATTGCATTCATATGCTTAAAATCCATAGTTCTTGACA
TAATGGAAAATCTTTCTTTTAGCATCCAAGATTCAACCTATCTTAATATCCACTGTTGGCATTCA
CATCAGAT
Found at i:25285325 original size:2 final size:2
Alignment explanation
Indices: 25285318--25285346 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25285308 GAAGCTTTAT
25285318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25285347 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25285351 original size:2 final size:2
Alignment explanation
Indices: 25285346--25285397 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
25285336 TATATATATA
25285346 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
25285388 TG TG TAG TG T
1 TG TG T-G TG T
25285398 TACTCTCTGC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:25294152 original size:25 final size:24
Alignment explanation
Indices: 25294102--25294152 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
25294092 TTAATAATTA
*
25294102 TTTTTTTATATATAAAATCAATTT
1 TTTTTTTATATATAAAATCAACTT
* *
25294126 TTTTTTTAATATATAATATCTACTT
1 TTTTTTT-ATATATAAAATCAACTT
25294151 TT
1 TT
25294153 GAATTCTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTTTTATATATAAAATCAACTT
Found at i:25295976 original size:29 final size:29
Alignment explanation
Indices: 25295923--25295978 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
25295913 TTTGGCTCAA
*
25295923 AATAAAAATATAAAGACTTGATTGAATGC
1 AATAAAAATATAAAGACTTCATTGAATGC
* *
25295952 AATAAAAATATAATGACTTCTTTGAAT
1 AATAAAAATATAAAGACTTCATTGAAT
25295979 TTTTTTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (29 bp):
AATAAAAATATAAAGACTTCATTGAATGC
Found at i:25298349 original size:208 final size:208
Alignment explanation
Indices: 25297986--25298546 Score: 856
Period size: 208 Copynumber: 2.7 Consensus size: 208
25297976 TTATTGATAA
* * * * * *
25297986 TAAGTGATAAGACGTCAATGTTCTCTTAATGAATTATTGTGGTCTTACTTTTTATCCTATGTAAT
1 TAAGTGATAAGACATCAATGCTCTCTTAATGAATTATTGTGATCCTACTCTCTATCCTATGTAAT
* * * * *
25298051 TCAATTATTACATTTTGAAGTATTACAGCAAGATAAGTAAAAATGATAAACATGTATCTTATGCT
66 TCAATTATTATATTATAAATTATTACAACAAGATAAGTAAAAATGATAAACATGTATCTTATGCT
* * *
25298116 TAATTTGTTATTTATGCCCTTTAATC-ACATTGCATGTAAAATTATGAATCATTTACTA-ATAAC
131 TAATTTGTTATTTATGCCCTTTAATCAACATT-AATGTAAAACTATAAATCATTTAC-AGATAAC
*
25298179 ATTTCATTAAACAGT
194 ATTTCATTAAACAGG
* * * *
25298194 TAAGTGATAAGACATCAATGCTCTCTTAATGAATTATTGTGTTCCTACTCTCTATGCTGTATAAT
1 TAAGTGATAAGACATCAATGCTCTCTTAATGAATTATTGTGATCCTACTCTCTATCCTATGTAAT
* *
25298259 TTAATTATTATATTATAAATTATTACAATAAGATAAGTAAAAATGATAAACATGTATCTTATGCT
66 TCAATTATTATATTATAAATTATTACAACAAGATAAGTAAAAATGATAAACATGTATCTTATGCT
* * *
25298324 TAATTTGCTATTTATGCCTTTTAATCAACCTTAATGTAAAACTATAAATCATTTACAGATAACAT
131 TAATTTGTTATTTATGCCCTTTAATCAACATTAATGTAAAACTATAAATCATTTACAGATAACAT
25298389 TTCATTAAACAGG
196 TTCATTAAACAGG
* *
25298402 TAAGTGATAAGACATCAATGCTCTTTTAATGAATTATTGTGATCCTACTCTCTATCCAATGTAAT
1 TAAGTGATAAGACATCAATGCTCTCTTAATGAATTATTGTGATCCTACTCTCTATCCTATGTAAT
25298467 TCAATTATTATATTATAAATTATTACAACAAGATAAGTAAAAATGATAAACATGTATCTTATGCT
66 TCAATTATTATATTATAAATTATTACAACAAGATAAGTAAAAATGATAAACATGTATCTTATGCT
25298532 TAATTTGTTATTTAT
131 TAATTTGTTATTTAT
25298547 CTGAATGGAA
Statistics
Matches: 319, Mismatches: 32, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
207 1 0.00
208 314 0.98
209 4 0.01
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.40
Consensus pattern (208 bp):
TAAGTGATAAGACATCAATGCTCTCTTAATGAATTATTGTGATCCTACTCTCTATCCTATGTAAT
TCAATTATTATATTATAAATTATTACAACAAGATAAGTAAAAATGATAAACATGTATCTTATGCT
TAATTTGTTATTTATGCCCTTTAATCAACATTAATGTAAAACTATAAATCATTTACAGATAACAT
TTCATTAAACAGG
Found at i:25300541 original size:18 final size:18
Alignment explanation
Indices: 25300509--25300543 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25300499 GTGGGAGGCA
*
25300509 GAGGAAGAAGTGGAGGAT
1 GAGGAAGAAGAGGAGGAT
*
25300527 GAGGAAGATGAGGAGGA
1 GAGGAAGAAGAGGAGGA
25300544 AGATGTAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.51, T:0.09
Consensus pattern (18 bp):
GAGGAAGAAGAGGAGGAT
Found at i:25312278 original size:26 final size:25
Alignment explanation
Indices: 25312249--25312330 Score: 94
Period size: 25 Copynumber: 3.2 Consensus size: 25
25312239 GGAGCTCATT
25312249 GGTGCTCAGCCAAAAGAGGGGAGATC
1 GGTGCTC-GCCAAAAGAGGGGAGATC
*
25312275 GGTGCTCTCCAAAAGAGGGGAGATC
1 GGTGCTCGCCAAAAGAGGGGAGATC
* ** *
25312300 GATGCTC-CCAATGGAGGGGAGCATT
1 GGTGCTCGCCAAAAGAGGGGAG-ATC
25312325 GGTGCT
1 GGTGCT
25312331 TCTTTAGGGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
24 12 0.24
25 30 0.61
26 7 0.14
ACGTcount: A:0.26, C:0.20, G:0.38, T:0.17
Consensus pattern (25 bp):
GGTGCTCGCCAAAAGAGGGGAGATC
Found at i:25314636 original size:42 final size:41
Alignment explanation
Indices: 25314590--25314731 Score: 142
Period size: 42 Copynumber: 3.4 Consensus size: 41
25314580 ACTCCCACTA
* * *
25314590 GCACATGGCTGGGTCAGCATCGACTTATGTGCACTCTTACTC
1 GCACATAGCTGGGTCAGCATCGGCTTATGCGCACTC-TACTC
* * **
25314632 GCACATAG-TCGAGTCAGTATCGGCTTATGCGCACTCCCCATC
1 GCACATAGCT-GGGTCAGCATCGGCTTATGCGCACTCTAC-TC
* *
25314674 GCACATAGCCGGGTCAGCATCGGCTTATGCACACTCCTACTC
1 GCACATAGCTGGGTCAGCATCGGCTTATGCGCACT-CTACTC
* *
25314716 GCATATAGCCGGGTCA
1 GCACATAGCTGGGTCA
25314732 ATATCATTAC
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
41 2 0.02
42 78 0.95
43 2 0.02
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.24
Consensus pattern (41 bp):
GCACATAGCTGGGTCAGCATCGGCTTATGCGCACTCTACTC
Found at i:25318080 original size:39 final size:39
Alignment explanation
Indices: 25318032--25318107 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
25318022 TTTACAGGTG
*
25318032 ATTGATTTGAGAGATGAACTAAAAGCTTATAGTTGATTT
1 ATTGATTTGAGAGATGAACTAAAAGCTTAAAGTTGATTT
25318071 ATTGATTTGAGAGATGAACTAAAAGCTTAAAGTTGAT
1 ATTGATTTGAGAGATGAACTAAAAGCTTAAAGTTGAT
25318108 AGTTTGAGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (39 bp):
