Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold23
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: 3824748
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 177433 characters in sequence are not A, C, G, or T
File 12 of 14
Found at i:3107182 original size:34 final size:35
Alignment explanation
Indices: 3107125--3107191 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3107115 CAAACACAAG
*
3107125 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3107160 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3107192 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3107183 original size:14 final size:14
Alignment explanation
Indices: 3107160--3107199 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3107150 ACAGAAAAGT
*
3107160 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
3107174 AAATCATTTTACGG
1 AAAACATTTTACAG
3107188 AAAACATTTTAC
1 AAAACATTTTAC
3107200 TGGCAATCAN
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:3112484 original size:14 final size:16
Alignment explanation
Indices: 3112444--3112487 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
3112434 TTTTCAACAT
*
3112444 AAATTAAACTTAATTCA
1 AAATTAAA-TAAATTCA
3112461 AAATTAAATAAATT-A
1 AAATTAAATAAATTCA
3112476 AAA-TAAATAAAT
1 AAATTAAATAAAT
3112488 ATGGCTTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.35
15 4 0.15
16 5 0.19
17 8 0.31
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTAAATAAATTCA
Found at i:3115853 original size:16 final size:16
Alignment explanation
Indices: 3115832--3115864 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3115822 TTCGCTGTAT
3115832 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
3115848 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
3115864 T
1 T
3115865 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:3121192 original size:37 final size:37
Alignment explanation
Indices: 3121151--3121350 Score: 110
Period size: 37 Copynumber: 5.4 Consensus size: 37
3121141 AAGGCAAAAA
*
3121151 AAAAATGAACATGGGAGATTCCCTGCAAAGCAAAGAC
1 AAAAATGAACATGAGAGATTCCCTGCAAAGCAAAGAC
* * * *
3121188 AAAAATAAACAAGAGTGATTCCCTGCCAAAAGC-AA-TC
1 AAAAATGAACATGAGAGATTCCCTG-C-AAAGCAAAGAC
* * * *
3121225 AATAATGAATAGTGA-A-ATTCCCTACAGAGCAAAGAC
1 AAAAATGAACA-TGAGAGATTCCCTGCAAAGCAAAGAC
* * * * *
3121261 ATAAATGAACATAAGTGATTCTCTGCCAAAAGC-AA-CC
1 AAAAATGAACATGAGAGATTCCCTG-C-AAAGCAAAGAC
* * * *
3121298 AAGAATGAACAGTGA-AG-TTTCCTGCCAAGCAAAGAT
1 AAAAATGAACA-TGAGAGATTCCCTGCAAAGCAAAGAC
*
3121334 AAAAATAAACAGTGAGA
1 AAAAATGAACA-TGAGA
3121351 TACCCTATAA
Statistics
Matches: 117, Mismatches: 33, Indels: 26
0.66 0.19 0.15
Matches are distributed among these distances:
34 8 0.07
35 8 0.07
36 34 0.29
37 48 0.41
38 10 0.09
39 9 0.08
ACGTcount: A:0.47, C:0.18, G:0.17, T:0.17
Consensus pattern (37 bp):
AAAAATGAACATGAGAGATTCCCTGCAAAGCAAAGAC
Found at i:3121256 original size:73 final size:72
Alignment explanation
Indices: 3121154--3121344 Score: 213
Period size: 73 Copynumber: 2.6 Consensus size: 72
3121144 GCAAAAAAAA
* * *
3121154 AATGAACATGGGAGATTCCCTGCAAAGCAAAGACAAAAATAAACA-AGAGTGATTCCCTGCCAAA
1 AATGAACA-GTGAAATTCCCTAC-AAGCAAAGACAAAAATAAACATA-AGTGATTCCCTGCCAAA
* *
3121218 AGCAATCAAT
63 AGCAACCAAG
* * * *
3121228 AATGAATAGTGAAATTCCCTACAGAGCAAAGACATAAATGAACATAAGTGATTCTCTGCCAAAAG
1 AATGAACAGTGAAATTCCCTACA-AGCAAAGACAAAAATAAACATAAGTGATTCCCTGCCAAAAG
3121293 CAACCAAG
65 CAACCAAG
* * * *
3121301 AATGAACAGTGAAGTTTCCTGCCAAGCAAAGATAAAAATAAACA
1 AATGAACAGTGAAATTCCCT-ACAAGCAAAGACAAAAATAAACA
3121345 GTGAGATACC
Statistics
Matches: 98, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
72 1 0.01
73 87 0.89
74 10 0.10
ACGTcount: A:0.47, C:0.19, G:0.17, T:0.18
Consensus pattern (72 bp):
AATGAACAGTGAAATTCCCTACAAGCAAAGACAAAAATAAACATAAGTGATTCCCTGCCAAAAGC
AACCAAG
Found at i:3121662 original size:12 final size:13
Alignment explanation
Indices: 3121642--3121688 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
3121632 TTAAAACAAA
3121642 TCAAATTTAATTT
1 TCAAATTTAATTT
3121655 TC-AATTTAAGTTT
1 TCAAATTTAA-TTT
*
3121668 TCAAATTTTATTTT
1 TCAAA-TTTAATTT
3121682 TCAAATT
1 TCAAATT
3121689 ACGACTTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 7 0.23
13 9 0.30
14 10 0.33
15 4 0.13
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (13 bp):
TCAAATTTAATTT
Found at i:3121821 original size:10 final size:10
Alignment explanation
Indices: 3121807--3121848 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
3121797 AAATTTATTT
3121807 AAATTATTAA
1 AAATTATTAA
*
3121817 TAATTA-TAA
1 AAATTATTAA
3121826 AAACTTATTAA
1 AAA-TTATTAA
*
3121837 AAATTAATAA
1 AAATTATTAA
3121847 AA
1 AA
3121849 TTTCTAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 5 0.19
10 16 0.59
11 6 0.22
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATTATTAA
Found at i:3121833 original size:20 final size:21
Alignment explanation
Indices: 3121810--3121848 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3121800 TTTATTTAAA
*
3121810 TTATTAATAATT-ATAAAAAC
1 TTATTAAAAATTAATAAAAAC
3121830 TTATTAAAAATTAATAAAA
1 TTATTAAAAATTAATAAAA
3121849 TTTCTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TTATTAAAAATTAATAAAAAC
Found at i:3123018 original size:3 final size:3
Alignment explanation
Indices: 3123010--3123046 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3123000 AACGAATGAA
3123010 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3123047 CACCTAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3123165 original size:31 final size:31
Alignment explanation
Indices: 3123122--3123183 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
3123112 ATTATTATTG
3123122 AACTATTCGAAAATTTTCATTTAAATCACTA
1 AACTATTCGAAAATTTTCATTTAAATCACTA
* *
3123153 AACTGTTCGAAAATTTTTATTTAAATCACTA
1 AACTATTCGAAAATTTTCATTTAAATCACTA
3123184 GGTCGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (31 bp):
AACTATTCGAAAATTTTCATTTAAATCACTA
Found at i:3127402 original size:21 final size:21
Alignment explanation
Indices: 3127369--3127410 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3127359 CTTTAAATCC
3127369 AAAAAATAAAAATATT-TTTAA
1 AAAAAATAAAAAT-TTATTTAA
**
3127390 AAAAAATTTAAATTTATTTAA
1 AAAAAATAAAAATTTATTTAA
3127411 TATATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAATAAAAATTTATTTAA
Found at i:3138342 original size:20 final size:20
Alignment explanation
Indices: 3138317--3138356 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3138307 CGTAAAATGA
*
3138317 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
3138337 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
3138357 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:3138346 original size:34 final size:35
Alignment explanation
Indices: 3138302--3138368 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3138292 CAGTAAAATA
*
3138302 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
3138336 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
3138369 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:3138372 original size:14 final size:15
Alignment explanation
Indices: 3138296--3138372 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
3138286 AATTGCCAGT
* *
3138296 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
3138310 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
3138324 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
3138344 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
3138359 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
3138373 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:3140695 original size:33 final size:33
Alignment explanation
Indices: 3140653--3140717 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
3140643 TGGTTGAAAG
*
3140653 GATTGCTAGTACTTTTCTAGTGCTATGAGTCTA
1 GATTGCTAGTACTTTTCTAGTGCTACGAGTCTA
3140686 GATTGCTAGTACTTTTCTAGTGCTACGAGTCT
1 GATTGCTAGTACTTTTCTAGTGCTACGAGTCT
3140718 TTATTTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.42
Consensus pattern (33 bp):
GATTGCTAGTACTTTTCTAGTGCTACGAGTCTA
Found at i:3141571 original size:30 final size:30
Alignment explanation
Indices: 3141537--3141600 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
3141527 GCAAAAAAAA
*
3141537 TCTCAATTTTCTCCCTAAATTTCTCAAAGC
1 TCTCAAATTTCTCCCTAAATTTCTCAAAGC
* *
3141567 TCTCAAATTTCTCCTTAAATTTCTCAAATC
1 TCTCAAATTTCTCCCTAAATTTCTCAAAGC
3141597 TCTC
1 TCTC
3141601 TTTAATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.30, G:0.02, T:0.42
Consensus pattern (30 bp):
TCTCAAATTTCTCCCTAAATTTCTCAAAGC
Found at i:3146835 original size:15 final size:15
Alignment explanation
Indices: 3146815--3146853 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3146805 TTATTTTAAC
*
3146815 AAAACCCTAACCCTA
1 AAAACCCTAACCCAA
*
3146830 AAAACCCTAATCCAA
1 AAAACCCTAACCCAA
*
3146845 AAAATCCTA
1 AAAACCCTA
3146854 GGGACTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAACCCTAACCCAA
Found at i:3147751 original size:2 final size:2
Alignment explanation
Indices: 3147744--3147769 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3147734 AAATTACCTT
3147744 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
3147770 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3148516 original size:33 final size:31
Alignment explanation
Indices: 3148479--3148540 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
3148469 TTTTCTAATT
3148479 TTTTATGGGTTGTAATAAATTGTTTTTATAAAA
1 TTTTATGGGTTGTAATAAA-T-TTTTTATAAAA
* * *
3148512 TTTTATGGTTTTTAATTAATTTTTTATAA
1 TTTTATGGGTTGTAATAAATTTTTTATAA
3148541 TTATTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 9 0.35
32 1 0.04
33 16 0.62
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (31 bp):
TTTTATGGGTTGTAATAAATTTTTTATAAAA
Found at i:3148602 original size:30 final size:31
Alignment explanation
Indices: 3148531--3148603 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
3148521 TTTTAATTAA
3148531 TTTTTTATAATTATTATAAATTTTAATGATT
1 TTTTTTATAATTATTATAAATTTTAATGATT
*** * *
3148562 TTTAAAATAATT-TTATAAGTTTTTTATG-TT
1 TTTTTTATAATTATTATAA-ATTTTAATGATT
3148592 TTTTTTATAATT
1 TTTTTTATAATT
3148604 CTAGAATGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (31 bp):
TTTTTTATAATTATTATAAATTTTAATGATT
Found at i:3154609 original size:11 final size:11
Alignment explanation
Indices: 3154593--3154623 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3154583 TATATATATT
3154593 TAAAAATTATA
1 TAAAAATTATA
*
3154604 TAAAAATAATA
1 TAAAAATTATA
3154615 TAAAAATTA
1 TAAAAATTA
3154624 ATACGGGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:3156100 original size:12 final size:12
Alignment explanation
Indices: 3156083--3156110 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3156073 TATACATTAT
3156083 AAAAAATATATA
1 AAAAAATATATA
3156095 AAAAAATATATA
1 AAAAAATATATA
3156107 AAAA
1 AAAA
3156111 TATGAACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAATATATA
Found at i:3156103 original size:10 final size:10
