Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009568.1 Hibiscus syriacus cultivar Beakdansim tig00116927_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 696633
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:240616 original size:23 final size:24
Alignment explanation
Indices: 240568--240630 Score: 101
Period size: 23 Copynumber: 2.7 Consensus size: 24
240558 CAAGTATTAT
*
240568 ATCAGAATCCAGGTCATGTATCAG
1 ATCAGAATCCAGGTCATATATCAG
*
240592 ATCAGAATCCATGTCA-ATATCAG
1 ATCAGAATCCAGGTCATATATCAG
240615 ATCAGAATCCAGGTCA
1 ATCAGAATCCAGGTCA
240631 GGTATCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 21 0.58
24 15 0.42
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAGAATCCAGGTCATATATCAG
Found at i:243164 original size:13 final size:14
Alignment explanation
Indices: 243146--243176 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
243136 CAACGGTCAA
243146 CGGGTCAAT-GGGT
1 CGGGTCAATCGGGT
243159 CGGGTCAATCGGGT
1 CGGGTCAATCGGGT
243173 CGGG
1 CGGG
243177 GCGGGTTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.13, C:0.19, G:0.48, T:0.19
Consensus pattern (14 bp):
CGGGTCAATCGGGT
Found at i:243215 original size:23 final size:23
Alignment explanation
Indices: 243155--243223 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
243145 ACGGGTCAAT
*
243155 GGGTCGGGTCAATCGGGTCGGGGC
1 GGGTCGGGTCAA-CGGGTCGGGTC
* * **
243179 GGGTTGAGAAAACGGGTCGGGTC
1 GGGTCGGGTCAACGGGTCGGGTC
243202 GGGTCGGGTCAACGGGTCGGGT
1 GGGTCGGGTCAACGGGTCGGGT
243224 TGTGACCGGT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 28 0.78
24 8 0.22
ACGTcount: A:0.13, C:0.17, G:0.52, T:0.17
Consensus pattern (23 bp):
GGGTCGGGTCAACGGGTCGGGTC
Found at i:243234 original size:23 final size:23
Alignment explanation
Indices: 243189--243236 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
243179 GGGTTGAGAA
* *
243189 AACGGGTCGGGTCGGGTCGGGTC
1 AACGGGTCGGGTCGGGACCGGTC
* *
243212 AACGGGTCGGGTTGTGACCGGTC
1 AACGGGTCGGGTCGGGACCGGTC
243235 AA
1 AA
243237 ACCGGTCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.19
Consensus pattern (23 bp):
AACGGGTCGGGTCGGGACCGGTC
Found at i:263722 original size:28 final size:28
Alignment explanation
Indices: 263689--263754 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
263679 ATTCCATAAC
263689 AGAGTTTTGACTATTAGTTCCCAGACCT
1 AGAGTTTTGACTATTAGTTCCCAGACCT
* *
263717 TGAGTTTTGACTATTAGTTCCCGGACCT
1 AGAGTTTTGACTATTAGTTCCCAGACCT
263745 AGAGTTTTGA
1 AGAGTTTTGA
263755 TGTTTGAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (28 bp):
AGAGTTTTGACTATTAGTTCCCAGACCT
Found at i:266097 original size:32 final size:32
Alignment explanation
Indices: 266061--266143 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
266051 TCATAATAGT
*
266061 TAAAATGATGATATAATATGTACTAAATTATC
1 TAAAATGATAATATAATATGTACTAAATTATC
* * ** *
266093 TAAAATAATAACATAATATGTGTTACATTATC
1 TAAAATGATAATATAATATGTACTAAATTATC
*
266125 TAAAATGATAATATGATAT
1 TAAAATGATAATATAATAT
266144 ATATTATGTC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.37
Consensus pattern (32 bp):
TAAAATGATAATATAATATGTACTAAATTATC
Found at i:268938 original size:2 final size:2
Alignment explanation
Indices: 268931--268957 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
268921 ATTATATCAG
268931 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 T
268958 GTTACATTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:271796 original size:12 final size:12
Alignment explanation
Indices: 271779--271806 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
271769 GGACTTTTTG
271779 GAAAATTGAGAA
1 GAAAATTGAGAA
271791 GAAAATTGAGAA
1 GAAAATTGAGAA
271803 GAAA
1 GAAA
271807 TGGAGTATAA
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:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (12 bp):
GAAAATTGAGAA
Found at i:274852 original size:22 final size:22
Alignment explanation
Indices: 274815--274858 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
274805 ACCTCATTTC
*
274815 TTAATAAAAAAATAAATAAATA
1 TTAATAAAAAAATAAAAAAATA
* *
274837 TTAATAAAACATTAAAAAAATA
1 TTAATAAAAAAATAAAAAAATA
274859 ATATATATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
TTAATAAAAAAATAAAAAAATA
Found at i:274877 original size:22 final size:22
Alignment explanation
Indices: 274852--274903 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
274842 AAAACATTAA
*
274852 AAAAATAATATATATAATTTA-T
1 AAAAATAAAATAT-TAATTTATT
*
274874 AAAAATAAAATATTTATTTATTT
1 AAAAATAAAATATTAATTTA-TT
274897 AAAAATA
1 AAAAATA
274904 TCAGAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 12 0.46
23 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATAAAATATTAATTTATT
Found at i:275092 original size:15 final size:15
Alignment explanation
Indices: 275072--275101 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
275062 ATATATATTT
275072 GTAATAATAATAATA
1 GTAATAATAATAATA
*
275087 GTAATAGTAATAATA
1 GTAATAATAATAATA
275102 ATAAATAAAT
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:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (15 bp):
GTAATAATAATAATA
Found at i:276700 original size:21 final size:21
Alignment explanation
Indices: 276676--276718 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
276666 TAATAATAAA
276676 TAATAATAA-TATATATTATAT
1 TAATAATAATTAT-TATTATAT
* *
276697 TAATTATTATTATTATTATAT
1 TAATAATAATTATTATTATAT
276718 T
1 T
276719 TATGAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATAATAATTATTATTATAT
Found at i:276916 original size:46 final size:46
Alignment explanation
Indices: 276841--277335 Score: 891
Period size: 46 Copynumber: 10.8 Consensus size: 46
276831 GACGGAAATG
* * *
276841 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCAAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
276887 TTTGAAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
276933 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* *
276979 TTTGAAAACATCATGCACTGAAAGACTTACAGATGACCCAAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
277025 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCAAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
**
277071 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCTAAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
277117 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
277163 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
277209 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
277255 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* *
277301 TTTGAAAACATCATGTACTGAAAGACTTACAGATG
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATG
277336 CGGGAAATAG
Statistics
Matches: 436, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 436 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (46 bp):
TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
Found at i:277888 original size:25 final size:25
Alignment explanation
Indices: 277854--277914 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
277844 CTTGTATCTT
*
277854 TGTTTCATTTAAGTCTCAGAAGAAA
1 TGTTTCATTTAAGTCTAAGAAGAAA
277879 TGTTTCATTTAAGTCTAAGAAGAAA
1 TGTTTCATTTAAGTCTAAGAAGAAA
277904 TGTTTCATTTA
1 TGTTTCATTTA
277915 TGGAACTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (25 bp):
TGTTTCATTTAAGTCTAAGAAGAAA
Found at i:282974 original size:75 final size:75
Alignment explanation
Indices: 282865--283031 Score: 226
Period size: 75 Copynumber: 2.2 Consensus size: 75
282855 GGCCTTAAAC
* * * *** * * * *
282865 ATGCCCCAACATTGGCTAATACAAGCATTCAAAATGCGTCAACATTCTTTATTCTGATTGAAAGG
1 ATGCCCCAACATTTGCTGATATAAATGTTCAAAATACATCAACATTCATGATTCTGATTGAAAGG
282930 GGCTTTCAGT
66 GGCTTTCAGT
* *
282940 ATGCCCCAGCATTTGCTGATATAAATGTTCAAAATACATCAACATTCATGATTCTGATTGAGAGG
1 ATGCCCCAACATTTGCTGATATAAATGTTCAAAATACATCAACATTCATGATTCTGATTGAAAGG
283005 GGCTTTCAGT
66 GGCTTTCAGT
283015 ATGCCCCAACATTTGCT
1 ATGCCCCAACATTTGCT
283032 TTTTGTTAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 79 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (75 bp):
ATGCCCCAACATTTGCTGATATAAATGTTCAAAATACATCAACATTCATGATTCTGATTGAAAGG
GGCTTTCAGT
Found at i:288445 original size:14 final size:14
Alignment explanation
Indices: 288426--288452 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
288416 TTAACAAATA
288426 AAAAATGTAAATGC
1 AAAAATGTAAATGC
288440 AAAAATGTAAATG
1 AAAAATGTAAATG
288453 TAAATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.15, T:0.22
Consensus pattern (14 bp):
AAAAATGTAAATGC
Found at i:291823 original size:3 final size:3
Alignment explanation
Indices: 291817--291849 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
291807 TATATATTTG
*
291817 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
291850 ATAAATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:293423 original size:3 final size:3
Alignment explanation
Indices: 293415--293459 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
293405 TATATTTATT
* *
293415 TAA TAA TAA TAAA TAA TAA TAA TAA TAA TATA TTA TAT TAA TAA T
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA T
293460 TATTATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 31 0.86
4 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:293439 original size:19 final size:19
Alignment explanation
