Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007996.1 Hibiscus syriacus cultivar Beakdansim tig00110446_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 213188
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:745 original size:39 final size:38
Alignment explanation
Indices: 691--794 Score: 147
Period size: 39 Copynumber: 2.7 Consensus size: 38
681 AACTTGTAAG
*
691 GTTGGAATCCTCAGTACTTTGGTATCTAGTGTGATAGGA
1 GTTGGAATCCTCAGTACTTTGGTATCTAGTGTGATA-CA
* * *
730 GTTGGAATCCACAGTACTTTGGTACCTAGTTTGATACA
1 GTTGGAATCCTCAGTACTTTGGTATCTAGTGTGATACA
768 GTTGGAATCCTC-GATACTTTGGTATCT
1 GTTGGAATCCTCAG-TACTTTGGTATCT
795 GATGTAAACT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
37 1 0.02
38 24 0.41
39 33 0.57
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (38 bp):
GTTGGAATCCTCAGTACTTTGGTATCTAGTGTGATACA
Found at i:2121 original size:7 final size:8
Alignment explanation
Indices: 2107--2131 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2097 AAAATATATA
2107 AAATTTTT
1 AAATTTTT
2115 AAATTTTT
1 AAATTTTT
2123 AAATTTTT
1 AAATTTTT
2131 A
1 A
2132 GAAGAAATAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
AAATTTTT
Found at i:9795 original size:31 final size:31
Alignment explanation
Indices: 9749--9816 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
9739 AGGAGAAATG
* * *
9749 GTCCCTAAGATTATTGATTCGTTTGATTTTA
1 GTCCCTAAGATTATTGATCCGTTCGATTGTA
* *
9780 GTCCTTAATATTATTGATCCGTTCGATTGTA
1 GTCCCTAAGATTATTGATCCGTTCGATTGTA
9811 GTCCCT
1 GTCCCT
9817 CAACCATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.46
Consensus pattern (31 bp):
GTCCCTAAGATTATTGATCCGTTCGATTGTA
Found at i:10351 original size:16 final size:17
Alignment explanation
Indices: 10330--10362 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
10320 TTAATAGAAA
10330 ATATAAAAAA-TTAAAT
1 ATATAAAAAATTTAAAT
10346 ATATAAAAAATTTAAAT
1 ATATAAAAAATTTAAAT
10363 TTTTAGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATTTAAAT
Found at i:11218 original size:35 final size:35
Alignment explanation
Indices: 11161--11263 Score: 134
Period size: 35 Copynumber: 2.9 Consensus size: 35
11151 AGGGCTGATG
* *
11161 TACATAGTTTTATTGGAGATCGTTGCACATTCACT
1 TACATAGTTTTATTGGAAATCGTTGCACACTCACT
* * **
11196 TGCATGGTTTTATTGGAAATCGTTGCACACTCGTT
1 TACATAGTTTTATTGGAAATCGTTGCACACTCACT
* *
11231 TACATAGTTTTACTGGAAATCGTTGTACACTCA
1 TACATAGTTTTATTGGAAATCGTTGCACACTCA
11264 TTATTTTAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 57 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (35 bp):
TACATAGTTTTATTGGAAATCGTTGCACACTCACT
Found at i:11792 original size:39 final size:39
Alignment explanation
Indices: 11733--11812 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
11723 AACTTGTAAG
* * *
11733 GTTGGAATCCTCAGTACTTTGGTATCTAGTGTGATAGAA
1 GTTGGAATCCACAGTACTTTGGTAGCTAGTGTGATACAA
* *
11772 GTTGGAATCCACAGTTCTTTGGTAGCTAGTTTGATACAA
1 GTTGGAATCCACAGTACTTTGGTAGCTAGTGTGATACAA
11811 GT
1 GT
11813 CCGCAGTGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (39 bp):
GTTGGAATCCACAGTACTTTGGTAGCTAGTGTGATACAA
Found at i:11830 original size:33 final size:33
Alignment explanation
Indices: 11783--11845 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
11773 TTGGAATCCA
* *
11783 CAGTTCTTTGGTAGCTAGTTTGATACAAGTCCG
1 CAGTGCTTTGGTAGCTAGTTTGATAAAAGTCCG
11816 CAGTGCTTTGGTAGCTAGTTTGATAAAAGT
1 CAGTGCTTTGGTAGCTAGTTTGATAAAAGT
11846 TGGAAACCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (33 bp):
CAGTGCTTTGGTAGCTAGTTTGATAAAAGTCCG
Found at i:13733 original size:60 final size:60