ATTGATTTGAGAGATGAACTAAAAGCTTAAAGTTGATTT
Found at i:25318114 original size:34 final size:37
Alignment explanation
Indices: 25318034--25318129 Score: 126
Period size: 39 Copynumber: 2.6 Consensus size: 37
25318024 TACAGGTGAT
*
25318034 TGATTTGAGAGATGAACTAAAAGCTTATAGTTGATTTA
1 TGATTTGAGAGATGAACTAAAAGCTTAAAGTTGA-TTA
25318072 TTGATTTGAGAGATGAACTAAAAGCTTAAAGTTGA-TA
1 -TGATTTGAGAGATGAACTAAAAGCTTAAAGTTGATTA
* *
25318109 -G-TTTGAGGGATAAACTAAAAG
1 TGATTTGAGAGATGAACTAAAAG
25318130 GTCATTTTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
34 18 0.33
35 1 0.02
37 2 0.04
39 33 0.61
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (37 bp):
TGATTTGAGAGATGAACTAAAAGCTTAAAGTTGATTA
Found at i:25321524 original size:2 final size:2
Alignment explanation
Indices: 25321517--25321556 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
25321507 CCCATTCTTT
25321517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25321557 AAAATAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25328225 original size:2 final size:2
Alignment explanation
Indices: 25328218--25328243 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25328208 CTTCTCGCCA
25328218 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
25328244 CAGCTTTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25358893 original size:64 final size:63
Alignment explanation
Indices: 25358674--25358924 Score: 297
Period size: 63 Copynumber: 4.0 Consensus size: 63
25358664 CCTGGCAAAA
* * *
25358674 TTGTTATCCAGCCATTTTCAAGAGTGGGGACTGGTTGGGGTTGCTCCATGGATCTACCATATT
1 TTGTTATCCAGCCATTTTCAAGAGTGGGGACTGGTTTGGATAGCTCCATGGATCTACCATATT
* * * *** **
25358737 TTGTTATCCAGCCCTTTTCAAGAGTGTGGAGTGGTTTGGATAGCTCGGGGGATCTACTTTATT
1 TTGTTATCCAGCCATTTTCAAGAGTGGGGACTGGTTTGGATAGCTCCATGGATCTACCATATT
* * * * * *
25358800 TTGTTATCCAGCCATTGTCAAGAGAGGGGACCGGTTTAGG-CAGCTCCATGGAACTATCCATACT
1 TTGTTATCCAGCCATTTTCAAGAGTGGGGACTGGTTT-GGATAGCTCCATGGATCTA-CCATATT
* *
25358864 TTGCTATCCAGCCATTTTCAGGAGTGGGGACTGGTTTGGATAGCTCCATGGATCTAACCAT
1 TTGTTATCCAGCCATTTTCAAGAGTGGGGACTGGTTTGGATAGCTCCATGGATCT-ACCAT
25358925 GAAAGATGCT
Statistics
Matches: 152, Mismatches: 32, Indels: 7
0.80 0.17 0.04
Matches are distributed among these distances:
63 96 0.63
64 55 0.36
65 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.33
Consensus pattern (63 bp):
TTGTTATCCAGCCATTTTCAAGAGTGGGGACTGGTTTGGATAGCTCCATGGATCTACCATATT
Found at i:25358908 original size:127 final size:126
Alignment explanation
Indices: 25358674--25358909 Score: 337
Period size: 126 Copynumber: 1.9 Consensus size: 126
25358664 CCTGGCAAAA
* * * * ** * *
25358674 TTGTTATCCAGCCATTTTCAAGAGTGGGGACTGGTTGGGGTTGCTCCATGGATCTACCATATTTT
1 TTGTTATCCAGCCATTGTCAAGAGAGGGGACCGGTTGAGGCAGCTCCATGGAACTACCATACTTT
* * * *
25358739 GTTATCCAGCCCTTTTCAAGAGTGTGGAGTGGTTTGGATAGCTCGGGGGATCTACTTTATT
66 GCTATCCAGCCATTTTCAAGAGTGGGGACTGGTTTGGATAGCTCGGGGGATCTACTTTATT
*
25358800 TTGTTATCCAGCCATTGTCAAGAGAGGGGACCGGTTTAGGCAGCTCCATGGAACTATCCATACTT
1 TTGTTATCCAGCCATTGTCAAGAGAGGGGACCGGTTGAGGCAGCTCCATGGAACTA-CCATACTT
*
25358865 TGCTATCCAGCCATTTTCAGGAGTGGGGACTGGTTTGGATAGCTC
65 TGCTATCCAGCCATTTTCAAGAGTGGGGACTGGTTTGGATAGCTC
25358910 CATGGATCTA
Statistics
Matches: 95, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
126 48 0.51
127 47 0.49
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (126 bp):
TTGTTATCCAGCCATTGTCAAGAGAGGGGACCGGTTGAGGCAGCTCCATGGAACTACCATACTTT
GCTATCCAGCCATTTTCAAGAGTGGGGACTGGTTTGGATAGCTCGGGGGATCTACTTTATT
Found at i:25358917 original size:127 final size:126
Alignment explanation
Indices: 25358674--25358919 Score: 330
Period size: 127 Copynumber: 1.9 Consensus size: 126
25358664 CCTGGCAAAA
* * * * ** * *
25358674 TTGTTATCCAGCCATTTTCAAGAGTGGGGACTGGTTGGGGTTGCTCCATGGATCTACCATATTTT
1 TTGTTATCCAGCCATTGTCAAGAGAGGGGACCGGTTGAGGCAGCTCCATGGAACTACCATACTTT
* * * * **
25358739 GTTATCCAGCCCTTTTCAAGAGTGTGGAGTGGTTTGGATAGCTCGGGGGATCTACTTTATT
66 GCTATCCAGCCATTTTCAAGAGTGGGGACTGGTTTGGATAGCTCCAGGGATCTACTTTATT
*
25358800 TTGTTATCCAGCCATTGTCAAGAGAGGGGACCGGTTTAGGCAGCTCCATGGAACTATCCATACTT
1 TTGTTATCCAGCCATTGTCAAGAGAGGGGACCGGTTGAGGCAGCTCCATGGAACTA-CCATACTT
* *
25358865 TGCTATCCAGCCATTTTCAGGAGTGGGGACTGGTTTGGATAGCTCCATGGATCTA
65 TGCTATCCAGCCATTTTCAAGAGTGGGGACTGGTTTGGATAGCTCCAGGGATCTA
25358920 ACCATGAAAG
Statistics
Matches: 102, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
126 48 0.47
127 54 0.53
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (126 bp):
TTGTTATCCAGCCATTGTCAAGAGAGGGGACCGGTTGAGGCAGCTCCATGGAACTACCATACTTT
GCTATCCAGCCATTTTCAAGAGTGGGGACTGGTTTGGATAGCTCCAGGGATCTACTTTATT
Found at i:25371661 original size:16 final size:17
Alignment explanation
Indices: 25371640--25371676 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
25371630 TCGAAAAGAA
25371640 ACAGCAGAG-GAAGATC
1 ACAGCAGAGAGAAGATC
*
25371656 ACAGCAGAGAGAGGATC
1 ACAGCAGAGAGAAGATC
25371673 ACAG
1 ACAG
25371677 TAATCTCAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.43, C:0.19, G:0.32, T:0.05
Consensus pattern (17 bp):
ACAGCAGAGAGAAGATC
Found at i:25407536 original size:6 final size:6
Alignment explanation
Indices: 25407525--25407551 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
25407515 CTAGGTTGGC
25407525 CTGGTG CTGGTG CTGGTG CTGGTG CTG
1 CTGGTG CTGGTG CTGGTG CTGGTG CTG
25407552 CTGGTGCAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.48, T:0.33
Consensus pattern (6 bp):
CTGGTG
Found at i:25407563 original size:6 final size:6
Alignment explanation
Indices: 25407554--25407600 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
25407544 TGGTGCTGCT
* * *
25407554 GGTGCA GGTGGA GGTGGA GGTGGA GGTGGG GGTGGA GGTGGG GGTGG
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGG
25407601 CAAAGGGGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.11, C:0.02, G:0.70, T:0.17
Consensus pattern (6 bp):
GGTGGA
Found at i:25407569 original size:21 final size:21
Alignment explanation