Indices: 293415--293459 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
293405 TATATTTATT
293415 TAATAATAATAAATAATAA
1 TAATAATAATAAATAATAA
* * *
293434 TAATAATAATATATTATAT
1 TAATAATAATAAATAATAA
293453 TAATAAT
1 TAATAAT
293460 TATTATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATAATAATAAATAATAA
Found at i:293456 original size:16 final size:16
Alignment explanation
Indices: 293437--293470 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
293427 ATAATAATAA
293437 TAATAATATATTA-TAT
1 TAATAAT-TATTATTAT
293453 TAATAATTATTATTAT
1 TAATAATTATTATTAT
293469 TA
1 TA
293471 TATTTATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATAATTATTATTAT
Found at i:296781 original size:41 final size:41
Alignment explanation
Indices: 296724--296837 Score: 196
Period size: 41 Copynumber: 2.8 Consensus size: 41
296714 ACCCCAAAGG
* *
296724 CCCAAAC-ACAAC-AAAACACACACAAACACCCATACATAC
1 CCCAAACTACAACAAAAACTCACACCAACACCCATACATAC
296763 CCCAAACTACAACAAAAACTCACACCAACACCCATACATAC
1 CCCAAACTACAACAAAAACTCACACCAACACCCATACATAC
296804 CCCAAACTACAACAAAAACTCACACCAACACCCA
1 CCCAAACTACAACAAAAACTCACACCAACACCCA
296838 ATGACAACGA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
39 7 0.10
40 5 0.07
41 59 0.83
ACGTcount: A:0.51, C:0.42, G:0.00, T:0.07
Consensus pattern (41 bp):
CCCAAACTACAACAAAAACTCACACCAACACCCATACATAC
Found at i:297256 original size:23 final size:22
Alignment explanation
Indices: 297228--297292 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
297218 AAGGAGTTGA
*
297228 AATATTATTAACTATATATTCAT
1 AATATTATTAACTATAAATT-AT
* *
297251 TATATT-CTAAC-ATAAATTAT
1 AATATTATTAACTATAAATTAT
*
297271 AATATTATTAACTATAATTTAT
1 AATATTATTAACTATAAATTAT
297293 TTTTTTTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 7 0.21
21 10 0.29
22 12 0.35
23 5 0.15
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATTATTAACTATAAATTAT
Found at i:297289 original size:21 final size:22
Alignment explanation
Indices: 297228--297289 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
297218 AAGGAGTTGA
297228 AATATTATTAACTATATATTCAT
1 AATATTATTAACTATA-ATTCAT
* *
297251 TATATT-CTAAC-ATAAATT-AT
1 AATATTATTAACTAT-AATTCAT
297271 AATATTATTAACTATAATT
1 AATATTATTAACTATAATT
297290 TATTTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 7 0.22
21 13 0.41
22 7 0.22
23 5 0.16
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATTATTAACTATAATTCAT
Found at i:311116 original size:14 final size:14
Alignment explanation
Indices: 311097--311139 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
311087 TGGCATCGAC
*
311097 ATTAATCACTTAGA
1 ATTAATAACTTAGA
311111 ATTAATAACTTAGA
1 ATTAATAACTTAGA
311125 ATTAATAACTTAGA
1 ATTAATAACTTAGA
311139 A
1 A
311140 CTATACGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (14 bp):
ATTAATAACTTAGA
Found at i:315199 original size:21 final size:22
Alignment explanation
Indices: 315175--315220 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
315165 ATTAAAATAA
*
315175 TTTGTAAA-TTAATTTAATAGT
1 TTTGGAAAGTTAATTTAATAGT
* *
315196 TTTGGAAAGTTATTTTAGTAGT
1 TTTGGAAAGTTAATTTAATAGT
315218 TTT
1 TTT
315221 AAAGTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.54
Consensus pattern (22 bp):
TTTGGAAAGTTAATTTAATAGT
Found at i:315361 original size:60 final size:59
Alignment explanation
Indices: 315263--315442 Score: 207
Period size: 60 Copynumber: 3.0 Consensus size: 59
315253 TGCATCATAT
*
315263 TTCCTTAAACTATGACTCTCATTTTAAATTAGTCTTTAAACTTTTAAATACTTCAATTTC
1 TTCCTTAAACTATGACTCTCATTATAAATTAGTCTTTAAACTTTTAAATA-TTCAATTTC
* * *
315323 TTCCTTAAACTATGACTCTCATTATAAATTAGTATTTAAACTTTTGAACATTCTAATTTC
1 TTCCTTAAACTATGACTCTCATTATAAATTAGTCTTTAAACTTTTAAATATTC-AATTTC
* ** * * * * ** *
315383 ATCCCCAAATTATGAATTTCATTCTAAATTAGTCCCTAAACTTTTAGATATTTCAATTTC
1 TTCCTTAAACTATGACTCTCATTATAAATTAGTCTTTAAACTTTTAAATA-TTCAATTTC
315443 ATCCCAAATT
Statistics
Matches: 101, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
59 3 0.03
60 95 0.94
61 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.44
Consensus pattern (59 bp):
TTCCTTAAACTATGACTCTCATTATAAATTAGTCTTTAAACTTTTAAATATTCAATTTC
Found at i:315699 original size:41 final size:41
Alignment explanation
Indices: 315653--315878 Score: 244
Period size: 41 Copynumber: 5.6 Consensus size: 41
315643 AAAAAACGCT
* * *
315653 GCTAAATACTCGTATTTTAGTGGCGTTTTTATATAAACATC
1 GCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACATC
* * * *
315694 GCTAAACAAT-GTACTTTAGTAGCGTTTTTATACAAACACC
1 GCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACATC
* * *
315734 GCTAAAGA-TTGTACTTTAGTGGC-ATTTTATACAAACGTC
1 GCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACATC
* *
315773 GCTAAAGACTCGTACTTTAGTGGTGTTTTTATACAAACGTC
1 GCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACATC
* * * ** *
315814 ACTATAGACTAGTGTTTTAGTGGCGTTTTGATACAAACA-C
1 GCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACATC
*
315854 TGTTAAAGACTCGTACTTTAGTGGC
1 -GCTAAAGACTCGTACTTTAGTGGC
315879 ATTTGTTTTT
Statistics
Matches: 153, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
39 22 0.14
40 59 0.39
41 72 0.47
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (41 bp):
GCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACATC
Found at i:315789 original size:80 final size:80
Alignment explanation
Indices: 315654--315875 Score: 214
Period size: 80 Copynumber: 2.7 Consensus size: 80
315644 AAAAACGCTG
* * * * * * *
315654 CTAAATACTCGTATTTTAGTGGCGTTTTTATATAAACATCGCTAAACAAT-GTACTTTAGTAGCG
1 CTAAAGACTAGTACTTTAGTGGC-ATTTTATACAAAC-TCGCTAAAGACTCGTACTTTAGTAGCG
*
315718 TTTTTATACAAACACCG
64 TTTTTATACAAACACCA
* * *
315735 CTAAAGA-TTGTACTTTAGTGGCATTTTATACAAACGTCGCTAAAGACTCGTACTTTAGTGGTGT
1 CTAAAGACTAGTACTTTAGTGGCATTTTATACAAAC-TCGCTAAAGACTCGTACTTTAGTAGCGT
**
315799 TTTTATACAAACGTCA
65 TTTTATACAAACACCA
* ** * * *
315815 CTATAGACTAGTGTTTTAGTGGCGTTTTGATACAAACACTGTTAAAGACTCGTACTTTAGT
1 CTAAAGACTAGTACTTTAGTGGCATTTT-ATACAAACTC-GCTAAAGACTCGTACTTTAGT
315876 GGCATTTGTT
Statistics
Matches: 117, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 21 0.18
80 45 0.38
81 23 0.20
82 28 0.24
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (80 bp):
CTAAAGACTAGTACTTTAGTGGCATTTTATACAAACTCGCTAAAGACTCGTACTTTAGTAGCGTT
TTTATACAAACACCA
Found at i:315969 original size:25 final size:25
Alignment explanation
Indices: 315937--315995 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
315927 CCTTTAACAC
315937 TTTTTCATTTTCCCACTTCACCTAT
1 TTTTTCATTTTCCCACTTCACCTAT
315962 TTTTTCATTTTCCCACTTCACCTAT
1 TTTTTCATTTTCCCACTTCACCTAT
315987 TTTTTCATT
1 TTTTTCATT
315996 CTAGCCGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.15, C:0.29, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTTCATTTTCCCACTTCACCTAT
Found at i:317434 original size:42 final size:43
Alignment explanation
Indices: 317275--317435 Score: 150
Period size: 43 Copynumber: 3.8 Consensus size: 43
317265 GTTTGAGAAC
* *
317275 AAAAAACGCCGCAATAGGTCAATATCTATTA-CGACGTTTTTTG
1 AAAAAACGCCGCAAAAGGTCAATATCTA-TAGCGACGTTTTTAG
* * * * *
317318 AACAAACGCCACAAAAGGTCGATATCTATAGCGGCGTTTTTGG
1 AAAAAACGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTAG
* * * *
317361 AATAAACGCCGCAAAAAGT-TATGA-CATATAGCGACGTTTCTAG
1 AAAAAACGCCGCAAAAGGTCAAT-ATC-TATAGCGACGTTTTTAG
* *
317404 AAAAAACACTGCAAAAGGTC-ATATCTATAGCG
1 AAAAAACGCCGCAAAAGGTCAATATCTATAGCG
317436 GCATTTTTGG
Statistics
Matches: 96, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
42 13 0.14
43 83 0.86
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (43 bp):
AAAAAACGCCGCAAAAGGTCAATATCTATAGCGACGTTTTTAG
Found at i:317452 original size:34 final size:34
Alignment explanation
Indices: 317414--317479 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
317404 AAAAAACACT
* *
317414 GCAAAAGGTCATATCTATAGCGGCATTTTTGGTC
1 GCAAAAGGTCAGACCTATAGCGGCATTTTTGGTC
*
317448 GCAAAAGGTCAGACCTATAGCGGCGTTTTTGG
1 GCAAAAGGTCAGACCTATAGCGGCATTTTTGG
317480 ACACAAACAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (34 bp):
GCAAAAGGTCAGACCTATAGCGGCATTTTTGGTC
Found at i:317508 original size:43 final size:43
Alignment explanation
Indices: 317447--317563 Score: 180
Period size: 43 Copynumber: 2.7 Consensus size: 43
317437 CATTTTTGGT
*
317447 CGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACAC
1 CGCAAAAGGTCAGACCTATAGCGGCGTTTTTGAACACAAACAC
** *
317490 CGCAAAAGGTCAGACCTATAATGGCGTTTTTGAACACAAATAC
1 CGCAAAAGGTCAGACCTATAGCGGCGTTTTTGAACACAAACAC
* *
317533 CGCAAAAAGTCAGACCTATAGCGGAGTTTTT
1 CGCAAAAGGTCAGACCTATAGCGGCGTTTTT
317564 TTGATACAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (43 bp):
CGCAAAAGGTCAGACCTATAGCGGCGTTTTTGAACACAAACAC
Found at i:317563 original size:120 final size:120
Alignment explanation
Indices: 317329--317556 Score: 264
Period size: 120 Copynumber: 1.9 Consensus size: 120
317319 ACAAACGCCA
* * * * * *
317329 CAAAAGGTCGATATCTATAGCGGCGTTTTTGGAATAAACGCCGCAAAAAGTTATGACATATAGCG
1 CAAAAGGTCGAGACCTATAGCGGCGTTTTTGGAACAAACACCGCAAAAAGTCATGACATATAACG
* * * *
317394 ACGTTTCTAGAAAAAACACTGCAAAAGGTCATATCTATAGCGGCATTTTTGGTCG
66 ACGTTTCTAGAAAAAACACCGCAAAAAGTCAGACCTATAGCGGCATTTTTGGTCG
* * *
317449 CAAAAGGTC-AGACCTATAGCGGCGTTTTTGGACACAAACACCGCAAAAGGTCA-GACCTATAAT
1 CAAAAGGTCGAGACCTATAGCGGCGTTTTTGGA-ACAAACACCGCAAAAAGTCATGACATATAAC
* * *