Alignment explanation
Indices: 3156080--3156113 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3156070 ACATATACAT
3156080 TATAAAAAATA
1 TATAAAAAA-A
3156091 TATAAAAAAA
1 TATAAAAAAA
*
3156101 TATATAAAAA
1 TATAAAAAAA
3156111 TAT
1 TAT
3156114 GAACAAGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
TATAAAAAAA
Found at i:3160314 original size:18 final size:18
Alignment explanation
Indices: 3160293--3160339 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
3160283 ATATTTGGAT
3160293 TATAAAATATATA-AAAA
1 TATAAAATATATATAAAA
3160310 CTATAAAA-ATATTATAAAA
1 -TATAAAATATA-TATAAAA
3160329 TAT-AAATATAT
1 TATAAAATATAT
3160340 GTACGTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.27
18 15 0.58
19 4 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
TATAAAATATATATAAAA
Found at i:3160491 original size:3 final size:3
Alignment explanation
Indices: 3160485--3160537 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
3160475 GTATTAGAAG
*
3160485 AAT AAT AAT AAT AAT AAT AATT AAT -AT AAT AAT AGT AAT ATAT AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT A-AT AAT
3160531 -AT AAT AA
1 AAT AAT AA
3160538 CAAAGATAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 4 0.09
3 34 0.77
4 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:3160514 original size:21 final size:21
Alignment explanation
Indices: 3160489--3160537 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
3160479 TAGAAGAATA
3160489 ATAATAATAATAATA-ATTAAT
1 ATAATAATAATAATATA-TAAT
*
3160510 ATAATAATAGTAATATATAAT
1 ATAATAATAATAATATATAAT
3160531 ATAATAA
1 ATAATAA
3160538 CAAAGATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAATAATAATAATATATAAT
Found at i:3161760 original size:65 final size:66
Alignment explanation
Indices: 3161656--3161786 Score: 255
Period size: 65 Copynumber: 2.0 Consensus size: 66
3161646 AAAAGAACAG
3161656 AAAAATTTGAGCAAAATCGATCACCTTTCCCAAAATTGCTTTCCTGATTTTTTTT-TCTTGTATT
1 AAAAATTTGAGCAAAATCGATCACCTTTCCCAAAATTGCTTTCCTGATTTTTTTTCTCTTGTATT
3161720 T
66 T
3161721 AAAAATTTGAGCAAAATCGATCACCTTTCCCAAAATTGCTTTCCTGATTTTTTTTCTCTTGTATT
1 AAAAATTTGAGCAAAATCGATCACCTTTCCCAAAATTGCTTTCCTGATTTTTTTTCTCTTGTATT
3161786 T
66 T
3161787 TCTTTTTTAA
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
65 55 0.85
66 10 0.15
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.44
Consensus pattern (66 bp):
AAAAATTTGAGCAAAATCGATCACCTTTCCCAAAATTGCTTTCCTGATTTTTTTTCTCTTGTATT
T
Found at i:3162260 original size:8 final size:8
Alignment explanation
Indices: 3162247--3162271 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3162237 TATTCAAAAA
3162247 AAATAAAC
1 AAATAAAC
3162255 AAATAAAC
1 AAATAAAC
3162263 AAATAAAC
1 AAATAAAC
3162271 A
1 A
3162272 CTTCTTTTTT
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:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
AAATAAAC
Found at i:3162378 original size:86 final size:85
Alignment explanation
Indices: 3162280--3162444 Score: 208
Period size: 86 Copynumber: 1.9 Consensus size: 85
3162270 CACTTCTTTT
* * *
3162280 TTTTTTTGCACTCAATTAAGAACTTGAACTTTCAAAATACATAAAAA-AGGCTCTCAAACTTCTT
1 TTTTTTTGCACTCAATTAAGAACTTGAACTTTAAAAATACATAAAAATA--CCCTCAAAATTCTT
3162344 CAAAAGAAGCAATTAAGCCCCTG
64 CAAAA-AAGCAATTAAGCCCCTG
** * * * *
3162367 TTTTTTT-CACTCAATTGGGTATTTGAACTTTAAAAATGCATAAAAATACCCTCAAAATTTTTCA
1 TTTTTTTGCACTCAATTAAGAACTTGAACTTTAAAAATACATAAAAATACCCTCAAAATTCTTCA
3162431 AAAAAGCAATTAAG
66 AAAAAGCAATTAAG
3162445 TCCATGCACT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 11 0.16
85 16 0.24
86 33 0.49
87 8 0.12
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.33
Consensus pattern (85 bp):
TTTTTTTGCACTCAATTAAGAACTTGAACTTTAAAAATACATAAAAATACCCTCAAAATTCTTCA
AAAAAGCAATTAAGCCCCTG
Found at i:3162510 original size:20 final size:21
Alignment explanation
Indices: 3162458--3162513 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 21
3162448 ATGCACTTAT
*
3162458 TAAAAATTAGAAAAAAATTTTA
1 TAAAAATT-GTAAAAAATTTTA
*
3162480 TAAAAA--ATAAAAAA-TTTA
1 TAAAAATTGTAAAAAATTTTA
3162498 TAAAAATTGTAAAAAA
1 TAAAAATTGTAAAAAA
3162514 ATTGTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 10 0.34
19 6 0.21
20 7 0.24
22 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
TAAAAATTGTAAAAAATTTTA
Found at i:3162532 original size:20 final size:22
Alignment explanation
Indices: 3162486--3162533 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 22
3162476 TTTATAAAAA
3162486 ATAAAAAATTTATAAAAATTGT
1 ATAAAAAATTTATAAAAATTGT
* *
3162508 A-AAAAAA-TTGT-AAAATTTT
1 ATAAAAAATTTATAAAAATTGT
3162527 ATAAAAA
1 ATAAAAA
3162534 TCATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 8 0.35
20 8 0.35
21 6 0.26
22 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
ATAAAAAATTTATAAAAATTGT
Found at i:3162534 original size:30 final size:30
Alignment explanation
Indices: 3162489--3162546 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3162479 ATAAAAAATA
**
3162489 AAAAATTTATAAAAATTGTAAAAAAATTGT
1 AAAAATTTATAAAAATCATAAAAAAATTGT
*
3162519 AAAATTTTATAAAAATCATAAAAAAATT
1 AAAAATTTATAAAAATCATAAAAAAATT
3162547 AACGACCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAAATTTATAAAAATCATAAAAAAATTGT
Found at i:3162936 original size:19 final size:19
Alignment explanation
Indices: 3162901--3162974 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
3162891 GTTAAAGGAT
3162901 ATTTTTCTA-TATATTTTATA
1 ATTTTT-TACTAT-TTTTATA
3162921 ATTTTTTACTATTTTTATA
1 ATTTTTTACTATTTTTATA
** *
3162940 AAATTTTACAATTTTT-T-
1 ATTTTTTACTATTTTTATA
*
3162957 ATTTTTTTCTAATTTTTA
1 ATTTTTTACT-ATTTTTA
3162975 ATATTTGAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.14
18 7 0.16
19 22 0.50
20 9 0.20
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTTTACTATTTTTATA
Found at i:3175619 original size:19 final size:19
Alignment explanation
Indices: 3175578--3175622 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
3175568 ATTAGATTTT
* * *
3175578 TTTTTTAATATTTTTATTA
1 TTTTTTAAAATTTTAATAA
3175597 -TTTTTAAAATTTTAATAA
1 TTTTTTAAAATTTTAATAA
3175615 TTTTTTAA
1 TTTTTTAA
3175623 TCAAACCAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTAAAATTTTAATAA
Found at i:3182829 original size:102 final size:102
Alignment explanation
Indices: 3182617--3182821 Score: 295
Period size: 102 Copynumber: 2.0 Consensus size: 102
3182607 AAAATTAAAC
* * ** * * *
3182617 AAAAAAAATAAATTAGGAGTGTGTTGGGCTGGGTAACCGGGATGGGGTGCTTGGGTTGTCATTCC
1 AAAAATAATAAATTAAGAGTGTGTTGGGCTAAGTAACCGGGATGAGGTGCTTGAGTTATCATTCC
3182682 ACTTCGAGTCAAAAGGGCCAATACATTCTTAAACAAT
66 ACTTCGAGTCAAAAGGGCCAATACATTCTTAAACAAT
* * *
3182719 AAAAATAATAAATTAAGAGTGTGTTGGGCTAAGTAACTGGGGTGAGGTGTTTGAGTTATCATTCC
1 AAAAATAATAAATTAAGAGTGTGTTGGGCTAAGTAACCGGGATGAGGTGCTTGAGTTATCATTCC
*
3182784 ACTTCGCA-TCAAAAGGGCCAATACATTCTTAAATAAT
66 ACTTCG-AGTCAAAAGGGCCAATACATTCTTAAACAAT
3182821 A
1 A
3182822 TATATAATTC
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
102 90 0.99
103 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (102 bp):
AAAAATAATAAATTAAGAGTGTGTTGGGCTAAGTAACCGGGATGAGGTGCTTGAGTTATCATTCC
ACTTCGAGTCAAAAGGGCCAATACATTCTTAAACAAT
Found at i:3187378 original size:17 final size:16
Alignment explanation
Indices: 3187358--3187399 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3187348 AGAATTTTAA
3187358 AAAAATTAT-AGTTTTTT
1 AAAAATTATGAG--TTTT
*
3187375 AAAAATTTTGAGTTTT
1 AAAAATTATGAGTTTT
3187391 AAAAATTAT
1 AAAAATTAT
3187400 TTTGATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 12 0.55
17 8 0.36
18 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (16 bp):
AAAAATTATGAGTTTT
Found at i:3189383 original size:29 final size:29
Alignment explanation
Indices: 3189332--3189407 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
3189322 GTTTTAAGGA
* * * *
3189332 TAGTCCCTGTACTTATAAATTTGTGTGGATT
1 TAGTCCCTCTACTT-T-TATTTGTGTGAAAT
*
3189363 TAGTCCCTCTACTTTTATTTGTTTGAAAT
1 TAGTCCCTCTACTTTTATTTGTGTGAAAT
*
3189392 TAGTCTCTCTACTTTT
1 TAGTCCCTCTACTTTT
3189408 CAAATAACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 25 0.64
30 1 0.03
31 13 0.33
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (29 bp):
TAGTCCCTCTACTTTTATTTGTGTGAAAT
Found at i:3190530 original size:20 final size:21
Alignment explanation
Indices: 3190505--3190556 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
3190495 AGCAGTGGCG
*
3190505 GTGAGATTAGTTACTGTAG-C
1 GTGAGATTAGATACTGTAGAC
* *
3190525 GTGAGATTGGATACTGTAGAG
1 GTGAGATTAGATACTGTAGAC
3190546 GTGAGATTAGA
1 GTGAGATTAGA
3190557 AACAGCGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.31
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGAC
Found at i:3195836 original size:19 final size:19
Alignment explanation
Indices: 3195780--3195836 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
3195770 TTGACGAAAC
3195780 AATAACATAACTATATTTTAAA
1 AATAA-ATAA-TAT-TTTTAAA
* *
3195802 AA-AAATTAAAAATTTTAAA
1 AATAAA-TAATATTTTTAAA
3195821 AATAAATAATATTTTT
1 AATAAATAATATTTTT
3195837 TTTATAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 17 0.59
20 5 0.17
21 5 0.17
22 2 0.07
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAATAATATTTTTAAA
Found at i:3215715 original size:109 final size:109
Alignment explanation
Indices: 3215423--3215703 Score: 460
Period size: 109 Copynumber: 2.6 Consensus size: 109
3215413 ATATTTGGCA
* * * *
3215423 ATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCGAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
* *
3215485 CAAAACATTGCCTTATTTTGAAATTTTTAAAAGGATATTAAGTC
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
* *
3215529 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCTAAATG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
3215594 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
66 CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
*
3215638 ATTTGGTTGAACGAGAAAAATTGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
1 ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
3215703 C
66 C
3215704 TGAATATTGC
Statistics
Matches: 161, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
106 14 0.09
108 26 0.16
109 121 0.75
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (109 bp):
ATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACG
CAAAACATTGCCTTATTTTAAAATTTTTAAAAGGATATTAAGCC
Found at i:3217895 original size:44 final size:44
Alignment explanation
Indices: 3217710--3218080 Score: 221
Period size: 44 Copynumber: 8.6 Consensus size: 44
3217700 GGATGCGATC
* * * *
3217710 TGCTCTACTATTGCTTAGAGAGATAAGATCTACAATCTTCAACT
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACT
* * * * **** * *
3217754 TACTCCACTGCTGCTCAGGGAGATAGGAT-TGGTTTCTTTTGTC-
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTACAATC-TTCGACT
* * * ** *
3217797 TGCTCCGCTACTGTTTAGGAAGATAAGA-CT-TGA--TGCGA-T
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACT
*
3217836 CTGCTGCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACT
1 -TGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACT
* * *
3217881 TGCTCCACTACTGCTTAGGGAGATAGGATCTA-ATATCTTTGACC
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTACA-ATCTTCGACT
* * *** * *
3217925 TGATCCACTACTGCTTAGGGAGATAGGA-CT-GGTTGCTT-AAAT
1 TGCTCCACTACTGCTTAGGGAGATAAGATCTACAAT-CTTCGACT
* * * **
3217967 CTGCTTCACTACTGCTTAGGAAGATGAGAT-TCACCGTCTTCGA-T
1 -TGCTCCACTACTGCTTAGGGAGATAAGATCT-ACAATCTTCGACT
* * *
3218011 CTGCTCCACTACTGCTTAGGGAGATAGGATCTA-ATATCTTTGACC
1 -TGCTCCACTACTGCTTAGGGAGATAAGATCTACA-ATCTTCGACT
3218056 TGCTCCACTACTGCTTAGGGAGATA
1 TGCTCCACTACTGCTTAGGGAGATA
3218081 GGACTGGTGG
Statistics
Matches: 246, Mismatches: 61, Indels: 40
0.71 0.18 0.12
Matches are distributed among these distances:
39 2 0.01
40 24 0.10
41 2 0.01
42 3 0.01
43 55 0.22
44 156 0.63
45 4 0.02
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (44 bp):
TGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACT
Found at i:3218007 original size:131 final size:131
Alignment explanation
Indices: 3217834--3218170 Score: 525
Period size: 131 Copynumber: 2.6 Consensus size: 131
3217824 ACTTGATGCG
* * * *
3217834 ATCTGCTGCACTACTGCTTAGGGAGATAAGA-TCTACAATCTTCGA-CTTGCTCCACTACTGCTT
1 ATCTGCTTCACTACTGCTTAGGAAGATGAGATTC-ACAGTCTTCGATC-TGCTCCACTACTGCTT
*
3217897 AGGGAGATAGGATCTAATATCTTTGACCTGATCCACTACTGCTTAGGGAGATAGGACTGGTTGCT
64 AGGGAGATAGGATCTAATATCTTTGACCTGATCCACTACTGCTTAGGGAGATAGGACTGGTGGCT
3217962 TAA
129 TAA
*
3217965 ATCTGCTTCACTACTGCTTAGGAAGATGAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAG
1 ATCTGCTTCACTACTGCTTAGGAAGATGAGATTCACAGTCTTCGATCTGCTCCACTACTGCTTAG
*
3218030 GGAGATAGGATCTAATATCTTTGACCTGCTCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTA
66 GGAGATAGGATCTAATATCTTTGACCTGATCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTA
3218095 A
131 A
* * * * *
3218096 ATCTGCTTCACTACTGCCTAGGAAGATGAGATTCGCTGTCTTCGATCTGCTCTACTACCGCTTAG
1 ATCTGCTTCACTACTGCTTAGGAAGATGAGATTCACAGTCTTCGATCTGCTCCACTACTGCTTAG
*
3218161 GGATATAGGA
66 GGAGATAGGA
3218171 CTGGTGGCTT
Statistics
Matches: 191, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
131 188 0.98
132 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (131 bp):
ATCTGCTTCACTACTGCTTAGGAAGATGAGATTCACAGTCTTCGATCTGCTCCACTACTGCTTAG
GGAGATAGGATCTAATATCTTTGACCTGATCCACTACTGCTTAGGGAGATAGGACTGGTGGCTTA
A
Found at i:3218081 original size:44 final size:44
Alignment explanation
Indices: 3217836--3218083 Score: 272
Period size: 44 Copynumber: 5.7 Consensus size: 44
3217826 TTGATGCGAT
* *
3217836 CTGCTGCACTACTGCTTAGGGAGATAAGATCTACA-ATCTTCGAC
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTA-ATATCTTCGAC
* *
3217880 TTGCTCCACTACTGCTTAGGGAGATAGGATCTAATATCTTTGAC
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTAATATCTTCGAC
* ** ** *
3217924 CTGATCCACTACTGCTTAGGGAGATAGGA-CTGGT-TGCTTAAAT
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTAATAT-CTTCGAC
* * *** *
3217967 CTGCTTCACTACTGCTTAGGAAGAT-GAGAT-TCACCGTCTTCGAT
1 CTGCTCCACTACTGCTTAGGGAGATAG-GATCT-AATATCTTCGAC
*
3218011 CTGCTCCACTACTGCTTAGGGAGATAGGATCTAATATCTTTGAC
1 CTGCTCCACTACTGCTTAGGGAGATAGGATCTAATATCTTCGAC
3218055 CTGCTCCACTACTGCTTAGGGAGATAGGA
1 CTGCTCCACTACTGCTTAGGGAGATAGGA
3218084 CTGGTGGCTT
Statistics
Matches: 170, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
42 2 0.01
43 33 0.19
44 132 0.78
45 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (44 bp):
CTGCTCCACTACTGCTTAGGGAGATAGGATCTAATATCTTCGAC
Found at i:3218100 original size:87 final size:87
Alignment explanation
Indices: 3217834--3218205 Score: 299
Period size: 87 Copynumber: 4.3 Consensus size: 87
3217824 ACTTGATGCG
* * *
3217834 ATCTGCTGCACTACTGCTTAGGGAGATAAGATCTACA-ATCTTCGACTTGCTCCACTACTGCTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTA-ATATCTTCGACCTGCTCCACTACTGCTTA
* ** **
3217898 GGGAGATAGGATCTAATATCTTTG
65 GGGAGATAGGA-CTAGTGGCTTAA
* * ** ** * *
3217922 ACCTGATCCACTACTGCTTAGGGAGATAGGA-CTGGT-TGCTTAAATCTGCTTCACTACTGCTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAATAT-CTTCGACCTGCTCCACTACTGCTTA
* * ** * **
3217985 GGAAGAT-GAGATTCACCGTCTTCG
65 GGGAGATAG-GACT-AGTGGCTTAA
*
3218009 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAATATCTTTGACCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAATATCTTCGACCTGCTCCACTACTGCTTAG
*
3218074 GGAGATAGGACTGGTGGCTTAA
66 GGAGATAGGACTAGTGGCTTAA
* * * ** * * * *
3218096 ATCTGCTTCACTACTGCCTAGGAAGAT-GAGAT-TCGCTGTCTTCGATCTGCTCTACTACCGCTT
1 ATCTGCTCCACTACTGCTTAGGGAGATAG-GATCT-AATATCTTCGACCTGCTCCACTACTGCTT
* *
3218159 AGGGATATAGGACTGGTGGCTTAA
64 AGGGAGATAGGACTAGTGGCTTAA
*
3218183 ATCTGCTTCAC-ACTGCTTAGGGA
1 ATCTGCTCCACTACTGCTTAGGGA
3218206 AGATGAGATT
Statistics
Matches: 229, Mismatches: 46, Indels: 20
0.78 0.16 0.07
Matches are distributed among these distances:
86 15 0.07
87 152 0.66
88 60 0.26
89 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (87 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTAATATCTTCGACCTGCTCCACTACTGCTTAG
GGAGATAGGACTAGTGGCTTAA
Found at i:3218153 original size:44 final size:44
Alignment explanation
Indices: 3217832--3218170 Score: 169
Period size: 44 Copynumber: 7.8 Consensus size: 44
3217822 AGACTTGATG
* * **
3217832 CGATCTGCTGC-ACTACTGCTTAGGGAGATAAGA-TCTACAATCTT
1 CGATCTGCT-CTACTACTGCTTAGGAAGATAGGATTC-ACTGTCTT
* * * *
3217876 CGA-CTTGCTCCACTACTGCTTAGGGAGATAGGA-TCTAATATCTT
1 CGATC-TGCTCTACTACTGCTTAGGAAGATAGGATTC-ACTGTCTT
* * * * * * ***
3217920 TGACCTGATCCACTACTGCTTAGGGAGATAGGACTGGTTG-CTT
1 CGATCTGCTCTACTACTGCTTAGGAAGATAGGATTCACTGTCTT
** *
3217963 AAATCTGCT-TCACTACTGCTTAGGAAGAT-GAGATTCACCGTCTT
1 CGATCTGCTCT-ACTACTGCTTAGGAAGATAG-GATTCACTGTCTT
* * * *
3218007 CGATCTGCTCCACTACTGCTTAGGGAGATAGGA-TCTAATATCTT
1 CGATCTGCTCTACTACTGCTTAGGAAGATAGGATTC-ACTGTCTT
* * * * * ** *
3218051 TGACCTGCTCCACTACTGCTTAGGGAGATAGGACT-GGTGGCTT
1 CGATCTGCTCTACTACTGCTTAGGAAGATAGGATTCACTGTCTT
** * *
3218094 AAATCTGCT-TCACTACTGCCTAGGAAGAT-GAGATTCGCTGTCTT
1 CGATCTGCTCT-ACTACTGCTTAGGAAGATAG-GATTCACTGTCTT
* * *
3218138 CGATCTGCTCTACTACCGCTTAGGGATATAGGA
1 CGATCTGCTCTACTACTGCTTAGGAAGATAGGA
3218171 CTGGTGGCTT
Statistics
Matches: 231, Mismatches: 48, Indels: 32
0.74 0.15 0.10
Matches are distributed among these distances:
42 2 0.01
43 62 0.27
44 161 0.70
45 6 0.03
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (44 bp):
CGATCTGCTCTACTACTGCTTAGGAAGATAGGATTCACTGTCTT
Found at i:3220535 original size:16 final size:16
Alignment explanation
Indices: 3220514--3220604 Score: 60
Period size: 17 Copynumber: 5.3 Consensus size: 16
3220504 TGACCTCTCC
3220514 TTTTTCTTTTTCTTTT
1 TTTTTCTTTTTCTTTT
*
3220530 TTTTTCTTTTTGATTTT
1 TTTTTCTTTTT-CTTTT
3220547 TTTCTT-TTTTCTGCTTTT
1 TTT-TTCTTTT-T-CTTTT
**
3220565 GATTTTGATTTTT-TTTCT
1 --TTTTTCTTTTTCTTT-T
*
3220583 TTTTTCTTTTCCTTCTT
1 TTTTTCTTTTTCTT-TT
3220600 TTTTT
1 TTTTT
3220605 TTGCCTTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 17
0.72 0.07 0.20
Matches are distributed among these distances:
16 19 0.32
17 22 0.37
18 10 0.17
19 2 0.03
20 7 0.12
ACGTcount: A:0.03, C:0.12, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTTTCTTTTTCTTTT
Found at i:3220539 original size:15 final size:15
Alignment explanation
Indices: 3220514--3220555 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
3220504 TGACCTCTCC
**
3220514 TTTTTCTTTTTCTTTT
1 TTTTTCTTTTT-GATT
3220530 TTTTTCTTTTTGATT
1 TTTTTCTTTTTGATT
3220545 TTTTTCTTTTT
1 TTTTTCTTTTT
3220556 TCTGCTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (15 bp):
TTTTTCTTTTTGATT
Found at i:3220550 original size:31 final size:32
Alignment explanation
Indices: 3220514--3220593 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
3220504 TGACCTCTCC
* *
3220514 TTTTTCTTTTTCTTTTTTTTTCTTTTTGA-TT
1 TTTTTCTTTTTCTTTTCTTTTCATTTTGATTT
* * *
3220545 TTTTTCTTTTT-TCTGCTTTTGATTTTGATTT
1 TTTTTCTTTTTCTTTTCTTTTCATTTTGATTT
3220576 TTTTTCTTTTTTCTTTTC
1 TTTTTC-TTTTTCTTTTC
3220594 CTTCTTTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
30 12 0.31
31 19 0.49
32 5 0.13
33 3 0.08
ACGTcount: A:0.04, C:0.11, G:0.05, T:0.80
Consensus pattern (32 bp):
TTTTTCTTTTTCTTTTCTTTTCATTTTGATTT
Found at i:3220554 original size:24 final size:24
Alignment explanation
Indices: 3220520--3220605 Score: 70
Period size: 25 Copynumber: 3.6 Consensus size: 24
3220510 CTCCTTTTTC
3220520 TTTTTCTTTTTTTTTCTTTTTGATT
1 TTTTTC-TTTTTTTTCTTTTTGATT
*
3220545 TTTTTCTTTTTTCTGC-TTTTGA--
1 TTTTTCTTTTTT-TTCTTTTTGATT
** **
3220567 TTTTGATTTTTTTTCTTTTTTCTT
1 TTTTTCTTTTTTTTCTTTTTGATT
*
3220591 TTCCTTCTTTTTTTT
1 TT-TTTCTTTTTTTT
3220606 TGCCTTTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
21 2 0.04
22 14 0.30
24 14 0.30
25 17 0.36
ACGTcount: A:0.03, C:0.12, G:0.05, T:0.80
Consensus pattern (24 bp):
TTTTTCTTTTTTTTCTTTTTGATT
Found at i:3220554 original size:25 final size:24
Alignment explanation
Indices: 3220520--3220570 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
3220510 CTCCTTTTTC
* *
3220520 TTTTTCTTTTTTTTTCTTTTTGATT
1 TTTTTCTTTTTTCTGC-TTTTGATT
3220545 TTTTTCTTTTTTCTGCTTTTGATT
1 TTTTTCTTTTTTCTGCTTTTGATT
3220569 TT
1 TT
3220571 GATTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.04, C:0.10, G:0.06, T:0.80
Consensus pattern (24 bp):
TTTTTCTTTTTTCTGCTTTTGATT
Found at i:3224776 original size:3 final size:3
Alignment explanation
Indices: 3224768--3224802 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3224758 AAAATAAAAC
* *
3224768 TAA TAA TAA TAA TAG TAA TAA TAA TAG TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3224803 TGAAATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3224786 original size:12 final size:12
Alignment explanation
Indices: 3224771--3224802 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
3224761 ATAAAACTAA
3224771 TAATAATAATAG
1 TAATAATAATAG
3224783 TAATAATAATAG
1 TAATAATAATAG
3224795 TAATAATA
1 TAATAATA
3224803 TGAAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (12 bp):
TAATAATAATAG
Found at i:3225509 original size:222 final size:223
Alignment explanation
Indices: 3225122--3225566 Score: 874
Period size: 222 Copynumber: 2.0 Consensus size: 223
3225112 GGCAGCCCAA
*
3225122 AACGACGTCGTTTTGGAAGCCTATTTAAACTATTTTTTTTTTTAAAATTTTCATTCTTCCCTTCT
1 AACGACGTCGTTTTGGAAGCCTATTTAAACTATATTTTTTTTTAAAATTTTCATTCTTCCCTTCT
3225187 TCTCCAGAAAAAAAACAAAAATTTCTCTCAAGTCTCTCTCCCTTCCTCCTACCAGAGCCCAGAAA
66 TCTCCAGAAAAAAAACAAAAATTTCTCTCAAGTCTCTCTCCCTTCCTCCTACCAGAGCCCAGAAA
3225252 CCGGCGAACAGGGCCGCCACGTCGCCGCCGCGCCGGCCACCGTACATGGTGGCCGGAAAAAATCA
131 CCGGCGAACAGGGCCGCCACGTCGCCGCCGCGCCGGCCACCGTACATGGTGGCCGGAAAAAATCA
3225317 AAAGGTATGTTTTTTTTGGTTTTTTATG
196 AAAGGTATGTTTTTTTTGGTTTTTTATG
3225345 AACGACGTCGTTTTGGAAGCCTATTTAAACTA-ATTTTTTTTTAAAATTTTCATTCTTCCCTTCT
1 AACGACGTCGTTTTGGAAGCCTATTTAAACTATATTTTTTTTTAAAATTTTCATTCTTCCCTTCT
3225409 TCTCCAGAAAAAAAACAAAAATTTCTCTCAAGTCTCTCTCCCTTCCTCCTACCAGAGCCCAGAAA
66 TCTCCAGAAAAAAAACAAAAATTTCTCTCAAGTCTCTCTCCCTTCCTCCTACCAGAGCCCAGAAA
3225474 CCGGCGAACAGGGCCGCCACGTCGCCGCCGCGCCGGCCACCGTACATGGTGGCCGGAAAAAATCA
