Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009074.1 Hibiscus syriacus cultivar Beakdansim tig00112507_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: 2143704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:452894 original size:20 final size:20
Alignment explanation
Indices: 452864--452911 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
452854 AAATCATAAA
*
452864 TCCATAATAATTTCAAACTT
1 TCCAAAATAATTTCAAACTT
*
452884 TCCTAAATAATTTCAAACTT
1 TCCAAAATAATTTCAAACTT
452904 TCCAAAAT
1 TCCAAAAT
452912 CTTCATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.38
Consensus pattern (20 bp):
TCCAAAATAATTTCAAACTT
Found at i:454633 original size:30 final size:31
Alignment explanation
Indices: 454570--454651 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 31
454560 TAAAATATAT
454570 AACTTTT-CAAAA-TTATATTTTTAGTCCCTA
1 AACTTTTACAAAATTTATA-TTTTAGTCCCTA
*
454600 AACTTTTACAAAATTTATACTTTAG-CCAC-A
1 AACTTTTACAAAATTTATATTTTAGTCC-CTA
454630 AAC-TTTA-AAAATTTATATTTTA
1 AACTTTTACAAAATTTATATTTTA
454652 ATCACTGGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
28 14 0.30
29 4 0.09
30 13 0.28
31 11 0.23
32 5 0.11
ACGTcount: A:0.39, C:0.15, G:0.02, T:0.44
Consensus pattern (31 bp):
AACTTTTACAAAATTTATATTTTAGTCCCTA
Found at i:459758 original size:32 final size:32
Alignment explanation
Indices: 459722--459790 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
459712 AGTGGTTTTA
* * *
459722 TTGTGCATTATCTGAATATAATGCTAACTCTG
1 TTGTGCATTATCCGAATACAATACTAACTCTG
* * *
459754 TTGTGCATTCTCCGAATGCAATACTAACTTTG
1 TTGTGCATTATCCGAATACAATACTAACTCTG
459786 TTGTG
1 TTGTG
459791 ACTCATACAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (32 bp):
TTGTGCATTATCCGAATACAATACTAACTCTG
Found at i:461122 original size:32 final size:30
Alignment explanation
Indices: 461055--461126 Score: 108
Period size: 30 Copynumber: 2.3 Consensus size: 30
461045 ACGATACTCG
* *
461055 AACCCAAAAATTGGTATTTTAGGCTAAAAA
1 AACCCAAAATTTGGTATTTTAAGCTAAAAA
461085 AACCCAAAATTTGGTATTTTAAGCTAAAAAA
1 AACCCAAAATTTGGTATTTTAAGCT-AAAAA
461116 ACACCCAAAAT
1 A-ACCCAAAAT
461127 CATCATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 23 0.61
31 6 0.16
32 9 0.24
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.25
Consensus pattern (30 bp):
AACCCAAAATTTGGTATTTTAAGCTAAAAA
Found at i:464092 original size:13 final size:13
Alignment explanation
Indices: 464074--464099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
464064 AAGACGTATC
464074 AGGAACAATATTT
1 AGGAACAATATTT
464087 AGGAACAATATTT
1 AGGAACAATATTT
464100 GATGTTCATG
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:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AGGAACAATATTT
Found at i:465010 original size:36 final size:35
Alignment explanation
Indices: 464944--465011 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
464934 TCTTTTGACT
*
464944 AATTTAAATATATTATATTAGATTCGTGTAATATA
1 AATTTAAATATATTATATTAGATTCATGTAATATA
**
464979 AATTTAAA-ATATTATTTATTATTTTCATGTAAT
1 AATTTAAATATATTA--TATTAGATTCATGTAAT
465012 TAATTTTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 6 0.21
35 8 0.29
36 14 0.50
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (35 bp):
AATTTAAATATATTATATTAGATTCATGTAATATA
Found at i:469276 original size:60 final size:60
Alignment explanation
Indices: 469222--469335 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
469212 AATGGTCCTT
*
469222 TGACTATAATG-TGTTGTTTTATTGAGTTC-CCCGACTATCAAAAGTTACAAAATGGACCCC
1 TGACTATAA-GATATTGTTTTATTGAG-TCACCCGACTATCAAAAGTTACAAAATGGACCCC
* * * *
469282 TGACTATAAGATATTGTTTTGTTGAGTCACTCGACTATTAAAAGTTACACAATG
1 TGACTATAAGATATTGTTTTATTGAGTCACCCGACTATCAAAAGTTACAAAATG
469336 ATCACCTCAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (60 bp):
TGACTATAAGATATTGTTTTATTGAGTCACCCGACTATCAAAAGTTACAAAATGGACCCC
Found at i:469348 original size:60 final size:60
Alignment explanation
Indices: 469235--469348 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
469225 CTATAATGTG
* *
469235 TTGTTTTATTGAGTTCCCCGACTATCAAAAGTTACAAAATGGACCCCTGACTATAAGATA
1 TTGTTTTATTGAGTTCCCCGACTATCAAAAGTTACAAAATGGACACCTCACTATAAGATA
* * * *
469295 TTGTTTTGTTGAG-TCACTCGACTATTAAAAGTTACACAAT-GATCACCTCACTAT
1 TTGTTTTATTGAGTTC-CCCGACTATCAAAAGTTACAAAATGGA-CACCTCACTAT
469349 TCATTATGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 4 0.09
60 42 0.91
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (60 bp):
TTGTTTTATTGAGTTCCCCGACTATCAAAAGTTACAAAATGGACACCTCACTATAAGATA
Found at i:470233 original size:15 final size:15
Alignment explanation
Indices: 470196--470234 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
470186 AACATCTTTC
*
470196 TTAAATGATTTATTA
1 TTAAATGTTTTATTA
470211 TTAAATGTTTTATTA
1 TTAAATGTTTTATTA
470226 TTAAATGTT
1 TTAAATGTT
470235 ATATAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (15 bp):
TTAAATGTTTTATTA
Found at i:475867 original size:29 final size:29
Alignment explanation
Indices: 475830--475932 Score: 75
Period size: 29 Copynumber: 3.4 Consensus size: 29
475820 AAAAAGATTC
* *
475830 AATATTTTAGGTATTTATTTTGATCAAAA
1 AATACTTTAGGTAATTATTTTGATCAAAA
*
475859 AATACTTTAGGTACACT-TTTTGA-CTAAAA
1 AATACTTTAGGTA-ATTATTTTGATC-AAAA
* * * *
475888 AGATAAATTTAAGTACTTATTTTGATAAAAAA
1 A-AT-ACTTTAGGTAATTATTTTGAT-CAAAA
*
475920 AAAACTTTAGGTA
1 AATACTTTAGGTA
475933 CTTAAATAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
28 1 0.02
29 23 0.41
30 12 0.21
31 15 0.27
32 5 0.09
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.40
Consensus pattern (29 bp):
AATACTTTAGGTAATTATTTTGATCAAAA
Found at i:475934 original size:30 final size:30
Alignment explanation
Indices: 475835--475936 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
475825 GATTCAATAT
* * *
475835 TTTAGGTATTTATTTTGAT-CAAAAAATAC
1 TTTAGGTACTTATTTTGATAAAAAAAAAAC
* *
475864 TTTAGGTACACT-TTTTGACTAAAAAGATAAA-
1 TTTAGGTAC-TTATTTTGA-TAAAAA-AAAAAC
*
475895 TTTAAGTACTTATTTTGATAAAAAAAAAAC
1 TTTAGGTACTTATTTTGATAAAAAAAAAAC
475925 TTTAGGTACTTA
1 TTTAGGTACTTA
475937 AATAAAAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
29 18 0.31
30 20 0.34
31 17 0.29
32 3 0.05
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (30 bp):
TTTAGGTACTTATTTTGATAAAAAAAAAAC
Found at i:480936 original size:111 final size:111
Alignment explanation
Indices: 480807--481037 Score: 401
Period size: 111 Copynumber: 2.1 Consensus size: 111
480797 TCATTTCAAT
*
480807 AAAAAAAATATCAATTTAATTTATGACATGACAATGATTCCGTCGCAAATTTTGTTCAACTTTAA
1 AAAAAAAATATCAATTTAATTTATGACATCACAATGATTCCGTCGCAAATTTTGTTCAACTTTAA
480872 TTAAAATATTA-CAATTTAATTTCTGATGGAATAGTCATTCCGTCGG
66 TTAAAATA-TACCAATTTAATTTCTGATGGAATAGTCATTCCGTCGG
* *
480918 AAAAAAAATATCAATTTAATTTATGACATCACAATGATTCCGTTGGAAATTTTGTTCAACTTTAA
1 AAAAAAAATATCAATTTAATTTATGACATCACAATGATTCCGTCGCAAATTTTGTTCAACTTTAA
*
480983 TTAAAATATACCAATTTAATTTGTGATGGAATAGTCATTCCGTCGG
66 TTAAAATATACCAATTTAATTTCTGATGGAATAGTCATTCCGTCGG
481029 AAATAAAAA
1 AAA-AAAAA
481038 ATAACTACAT
Statistics
Matches: 114, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
110 2 0.02
111 107 0.94
112 5 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (111 bp):
AAAAAAAATATCAATTTAATTTATGACATCACAATGATTCCGTCGCAAATTTTGTTCAACTTTAA
TTAAAATATACCAATTTAATTTCTGATGGAATAGTCATTCCGTCGG
Found at i:485428 original size:18 final size:18
Alignment explanation
Indices: 485405--485449 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
485395 GCAAAGGTTA
485405 ATGCCCAAAGATAATGTC
1 ATGCCCAAAGATAATGTC
485423 ATGCCCAAAGATAATGTC
1 ATGCCCAAAGATAATGTC
485441 ATGCCCAAA
1 ATGCCCAAA
485450 AACATTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (18 bp):
ATGCCCAAAGATAATGTC
Found at i:487064 original size:31 final size:31
Alignment explanation
Indices: 487026--487093 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
487016 AAATATTTTT
*
487026 AAATTTGTGATGGAATATGTGGACCCATTAC
1 AAATTTGTGATGGAATATGTGGACCCATCAC
**
487057 AAATTTGTGATGGAATATGTGGATTCATCAC
1 AAATTTGTGATGGAATATGTGGACCCATCAC
487088 AAATTT
1 AAATTT
487094 ATGACAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (31 bp):
AAATTTGTGATGGAATATGTGGACCCATCAC
Found at i:487156 original size:31 final size:31
Alignment explanation
Indices: 487082--487157 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
487072 TATGTGGATT
* *
487082 CATCACAAATTTATGACAGATTCACCTATTC
1 CATCACAAATTTCTAACAGATTCACCTATTC
487113 CATCACAAATTTCTAACAGATTCACCTATTC
1 CATCACAAATTTCTAACAGATTCACCTATTC
*
487144 CGTCACAAATTTCT
1 CATCACAAATTTCT
487158 TACGGTCCTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (31 bp):
CATCACAAATTTCTAACAGATTCACCTATTC
Found at i:490740 original size:2 final size:2
Alignment explanation
Indices: 490683--490727 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
490673 AATGTGTAAG
490683 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
490725 AT A
1 AT A
490728 CAAAAGTATA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:490812 original size:63 final size:63
Alignment explanation
Indices: 490708--490834 Score: 209
Period size: 63 Copynumber: 2.0 Consensus size: 63
490698 TATATATATA
* *
490708 TATATATATATATATATATACAAAAGTATATATTTGACCATCTTACCTCAGGATTCTAGTAAG
1 TATAAATATATATATATATACAAAAGTATATATTTGACCATCTTACCTCAAGATTCTAGTAAG
* * *
490771 TATAAATATATATATATATATAAAAGTATATATTTGGCCATCTTACCTCAAGATTTTAGTAAG
1 TATAAATATATATATATATACAAAAGTATATATTTGACCATCTTACCTCAAGATTCTAGTAAG
490834 T
1 T
490835 GTACTAGAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.39
Consensus pattern (63 bp):
TATAAATATATATATATATACAAAAGTATATATTTGACCATCTTACCTCAAGATTCTAGTAAG
Found at i:493709 original size:37 final size:37
Alignment explanation
Indices: 493637--493709 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
493627 TATATTTTTT
*
493637 ATTTTGTAAAAAAAATTATATAAATATTATGAATTTA
1 ATTTTGTAAAAAAAATTATATAAATATTATCAATTTA
* * *
493674 ATTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 ATTTTGTAAAAAAAATTATATAAATATTAT-CAATTT
493710 GTAATATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 13 0.42
37 18 0.58
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
ATTTTGTAAAAAAAATTATATAAATATTATCAATTTA
Found at i:500963 original size:2 final size:2
Alignment explanation
Indices: 500956--501000 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
500946 TTTGAAAATG
500956 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
500998 TA T
1 TA T
501001 TTTTTTTTTT
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:501044 original size:34 final size:37
Alignment explanation
Indices: 501006--501079 Score: 109
Period size: 34 Copynumber: 2.1 Consensus size: 37
500996 TATATTTTTT
501006 TTTTTGAAAACGTATAT-A-ATATAG-TTTGAAAACA
1 TTTTTGAAAACGTATATGATATATAGTTTTGAAAACA
**
501040 TTTTTGAAAATTTATATGATATATAGTTTTGAAAACA
1 TTTTTGAAAACGTATATGATATATAGTTTTGAAAACA
501077 TTT
1 TTT
501080 ATATATTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
34 15 0.43
35 1 0.03
36 6 0.17
37 13 0.37
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.45
Consensus pattern (37 bp):
TTTTTGAAAACGTATATGATATATAGTTTTGAAAACA
Found at i:501069 original size:25 final size:27
Alignment explanation
Indices: 501041--501096 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
501031 TTGAAAACAT
501041 TTTTG-AAA-ATTTATATGA-TATATAG
1 TTTTGAAAACATTTATAT-ATTATATAG
501066 TTTTGAAAACATTTATATATTATATAG
1 TTTTGAAAACATTTATATATTATATAG
501093 TTTT
1 TTTT
501097 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.18
26 4 0.14
27 19 0.68
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (27 bp):
TTTTGAAAACATTTATATATTATATAG
Found at i:501098 original size:29 final size:27
Alignment explanation
Indices: 501040--501103 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
501030 TTTGAAAACA
501040 TTTTTG-AAAATTTATATGATATATAG
1 TTTTTGAAAAATTTATATGATATATAG
501066 -TTTTGAAAACATTTATAT-ATTATATAG
1 TTTTTGAAAA-ATTTATATGA-TATATAG
*
501093 TTTTTTAAAAA
1 TTTTTGAAAAA
501104 ATATTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
25 5 0.15
26 4 0.12
27 16 0.48
28 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.50
Consensus pattern (27 bp):
TTTTTGAAAAATTTATATGATATATAG
Found at i:501121 original size:37 final size:38
Alignment explanation
Indices: 501079--501170 Score: 114