Alignment explanation
Indices: 13661--13803 Score: 173
Period size: 60 Copynumber: 2.4 Consensus size: 60
13651 TATGACTCTA
**
13661 ATTCTAAATTAGTCCCTAAACTTTTAAATATTTCAATTCCATCCTTAAACTATG-GCTGTC
1 ATTCTAAATTAGTCCCTAAACTTTTAAATATTTCAATTCCATCCCCAAACTATGAGCT-TC
* * * * * *
13721 ATTCTAGATTAGT-CCTCAAATTTTTTAATATTTCATTTTCATCCCCAAACTATGATCTTC
1 ATTCTAAATTAGTCCCT-AAACTTTTAAATATTTCAATTCCATCCCCAAACTATGAGCTTC
*
13781 ATTCTAAATTAGTCCCCAAACTT
1 ATTCTAAATTAGTCCCTAAACTT
13804 CTTTGATGAA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
59 3 0.04
60 62 0.90
61 4 0.06
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (60 bp):
ATTCTAAATTAGTCCCTAAACTTTTAAATATTTCAATTCCATCCCCAAACTATGAGCTTC
Found at i:19935 original size:14 final size:14
Alignment explanation
Indices: 19893--19954 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
19883 CTATTCGTAT
*
19893 TATATTAATAAATA
1 TATAATAATAAATA
* *
19907 CATATTAATAAATA
1 TATAATAATAAATA
*
19921 TATAATATTAAATA
1 TATAATAATAAATA
*
19935 T-TAACTAAAAAATA
1 TATAA-TAATAAATA
19949 T-TAATA
1 TATAATA
19955 TGTTTTATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
13 5 0.12
14 36 0.88
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
TATAATAATAAATA
Found at i:19963 original size:67 final size:61
Alignment explanation
Indices: 19821--19964 Score: 135
Period size: 65 Copynumber: 2.2 Consensus size: 61
19811 AAAAATTAAG
* * * *
19821 AATATTTTTTAAATTAATAAAAATACAAATATATAAATAATATTTATATTAACAAAAAATT
1 AATATGTTTTATATTAATAAAAATACAAATAAATAAATAATATTAATATTAACAAAAAATT
* * ** *
19882 ACTATTCGTATTATATTAATAAATACATATTAATAAATATATAATATTAAATATTAACTAAAAAA
1 AATA-T-GTTTTATATTAATAAA-A-ATACAAATAAATAAATAATATT-AATATTAAC--AAAAA
19947 TATT
59 -ATT
19951 AATATGTTTTATAT
1 AATATGTTTTATAT
19965 ATTTATATTT
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
61 3 0.05
62 1 0.02
63 13 0.20
64 1 0.02
65 18 0.28
66 8 0.12
67 8 0.12
68 6 0.09
69 6 0.09
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (61 bp):
AATATGTTTTATATTAATAAAAATACAAATAAATAAATAATATTAATATTAACAAAAAATT
Found at i:21468 original size:39 final size:39
Alignment explanation
Indices: 21414--21518 Score: 149
Period size: 39 Copynumber: 2.7 Consensus size: 39
21404 AACTTGTAAG
**
21414 GTTGGAATCCTCAGTACTTTGGTATCTAGTGTGATAGGA
1 GTTGGAATCCTCAGTACTTTGGTATCTAGTGTGATACAA
* * *
21453 GTTGGAATCCACAGTACTTTGGTACCTAGTTTGATACAA
1 GTTGGAATCCTCAGTACTTTGGTATCTAGTGTGATACAA
21492 GTTGGAATCCTC-GATACTTTGGTATCT
1 GTTGGAATCCTCAG-TACTTTGGTATCT
21519 GATGTAAACA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 1 0.02
39 57 0.98
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (39 bp):
GTTGGAATCCTCAGTACTTTGGTATCTAGTGTGATACAA
Found at i:25940 original size:28 final size:28
Alignment explanation
Indices: 25909--25971 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
25899 TTTTAATAAG
*
25909 TTTTATTCAGTACCTAA-ATTTTAATTTT
1 TTTTATTCAATACCTAACA-TTTAATTTT
** *
25937 TTTTAAACAATACTTAACATTTAATTTT
1 TTTTATTCAATACCTAACATTTAATTTT
25965 TTTTATT
1 TTTTATT
25972 TTAGTATCGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTATTCAATACCTAACATTTAATTTT
Found at i:28350 original size:28 final size:28
Alignment explanation
Indices: 28296--28352 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
28286 CCTCACATTA
* *
28296 ATATATATATTTTTATAATTGTTTAATT
1 ATATATATATTTTTATAATTATATAATT
*
28324 ATATATAT-TTTTTGTTAATTATATAATT
1 ATATATATATTTTT-ATAATTATATAATT
28352 A
1 A
28353 GTCTATGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (28 bp):
ATATATATATTTTTATAATTATATAATT