Indices: 25407529--25407569 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25407519 GTTGGCCTGG
* *
25407529 TGCTGGTGCTGGTGCTGGTGC
1 TGCTGGTGCAGGTGCAGGTGC
*
25407550 TGCTGGTGCAGGTGGAGGTG
1 TGCTGGTGCAGGTGCAGGTG
25407570 GAGGTGGAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.15, G:0.51, T:0.29
Consensus pattern (21 bp):
TGCTGGTGCAGGTGCAGGTGC
Found at i:25410915 original size:15 final size:15
Alignment explanation
Indices: 25410897--25410929 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
25410887 GAGTTGCAAA
25410897 TGGTGGAG-GAGGAGG
1 TGGTGGAGAG-GGAGG
25410912 TGGTGGAGAGGGAGG
1 TGGTGGAGAGGGAGG
25410927 TGG
1 TGG
25410930 CAGTGGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.18, C:0.00, G:0.67, T:0.15
Consensus pattern (15 bp):
TGGTGGAGAGGGAGG
Found at i:25411087 original size:6 final size:6
Alignment explanation
Indices: 25411078--25411166 Score: 54
Period size: 6 Copynumber: 14.8 Consensus size: 6
25411068 TAGTGGTTAT
* * * * *
25411078 GGTGCA GGTGGA GGTGGA GGTGTA AGTGGCA -GTGGA GCTGGA GGTGGT
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGG-A GGTGGA GGTGGA GGTGGA
* * * * * * *
25411126 GGCGGA GGAGGA GGAGGA GGAGGT GGTGGT GGTGGT GGTGG
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGG
25411167 TTCTGGTGGA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
5 1 0.01
6 67 0.97
7 1 0.01
ACGTcount: A:0.16, C:0.04, G:0.62, T:0.18
Consensus pattern (6 bp):
GGTGGA
Found at i:25411236 original size:3 final size:3
Alignment explanation
Indices: 25411228--25411256 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
25411218 TGGTAGCACT
25411228 GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
25411257 CGGTGGTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:25433801 original size:5 final size:5
Alignment explanation
Indices: 25433791--25433816 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
25433781 ACTGATACGA
25433791 TCAGG TCAGG TCAGG TCAGG TCAGG T
1 TCAGG TCAGG TCAGG TCAGG TCAGG T
25433817 TTGGGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.23
Consensus pattern (5 bp):
TCAGG
Found at i:25451003 original size:418 final size:418
Alignment explanation
Indices: 25449927--25451594 Score: 2447
Period size: 420 Copynumber: 4.0 Consensus size: 418
25449917 AAATCTCTCC
* * * * *
25449927 TTCTCTCCTCAAATGAGTGTTATAAAAAAACAAAGCAACCGTCATTATTATAGTTGTAAAAATAA
1 TTCTCTCCCCAAATGAGTGTTATAAAAAAACAAAGCAACCATCATGATTATGGTTGTGAAAATAA
* * *
25449992 TTTAAATTTGATTGCTTAAATTTTATGCAGCATTTTTTTTTTGTGCGACAGTAGTATTTTTCATA
66 TTTAAATTTGATTGCTTAAATTTCATGCAGCATTTTTTTTTCGTGCGACAGTAGTTTTTTTCATA
* *
25450057 CACCACTATTCTCAAATGACAAAAGTTTAAGAGTCACCAACTTACTATTTAGATTTTATTTTAAA
131 CACCACTATTCTCAAATGACAAAAGTTTAAAAATCACCAACTTACTATTTAGATTTTATTTTAAA
* * * * * *
25450122 ATTCATAAAACGCTACAAAACATCATACACTCTTCAACAAATGCCAAACATGTTCATATCTTCTT
196 ATTCATGAAACGCCACAAAGCATCATACACTCTTCAACAAATACCAAACATATTCATCTCTTCTT
* * *
25450187 CAATGTTAGCAACAGTTCTTTAAAGATAATGATATAATATTATAAAGTCTAATAAATTTAAAATT
261 CAATGTTAGCAACAGTTCTTTAAAGATAGTGATATAACATTATAAACTCTAATAAATTTAAAATT
* *
25450252 TCGTACTGCATCATAACAAAATTAACATTCATTATAATGATGTTTGCAACAACGCCAAC-GTAGT
326 TCGTACTGCATCATAACAAAATTAACATTCATTGTAATGATGTCTGCAACAACGCCAACAGTAGT
* **
25450316 AAATTTTTT-TGTTTC-T-G-TTTCCTCT
391 AGATTTTTTGT-TTTCATGGTTTTTTTCT
* * * * * *
25450341 TTCTTTCCCCAAATAAGTGTTATAAAAAAACAAAGCAACCATTATGATTGTTGTTGTGAAAATAG
1 TTCTCTCCCCAAATGAGTGTTATAAAAAAACAAAGCAACCATCATGATTATGGTTGTGAAAATAA
* * *
25450406 TTTAAATTTGATTGCTTAAATTTCATACAGCATTTTTTTTTCGTGCGATAGTGGTTTTTTTCATA
66 TTTAAATTTGATTGCTTAAATTTCATGCAGCATTTTTTTTTCGTGCGACAGTAGTTTTTTTCATA
* * * *
25450471 TATCACTATTCTCAAATAACAAAAGTTTAAAAATCACCAACTTACTATTTAGATTTGATTTTAAA
131 CACCACTATTCTCAAATGACAAAAGTTTAAAAATCACCAACTTACTATTTAGATTTTATTTTAAA
* * *
25450536 ATTCATGAAACACCAAAAAGCATCATATACTCTTCAACAAA-AGCCAAACATATTCATCTCTTCT
196 ATTCATGAAACGCCACAAAGCATCATACACTCTTCAACAAATA-CCAAACATATTCATCTCTTCT
*
25450600 TCAATGTTAGCAACAGTTCTTTAAAGATAGTGATATAACATTATAAACTTTAATAAATTTAAAAT
260 TCAATGTTAGCAACAGTTCTTTAAAGATAGTGATATAACATTATAAACTCTAATAAATTTAAAAT
* * * * **
25450665 TTCATACTGCA-CTATAACAAAATTAACATTTATTGTAATGATGTTTGCAGCAGTGCCAACAGTA
325 TTCGTACTGCATC-ATAACAAAATTAACATTCATTGTAATGATGTCTGCAACAACGCCAACAGTA
25450729 GTAGATTTTTTAGTTTTCATGGTTTTTTTCT
389 GTAGATTTTTT-GTTTTCATGGTTTTTTTCT
*
25450760 CTCTCTCCCCAAATGAGTGTTATAAAAAAACAAAGCAACCATCATGATTATGGTTGTGAAAATAA
1 TTCTCTCCCCAAATGAGTGTTATAAAAAAACAAAGCAACCATCATGATTATGGTTGTGAAAATAA
* * * *
25450825 TTTAACTTTGATTGCTTAAATTTCATGTAGTA-TTTTTTTTCGTGTGACAGTAGTTTTTTTCATA
66 TTTAAATTTGATTGCTTAAATTTCATGCAGCATTTTTTTTTCGTGCGACAGTAGTTTTTTTCATA
* *
25450889 CACCATTATTCTTAAATGACAAAAGTTTAAAAATCACCAACTTACTATTTAGATTTTATTTTAAA
131 CACCACTATTCTCAAATGACAAAAGTTTAAAAATCACCAACTTACTATTTAGATTTTATTTTAAA
*
25450954 ATTCATTAAACGCCACAAAGCATCATACACTCTTCAACAAATACCAAACATATTCATCTCTTCTT
196 ATTCATGAAACGCCACAAAGCATCATACACTCTTCAACAAATACCAAACATATTCATCTCTTCTT
* * *
25451019 CAATGTTAGCAACAGTTCTTTAAAAATAGTGATATAACATTATAAACTCTAGTAAATTTACAATT
261 CAATGTTAGCAACAGTTCTTTAAAGATAGTGATATAACATTATAAACTCTAATAAATTTAAAATT
*
25451084 TCGTACTGCATCATAACAAAATTAACATTCATTGTAATGATGTCTGCAACAGCGCCAACAGTAGT
326 TCGTACTGCATCATAACAAAATTAACATTCATTGTAATGATGTCTGCAACAACGCCAACAGTAGT
25451149 AGATTTTTTGTTTTCCATGGTTTTTTCCTCT
391 AGATTTTTTGTTTT-CATGGTTTTTT--TCT
* * * * * * *
25451180 TTTTTTCTCCAAATTAGTGTTATAAAAAAACAAAACAACCATCATGATTATGATTGTGAAAATAG
1 TTCTCTCCCCAAATGAGTGTTATAAAAAAACAAAGCAACCATCATGATTATGGTTGTGAAAATAA
* *
25451245 TTTAAATTTGATTGCTTAAATTTCATGCAGCATTTTTTTTTCATGCAACAGTAG-TTTTTTCATA
66 TTTAAATTTGATTGCTTAAATTTCATGCAGCATTTTTTTTTCGTGCGACAGTAGTTTTTTTCATA
* * * *
25451309 CATCACAATTCTCAAATGACAAAAGTTTAAGAATCACCAACTTACAATTTAGATTTTATTTTAAA
131 CACCACTATTCTCAAATGACAAAAGTTTAAAAATCACCAACTTACTATTTAGATTTTATTTTAAA
* ** *
25451374 ATTCATGAAACGCCACAAAGCGTCATACACTCTTCAACAAATGTCAAACATGTTCATCTCTTCTT
196 ATTCATGAAACGCCACAAAGCATCATACACTCTTCAACAAATACCAAACATATTCATCTCTTCTT