Period size: 37 Copynumber: 2.4 Consensus size: 38
501069 TGAAAACATT
*
501079 TATATATTATATAGTTTTTTAAAAAATATTTTAAAA-A
1 TATATATTATATAATTTTTTAAAAAATATTTTAAAATA
* ** * * *
501116 TATATAATATATAATTTTTTTTAACATTTTTTAAAATC
1 TATATATTATATAATTTTTTAAAAAATATTTTAAAATA
501154 TATATATTATATAATTT
1 TATATATTATATAATTT
501171 CAAAAAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
37 30 0.65
38 16 0.35
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (38 bp):
TATATATTATATAATTTTTTAAAAAATATTTTAAAATA
Found at i:501239 original size:3 final size:3
Alignment explanation
Indices: 501226--501304 Score: 70
Period size: 3 Copynumber: 25.3 Consensus size: 3
501216 TATTTATATA
* *
501226 TAT TA- TAT TAT TAT ATAT TAT CAT TATT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * *
501272 TAT TGT AAT TATT TATT TAT AAT TAT TAT TAT T
1 TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT T
501305 TCTTATTTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
2 2 0.03
3 47 0.76
4 13 0.21
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:501261 original size:31 final size:30
Alignment explanation
Indices: 501226--501319 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 30
501216 TATTTATATA
501226 TATTAT-ATTATTATATATTATCATTATTTAT
1 TATTATAATTATTAT-TATT-TCATTATTTAT
* *
501257 TATTATCATTATTATTATTGTAATTATTTA-
1 TATTATAATTATTATTATT-TCATTATTTAT
501287 T-TTATAATTATTATTATTTC-TTATTTAAT
1 TATTATAATTATTATTATTTCATTATTT-AT
501316 TATT
1 TATT
501320 TTGTTCTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 6 0.11
28 2 0.04
29 17 0.31
30 3 0.05
31 19 0.35
32 8 0.15
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (30 bp):
TATTATAATTATTATTATTTCATTATTTAT
Found at i:501288 original size:35 final size:33
Alignment explanation
Indices: 501216--501320 Score: 101
Period size: 35 Copynumber: 3.2 Consensus size: 33
501206 TTTTTTAAAA
*
501216 TATTTATATA-TATTATATTATTA-TATATT-AT
1 TATTTATTTATTATTATATTATTATTAT-TTAAT
*
501247 CA-TTATTTATTATTATCATTATTATTATTGTAAT
1 TATTTATTTATTATTAT-ATTATTATTATT-TAAT
* *
501281 TATTTATTTATAATTATTATTATTTCTTATTTAAT
1 TATTTATTTATTATTA-TATTA-TTATTATTTAAT
501316 TATTT
1 TATTT
501321 TGTTCTTGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
30 6 0.10
31 7 0.11
32 8 0.13
33 4 0.07
34 3 0.05
35 25 0.41
36 8 0.13
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (33 bp):
TATTTATTTATTATTATATTATTATTATTTAAT
Found at i:508206 original size:165 final size:164
Alignment explanation
Indices: 507925--508868 Score: 1325
Period size: 165 Copynumber: 5.7 Consensus size: 164
507915 TAAACAAACT
* * * *
507925 ATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACGCTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * *
507990 GCTTCGATGGAACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACC
508055 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
130 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * ** *
508090 ATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGTCAAAGACCCTTAAGTTTGATTACACTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * * * *
508155 GCTTCAAGGGCATAACATTTACAGCATAACTCAAGGATAGAAGGGTTATCTGTCAGCAAAGACCT
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCT
508220 TTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * *
508254 ATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * * * * * *
508319 GCTACGAGAGCACATCATTTGCAGCATAACTGAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACC
508384 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
130 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
508419 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * *
508484 ACTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACC
* *
508549 TTCGAGTTCGACTACGCTCAACTCCAAGGCACATC
130 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* *
508584 ATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * * * *
508649 GCTTCAAGGGCATAACATTTACAGCATAACTTAAGGCTAGAAGGGTTATCTGTCAGCAAAGACCT
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCT
*
508714 TTGAGTTCGACTACGCTCAGCTTCAAGGCACATC
131 TTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * * ** * * * *
508748 ATTTGCAGTATAACTTAAGTCGAGAATGGCTATCTGCTAAAGACCTTCGAGTTCAATTATATTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * * * *
508813 ACTTAGA-GGCAAATCAAGTTTACAGCATAGCTCAAGG-TAAGAAGGGCTATCTGTCA
66 GCTTCGAGGGCACATC-A-TTTACAGCATAACTCAAGGCT-AGAAGGGTTATCTGTCA
508869 ATAAAATTGT
Statistics
Matches: 690, Mismatches: 84, Indels: 10
0.88 0.11 0.01
Matches are distributed among these distances:
163 6 0.01
164 246 0.36
165 438 0.63
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (164 bp):
ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCT
TTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:508527 original size:329 final size:326
Alignment explanation
Indices: 507925--508868 Score: 1336
Period size: 329 Copynumber: 2.9 Consensus size: 326
507915 TAAACAAACT
* *
507925 ATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACGCTCA
1 ATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* *
507990 GCTTCGATGGAACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGA-GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-CACC-AAAGACC
*
508055 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGC
128 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGC
* * * * *
508120 TATCTGTCAAAGACCCTTAAGTTTGATTACACTCAGCTTCAAGGGCATAA-CATTTACAGCATAA
193 TATCTGCCAAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCA-AATCATTTACAGCATAA
* * *
508184 CTCAAGGATAGAAGGGTTATCTGTCAGC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
257 CTCAAGG-TAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGG
508248 CACATC
321 CACATC
*
508254 ATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * *
508319 GCTACGAGAGCACATCATTTGCAGCATAACTGAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAG-GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-C-ACCAAAGACC
*
508384 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
128 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGC
* *
508449 TATCTGCCAAAGACCCCCAAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAGCATAAC
193 TATCTGCCAAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCAAATCATTTACAGCATAAC
* *
508514 TCAAGGCTAGAAGGGTTATCTATGACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGC
258 TCAAGG-TAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGC
508579 ACATC
322 ACATC
* * * *
508584 ATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCA
1 ATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * *
508649 GCTTCAAGGGCATAACATTTACAGCATAACTTAAGGCTAGAAGGGTTATCTGTCAGCAAAGACCT
66 GCTTCGA-GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-CACCAAAGACCT
* * *
508714 TTGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGTATAACTTAAGTCGAGAATGGCT
129 TTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCT
* * * * * * * *
508779 ATCTGCTAAAGACCTTCGAGTTCAATTATATTCAACTTAGA-GGCAAATCAAGTTTACAGCATAG
194 ATCTGCCAAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCAAATC-A-TTTACAGCATAA
*
508843 CTCAAGGTAAGAAGGGCTATCTGTCA
257 CTCAAGGT-AGAAGGGTTATCTGTCA
508869 ATAAAATTGT
Statistics
Matches: 549, Mismatches: 58, Indels: 15
0.88 0.09 0.02
Matches are distributed among these distances:
328 9 0.02
329 361 0.66
330 178 0.32
331 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (326 bp):
ATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCACCAAAGACCTTT
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTAT
CTGCCAAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCAAATCATTTACAGCATAACTCA
AGGTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACAT
C
Found at i:509553 original size:39 final size:37
Alignment explanation
Indices: 509510--509682 Score: 132
Period size: 37 Copynumber: 4.8 Consensus size: 37
509500 ATATTATATG
*
509510 ATATATAATATAT-GTTTTTTTCGAAAACATTTTAAAAAT
1 ATATATAATATATAG--TCTTT-GAAAACATTTTAAAAAT
*
509549 ATATATAATATATAGTCTTTGAAAACATTTTGAAAAT
1 ATATATAATATATAGTCTTTGAAAACATTTTAAAAAT
* * * * *
509586 GTATATAATATATA-----T--ATATATTTTGAAAAC
1 ATATATAATATATAGTCTTTGAAAACATTTTAAAAAT
* *
509616 GTATATAATATATAGT-TTTGAAAAACATTTTTGAAAAT
1 ATATATAATATATAGTCTTTG-AAAACA-TTTTAAAAAT
* *
509654 TTATATGATATATAGT-TTTGAAAACATTT
1 ATATATAATATATAGTCTTTGAAAACATTT
509683 ATATATTATA
Statistics
Matches: 114, Mismatches: 11, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
30 26 0.23
32 1 0.01
34 1 0.01
36 3 0.03
37 38 0.33
38 31 0.27
39 13 0.11
40 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
ATATATAATATATAGTCTTTGAAAACATTTTAAAAAT
Found at i:509659 original size:38 final size:37
Alignment explanation
Indices: 509606--509682 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 37
509596 TATATATATA
509606 TTTTGAAAACGTATATAATATATAGTTTTGAAAAACAT
1 TTTTGAAAACGTATATAATATATAGTTTTG-AAAACAT
** *
509644 TTTTGAAAATTTATATGATATATAGTTTTGAAAACAT
1 TTTTGAAAACGTATATAATATATAGTTTTGAAAACAT
509681 TT
1 TT
509683 ATATATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 9 0.25
38 27 0.75
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (37 bp):
TTTTGAAAACGTATATAATATATAGTTTTGAAAACAT
Found at i:509701 original size:29 final size:27
Alignment explanation
Indices: 509643--509706 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
509633 TTGAAAAACA
509643 TTTTTG-AAAATTTATATGATATATAG
1 TTTTTGAAAAATTTATATGATATATAG
509669 -TTTTGAAAACATTTATAT-ATTATATAG
1 TTTTTGAAAA-ATTTATATGA-TATATAG
*
509696 TTTTTTAAAAA
1 TTTTTGAAAAA
509707 ATATTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
25 5 0.15
26 4 0.12
27 16 0.48
28 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.50
Consensus pattern (27 bp):
TTTTTGAAAAATTTATATGATATATAG
Found at i:509762 original size:39 final size:38
Alignment explanation
Indices: 509682--509774 Score: 116
Period size: 38 Copynumber: 2.4 Consensus size: 38
509672 TGAAAACATT
*
509682 TATATATTATAT-AGTTTTTTAAAAAATATTTTAAAAA
1 TATATATTATATAATTTTTTTAAAAAATATTTTAAAAA
* * * * *
509719 TATATAATATATAATTTTTTTTAAACATTTTTTAAAATC
1 TATATATTATATAATTTTTTTAAAAAATATTTTAAAA-A
509758 TATATATTATATAATTT
1 TATATATTATATAATTT
509775 CAAAAAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 11 0.23
38 20 0.43
39 16 0.34
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (38 bp):
TATATATTATATAATTTTTTTAAAAAATATTTTAAAAA
Found at i:509847 original size:3 final size:3
Alignment explanation
Indices: 509834--509912 Score: 74
Period size: 3 Copynumber: 26.3 Consensus size: 3
509824 TTTATATATA
* *
509834 TAT TA- TAT TAT TA- TAT TAT TAT CAT TATT TAT TAT TAT CATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT
* *
509879 TAT TAT TGT AAT TAT T-T TATT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT T
509913 TCTTATTTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
2 6 0.10
3 48 0.77
4 8 0.13
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:509880 original size:37 final size:35
Alignment explanation
Indices: 509822--509927 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 35
509812 TTTTTTAAAA
509822 TATTTA-TATATATATTATATTATTATATTATTATCAT
1 TATTTATTAT-TATATT-TATTATTATATTATTAT-AT
*
509859 TATTTATTATTATCATTTATTATTAT-TGTAATTATTT
1 TATTTATTATTAT-ATTTATTATTATAT-T-ATTATAT
*
509896 TATTTATTATTATTATTTCTTATT-TAATTATT
1 TATTTATTATTA-TATTTATTATTAT-ATTATT
509928 TTGTTCTTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
36 5 0.08
37 42 0.70
38 13 0.22
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (35 bp):
TATTTATTATTATATTTATTATTATATTATTATAT
Found at i:509902 original size:9 final size:8
Alignment explanation
Indices: 509834--509929 Score: 54
Period size: 8 Copynumber: 11.8 Consensus size: 8
509824 TTTATATATA
*
509834 TATTATAT
1 TATTTTAT
*
509842 TATTATAT
1 TATTTTAT
*
509850 TATTATCAT
1 TATT-TTAT
509859 TA-TTTAT
1 TATTTTAT
*
509866 TATTATCAT
1 TATT-TTAT
*
509875 T-TATTAT
1 TATTTTAT
*
509882 TATTGTAAT
1 TATT-TTAT
509891 TATTTTATT
1 TATTTTA-T
509900 TATTATTAT
1 TATT-TTAT
*
509909 TA-TTTCT
1 TATTTTAT
*
509916 TATTTAAT
1 TATTTTAT
509924 TATTTT
1 TATTTT
509930 GTTCTTATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 16
0.70 0.14 0.17
Matches are distributed among these distances:
7 14 0.21
8 27 0.40
9 23 0.34
10 3 0.04
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (8 bp):
TATTTTAT
Found at i:509913 original size:13 final size:13
Alignment explanation
Indices: 509839--509919 Score: 94
Period size: 13 Copynumber: 6.3 Consensus size: 13
509829 ATATATATTA
509839 TATTATTATATTAT
1 TATTATTAT-TTAT
*
509853 TATCATTATTTAT
1 TATTATTATTTAT
*
509866 TATTATCATTTAT
1 TATTATTATTTAT
* *
509879 TATTATT-GTAAT
1 TATTATTATTTAT
509891 TATT-TTATTTAT
1 TATTATTATTTAT
*
509903 TATTATTATTTCT
1 TATTATTATTTAT
509916 TATT
1 TATT
509920 TAATTATTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 14 0.25
13 32 0.57
14 8 0.14
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (13 bp):
TATTATTATTTAT
Found at i:509918 original size:7 final size:7
Alignment explanation
Indices: 509822--509928 Score: 75
Period size: 6 Copynumber: 15.7 Consensus size: 7
509812 TTTTTTAAAA
509822 TATTTAT
1 TATTTAT
*
509829 ATATATAT
1 -TATTTAT
509837 TATATTAT
1 TAT-TTAT
509845 TATATTAT
1 TAT-TTAT
*
509853 TA-TCAT
1 TATTTAT
509859 TATTTAT
1 TATTTAT
509866 TA-TTAT
1 TATTTAT
*
509872 CATTTAT
1 TATTTAT
509879 TA-TTAT
1 TATTTAT
* *
509885 T-GTAAT
1 TATTTAT
509891 TA-TT-T
1 TATTTAT
509896 TATTTAT
1 TATTTAT
509903 TA-TTAT
1 TATTTAT
*
509909 TATTTCT
1 TATTTAT
509916 TATTTAAT
1 TATTT-AT
509924 TATTT
1 TATTT
509929 TGTTCTTATT
Statistics
Matches: 80, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
5 3 0.04
6 28 0.35
7 24 0.30
8 25 0.31
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (7 bp):
TATTTAT
Found at i:510597 original size:18 final size:18
Alignment explanation
Indices: 510571--510605 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
510561 AACGCAAAAT
* *
510571 AAACCAAAACAACAGCAA
1 AAACAAAAACAAAAGCAA
510589 AAACAAAAACAAAAGCA
1 AAACAAAAACAAAAGCA
510606 GACAGCCCCG
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:0.71, C:0.23, G:0.06, T:0.00
Consensus pattern (18 bp):
AAACAAAAACAAAAGCAA
Found at i:512674 original size:28 final size:29
Alignment explanation
Indices: 512592--512692 Score: 105
Period size: 31 Copynumber: 3.4 Consensus size: 29
512582 TTCATTTAAG
* *
512592 TACCTAAAATATTTTTTGGTCAAAATAAA
1 TACCTAAAATATTTTATAGTCAAAATAAA
* *
512621 TACCTAAAATTATATTTCTAGCCAAAATAAA
1 TACCTAAAA-TAT-TTTATAGTCAAAATAAA
* **
512652 TACCTAAAGTATTTTAT-GTCAAAATAGG
1 TACCTAAAATATTTTATAGTCAAAATAAA
*
512680 TACCTAAACTATT
1 TACCTAAAATATT
512693 CAAACTTTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 20 0.33
29 13 0.21
30 6 0.10
31 22 0.36
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (29 bp):
TACCTAAAATATTTTATAGTCAAAATAAA
Found at i:512824 original size:27 final size:27
Alignment explanation
Indices: 512789--512840 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
512779 TTTAGATACC
*
512789 TATTTTGATCAAAAAATACTTTAAACT
1 TATTTTGATAAAAAAATACTTTAAACT
512816 TATTTTGATAAAAAAATACTTTAAA
1 TATTTTGATAAAAAAATACTTTAAA
512841 TATTTAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (27 bp):
TATTTTGATAAAAAAATACTTTAAACT
Found at i:512854 original size:26 final size:26
Alignment explanation
Indices: 512799--512858 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
512789 TATTTTGATC
**
512799 AAAAAATACTTTAAACTTATTTTGATA
1 AAAAAATACTTTAAAC-TATTTAAATA
512826 AAAAAATACTTTAAA-TATTTAAATGA
1 AAAAAATACTTTAAACTATTTAAAT-A
512852 AAAAAAT
1 AAAAAAT
512859 GATGTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 7 0.23
26 8 0.27
27 15 0.50
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (26 bp):
AAAAAATACTTTAAACTATTTAAATA
Found at i:514251 original size:23 final size:23
Alignment explanation
Indices: 514225--514269 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
514215 ATCAAAAAAC
*
514225 GTGCCACA-AAGGCAAAGATAAAT
1 GTGCAACACAAGG-AAAGATAAAT
*
514248 GTGCAACACAAGGATAGATAAA
1 GTGCAACACAAGGAAAGATAAA
514270 CTTTATCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.13
Consensus pattern (23 bp):
GTGCAACACAAGGAAAGATAAAT
Found at i:515136 original size:43 final size:43
Alignment explanation
Indices: 515087--515460 Score: 412
Period size: 43 Copynumber: 8.7 Consensus size: 43
515077 CAATAGGTCA
* *
515087 AGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTTG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTG
* ** * *
515130 ATATCTATAGCAACGTTTTTGGAACAAACGTCGCAAAAGGTTG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTG
* * *
515173 ATATCTATAGCGGCGTTTTTGGAACAAACACCGCAAAATATTG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTG
* * * * *
515216 ATATCTATAGCAGCATTTTTGGAACAAACGTCGCAAAAGATCG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTG
** *
515259 AGATCTATAGCGGCG-TTTTGGAACAAACGCCATAAAAGATCG
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTG
* * * * * **
515301 AGACCTATAGCAGTGTTTTTGGAACAATCACCGCAAAAGATCA
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTG
* * *
515344 AGATCTATAGCGGCATTTTTGGAACAAACGCCTCAAAAGA-TA
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTG
* * ** * *
515386 AGATCTATTGTGGCGTTTTTGGAACAAACGTTGCAAAAG-GTC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTG
515428 AGATCTATAGCGGCGTTTTTGGATACAAACGCC
1 AGATCTATAGCGGCGTTTTTGGA-ACAAACGCC
515461 ACTAATTATC
Statistics
Matches: 278, Mismatches: 50, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
42 92 0.33
43 186 0.67
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (43 bp):
AGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTG
Found at i:515196 original size:86 final size:86
Alignment explanation
Indices: 515073--515460 Score: 467
Period size: 86 Copynumber: 4.5 Consensus size: 86
515063 AACAAAAAAT
* * * * * *
515073 GTCGCAATAGGTCAAGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTTGATATCTAT
1 GTCGCAAAAGATCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTGAGATCTAT
*
515138 AGCAACGTTTTTGGAACAAAC
66 AGCAGCGTTTTTGGAACAAAC
* * * * * *
515159 GTCGCAAAAGGTTGATATCTATAGCGGCGTTTTTGGAACAAACACCGCAAAATATTGATATCTAT
1 GTCGCAAAAGATCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTGAGATCTAT
*
515224 AGCAGCATTTTTGGAACAAAC
66 AGCAGCGTTTTTGGAACAAAC
** * *
515245 GTCGCAAAAGATCGAGATCTATAGCGGCG-TTTTGGAACAAACGCCATAAAAGATCGAGACCTAT
1 GTCGCAAAAGATCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTGAGATCTAT
* *
515309 AGCAGTGTTTTTGGAACAATC
66 AGCAGCGTTTTTGGAACAAAC
** * * * *
515330 ACCGCAAAAGATCAAGATCTATAGCGGCATTTTTGGAACAAACGCCTCAAAAGA-TAAGATCTAT
1 GTCGCAAAAGATCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTGAGATCTAT
* **
515394 TGTGGCGTTTTTGGAACAAAC
66 AGCAGCGTTTTTGGAACAAAC
* *
515415 GTTGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATACAAACGCC
1 GTCGCAAAAGATCGAGATCTATAGCGGCGTTTTTGGA-ACAAACGCC
515461 ACTAATTATC
Statistics
Matches: 258, Mismatches: 42, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
84 22 0.09
85 112 0.43
86 124 0.48
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (86 bp):
GTCGCAAAAGATCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGATTGAGATCTAT
AGCAGCGTTTTTGGAACAAAC
Found at i:515350 original size:128 final size:128
Alignment explanation
Indices: 515075--515457 Score: 437
Period size: 128 Copynumber: 3.0 Consensus size: 128
515065 CAAAAAATGT
* * * *
515075 CGCAATAGGTCAAGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTTGATATCTATAG
1 CGCAAAAGATCAAGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAA-GATGAGATCTATAG
** * * * * * * *
515140 CAACGTTTTTGGAACAAACGTCGCAAAAGGTTGATATCTATAGCGGCGTTTTTGGAACAAACAC
65 CGGCGTTTTTGGAACAAACGCCACAAAAGATCGAGACCTATAGCAGCGTTTTTGGAACAAACAC
* ** * * *
515204 CGCAAAATATTGATATCTATAGCAGCATTTTTGGAACAAACGTCGCAAAAGATCGAGATCTATAG
1 CGCAAAAGATCAAGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGAT-GAGATCTATAG
* * *
515269 CGGCG-TTTTGGAACAAACGCCATAAAAGATCGAGACCTATAGCAGTGTTTTTGGAACAATCAC
65 CGGCGTTTTTGGAACAAACGCCACAAAAGATCGAGACCTATAGCAGCGTTTTTGGAACAAACAC
* * * *
515332 CGCAAAAGATCAAGATCTATAGCGGCATTTTTGGAACAAACGCCTCAAAAGATAAGATCTATTGT
1 CGCAAAAGATCAAGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGATGAGATCTATAGC
*** * * *
515397 GGCGTTTTTGGAACAAACGTTGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATACAAAC
66 GGCGTTTTTGGAACAAACGCCACAAAAGATCGAGACCTATAGCAGCGTTTTTGGA-ACAAAC
515458 GCCACTAATT
Statistics
Matches: 210, Mismatches: 41, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
127 33 0.16
128 122 0.58
129 55 0.26
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (128 bp):
CGCAAAAGATCAAGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGATGAGATCTATAGC
GGCGTTTTTGGAACAAACGCCACAAAAGATCGAGACCTATAGCAGCGTTTTTGGAACAAACAC
Found at i:516544 original size:3 final size:3
Alignment explanation
Indices: 516449--516528 Score: 92
Period size: 3 Copynumber: 27.0 Consensus size: 3
516439 TCCATTTGTT
* * * *
516449 TTA TTT TTA CTA TTA CTA TTA TTA TTA TT- TTT TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
516496 TTA ATA TTA TTA TTA TTA TTTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
516529 ATAAATTTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 4 0.06
3 58 0.89
4 3 0.05
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:516927 original size:20 final size:20
Alignment explanation
Indices: 516898--516935 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
516888 CAACTAGTAG
* *
516898 GGTGAGTCACCACATAGCTC
1 GGTGACTCACCAAATAGCTC
516918 GGTGACTCACCAAATAGC
1 GGTGACTCACCAAATAGC
516936 CACCCTTTAC
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:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (20 bp):
GGTGACTCACCAAATAGCTC
Found at i:518162 original size:13 final size:16
Alignment explanation
Indices: 518144--518186 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
518134 CTATTTTCTG
*
518144 ATATTTTAAA-TAAAT
1 ATATTTTAAATTATAT
518159 AT-TTTTAAATTATAT
1 ATATTTTAAATTATAT
518174 ATATTTT-AATTAT
1 ATATTTTAAATTAT
518187 TTTTAGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 7 0.28
15 14 0.56
16 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTTTAAATTATAT
Found at i:518624 original size:21 final size:21
Alignment explanation
Indices: 518598--518953 Score: 122
Period size: 21 Copynumber: 16.6 Consensus size: 21
518588 GATTTACATA
518598 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
518619 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* **
518640 TTCGCGTTGCGATTTTCCAAATTCG
1 TTCGCATTGCGATAGTCC-AA---G
* * * * *
518665 ACTATCGCAATGCGA-ACTTCGAC
1 --T-TCGCATTGCGATAGTCCAAG
518688 TATCGCATTGCGATAGTCCAAG
1 T-TCGCATTGCGATAGTCCAAG
* *
518710 TTTGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* ** *
518731 TTCGCGTTGCGATTTTCCAAA
1 TTCGCATTGCGATAGTCCAAG
* * * * * *
518752 TTCGACTATCGCAACACGAACTTCGAC
1 TTCG-C-ATTGCGATA-G---TCCAAG
* *
518779 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
*
518800 TTCGCATTGCGATAGTTCAAG
1 TTCGCATTGCGATAGTCCAAG
518821 TTCGC----CGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*** *
518838 TTCATGTTGCGATAGTCAAAG
1 TTCGCATTGCGATAGTCCAAG
* ** *
518859 TTCGCGTTGCGATTTTCCAAA
1 TTCGCATTGCGATAGTCCAAG
*
518880 TTCG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
518899 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCATTGCGA--TAGTCCAAG
* *
518922 TTCG--TTCCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
518941 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
518954 TTATTCCAAA
Statistics
Matches: 243, Mismatches: 64, Indels: 56
0.67 0.18 0.15
Matches are distributed among these distances:
17 14 0.06
19 25 0.10
20 13 0.05
21 141 0.58
22 9 0.04
23 14 0.06
25 1 0.00
26 6 0.02
27 8 0.03
28 12 0.05
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:518650 original size:42 final size:42
Alignment explanation
Indices: 518598--518962 Score: 191
Period size: 42 Copynumber: 8.5 Consensus size: 42
518588 GATTTACATA
* *
518598 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAGTTCGCATTGCGATAGTCGAAG
* * * *
518640 TTCGCGTTGCGATTTTCCAAATTCGACTATCGCAATGCGA-ACTTCG-AC
1 TTCGCGTTGCGATATTCC-AA---G--T-TCGCATTGCGATA-GTCGAAG
* * *
518688 TATCGCATTGCGATAGTCCAAGTTTGCATTGCGATAGTCGAAG
1 T-TCGCGTTGCGATATTCCAAGTTCGCATTGCGATAGTCGAAG
* * * * * *
518731 TTCGCGTTGCGATTTTCCAAATTCGACTATCGCAACACGAACTTCG-AC
1 TTCGCGTTGCGATATTCCAAGTTCG-C-ATTGCGATA-G----TCGAAG
* *