317512 GGCGTTT-TTGAACACAAATACCGCAAAAAGTCAGACCTATAGCGG
65 GACGTTTCTAGAA-A-AAACACCGCAAAAAGTCAGACCTATAGCGG
317557 AGTTTTTTTG
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
118 4 0.04
119 35 0.39
120 50 0.56
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.23
Consensus pattern (120 bp):
CAAAAGGTCGAGACCTATAGCGGCGTTTTTGGAACAAACACCGCAAAAAGTCATGACATATAACG
ACGTTTCTAGAAAAAACACCGCAAAAAGTCAGACCTATAGCGGCATTTTTGGTCG
Found at i:322487 original size:41 final size:41
Alignment explanation
Indices: 322442--322894 Score: 498
Period size: 41 Copynumber: 11.0 Consensus size: 41
322432 TGTGGATAAG
* * *
322442 GTACGAGTCTTTAGCGGCGTTTGTATAAAAATGTCAATAAA
1 GTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA
*
322483 GTACGAGTCTTTAGCGGCGTTTGTATAAAAATG-CACTAAA
1 GTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA
* ** * *
322523 TTACGAGTCTTTAGCAACGTTTGTAAACACAAACGCCACTATA
1 GTACGAGTCTTTAGCGGCGTTTGTATA-A-AAACGCCACTAAA
* * * * * *
322566 GTACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTAAA
1 GTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA
* *
322607 GTACGCGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAA
1 GTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA
*
322648 GTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA
1 GTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA
* * * *
322689 TTATGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCACTATA
1 GTACGAGTCTTTAGCGGCGTTTGTATA-A-AAACGCCACTAAA
* * * *
322732 GTAC-ATGTGTATAACGGCGTTTGTATAAAAAAGCCACTAAA
1 GTACGA-GTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA
* * * * *
322773 GTACAATTCTATAGCGGTGTTTGTATAAAAATGCCACTAAA
1 GTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA
* *
322814 TTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCTACTAAA
1 GTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA
* * *
322855 GTACTACTCTTTTGCGGCGTTTGT-TGAAAAAACGCCACTA
1 GTACGAGTCTTTAGCGGCGTTTGTAT--AAAAACGCCACTA
322895 TCGATGAACC
Statistics
Matches: 346, Mismatches: 57, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
40 30 0.09
41 240 0.69
42 21 0.06
43 55 0.16
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (41 bp):
GTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA
Found at i:322751 original size:166 final size:166
Alignment explanation
Indices: 322442--322895 Score: 655
Period size: 166 Copynumber: 2.7 Consensus size: 166
322432 TGTGGATAAG
* * *
322442 GTACGAGTCTTTAGCGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTAGCGGCGTTTGT
1 GTACGAGTCTTTAGCGGAGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT
* * **
322507 ATAAAAATG-CACTAAATTACGAGTCTTTAGCAACGTTTGTAAACACAAACGCCACTATAGTACA
66 ATAAAAACGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCACTATAGTACA
*
322571 AGTGTATAACGGCGTTTGAATAAAAATGCCACTAAA
131 AGTGTATAACGGCGTTTGAATAAAAAAGCCACTAAA
* * *
322607 GTACGCGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGT
1 GTACGAGTCTTTAGCGGAGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT
322672 ATAAAAACGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCACTATAGTACA
66 ATAAAAACGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCACTATAGTACA
* *
322737 TGTGTATAACGGCGTTTGTATAAAAAAGCCACTAAA
131 AGTGTATAACGGCGTTTGAATAAAAAAGCCACTAAA
* * * * *
322773 GTACAATTCTATAGCGGTGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTTTGT
1 GTACGAGTCTTTAGCGGAGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT
* * * * *
322838 ATAAAAACGCTACTAAAGTACT-ACTCTTTTGCGGCGTTTGTTGAA-A-AAACGCCACTAT
66 ATAAAAACGCCACTAAATTA-TGAGTCTTTAGCGGCGTTTG-TAAACACAAACGCCACTAT
322896 CGATGAACCT
Statistics
Matches: 260, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
165 79 0.30
166 177 0.68
167 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (166 bp):
GTACGAGTCTTTAGCGGAGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT
ATAAAAACGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTAAACACAAACGCCACTATAGTACA
AGTGTATAACGGCGTTTGAATAAAAAAGCCACTAAA
Found at i:324020 original size:12 final size:12
Alignment explanation
Indices: 323993--324031 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
323983 TTTTTTATAC
*
323993 TTTCTCTTATTAT
1 TTTCTCTTCTT-T
*
324006 TTTCTTTTCTTT
1 TTTCTCTTCTTT
324018 TTTCTCTTCTTT
1 TTTCTCTTCTTT
324030 TT
1 TT
324032 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTCTCTTCTTT
Found at i:325274 original size:18 final size:17
Alignment explanation
Indices: 325251--325284 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
325241 CTGCTATTAG
325251 TGAACCGATCGGAACCGT
1 TGAACCGATC-GAACCGT
*
325269 TGAACCGTTCGAACCG
1 TGAACCGATCGAACCG
325285 AACCGGCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (17 bp):
TGAACCGATCGAACCGT
Found at i:345858 original size:19 final size:19
Alignment explanation
Indices: 345828--345875 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
345818 AAATAGAGAT
** *
345828 ATCAGA-ATCATAGTAGAG
1 ATCAGAGATCATAACAGAA
345846 ATCAGAGATCATAACAGAA
1 ATCAGAGATCATAACAGAA
345865 ATCAGAGATCA
1 ATCAGAGATCA
345876 GAACTATATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (19 bp):
ATCAGAGATCATAACAGAA
Found at i:346687 original size:21 final size:21
Alignment explanation
Indices: 346663--346717 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
346653 CTCGGAGGGA
346663 ACCGATTCCCCCCAAGGGGGT
1 ACCGATTCCCCCCAAGGGGGT
346684 ACCGATTCCCCCCAAGGGGGT
1 ACCGATTCCCCCCAAGGGGGT
346705 ACCGATTCCCCCC
1 ACCGATTCCCCCC
346718 TGTTCAACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.18, C:0.44, G:0.24, T:0.15
Consensus pattern (21 bp):
ACCGATTCCCCCCAAGGGGGT
Found at i:347468 original size:181 final size:179
Alignment explanation
Indices: 347150--347509 Score: 686
Period size: 181 Copynumber: 2.0 Consensus size: 179
347140 AAAAGAGTGT
347150 TCTCAAGAGTTGGGGTTACTCTTGAGGGAATTGTAAGGTTATCTCTTTGGCCTCAAAAGAAACAA
1 TCTCAAGAGTTGGGGTTACTCTTGAGGGAATTGTAAGGTTATCTCTTTGGCCTCAAAAGAAACAA
347215 ATTAGTGAATTTGTTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGTTTG
66 ATTAGTGAATTTGTTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGTTTG
347280 AGAAAGTCGAACCACTGTAAATCGCTGTGC-AATACTTTCAATTCTCTG
131 AGAAAGTCGAACCACTGTAAATCGCTGTGCAAATACTTTCAATTCTCTG
347328 TCTCAAGAGTTGGGGTATACTCTTGAGGGAATTGTAAGGTTATCTCTTTGGCCTCAAAAGAAGAA
1 TCTCAAGAGTTGGGGT-TACTCTTGAGGGAATTGTAAGGTTATCTCTTTGGCCTCAAAAG-A-AA
347393 CAAATTAGTGAATTTGTTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGT
63 CAAATTAGTGAATTTGTTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGT
347458 TTGAGAAAGTCGAACCACTGTAAATCGCTGTGCAAATACTTTCAATTCTCTG
128 TTGAGAAAGTCGAACCACTGTAAATCGCTGTGCAAATACTTTCAATTCTCTG
347510 CAAAAGCTTC
Statistics
Matches: 178, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
178 16 0.09
179 43 0.24
180 1 0.01
181 100 0.56
182 18 0.10
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.32
Consensus pattern (179 bp):
TCTCAAGAGTTGGGGTTACTCTTGAGGGAATTGTAAGGTTATCTCTTTGGCCTCAAAAGAAACAA
ATTAGTGAATTTGTTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGTTTG
AGAAAGTCGAACCACTGTAAATCGCTGTGCAAATACTTTCAATTCTCTG
Found at i:353511 original size:21 final size:21
Alignment explanation
Indices: 353486--353531 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
353476 ATCGATGAAG
353486 CCGAAGATGAGCCTGATCAGC
1 CCGAAGATGAGCCTGATCAGC
353507 CCGAAGATGAGCCTGATCAGC
1 CCGAAGATGAGCCTGATCAGC
353528 CCGA
1 CCGA
353532 GGAGCAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.13
Consensus pattern (21 bp):
CCGAAGATGAGCCTGATCAGC
Found at i:353875 original size:15 final size:15
Alignment explanation
Indices: 353835--353875 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
353825 TTGTTTCAAC
* *
353835 ATTTTGAATTGTTTG
1 ATTTTGGATTGTTGG
353850 ATTTGTGGATTGTTGG
1 ATTT-TGGATTGTTGG
353866 ATTTTGGATT
1 ATTTTGGATT
353876 TATGAATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (15 bp):
ATTTTGGATTGTTGG
Found at i:356309 original size:18 final size:18
Alignment explanation
Indices: 356286--356325 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
356276 AATTTACGTT
356286 AGAAACTAAACTTAATTG
1 AGAAACTAAACTTAATTG
*
356304 AGAAACTGAACTTAATTG
1 AGAAACTAAACTTAATTG
356322 AGAA
1 AGAA
356326 CCAACTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (18 bp):
AGAAACTAAACTTAATTG
Found at i:357071 original size:2 final size:2
Alignment explanation
Indices: 357064--357111 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
357054 TATTTGTTTA
357064 AT 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 AT
357106 AT AT AT
1 AT AT AT
357112 GGAGTAGGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:364518 original size:23 final size:23
Alignment explanation
Indices: 364492--364543 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
364482 CAAATGTTCT
* * *
364492 GACCAGGCCGGGACCAATGAGCG
1 GACCAGGCCAGAACCAATAAGCG
*
364515 GACCAGGTCAGAACCAATAAGCG
1 GACCAGGCCAGAACCAATAAGCG
364538 GACCAG
1 GACCAG
364544 TCCGCCCGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.29, G:0.33, T:0.06
Consensus pattern (23 bp):
GACCAGGCCAGAACCAATAAGCG
Found at i:364858 original size:14 final size:14
Alignment explanation
Indices: 364819--364860 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
364809 TTCGATTATA
* *
364819 TGTTCGTTTATATT
1 TGTTCATTTATGTT
*