131 CCGGCGAACAGGGCCGCCACGTCGCCGCCGCGCCGGCCACCGTACATGGTGGCCGGAAAAAATCA
3225539 AAAGGTATGTTTTTTTTGGTTTTTTATG
196 AAAGGTATGTTTTTTTTGGTTTTTTATG
3225567 TGTTATAAAT
Statistics
Matches: 221, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
222 189 0.86
223 32 0.14
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.31
Consensus pattern (223 bp):
AACGACGTCGTTTTGGAAGCCTATTTAAACTATATTTTTTTTTAAAATTTTCATTCTTCCCTTCT
TCTCCAGAAAAAAAACAAAAATTTCTCTCAAGTCTCTCTCCCTTCCTCCTACCAGAGCCCAGAAA
CCGGCGAACAGGGCCGCCACGTCGCCGCCGCGCCGGCCACCGTACATGGTGGCCGGAAAAAATCA
AAAGGTATGTTTTTTTTGGTTTTTTATG
Found at i:3225665 original size:17 final size:16
Alignment explanation
Indices: 3225624--3225666 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3225614 CAAAATAGTT
*
3225624 AGAAAAAAAGAGAAAA
1 AGAAAAAAATAGAAAA
*
3225640 A-ATAAAAATAGAAAA
1 AGAAAAAAATAGAAAA
3225655 AGAAAATAAATA
1 AGAAAA-AAATA
3225667 TACCGAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 13 0.59
16 4 0.18
17 5 0.23
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (16 bp):
AGAAAAAAATAGAAAA
Found at i:3226026 original size:74 final size:73
Alignment explanation
Indices: 3225861--3226006 Score: 247
Period size: 74 Copynumber: 2.0 Consensus size: 73
3225851 GCAGGTACCT
*
3225861 TGACGAGACAAGGCAAGTGGGCGAGCGGTGGAGCAGAGAGTAGGCGATGGGACGTGCGCGGCGAC
1 TGACGAGACAAGGCAAGTGGGCGAGCGGTGGAGCAGAGAGTAGGCGATGGGACGTGCGCGACGAC
* *
3225926 CAGTAGCC
66 CAGCAGAC
*
3225934 TTGACGAGACAAGGCAAGTGGGCGAGCGGTGGAGCAGAGAGTAGGCGATGGGACGTGCGCGACGG
1 -TGACGAGACAAGGCAAGTGGGCGAGCGGTGGAGCAGAGAGTAGGCGATGGGACGTGCGCGACGA
3225999 CCAGCAGA
65 CCAGCAGA
3226007 ACGGCGGTGG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.25, C:0.20, G:0.45, T:0.10
Consensus pattern (73 bp):
TGACGAGACAAGGCAAGTGGGCGAGCGGTGGAGCAGAGAGTAGGCGATGGGACGTGCGCGACGAC
CAGCAGAC
Found at i:3236249 original size:73 final size:74
Alignment explanation
Indices: 3236058--3236252 Score: 304
Period size: 74 Copynumber: 2.6 Consensus size: 74
3236048 TTTTTTTTAT
* ** *
3236058 TTTTTACATCAATAATAT-CTTATTTACAATTTACAAAAAAAATGAAAATATTGTTTGTATTGTA
1 TTTTTACATCAATAATATAATTATTTACAATTTAC-CCAAAAATGAAAATATTGTTTGTACTGTA
*
3236122 TTTTATTGTA
65 TTCTATTGTA
* *
3236132 TTTTTACATCAATAATATATTTAGTTACAATTTACCCAAAAATGAAAATATTGTTTGTACTGTAT
1 TTTTTACATCAATAATATAATTATTTACAATTTACCCAAAAATGAAAATATTGTTTGTACTGTAT
3236197 TCTATTGTA
66 TCTATTGTA
3236206 -TTTTACATCAATAATATAATTATTTACAATTTACCCAAAAATGAAAA
1 TTTTTACATCAATAATATAATTATTTACAATTTACCCAAAAATGAAAA
3236253 AATGAAAAAA
Statistics
Matches: 112, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
73 45 0.40
74 53 0.47
75 14 0.12
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.44
Consensus pattern (74 bp):
TTTTTACATCAATAATATAATTATTTACAATTTACCCAAAAATGAAAATATTGTTTGTACTGTAT
TCTATTGTA
Found at i:3240786 original size:26 final size:25
Alignment explanation
Indices: 3240749--3240806 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
3240739 TATTTTCTTG
*
3240749 AAAATTTACCAGAGGCAAAATCGTC
1 AAAATTTACCAGAGGCAAAATCATC
* * *
3240774 AAAATTATACCAGGGGTAAAATCATT
1 AAAATT-TACCAGAGGCAAAATCATC
3240800 AAAATTT
1 AAAATTT
3240807 TACTGGGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.26
Consensus pattern (25 bp):
AAAATTTACCAGAGGCAAAATCATC
Found at i:3246871 original size:29 final size:29
Alignment explanation
Indices: 3246811--3246880 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
3246801 CACGATAACG
**
3246811 TAAGTGACTAAAATGTAACATTTCAAATA
1 TAAGTGACTAAAATGTAACATGACAAATA
*
3246840 TAAGTGACTAAAATGTAATATGAGACAAATA
1 TAAGTGACTAAAATGTAACAT--GACAAATA
*
3246871 AAAGTGACTA
1 TAAGTGACTA
3246881 TCTAAATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 20 0.57
31 15 0.43
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (29 bp):
TAAGTGACTAAAATGTAACATGACAAATA
Found at i:3252363 original size:5 final size:5
Alignment explanation
Indices: 3252343--3252376 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
3252333 TATAAAATAC
3252343 ATAAT AT-AT A-AAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
3252377 GAAAATTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 6 0.22
5 21 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:3253200 original size:89 final size:89
Alignment explanation
Indices: 3253069--3253310 Score: 253
Period size: 89 Copynumber: 2.7 Consensus size: 89
3253059 ATGTAAAAAG
* * ** * *
3253069 TCTTCAAAATTTTCCAAAAAAAGCTATTAAGTCTCTACTTTTTTTGGCACTTAATTGGGTAATTG
1 TCTT-AAAATTTT-CAAAAAAAGCAATTAAGTCCCTTTTTTTTTTTGCACTCAATTGGGTAATTG
* *
3253134 AAAGTTT-AAAATGCATAAAAAAGGC
64 AAACTTTCAAAATACATAAAAAAGGC
*
3253159 TCTTAAAAATTTTCAAAAAAAGCAATTAAGTCCCTTTTTTTTTTTGCACTCAATTGGGTACTTG-
1 TCTT-AAAATTTTCAAAAAAAGCAATTAAGTCCCTTTTTTTTTTTGCACTCAATTGGGTAATTGA
*
3253223 AACTTTCAAAATACATCAAAAAGGC
65 AACTTTCAAAATACATAAAAAAGGC
* * * * * *
3253248 -CCTCAAA-CTT-AAAAAAA-AAATTAAGCCCCTATTTTTTTTTTTGCACTCAATTGGGTATTTG
1 TCTTAAAATTTTCAAAAAAAGCAATTAAGTCCC--TTTTTTTTTTTGCACTCAATTGGGTAATTG
3253309 AA
64 AA
3253311 CTACCAAAAT
Statistics
Matches: 131, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
84 10 0.08
85 7 0.05
86 31 0.24
87 4 0.03
88 7 0.05
89 60 0.46
90 12 0.09
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (89 bp):
TCTTAAAATTTTCAAAAAAAGCAATTAAGTCCCTTTTTTTTTTTGCACTCAATTGGGTAATTGAA
ACTTTCAAAATACATAAAAAAGGC
Found at i:3253540 original size:18 final size:17
Alignment explanation
Indices: 3253499--3253542 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3253489 TTTTTTTTTC
3253499 TAATTTTTAATAAATTA
1 TAATTTTTAATAAATTA
* *
3253516 TATATTTTTATTAAAATTT
1 TA-ATTTTTAAT-AAATTA
3253535 TAATTTTT
1 TAATTTTT
3253543 TTTTTTGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 14 0.61
19 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTTTTAATAAATTA
Found at i:3253826 original size:92 final size:91
Alignment explanation
Indices: 3253654--3253823 Score: 238
Period size: 92 Copynumber: 1.9 Consensus size: 91
3253644 AAATGACCTG
* * ** * *
3253654 TTTTATGTATTTTGATAGTTCAAGTGTCCAATTGAGTGCAAGAAAAAAAAGTAGGGGCTTAATTG
1 TTTTATGTATTTTGAAAGTTAAAGCATCCAATTGAGTGCAAGAAAAAAAAGTAGAGACTTAATTG
3253719 CTTTTTTCGAAAAAATTTGAAGGCCC
66 CTTTTTTCGAAAAAATTTGAAGGCCC
3253745 TTTTGATGTATTTTGAAAGTTAAAGCATCCAATTGAGTGCAA-AAAAAAAA-T-GCAGACTTAAT
1 TTTT-ATGTATTTTGAAAGTTAAAGCATCCAATTGAGTGCAAGAAAAAAAAGTAG-AGACTTAAT
*
3253807 TGCTTTTTTTGAAAAAA
64 TGCTTTTTTCGAAAAAA
3253824 AATAGAGAGC
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
89 1 0.01
90 24 0.34
91 12 0.17
92 33 0.47
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35
Consensus pattern (91 bp):
TTTTATGTATTTTGAAAGTTAAAGCATCCAATTGAGTGCAAGAAAAAAAAGTAGAGACTTAATTG
CTTTTTTCGAAAAAATTTGAAGGCCC
Found at i:3261916 original size:18 final size:19
Alignment explanation
Indices: 3261893--3261931 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3261883 AATATATATT
3261893 TTTAGTTT-TAATGGTTTA
1 TTTAGTTTATAATGGTTTA
*
3261911 TTTAGTTTATAGTGGTTTA
1 TTTAGTTTATAATGGTTTA
3261930 TT
1 TT
3261932 ATGTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.62
Consensus pattern (19 bp):
TTTAGTTTATAATGGTTTA
Found at i:3262440 original size:19 final size:19
Alignment explanation
Indices: 3262398--3262441 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3262388 ACAAATAATT
3262398 TAAAAAATATAAAATTTAA
1 TAAAAAATATAAAATTTAA
* *
3262417 AAAAAAAT-TAAAAGTTTCA
1 TAAAAAATATAAAA-TTTAA
3262436 TAAAAA
1 TAAAAA
3262442 TTCAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAAAAATATAAAATTTAA
Found at i:3264913 original size:99 final size:98
Alignment explanation
Indices: 3264742--3264940 Score: 371
Period size: 99 Copynumber: 2.0 Consensus size: 98
3264732 ATTATTCATA
* *
3264742 ATACATATGATTACTCATATGGAAATTTACAAAGTCTTCATTTTGAAGATCCAAGAAATTCCTGT
1 ATACATATGATTACTCATATAGAAATTTACAAAGTCTTCATTTTGAAGATCCAAGAAATTCATGT
3264807 TTGAGACTTTTAATTTAATACTTTTTTTATTTTC
66 TTGAGACTTTTAATTTAATAC-TTTTTTATTTTC
3264841 ATACATATGATTACTCATATAGAAATTTACAAAGTCTTCATTTTGAAGATCCAAGAAATTCATGT
1 ATACATATGATTACTCATATAGAAATTTACAAAGTCTTCATTTTGAAGATCCAAGAAATTCATGT
3264906 TTGAGACTTTTAATTTAATACTTTTTTATTTTC
66 TTGAGACTTTTAATTTAATACTTTTTTATTTTC
3264939 AT
1 AT
3264941 TTTTAATTAA
Statistics
Matches: 98, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
98 14 0.14
99 84 0.86
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (98 bp):
ATACATATGATTACTCATATAGAAATTTACAAAGTCTTCATTTTGAAGATCCAAGAAATTCATGT
TTGAGACTTTTAATTTAATACTTTTTTATTTTC
Found at i:3272336 original size:350 final size:350
Alignment explanation
Indices: 3271695--3272394 Score: 1400
Period size: 350 Copynumber: 2.0 Consensus size: 350
3271685 GATAAAATAT
3271695 GAAATTGATACCAATATAAAATTTTAACACGAATATTTTATGGCATCATCAATAATTCAATTTAA
1 GAAATTGATACCAATATAAAATTTTAACACGAATATTTTATGGCATCATCAATAATTCAATTTAA
3271760 TAGAAATTTATAAAAATTTAATATGATTAAACAGTTCAATAACATAAATAGTATAAAGTGTAAAA
66 TAGAAATTTATAAAAATTTAATATGATTAAACAGTTCAATAACATAAATAGTATAAAGTGTAAAA
3271825 TTTAATTTAATAATATAAATAGTATATATAAATACTATTTAGGTTTAGGGATCTTTTTTTGGATG
131 TTTAATTTAATAATATAAATAGTATATATAAATACTATTTAGGTTTAGGGATCTTTTTTTGGATG
3271890 ATTTTTTATTTGGGGGTAAAGAGAGAAAAGTTAAAGTTTAGGAAAAATATAAAAAGCTTTGAGGG
196 ATTTTTTATTTGGGGGTAAAGAGAGAAAAGTTAAAGTTTAGGAAAAATATAAAAAGCTTTGAGGG
3271955 TTAGAGGAGTAAAATTTTGGGGGGAAGTAAATGGGGGAAAAATATTTTTAAAAAAATTGAGGGGG
261 TTAGAGGAGTAAAATTTTGGGGGGAAGTAAATGGGGGAAAAATATTTTTAAAAAAATTGAGGGGG
3272020 GGGGATGGGTTTGGGGTAGATGGGG
326 GGGGATGGGTTTGGGGTAGATGGGG
3272045 GAAATTGATACCAATATAAAATTTTAACACGAATATTTTATGGCATCATCAATAATTCAATTTAA
1 GAAATTGATACCAATATAAAATTTTAACACGAATATTTTATGGCATCATCAATAATTCAATTTAA
3272110 TAGAAATTTATAAAAATTTAATATGATTAAACAGTTCAATAACATAAATAGTATAAAGTGTAAAA
66 TAGAAATTTATAAAAATTTAATATGATTAAACAGTTCAATAACATAAATAGTATAAAGTGTAAAA
3272175 TTTAATTTAATAATATAAATAGTATATATAAATACTATTTAGGTTTAGGGATCTTTTTTTGGATG
131 TTTAATTTAATAATATAAATAGTATATATAAATACTATTTAGGTTTAGGGATCTTTTTTTGGATG
3272240 ATTTTTTATTTGGGGGTAAAGAGAGAAAAGTTAAAGTTTAGGAAAAATATAAAAAGCTTTGAGGG
196 ATTTTTTATTTGGGGGTAAAGAGAGAAAAGTTAAAGTTTAGGAAAAATATAAAAAGCTTTGAGGG
3272305 TTAGAGGAGTAAAATTTTGGGGGGAAGTAAATGGGGGAAAAATATTTTTAAAAAAATTGAGGGGG
261 TTAGAGGAGTAAAATTTTGGGGGGAAGTAAATGGGGGAAAAATATTTTTAAAAAAATTGAGGGGG
3272370 GGGGATGGGTTTGGGGTAGATGGGG
326 GGGGATGGGTTTGGGGTAGATGGGG
3272395 TAGGGGTGAG
Statistics
Matches: 350, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
350 350 1.00
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (350 bp):
GAAATTGATACCAATATAAAATTTTAACACGAATATTTTATGGCATCATCAATAATTCAATTTAA
TAGAAATTTATAAAAATTTAATATGATTAAACAGTTCAATAACATAAATAGTATAAAGTGTAAAA
TTTAATTTAATAATATAAATAGTATATATAAATACTATTTAGGTTTAGGGATCTTTTTTTGGATG
ATTTTTTATTTGGGGGTAAAGAGAGAAAAGTTAAAGTTTAGGAAAAATATAAAAAGCTTTGAGGG
TTAGAGGAGTAAAATTTTGGGGGGAAGTAAATGGGGGAAAAATATTTTTAAAAAAATTGAGGGGG
GGGGATGGGTTTGGGGTAGATGGGG
Found at i:3272505 original size:19 final size:18
Alignment explanation
Indices: 3272468--3272506 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3272458 ACGAATCAAG