518779 TATCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTTC-AAG
1 T-TCGCGTTGCGATATTCCA-AGTTCGCATTGCGATAG-TCGAAG
* *** *
518821 TTCGC----CGATAGTCCAAGTTCATGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATATTCCAAGTTCGCATTGCGATAGTCGAAG
* *
518859 TTCGCGTTGCGATTTTCCAAATTCG--TTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAGTTCGCATTGCGATAGTCGAAG
* *
518899 TTCGCGTTGCGATTTATTCCAAATTCG--TTCCGATAGTCGAAG
1 TTCGCGTTGCGA--TATTCCAAGTTCGCATTGCGATAGTCGAAG
518941 TTCGCGTTGCGATTTATTCCAA
1 TTCGCGTTGCGA--TATTCCAA
518963 ATTTGTTGCG
Statistics
Matches: 253, Mismatches: 40, Indels: 60
0.72 0.11 0.17
Matches are distributed among these distances:
37 7 0.03
38 23 0.09
40 26 0.10
41 4 0.02
42 111 0.44
43 7 0.03
44 6 0.02
45 3 0.01
46 7 0.03
47 1 0.00
48 16 0.06
49 42 0.17
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (42 bp):
TTCGCGTTGCGATATTCCAAGTTCGCATTGCGATAGTCGAAG
Found at i:518699 original size:49 final size:49
Alignment explanation
Indices: 518641--518794 Score: 137
Period size: 49 Copynumber: 3.3 Consensus size: 49
518631 TAGTCGAAGT
*
518641 TCGCGTTGCGATTTTCCAAATTCGACTATCGCAATGCGAACTTCGACTA
1 TCGCATTGCGATTTTCCAAATTCGACTATCGCAATGCGAACTTCGACTA
** * * * *
518690 TCGCATTGCGATAGTCC-AA---G--T-TTGCATTGCGATA-GTCGAAGT-
1 TCGCATTGCGATTTTCCAAATTCGACTATCGCAATGCGA-ACTTCG-ACTA
* **
518732 TCGCGTTGCGATTTTCCAAATTCGACTATCGCAACACGAACTTCGACTA
1 TCGCATTGCGATTTTCCAAATTCGACTATCGCAATGCGAACTTCGACTA
518781 TCGCATTGCGATTT
1 TCGCATTGCGATTT
518795 ACATATTCGC
Statistics
Matches: 77, Mismatches: 17, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
42 26 0.34
43 6 0.08
45 1 0.01
46 1 0.01
48 6 0.08
49 37 0.48
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (49 bp):
TCGCATTGCGATTTTCCAAATTCGACTATCGCAATGCGAACTTCGACTA
Found at i:518705 original size:91 final size:91
Alignment explanation
Indices: 518599--518825 Score: 370
Period size: 91 Copynumber: 2.5 Consensus size: 91
518589 ATTTACATAT
518599 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTC
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTC
**
518664 GACTATCGCAATGCGAACTTCGACTA
66 GACTATCGCAACACGAACTTCGACTA
*
518690 TCGCATTGCGATAGTCCAAGTTTGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTC
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTC
518755 GACTATCGCAACACGAACTTCGACTA
66 GACTATCGCAACACGAACTTCGACTA
* *
518781 TCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTTC-AAGTTCGC
1 TCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAG-TCGAAGTTCGC
518826 CGATAGTCCA
Statistics
Matches: 128, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
90 25 0.20
91 103 0.80
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (91 bp):
TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTC
GACTATCGCAACACGAACTTCGACTA
Found at i:518963 original size:42 final size:42
Alignment explanation
Indices: 518843--518977 Score: 229
Period size: 42 Copynumber: 3.3 Consensus size: 42
518833 CCAAGTTCAT
*
518843 GTTGCGATAGTCAAAGTTCGCGTTGCGA-TT-TTCCAAATTC
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
518883 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
* *
518925 GTTCCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTT
1 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
518967 GTTGCGATAGT
1 GTTGCGATAGT
518978 GCAAAATCGC
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
40 27 0.30
41 2 0.02
42 60 0.67
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTC
Found at i:519732 original size:21 final size:21
Alignment explanation
Indices: 519707--519778 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
519697 ATTTTGGGCT
519707 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
519728 ATCGCAACGTGAACTTCGACT--
1 ATCGCAAC--GAATTTGGAATAA
*
519749 ACCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
519770 ATCGCAACG
1 ATCGCAACG
519779 CGAACTTCGA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
19 8 0.21
21 23 0.59
23 8 0.21
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:519768 original size:42 final size:42
Alignment explanation
Indices: 519709--519791 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
519699 TTTGGGCTAT
*
519709 CGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACTAC
1 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTAC
519751 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
1 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTA
519792 TCGTAACTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (42 bp):
CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTAC
Found at i:519794 original size:21 final size:21
Alignment explanation
Indices: 519728--519794 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
519718 TTTGGAATAA
*
519728 ATCGCAACGTGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * * *
519749 ACCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
519768 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
519791 ATCG
1 ATCG
519795 TAACTAACTT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
19 8 0.24
21 16 0.48
23 9 0.27
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:519814 original size:42 final size:42
Alignment explanation
Indices: 519709--519814 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
519699 TTTGGGCTAT
* * * *
519709 CGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACTAC
1 CGCAACGAACTTGAAAAAAATCGCAACGCGAACTTCGACTAC
* * * *
519751 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTAT
1 CGCAACGAACTTGAAAAAAATCGCAACGCGAACTTCGACTAC
* *
519793 CGTAACTAACTTGAAAAAAATC
1 CGCAACGAACTTGAAAAAAATC
519815 TGTTGAGTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.22
Consensus pattern (42 bp):
CGCAACGAACTTGAAAAAAATCGCAACGCGAACTTCGACTAC
Found at i:520903 original size:21 final size:21
Alignment explanation
Indices: 520879--520989 Score: 154
Period size: 21 Copynumber: 5.3 Consensus size: 21
520869 AACTTGGACT
520879 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
520900 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
520921 ATCGCAACGCAAACTTCGACT--
1 ATCGCAACG--AATTTGGAATAA
*
520942 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
520963 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
520984 ATCGCA
1 ATCGCA
520990 GCGCGAACTT
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
19 8 0.10
21 65 0.81
23 7 0.09
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:520936 original size:63 final size:63
Alignment explanation
Indices: 520856--521013 Score: 271
Period size: 63 Copynumber: 2.5 Consensus size: 63
520846 GTTTTCAACA
* * *
520856 AAATCACAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAAT
1 AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGAATTTGGAAT
*
520919 AAATCGCAACGCAAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGAATTTGGAAT
1 AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGAATTTGGAAT
*
520982 AAATCGCAGCGCGAACTTCGACTATCGCAACG
1 AAATCGCAACGCGAACTTCGACTATCGCAACG
521014 CGAACTTCGA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 89 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (63 bp):
AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGAATTTGGAAT
Found at i:521008 original size:21 final size:21
Alignment explanation
Indices: 520921--521059 Score: 133
Period size: 21 Copynumber: 6.6 Consensus size: 21
520911 TTTGGAATAA
*
520921 ATCGCAACGCAAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
520942 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
* * *
520961 AAATCGCAA--CGAATTTGGAAT
1 --ATCGCAACGCGAACTTCGACT
*
520982 AAATCGCAGCGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
521005 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
521026 ATCGCAATGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
521047 ATCGCAATGCGAA
1 ATCGCAACGCGAA
521060 TATGTAAATC
Statistics
Matches: 104, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
19 9 0.09
21 86 0.83
23 9 0.09
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:521009 original size:42 final size:40
Alignment explanation
Indices: 520866--521053 Score: 123
Period size: 42 Copynumber: 4.5 Consensus size: 40
520856 AAATCACAAC
* *
520866 GCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCA
1 GCGAACTTGGACTATCGCAACGAACTTCGAATAAATCGCA
* * * *
520906 ACGAATTTGGAATAAATCGCAACGCAAACTTCGACT--ATCGCA
1 GCGAACTTGGACT--ATCGCAACG--AACTTCGAATAAATCGCA
* * * *
520948 ACGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCA
1 GCGAACTTGGACT--ATCGCAACGAACTTCGAATAAATCGCA
* *
520990 GCGCGAACTTCGACTATCGCAACGCGAACTTCGACT--ATCGCAA
1 --GCGAACTTGGACTATCGCAA--CGAACTTCGAATAAATCGC-A
*
521033 TGCGAACTTCGACTATCGCAA
1 -GCGAACTTGGACTATCGCAA
521054 TGCGAATATG
Statistics
Matches: 120, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
40 17 0.14
42 76 0.63
43 1 0.01
44 26 0.22
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (40 bp):
GCGAACTTGGACTATCGCAACGAACTTCGAATAAATCGCA
Found at i:523927 original size:183 final size:182
Alignment explanation
Indices: 523327--524101 Score: 1082
Period size: 183 Copynumber: 4.3 Consensus size: 182
523317 AGGTAAAAAT
*
523327 ATGACAAAATCGGT-AA-AACGATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATC
1 ATGACAAAACCGGTAAAGAAC--TACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATC
*
523390 -AACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAA
64 GAA-ACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAA
* *
523454 ATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA-CATGTCTAAAAA
128 ATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATC-GGTCT-CAAA
* *
523510 ATGACAAAACCGGTAAA-AAATACCGGATATGTTGAAAGTATCGATAATTTAATATAAGTATCGA
1 ATGACAAAACCGGTAAAGAACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGA
* *
523574 AATTTTTTTGGAATTT-AAA-AG-AGAAGTTATAGCTCCTATAAAGTGTCGATACTTTAAAAAAA
66 AA--CTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAA
* * * *
523636 TGTATCGATCTATAACAATATAACAGGTAAAAATATGATAAAATCGATCCCAAA
129 TGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAA
* ** *
523690 ATGACAAATCCGGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGA
1 ATGACAAAACCGGTAAAGAACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGA
* * * **
523755 CACTTTCT-AAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATGAAAAT
66 AACTTT-TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAAT
* * * * *
523819 TTATCGATCCGTAACAATATAACAGCTAAAAAAAATGATAAAATCGGTCTCAAA
130 GTATCGATCCATAACAATATAACAGGT-AAAAATATGACAAAATCGGTCTCAAA
* *
523873 ATGACAAAACCGATAAAGAACTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGA
1 ATGACAAAACCGGTAAAGAACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGA
*
523938 AACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAATATG
66 AACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATG
* * *
524003 TATCGATCTATTACAATATAACAGGTAAAAATATGACAAAATTGGTCTCAAA
131 TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAA
* ** *
524055 ATGACAAAACCGGTAAAGCACTATTGAATATGTTGAAAGTGTCGATA
1 ATGACAAAACCGGTAAAGAACTACCGGATATGTTGAAAGTGTCGATA
524102 CTTGAATAAG
Statistics
Matches: 523, Mismatches: 57, Indels: 25
0.86 0.09 0.04
Matches are distributed among these distances:
179 8 0.02
180 23 0.04
181 127 0.24
182 172 0.33
183 178 0.34
184 15 0.03
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (182 bp):
ATGACAAAACCGGTAAAGAACTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGA
AACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATG
TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAA
Found at i:524556 original size:19 final size:19
Alignment explanation
Indices: 524534--524608 Score: 87
Period size: 19 Copynumber: 3.9 Consensus size: 19
524524 CTTTTATTTA
524534 ATATTATAGGTAAAAAATG
1 ATATTATAGGTAAAAAATG
*
524553 ATATTATAGGTAAACAATG
1 ATATTATAGGTAAAAAATG
* * * *
524572 ATATTACATGTAGAAAGTG
1 ATATTATAGGTAAAAAATG
* *
524591 ATATTCTAGGTAGAAAAT
1 ATATTATAGGTAAAAAAT
524609 AAATATGGAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.47, C:0.04, G:0.17, T:0.32
Consensus pattern (19 bp):
ATATTATAGGTAAAAAATG
Found at i:525347 original size:29 final size:29
Alignment explanation
Indices: 525305--525366 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
525295 TGCAGCATAA