Found at i:28782 original size:3 final size:3
Alignment explanation
Indices: 28776--28821 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
28766 TTGTAGCAGT
28776 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28822 GTTAGTTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29723 original size:16 final size:16
Alignment explanation
Indices: 29704--29734 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29694 AAAAAAAAAC
29704 GATATACATAAAAGGA
1 GATATACATAAAAGGA
29720 GATATACATAAAAGG
1 GATATACATAAAAGG
29735 GTAAACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.19
Consensus pattern (16 bp):
GATATACATAAAAGGA
Found at i:29876 original size:31 final size:32
Alignment explanation
Indices: 29811--29876 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
29801 AGGGGAAATG
* * *
29811 GTCCCTAATGTTGTTGATCCGTTTGATTTTTA
1 GTCCCTAATATTATTGATCCGTTCGATTTTTA
29843 GTCCCTAATATTATTGATCCGTTCGA-TTTTA
1 GTCCCTAATATTATTGATCCGTTCGATTTTTA
29874 GTC
1 GTC
29877 TCTCAGCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 8 0.26
32 23 0.74
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (32 bp):
GTCCCTAATATTATTGATCCGTTCGATTTTTA
Found at i:32718 original size:29 final size:29
Alignment explanation
Indices: 32676--32772 Score: 185
Period size: 29 Copynumber: 3.3 Consensus size: 29
32666 CAGTATACAA
32676 GGACTAAATTTTAACAAATTAGAATAAAT
1 GGACTAAATTTTAACAAATTAGAATAAAT
32705 GGACTAAATTTTAACAAATTAGAATAAAT
1 GGACTAAATTTTAACAAATTAGAATAAAT
32734 GGACTAAATTTTAACAAATTAGAATAAAT
1 GGACTAAATTTTAACAAATTAGAATAAAT
*
32763 GGACTGAATT
1 GGACTAAATT
32773 CTACAAAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.31
Consensus pattern (29 bp):
GGACTAAATTTTAACAAATTAGAATAAAT
Found at i:37045 original size:26 final size:26
Alignment explanation
Indices: 37015--37065 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
37005 AATGTACTCT
37015 CATTTTAATTTAATCA-TCAAATTTTA
1 CATTTTAATTTAATCATTC-AATTTTA
*
37041 CATTTTAATTTATTCATTCAATTTT
1 CATTTTAATTTAATCATTCAATTTT
37066 GAAATTTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (26 bp):
CATTTTAATTTAATCATTCAATTTTA
Found at i:37864 original size:20 final size:20
Alignment explanation
Indices: 37839--37880 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
37829 CTTAACAGTG
37839 AATGATCAAAATAAAATTAA
1 AATGATCAAAATAAAATTAA
37859 AATGATCAAAATAAAATTAA
1 AATGATCAAAATAAAATTAA
37879 AA
1 AA
37881 CGTAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (20 bp):
AATGATCAAAATAAAATTAA
Found at i:38343 original size:65 final size:65
Alignment explanation
Indices: 38266--38387 Score: 208
Period size: 65 Copynumber: 1.9 Consensus size: 65
38256 AATCCAAACC
*
38266 CGATAAAGATGCCTTCACCCATCCCTCCCTCGGTCTATCCGTTGAGTCAAGGAATGAATGAGTGG
1 CGATAAAGATGCCTTCACCCATCCCTCCCTCGGTCTATCCGTTGACTCAAGGAATGAATGAGTGG
* * *
38331 CGATAAGGATGCCTTCACCCGTCCCTCCCTCGGTCTGTCCGTTGACTCAAGGAATGA
1 CGATAAAGATGCCTTCACCCATCCCTCCCTCGGTCTATCCGTTGACTCAAGGAATGA
38388 GTGACGATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (65 bp):
CGATAAAGATGCCTTCACCCATCCCTCCCTCGGTCTATCCGTTGACTCAAGGAATGAATGAGTGG
Found at i:38396 original size:61 final size:63
Alignment explanation
Indices: 38266--38402 Score: 197
Period size: 65 Copynumber: 2.2 Consensus size: 63
38256 AATCCAAACC
* * *
38266 CGATAAAGATGCCTTCACCCATCCCTCCCTCGGTCTATCCGTTGAGTCAAGGAATGAATGAGTGG
1 CGATAAGGATGCCTTCACCCATCCCTCCCTCGGTCTATCCGTTGACTCAAGG-A-GAATGAGTGA
* *
38331 CGATAAGGATGCCTTCACCCGTCCCTCCCTCGGTCTGTCCGTTGACTCAA-G-GAATGAGTGA
1 CGATAAGGATGCCTTCACCCATCCCTCCCTCGGTCTATCCGTTGACTCAAGGAGAATGAGTGA