* *
3272468 TTATTCGAGTTAATCGAA
1 TTATTCGAATCAATCGAA
3272486 TTATTCGAATCAACTCGAA
1 TTATTCGAATCAA-TCGAA
3272505 TT
1 TT
3272507 TTGTTTTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (18 bp):
TTATTCGAATCAATCGAA
Found at i:3273347 original size:19 final size:20
Alignment explanation
Indices: 3273310--3273348 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3273300 AAGTGGGAGG
*
3273310 AAGTAAAAATATTTGGGGGA
1 AAGTAAAAAGATTTGGGGGA
*
3273330 AAGTAAAAAGGTTTGGGGG
1 AAGTAAAAAGATTTGGGGG
3273349 TTTGAGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.36, T:0.23
Consensus pattern (20 bp):
AAGTAAAAAGATTTGGGGGA
Found at i:3275862 original size:27 final size:26
Alignment explanation
Indices: 3275830--3275911 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 26
3275820 AGACAGTCAT
* *
3275830 TTCATATTTTGCCACAAAGGCATTCC
1 TTCATATTGTACCACAAAGGCATTCC
* *
3275856 TTCCATATTGCACCACAAGGGCATTCC
1 TT-CATATTGTACCACAAAGGCATTCC
**
3275883 ATTCATATTGTACCACAAAGTTATTCC
1 -TTCATATTGTACCACAAAGGCATTCC
3275910 TT
1 TT
3275912 ATCTATCGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
26 4 0.09
27 40 0.87
28 2 0.04
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (26 bp):
TTCATATTGTACCACAAAGGCATTCC
Found at i:3278133 original size:13 final size:13
Alignment explanation
Indices: 3278112--3278145 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3278102 TCTTTGATTT
3278112 ATTATTTTATTTTA
1 ATTA-TTTATTTTA
*
3278126 GTTATTTATTTTA
1 ATTATTTATTTTA
3278139 ATTATTT
1 ATTATTT
3278146 TATCTGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
ATTATTTATTTTA
Found at i:3289006 original size:2 final size:2
Alignment explanation
Indices: 3288999--3289028 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3288989 TTGATATTTC
3288999 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
3289029 CTAACTCAGG
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):
AT
Found at i:3291028 original size:2 final size:2
Alignment explanation
Indices: 3291021--3291048 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3291011 NNNNNATTGC
3291021 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
3291049 CATTAACTGA
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:3307093 original size:85 final size:85
Alignment explanation
Indices: 3306950--3307113 Score: 310
Period size: 85 Copynumber: 1.9 Consensus size: 85
3306940 CGAACGGTCT
3306950 TCTCCGTTATTCTTGTACTACAAACCGCTTCAAGTGTGGGCTCGAACAATTACGAACCAAACATA
1 TCTCCGTTATTCTTGTACTACAAACCGCTTCAAGTGTGGGCTCGAACAATTACGAACCAAACATA
3307015 AAACCAAAAATAATGTCTTC
66 AAACCAAAAATAATGTCTTC
*
3307035 TCTCCGTTATTCTTGTACTACAAACTGCTTCAAGTGTGGGCTCGAACAATTACGAACCAAACATA
1 TCTCCGTTATTCTTGTACTACAAACCGCTTCAAGTGTGGGCTCGAACAATTACGAACCAAACATA
*
3307100 AAACTAAAAATAAT
66 AAACCAAAAATAAT
3307114 TTTCTTACTT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 77 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (85 bp):
TCTCCGTTATTCTTGTACTACAAACCGCTTCAAGTGTGGGCTCGAACAATTACGAACCAAACATA
AAACCAAAAATAATGTCTTC
Found at i:3309539 original size:3 final size:3
Alignment explanation
Indices: 3309504--3309586 Score: 55
Period size: 3 Copynumber: 28.0 Consensus size: 3
3309494 TTTAGCACTT
* * ***
3309504 TTA TTA TT- TTA GTTAA TTA TT- TTA ATG TTA TTA TTA TTA TTA GCG
1 TTA TTA TTA TTA -TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
3309549 TTG TCA TTA TTA TTA TTA TTA TTA CTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3309587 ATATAATTGC
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
2 6 0.10
3 50 0.82
4 4 0.07
5 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:3314150 original size:9 final size:9
Alignment explanation
Indices: 3314138--3314188 Score: 93
Period size: 9 Copynumber: 5.6 Consensus size: 9
3314128 ATAAAACAAT
3314138 AAAAAAAAG
1 AAAAAAAAG
3314147 AAAAAAAAG
1 AAAAAAAAG
3314156 AAAAAAAAG
1 AAAAAAAAG
3314165 AAAAAAAAG
1 AAAAAAAAG
3314174 AAAAAAAATG
1 AAAAAAAA-G
3314184 AAAAA
1 AAAAA
3314189 GGAGAGGCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
9 35 0.85
10 6 0.15
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:3314188 original size:1 final size:1
Alignment explanation
Indices: 3314138--3314181 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
3314128 ATAAAACAAT
* * * *
3314138 AAAAAAAAGAAAAAAAAGAAAAAAAAGAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3314182 TGAAAAAGGA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:3315005 original size:8 final size:8
Alignment explanation
Indices: 3314992--3315027 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
3314982 AGTCGAACAA
3314992 AAAAAATG
1 AAAAAATG
3315000 AAAAAAATG
1 -AAAAAATG
3315009 -AAAAATG
1 AAAAAATG
3315016 AAAAAATG
1 AAAAAATG
3315024 AAAA
1 AAAA
3315028 GTAAAAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.27
8 11 0.42
9 8 0.31
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:3315005 original size:9 final size:9
Alignment explanation
Indices: 3314991--3315027 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
3314981 GAGTCGAACA
3314991 AAAAAAATG
1 AAAAAAATG
3315000 AAAAAAATG
1 AAAAAAATG
3315009 --AAAAATG
1 AAAAAAATG
3315016 -AAAAAATG
1 AAAAAAATG
3315024 AAAA
1 AAAA
3315028 GTAAAAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.27
8 7 0.27
9 12 0.46
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAAAAATG
Found at i:3315014 original size:16 final size:15
Alignment explanation
Indices: 3314993--3315027 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3314983 GTCGAACAAA
3314993 AAAAATGAAAAAAATG
1 AAAAATG-AAAAAATG
3315009 AAAAATGAAAAAATG
1 AAAAATGAAAAAATG
3315024 AAAA
1 AAAA
3315028 GTAAAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (15 bp):
AAAAATGAAAAAATG
Found at i:3315034 original size:15 final size:15
Alignment explanation
Indices: 3314993--3315034 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
3314983 GTCGAACAAA
3314993 AAAAATGAAAAAAATG
1 AAAAAT-AAAAAAATG
*
3315009 AAAAATGAAAAAATG
1 AAAAATAAAAAAATG
*
3315024 AAAAGTAAAAA
1 AAAAATAAAAA
3315035 TGGAGAGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAAAATG
Found at i:3315191 original size:43 final size:42
Alignment explanation
Indices: 3315111--3315212 Score: 98
Period size: 43 Copynumber: 2.4 Consensus size: 42
3315101 GAAAATGTCT
** * * * *
3315111 GCTCAAATTTTTGATCATGGTGGGACATTAGGTGATCAGAG-C
1 GCTCAAA-TTTTGATCAAAGTGGGACATGAGGCGATCAAAGAA
* *
3315153 GACTCAAATTTTGGATCAAATTGGGGCATGAGGCGATCAAAGAA
1 G-CTCAAATTTT-GATCAAAGTGGGACATGAGGCGATCAAAGAA
3315197 GCTCAAATTTTGATCA
1 GCTCAAATTTTGATCA
3315213 GATCAGGGCA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
42 10 0.20
43 38 0.78
44 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.28
Consensus pattern (42 bp):
GCTCAAATTTTGATCAAAGTGGGACATGAGGCGATCAAAGAA
Found at i:3316388 original size:46 final size:46
Alignment explanation
Indices: 3316328--3316645 Score: 438
Period size: 46 Copynumber: 6.9 Consensus size: 46
3316318 CAATGAAGTT
*
3316328 GCAGATCTTTTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATA
1 GCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATA
** * *
3316374 ATAGATCTTGTCTTCCTGTACTTGGCAGCGGAGGAGATCGAATATA
1 GCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATA
* *
3316420 GTAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATTGAAGATA
1 GCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATA
3316466 GCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATA
1 GCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATA
* * ** * *
3316512 GCAGATCTTATCTTTCTGTATTTGGCAGCAAAAGAGATCAAAGATA
1 GCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATA
* * **
3316558 GCAGATCTTGTCTTCCTATATTTGGCAGCGGAGAAGATTAAAGATA
1 GCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATA
* * * * *
3316604 GCAGATCATGTTTTCCTATATTTAGCAGCGGAGTAGATCGAA
1 GCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAA
3316646 AATGGTGAAT
Statistics
Matches: 241, Mismatches: 31, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 241 1.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (46 bp):
GCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGATA
Found at i:3316862 original size:44 final size:44
Alignment explanation
Indices: 3316684--3316867 Score: 108
Period size: 44 Copynumber: 4.2 Consensus size: 44
3316674 TGGAGAAGTG
* * * *
3316684 GATTTAAGCCATTAG-TCCTATCACCCTAAGCAGTAGTGGAGTA
1 GATTGAAGCCATTAGATCCTATCTCCCTAAGCAGTAGTGAAGCA
* * * *
3316727 GGTTGAAG--ATTACAGATTCTGTCTCCCTAAGCAGTAGTGGAGCA
1 GATTGAAGCCATT--AGATCCTATCTCCCTAAGCAGTAGTGAAGCA
* ** * * * * * *
3316771 GATCGAAGATAGT-GAATCTTATCTTCCC-AAGATAGTGGAGAAACA
1 GATTGAAGCCATTAG-ATCCTATC-TCCCTAAG-CAGTAGTGAAGCA
* *
3316816 GATTTAAGCCATTAGATCCTGTCTCCCTAAGCAGTAGTGAAGCA
1 GATTGAAGCCATTAGATCCTATCTCCCTAAGCAGTAGTGAAGCA
*
3316860 GATCGAAG
1 GATTGAAG
3316868 ACAGTAAATC
Statistics
Matches: 101, Mismatches: 30, Indels: 19
0.67 0.20 0.13
Matches are distributed among these distances:
41 3 0.03
43 9 0.09
44 57 0.56
45 29 0.29
46 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (44 bp):
GATTGAAGCCATTAGATCCTATCTCCCTAAGCAGTAGTGAAGCA
Found at i:3316888 original size:45 final size:44
Alignment explanation
Indices: 3316750--3316888 Score: 109
Period size: 45 Copynumber: 3.1 Consensus size: 44
3316740 AGATTCTGTC
* * *
3316750 TCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGTGAATCTTATCT
1 TCCCTAAGCAGTAGTGAAGCAGATCGAAGACAGTAAATCTTAT-T
* * * * ** * * * * * *
3316795 TCCC-AAGATAGTGGAGAAACAGATTTAAGCCATTAGATCCTGTC
1 TCCCTAAG-CAGTAGTGAAGCAGATCGAAGACAGTAAATCTTATT
3316839 TCCCTAAGCAGTAGTGAAGCAGATCGAAGACAGTAAATCTTACTT
1 TCCCTAAGCAGTAGTGAAGCAGATCGAAGACAGTAAATCTTA-TT
3316884 TCCCT
1 TCCCT
3316889 GGCAGTACAG
Statistics
Matches: 64, Mismatches: 27, Indels: 6
0.66 0.28 0.06
Matches are distributed among these distances:
44 30 0.47
45 34 0.53
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (44 bp):
TCCCTAAGCAGTAGTGAAGCAGATCGAAGACAGTAAATCTTATT
Found at i:3316979 original size:51 final size:51
Alignment explanation
Indices: 3316907--3317787 Score: 262
Period size: 51 Copynumber: 17.4 Consensus size: 51
3316897 AGTGGAACAA
* * * *
3316907 ATTGAATCTACAATGGCGAATCTCGTTTTCCTTGACATTACAATTTAAAGG
1 ATTGAAGCCACAACGGCGAATCTCGTTTTCCTTGACATTGCAATTTAAAGG
* * * * ** * ****
3316958 ATTGAAGCCACAACGGTGAATCT--TACTT-CTCAGGCGGTGGAGCGGAATA-G
1 ATTGAAGCCACAACGGCGAATCTCGT-TTTCCT-TGACATTGCAATTTAA-AGG
* * *
3317008 ATTGAAGCTACAACGACGAATCTCGTTTTCCCTGACATTGCAATTTAAAGG
1 ATTGAAGCCACAACGGCGAATCTCGTTTTCCTTGACATTGCAATTTAAAGG
* ** * *** *
3317059 ATTGAAGCCACAACGGCAAATCT--TATTT-CTTAGACGGTG-TAGCGAAACAG
1 ATTGAAGCCACAACGGCGAATCTCGT-TTTCCTT-GACATTGCAATTTAAA-GG
* * *
3317109 ATTGAAGCTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGG
1 ATTGAAGCCACAACGGCGAATCTCGTTTTCCTTGACATTGCAATTTAAAGG
* * * ** * *** *
3317160 ATTGAAGCCATAACGGCGAATCT--TACTT-CTCAGGTAGTGC-AGCGAAATAG
1 ATTGAAGCCACAACGGCGAATCTCGT-TTTCCT-TGACATTGCAATTTAAA-GG