364833 TGTTCAGTTATGTT
1 TGTTCATTTATGTT
364847 TGTTCATTTATGTT
1 TGTTCATTTATGTT
364861 CAAACAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.14, C:0.07, G:0.17, T:0.62
Consensus pattern (14 bp):
TGTTCATTTATGTT
Found at i:379390 original size:201 final size:198
Alignment explanation
Indices: 379048--379450 Score: 754
Period size: 201 Copynumber: 2.0 Consensus size: 198
379038 CGTGGGAGGA
*
379048 GATTTCAATGGATTATACATTCTGATGAGAAAAAGGGGGGGGCGGAAACCGGTCAGAAGCCATAT
1 GATTTCAATGGATTATACATTCTGATGAGAAAAAGAGGGGGGCGGAAACCGGTCAGAAGCCATAT
379113 GGAGGAATTTCAATGCCTTCGCGGAGCCGATCTGTGAGATATTCGGCCTAGAGTTGGTTGGTTCT
66 GGAGGAATTTCAATGCCTTCGCGGAGCCGATCTGTGAGATATTCGGCCTAGAGTTGGTTGGTTCT
379178 CTTGGGCAAGTGGTACCCGGGCTAAAACTTATGTTTGCGAGAGAATCGATAGATTTGTGGCAAAA
131 CTTGGGCAAGTGGTACCCGGGCTAAAACTTATGTTTGCGAGAGAATCGATAGATTTGTGGCAAAA
379243 AAT
196 AAT
379246 GATTTCAATGAGATTATACATTCTGATGAG-AAAAGAGGGGGGCGGAAACCGGTCAGAAGCCATA
1 GATTTCAATG-GATTATACATTCTGATGAGAAAAAGAGGGGGGCGGAAACCGGTCAGAAGCCATA
379310 TGGAGGAATTTTTTCAATGCCTTCGCGGAGCCGATCTGTGAGATATTCGGCCTAGAGTTGGTTGG
65 TGGAGGAA---TTTCAATGCCTTCGCGGAGCCGATCTGTGAGATATTCGGCCTAGAGTTGGTTGG
379375 TTCTCTTGGGCAAGTGGTACCCGGGCTAAAACTTATGTTTGCGAGAGAATCGATAGATTTGTGGC
127 TTCTCTTGGGCAAGTGGTACCCGGGCTAAAACTTATGTTTGCGAGAGAATCGATAGATTTGTGGC
379440 AAAAAAT
192 AAAAAAT
379447 GATT
1 GATT
379451 GGAGGCTCAT
Statistics
Matches: 200, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
198 51 0.25
199 19 0.09
201 130 0.65
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (198 bp):
GATTTCAATGGATTATACATTCTGATGAGAAAAAGAGGGGGGCGGAAACCGGTCAGAAGCCATAT
GGAGGAATTTCAATGCCTTCGCGGAGCCGATCTGTGAGATATTCGGCCTAGAGTTGGTTGGTTCT
CTTGGGCAAGTGGTACCCGGGCTAAAACTTATGTTTGCGAGAGAATCGATAGATTTGTGGCAAAA
AAT
Found at i:383963 original size:21 final size:21
Alignment explanation
Indices: 383909--383963 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
383899 CGATATCCGG
*
383909 TATCGCAACGCAAACTTCGAC
1 TATCGCAACGCGAACTTCGAC
*
383930 TATCGCAACGCGAACTTGGAC
1 TATCGCAACGCGAACTTCGAC
*
383951 TATCGCAATGCGA
1 TATCGCAACGCGA
383964 TTTACATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (21 bp):
TATCGCAACGCGAACTTCGAC
Found at i:383998 original size:21 final size:21
Alignment explanation
Indices: 383972--384058 Score: 97
Period size: 21 Copynumber: 4.2 Consensus size: 21
383962 GATTTACATA
383972 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
383993 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * ** *
384014 TTTGCGTTGCGATTTTCCAAA
1 TTCGCATTGCGATAGTCCAAG
* *
384035 TACG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
384054 TTCGC
1 TTCGC
384059 GCGAGACGAC
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
19 14 0.26
21 39 0.74
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:384079 original size:6 final size:6
Alignment explanation
Indices: 384064--384102 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
384054 TTCGCGCGAG
384064 ACGA-C ACGACC ACGACC ACGACC ACGACC ACGACC ACGA
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGA
384103 GACGACACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.36, C:0.46, G:0.18, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:384091 original size:18 final size:17
Alignment explanation
Indices: 384064--384112 Score: 73
Period size: 18 Copynumber: 2.9 Consensus size: 17
384054 TTCGCGCGAG
384064 ACGACACGACCACGACC
1 ACGACACGACCACGACC
384081 ACGACCACGACCACGACC
1 ACGA-CACGACCACGACC
*
384099 ACGAGACGA-CACGA
1 ACGACACGACCACGA
384113 GACGAGACGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 5 0.17
17 8 0.27
18 17 0.57
ACGTcount: A:0.37, C:0.43, G:0.20, T:0.00
Consensus pattern (17 bp):
ACGACACGACCACGACC
Found at i:384113 original size:10 final size:10
Alignment explanation
Indices: 384093--384126 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
384083 GACCACGACC
384093 ACGACCACGAG
1 ACGA-CACGAG
384104 ACGACACGAG
1 ACGACACGAG
*
384114 ACGAGACGAG
1 ACGACACGAG
384124 ACG
1 ACG
384127 GACGGCGGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.38, C:0.29, G:0.32, T:0.00
Consensus pattern (10 bp):
ACGACACGAG
Found at i:386950 original size:17 final size:18
Alignment explanation
Indices: 386903--386950 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
386893 AGATTGGTGC
386903 AATTGATTTCTTCTGAGA
1 AATTGATTTCTTCTGAGA
386921 AATTGATTTCTTCTGAGA
1 AATTGATTTCTTCTGAGA
386939 AATTGA-TTCTTC
1 AATTGATTTCTTC
386951 GACTTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 6 0.20
18 24 0.80
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (18 bp):
AATTGATTTCTTCTGAGA
Found at i:387487 original size:80 final size:77
Alignment explanation
Indices: 387357--387514 Score: 289
Period size: 80 Copynumber: 2.0 Consensus size: 77
387347 TTTCATCAGA
387357 ATATTTCCTATGCTTAACATTCTGGTTGTTTCTTTTTGCTTCTGACAGAGAGATTGCATTTGATG
1 ATATTTCCTATGCTTAACATTCTGGTTGTTTCTTTTTGCTTCTGACAGAGAGATTGCATTTGAT-
387422 AGATATAGAAGAGG
65 -GATATAGAAGAGG
387436 ATATTTCCTATGCTTAACATTCTGGTTGGTTTCTTTTTGCTTCTGACAGAGAGATTGCATTTGAT
1 ATATTTCCTATGCTTAACATTCTGGTT-GTTTCTTTTTGCTTCTGACAGAGAGATTGCATTTGAT
387501 GATATAGAAGAGG
65 GATATAGAAGAGG
387514 A
1 A
387515 AGGTGTTATA
Statistics
Matches: 78, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
78 14 0.18
79 27 0.35
80 37 0.47
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.41
Consensus pattern (77 bp):
ATATTTCCTATGCTTAACATTCTGGTTGTTTCTTTTTGCTTCTGACAGAGAGATTGCATTTGATG
ATATAGAAGAGG
Found at i:391253 original size:51 final size:51
Alignment explanation
Indices: 391188--391437 Score: 292
Period size: 51 Copynumber: 5.0 Consensus size: 51
391178 GTGTGCTCCC
* *
391188 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCCAGTAAGT
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGA
* * * *
391239 CTCATCAGCGAAGTGATGAGAAAAACCAATCCGGGGCAACCTCGAGTAAGA
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGA
* * * *
391290 CTCATCAGCCAAGTGATAAGAAGAACCAAT-CAGGGCAACCTTGAGTAAGA
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGA
* * * * * * *
391340 --C-TCAGCAAAATGATGAGGACAACCAATCCAGAGAGACCTTGAATAAGA
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGA
* * *
391388 GTCATCAGCAAAGGGATGAGAAGAACCAATCCGGGGAAACCTCGAGTAAG
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAG
391438 CTTAAAAGAA
Statistics
Matches: 166, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
47 21 0.13
48 17 0.10
50 19 0.11
51 109 0.66
ACGTcount: A:0.40, C:0.22, G:0.24, T:0.14
Consensus pattern (51 bp):
CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGA
Found at i:391393 original size:98 final size:101
Alignment explanation
Indices: 391188--391438 Score: 303
Period size: 98 Copynumber: 2.5 Consensus size: 101
391178 GTGTGCTCCC
* * * *
391188 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCCAGTAAGTCTCATCAGCGAAGT
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAG-CACATCAGCAAAAT
* * *
391253 GATGAGAAAAACCAATCCGGGGCAACCTCGAGTAAGA
65 GATGAGAAAAACCAATCCAGAGCAACCTCGAATAAGA
* * * *
391290 CTCATCAGCCAAGTGATAAGAAGAACCAAT-CAGGGCAACCTTGAGTAAG-AC-TCAGCAAAATG
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGCACATCAGCAAAATG
* * *
391352 ATGAGGACAACCAATCCAGAG-AGACCTTGAATAAGA
66 ATGAGAAAAACCAATCCAGAGCA-ACCTCGAATAAGA
* * *
391388 GTCATCAGCAAAGGGATGAGAAGAACCAATCCGGGGAAACCTCGAGTAAGC
1 CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGC
391439 TTAAAAGAAA
Statistics
Matches: 125, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
97 1 0.01
98 63 0.50
99 17 0.14
101 16 0.13
102 28 0.22
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.14
Consensus pattern (101 bp):
CTCATCAGCAAAGTGATGAGAAGAACCAATCCAGGGAAACCTCGAGTAAGCACATCAGCAAAATG
ATGAGAAAAACCAATCCAGAGCAACCTCGAATAAGA
Found at i:416352 original size:36 final size:36
Alignment explanation
Indices: 416278--416364 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
416268 CACCCCTAGC
* ** *
416278 GAACATGTTCGTTTATATGTTCATGAATGTATTCAT
1 GAACATGTTCATTTATATGTTCACAAAAGTATTCAT
* * *
416314 GAACATGTTTATTTATATGTTCACAAAAGTGTTTAT
1 GAACATGTTCATTTATATGTTCACAAAAGTATTCAT
* *
416350 GAACAAGTTCGTTTA
1 GAACATGTTCATTTA
416365 ACGTTCATTA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (36 bp):
GAACATGTTCATTTATATGTTCACAAAAGTATTCAT
Found at i:416648 original size:24 final size:24
Alignment explanation
Indices: 416630--416699 Score: 131
Period size: 24 Copynumber: 2.9 Consensus size: 24
416620 GAACGAGTTG
*
416630 ATAAATGAGCTCATAAACGAACTC
1 ATAAACGAGCTCATAAACGAACTC
416654 ATAAACGAGCTCATAAACGAACTC
1 ATAAACGAGCTCATAAACGAACTC
416678 ATAAACGAGCTCATAAACGAAC
1 ATAAACGAGCTCATAAACGAAC
416700 CGAACACACC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.13, T:0.17
Consensus pattern (24 bp):
ATAAACGAGCTCATAAACGAACTC
Found at i:416654 original size:12 final size:12
Alignment explanation
Indices: 416639--416699 Score: 104
Period size: 12 Copynumber: 5.1 Consensus size: 12
416629 GATAAATGAG
416639 CTCATAAACGAA
1 CTCATAAACGAA
*
416651 CTCATAAACGAG
1 CTCATAAACGAA
416663 CTCATAAACGAA
1 CTCATAAACGAA
*
416675 CTCATAAACGAG
1 CTCATAAACGAA
416687 CTCATAAACGAA
1 CTCATAAACGAA
416699 C
1 C
416700 CGAACACACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.16
Consensus pattern (12 bp):
CTCATAAACGAA
Found at i:416670 original size:36 final size:36