38392 CGATAAGGATG
1 CGATAAGGATG
38403 AAATTAAGAG
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
61 20 0.30
64 1 0.01
65 46 0.69
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.24
Consensus pattern (63 bp):
CGATAAGGATGCCTTCACCCATCCCTCCCTCGGTCTATCCGTTGACTCAAGGAGAATGAGTGA
Found at i:40030 original size:6 final size:6
Alignment explanation
Indices: 40019--40044 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40009 AGAGGGAATT
40019 AGTGGA AGTGGA AGTGGA AGTGGA AG
1 AGTGGA AGTGGA AGTGGA AGTGGA AG
40045 GTCAAGGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (6 bp):
AGTGGA
Found at i:40548 original size:26 final size:28
Alignment explanation
Indices: 40519--40583 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
40509 AAATCAATCT
*
40519 ATAAAATTCAGTGAAT-AAAT-TAAAAA
1 ATAAAATTCAGTGAATGAAATAAAAAAA
* *
40545 ATAAAAAT-AGTGAGTGAAATAAAAAAA
1 ATAAAATTCAGTGAATGAAATAAAAAAA
40572 ATAAAATTCAGT
1 ATAAAATTCAGT
40584 TATCAAACAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 6 0.19
26 11 0.34
27 12 0.38
28 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.11, T:0.25
Consensus pattern (28 bp):
ATAAAATTCAGTGAATGAAATAAAAAAA
Found at i:45361 original size:40 final size:40
Alignment explanation
Indices: 45306--45384 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
45296 ACCGAATTGT
45306 CCAATCATGCTCACATCAGCTCCACCTTCCAGAGCCTCCA
1 CCAATCATGCTCACATCAGCTCCACCTTCCAGAGCCTCCA
*
45346 CCAATCATGCTCACATCAGCTCCAGCTTCCAGAGCCTCC
1 CCAATCATGCTCACATCAGCTCCACCTTCCAGAGCCTCC
45385 CCGGACCTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.24, C:0.44, G:0.11, T:0.20
Consensus pattern (40 bp):
CCAATCATGCTCACATCAGCTCCACCTTCCAGAGCCTCCA
Found at i:51081 original size:35 final size:35
Alignment explanation
Indices: 51033--51144 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
51023 TCTAAACCTT
* * *
51033 AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* * *
51068 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* * *
51103 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
51138 AAATTGA
1 AAATTGA
51145 GGACTATTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
Found at i:52230 original size:6 final size:6
Alignment explanation
Indices: 52221--52252 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
52211 CAACGTTCTG
*
52221 CTAATT CTAATT CTAATT CTAATT TTAATT CT
1 CTAATT CTAATT CTAATT CTAATT CTAATT CT
52253 TGGTTTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (6 bp):
CTAATT
Found at i:53227 original size:4 final size:4
Alignment explanation
Indices: 53218--53244 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
53208 CAATGCATGT
53218 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
53245 GTTGAACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:53269 original size:13 final size:13
Alignment explanation
Indices: 53251--53277 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53241 AATAGTTGAA
53251 CAGTCTTCATATG
1 CAGTCTTCATATG
53264 CAGTCTTCATATG
1 CAGTCTTCATATG
53277 C
1 C
53278 GCGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:62180 original size:18 final size:18
Alignment explanation
Indices: 62143--62189 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
62133 TATGGAATTG
*
62143 GATTCCAATT-CTTGACA
1 GATTCCAATTCCTTCACA
62160 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
62178 GATTCCAATTCC
1 GATTCCAATTCC
62190 CTCATAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:62709 original size:2 final size:2
Alignment explanation