* * * * **
3317210 ATTGAAGCTACAACGGTGAATCTCGTTTTCCCTGACATTACAATTTAAAAT
1 ATTGAAGCCACAACGGCGAATCTCGTTTTCCTTGACATTGCAATTTAAAGG
* * ** ****
3317261 ATTGAAGCCACAACGGCGAAT-T--TTACTT-CTCAGGCGGTGCAGCGGAACA-G
1 ATTGAAGCCACAACGGCGAATCTCGTT--TTCCT-TGACATTGCAATTTAA-AGG
* ** * *
3317311 ATTAAAGTTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGG
1 ATTGAAGCCACAACGGCGAATCTCGTTTTCCTTGACATTGCAATTTAAAGG
* * * * * ** *** *
3317362 ATTGACGCCACAACGGTGAATCT--TACTT-CTCAGGCGGTGC-AGCGAAACAG
1 ATTGAAGCCACAACGGCGAATCTCGT-TTTCCT-TGACATTGCAATTTAAA-GG
* * * *
3317412 ATTGAAGCTACAATGACGAATCTCGTTTTCCCTGACATTGCAATTTAAAGG
1 ATTGAAGCCACAACGGCGAATCTCGTTTTCCTTGACATTGCAATTTAAAGG
* * ** ****
3317463 ATTGAAGCCACAACGGCGAATCT--TCTTT-CTCAGGCGGTGCAGCAGAACA-G
1 ATTGAAGCCACAACGGCGAATCTCGT-TTTCCT-TGACATTGCAATTTAA-AGG
* * * * * *
3317513 ATTGAGGCTACAATGACGAATCTTGTTTTCCCTGACATTGCAATTTAAAGG
1 ATTGAAGCCACAACGGCGAATCTCGTTTTCCTTGACATTGCAATTTAAAGG
* * * ** * *** *
3317564 ATTGAAGCCACAACGGCAAATCT--TACTT-CTCAGACGGTG-TAGCGAAACAG
1 ATTGAAGCCACAACGGCGAATCTCGT-TTTCCT-TGACATTGCAATTTAAA-GG
* * * *
3317614 ATTGAAGCTACAATGGCAAATCTCGTTTTCCCTGACATTGCAATTTAAAGG
1 ATTGAAGCCACAACGGCGAATCTCGTTTTCCTTGACATTGCAATTTAAAGG
* * * * ** *** *
3317665 ATTGAAGCCACAACGGTGAATCT--TACTT-CTCAGGCGGTGC-AGCGAAACAG
1 ATTGAAGCCACAACGGCGAATCTCGT-TTTCCT-TGACATTGCAATTTAAA-GG
* * * *
3317715 ATTGAAGCTACAACGGCGAATCTCGTTTTCCCTGTCCTTGCAATTTAAAGG
1 ATTGAAGCCACAACGGCGAATCTCGTTTTCCTTGACATTGCAATTTAAAGG
*
3317766 ATTGAAGCCACAACGGTGAATC
1 ATTGAAGCCACAACGGCGAATC
3317788 CTACTTCTCA
Statistics
Matches: 557, Mismatches: 215, Indels: 116
0.63 0.24 0.13
Matches are distributed among these distances:
48 2 0.00
49 37 0.07
50 231 0.41
51 249 0.45
52 36 0.06
53 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (51 bp):
ATTGAAGCCACAACGGCGAATCTCGTTTTCCTTGACATTGCAATTTAAAGG
Found at i:3317082 original size:101 final size:101
Alignment explanation
Indices: 3316902--3317819 Score: 1390
Period size: 101 Copynumber: 9.1 Consensus size: 101
3316892 AGTACAGTGG
* * * *
3316902 AACAAATTGAATCTACAATGGCGAATCTCGTTTTCCTTGACATTACAATTTAAAGGATTGAAGCC
1 AACAGATTGAAGCTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
* * *
3316967 ACAACGGTGAATCTTACTTCTCAGGCGGTGGAGCGG
66 ACAACGGCGAATCTTACTTCTCAGGCGGTGCAGCGA
* * *
3317003 AATAGATTGAAGCTACAACGACGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
1 AACAGATTGAAGCTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
* * * * *
3317068 ACAACGGCAAATCTTATTTCTTAGACGGTGTAGCGA
66 ACAACGGCGAATCTTACTTCTCAGGCGGTGCAGCGA
3317104 AACAGATTGAAGCTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
1 AACAGATTGAAGCTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
* **
3317169 ATAACGGCGAATCTTACTTCTCAGGTAGTGCAGCGA
66 ACAACGGCGAATCTTACTTCTCAGGCGGTGCAGCGA
* * * * **
3317205 AATAGATTGAAGCTACAACGGTGAATCTCGTTTTCCCTGACATTACAATTTAAAATATTGAAGCC
1 AACAGATTGAAGCTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
* *
3317270 ACAACGGCGAATTTTACTTCTCAGGCGGTGCAGCGG
66 ACAACGGCGAATCTTACTTCTCAGGCGGTGCAGCGA
* * *
3317306 AACAGATTAAAGTTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGACGCC
1 AACAGATTGAAGCTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
*
3317371 ACAACGGTGAATCTTACTTCTCAGGCGGTGCAGCGA
66 ACAACGGCGAATCTTACTTCTCAGGCGGTGCAGCGA
*
3317407 AACAGATTGAAGCTACAATGACGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
1 AACAGATTGAAGCTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
3317472 ACAACGGCGAATCTT-CTTTCTCAGGCGGTGCAGC-A
66 ACAACGGCGAATCTTAC-TTCTCAGGCGGTGCAGCGA
* * *
3317507 GAACAGATTGAGGCTACAATGACGAATCTTGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGC
1 -AACAGATTGAAGCTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGC
* * *
3317572 CACAACGGCAAATCTTACTTCTCAGACGGTGTAGCGA
65 CACAACGGCGAATCTTACTTCTCAGGCGGTGCAGCGA
*
3317609 AACAGATTGAAGCTACAATGGCAAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
1 AACAGATTGAAGCTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
*
3317674 ACAACGGTGAATCTTACTTCTCAGGCGGTGCAGCGA
66 ACAACGGCGAATCTTACTTCTCAGGCGGTGCAGCGA
* * *
3317710 AACAGATTGAAGCTACAACGGCGAATCTCGTTTTCCCTGTCCTTGCAATTTAAAGGATTGAAGCC
1 AACAGATTGAAGCTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
* * * *
3317775 ACAACGGTGAATCCTACTTCTCAGACGGTGCAGCAA
66 ACAACGGCGAATCTTACTTCTCAGGCGGTGCAGCGA
3317811 AACAGATTG
1 AACAGATTG
3317820 CAGCCAAAAA
Statistics
Matches: 740, Mismatches: 73, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
100 2 0.00
101 736 0.99
102 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (101 bp):
AACAGATTGAAGCTACAATGGCGAATCTCGTTTTCCCTGACATTGCAATTTAAAGGATTGAAGCC
ACAACGGCGAATCTTACTTCTCAGGCGGTGCAGCGA
Found at i:3319513 original size:5 final size:5
Alignment explanation
Indices: 3319503--3319528 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3319493 TGAGCATTCG
3319503 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
3319529 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:3320086 original size:29 final size:31
Alignment explanation
Indices: 3320048--3320106 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
3320038 GGAGGTGGGA
3320048 TGGGAAGGGAAT-AAAAGTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAAGTTTAGGGGAAAAG
* * *
3320078 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAAGTTTAGGGGAAAA
3320107 TAAAATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAAGTTTAGGGGAAAAG
Found at i:3320341 original size:9 final size:9
Alignment explanation
Indices: 3320327--3320363 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
3320317 TATAGTTTGA
3320327 TATTCGAAT
1 TATTCGAAT
3320336 TATTCGAAT
1 TATTCGAAT
*
3320345 TATTCGAGT
1 TATTCGAAT
3320354 TATTCGAAT
1 TATTCGAAT
3320363 T
1 T
3320364 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:3322623 original size:69 final size:69
Alignment explanation
Indices: 3322512--3322671 Score: 230
Period size: 69 Copynumber: 2.3 Consensus size: 69
3322502 ATTCACAAAT
* * * * * *
3322512 ATTTGGATAGCAGTAAAAACATTTGGACAGCATTGACTTGTACCAAACATGGACAGCATTTAAGC
1 ATTTGGACAGCATTAATAACATTCGGACAGCATTGACTTGTACCAAAAATGGACAACATTTAAGC
*
3322577 ATTA
66 ACTA
* *
3322581 ATTTGGACAGCATTAATAACATTCGGATAGCATTGATTTGTACCAAAAATGGACAACATTTAAGC
1 ATTTGGACAGCATTAATAACATTCGGACAGCATTGACTTGTACCAAAAATGGACAACATTTAAGC
3322646 ACTA
66 ACTA
*
3322650 AGTTGGACAGCATTAATAACAT
1 ATTTGGACAGCATTAATAACAT
3322672 GTAAAAATAG
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 81 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (69 bp):
ATTTGGACAGCATTAATAACATTCGGACAGCATTGACTTGTACCAAAAATGGACAACATTTAAGC
ACTA
Found at i:3325590 original size:12 final size:12
Alignment explanation
Indices: 3325562--3325599 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3325552 TTTTTCACTG
*
3325562 TTTTGCTACTA-
1 TTTTCCTACTAT
3325573 TTTTCCTACTAT
1 TTTTCCTACTAT
*
3325585 TTTTCCAACTAT
1 TTTTCCTACTAT
3325597 TTT
1 TTT
3325600 GCTGTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.58
Consensus pattern (12 bp):
TTTTCCTACTAT
Found at i:3326948 original size:3 final size:3
Alignment explanation
Indices: 3326940--3326988 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
3326930 CCATTTTCAC
*
3326940 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAC CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
3326988 C
1 C
3326989 TATCTCTTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:3328425 original size:76 final size:76
Alignment explanation
Indices: 3328338--3328487 Score: 221
Period size: 76 Copynumber: 2.0 Consensus size: 76
3328328 AACTTAATAC
* * ** *
3328338 ATTTTTTTGTAT-AACCACAAGTGTCCTTATAGATTTTTTATTTTACAATATAATTTAATATATT
1 ATTTTTTTGTATGAA-CACAAGTGTCCTTACAGATTTTTTATTTTAAAATATAACCTAATATAAT
3328402 TTTAATATTTTA
65 TTTAATATTTTA
* *
3328414 ATTTTTTTGTATGAACACAAGTGTCCTTGCCGATTTTTTATTTTAAAATATAACCTAATATAATT
1 ATTTTTTTGTATGAACACAAGTGTCCTTACAGATTTTTTATTTTAAAATATAACCTAATATAATT
3328479 TTAATATTT
66 TTAATATTT
3328488 ACATTTCTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
76 64 0.97
77 2 0.03
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (76 bp):
ATTTTTTTGTATGAACACAAGTGTCCTTACAGATTTTTTATTTTAAAATATAACCTAATATAATT
TTAATATTTTA
Found at i:3333642 original size:20 final size:21
Alignment explanation
Indices: 3333614--3333656 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3333604 AGGAGCGCCA
3333614 CAGCAAGCCCTCAAG-CGCACC
1 CAGCAAGCCC-CAAGTCGCACC
*
3333635 CAGC-AGCCCCACGTCGCACC
1 CAGCAAGCCCCAAGTCGCACC
3333655 CA
1 CA
3333657 ACGCCTCCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 13 0.65
21 4 0.20
ACGTcount: A:0.26, C:0.51, G:0.19, T:0.05
Consensus pattern (21 bp):
CAGCAAGCCCCAAGTCGCACC
Found at i:3345252 original size:17 final size:17
Alignment explanation
Indices: 3345223--3345255 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3345213 TTATATTATG
3345223 TTATTAGTTTTGTATTA
1 TTATTAGTTTTGTATTA
3345240 TTATT-GTTATTGTATT
1 TTATTAGTT-TTGTATT
3345256 TCTATTTTNN
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (17 bp):
TTATTAGTTTTGTATTA
Found at i:3349500 original size:1 final size:1
Alignment explanation
Indices: 3349489--3349569 Score: 63
Period size: 1 Copynumber: 81.0 Consensus size: 1
3349479 CTGATCTTTC
* * * * * * * * *
3349489 AAAATAAAAAAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
3349554 AGAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAA
3349570 GGTAGAGGTC
Statistics
Matches: 58, Mismatches: 22, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.86, C:0.09, G:0.04, T:0.01
Consensus pattern (1 bp):
A
Found at i:3349569 original size:6 final size:6
Alignment explanation
Indices: 3349489--3349550 Score: 101
Period size: 6 Copynumber: 10.7 Consensus size: 6
3349479 CTGATCTTTC
*
3349489 AAAATA AAAA-A AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
3349536 AAAACA AAAA-A AAAA
1 AAAACA AAAACA AAAA
3349551 GAAAGAAAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
5 10 0.18
6 45 0.82
ACGTcount: A:0.87, C:0.11, G:0.00, T:0.02
Consensus pattern (6 bp):
AAAACA
Found at i:3350431 original size:20 final size:19
Alignment explanation
Indices: 3350408--3350451 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
3350398 AAAAAATAAA
3350408 AAAAATGAATGAAAA-AAATG
1 AAAAATGAA--AAAAGAAATG
3350428 AAAAATGAAAAAAGAAATG
1 AAAAATGAAAAAAGAAATG
3350447 AAAAA
1 AAAAA
3350452 GTAAAAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.17
19 10 0.43
20 9 0.39
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (19 bp):
AAAAATGAAAAAAGAAATG
Found at i:3351217 original size:176 final size:176
Alignment explanation
Indices: 3350923--3353899 Score: 5265
Period size: 176 Copynumber: 16.9 Consensus size: 176
3350913 ATTGGAATAA
3350923 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
3350988 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3351053 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
3351099 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