25451439 CAATGTTAGCAACAGTTCTTTAAAGATAGTGATATAACATTATAAACTCTAATAAATTTAAAATT
261 CAATGTTAGCAACAGTTCTTTAAAGATAGTGATATAACATTATAAACTCTAATAAATTTAAAATT
* * * * *
25451504 TCGCACTGCACCATAACAAAATTAACATTCATTGTAATGATGTCTGCAGCAATGCCAATAGTAGT
326 TCGTACTGCATCATAACAAAATTAACATTCATTGTAATGATGTCTGCAACAACGCCAACAGTAGT
*
25451569 ACATTTTTT-TATTTCTATGGTTTTTT
391 AGATTTTTTGT-TTTC-ATGGTTTTTT
25451595 CTCACAGAAA
Statistics
Matches: 1126, Mismatches: 112, Indels: 26
0.89 0.09 0.02
Matches are distributed among these distances:
413 1 0.00
414 340 0.30
415 13 0.01
416 4 0.00
417 7 0.01
418 287 0.25
419 96 0.09
420 360 0.32
421 18 0.02
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (418 bp):
TTCTCTCCCCAAATGAGTGTTATAAAAAAACAAAGCAACCATCATGATTATGGTTGTGAAAATAA
TTTAAATTTGATTGCTTAAATTTCATGCAGCATTTTTTTTTCGTGCGACAGTAGTTTTTTTCATA
CACCACTATTCTCAAATGACAAAAGTTTAAAAATCACCAACTTACTATTTAGATTTTATTTTAAA
ATTCATGAAACGCCACAAAGCATCATACACTCTTCAACAAATACCAAACATATTCATCTCTTCTT
CAATGTTAGCAACAGTTCTTTAAAGATAGTGATATAACATTATAAACTCTAATAAATTTAAAATT
TCGTACTGCATCATAACAAAATTAACATTCATTGTAATGATGTCTGCAACAACGCCAACAGTAGT
AGATTTTTTGTTTTCATGGTTTTTTTCT
Found at i:25452239 original size:22 final size:21
Alignment explanation
Indices: 25452214--25452289 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 21
25452204 ATTGCTCATA
25452214 TTTTGTGCAACACTTGTTTTTT
1 TTTTGTGCAACA-TTGTTTTTT
* *
25452236 TTTTCGTGCCACATCAGTTTTTT
1 TTTT-GTGCAACAT-TGTTTTTT
* *
25452259 TTTCGTGCAGGA-ATTTTTTTTT
1 TTTTGTGCA--ACATTGTTTTTT
25452281 TTTTGTGCA
1 TTTTGTGCA
25452290 CCTGATAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
22 23 0.53
23 19 0.44
24 1 0.02
ACGTcount: A:0.13, C:0.14, G:0.16, T:0.57
Consensus pattern (21 bp):
TTTTGTGCAACATTGTTTTTT
Found at i:25453298 original size:169 final size:169
Alignment explanation
Indices: 25453019--25453358 Score: 590
Period size: 169 Copynumber: 2.0 Consensus size: 169
25453009 AAATCTCACA
* * *
25453019 TCGGCTATATACTAGAGTGATATTGGGCGTATAAGGATTCACACCACCTTCAACCTGTGAGGCAT
1 TCGGCTATATACTAGAGTGATATTGGGCATATAAAGATTCACACCACCTTCAACCTATGAGGCAT
25453084 TTTTTGTAGACAAAACCAATGATGTGGATAGTGATAGTTGGAAGTTTCTCATCAATGTGGGATTG
66 TTTTTGTAGACAAAACCAATGATGTGGATAGTGATAGTTGGAAGTTTCTCATCAATGTGGGATTG
* *
25453149 GCTCTACCCGTTGGGAGTATTATCTCGACAATGTGAGAT
131 ACTCTACCCGTTCGGAGTATTATCTCGACAATGTGAGAT
* *
25453188 TCGGCTATATACTAGAGTGATATTGGGTATATAAAGATTCATACCACCTTCAACCTATGAGGCAT
1 TCGGCTATATACTAGAGTGATATTGGGCATATAAAGATTCACACCACCTTCAACCTATGAGGCAT
*
25453253 TTTTTGTAGACAAAACCAGTGATGTGGATAGTGATAGTTGGAAGTTTCTCATCAATGTGGGATTG
66 TTTTTGTAGACAAAACCAATGATGTGGATAGTGATAGTTGGAAGTTTCTCATCAATGTGGGATTG
* *
25453318 ACTCTACCCGTTCGGAGTATTATCTCTACGATGTGAGAT
131 ACTCTACCCGTTCGGAGTATTATCTCGACAATGTGAGAT
25453357 TC
1 TC
25453359 ACGTCCATGC
Statistics
Matches: 161, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
169 161 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (169 bp):
TCGGCTATATACTAGAGTGATATTGGGCATATAAAGATTCACACCACCTTCAACCTATGAGGCAT
TTTTTGTAGACAAAACCAATGATGTGGATAGTGATAGTTGGAAGTTTCTCATCAATGTGGGATTG
ACTCTACCCGTTCGGAGTATTATCTCGACAATGTGAGAT
Found at i:25453684 original size:113 final size:113
Alignment explanation
Indices: 25453527--25453752 Score: 346
Period size: 113 Copynumber: 2.0 Consensus size: 113
25453517 ATGCTAATAT
* * * * *
25453527 GTAAATTGGATATTTGAGTTGGTTGATAAATACTGTTTATAGATTTATCGATGTTTATTCAATTC
1 GTAAATCGGATATTTGAGTTGGTTGATAAATACCGTTTAGAGATTTATCAATATTTATTCAATTC
* * *
25453592 TATACTTATTTTCTCTTTTGTTGATTGATCACTAGGAATATGAGATTG
66 TATACTTATTTCCTCTTTTGTTGATTGATCACCAGGAAAATGAGATTG
25453640 GTAAATCGGATATTT-AGGTTGGTTGATAAATACCGTTTAGAGATTTATCAATATTTATTCAATT
1 GTAAATCGGATATTTGA-GTTGGTTGATAAATACCGTTTAGAGATTTATCAATATTTATTCAATT
* *
25453704 TTATACTTATTTCCTCTTTTGTTGATTGATCACCATGAAAATGAGATTG
65 CTATACTTATTTCCTCTTTTGTTGATTGATCACCAGGAAAATGAGATTG
25453753 AGTGTTTAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
112 1 0.01
113 101 0.99
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (113 bp):
GTAAATCGGATATTTGAGTTGGTTGATAAATACCGTTTAGAGATTTATCAATATTTATTCAATTC
TATACTTATTTCCTCTTTTGTTGATTGATCACCAGGAAAATGAGATTG
Found at i:25465805 original size:20 final size:20
Alignment explanation
Indices: 25465776--25465813 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25465766 TATATATTAC
*
25465776 ATACACATACATTTACATAT
1 ATACACATACATATACATAT
*
25465796 ATACATATACATATACAT
1 ATACACATACATATACAT
25465814 GATTAATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (20 bp):
ATACACATACATATACATAT
Found at i:25488393 original size:16 final size:16
Alignment explanation
Indices: 25488354--25488385 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25488344 AACAAATCAT
25488354 GACATCATTTTATGAC
1 GACATCATTTTATGAC
25488370 GACATCATTTTATGAC
1 GACATCATTTTATGAC
25488386 TGCATCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
GACATCATTTTATGAC
Found at i:25492797 original size:2 final size:2
Alignment explanation
Indices: 25492790--25492829 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
25492780 TTATATGTTA
25492790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25492830 GAAAAGGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25521422 original size:25 final size:23
Alignment explanation
Indices: 25521393--25521438 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
25521383 TAAAAATTAT
*
25521393 TTTAAAATTTTTTATAATATAAATG
1 TTTAAAA-CTTTT-TAATATAAATG
*
25521418 TTTAATACTTTTTAATATAAA
1 TTTAAAACTTTTTAATATAAA
25521439 AGATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 4 0.21
25 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTAAAACTTTTTAATATAAATG
Found at i:25537587 original size:2 final size:2
Alignment explanation
Indices: 25537580--25537615 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
25537570 CATGCAATTA
25537580 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
25537616 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:25539451 original size:25 final size:25