Indices: 62702--62744 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
62692 TTACATCAAA
*
62702 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
62745 CTTAATCATC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:63018 original size:28 final size:29
Alignment explanation
Indices: 62987--63082 Score: 72
Period size: 31 Copynumber: 3.2 Consensus size: 29
62977 ATTTAATAAT
* *
62987 TATAATAATT-AATTTTATTAAATTATTA
1 TATAATAATTAAATTTAATCAAATTATTA
*
63015 TATAAAAATATTAAATTTAATCAAATTATTA
1 TAT-AATA-ATTAAATTTAATCAAATTATTA
* *
63046 CAAAATAATTTTAAAATTGT-ATCAAATTATTA
1 TATAATAA--TT-AAATT-TAATCAAATTATTA
63078 T-TAAT
1 TATAAT
63083 TTTTTGTTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
28 3 0.06
29 4 0.08
30 6 0.11
31 22 0.42
32 17 0.32
33 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (29 bp):
TATAATAATTAAATTTAATCAAATTATTA
Found at i:63032 original size:31 final size:32
Alignment explanation
Indices: 62997--63078 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
62987 TATAATAATT
*
62997 AATTTTATTAAATTATTATATAAA-AATATT-A
1 AATTTTATCAAATTATTATA-AAATAATATTAA
* * *
63028 AATTTAATCAAATTATTACAAAATAATTTTAA
1 AATTTTATCAAATTATTATAAAATAATATTAA
*
63060 AATTGTATCAAATTATTAT
1 AATTTTATCAAATTATTAT
63079 TAATTTTTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 3 0.07
31 22 0.52
32 17 0.40
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (32 bp):
AATTTTATCAAATTATTATAAAATAATATTAA
Found at i:69073 original size:24 final size:26
Alignment explanation
Indices: 69025--69074 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
69015 TATGTTCAAA
69025 TTAAAAAAAATAATTATCAATAATTTG
1 TTAAAAAAAATAATTA-CAATAATTTG
*
69052 TTAAAATAAATAATTA-AA-AATTT
1 TTAAAAAAAATAATTACAATAATTT
69075 CAAATCATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 2 0.09
27 15 0.68
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
TTAAAAAAAATAATTACAATAATTTG
Found at i:90215 original size:70 final size:71
Alignment explanation
Indices: 90136--90274 Score: 228
Period size: 70 Copynumber: 2.0 Consensus size: 71
90126 AGTAAGATAT
* *
90136 AACAGAATTTTATGTTTTATATATT-ACAAAATAGAAATGGATAATGATGATTAACATTGATAAT
1 AACAGAATTTTATATTTTATATATTAAAAAAATA-AAATGGATAATGATGATTAACATTGATAAT
90200 ATTTTGC
65 ATTTTGC
*
90207 AACA-AATTTTATATTTTATATATTAAAAAAATAAAATGGATAATGATGATTAGCATTGATAATA
1 AACAGAATTTTATATTTTATATATTAAAAAAATAAAATGGATAATGATGATTAACATTGATAATA
90271 TTTT
66 TTTT
90275 TCAATTTCTA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
70 53 0.83
71 11 0.17
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (71 bp):
AACAGAATTTTATATTTTATATATTAAAAAAATAAAATGGATAATGATGATTAACATTGATAATA
TTTTGC
Found at i:94292 original size:21 final size:21
Alignment explanation
Indices: 94266--94307 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
94256 ATTCGTTTGT
94266 AATTTCTTTAACACTCTGTGC
1 AATTTCTTTAACACTCTGTGC
94287 AATTTCTTTAACACTCTGTGC
1 AATTTCTTTAACACTCTGTGC
94308 CTATATACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.43
Consensus pattern (21 bp):
AATTTCTTTAACACTCTGTGC
Found at i:94468 original size:30 final size:30
Alignment explanation
Indices: 94434--94491 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
94424 TTAAATATAT
94434 AAATT-AAAATTTAGGATA-TAAAATGTATCA
1 AAATTGAAAATTTAGG-TACT-AAATGTATCA
*
94464 AAATTGATAATTTAGGTACTAAATGTAT
1 AAATTGAAAATTTAGGTACTAAATGTAT
94492 TAATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (30 bp):
AAATTGAAAATTTAGGTACTAAATGTATCA
Found at i:96486 original size:26 final size:25
Alignment explanation
Indices: 96457--96515 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