525305 AAAGGGTGAATTTATTAATTGAACACCTT
1 AAAGGGTGAATTTATTAATTGAACACCTT
525334 AAAGGGTGAATTTATTAATTGAACACCTT
1 AAAGGGTGAATTTATTAATTGAACACCTT
525363 AAAG
1 AAAG
525367 AGAAGGATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (29 bp):
AAAGGGTGAATTTATTAATTGAACACCTT
Found at i:527980 original size:19 final size:19
Alignment explanation
Indices: 527956--528001 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
527946 ATAGGGTTAG
527956 TTTTGTATAAGATTTATAA
1 TTTTGTATAAGATTTATAA
*
527975 TTTTGTATACGATTTATAA
1 TTTTGTATAAGATTTATAA
527994 TTTTGTAT
1 TTTTGTAT
528002 GTGAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTTGTATAAGATTTATAA
Found at i:528715 original size:199 final size:200
Alignment explanation
Indices: 528374--529671 Score: 1971
Period size: 199 Copynumber: 6.5 Consensus size: 200
528364 GTAAACTTAT
* * * * *
528374 GTGTCGATACATTTATAACAAGTATCGATCCTAAAAACATCGAAACCCATAATTATAATGTAAAA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAATA
* * * * *
528439 GGTAAATTAACAATTTAACCGGTCTAAATATACCGATTTTTGAGAAAATAGGTATACAAAAAATA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * *
528504 TCGAAACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACCA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGCACGA
528569 AAAGA
196 AAAGA
* *
528574 -TGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAATA
528638 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * *
528703 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCTAGTGCATGA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGCACGA
*
528768 AAAAA
196 AAAGA
* * * * *
528773 GTGTCGATACATTTATAACAAATGTCGATCCCAAAAAACATGGAAACTCATAATTATAATGTAAT
1 GTGTCGATACATTTATAACAAGTGTCGATCCC-AAAAACATCGAAACCCAAAATTTTAATGTAAT
* *
528838 AGGTAAATTAACAATGTAACCAGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGT
65 AGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGT
528903 ATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGCAC-
130 ATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGCACG
*
528967 AAAAAA
195 AAAAGA
* * * * *
528973 GTTTCAATACATTTATAATAAGTGTCGTTCCCAAAAACATTGAAACCCAAAATTTTAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAATA
*
529038 GGTAAATTAACAATGTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* *
529103 TCGACACAAATAAAACAAGTGTCAATACTTTTTGTCCAAAATGTATTTCTAAACCAAGTGCACGA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGCACGA
*
529168 ATA-A
196 AAAGA
*
529172 GTGTCGATACATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAATA
*
529237 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTACAAAAAGTA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* *
529302 TCGACACAAATAAAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCTAAACCAAGTGCACGA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGCACGA
*
529367 ATA-A
196 AAAGA
* * * *
529371 GTGTCGATACATTTATAACAAGTATCGATCCTAAGAACATCGAAACACAAAATTTTAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAATA
* * ** * * *
529436 GGTCATTTTGCAATGTAACCGGTATAATTATACCGGTTTTTGAGAAAACAGATGT--AAAAAGTA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
*
529499 TCGATACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGCACGA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGCACGA
529564 AAA-A
196 AAAGA
* * *
529568 GTGTCGATACATTTATAACAAGTATCGATCCTAAGAACATCGAAACCCAAAATTTTAATGTAATA
1 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAATA
* * ** * * *
529633 GGTCATTTTGCAATGTAACCGGTATAATTATACCTGTTT
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTT
529672 AATTTGAAAA
Statistics
Matches: 1034, Mismatches: 61, Indels: 9
0.94 0.06 0.01
Matches are distributed among these distances:
197 175 0.17
199 639 0.62
200 66 0.06
201 154 0.15
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (200 bp):
GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAATA
GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGCACGA
AAAGA
Found at i:529148 original size:400 final size:396
Alignment explanation
Indices: 528374--529671 Score: 1988
Period size: 400 Copynumber: 3.3 Consensus size: 396
528364 GTAAACTTAT
* *
528374 GTGTCGATACATTTATAACAAGTATCGATCCTAAAAACATCGAAACCCATAATTATAATGTAAAA
1 GTGTCGATACATTTATAACAAGTATCGATCCTAAAAACATCGAAACCCAAAATTATAATGTAATA
* * * *
528439 GGTAAATTAACAATTTAACCGGTCTAAATATACCGATTTTTGAGAAAATAGGTATACAAAAAATA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCG-TTTTTGAGAAAACAGGTGTACAAAAAGTA
* *
528504 TCGAAACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACCA
130 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACAA
* *
528569 AAAGATGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
195 AAAG-TGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGT
528634 AATAGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAA
259 AATAGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAA
* *
528699 AGTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCTAGTGC
324 AGTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGC
*
528764 ATGAAAAAA
389 ACG-AAAAA
* * * * * *
528773 GTGTCGATACATTTATAACAAATGTCGATCCCAAAAAACATGGAAACTCATAATTATAATGTAAT
1 GTGTCGATACATTTATAACAAGTATCGAT-CCTAAAAACATCGAAACCCAAAATTATAATGTAAT
*
528838 AGGTAAATTAACAATGTAACCAGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGT
65 AGGTAAATTAACAATGTAACCGGTCTAAATATACC-GTTTTTGAGAAAACAGGTGTACAAAAAGT
*
528903 ATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGCACA
129 ATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCAC-
* * * * *
528968 AAAAAGTTTCAATACATTTATAATAAGTGTCGTTCCCAAAAACATTGAAACCCAAAATTTTAATG
193 AAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATG
*
529033 TAATAGGTAAATTAACAATGTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAA
258 TAATAGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAA
* *
529098 AAGTATCGACACAAATAAAACAAGTGTCAATACTTTTTGTCCAAAATGTATTTCTAAACCAAGTG
323 AAGTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTG
*
529163 CACGAATAA
388 CACGAAAAA
* * * *
529172 GTGTCGATACATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCTAAAAACATCGAAACCCAAAATTATAATGTAATA
*
529237 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACATGTGTACAAAAAGTA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACC-GTTTTTGAGAAAACAGGTGTACAAAAAGTA
*
529302 TCGACACAAATAAAACAAGTGTCGATACTTTTTGTCCAGAATGTATTTCTAAACCAAGTGCACGA
130 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCAC-A
* * * * *
529367 ATAAGTGTCGATACATTTATAACAAGTATCGATCCTAAGAACATCGAAACACAAAATTTTAATGT
194 AAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGT
* * ** * * *
529432 AATAGGTCATTTTGCAATGTAACCGGTATAATTATACCGGTTTTTGAGAAAACAGATGT--AAAA
259 AATAGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAA
*
529495 AGTATCGATACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGC
324 AGTATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGC
529560 ACGAAAAA
389 ACGAAAAA
* *
529568 GTGTCGATACATTTATAACAAGTATCGATCCTAAGAACATCGAAACCCAAAATTTTAATGTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCTAAAAACATCGAAACCCAAAATTATAATGTAATA
* * ** * *
529633 GGTCATTTTGCAATGTAACCGGTATAATTATACCTGTTT
66 GGTAAATTAACAATGTAACCGGTCTAAATATACC-GTTT
529672 AATTTGAAAA
Statistics
Matches: 822, Mismatches: 74, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
396 166 0.20
398 261 0.32
399 58 0.07
400 331 0.40
401 6 0.01
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (396 bp):
GTGTCGATACATTTATAACAAGTATCGATCCTAAAAACATCGAAACCCAAAATTATAATGTAATA
GGTAAATTAACAATGTAACCGGTCTAAATATACCGTTTTTGAGAAAACAGGTGTACAAAAAGTAT
CGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCACAAA
AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAA
TAGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAG
TATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGTATTTCTAAACCAAGTGCAC
GAAAAA
Found at i:531083 original size:21 final size:21
Alignment explanation
Indices: 531059--531101 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
531049 TCATTGCTCA
*
531059 ATGAAGTCTCCATGTTGCGTG
1 ATGAAGTCTCCATATTGCGTG
*
531080 ATGAAGTCTCTATATTGCGTG
1 ATGAAGTCTCCATATTGCGTG
531101 A
1 A
531102 CGAATTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (21 bp):
ATGAAGTCTCCATATTGCGTG
Found at i:531252 original size:3 final size:3
Alignment explanation
Indices: 531220--531269 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
531210 CAAGCGGTCA
* * * * *
531220 ATG AAG ATG ACG ATG AAG ATG AAG AAG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
531268 AT
1 AT
531270 CCAAACAAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.42, C:0.02, G:0.32, T:0.24
Consensus pattern (3 bp):
ATG
Found at i:532597 original size:24 final size:24
Alignment explanation
Indices: 532546--532598 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
532536 TTTCATTTAT
* * *
532546 AATTAGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
532570 AATTTGAGTTTGAATTTAAATATA
1 AATTTGAGTTTGAATTTAAATATA
532594 AATTT
1 AATTT
532599 CGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:533117 original size:200 final size:198
Alignment explanation
Indices: 532772--533471 Score: 960
Period size: 200 Copynumber: 3.5 Consensus size: 198
532762 TATTCATTCA
* * *
532772 TGTCGATATATATTGTCCATAATGTA-TTTCCAAACCAAGTGCACGAGAAAAGTGTCGATACATT
1 TGTCGATACATTTTGTCCATAATGTATTTTCCAAACCAAGTGCAC-AAAAAAGTGTCGATACATT
* * *
532836 TATAACAAGTATCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAAGTAAATTAACAA
65 TATAACAAGTGTCGATACCAAAAACATCGAAACACATAATTATAATGTAATAGGTAAATTAACAA
* *
532901 TGTAACCAGTCTAAATAAACCGGTTTTTGAGAAAACAAGTATACATAAAGCATCGACACAAATCC
130 TGTAACGA-TCTAAATAAACCGGTTTTTGAGAAAA-AAGTATACATAAAGTATCGACACAAATCC
532966 AACAAG
193 AACAAG
* * *
532972 TGTCGATACATTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTT
1 TGTCGATACATTTTGTCCATAATGTATTTTCCAAACCAAGTGCACAAAAAAGTGTCGATACATTT
* * * * *
533037 CTAACAAGTGTCGATACTAAAATCATCGAAACACATAGA-TATAATATAATAGGTAAAATAACAA
66 ATAACAAGTGTCGATACCAAAAACATCGAAACACATA-ATTATAATGTAATAGGTAAATTAACAA
* * *
533101 TGTAATCGACCTAAATACACCGGTTTATGAGAAAAAAGTATACATAAAGTATCGACACAAATCCA
130 TGTAA-CGATCTAAATAAACCGGTTTTTGAGAAAAAAGTATACATAAAGTATCGACACAAATCCA
533166 ACAAG
194 ACAAG
* * *
533171 TGTCGAAACTTTTTGTCCATAATGTATTTTCCAAACCAA-TGCACAAAAAAGTTTCGATACATTT
1 TGTCGATACATTTTGTCCATAATGTATTTTCCAAACCAAGTGCACAAAAAAGTGTCGATACATTT
* * * * * *
533235 ATAACATGTGTCGATCCCAAATACATCGAAAC-CTATAATTATAATGTAATAGGTCACTTTACAA
66 ATAACAAGTGTCGATACCAAAAACATCGAAACAC-ATAATTATAATGTAATAGGTAAATTAACAA
* * ** *
533299 TGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATC
130 TGTAA-CGATCTAAATAAACCGGTTTT-TGAGAAAA-AAGTATACATAAAGTATCGACACAAATC
533364 CAACAAG
192 CAACAAG
*
533371 TGTCGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACAACAAAA-TGTCGATACATT
1 TGTCGATACATTTTGTCCATAATGTATTTTCCAAACCAAGTGCACAA-AAAAGTGTCGATACATT
*
533435 TATAACAAGTGTCGATACAAAAAACATCGAAACACAT
65 TATAACAAGTGTCGATACCAAAAACATCGAAACACAT
533472 CGGCCTAAAT
Statistics
Matches: 440, Mismatches: 50, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
197 2 0.00
198 91 0.21
199 78 0.18
200 194 0.44
201 70 0.16
202 5 0.01
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (198 bp):
TGTCGATACATTTTGTCCATAATGTATTTTCCAAACCAAGTGCACAAAAAAGTGTCGATACATTT
ATAACAAGTGTCGATACCAAAAACATCGAAACACATAATTATAATGTAATAGGTAAATTAACAAT
GTAACGATCTAAATAAACCGGTTTTTGAGAAAAAAGTATACATAAAGTATCGACACAAATCCAAC
AAG
Found at i:533597 original size:166 final size:166
Alignment explanation
Indices: 533323--533637 Score: 558
Period size: 166 Copynumber: 1.9 Consensus size: 166
533313 ATTTACCGGT
* ** *
533323 TTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTTTTTGTC
1 TTTATGAGAAAACAAATATACATAAAGTATCAACACAAATCCAACAAGTGTCGATACTTTTTGTC
533388 CATAATGTATTTTCCAAACCAAGTGCACAACAAAATGTCGATACATTTATAACAAGTGTCGATAC
66 CATAATGTATTTTCCAAACCAAGTGCACAACAAAATGTCGATACATTTATAACAAGTGTCGATAC
533453 AAAAAACATCGAAACACATCGGCCTAAATACATCGG
131 AAAAAACATCGAAACACATCGGCCTAAATACATCGG
*
533489 TTTATGAGAAAACAAATATACATAAAGTATCAACACAAATTCAACAAGTGTCGATACTTTTTGTC
1 TTTATGAGAAAACAAATATACATAAAGTATCAACACAAATCCAACAAGTGTCGATACTTTTTGTC
* *
533554 CATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGATAC
66 CATAATGTATTTTCCAAACCAAGTGCACAACAAAATGTCGATACATTTATAACAAGTGTCGATAC
*