Alignment explanation
Indices: 25539423--25539483 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
25539413 TATAGAATTA
25539423 AAAATATAATAATTTA-ATGTTAAT
1 AAAATATAATAATTTATATGTTAAT
* *
25539447 GAAAA-ATTAAGAATTTATATTTTAAT
1 -AAAATA-TAATAATTTATATGTTAAT
25539473 AAAATA-AATAA
1 AAAATATAATAA
25539484 AATGATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
24 5 0.17
25 17 0.57
26 8 0.27
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (25 bp):
AAAATATAATAATTTATATGTTAAT
Found at i:25539451 original size:26 final size:26
Alignment explanation
Indices: 25539421--25539483 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
25539411 TTTATAGAAT
25539421 TAAAAATATAATAATTTA-ATGTTAA
1 TAAAAATATAATAATTTATATGTTAA
* *
25539446 TGAAAAAT-TAAGAATTTATATTTTAA
1 T-AAAAATATAATAATTTATATGTTAA
25539472 T-AAAATA-AATAA
1 TAAAAATATAATAA
25539484 AATGATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 9 0.28
25 10 0.31
26 13 0.41
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (26 bp):
TAAAAATATAATAATTTATATGTTAA
Found at i:25556204 original size:131 final size:131
Alignment explanation
Indices: 25555964--25556225 Score: 434
Period size: 131 Copynumber: 2.0 Consensus size: 131
25555954 TCTACTCCGG
* * * *
25555964 GCTCATCCAGGCGTGGTTGGGCAGTTCCTATGTAGGAACCATTCCATAGAATCATATATAGAACC
1 GCTCATCCAGGCGTGGTCGGGCAGTTCCGATGTAGGAACCATTCCAGAGAATCATATACAGAACC
* * *
25556029 AGATTATTGTATTTAGAATATCCGGTATAATATACAGAACGAATCAAAATACGTATGGAAGTATT
66 AGATTATTGTATTTAGAATATCCGGTATAATATACAGAAAGAATCAAAATACATATAGAAGTATT
25556094 A
131 A
*
25556095 GCTCATCCAGGCGTGGTCGGGCAGTTCCGATGTAGGAACCATTCCAGAGAATCATATACAGAATC
1 GCTCATCCAGGCGTGGTCGGGCAGTTCCGATGTAGGAACCATTCCAGAGAATCATATACAGAACC
* *
25556160 AGATTATTGTATTTGGAATATCCGGTATAATATATAGAAAGAATCAAAATACATATAGAAGTATT
66 AGATTATTGTATTTAGAATATCCGGTATAATATACAGAAAGAATCAAAATACATATAGAAGTATT
25556225 A
131 A
25556226 CTTTATTCGA
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 121 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (131 bp):
GCTCATCCAGGCGTGGTCGGGCAGTTCCGATGTAGGAACCATTCCAGAGAATCATATACAGAACC
AGATTATTGTATTTAGAATATCCGGTATAATATACAGAAAGAATCAAAATACATATAGAAGTATT
A
Found at i:25559490 original size:2 final size:2
Alignment explanation
Indices: 25559483--25559559 Score: 65
Period size: 2 Copynumber: 40.0 Consensus size: 2
25559473 GAGAACAGTT
* *
25559483 AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG -G AA AG -G TG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
25559522 -G ATT NG TAG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG
1 AG A-G AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25559560 GAAAGGTGGA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
1 5 0.08
2 56 0.90
3 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.47, T:0.05
Consensus pattern (2 bp):
AG
Found at i:25559549 original size:46 final size:45
Alignment explanation
Indices: 25559482--25559571 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 45
25559472 AGAGAACAGT
25559482 TAGAGAGAGAGAGAGAGAGAGAGAGAGAAGAGGAAAGGTGGATTNG
1 TAGAGAGAGAGAGAGAGAGAGAGAGAGAAGAGGAAAGGTGGATT-G
25559528 TAGAGAGAGAGAGAGAGAGAGAGAGAGAAGAGGAAAGGTGGATT
1 TAGAGAGAGAGAGAGAGAGAGAGAGAGAAGAGGAAAGGTGGATT
25559572 AAAGGCTAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.44, C:0.00, G:0.46, T:0.09
Consensus pattern (45 bp):
TAGAGAGAGAGAGAGAGAGAGAGAGAGAAGAGGAAAGGTGGATTG
Found at i:25562223 original size:30 final size:30
Alignment explanation
Indices: 25562187--25562247 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
25562177 ATCCATCACT
*
25562187 TTGTGTCCCAAGCAATCAATCAGTAATTAA
1 TTGTGTCCCAAACAATCAATCAGTAATTAA
*
25562217 TTGTGTCCCAAACAATCAATTAGTAATTAA
1 TTGTGTCCCAAACAATCAATCAGTAATTAA
25562247 T
1 T
25562248 ACCTAGAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (30 bp):
TTGTGTCCCAAACAATCAATCAGTAATTAA
Found at i:25562378 original size:21 final size:23
Alignment explanation
Indices: 25562348--25562401 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
25562338 AATCAATTAA
* *
25562348 TAAATTAAATATT-TAAGTAT-T
1 TAAATAAAATATTGTAAATATAT
25562369 TAAATAAAATATTGTAAATATAT
1 TAAATAAAATATTGTAAATATAT
*
25562392 TATATAAAAT
1 TAAATAAAAT
25562402 TAATATACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 12 0.43
22 6 0.21
23 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TAAATAAAATATTGTAAATATAT
Found at i:25565356 original size:30 final size:30
Alignment explanation
Indices: 25565264--25565358 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
25565254 AGATATGAAA
* *
25565264 GTGTAACAA-AATA--TTTTTGAATATGGT
1 GTGTAACAATAATATTTTTTTCAAAATGGT
* * *
25565291 GTGTAATAATAATATTTTTTTCAACATAGT
1 GTGTAACAATAATATTTTTTTCAAAATGGT
* * *
25565321 ATGTAACAATAGTATTTTTTTCAAAATGGC
1 GTGTAACAATAATATTTTTTTCAAAATGGT
25565351 GTGTAACA
1 GTGTAACA
25565359 GCCTTTTTTA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
27 8 0.15
28 4 0.07
30 42 0.78
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (30 bp):
GTGTAACAATAATATTTTTTTCAAAATGGT
Found at i:25565451 original size:24 final size:24
Alignment explanation
Indices: 25565410--25565516 Score: 133
Period size: 24 Copynumber: 4.5 Consensus size: 24
25565400 TATGTAACAA
* ** *
25565410 TAATATTTTTTTCAACATGGCGTG
1 TAATATGTTTTTGTACATGACGTG
25565434 TAATATGTTTTTGTACATGACGTG
1 TAATATGTTTTTGTACATGACGTG
* *
25565458 TTACATGTTTTTGTACATGACGTG
1 TAATATGTTTTTGTACATGACGTG
* *
25565482 TCACATGTTTTTGTACATGACGTG
1 TAATATGTTTTTGTACATGACGTG
*
25565506 TCATATGTTTT
1 TAATATGTTTT
25565517 ATGTTTCTGT
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 75 1.00
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (24 bp):
TAATATGTTTTTGTACATGACGTG
Found at i:25565467 original size:78 final size:79
Alignment explanation
Indices: 25565314--25565476 Score: 224
Period size: 80 Copynumber: 2.1 Consensus size: 79
25565304 ATTTTTTTCA