3351164 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3351229 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
3351275 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
3351340 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3351405 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
3351451 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
3351516 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3351581 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
3351627 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
3351692 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3351757 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
3351803 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
3351868 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3351933 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
3351979 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
3352044 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3352109 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
3352155 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
3352220 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3352285 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
3352331 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
3352396 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3352461 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
3352507 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
3352572 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3352637 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
3352683 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
3352748 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3352813 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
3352859 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
3352924 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3352989 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
3353035 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
*
3353100 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTGACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
* *
3353165 CAGGTCGAAGACACAAACCTTGTCTCTCTCGGTTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
* * * * * *
3353211 GTTGAAGACAAAAGATCTTGCCTTCACTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTG
1 GTTGAAGACAACAGATCTTGCCTTC-CTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTA
* * * * * * * *
3353276 CCTCTCTCAGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAA
65 CCTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAA
* * * * * *
3353341 GTAAGTCAAAGACACAAACCTTACCTCTTTCGGTTGTGATGGAGCTG
130 GCAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
* * * * * * * * * *
3353388 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
* * * * * * *
3353453 CTCTCTCGGTTGTGATGGAGTTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGATAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
3353518 CAGGTCGAAGACACAAACCTTGCCTCTCTC-GATTGTGATGGAGCTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAG-TTGTGATGGAGCTG
* * * * * * *
3353564 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
* * * * * *
3353629 CTCTCTCGGTTGTGATGAAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAG
66 CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
* * *
3353694 CAGGTCGAAGACACAAACCTTACCTCTCTCGGTTGTGATGGAGGTG
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
* * ** * * * *
3353740 GTTGAAGAAAAAAGATCTTGCCTT-CTGGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTG
1 GTTGAAGACAACAGATCTTGCCTTCCT-ACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTA
* * * * *
3353804 CCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAA
65 CCTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAA
* * *
3353869 GCAGGTTGAAGACACAAGCCTTACCTCTCTC
130 GCAGGTCGAAGACACAAACCTTGCCTCTCTC
3353900 TGTTTTAGTG
Statistics
Matches: 2745, Mismatches: 52, Indels: 8
0.98 0.02 0.00
Matches are distributed among these distances:
175 3 0.00
176 2586 0.94
177 156 0.06
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (176 bp):
GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
CTCTTTCGGTTGTGATGGAGCTGGTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAG
CAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTGATGGAGCTG
Found at i:3353912 original size:88 final size:88
Alignment explanation
Indices: 3350923--3353899 Score: 4318
Period size: 88 Copynumber: 33.8 Consensus size: 88
3350913 ATTGGAATAA
* * * * * *
3350923 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3350988 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3351011 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3351076 CTCTCTCAGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3351099 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3351164 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3351187 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3351252 CTCTCTCAGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3351275 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3351340 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3351363 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3351428 CTCTCTCAGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3351451 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3351516 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3351539 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3351604 CTCTCTCAGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3351627 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3351692 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3351715 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3351780 CTCTCTCAGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3351803 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3351868 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3351891 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3351956 CTCTCTCAGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3351979 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3352044 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3352067 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3352132 CTCTCTCAGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3352155 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3352220 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3352243 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3352308 CTCTCTCAGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3352331 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3352396 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3352419 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3352484 CTCTCTCAGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3352507 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3352572 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3352595 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3352660 CTCTCTCAGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3352683 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3352748 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3352771 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3352836 CTCTCTCAGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3352859 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3352924 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3352947 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3353012 CTCTCTCAGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3353035 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3353100 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3353123 GTTTAAGATAAAATATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGT
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
3353188 CTCTCTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
3353211 GTTGAAGACAAAAGATCTTGCCTTCACTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTG
1 GTTGAAGACAAAAGATCTTGCCTTC-CTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTG
*
3353276 CCTCTCTCAGTTGTGATGGAGCTG
65 CCTCTCTCGGTTGTGATGGAGCTG
* * * * * *
3353300 GTTGAAGACAACAGATCTTGCCTTCCTACATTGACAGCGAAGTAAGTCAAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3353365 CTCTTTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
3353388 GTTTAAGATAAAATATCTTGCCTTCCTGCATTTACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3353453 CTCTCTCGGTTGTGATGGAGTTG
66 CTCTCTCGGTTGTGATGGAGCTG
*
3353476 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGATAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3353541 CTCTCTCGATTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
*
3353564 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3353629 CTCTCTCGGTTGTGATGAAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
*
3353652 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
3353717 CTCTCTCGGTTGTGATGGAGGTG
66 CTCTCTCGGTTGTGATGGAGCTG
* *
3353740 GTTGAAGAAAAAAGATCTTGCCTT-CTGGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTG
1 GTTGAAGACAAAAGATCTTGCCTTCCT-GCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTG
3353804 CCTCTCTCGGTTGTGATGGAGCTG
65 CCTCTCTCGGTTGTGATGGAGCTG
* * *
3353828 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTTGAAGACACAAGCCTTAC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
3353893 CTCTCTC
66 CTCTCTC
3353900 TGTTTTAGTG
Statistics
Matches: 2538, Mismatches: 348, Indels: 6
0.88 0.12 0.00
Matches are distributed among these distances:
87 2 0.00
88 2449 0.96
89 87 0.03
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (88 bp):
GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
CTCTCTCGGTTGTGATGGAGCTG
Found at i:3354057 original size:132 final size:132
Alignment explanation
Indices: 3353905--3354252 Score: 572
Period size: 132 Copynumber: 2.6 Consensus size: 132
3353895 CTCTCTGTTT
* * *
3353905 TAGTGGAGTAGGTTAAAGATTGCATATTCTGTCACCCTATGCAGTAGTGGAGTAGATCAAAGATG
1 TAGTGGAGTAGGTTAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATG
* * *
3353970 GTGAATCTTATCTTCCCAGTACAGTGGGGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGT
66 GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAAT
3354035 AG
131 AG
* *
3354037 TAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATG
1 TAGTGGAGTAGGTTAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATG
3354102 GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAAT
66 GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAAT
3354167 AG
131 AG
* * * *
3354169 TAGTGGAATATGTCAAAGATTGTAGATTCTGT-ATCCCTAAGCAGTAGTGGAGCAGATCAAAGAT
1 TAGTGGAGTAGGTTAAAGATTGCAGATTCTGTCA-CCCTAAGCAGTAGTGGAGCAGATCAAAGAT
3354233 GGTGAATCTTATCTTCCCAA
65 GGTGAATCTTATCTTCCCAA
3354253 GATAGTAGGG
Statistics