96447 TATAGGTACC
96457 TATTTTGACAAAATATTTTAGATACT
1 TATTTTGACAAAA-ATTTTAGATACT
** * *
96483 TATTTTGA-TTAAATTTTAGGTATT
1 TATTTTGACAAAAATTTTAGATACT
96507 TATTTTGAC
1 TATTTTGAC
96516 TAGAAAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 18 0.64
25 2 0.07
26 8 0.29
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.53
Consensus pattern (25 bp):
TATTTTGACAAAAATTTTAGATACT
Found at i:102685 original size:24 final size:24
Alignment explanation
Indices: 102658--102730 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
102648 CGTTCATTTA
102658 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
102682 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
102706 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
102730 C
1 C
102731 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:102687 original size:14 final size:14
Alignment explanation
Indices: 102668--102723 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
102658 CGTTCGTGAA
102668 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
102682 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
102696 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
102706 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
102720 CGTT
1 CGTT
102724 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:102740 original size:24 final size:23
Alignment explanation
Indices: 102669--102743 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
102659 GTTCGTGAAC
* *
102669 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
102693 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
102717 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
102741 GTT
1 GTT
102744 TAACCCAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:103487 original size:10 final size:10
Alignment explanation
Indices: 103472--103546 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
103462 GGGTCTCCAA
103472 CGTTTATGTT
1 CGTTTATGTT
103482 CGTTTATGTT
1 CGTTTATGTT
103492 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
103503 ATGTTCGTGTT
1 -CGTTTATGTT
103514 CGTTTATGTT
1 CGTTTATGTT
103524 CG----TGTT
1 CGTTTATGTT
103530 CGTTTATGTT
1 CGTTTATGTT
103540 CGTTTAT
1 CGTTTAT
103547 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:103503 original size:16 final size:16
Alignment explanation
Indices: 103478--103542 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
103468 CCAACGTTTA
103478 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
103494 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
103510 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
103526 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
103542 T
1 T
103543 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:103633 original size:16 final size:16
Alignment explanation
Indices: 103612--103644 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
103602 AAAAAAATTT
103612 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
103628 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
103644 T
1 T
103645 CTATTTATTA
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:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:105518 original size:30 final size:30
Alignment explanation
Indices: 105482--105555 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
105472 CAGCGAAGCC
*
105482 TCATTGGCATGTTTACTGAATTCATCAATA
1 TCATTGGCATGTTCACTGAATTCATCAATA
*
105512 TCATTGGCATGTTCACTGAATTCATCCATA
1 TCATTGGCATGTTCACTGAATTCATCAATA
105542 TCATTGGCATGTTC
1 TCATTGGCATGTTC