Alignment explanation
Indices: 416621--416697 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
416611 AACATAAATG
* * * *
416621 AACGAGTTGATAAATGAGCTCATAAACGAACTCATA
1 AACGAGCTCATAAACGAACTCATAAACGAACTCATA
*
416657 AACGAGCTCATAAACGAACTCATAAACGAGCTCATA
1 AACGAGCTCATAAACGAACTCATAAACGAACTCATA
416693 AACGA
1 AACGA
416698 ACCGAACACA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (36 bp):
AACGAGCTCATAAACGAACTCATAAACGAACTCATA
Found at i:420936 original size:16 final size:16
Alignment explanation
Indices: 420915--420946 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
420905 TCTTGGGTTC
420915 AGAGAATGATTTGATT
1 AGAGAATGATTTGATT
420931 AGAGAATGATTTGATT
1 AGAGAATGATTTGATT
420947 TGATCTTATC
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:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (16 bp):
AGAGAATGATTTGATT
Found at i:423218 original size:40 final size:40
Alignment explanation
Indices: 423148--423227 Score: 153
Period size: 39 Copynumber: 2.0 Consensus size: 40
423138 TTTTTTTTAA
423148 ATCAGTTAAGGTTGGGTCGGGTCATATTTTTTAAGGGATG
1 ATCAGTTAAGGTTGGGTCGGGTCATATTTTTTAAGGGATG
423188 ATCAG-TAAGGTTGGGTCGGGTCATATTTTTTAAGGGATG
1 ATCAGTTAAGGTTGGGTCGGGTCATATTTTTTAAGGGATG
423227 A
1 A
423228 ACTCGGTCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 35 0.88
40 5 0.12
ACGTcount: A:0.24, C:0.07, G:0.33, T:0.36
Consensus pattern (40 bp):
ATCAGTTAAGGTTGGGTCGGGTCATATTTTTTAAGGGATG
Found at i:424148 original size:56 final size:54
Alignment explanation
Indices: 424051--424158 Score: 198
Period size: 56 Copynumber: 2.0 Consensus size: 54
424041 TTTCTATTAA
424051 ACTTTAATCTATTTATAGGATATGATAATTTTAATTCAATAATCTCACATAATT
1 ACTTTAATCTATTTATAGGATATGATAATTTTAATTCAATAATCTCACATAATT
424105 ACTTTAATCTATTTATTAGGATATGATAAATTTTAATTCAATAATCTCACATAA
1 ACTTTAATCTATTTA-TAGGATATGAT-AATTTTAATTCAATAATCTCACATAA
424159 CTATACCACT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 15 0.29
55 11 0.21
56 26 0.50
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.44
Consensus pattern (54 bp):
ACTTTAATCTATTTATAGGATATGATAATTTTAATTCAATAATCTCACATAATT
Found at i:424265 original size:19 final size:20
Alignment explanation
Indices: 424241--424279 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
424231 TAGATGATTA
*
424241 TTTTATATTTTTTAA-AATT
1 TTTTATAATTTTTAATAATT
424260 TTTTATAATTTTTAATAATT
1 TTTTATAATTTTTAATAATT
424280 AAAAGAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATAATTTTTAATAATT
Found at i:425732 original size:24 final size:23
Alignment explanation
Indices: 425681--425732 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
425671 AGATATCATT
425681 GAAATTATCTCTATATATATAAG
1 GAAATTATCTCTATATATATAAG
*
425704 G-AATTATCTCTCTATATATAAG
1 GAAATTATCTCTATATATATAAG
425726 GTAAATT
1 G-AAATT
425733 TACATTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 21 0.81
23 1 0.04
24 4 0.15
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (23 bp):
GAAATTATCTCTATATATATAAG
Found at i:428420 original size:92 final size:92
Alignment explanation
Indices: 428311--428502 Score: 350
Period size: 92 Copynumber: 2.1 Consensus size: 92
428301 GAAAAATATA
*
428311 AATATGATCACACAAATAAAT-AATGAGATTTTATATATATCTTAAATCTAGTATATATATTTAA
1 AATAT-ATCACAAAAATAAATAAATGAGATTTT-TATATATCTTAAATCTAGTATATATATTTAA
428375 AATTTTATTATATTCTAGAATATTTTTCT
64 AATTTTATTATATTCTAGAATATTTTTCT
428404 AATATATCACAAAAATAAATAAATGAGATTTTTATATATCTTAAATCTAGTATATATATTTAAAA
1 AATATATCACAAAAATAAATAAATGAGATTTTTATATATCTTAAATCTAGTATATATATTTAAAA
428469 TTTTATTATATTCTAGAATATTTTTCT
66 TTTTATTATATTCTAGAATATTTTTCT
428496 AATATAT
1 AATATAT
428503 TTTCGAAATC
Statistics
Matches: 97, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
92 81 0.84
93 16 0.16
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (92 bp):
AATATATCACAAAAATAAATAAATGAGATTTTTATATATCTTAAATCTAGTATATATATTTAAAA
TTTTATTATATTCTAGAATATTTTTCT
Found at i:436189 original size:16 final size:17
Alignment explanation
Indices: 436145--436193 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
436135 TTTTTTTTCT
*
436145 TTTTTTAAAAAAAAAAC
1 TTTTTTAAAAAATAAAC
** *
436162 TTTTTTTTAAAATATA-
1 TTTTTTAAAAAATAAAC
436178 TTTTTTAAAAAATAAA
1 TTTTTTAAAAAATAAA
436194 AGTTCTTTTA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTTTTAAAAAATAAAC
Found at i:440128 original size:106 final size:106
Alignment explanation
Indices: 440009--441332 Score: 1976
Period size: 106 Copynumber: 12.6 Consensus size: 106
439999 TGTGCACGAT
* * *
440009 TCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCATTCGCTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * ** *
440074 TCGGCCCTGAGATTGAGAAACTGTTTATTGACAACCAGCGG
66 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
*
440115 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * * ** *
440180 TCGGCCCTGAGATTGGGAAACTGTTTATTGACAACCAGCGG
66 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
*
440221 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * * ** *
440286 TCGGCCCTGAGATTGGGAAACTGTTTATTGACAACCAGCGG
66 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
*
440327 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
440392 TTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
66 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
440433 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
440498 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGTGG
66 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
*
440539 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* *
440604 TTGGCTCTGAATTTGAGAAGTTGGTTATTGACAACCAGCGG
66 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
440645 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* *
440710 TTGGCTTTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
66 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
*
440751 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
*
440816 TTGG----GAAATT----A--T--TTATTGACAACCAGCGG
66 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
* *
440845 TCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * * *
440910 TTGACTCTGAAATTGAGAAGTT-GTTGTTGACAAGCAGCGG
66 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
440950 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * *
441015 TTGGCTCTGAAATTGAGAAGTT-GTTGTTGACAACCAGCAG
66 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
* * *
441055 TCCCTTCGTCGTGAAGTCGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * *
441120 TTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAACGG
66 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
* *
441161 TCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * * * *
441226 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAATCAGCCG
66 TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
* * * * * * * *
441267 CCCCTTCGTCATGAAGTTGAGCTTGTGTTGTCTTGGA-TTCAAGATCCTTCATTGAGAAGTTGAA
1 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
441331 AT
65 AT
441333 TTACTCTCGA
Statistics
Matches: 1149, Mismatches: 56, Indels: 26
0.93 0.05 0.02
Matches are distributed among these distances:
94 82 0.07
96 1 0.00
98 7 0.01
102 7 0.01
104 1 0.00
105 199 0.17
106 848 0.74
107 4 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
TCGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
Found at i:440877 original size:94 final size:96
Alignment explanation
Indices: 440734--441229 Score: 609
Period size: 105 Copynumber: 4.9 Consensus size: 96
440724 GAGAAGTTGG
440734 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCT
1 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCT
440799 TCGTTGTGAAGTTGAAATTGGGAAATT-A-T
66 TCGTTGTGAAGTTGAAATTGGGAAATTAAGT
* * *
440828 TTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCT
1 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCT
*
440893 TCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTT
66 TCGTTGTGAAGTTGAAATTG----GGAAATT---AAG-T
* * *
440932 GTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
1 -TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCC
440997 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTT
65 TTCGTTGTGAAGTTGAAATTGG----GAAATT---AAG-T
* * *
441037 GTTGTTGACAACCAGCAGTCCCTTCGTCGTGAAGTCGAACTTACGTTGTCTGGAGTCCAATATCC
1 -TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCC
*
441102 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGT
65 TTCGTTGTGAAGTTGAAATTGG----GAAATT---AA---GT
*
441144 TTATTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCT
1 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCT
*
441209 TCGCTGTGAAGTTGAAATTGG
66 TCGTTGTGAAGTTGAAATTGG
441230 CTCTGAAATT
Statistics
Matches: 366, Mismatches: 18, Indels: 24
0.90 0.04 0.06
Matches are distributed among these distances:
94 82 0.22
98 6 0.02
102 1 0.00
104 1 0.00
105 192 0.52
106 82 0.22
107 1 0.00
108 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (96 bp):
TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCT
TCGTTGTGAAGTTGAAATTGGGAAATTAAGT
Found at i:441205 original size:211 final size:211
Alignment explanation
Indices: 440811--441339 Score: 792
Period size: 211 Copynumber: 2.5 Consensus size: 211
440801 GTTGTGAAGT
* * * * *
440811 TGAAATTGGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCAGTCCCTTCGTCATGAAGTTGAACTTGCGTTGT