533619 TAAAAACATCGAAACACAT
131 AAAAAACATCGAAACACAT
533638 AGATATAATG
Statistics
Matches: 141, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
166 141 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.27
Consensus pattern (166 bp):
TTTATGAGAAAACAAATATACATAAAGTATCAACACAAATCCAACAAGTGTCGATACTTTTTGTC
CATAATGTATTTTCCAAACCAAGTGCACAACAAAATGTCGATACATTTATAACAAGTGTCGATAC
AAAAAACATCGAAACACATCGGCCTAAATACATCGG
Found at i:533811 original size:366 final size:365
Alignment explanation
Indices: 533105--533837 Score: 1139
Period size: 366 Copynumber: 2.0 Consensus size: 365
533095 TAACAATGTA
* *
533105 ATCGACCTAAATACACCGGTTTATGAGAAAAAAGTATACATAAAGTATCGACACAAATCCAACAA
1 ATCGACCTAAATACACCGGTTTATGAGAAAAAAATATACATAAAGTATCAACACAAATCCAACAA
*
533170 GTGTCGAAACTTTTTGTCCATAATGTATTTTCCAAACCAATGCACAAAAAAGTTTCGATACATTT
66 GTGTCGAAACTTTTTGTCCATAATGTATTTTCCAAACCAATGCACAAAAAAGTGTCGATACATTT
* * * * ** *
533235 ATAACATGTGTCGATCCCAAATACATCGAAACCTATAATTATAATGTAATAGGTCACTTTACAAT
131 ATAACAAGTGTCGATACCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAAATAACAAT
* ** ** * * *
533300 GTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTATACATAAAGTATCGACACAAATCC
196 GTAACCAGACTAAATACACCGGATTTATGAGAAAACAGATATACATAAAGTATCGACACAAATCC
533365 AACAAGTGTCGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACAACAAAATGTCGAT
261 AACAAGTGTCGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACAACAAAATGTCGAT
533430 ACATTTATAACAAGTGTCGATACAAAAAACATCGAAACAC
326 ACATTTATAACAAGTGTCGATACAAAAAACATCGAAACAC
* * *
533470 ATCGGCCTAAATACATCGGTTTATGAGAAAACAAATATACATAAAGTATCAACACAAATTCAACA
1 ATCGACCTAAATACACCGGTTTATGAGAAAA-AAATATACATAAAGTATCAACACAAATCCAACA
* * *
533535 AGTGTCGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACAT
65 AGTGTCGAAACTTTTTGTCCATAATGTATTTTCCAAACCAA-TGCACAAAAAAGTGTCGATACAT
*
533600 TTATAACAAGTGTCGATACTAAAAACATCGAAACAC-ATAGA-TATAATGTAATAGGTAAAATAA
129 TTATAACAAGTGTCGATACCAAAAACATCGAAAC-CTATA-ATTATAATGTAATAGGTAAAATAA
533663 CAATGTAACCAGACTAAATACACC-GATTTATGAGAAAACAGATATACATAAAGTATCGACACAA
192 CAATGTAACCAGACTAAATACACCGGATTTATGAGAAAACAGATATACATAAAGTATCGACACAA
* * *
533727 ATCCAACAAGTGTTGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGT
257 ATCCAACAAGTGTCGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACAACAAAATGT
* *
533792 CGATATATTTATAACAAGTGTCGATACTAAAAACATCGAAACAC
322 CGATACATTTATAACAAGTGTCGATACAAAAAACATCGAAACAC
533836 AT
1 AT
533838 AGATATAATG
Statistics
Matches: 334, Mismatches: 30, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
365 29 0.09
366 213 0.64
367 90 0.27
368 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (365 bp):
ATCGACCTAAATACACCGGTTTATGAGAAAAAAATATACATAAAGTATCAACACAAATCCAACAA
GTGTCGAAACTTTTTGTCCATAATGTATTTTCCAAACCAATGCACAAAAAAGTGTCGATACATTT
ATAACAAGTGTCGATACCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAAATAACAAT
GTAACCAGACTAAATACACCGGATTTATGAGAAAACAGATATACATAAAGTATCGACACAAATCC
AACAAGTGTCGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACAACAAAATGTCGAT
ACATTTATAACAAGTGTCGATACAAAAAACATCGAAACAC
Found at i:533868 original size:200 final size:199
Alignment explanation
Indices: 533476--534069 Score: 712
Period size: 200 Copynumber: 3.0 Consensus size: 199
533466 ACACATCGGC
* * * *
533476 CTAAATACATCGGTTTATGAGAAAACAAATATACATAAAGTATCAACACAAATTCAACAAGTGTC
1 CTAAATACACCGATTTATGAGAAAACAGATATACATAAAGTATCGACACAAA-TCAACAAGTGTC
533541 GATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAA
65 GATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAA
* ** *
533606 CAAGTGTCGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAA
130 CAAGTGTCGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTCACTTTACAATGTAA
533671 CCAGA
195 CCAGA
*
533676 CTAAATACACCGATTTATGAGAAAACAGATATACATAAAGTATCGACACAAATCCAACAAGTGTT
1 CTAAATACACCGATTTATGAGAAAACAGATATACATAAAGTATCGACACAAAT-CAACAAGTGTC
*
533741 GATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATATATTTATAA
65 GATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAA
533806 CAAGTGTCGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTCACTTTACAATGTAA
130 CAAGTGTCGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTCACTTTACAATGTAA
* *
533871 CCGGT
195 CCAGA
* ** * * ** * * ** ** ***
533876 TTAAATTTACTGGTTTTATGAGCTAATAGGTATACATAAAGTATCGACACTTTATTTATTTGTGT
1 CTAAATACAC-CGATTTATGAGAAAACAGATATACATAAAGTATCGACAC-AAATCAACAAGTGT
* * * * * * *
533941 CGATACTTTTTATCCATAATG-AATTCCCAAACTATGTGCACCCATAAAGTGTCGATACATTTAT
64 CGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCA-CGACAAAGTGTCGATACATTTA-
* * * * * *
534005 TAA-AAGTATC-A-ACCCAAATACATCGAGAC-CAAAAATTATAATGTAATAGGTCACTTTACAA
127 TAACAAGTGTCGATA-CTAAAAACATCGAAACACATAGA-TATAATGTAATAGGTCACTTTACAA
534066 TGTA
190 TGTA
534070 TCCGGTTTAA
Statistics
Matches: 344, Mismatches: 43, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
199 6 0.02
200 251 0.73
201 82 0.24
202 5 0.01
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (199 bp):
CTAAATACACCGATTTATGAGAAAACAGATATACATAAAGTATCGACACAAATCAACAAGTGTCG
ATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAAC
AAGTGTCGATACTAAAAACATCGAAACACATAGATATAATGTAATAGGTCACTTTACAATGTAAC
CAGA
Found at i:534096 original size:200 final size:201
Alignment explanation
Indices: 533536--534286 Score: 659
Period size: 200 Copynumber: 3.7 Consensus size: 201
533526 AATTCAACAA
* * * * *
533536 GTGTCGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCA-CGACAAAGTGTCGATACAT
1 GTGTCGATACTTTTTGTCCATAATG-AATTCCCAAACCATGTGCACCCATAAAGTGTCGATACAT
* * * * * * * ** *
533600 TTA-TAACAAGTGTCGATA-CTAAAAACATCGAAACACATAGA-TATAATGTAATAGGTAAAATA
65 TTATTAA-AAGTATC-A-ACCCAAATACATCGAGAC-CAAAAATTATAATGTAATAGGTCACTTT
* ** ** * * * * *
533662 ACAATGTAACCAGACTAAATACA-C-CGATTTATGAGAAAACAGATATACATAAAGTATCGACAC
126 ACAATGTAACCGGTTTAAATTTATCTAGTTTTATGAGCAAATAGGTATACATAAAGTATCGACAC
*** * ***
533725 -AAATCCAACAA
191 TTTTTGC-ATTT
* * * * * * *
533736 GTGTTGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCA-CGACAAAGTGTCGATATAT
1 GTGTCGATACTTTTTGTCCATAATG-AATTCCCAAACCATGTGCACCCATAAAGTGTCGATACAT
* * * * * *
533800 TTA-TAACAAGTGTCGATA-CTAAAAACATCGAAACACATAGA-TATAATGTAATAGGTCACTTT
65 TTATTAA-AAGTATC-A-ACCCAAATACATCGAGAC-CAAAAATTATAATGTAATAGGTCACTTT
* *
533862 ACAATGTAACCGGTTTAAATTTA-CTGGTTTTATGAGCTAATAGGTATACATAAAGTATCGACAC
126 ACAATGTAACCGGTTTAAATTTATCTAGTTTTATGAGCAAATAGGTATACATAAAGTATCGACAC
*
533926 TTTATT-TATTT
191 TTT-TTGCATTT
* *
533937 GTGTCGATACTTTTTATCCATAATGAATTCCCAAACTATGTGCACCCATAAAGTGTCGATACATT
1 GTGTCGATACTTTTTGTCCATAATGAATTCCCAAACCATGTGCACCCATAAAGTGTCGATACATT
534002 TATTAAAAGTATCAACCCAAATACATCGAGACCAAAAATTATAATGTAATAGGTCACTTTACAAT
66 TATTAAAAGTATCAACCCAAATACATCGAGACCAAAAATTATAATGTAATAGGTCACTTTACAAT
* * * * *
534067 GTATCCGGTTTAAATTTATC-AGTTTTATGAGCAAATAGGTCTACGTAATGTATCGATACTTTTT
131 GTAACCGGTTTAAATTTATCTAGTTTTATGAGCAAATAGGTATACATAAAGTATCGACACTTTTT
534131 GCATTT
196 GCATTT
* * * * * *
534137 GTGTCGATACTTTATGTCCATAATGAA-TGCCAAACGATGTCCACGCATAAAGTGTCTATACATT
1 GTGTCGATACTTTTTGTCCATAATGAATTCCCAAACCATGTGCACCCATAAAGTGTCGATACATT
* * * *** *
534201 TATAAAAAGTATTGACCCCAAATACATCGAGACTGGAAATTATAATGTAATAGGTCAATTTACAA
66 TATTAAAAGTA-TCAACCCAAATACATCGAGACCAAAAATTATAATGTAATAGGTCACTTTACAA
*
534266 TGTAACCGGTTGAAATTTATC
130 TGTAACCGGTTTAAATTTATC
534287 GGTGTAAATA
Statistics
Matches: 478, Mismatches: 63, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
199 49 0.10
200 342 0.72
201 83 0.17
202 3 0.01
203 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (201 bp):
GTGTCGATACTTTTTGTCCATAATGAATTCCCAAACCATGTGCACCCATAAAGTGTCGATACATT
TATTAAAAGTATCAACCCAAATACATCGAGACCAAAAATTATAATGTAATAGGTCACTTTACAAT
GTAACCGGTTTAAATTTATCTAGTTTTATGAGCAAATAGGTATACATAAAGTATCGACACTTTTT
GCATTT
Found at i:534305 original size:200 final size:199
Alignment explanation
Indices: 533841--534330 Score: 662
Period size: 200 Copynumber: 2.5 Consensus size: 199
533831 AACACATAGA
*
533841 TATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTA-CTGGTTTTATGAGCTAATAG
1 TATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTATC-GGTTTTATGAGCAAATAG
* * * *
533905 GTATACATAAAGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCA
65 GTCTACATAATGTATCGACACTTT-TTCATTTGTGTCGATACTTTATATCCATAATGAATTCCCA
* * *
533970 AACTATGTGCACCCATAAAGTGTCGATACATTTATTAAAAGTATCAACCCAAATACATCGAGACC
129 AACGATGTCCACCCATAAAGTGTCGATACATTTATAAAAAGTATCAACCCAAATACATCGAGACC
534035 AAAAAT
194 AAAAAT
* *
534041 TATAATGTAATAGGTCACTTTACAATGTATCCGGTTTAAATTTATCAGTTTTATGAGCAAATAGG
1 TATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTATCGGTTTTATGAGCAAATAGG
* * * *
534106 TCTACGTAATGTATCGATACTTTTTGCATTTGTGTCGATACTTTATGTCCATAATGAA-TGCCAA
66 TCTACATAATGTATCGACACTTTTT-CATTTGTGTCGATACTTTATATCCATAATGAATTCCCAA
* * * * *
534170 ACGATGTCCACGCATAAAGTGTCTATACATTTATAAAAAGTATTGACCCCAAATACATCGAGACT
130 ACGATGTCCACCCATAAAGTGTCGATACATTTATAAAAAGTA-TCAACCCAAATACATCGAGACC
**
534235 GGAAAT
194 AAAAAT
* * ** *
534241 TATAATGTAATAGGTCAATTTACAATGTAACCGGTTGAAATTTATCGGTGTAAAT-AGAAAATAG
1 TATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTATCGGT-TTTATGAGCAAATAG
* *
534305 GTCAACATAATGTGTCGACACTTTTT
65 GTCTACATAATGTATCGACACTTTTT
534331 AAATTCATGT
Statistics
Matches: 254, Mismatches: 32, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
199 44 0.17
200 206 0.81
201 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (199 bp):
TATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTATCGGTTTTATGAGCAAATAGG
TCTACATAATGTATCGACACTTTTTCATTTGTGTCGATACTTTATATCCATAATGAATTCCCAAA
CGATGTCCACCCATAAAGTGTCGATACATTTATAAAAAGTATCAACCCAAATACATCGAGACCAA
AAAT
Found at i:538159 original size:87 final size:87
Alignment explanation
Indices: 538058--538220 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
538048 AAATAGGTCA
* *
538058 ATATAAGCGCTACCTATTACATTATATAAGTGCTACATAATATGTTATTGTACTTGGTAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACATAATATGTTATTGTACTTGATAATATTT
538123 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* *
538145 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACATAATATGTTATTGTACTTGATAATATTT
538210 CCGGTTAAATG
66 CCGGTTAAATG
538221 ATATAACATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACATAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:538192 original size:23 final size:23
Alignment explanation
Indices: 538142--538186 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
538132 TGCCTATTTT
*
538142 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
538165 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
538187 TGTTATTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:539495 original size:21 final size:21
Alignment explanation
Indices: 539471--539515 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
539461 ATTCACCATT
539471 GGGATCACGATTTTCATCCTA
1 GGGATCACGATTTTCATCCTA
*
539492 GGGATCGCGATTTTCATCCTA
1 GGGATCACGATTTTCATCCTA
539513 GGG
1 GGG
539516 TTTGCGGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (21 bp):
GGGATCACGATTTTCATCCTA
Found at i:542408 original size:19 final size:18
Alignment explanation
Indices: 542376--542414 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
542366 TGTTAAATTA
*
542376 TATTATGTTAATATTTAT
1 TATTATGTTAATATTAAT
*
542394 TATTAATGTTTATATTAAT
1 TATT-ATGTTAATATTAAT
542413 TA
1 TA
542415 AGATTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
TATTATGTTAATATTAAT
Found at i:543149 original size:14 final size:15
Alignment explanation
Indices: 543122--543150 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
543112 ATGATGTGGA
543122 CCTTGAAGACATGCC
1 CCTTGAAGACATGCC
543137 CCTTGAA-ACATGCC
1 CCTTGAAGACATGCC
543151 TTCTTACGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.21
Consensus pattern (15 bp):
CCTTGAAGACATGCC
Found at i:547021 original size:61 final size:61
Alignment explanation
Indices: 546922--547062 Score: 219
Period size: 61 Copynumber: 2.3 Consensus size: 61
546912 ATTCGACATG
* * *
546922 GTTCCTTCTTGGTGAGGAACACTAGTCGTTCTTGAAGGATTGTGAATATGAAGACAATGTT
1 GTTCCTTCTTGCTGAGGAAAACTAGTCGTTCTTAAAGGATTGTGAATATGAAGACAATGTT
* * *
546983 GTTCCTTCTAGCTGAGGAAAACTAGTCGTTCTTAAAGGATTTTGAATTTGAAGACAATGTT
1 GTTCCTTCTTGCTGAGGAAAACTAGTCGTTCTTAAAGGATTGTGAATATGAAGACAATGTT
*
547044 GTTCCTTTTTGCTGAGGAA