105556 TATTACCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (30 bp):
TCATTGGCATGTTCACTGAATTCATCAATA
Found at i:106687 original size:32 final size:32
Alignment explanation
Indices: 106649--106711 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
106639 ATTAAAAGTA
106649 TTGTTATAAATAGATCGACGATCATTACACAC
1 TTGTTATAAATAGATCGACGATCATTACACAC
*
106681 TTGTTATAAATAGATCGATGATCATTACACA
1 TTGTTATAAATAGATCGACGATCATTACACA
106712 TTAAACGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (32 bp):
TTGTTATAAATAGATCGACGATCATTACACAC
Found at i:113613 original size:60 final size:60
Alignment explanation
Indices: 113501--113613 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
113491 ATAATCGGGT
* *
113501 GATCATTTTAAAGCTTTTAATAGTCGAGAGACTCAACAAAGCAACACTCTATAGTCAGAG
1 GATCATTTTAAAGCTTTTAATAGTCAAGAGACTCAACAAAGCAACACACTATAGTCAGAG
* * *
113561 GATCATTTTGTAA-CTTTTAATAGTCAAG-GAACTGAATAAAGC-ACTACACTATA
1 GATCATTTT-AAAGCTTTTAATAGTCAAGAG-ACTCAACAAAGCAAC-ACACTATA
113614 ATCGGGGACC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
59 3 0.07
60 40 0.89
61 2 0.04
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (60 bp):
GATCATTTTAAAGCTTTTAATAGTCAAGAGACTCAACAAAGCAACACACTATAGTCAGAG
Found at i:117209 original size:60 final size:60
Alignment explanation
Indices: 117110--117226 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
117100 CATACGTCCC
* * * *
117110 CAAACTATGATATTCATTCTAAATTCATCCTTAAACTTTTGAATATTCTAATTTCATACT
1 CAAACTATGATACTCATTCTAAATTCATCATTAAACTTTTGAACATTCTAACTTCATACT
* * * * *
117170 CAAATTATGATACTCATTCTAAATT-AGTTATTGAGCTTTTGAACCTTCTAACTTCAT
1 CAAACTATGATACTCATTCTAAATTCA-TCATTAAACTTTTGAACATTCTAACTTCAT
117227 TCCAAATATG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 1 0.02
60 46 0.98
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (60 bp):
CAAACTATGATACTCATTCTAAATTCATCATTAAACTTTTGAACATTCTAACTTCATACT
Found at i:123626 original size:29 final size:31
Alignment explanation
Indices: 123578--123643 Score: 118
Period size: 29 Copynumber: 2.2 Consensus size: 31
123568 GTAACTTTCA
123578 ATAGTCGAGGAATTTAATAAAACAACATTCT
1 ATAGTCGAGGAATTTAATAAAACAACATTCT
123609 ATAGTCGA-G-ATTTAATAAAACAACATTCT
1 ATAGTCGAGGAATTTAATAAAACAACATTCT
123638 ATAGTC
1 ATAGTC
123644 AAAGGATCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 26 0.74
30 1 0.03
31 8 0.23
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (31 bp):
ATAGTCGAGGAATTTAATAAAACAACATTCT
Found at i:129193 original size:16 final size:17
Alignment explanation
Indices: 129164--129197 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
129154 CATTTTGTTT
129164 TTATTTTATATTTTAAA
1 TTATTTTATATTTTAAA
129181 TTATTTT-TATTTTAAA
1 TTATTTTATATTTTAAA
129197 T
1 T
129198 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTTTATATTTTAAA
Found at i:138036 original size:58 final size:59
Alignment explanation
Indices: 137963--138108 Score: 170
Period size: 60 Copynumber: 2.5 Consensus size: 59
137953 TATTTAGGGT
* * * *
137963 AAAG-TACACAAATGGTCCCCGACTATTGA-TGTTGATTTGTTGAGTCCCTCGATTATTA
1 AAAGTTACA-AAATGGTCCTCGACTATTGAGTGTTGATTTCTTGAGTCCCTCGACTACTA
* * * *
138021 AAAGTTATAAAATGGTCCTTCGACTATAGAGTGTTGTTTTCTTGAGTCTCTCGACTACTA
1 AAAGTTACAAAATGGTCC-TCGACTATTGAGTGTTGATTTCTTGAGTCCCTCGACTACTA
*
138081 AAAGTTGCAAAATGGTCACTCGACTATT
1 AAAGTTACAAAATGGTC-CTCGACTATT
138109 CATATGTTCT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
58 13 0.18
59 12 0.16
60 47 0.64
61 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCCTCGACTATTGAGTGTTGATTTCTTGAGTCCCTCGACTACTA