* *
440876 CTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTGTTGAC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTATTGAC
* * * *
440941 AAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
131 AACCAACGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTG
441006 AAGTTGAAATTGGCTC
196 AAGTTGAAATTGGCTC
* * *
441022 TGAAATTGAGAAGTTG-TTGTTGACAACCAGCAGTCCCTTCGTCGTGAAGTCGAACTTACGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCAGTCCCTTCGTCATGAAGTTGAACTTGCGTTGT
* *
441086 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTG-TTATTGA
441151 CAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGT
130 CAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGT
441216 GAAGTTGAAATTGGCTC
195 GAAGTTGAAATTGGCTC
* * * * *
441233 TGAAATTGAGAAGTTGTTTGTTGACAATCAGCCGCCCCTTCGTCATGAAGTTGAGCTTGTGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCAGTCCCTTCGTCATGAAGTTGAACTTGCGTTGT
* * * * *
441298 CTTGGA-TTCAAGATCCTTCATTGAGAAGTTGAAATTTACTCT
66 C-TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
441340 CGAGCAAATT
Statistics
Matches: 284, Mismatches: 31, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
210 97 0.34
211 113 0.40
212 70 0.25
213 4 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (211 bp):
TGAAATTGAGAAGTTGTTTGTTGACAACCAGCAGTCCCTTCGTCATGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTATTGAC
AACCAACGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGCTGTG
AAGTTGAAATTGGCTC
Found at i:441333 original size:106 final size:106
Alignment explanation
Indices: 440811--441333 Score: 782
Period size: 105 Copynumber: 5.0 Consensus size: 106
440801 GTTGTGAAGT
* * * * *
440811 TGAAATTGGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
440876 CTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
440917 TGAAATTGAGAAGTTG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
440981 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
441022 TGAAATTGAGAAGTTG-TTGTTGACAACCAGCAGTCCCTTCGTCGTGAAGTCGAACTTACGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
441086 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
441127 TGAAATTGAGAAGTTGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
441192 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * * * * *
441233 TGAAATTGAGAAGTTGTTTGTTGACAATCAGCCGCCCCTTCGTCATGAAGTTGAGCTTGTGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * * *
441298 CTTGGA-TTCAAGATCCTTCATTGAGAAGTTGAAATT
66 C-TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
441334 TACTCTCGAG
Statistics
Matches: 384, Mismatches: 31, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
105 200 0.52
106 180 0.47
107 4 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (106 bp):
TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:448073 original size:17 final size:17
Alignment explanation
Indices: 448011--448078 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 17
448001 ACTAAATAGA
448011 TAATTTAAA-A-ATAAT
1 TAATTTAAATAGATAAT
* * *
448026 ATTATTTCAAATAAATAAA
1 -TAATTT-AAATAGATAAT
*
448045 TAA-TTGAATAGATAAT
1 TAATTTAAATAGATAAT
448061 TAATTTAAATAGATAAT
1 TAATTTAAATAGATAAT
448078 T
1 T
448079 TAAAAATAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
16 16 0.39
17 18 0.44
18 3 0.07
19 4 0.10
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (17 bp):
TAATTTAAATAGATAAT
Found at i:452332 original size:13 final size:13
Alignment explanation
Indices: 452291--452334 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
452281 TATTTAGTAC
*
452291 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
452304 TGTTTATTGGACT
1 TTTTTATTGTAAT
452317 TTTTTATTGTAAT
1 TTTTTATTGTAAT
452330 TTTTT
1 TTTTT
452335 TATTTATCAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:461931 original size:31 final size:31
Alignment explanation
Indices: 461895--461962 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
461885 TCATAAAACA
461895 TAAGATATGGGCA-TTTTCATTTTCATTTAAT
1 TAAGATATGGGCACTTTT-ATTTTCATTTAAT
* ** * *
461926 TAAGATGTGGTTACTTTTGTTTTTATTTAAT
1 TAAGATATGGGCACTTTTATTTTCATTTAAT
461957 TAAGAT
1 TAAGAT
461963 GTAATCAACC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (31 bp):
TAAGATATGGGCACTTTTATTTTCATTTAAT
Found at i:462062 original size:29 final size:29
Alignment explanation
Indices: 461988--462068 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
461978 CAATTGCCAT
*
461988 TAACATTAATTAAAT-AT-TTTGATATAA
1 TAACATTAATTAAATGTTATTTGATATAA
* **
462015 TCACACATTTGA-TCCATGTTATTTGATATAA
1 T-A-ACA-TTAATTAAATGTTATTTGATATAA
462046 TAACATTAATTAAATGTTATTTG
1 TAACATTAATTAAATGTTATTTG
462069 CACATTTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
27 1 0.02
28 4 0.10
29 20 0.49
30 5 0.12
31 11 0.27
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (29 bp):
TAACATTAATTAAATGTTATTTGATATAA
Found at i:472841 original size:2 final size:2
Alignment explanation
Indices: 472834--472869 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
472824 ATAAATTAGA
472834 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
472870 TAGCACTTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:476408 original size:32 final size:32
Alignment explanation
Indices: 476372--476438 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
476362 TATGAAAATT
* * **
476372 TATCACGCCATTACATTAGATGACGTGATACA
1 TATCACGCCATCACATCAGATGACACGATACA
*
476404 TATCACGTCATCACATCAGATGACACGATACA
1 TATCACGCCATCACATCAGATGACACGATACA
476436 TAT
1 TAT
476439 TACATTATCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (32 bp):
TATCACGCCATCACATCAGATGACACGATACA
Found at i:477310 original size:15 final size:15
Alignment explanation
Indices: 477290--477320 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
477280 GGATTTTGAC
*
477290 GGAGCGGGCTTAAAA
1 GGAGCGGGCTAAAAA
477305 GGAGCGGGCTAAAAA
1 GGAGCGGGCTAAAAA
477320 G
1 G
477321 CCCGCATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.42, T:0.10
Consensus pattern (15 bp):
GGAGCGGGCTAAAAA
Found at i:477600 original size:2 final size:2
Alignment explanation
Indices: 477595--477636 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
477585 TTAATCATTA
477595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
477637 ATTACTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:480939 original size:24 final size:24
Alignment explanation
Indices: 480894--480954 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
480884 ATGATAAACT
* * ** *
480894 AACACAAATAAACGAATGTAAATG
1 AACATAAACAAACGAACATAAATA
*
480918 AATATAAACAAACGAACATAAATA
1 AACATAAACAAACGAACATAAATA
*
480942 AACGTAAACAAAC
1 AACATAAACAAAC
480955 ATAAAATTGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (24 bp):
AACATAAACAAACGAACATAAATA
Found at i:483541 original size:2 final size:2
Alignment explanation
Indices: 483534--483565 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
483524 AAGCTTTTAC
483534 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
483566 CATAGCATAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:495482 original size:14 final size:14
Alignment explanation
Indices: 495465--495494 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
495455 TACCATTGTT
495465 CTCATATAGATCTC
1 CTCATATAGATCTC
*
495479 CTCATCTAGATCTC
1 CTCATATAGATCTC
495493 CT
1 CT
495495 TTAAAAAATG
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:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (14 bp):
CTCATATAGATCTC
Found at i:500755 original size:22 final size:20
Alignment explanation
Indices: 500730--500773 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
500720 AAATACGTTA
*
500730 TAAAAGTAAATAAAAATATATT
1 TAAAAATAAAT-AAAAT-TATT
*
500752 TAAAAATAGATAAAATTATT
1 TAAAAATAAATAAAATTATT
500772 TA
1 TA
500774 TTATTTCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
TAAAAATAAATAAAATTATT
Found at i:500988 original size:16 final size:16
Alignment explanation
Indices: 500967--500999 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
500957 AATACTAATA
500967 ATTAATTCAAA-AAAAT
1 ATTAATT-AAACAAAAT
500983 ATTAATTAAACAAAAT
1 ATTAATTAAACAAAAT
500999 A
1 A
501000 AAATAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAATTAAACAAAAT
Found at i:501579 original size:31 final size:31
Alignment explanation
Indices: 501541--501605 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
501531 AAAAAACAAT
501541 TTAGAATGCTAATG-TGA-AATAATTTAAGAAA
1 TTAGAATG-TAATGATGATAA-AATTTAAGAAA
*
501572 TTAGAATGTTATGATGATAAAATTTAAGAAA
1 TTAGAATGTAATGATGATAAAATTTAAGAAA
501603 TTA
1 TTA
501606 TGAAATGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 4 0.13
31 25 0.81
32 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (31 bp):
TTAGAATGTAATGATGATAAAATTTAAGAAA
Found at i:502485 original size:19 final size:19
Alignment explanation
Indices: 502457--502505 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
502447 GCCACTATTT
* *
502457 TGGTTCCCAATCAAAAATA
1 TGGTTTCCAACCAAAAATA
* *
502476 TGGTTTCCAACCGAAAATC
1 TGGTTTCCAACCAAAAATA
*
502495 TGGTTTTCAAC
1 TGGTTTCCAAC
502506 TTAAAATTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (19 bp):
TGGTTTCCAACCAAAAATA
Found at i:502530 original size:19 final size:19
Alignment explanation
Indices: 502479--502533 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