* *
25565314 ACATAGTATGTAACAATAGTATTTTTTTCAAAATGGCGTGTAACAGCCTTTTTTAACCATGACGT
1 ACATGGTATGTAACAATAATATTTTTTTCAAAATGGCGTGTAACAG-CTTTTTTAACCATGACGT
25565379 GTAACATGTTTTTAT
65 GTAACATGTTTTTAT
* *
25565394 ACATGGTATGTAACAATAATATTTTTTTCAACATGGCGTGTAATATG-TTTTTGT-A-CATGACG
1 ACATGGTATGTAACAATAATATTTTTTTCAAAATGGCGTGTAACA-GCTTTTT-TAACCATGACG
* *
25565456 TGTTACATGTTTTTGT
64 TGTAACATGTTTTTAT
25565472 ACATG
1 ACATG
25565477 ACGTGTCACA
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
78 26 0.35
79 6 0.08
80 42 0.56
81 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (79 bp):
ACATGGTATGTAACAATAATATTTTTTTCAAAATGGCGTGTAACAGCTTTTTTAACCATGACGTG
TAACATGTTTTTAT
Found at i:25565528 original size:31 final size:31
Alignment explanation
Indices: 25565486--25565546 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
25565476 GACGTGTCAC
* *
25565486 ATGTTTTTGTACATGACGTGTCATATGTTTT
1 ATGTTTCTGTACATGACGTGTCACATGTTTT
25565517 ATGTTTCTGTACATGACGTGTCACATGTTT
1 ATGTTTCTGTACATGACGTGTCACATGTTT
25565547 CTGTACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.48
Consensus pattern (31 bp):
ATGTTTCTGTACATGACGTGTCACATGTTTT
Found at i:25565601 original size:24 final size:24
Alignment explanation
Indices: 25565573--25565652 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
25565563 ACAACCTAAC
* * *
25565573 CATGACATATTACATGTTTTTGCA
1 CATGACATATAACATATTTTTGTA
* *
25565597 CATGACGTGTAACATATTTTTGTA
1 CATGACATATAACATATTTTTGTA
*
25565621 CAT-AGCATATAACATATTTTTATA
1 CATGA-CATATAACATATTTTTGTA
25565645 CATGACAT
1 CATGACAT
25565653 GTAATATCAT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
23 1 0.02
24 44 0.96
25 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (24 bp):
CATGACATATAACATATTTTTGTA
Found at i:25573604 original size:27 final size:26
Alignment explanation
Indices: 25573554--25573608 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
25573544 ATCCATCACT
**
25573554 TTGTATCCCAAACAATTTAGTACTTAA
1 TTGTATCCCAAACAATCAAGTAC-TAA
* *
25573581 TTGTGTCCCAAACAATCAATTACTAA
1 TTGTATCCCAAACAATCAAGTACTAA
25573607 TT
1 TT
25573609 AATACCTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (26 bp):
TTGTATCCCAAACAATCAAGTACTAA
Found at i:25573810 original size:31 final size:29
Alignment explanation
Indices: 25573766--25573851 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 29
25573756 ATATATTACA
*
25573766 TATTATTAATAA-TTAAAATTAATATATATT
1 TATTTTTAATAATTTAAAATTAA-ATA-ATT
* *
25573796 TATTTTTAATTAATTTTAATTTAAATAATT
1 TATTTTTAA-TAATTTAAAATTAAATAATT
*
25573826 TAATTTTTAA-AATTTTAAAATCAAAT
1 T-ATTTTTAATAA-TTTAAAATTAAAT
25573852 TAGTTAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
29 2 0.04
30 22 0.48
31 14 0.30
32 8 0.17
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (29 bp):
TATTTTTAATAATTTAAAATTAAATAATT
Found at i:25573843 original size:29 final size:31
Alignment explanation
Indices: 25573766--25573843 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
25573756 ATATATTACA
* * *
25573766 TATTATTAATAA-TTAAAATTAATATATATT
1 TATTTTTAATAATTTTAATTTAATATATATT
25573796 TATTTTTAATTAATTTTAATTTAA-ATA-ATT
1 TATTTTTAA-TAATTTTAATTTAATATATATT
25573826 TAATTTTTAA-AATTTTAA
1 T-ATTTTTAATAATTTTAA
25573844 AATCAAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 8 0.19
30 12 0.29
31 14 0.33
32 8 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
TATTTTTAATAATTTTAATTTAATATATATT
Found at i:25575967 original size:18 final size:20
Alignment explanation
Indices: 25575926--25575967 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
25575916 ATATATAAAT
*
25575926 TATTTAAATTTAATTTATTA
1 TATTTAAATTAAATTTATTA
25575946 -ATTT-AATTAAATTT-TTA
1 TATTTAAATTAAATTTATTA
25575963 TATTT
1 TATTT
25575968 TTATTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 3 0.15
18 13 0.65
19 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTAAATTAAATTTATTA
Found at i:25578041 original size:14 final size:14
Alignment explanation
Indices: 25578024--25578053 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25578014 ATTACTAGTC
*
25578024 TCAGGCTTCTAGCT
1 TCAGGCTTCAAGCT
25578038 TCAGGCTTCAAGCT
1 TCAGGCTTCAAGCT
25578052 TC
1 TC
25578054 GAATCTCTCT
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:0.17, C:0.30, G:0.20, T:0.33
Consensus pattern (14 bp):
TCAGGCTTCAAGCT
Found at i:25590687 original size:7 final size:7
Alignment explanation
Indices: 25590675--25590700 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
25590665 ACCTACCAAA
25590675 AAAGAAG
1 AAAGAAG
25590682 AAAGAAG
1 AAAGAAG
25590689 AAAGAAG
1 AAAGAAG
25590696 AAAGA
1 AAAGA
25590701 TTGAGCCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:25600915 original size:20 final size:20
Alignment explanation
Indices: 25600865--25600920 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
25600855 ATCAAATAAT
25600865 TTAAATATTAATGTATTTTAAA
1 TTAAATATTAA--TATTTTAAA
* *
25600887 --AATTTTTAATATTTTAAA
1 TTAAATATTAATATTTTAAA
25600905 TTAAATATTAATATTT
1 TTAAATATTAATATTT
25600921 ATCAAATCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
18 9 0.32
20 19 0.68
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTAAATATTAATATTTTAAA
Found at i:25605480 original size:2 final size:2
Alignment explanation
Indices: 25605475--25605506 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25605465 GACAAAAACT
25605475 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25605507 TATTATCACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25606455 original size:3 final size:3
Alignment explanation
Indices: 25606447--25606481 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
25606437 GAATTCGGAG
* *
25606447 GAT GAT GAT GAT GAT GAT GTT GAT GAT GAG GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
25606482 GAAGTCATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.37, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:25606845 original size:13 final size:13