1 GTTCCTTCTTGCTGAGGAA
547063 GTCTAATTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 72 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (61 bp):
GTTCCTTCTTGCTGAGGAAAACTAGTCGTTCTTAAAGGATTGTGAATATGAAGACAATGTT
Found at i:547598 original size:66 final size:65
Alignment explanation
Indices: 547520--547685 Score: 165
Period size: 67 Copynumber: 2.5 Consensus size: 65
547510 TCTCAAGCAC
* * * *
547520 GACAAAACTTTATTTCAAAAAAAACAATCTCAAATGTT-AGTGTCTTAAGGAATATTGTCTCAAG
1 GACAAAA-TTTATTT-AAAAAAAACAATCTCAAATGTTCA-TGTCTTAAGGAAGATTATCTAAAA
547584 TGA
63 TGA
* * *
547587 GACGAAATTTATTTTTAAGAAAAAA-AATATCAAGTGTTCATGTCTTAAGGAAGATTATCTAAAA
1 GACAAAATTTA--TTTAA-AAAAAACAATCTCAAATGTTCATGTCTTAAGGAAGATTATCTAAAA
547651 TGA
63 TGA
* * *
547654 GACAAAATTTGTATTGAGAAAAACAATCTCAA
1 GACAAAATTTAT-TTAAAAAAAACAATCTCAA
547686 GTGAAAACAA
Statistics
Matches: 81, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
65 6 0.07
66 14 0.17
67 51 0.63
68 10 0.12
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.31
Consensus pattern (65 bp):
GACAAAATTTATTTAAAAAAAACAATCTCAAATGTTCATGTCTTAAGGAAGATTATCTAAAATGA
Found at i:547610 original size:67 final size:66
Alignment explanation
Indices: 547539--547685 Score: 170
Period size: 67 Copynumber: 2.2 Consensus size: 66
547529 TTATTTCAAA
* * * * * * *
547539 AAAAACAATCTCAAATGTT-AGTGTCTTAAGGAATATTGTCTCAAGTGAGACGAAATTTATTTTT
1 AAAAACAATCTCAAATGTTCA-TGTCTTAAGGAAGATTATCTAAAATGAGACAAAATTT-GTATT
547603 AAG
64 AAG
* * * *
547606 AAAAAAAATATCAAGTGTTCATGTCTTAAGGAAGATTATCTAAAATGAGACAAAATTTGTATTGA
1 AAAAACAATCTCAAATGTTCATGTCTTAAGGAAGATTATCTAAAATGAGACAAAATTTGTATTAA
547671 G
66 G
547672 AAAAACAATCTCAA
1 AAAAACAATCTCAA
547686 GTGAAAACAA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
66 17 0.26
67 48 0.73
68 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (66 bp):
AAAAACAATCTCAAATGTTCATGTCTTAAGGAAGATTATCTAAAATGAGACAAAATTTGTATTAA
G
Found at i:552319 original size:21 final size:21
Alignment explanation
Indices: 552293--552348 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
552283 TATTTAGGTG
552293 TTATATAAGCTTAAGGAAAGC
1 TTATATAAGCTTAAGGAAAGC
*
552314 TTATATAAGCTTAAGGAAAGT
1 TTATATAAGCTTAAGGAAAGC
552335 TTATATAAGCTTAA
1 TTATATAAGCTTAA
552349 AACTATAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (21 bp):
TTATATAAGCTTAAGGAAAGC
Found at i:553241 original size:2 final size:2
Alignment explanation
Indices: 553234--553263 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
553224 AGTAGATGAG
553234 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
553264 AGTTAATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:557085 original size:44 final size:44
Alignment explanation
Indices: 557017--557149 Score: 194
Period size: 44 Copynumber: 3.0 Consensus size: 44
557007 CTTGTATTCA
** * *
557017 TGGATGATATAAGCCTTCACAAATGCCCCAACATTTATCATTTC
1 TGGATGATATGGGCCTTCAAAAATGCCCCAACACTTATCATTTC
* * *
557061 TGGATGATATGGGCCTTTAAAAATGCCCTAACACTTATCATTTT
1 TGGATGATATGGGCCTTCAAAAATGCCCCAACACTTATCATTTC
*
557105 TGAATGATATGGGCCTTCAAAAATGCCCCAACACTTATCATTTC
1 TGGATGATATGGGCCTTCAAAAATGCCCCAACACTTATCATTTC
557149 T
1 T
557150 CGGTCCATCA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 78 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
TGGATGATATGGGCCTTCAAAAATGCCCCAACACTTATCATTTC
Found at i:560058 original size:30 final size:30
Alignment explanation
Indices: 559999--560058 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
559989 ATGCATGTGA
* *
559999 AAATGTTCAAATAAATGCATAATAGAATAT
1 AAATATTCAAATAAATGCATAATAAAATAT
560029 AAATATTCAAATACATATGCA-AA-AAAATAT
1 AAATATTCAAATA-A-ATGCATAATAAAATAT
560059 TGATCCCAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 18 0.69
31 3 0.12
32 5 0.19
ACGTcount: A:0.57, C:0.08, G:0.07, T:0.28
Consensus pattern (30 bp):
AAATATTCAAATAAATGCATAATAAAATAT
Found at i:560906 original size:17 final size:17
Alignment explanation
Indices: 560884--560918 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
560874 GGTGGTCGTT
560884 CTACGGTACACTACATG
1 CTACGGTACACTACATG
560901 CTACGGTACACTACATG
1 CTACGGTACACTACATG
560918 C
1 C
560919 ATGGTTTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (17 bp):
CTACGGTACACTACATG
Found at i:575696 original size:15 final size:15
Alignment explanation
Indices: 575676--575726 Score: 102
Period size: 15 Copynumber: 3.4 Consensus size: 15
575666 GCTCCGTTTC
575676 TGATATAATTTATGT
1 TGATATAATTTATGT
575691 TGATATAATTTATGT
1 TGATATAATTTATGT
575706 TGATATAATTTATGT
1 TGATATAATTTATGT
575721 TGATAT
1 TGATAT
575727 GTATCTGAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (15 bp):
TGATATAATTTATGT
Found at i:577852 original size:24 final size:24
Alignment explanation
Indices: 577825--577932 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
577815 AATTATTTTA
*
577825 TCTGATTTCCGACTTGAATTCTGT
1 TCTGATTTCTGACTTGAATTCTGT
* * *
577849 TCTGA-TACATAACCTGAATTCTGT
1 TCTGATTTC-TGACTTGAATTCTGT
*
577873 TCTGATTTCTGA-TCTGGATTCTGT
1 TCTGATTTCTGACT-TGAATTCTGT
* * *
577897 TCTGATATCTG-TTCTGAATTTTGT
1 TCTGATTTCTGACT-TGAATTCTGT
*
577921 TTTGATTTCTGA
1 TCTGATTTCTGA
577933 TATCTCCGTT
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
23 2 0.03
24 62 0.94
25 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGACTTGAATTCTGT
Found at i:577877 original size:12 final size:12
Alignment explanation
Indices: 577862--577931 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
577852 GATACATAAC
577862 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
577874 CTGATTTCTGAT
1 CTGAATTCTGTT
*
577886 CTGGATTCTGTT
1 CTGAATTCTGTT
577898 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
*
577910 CTGAATTTTGTT
1 CTGAATTCTGTT
* *
577922 TTGATTTCTG
1 CTGAATTCTG
577932 ATATCTCCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.53
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:578097 original size:2 final size:2
Alignment explanation
Indices: 578090--578130 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
578080 GGGATGAGGG
578090 TA 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 TA T
578131 GTTTTAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:580023 original size:13 final size:13
Alignment explanation
Indices: 580019--580048 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
580009 CCGTTGACCC
580019 GACCCGACCCGTT
1 GACCCGACCCGTT
580032 GACCCGACCCGTT
1 GACCCGACCCGTT
580045 GACC
1 GACC
580049 GTTGACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:580042 original size:18 final size:18
Alignment explanation
Indices: 579997--580042 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
579987 TCATAACCCA
*
579997 ACCCGACCCAACCCGTTG
1 ACCCGACCCGACCCGTTG
580015 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
580033 ACCCGACCCG
1 ACCCGACCCG
580043 TTGACCGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.52, G:0.20, T:0.09
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:582525 original size:24 final size:24
Alignment explanation
Indices: 582498--582605 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
582488 AATTATTTTA
*
582498 TCTGATTTCCGACTTGAATTCTGT
1 TCTGATTTCTGACTTGAATTCTGT
* *
582522 TCTGA-TACATGACCTGAATTCTGT
1 TCTGATTTC-TGACTTGAATTCTGT
* *
582546 TTTGATTTCTGA-TCTGGATTCTGT
1 TCTGATTTCTGACT-TGAATTCTGT
* * *
582570 TCTGATATCTG-TTCTGAATTCTAT
1 TCTGATTTCTGACT-TGAATTCTGT
*
582594 TTTGATTTCTGA
1 TCTGATTTCTGA
582606 TATCTCCGTT
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
23 2 0.03
24 62 0.94
25 2 0.03
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGACTTGAATTCTGT
Found at i:582555 original size:12 final size:12
Alignment explanation
Indices: 582540--582604 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
582530 ATGACCTGAA
582540 TTCTGTTTTGAT
1 TTCTGTTTTGAT
* *
582552 TTCTGATCTGGA-
1 TTCTG-TTTTGAT
*
582564 TTCTGTTCTGAT
1 TTCTGTTTTGAT
* * *
582576 ATCTGTTCTGAA
1 TTCTGTTTTGAT
*
582588 TTCTATTTTGAT
1 TTCTGTTTTGAT
582600 TTCTG
1 TTCTG
582605 ATATCTCCGT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
11 3 0.08
12 32 0.82
13 4 0.10
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.55
Consensus pattern (12 bp):
TTCTGTTTTGAT
Found at i:582567 original size:48 final size:48
Alignment explanation
Indices: 582515--582606 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
582505 TCCGACTTGA
*
582515 ATTCTGTTCTGATA-CATGACCTGAATTCTGTTTTGATTTCTGATCTGG
1 ATTCTGTTCTGATATC-TGACCTGAATTCTATTTTGATTTCTGATCTGG
**
582563 ATTCTGTTCTGATATCTGTTCTGAATTCTATTTTGATTTCTGAT
1 ATTCTGTTCTGATATCTGACCTGAATTCTATTTTGATTTCTGAT
582607 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.50
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTGACCTGAATTCTATTTTGATTTCTGATCTGG
Found at i:582780 original size:2 final size:2
Alignment explanation
Indices: 582775--582810 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
582765 GGTATATATA
582775 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
582811 CTTTAAAAGA
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:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:585293 original size:7 final size:7
Alignment explanation
Indices: 585281--585306 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
585271 TATAAATTAT
585281 TATTTTA
1 TATTTTA
585288 TATTTTA
1 TATTTTA
585295 TATTTTA
1 TATTTTA
585302 TATTT
1 TATTT
585307 ATCTATAAAA
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTTTA
Found at i:590644 original size:29 final size:29
Alignment explanation
Indices: 590610--590680 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
590600 AAAAATACAT
*
590610 ATATTTTTAAAACAGTAACAATTTAGAAC
1 ATATTTTTAAAACAATAACAATTTAGAAC
590639 ATATTTTTAAAACAATAACAATTTAGAAC
1 ATATTTTTAAAACAATAACAATTTAGAAC
590668 ATATTTTTAAAAC
1 ATATTTTTAAAAC
590681 CATATTAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (29 bp):
ATATTTTTAAAACAATAACAATTTAGAAC
Found at i:592796 original size:5 final size:5
Alignment explanation
Indices: 592786--592810 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
592776 CTAATTTTTT
592786 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
592811 TAACTTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:592848 original size:28 final size:30
Alignment explanation
Indices: 592799--592861 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
592789 TAATATAATA
592799 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
*
592829 TAATAT-A-ATATAATTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
592857 TAATA
1 TAATA
592862 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:592864 original size:21 final size:21
Alignment explanation
Indices: 592838--592881 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
592828 CTAATATAAT
592838 ATAATTTAAACTAACAAACTA
1 ATAATTTAAACTAACAAACTA
*
592859 ATAATTTATACTAACAAACTA
1 ATAATTTAAACTAACAAACTA
592880 AT
1 AT
592882 TAACTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAATTTAAACTAACAAACTA
Found at i:592868 original size:28 final size:28
Alignment explanation
Indices: 592803--592868 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
592793 ATAATATAAT
592803 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
*
592831 AT-ATAATATAATTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
592859 ATAATTTATA
1 ATAATATATA
592869 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:594985 original size:30 final size:30
Alignment explanation
Indices: 594883--594987 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 30
594873 AGTTGATGAT
* * *
594883 GTGACAGATACACGTAGACTAAATGTTGAC
1 GTGACAGATTCACATAGACTAAATATTGAC
* ** * *
594913 TTGACAGAACCACATAAACTAAATACTGAC
1 GTGACAGATTCACATAGACTAAATATTGAC
**
594943 GTGGTAGATTCACATAGACTAAATATTGAC
1 GTGACAGATTCACATAGACTAAATATTGAC
594973 GTGACATG-TTCACAT
1 GTGACA-GATTCACAT
594988 GTGACGCCAC
Statistics
Matches: 58, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 57 0.98
31 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (30 bp):
GTGACAGATTCACATAGACTAAATATTGAC
Found at i:597521 original size:30 final size:30
Alignment explanation
Indices: 597485--597598 Score: 174
Period size: 30 Copynumber: 3.8 Consensus size: 30
597475 GTTTTATGTC
*
597485 CACATTTAAGATGTTCATGCATACAGTCAT