Matches: 201, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
131 1 0.00
132 200 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (132 bp):
TAGTGGAGTAGGTTAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATG
GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAAT
AG
Found at i:3355670 original size:3 final size:3
Alignment explanation
Indices: 3355655--3355734 Score: 63
Period size: 3 Copynumber: 26.3 Consensus size: 3
3355645 ATCATTTTGT
* * *
3355655 TTA TTA TTT TTA TTA TTTA TTA TTA TTA TCT- TTA CTA TTA CTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* * * * *
3355701 GTA TTA TTA CTA ATA TTA TTA TTA CTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3355735 ATTTACACTT
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
2 1 0.02
3 54 0.92
4 4 0.07
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:3359589 original size:44 final size:44
Alignment explanation
Indices: 3359434--3359629 Score: 259
Period size: 44 Copynumber: 4.5 Consensus size: 44
3359424 CAGTGGAATC
*
3359434 GATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTA
1 GATCGAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTA
* * * * * * *
3359478 GATCAAAGATAGCAGATCTTGTCTTCCTATACTGGTGGCGAGGTA
1 GATCGAAGATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTA
* * *
3359523 GATCGAAGAAAGAAGATCTTGTCTTCATTTATTGGCGTGAAGTA
1 GATCGAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTA
*
3359567 GATCGAAGATAGCAGATTTTGTCTTCATGTATTGGCGTGAAGTA
1 GATCGAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTA
*
3359611 GATCGAAGATA-CAAATCTT
1 GATCGAAGATAGCAGATCTT
3359630 ATCCCCCTGA
Statistics
Matches: 128, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
43 6 0.05
44 87 0.68
45 35 0.27
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (44 bp):
GATCGAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTA
Found at i:3367886 original size:28 final size:28
Alignment explanation
Indices: 3367846--3367904 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
3367836 ACCATACCAA
*
3367846 CCTTTCTAGTCCTCTAATTTGTGTCGGG
1 CCTTTCTAGTCCTATAATTTGTGTCGGG
*
3367874 CCTTTCTAGTCCTATAATTTGTGTCGTG
1 CCTTTCTAGTCCTATAATTTGTGTCGGG
3367902 CCT
1 CCT
3367905 AAGTATGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (28 bp):
CCTTTCTAGTCCTATAATTTGTGTCGGG
Found at i:3368080 original size:27 final size:25
Alignment explanation
Indices: 3368050--3368100 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
3368040 TTAAATTTTT
*
3368050 TTTAAAAATATTTATTTTATTTTAATA
1 TTTAAAAAT-TTTATATT-TTTTAATA
*
3368077 TTTAATAATTTTATATTTTTTAAT
1 TTTAAAAATTTTATATTTTTTAAT
3368101 TGTTGAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTAAAAATTTTATATTTTTTAATA
Found at i:3368194 original size:147 final size:147
Alignment explanation
Indices: 3367981--3368272 Score: 568
Period size: 147 Copynumber: 2.0 Consensus size: 147
3367971 TTTATGAAAA
3367981 TCTGTCCATATTTGTAACAGATTAACCCAAACCTATTTTAGACCTACCCATTTTATTTTTTAAAT
1 TCTGTCCATATTTGTAACAGATTAACCCAAACCTATTTTAGACCTACCCATTTTATTTTTTAAAT
3368046 TTTTTTTAAAAATATTTATTTTATTTTAATATTTAATAATTTTATATTTTTTAATTG-TTGAAAG
66 TTTTTTTAAAAATATTTATTTTATTTTAATATTTAATAATTTTATATTTTTTAATTGATTGAAAG
3368110 ATTTTTTATATAGTTAAG
131 A-TTTTTATATAGTTAAG
3368128 TCTGTCCATATTTGTAACAGATTAACCCAAACCTATTTTAGACCTACCCATTTTATTTTTTAAAT
1 TCTGTCCATATTTGTAACAGATTAACCCAAACCTATTTTAGACCTACCCATTTTATTTTTTAAAT
3368193 TTTTTTTAAAAATATTTATTTTATTTTAATATTTAATAATTTTATATTTTTTAATTGATTGAAAG
66 TTTTTTTAAAAATATTTATTTTATTTTAATATTTAATAATTTTATATTTTTTAATTGATTGAAAG
3368258 ATTTTTATATAGTTA
131 ATTTTTATATAGTTA
3368273 TCTTAACATT
Statistics
Matches: 144, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
147 136 0.94
148 8 0.06
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.52
Consensus pattern (147 bp):
TCTGTCCATATTTGTAACAGATTAACCCAAACCTATTTTAGACCTACCCATTTTATTTTTTAAAT
TTTTTTTAAAAATATTTATTTTATTTTAATATTTAATAATTTTATATTTTTTAATTGATTGAAAG
ATTTTTATATAGTTAAG
Found at i:3368227 original size:27 final size:25
Alignment explanation
Indices: 3368197--3368247 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
3368187 TTAAATTTTT
*
3368197 TTTAAAAATATTTATTTTATTTTAATA
1 TTTAAAAAT-TTTATATT-TTTTAATA
*
3368224 TTTAATAATTTTATATTTTTTAAT
1 TTTAAAAATTTTATATTTTTTAAT
3368248 TGATTGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTAAAAATTTTATATTTTTTAATA
Found at i:3371468 original size:17 final size:17
Alignment explanation
Indices: 3371446--3371479 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3371436 CAATAAAGTC
3371446 TAATATTATTATATTAA
1 TAATATTATTATATTAA
* *
3371463 TAATATTTTTATTTTAA
1 TAATATTATTATATTAA
3371480 ATTTAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATATTATTATATTAA
Found at i:3372810 original size:6 final size:6
Alignment explanation
Indices: 3372786--3372822 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
3372776 TAAACCTGCC
*
3372786 TTTCCT TTTC-T TTTC-T TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
3372823 AATATTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:3380092 original size:18 final size:18
Alignment explanation
Indices: 3380053--3380114 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
3380043 TCATAAAAAG
**
3380053 TAAAATTTTAAATTTCAT-
1 TAAAATTTTAAAAAT-ATA
3380071 TAAAATTTTAAAAATATA
1 TAAAATTTTAAAAATATA
3380089 TAAAATTAAACTTAAAAATATA
1 TAAAATT----TTAAAAATATA
3380111 TAAA
1 TAAA
3380115 TTCTATCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 2 0.05
18 20 0.54
22 15 0.41
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTTAAAAATATA
Found at i:3382896 original size:22 final size:23
Alignment explanation
Indices: 3382843--3382896 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 23
3382833 GATGAAATCG
*
3382843 AAATTAAATTATAATTTTTATGAT
1 AAATTAAA-TATAATTTTCATGAT
* *
3382867 AAA-AAAATATAA-TTTCATTAT
1 AAATTAAATATAATTTTCATGAT
3382888 AAATTAAAT
1 AAATTAAAT
3382897 TTTAAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 10 0.40
22 9 0.36
23 3 0.12
24 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
AAATTAAATATAATTTTCATGAT
Found at i:3385576 original size:31 final size:32
Alignment explanation
Indices: 3385527--3385590 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
3385517 ATACCTATAC
*
3385527 TATTTTTTTCTATCAATTTGGCCCTTATACTT
1 TATTTTTGTCTATCAATTTGGCCCTTATACTT
* *
3385559 TATTTTTGT-TATTAATTTGGCCCTTGTACTT
1 TATTTTTGTCTATCAATTTGGCCCTTATACTT
3385590 T
1 T
3385591 GATTATGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 21 0.72
32 8 0.28
ACGTcount: A:0.17, C:0.16, G:0.09, T:0.58
Consensus pattern (32 bp):
TATTTTTGTCTATCAATTTGGCCCTTATACTT
Found at i:3389974 original size:18 final size:21
Alignment explanation
Indices: 3389951--3389998 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 21
3389941 TCTTTCTAGC
3389951 TTATTTTTATTT-ATTAA-A-
1 TTATTTTTATTTAATTAATAT
*
3389969 TTATTTTTCTTTAATTAATAT
1 TTATTTTTATTTAATTAATAT
3389990 TTATTTTTA
1 TTATTTTTA
3389999 AAATTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 5 0.20
20 1 0.04
21 8 0.32
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTATTTTTATTTAATTAATAT
Found at i:3390180 original size:23 final size:22
Alignment explanation
Indices: 3390154--3390215 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
3390144 CCCTGTATAG
*
3390154 TATGTGAACCGTACATGTTTAGT
1 TATGTGAACCATACATGTTTA-T
* *
3390177 TATGTGAAACATACTTGTTTAT
1 TATGTGAACCATACATGTTTAT
* *
3390199 TATGCGAACCCTACATG
1 TATGTGAACCATACATG
3390216 ATAAAATATG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (22 bp):
TATGTGAACCATACATGTTTAT
Found at i:3390481 original size:181 final size:181
Alignment explanation
Indices: 3390177--3390544 Score: 709
Period size: 181 Copynumber: 2.0 Consensus size: 181
3390167 CATGTTTAGT
3390177 TATGTGAAACATACTTGTTTATTATGCGAACCCTACATGATAAAATATGTGAACCCTAGGCACAT
1 TATGTGAAACATACTTGTTTATTATGCGAACCCTACATGATAAAATATGTGAACCCTAGGCACAT
3390242 GCTACATAGGACGAGCGAACCCGATATAGTATGCAGATCGTACATGTTTAATTATGCAAACTGTA
66 GCTACATAGGACGAGCGAACCCGATATAGTATGCAGATCGTACATGTTTAATTATGCAAACTGTA
*
3390307 TGTGCGAGCCCTTATGAGCAAGCCTATGTGCGAAACCCAATCTGTGAGCCC
131 TGTGCGAGCCCGTATGAGCAAGCCTATGTGCGAAACCCAATCTGTGAGCCC
*
3390358 TATGTGAAACATACTTGTTTATTATGCGAACCCTATATGATAAAATATGTGAACCCTAGGCACAT
1 TATGTGAAACATACTTGTTTATTATGCGAACCCTACATGATAAAATATGTGAACCCTAGGCACAT
3390423 GCTACATAGGACGAGCGAACCCGATATAGTATGCAGATCGTACATGTTTAATTATGCAAACTGTA
66 GCTACATAGGACGAGCGAACCCGATATAGTATGCAGATCGTACATGTTTAATTATGCAAACTGTA
*
3390488 TGTGCGAGCCCGTATGAGCGAGCCTATGTGCGAAACCCAATCTGTGAGCCC
131 TGTGCGAGCCCGTATGAGCAAGCCTATGTGCGAAACCCAATCTGTGAGCCC
3390539 TATGTG
1 TATGTG
3390545 TGAGCCTGTG
Statistics
Matches: 184, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
181 184 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (181 bp):
TATGTGAAACATACTTGTTTATTATGCGAACCCTACATGATAAAATATGTGAACCCTAGGCACAT
GCTACATAGGACGAGCGAACCCGATATAGTATGCAGATCGTACATGTTTAATTATGCAAACTGTA
TGTGCGAGCCCGTATGAGCAAGCCTATGTGCGAAACCCAATCTGTGAGCCC
Found at i:3390595 original size:13 final size:13
Alignment explanation
Indices: 3390576--3390630 Score: 56
Period size: 14 Copynumber: 4.0 Consensus size: 13
3390566 ATGTACAAAC
3390576 CCCCTAAGTGTGA
1 CCCCTAAGTGTGA
* *
3390589 TCCCTAATGAGTGAA
1 CCCCTAA-GTGTG-A
*
3390604 CCCCTAGGTGTGA
1 CCCCTAAGTGTGA
3390617 CCCCTAAAGTGTGA
1 CCCCT-AAGTGTGA
3390631 ACCCACATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
13 12 0.36
14 15 0.45
15 6 0.18
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (13 bp):
CCCCTAAGTGTGA
Found at i:3390614 original size:28 final size:28
Alignment explanation
Indices: 3390576--3390634 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
3390566 ATGTACAAAC
* *
3390576 CCCCTAAGTGTGATCCCTAATGAGTGAA
1 CCCCTAAGTGTGACCCCTAAAGAGTGAA
* *
3390604 CCCCTAGGTGTGACCCCTAAAGTGTGAA
1 CCCCTAAGTGTGACCCCTAAAGAGTGAA
3390632 CCC
1 CCC
3390635 ACATGAGCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (28 bp):
CCCCTAAGTGTGACCCCTAAAGAGTGAA
Found at i:3392659 original size:30 final size:30
Alignment explanation
Indices: 3392625--3392692 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
3392615 AAATATAGTT
3392625 TTTTTTATATATTTTTAAAAATAATTTCAA
1 TTTTTTATATATTTTTAAAAATAATTTCAA
3392655 TTTTTTATATATTTTTAAAAATAATTTCAA
1 TTTTTTATATATTTTTAAAAATAATTTCAA
3392685 TTTTTTAT
1 TTTTTTAT
3392693 CATTTTATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTTTATATATTTTTAAAAATAATTTCAA
Found at i:3404092 original size:27 final size:27
Alignment explanation
Indices: 3404023--3404085 Score: 119
Period size: 26 Copynumber: 2.4 Consensus size: 27
3404013 TCTCATTCCT
3404023 ATTTTACCCCCAATAAAA-TTTTGACC
1 ATTTTACCCCCAATAAAATTTTTGACC
3404049 ATTTTACCCCCAATAAAATTTTTGACC
1 ATTTTACCCCCAATAAAATTTTTGACC
3404076 ATTTTACCCC
1 ATTTTACCCC
3404086 TAGTAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 18 0.50
27 18 0.50
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.37
Consensus pattern (27 bp):
ATTTTACCCCCAATAAAATTTTTGACC
Done.