Alignment explanation
Indices: 25606827--25606854 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
25606817 GAGTAGGAGG
25606827 AGCAGCAGCAGCC
1 AGCAGCAGCAGCC
25606840 AGCAGCAGCAGCC
1 AGCAGCAGCAGCC
25606853 AG
1 AG
25606855 TCAGTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (13 bp):
AGCAGCAGCAGCC
Found at i:25616197 original size:24 final size:24
Alignment explanation
Indices: 25616166--25616211 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
25616156 CCAAATCATC
25616166 TAAACAAT-TGATTATTTTGAACA
1 TAAACAATGTGATTATTTTGAACA
25616189 TAAAGCAATGTGATTATTTTGAA
1 TAAA-CAATGTGATTATTTTGAA
25616212 TTTAGAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
24 4 0.19
25 13 0.62
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (24 bp):
TAAACAATGTGATTATTTTGAACA
Found at i:25621609 original size:47 final size:48
Alignment explanation
Indices: 25621555--25621657 Score: 145
Period size: 48 Copynumber: 2.2 Consensus size: 48
25621545 TACAATTCAG
* *
25621555 ATCAAATTATACTCCTATCTAATTTA-ATCCAAATCTAAATATACTTA
1 ATCAAATTATACTCCTATCTAATGTATATCCAAATCTAAATAAACTTA
** * *
25621602 ATCAAATTATACTTTTATTTAATGTATATCCAAATTTAAATAAACTTA
1 ATCAAATTATACTCCTATCTAATGTATATCCAAATCTAAATAAACTTA
25621650 ATCAAATT
1 ATCAAATT
25621658 TAAGAGATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
47 22 0.45
48 27 0.55
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.41
Consensus pattern (48 bp):
ATCAAATTATACTCCTATCTAATGTATATCCAAATCTAAATAAACTTA
Found at i:25621675 original size:67 final size:67
Alignment explanation
Indices: 25621601--25621794 Score: 255
Period size: 67 Copynumber: 2.9 Consensus size: 67
25621591 AAATATACTT
* * * * * *
25621601 AATCAAATTATACTTTTATTTAATGTATATCCAAATTTAAATAAACTTAATCAAATTTAAGAGAT
1 AATCAAATTATACTTTTATATAATTTATATCAAAATCTAAATATACATAATCAAATTTAAGAG-T
25621666 T-A
65 TCA
* *
25621668 AATCAAATTATACTTTTATATAATTTATATCAAAATCTAAACATGCATAATCAAATTTAAGAGTT
1 AATCAAATTATACTTTTATATAATTTATATCAAAATCTAAATATACATAATCAAATTTAAGAGTT
25621733 CA
66 CA
* * * * *
25621735 GATCAAATTATACTCTTATCTAATTTACATCTAAATCTAAATATACATAATCAAATTTAA
1 AATCAAATTATACTTTTATATAATTTATATCAAAATCTAAATATACATAATCAAATTTAA
25621795 TAGTCTTATG
Statistics
Matches: 111, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
66 2 0.02
67 109 0.98
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.39
Consensus pattern (67 bp):
AATCAAATTATACTTTTATATAATTTATATCAAAATCTAAATATACATAATCAAATTTAAGAGTT
CA
Found at i:25629310 original size:17 final size:19
Alignment explanation
Indices: 25629273--25629313 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
25629263 ATATGATAAT
*
25629273 TAAATTAAAGTTTTTATTA
1 TAAATTAAAGATTTTATTA
25629292 TAAATTAAA-ATTTTA-TA
1 TAAATTAAAGATTTTATTA
25629309 TAAAT
1 TAAAT
25629314 ACAAGAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 5 0.24
19 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TAAATTAAAGATTTTATTA
Found at i:25630190 original size:6 final size:6
Alignment explanation
Indices: 25630181--25630218 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
25630171 CTGACTCTTC
25630181 TTCTCT TTCT-T CTTCTCT TTCTCT TTCTCT TTCTCT TT
1 TTCTCT TTCTCT -TTCTCT TTCTCT TTCTCT TTCTCT TT
25630219 ATCCTTGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 1 0.03
6 28 0.93
7 1 0.03
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTCTCT
Found at i:25630193 original size:12 final size:12
Alignment explanation
Indices: 25630176--25630214 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
25630166 TGACTCTGAC
25630176 TCTTCTTCTCTT
1 TCTTCTTCTCTT
25630188 TCTTCTTCTCTT
1 TCTTCTTCTCTT
25630200 TC-TCTTTCTCTT
1 TCTTC-TTCTCTT
25630212 TCT
1 TCT
25630215 CTTTATCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 2 0.08
12 23 0.92
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
TCTTCTTCTCTT
Found at i:25630204 original size:18 final size:18
Alignment explanation
Indices: 25630181--25630232 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
25630171 CTGACTCTTC
25630181 TTCTCTTTCTTCTTCTCT
1 TTCTCTTTCTTCTTCTCT
25630199 TTCTCTTTC-TCTTTCTCT
1 TTCTCTTTCTTC-TTCTCT
*
25630217 TTATCCTTGTCTTCTT
1 TTCT-CTT-TCTTCTT
25630233 GATGTTTTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 2 0.07
18 18 0.62
19 3 0.10
20 4 0.14
21 2 0.07
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (18 bp):
TTCTCTTTCTTCTTCTCT
Found at i:25633594 original size:2 final size:2
Alignment explanation
Indices: 25633583--25633623 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
25633573 ATTCATGCTA
25633583 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
25633624 AGTTTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25665294 original size:3 final size:3
Alignment explanation
Indices: 25665288--25665340 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
25665278 GATTGCCATC
* *
25665288 ATG ATG ATG ATG ATG GTG ATG GTG AATG AATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG -ATG -ATG ATG ATG ATG ATG ATG
*
25665335 GTG ATG
1 ATG ATG
25665341 GTGCCTCGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:25669815 original size:68 final size:69
Alignment explanation
Indices: 25669706--25669840 Score: 218
Period size: 68 Copynumber: 2.0 Consensus size: 69
25669696 GATAGGACAC
* * * *
25669706 GACAAAGAGTCGCCGGAAGGCTCCAATTCTTCTTTCCCAACTA-TATATATATATATATATATAT
1 GACAAAGAGTCACCAGAAAGCTCCAAGTCTTCTTTCCCAACTACTATATATATATATATATATAT
25669770 ACAT
66 ACAT
25669774 GACAAAGAGTCACCAGAAAGCTCCAAGTCTTCTTTCCCAACTACGTATATATATATATATATATA
1 GACAAAGAGTCACCAGAAAGCTCCAAGTCTTCTTTCCCAACTAC-TATATATATATATATATATA
25669839 TA
65 TA
25669841 TATATAATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 39 0.64
70 22 0.36
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (69 bp):
GACAAAGAGTCACCAGAAAGCTCCAAGTCTTCTTTCCCAACTACTATATATATATATATATATAT
ACAT
Found at i:25669826 original size:2 final size:2
Alignment explanation