1 CACATTTAAGATGATCATGCATACAGTCAT
597515 CACATTTAAGATGATCATGCATACAGTCAT
1 CACATTTAAGATGATCATGCATACAGTCAT
* *
597545 CACATTTAAGATGATCATGCATAGAATCAT
1 CACATTTAAGATGATCATGCATACAGTCAT
* *
597575 CATATTTAAAGATGTTCATGCATA
1 CACATTT-AAGATGATCATGCATA
597599 TAACCATCTT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 63 0.81
31 15 0.19
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (30 bp):
CACATTTAAGATGATCATGCATACAGTCAT
Found at i:600173 original size:2 final size:2
Alignment explanation
Indices: 600166--600193 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
600156 ACCATAAACG
600166 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
600194 TATTCTTTTC
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):
AT
Found at i:600766 original size:8 final size:8
Alignment explanation
Indices: 600753--600777 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
600743 GAGTATCTCG
600753 AAATTTCA
1 AAATTTCA
600761 AAATTTCA
1 AAATTTCA
600769 AAATTTCA
1 AAATTTCA
600777 A
1 A
600778 CTCGACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (8 bp):
AAATTTCA
Found at i:602516 original size:13 final size:13
Alignment explanation
Indices: 602498--602523 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
602488 TCAAATGGAA
602498 AAAAATTAAAATT
1 AAAAATTAAAATT
602511 AAAAATTAAAATT
1 AAAAATTAAAATT
602524 TTAAAAGTAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATTAAAATT
Found at i:603575 original size:18 final size:17
Alignment explanation
Indices: 603535--603573 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
603525 GAAAAAAAAT
603535 CCCCCGATTCCAAGCTA
1 CCCCCGATTCCAAGCTA
603552 CCCCCGATTCCAAGCTA
1 CCCCCGATTCCAAGCTA
603569 CCCCC
1 CCCCC
603574 CGCTGCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.21, C:0.54, G:0.10, T:0.15
Consensus pattern (17 bp):
CCCCCGATTCCAAGCTA
Found at i:604681 original size:106 final size:106
Alignment explanation
Indices: 604496--605965 Score: 2374
Period size: 106 Copynumber: 13.9 Consensus size: 106
604486 TATTGTTCCA
* * * * * *
604496 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTTTGGAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
* *
604561 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGG
66 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * * *
604602 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
* *
604667 CAGCGATCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
604708 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
604773 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
604814 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
604879 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
*
604920 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
* *
604985 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * *
605026 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
605091 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
605132 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
* * * *
605197 CGGCGGTCCCTTCATCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * *
605238 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
605303 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
605344 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
* *
605409 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
605450 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
*
605514 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * * *
605555 AGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTCGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
*
605619 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * *
605660 AGTCAAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAGATTGAGAAA-TGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
*
605724 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * **
605765 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAA-TGTTCATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
*
605829 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* * * *
605870 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAGATTGAGAAGTTGTTTGTTGACAAT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
* * * *
605935 CAGCCGCCCCTTCGTCATGAAGTTGAGCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
605966 GAATTGGATA
Statistics
Matches: 1282, Mismatches: 80, Indels: 4
0.94 0.06 0.00
Matches are distributed among these distances:
105 404 0.32
106 878 0.68
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
Found at i:606131 original size:361 final size:359
Alignment explanation
Indices: 605660--606325 Score: 1089
Period size: 361 Copynumber: 1.8 Consensus size: 359
605650 CGTTGTCTAG
* * *
605660 AGTCAAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAGATTGAGAAATGTTTGTTGACAACC
1 AGTCAAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGAGATTGAGAAATGTTTATTGACAACC
*
605725 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGT
*
605790 TGAAATTGACTCTGAAATCGAGAAATGTTCATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
131 CGAAATTGACTCTGAAATCGAGAAATGTTCATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
*
605855 ACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAGATTGAGAAG
196 ACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAA-
* * * *
605920 TTGTTTGTTGACAATCAGCCGCCCCTTCGTCATGAAGTTGAGCTTGGAATTGGATATCCTTCCTC
260 ATGTTTATTGACAACCAGCCGCCCCTTCGTCATGAAGTTGAACTTGGAATTGGATATCCTTCCTC
605985 GTGAAGTTGAAATCCAAGTAAGTTGTATTGTTCCA
325 GTGAAGTTGAAATCCAAGTAAGTTGTATTGTTCCA
* * * * *
606020 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGGTTTGGGAAATTGTTTATTGACAAC
1 AGTCAAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGAGATTGAGAAA-TGTTTATTGACAAC
*
606085 CAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAG
* * * *
606150 TCGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
130 TCGAAATTGACTCTGAAATCGAGAAATGTTCATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
* *
606215 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA
195 AACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAA
* * *
606280 ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
260 ATGTTTATTGACAACCAGCCGCCCCTTCGTCATGAAGTTGAACTTG
606326 CGTTGTCTGG
Statistics
Matches: 280, Mismatches: 25, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
360 82 0.29
361 198 0.71
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (359 bp):
AGTCAAATATCCTCCGTCGTGAAGTTGAAATTGACTCTGAGATTGAGAAATGTTTATTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGT
CGAAATTGACTCTGAAATCGAGAAATGTTCATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
ACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAA
TGTTTATTGACAACCAGCCGCCCCTTCGTCATGAAGTTGAACTTGGAATTGGATATCCTTCCTCG
TGAAGTTGAAATCCAAGTAAGTTGTATTGTTCCA
Found at i:606219 original size:105 final size:105
Alignment explanation
Indices: 606020--606578 Score: 938
Period size: 105 Copynumber: 5.3 Consensus size: 105
606010 TATTGTTCCA
* * ***
606020 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGGTTTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTATTGACAAC
*
606085 CAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
606126 AGTCCAATATCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACC
606191 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
606231 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACC
606296 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
606336 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAAC
* * * *
606401 CAGCGGTCCCTTCATCGTGAAGTTGAATTTGTGTTGTATGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
606442 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACC
*
606507 AGCGGTCCCTTCGTCGTGAAGTTGCACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
606547 AGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATT
606579 TGACTCTAAA
Statistics
Matches: 425, Mismatches: 27, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
105 284 0.67
106 141 0.33
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:606269 original size:211 final size:211
Alignment explanation
Indices: 606020--606578 Score: 949
Period size: 211 Copynumber: 2.6 Consensus size: 211
606010 TATTGTTCCA
* * *** *
606020 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGGTTTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTATTGACAAC
*
606085 CAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* * * *
606150 TCGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
130 TTGAAATTGGCTATGAAATTGGGAAGATATTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTT
*
606214 GAACTTGCGTTGTCTGG
195 GAACTTGCGTTGTATGG
606231 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACC
606296 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
606361 TGAAATTGGCTATGAAATTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTG
131 TGAAATTGGCTATGAAATTGGGAAGATATTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTG
* *
606426 AATTTGTGTTGTATGG
196 AACTTGCGTTGTATGG
*
606442 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACC
*
606507 AGCGGTCCCTTCGTCGTGAAGTTGCACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
606572 TGAAATT
131 TGAAATT
606579 TGACTCTAAA
Statistics
Matches: 330, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
210 101 0.31
211 229 0.69
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (211 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTATGAAATTGGGAAGATATTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTG
AACTTGCGTTGTATGG
Found at i:608393 original size:26 final size:25
Alignment explanation
Indices: 608339--608390 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
608329 TTGATGAGAC
*
608339 ATGTGAATGTAAAAAAAGGAAAACTA
1 ATGTGAATGTAAAAAAA-GAAAACAA
*
608365 ATGTGAATGTAAAGAAAA-ATAACAA
1 ATGTGAATGTAAA-AAAAGAAAACAA
608390 A
1 A
608391 ATGCATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 6 0.26
26 13 0.57
27 4 0.17
ACGTcount: A:0.60, C:0.04, G:0.17, T:0.19
Consensus pattern (25 bp):
ATGTGAATGTAAAAAAAGAAAACAA
Found at i:610145 original size:13 final size:13
Alignment explanation
Indices: 610127--610152 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
610117 ATCAAATGGA
610127 AAAAATTAAAATT
1 AAAAATTAAAATT
610140 AAAAATTAAAATT
1 AAAAATTAAAATT
610153 TTAAAAGTAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATTAAAATT
Found at i:611201 original size:18 final size:17
Alignment explanation
Indices: 611163--611202 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
611153 CGAAAAAAAT
611163 CCCCCGATTCCAAGCTA
1 CCCCCGATTCCAAGCTA
611180 CCCCCGATTCCAAGCTA
1 CCCCCGATTCCAAGCTA
611197 CCCCCG
1 CCCCCG
611203 CTGCCTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.53, G:0.12, T:0.15
Consensus pattern (17 bp):
CCCCCGATTCCAAGCTA
Found at i:611553 original size:7 final size:7
Alignment explanation
Indices: 611541--611575 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
611531 CTTCATCTTT
611541 TACCTTC
1 TACCTTC
611548 TACCTTC
1 TACCTTC
611555 TACCTTC
1 TACCTTC
*
611562 TACGTTC
1 TACCTTC
611569 TACCTTC
1 TACCTTC
611576 AAACTCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.14, C:0.40, G:0.03, T:0.43
Consensus pattern (7 bp):
TACCTTC
Found at i:615703 original size:29 final size:29
Alignment explanation
Indices: 615671--615852 Score: 142
Period size: 30 Copynumber: 6.1 Consensus size: 29
615661 ATCGGGTGAC
* **
615671 ATTTTAGGAA-TTAATTTGAAATGGGTGCT
1 ATTTT-GGAATTTAATTCGAAAAAGGTGCT
* * **
615700 ATTTCAGGAATTTAATTCTAAAAAAAGGTTTT
1 ATTT-TGGAATTTAATTC--GAAAAAGGTGCT
615732 ATTTTGAGAATTTAATTCG--AAA-GTGCT
1 ATTTTG-GAATTTAATTCGAAAAAGGTGCT
*
615759 ATTTTTGGAATTTAATTCGAAAAAAGTGCT
1 A-TTTTGGAATTTAATTCGAAAAAGGTGCT
615789 ATTTTGGGAATTTAATTCGAAAAAAGGTGCT
1 ATTTT-GGAATTTAATTCG-AAAAAGGTGCT
**
615820 ATTTTGGTAA-TT-ATTTTAAAAAGGGTGCT
1 ATTTTGG-AATTTAATTCGAAAAA-GGTGCT
615849 ATTT
1 ATTT
615853 CTGTAAAATG
Statistics
Matches: 126, Mismatches: 14, Indels: 26
0.76 0.08 0.16
Matches are distributed among these distances:
27 16 0.13
28 13 0.10
29 28 0.22
30 29 0.23
31 18 0.14
32 22 0.17
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (29 bp):
ATTTTGGAATTTAATTCGAAAAAGGTGCT
Done.