502469 AAAAATATGG
*
502479 TTTCCAACCGAAAATCTGGT
1 TTTCC-ACCGAAAATCTGAT
* ** *
502499 TTTCAACTTAAAATTTGAT
1 TTTCCACCGAAAATCTGAT
502518 TTTCCACCGAAAATCT
1 TTTCCACCGAAAATCT
502534 AGGTCGTAAC
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (19 bp):
TTTCCACCGAAAATCTGAT
Found at i:503431 original size:2 final size:2
Alignment explanation
Indices: 503419--503460 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
503409 ATTTGAAAAT
*
503419 TA TA AA 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
503461 AACTGAGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:504116 original size:18 final size:18
Alignment explanation
Indices: 504095--504141 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
504085 TCCAGCTCCT
*
504095 GCACCACCACCGAACCCA
1 GCACCCCCACCGAACCCA
* *
504113 GCACCCCCTCCGAATCCA
1 GCACCCCCACCGAACCCA
504131 GCACCCCCACC
1 GCACCCCCACC
504142 TACCCCACCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.60, G:0.11, T:0.04
Consensus pattern (18 bp):
GCACCCCCACCGAACCCA
Found at i:510379 original size:21 final size:21
Alignment explanation
Indices: 510285--510386 Score: 107
Period size: 21 Copynumber: 4.9 Consensus size: 21
510275 GTCCGACTCA
*
510285 CTGTCATCGTTCAAGAGGCCT
1 CTGTCATCGTTCAAGAGGCCC
*
510306 CT-CCTATCGTTCAAGAGGCCC
1 CTGTC-ATCGTTCAAGAGGCCC
* ** *
510327 CTATCATCCCTCAAGAGTCCC
1 CTGTCATCGTTCAAGAGGCCC
* *
510348 CTCTCACCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGCCC
*
510369 CTGTCATCGTTGAAGAGG
1 CTGTCATCGTTCAAGAGG
510387 TCCTTCCCAC
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.25
Consensus pattern (21 bp):
CTGTCATCGTTCAAGAGGCCC
Found at i:510385 original size:42 final size:42
Alignment explanation
Indices: 510285--510406 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
510275 GTCCGACTCA
* *
510285 CTGTCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGCCCCTCCTACCGTTCAAGAGGCCC
* ** *
510327 CTATCATCCCTCAAGAGTCCCCT-CTCACCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGCCCCTCCT-ACCGTTCAAGAGGCCC
* * * * *
510369 CTGTCATCGTTGAAGAGGTCCTTCCCACCATTCAAGAG
1 CTGTCATCGTTCAAGAGGCCCCTCCTACCGTTCAAGAG
510407 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
41 2 0.03
42 60 0.95
43 1 0.02
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGGCCCCTCCTACCGTTCAAGAGGCCC
Found at i:511862 original size:2 final size:2
Alignment explanation
Indices: 511839--511889 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
511829 TTTTCCTCTT
*
511839 TA TA T- TA TA T- TA TT TA -A 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
511878 TA TA TA TA TA TA
1 TA TA TA TA TA TA
511890 AAATTAAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:511980 original size:22 final size:21
Alignment explanation
Indices: 511958--512003 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
511948 AAATTTATTA
511958 AAATTTAAAAAATATATAATT
1 AAATTTAAAAAATATATAATT
* *
511979 AAATTT-CAAAA-GTATAATT
1 AAATTTAAAAAATATATAATT
511998 AAATTT
1 AAATTT
512004 CAAATGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 13 0.57
20 4 0.17
21 6 0.26
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATTTAAAAAATATATAATT
Found at i:512954 original size:19 final size:19
Alignment explanation
Indices: 512919--512980 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
512909 TTCCCAATAA
* *
512919 AAAATATGGGTTCCAACCG
1 AAAATATGGTTTTCAACCG
**
512938 AAAATATGGTTTTCAACTT
1 AAAATATGGTTTTCAACCG
* * *
512957 AAAATCTGATTTTCAAACG
1 AAAATATGGTTTTCAACCG
512976 AAAAT
1 AAAAT
512981 CTAGCTCGTA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (19 bp):
AAAATATGGTTTTCAACCG
Found at i:514380 original size:30 final size:30
Alignment explanation
Indices: 514322--514389 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
514312 TCCTCCAAGC
514322 CCACCACCAGCTCCACCGCCAAACCCACCA
1 CCACCACCAGCTCCACCGCCAAACCCACCA
* * * ** *
514352 CCAGCACCTGCTCCACCGCCGAGTCCACCT
1 CCACCACCAGCTCCACCGCCAAACCCACCA
514382 CCACCACC
1 CCACCACC
514390 GAACCCCCCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.59, G:0.10, T:0.07
Consensus pattern (30 bp):
CCACCACCAGCTCCACCGCCAAACCCACCA
Found at i:514459 original size:17 final size:17
Alignment explanation
Indices: 514433--514465 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
514423 TGCACCACCA
514433 CCGAACCCAGCACCCCT
1 CCGAACCCAGCACCCCT
*
514450 CCGAATCCAGCACCCC
1 CCGAACCCAGCACCCC
514466 CACTAGGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.58, G:0.12, T:0.06
Consensus pattern (17 bp):
CCGAACCCAGCACCCCT
Found at i:515446 original size:32 final size:35
Alignment explanation
Indices: 515410--515488 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
515400 GGTGTGGGGA
515410 TGGATTTGAAAA-TGTACCCGCG-TGGGCAGGT-G
1 TGGATTTGAAAATTGTACCCGCGATGGGCAGGTGG
* *
515442 TGGATTTGAAAATTTGTACCCGTGATGGGCGGGTGG
1 TGGATTTGAAAA-TTGTACCCGCGATGGGCAGGTGG
515478 TGGA-TTGAAAA
1 TGGATTTGAAAA
515489 ATATTATGTG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
32 12 0.29
34 9 0.22
35 15 0.37
36 5 0.12
ACGTcount: A:0.24, C:0.11, G:0.37, T:0.28
Consensus pattern (35 bp):
TGGATTTGAAAATTGTACCCGCGATGGGCAGGTGG
Found at i:518139 original size:2 final size:2
Alignment explanation
Indices: 518132--518156 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
518122 TGTCCAAGTA
518132 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
518157 ATAGCTAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:528824 original size:18 final size:18
Alignment explanation
Indices: 528801--528836 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
528791 CATCTTAAAA
* *
528801 ATTTTAATTTTTTTTTAT
1 ATTTTAAGTATTTTTTAT
528819 ATTTTAAGTATTTTTTAT
1 ATTTTAAGTATTTTTTAT
528837 TGATTATCTT
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:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
ATTTTAAGTATTTTTTAT
Found at i:534837 original size:16 final size:14
Alignment explanation
Indices: 534807--534851 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
534797 ATACGATATG
*
534807 TATACTTTAATACA
1 TATACATTAATACA
534821 TATACATATACATACA
1 TATACAT-TA-ATACA
534837 TATACATTAATACA
1 TATACATTAATACA
534851 T
1 T
534852 GTACTAAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 12 0.43
15 4 0.14
16 12 0.43
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (14 bp):
TATACATTAATACA
Found at i:536546 original size:18 final size:17
Alignment explanation
Indices: 536507--536549 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
536497 ATTATATGGA
536507 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
536523 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
536541 TATTATTAT
1 TATTATTAT
536550 ATATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:536554 original size:2 final size:2
Alignment explanation
Indices: 536547--536615 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
536537 TTATTATTAT
536547 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
536589 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 T
536616 TTCATTTGAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:537127 original size:38 final size:37
Alignment explanation
Indices: 537076--537176 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 37
537066 AGTGAGAGGG
*
537076 TAGCTTTTCTATTTTTAAATATTTGTTGTATATATATA
1 TAGCTTTT-TATTTTTAAATATTTGATGTATATATATA
*
537114 TAGCTTATTTATTTTATTAATAATTTGATGTATATATATA
1 TAGCTT-TTTATTTT-TAAAT-ATTTGATGTATATATATA
*
537154 TA-TTTTTTCATTTTTCAAATATT
1 TAGCTTTTT-ATTTTT-AAATATT
537177 ACTATATATA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
38 19 0.35
39 16 0.30
40 19 0.35
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (37 bp):
TAGCTTTTTATTTTTAAATATTTGATGTATATATATA
Found at i:537151 original size:40 final size:38
Alignment explanation
Indices: 537076--537176 Score: 116
Period size: 40 Copynumber: 2.6 Consensus size: 38
537066 AGTGAGAGGG
*
537076 TAGCTTTTCTATTTTTAAATATTTGTTGTATATATATA
1 TAGCTTTTCTATTTTTAAATATTTGATGTATATATATA
*
537114 TAGCTTATT-TATTTTATTAATAATTTGATGTATATATATA
1 TAGCTT-TTCTATTTT-TAAAT-ATTTGATGTATATATATA
**
537154 TATTTTTTC-ATTTTTCAAATATT
1 TAGCTTTTCTATTTTT-AAATATT
537177 ACTATATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
38 16 0.30
39 16 0.30
40 21 0.40
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (38 bp):
TAGCTTTTCTATTTTTAAATATTTGATGTATATATATA
Found at i:537230 original size:9 final size:9
Alignment explanation
Indices: 537218--537242 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
537208 CCTTATCTTA
537218 TTTATTTAT
1 TTTATTTAT
537227 TTTATTTAT
1 TTTATTTAT
537236 TTTATTT
1 TTTATTT
537243 TTTCCCTTTT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTAT
Found at i:545529 original size:106 final size:105
Alignment explanation
Indices: 545398--546148 Score: 973
Period size: 106 Copynumber: 7.0 Consensus size: 105
545388 ATATCGCGCC
*
545398 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACCATTACCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATT-CCC
* * *
545463 AATTTCAGAGCTAATTTCAACTTTACAGCGAAGGATATTGG
65 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * **
545504 ACTCGAGACAATAAAAGTTCAACTTCACAACGAAGGGACGACTGTTTGTCAATAAACCACTTTTC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAA-CAATTCCC