Indices: 25669819--25669846 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25669809 CCCAACTACG
25669819 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25669847 ATTATTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25684813 original size:3 final size:3
Alignment explanation
Indices: 25684807--25684844 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
25684797 GAAGGAAGAA
* *
25684807 GAG GAG GGG GAG GAG GAG GAG GAG GAG GAG GAG AAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
25684845 AGTGGAGCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:25685173 original size:5 final size:5
Alignment explanation
Indices: 25685163--25685198 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
25685153 AATGTTTGCG
*
25685163 AGAAA AGAAA AGAAA AGAAA AGAAA GGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
25685199 TGGAGTATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:25685559 original size:25 final size:25
Alignment explanation
Indices: 25685531--25685598 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
25685521 AATAAAATTT
25685531 TTTTATATATAAAATAATTAATTAA
1 TTTTATATATAAAATAATTAATTAA
* *
25685556 TTTTGA-AT-TCAAAATATTTTATTAA
1 TTTT-ATATAT-AAAATAATTAATTAA
25685581 TTTTATATA-AAAA-AATTA
1 TTTTATATATAAAATAATTA
25685599 CTAATTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
23 3 0.09
24 6 0.17
25 25 0.71
26 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (25 bp):
TTTTATATATAAAATAATTAATTAA
Found at i:25687320 original size:27 final size:27
Alignment explanation
Indices: 25687288--25687345 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
25687278 AAATTATTTG
25687288 AATTCAATTACTTTGATTTGATTGATC
1 AATTCAATTACTTTGATTTGATTGATC
25687315 AATTCAATTACTTTGATTTGATTGATC
1 AATTCAATTACTTTGATTTGATTGATC
25687342 AATT
1 AATT
25687346 TTGATATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (27 bp):
AATTCAATTACTTTGATTTGATTGATC
Found at i:25695022 original size:2 final size:2
Alignment explanation
Indices: 25694963--25695007 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
25694953 CCCATTCTTT
25694963 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25695005 TA T
1 TA T
25695008 TATTGGTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25720464 original size:20 final size:20
Alignment explanation
Indices: 25720435--25720485 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
25720425 TTAATTAACA
25720435 TTTTATTTAAGATTATTA-ATT
1 TTTTATTTAA-ATT-TTATATT
25720456 TTTTA-TTAAATTTTATA-T
1 TTTTATTTAAATTTTATATT
25720474 TTTTATTTAAAT
1 TTTTATTTAAAT
25720486 ACAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.32
19 10 0.36
20 4 0.14
21 5 0.18
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTATTTAAATTTTATATT
Found at i:25728104 original size:73 final size:74
Alignment explanation
Indices: 25727967--25728119 Score: 254
Period size: 73 Copynumber: 2.0 Consensus size: 74
25727957 AAAAGACGAA
25727967 AAAAGCTTAGTCCTGAAAACTTTTAGAGAGAGAGAGAGAGAATGATGATGTTTAATTTTCGTAGG
1 AAAAGCTTAGTCCTGAAAACTTTT----A-AGAGAGAGAGAATGATGATGTTTAATTTTCGTAGG
25728032 CAAAAGTGCCCTCC
61 CAAAAGTGCCCTCC
25728046 AAAAGCTTAGTCCTGAAAACTTTT-AGAGAGAGAGAATGATGATGTTTAATTTTCGTAGGCAAAA
1 AAAAGCTTAGTCCTGAAAACTTTTAAGAGAGAGAGAATGATGATGTTTAATTTTCGTAGGCAAAA
25728110 GTGCCCTCC
66 GTGCCCTCC
25728119 A
1 A
25728120 GGTATGAAAC
Statistics
Matches: 74, Mismatches: 0, Indels: 6
0.93 0.00 0.08
Matches are distributed among these distances:
73 50 0.68
79 24 0.32
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.27
Consensus pattern (74 bp):
AAAAGCTTAGTCCTGAAAACTTTTAAGAGAGAGAGAATGATGATGTTTAATTTTCGTAGGCAAAA
GTGCCCTCC
Found at i:25770658 original size:24 final size:24
Alignment explanation
Indices: 25770631--25770709 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
25770621 GAAATGTTTA
25770631 TTCTTCTAAGATGGAAAGCAGATT
1 TTCTTCTAAGATGGAAAGCAGATT
* * * *
25770655 TTCTATCTTAAAGAAGG-ATGCGGTTT
1 TTCT-TC-T-AAGATGGAAAGCAGATT
*
25770681 ATTCTTCTAAGATGGAAAGGAGATT
1 -TTCTTCTAAGATGGAAAGCAGATT
25770706 TTCT
1 TTCT
25770710 ATCTTAAAGA
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
24 14 0.34
25 8 0.20
26 9 0.22
27 10 0.24
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (24 bp):
TTCTTCTAAGATGGAAAGCAGATT
Found at i:25770668 original size:27 final size:27
Alignment explanation
Indices: 25770638--25770719 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
25770628 TTATTCTTCT
25770638 AAGATGGAAAGCAGATTTTCTATCTTA
1 AAGATGGAAAGCAGATTTTCTATCTTA
* * * *
25770665 AAGAAGG-ATGCGGTTTATTCT-TC-T-
1 AAGATGGAAAGCAGATT-TTCTATCTTA
*
25770689 AAGATGGAAAGGAGATTTTCTATCTTA
1 AAGATGGAAAGCAGATTTTCTATCTTA
25770716 AAGA
1 AAGA
25770720 CAGATGTGGA
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
24 10 0.24
25 8 0.20
26 9 0.22
27 14 0.34
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (27 bp):
AAGATGGAAAGCAGATTTTCTATCTTA
Found at i:25773100 original size:11 final size:11
Alignment explanation
Indices: 25773084--25773113 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
25773074 TATATATATA
25773084 TTTATTTTTTT
1 TTTATTTTTTT
25773095 TTTATTTTTTT
1 TTTATTTTTTT
25773106 TTT-TTTTT
1 TTTATTTTT
25773114 GAAAGTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:25773112 original size:15 final size:15
Alignment explanation
Indices: 25773082--25773111 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
25773072 TATATATATA
25773082 TATTTATTTTTTTTT
1 TATTTATTTTTTTTT
25773097 TATTT-TTTTTTTTT
1 TATTTATTTTTTTTT
25773111 T
1 T
25773112 TTGAAAGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TATTTATTTTTTTTT
Found at i:25776335 original size:3 final size:3
Alignment explanation
Indices: 25776327--25776359 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
25776317 TTATAACTAA
25776327 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25776360 TAGTAAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.