* *
545569 AGTTTCATTTAGAGTCAATTTCAACTTCACAGCGAAAGATATTGG
65 AGTTTC----AGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
545614 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAAACAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAAC-AAACAA-TTCC
545679 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
64 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * **
545721 ACTCAAGACAACACAAGTTCAACTTCACATCGAAGGGACGTCTGGTTGTTAACAAACCACTTTTC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAA-CAATTCCC
**
545786 AGTTTCAGAGCCAATTTCAACTTCACAAAGAAGGATATTGG
65 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
545827 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAGCAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAA-TTCCC
* *
545892 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
65 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
545933 ACTCAAGACGACACAAGTTTAAATTCACAACGAAGGGACGACTGGTTGTTAACAAATAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAA-TTCCC
* *
545998 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
65 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * * *
546039 ACTCGAGACAACACAAACTCAACTTCATAGCGAAGGGGCGACTGGCTGTCAACAAACAATCTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAAT-TCCC
* * *
546104 AGTTCCGGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
65 AGTTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
546145 ACTC
1 ACTC
546149 GGAACAATAC
Statistics
Matches: 562, Mismatches: 72, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
105 4 0.01
106 380 0.68
107 87 0.15
110 79 0.14
111 12 0.02
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (105 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTCCCA
GTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:547476 original size:18 final size:17
Alignment explanation
Indices: 547437--547480 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
547427 ATTATATGGA
547437 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
547453 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
547471 TATTATTATT
1 TATTATTATT
547481 ATACGTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 13 0.54
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:547545 original size:2 final size:2
Alignment explanation
Indices: 547540--547584 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
547530 TATATTTTAT
547540 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
547582 TA T
1 TA T
547585 GTTTCTTTAA
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:547970 original size:41 final size:39
Alignment explanation
Indices: 547908--547984 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 39
547898 ATGACCCATT
* * *
547908 TTTTTGTTTTATTTTTAACTAAAGTCTCTCCCACTTTCCTC
1 TTTTTGTCTTATTTCTAACTAAAG-C-CCCCCACTTTCCTC
*
547949 TTTTTGTCTTATTTCTGACTAAAGCCCCCCACTTTC
1 TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTC
547985 GGTGAAGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 10 0.31
40 1 0.03
41 21 0.66
ACGTcount: A:0.17, C:0.27, G:0.06, T:0.49
Consensus pattern (39 bp):
TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTCCTC
Found at i:548075 original size:2 final size:2
Alignment explanation
Indices: 548068--548106 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
548058 TAATTTGATG
548068 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
548107 TTTCAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:548176 original size:9 final size:9
Alignment explanation
Indices: 548164--548188 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
548154 CCTTATCTTA
548164 TTTATTTAT
1 TTTATTTAT
548173 TTTATTTAT
1 TTTATTTAT
548182 TTTATTT
1 TTTATTT
548189 TTTCCCTTTT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTATTTAT
Found at i:551210 original size:22 final size:22
Alignment explanation
Indices: 551162--551203 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
551152 CTTTGTAATA
551162 GTGAGCGTTTAATGTCGAGAAT
1 GTGAGCGTTTAATGTCGAGAAT
*
551184 GTGAGTGTTTAATGTCGAGA
1 GTGAGCGTTTAATGTCGAGA
551204 GATTGAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.33
Consensus pattern (22 bp):
GTGAGCGTTTAATGTCGAGAAT
Found at i:557932 original size:2 final size:2
Alignment explanation
Indices: 557925--557951 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
557915 GTTGTTTTGC
557925 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
557952 ATTATGTATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:560849 original size:190 final size:190
Alignment explanation
Indices: 560526--560903 Score: 756
Period size: 190 Copynumber: 2.0 Consensus size: 190
560516 TTGTTGTTGA
560526 TCATTCAGTCCAGGTTAATGTGACAAGATCTGAAAATGCTCTACAAGCAAAACGGAACTCGAATT
1 TCATTCAGTCCAGGTTAATGTGACAAGATCTGAAAATGCTCTACAAGCAAAACGGAACTCGAATT
560591 TCAAAGGTACAAGGAGAGATTTGCTTTCATCAAATGGGGTTCATCTGCTTTCGAGAACATGCTTG
66 TCAAAGGTACAAGGAGAGATTTGCTTTCATCAAATGGGGTTCATCTGCTTTCGAGAACATGCTTG
560656 TTGTTCCTCCTGGTTCTGGAATTCTTCACATGGTAAACATGCATACGTGGAGATGTATGT
131 TTGTTCCTCCTGGTTCTGGAATTCTTCACATGGTAAACATGCATACGTGGAGATGTATGT
560716 TCATTCAGTCCAGGTTAATGTGACAAGATCTGAAAATGCTCTACAAGCAAAACGGAACTCGAATT
1 TCATTCAGTCCAGGTTAATGTGACAAGATCTGAAAATGCTCTACAAGCAAAACGGAACTCGAATT
560781 TCAAAGGTACAAGGAGAGATTTGCTTTCATCAAATGGGGTTCATCTGCTTTCGAGAACATGCTTG
66 TCAAAGGTACAAGGAGAGATTTGCTTTCATCAAATGGGGTTCATCTGCTTTCGAGAACATGCTTG
560846 TTGTTCCTCCTGGTTCTGGAATTCTTCACATGGTAAACATGCATACGTGGAGATGTAT
131 TTGTTCCTCCTGGTTCTGGAATTCTTCACATGGTAAACATGCATACGTGGAGATGTAT
560904 ATGTTCACAG
Statistics
Matches: 188, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 188 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (190 bp):
TCATTCAGTCCAGGTTAATGTGACAAGATCTGAAAATGCTCTACAAGCAAAACGGAACTCGAATT
TCAAAGGTACAAGGAGAGATTTGCTTTCATCAAATGGGGTTCATCTGCTTTCGAGAACATGCTTG
TTGTTCCTCCTGGTTCTGGAATTCTTCACATGGTAAACATGCATACGTGGAGATGTATGT
Found at i:562128 original size:9 final size:10
Alignment explanation
Indices: 562110--562170 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 10
562100 GTCTTTTTTA
562110 TATTATTTAAT
1 TATTA-TTAAT
562121 T-TTATTAAT
1 TATTATTAAT
562130 TATTATT-AT
1 TATTATTAAT
562139 TATTATTATTAT
1 TATTATTA--AT
562151 TATTATTAAAT
1 TATTATT-AAT
562162 TATATATTA
1 TAT-TATTA
562171 CAAATTTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
9 15 0.34
10 8 0.18
11 7 0.16
12 13 0.30
13 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTAAT
Found at i:562134 original size:3 final size:3
Alignment explanation
Indices: 562110--562158 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
562100 GTCTTTTTTA
*
562110 TAT TAT T-T AAT T-T TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
562154 TAT TA
1 TAT TA
562159 AATTATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:568194 original size:20 final size:20
Alignment explanation
Indices: 568165--568248 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 20
568155 CATTCCTATC
*
568165 TCTTTGAGACCTTGAAATAT
1 TCTTTGAGACCTTGAAACAT
*
568185 TCTTTTAGACCTTGAAACATTCCCT
1 TCTTTGAGACCTTGAAACA-----T
568210 CTCTTTGAGACCTTGAAACAT
1 -TCTTTGAGACCTTGAAACAT
**
568231 TCTTT-CCACCTTGAAACA
1 TCTTTGAGACCTTGAAACA
568249 CTGCATTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
19 11 0.21
20 22 0.42
21 1 0.02
25 1 0.02
26 18 0.34
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
TCTTTGAGACCTTGAAACAT
Found at i:568222 original size:46 final size:46
Alignment explanation
Indices: 568154--568248 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 46
568144 CCAATTTTTG
* *
568154 ACATTCCTATCTCTTTGAGACCTTGAAATATTCTTTTAGACCTTGAA
1 ACATTCCTATCTCTTTGAGACCTTGAAACATTC-TTTACACCTTGAA
* *
568201 ACATTCC-CTCTCTTTGAGACCTTGAAACATTCTTTCCACCTTGAA
1 ACATTCCTATCTCTTTGAGACCTTGAAACATTCTTTACACCTTGAA
568246 ACA
1 ACA
568249 CTGCATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 14 0.32
46 23 0.52
47 7 0.16
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.37
Consensus pattern (46 bp):
ACATTCCTATCTCTTTGAGACCTTGAAACATTCTTTACACCTTGAA
Found at i:570060 original size:12 final size:12
Alignment explanation
Indices: 570043--570117 Score: 51
Period size: 12 Copynumber: 5.6 Consensus size: 12
570033 GATTGAGAAA
570043 CATACATCAACT
1 CATACATCAACT
*
570055 CATACATACATATAT
1 CATACAT-CA-A-CT
570070 ACATACATCAACT
1 -CATACATCAACT
*
570083 CATACATACATATAT
1 CATACAT-CA-A-CT
*
570098 ACATACATCAACA
1 -CATACATCAACT
570111 CATACAT
1 CATACAT
570118 GCATGTTACA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
12 21 0.42
13 5 0.10
14 4 0.08
15 6 0.12
16 14 0.28
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (12 bp):
CATACATCAACT
Found at i:570061 original size:16 final size:16
Alignment explanation
Indices: 570042--570117 Score: 87
Period size: 16 Copynumber: 5.2 Consensus size: 16
570032 AGATTGAGAA
570042 ACATACATCAACTCAT
1 ACATACATCAACTCAT
570058 ACATACAT--A-T-AT
1 ACATACATCAACTCAT
570070 ACATACATCAACTCAT
1 ACATACATCAACTCAT
570086 ACATACAT--A-T-AT
1 ACATACATCAACTCAT
*
570098 ACATACATCAACACAT
1 ACATACATCAACTCAT
570114 ACAT
1 ACAT
570118 GCATGTTACA
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
12 20 0.39
13 2 0.04
14 4 0.08
15 1 0.02
16 24 0.47
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (16 bp):
ACATACATCAACTCAT
Done.