Found at i:141035 original size:12 final size:12
Alignment explanation
Indices: 141014--141061 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
141004 GGAGAAGCTG
*
141014 GAAGAGAAGAAA
1 GAAGAAAAGAAA
*
141026 GAGGAAAAGAAA
1 GAAGAAAAGAAA
* *
141038 GAAGAGAAGAAG
1 GAAGAAAAGAAA
141050 GAAGAAAAGAAA
1 GAAGAAAAGAAA
141062 TGATTTTTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
GAAGAAAAGAAA
Found at i:141041 original size:24 final size:24
Alignment explanation
Indices: 141014--141061 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
141004 GGAGAAGCTG
*
141014 GAAGAGAAGAAAGAGGAAAAGAAA
1 GAAGAGAAGAAAGAAGAAAAGAAA
*
141038 GAAGAGAAGAAGGAAGAAAAGAAA
1 GAAGAGAAGAAAGAAGAAAAGAAA
141062 TGATTTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (24 bp):
GAAGAGAAGAAAGAAGAAAAGAAA
Found at i:146309 original size:41 final size:40
Alignment explanation
Indices: 146243--146320 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
146233 CTTATGTTCG
*
146243 TTTTATTATCTAAATTTTTAATTTTTTTAAAGTCATATCCC
1 TTTTAATATCTAAATTTTT-ATTTTTTTAAAGTCATATCCC
*
146284 TTTTAATATCTAAACTTTATT-TTTTTTTAAATTCATA
1 TTTTAATATCTAAA-TTT-TTATTTTTTTAAAGTCATA
146321 CCCATGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 28 0.85
42 3 0.09
43 2 0.06
ACGTcount: A:0.31, C:0.10, G:0.01, T:0.58
Consensus pattern (40 bp):
TTTTAATATCTAAATTTTTATTTTTTTAAAGTCATATCCC
Found at i:146456 original size:26 final size:26
Alignment explanation
Indices: 146426--146477 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
146416 AATTTTTATT
*
146426 TGTTTTGAAATTAATGTTAGATTTTG
1 TGTTTTGAAATTAATGTTAAATTTTG
146452 TGTTTTGAAATTAATGTTAAATTTTG
1 TGTTTTGAAATTAATGTTAAATTTTG
146478 AATAGAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (26 bp):
TGTTTTGAAATTAATGTTAAATTTTG
Found at i:146546 original size:31 final size:31
Alignment explanation
Indices: 146483--146549 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
146473 TTTTGAATAG
*
146483 AAGTATTAAAATGAACAAAAATTAAAAGTTT
1 AAGTATTAAAATGAACAAAAATGAAAAGTTT
* * *
146514 AAGTATTAAAATAGATCAAAACTGATAA-TTT
1 AAGTATTAAAAT-GAACAAAAATGAAAAGTTT
146545 AAGTA
1 AAGTA
146550 CTAATCATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 20 0.65
32 11 0.35
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.30
Consensus pattern (31 bp):
AAGTATTAAAATGAACAAAAATGAAAAGTTT
Found at i:146689 original size:65 final size:66
Alignment explanation
Indices: 146571--146699 Score: 172
Period size: 65 Copynumber: 2.0 Consensus size: 66
146561 ATTTACCATA
* * * * *
146571 ATTATTAATTCTAATTATAATATTAAAAGAAATGAACAAAGATTGAAAATTTAAGTATTAAAACA
1 ATTATTAATTCAAATCATAATATTAAAAGAAATGAACAAAGAATAAAAATTTAAATATTAAAACA
146636 G
66 G
* *
146637 ATTA-TAATTCAAATCATAATCTTAAAAGAAATGAAGAAA-AATAAAAAGTTTAAATATTAAAAC
1 ATTATTAATTCAAATCATAATATTAAAAGAAATGAACAAAGAATAAAAA-TTTAAATATTAAAAC
146700 GGATCAAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
64 6 0.11
65 45 0.82
66 4 0.07
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (66 bp):
ATTATTAATTCAAATCATAATATTAAAAGAAATGAACAAAGAATAAAAATTTAAATATTAAAACA
G
Found at i:149410 original size:378 final size:371
Alignment explanation
Indices: 148481--150322 Score: 1790
Period size: 361 Copynumber: 5.0 Consensus size: 371
148471 TTTTTGCGGC
* * * * * *
148481 GCTAGAGGTTCCTCGACTGTATCAGCCGTCTTCCCAAAGTCGACTCTCGGTTGTTCTCTCC-CTT
1 GCTAGAGGTTCCTCAACAGTATCAGTCGTCTTCCCAAAGTCGACCCTCGGTTGATCTC-CCACTA
* * * *
148545 GAGGCGCATCCAGGCCACTAACAGCGCTGTTC-AGTGGATC---GTGTTTTGTCTCGTAGTTTCC
65 AAGGCGCCTCCAAGCCACTAACAG-ACTGTTCGA-TGGATCAATGTGTTTTGTCTCGTAGTTTCC
* * * *
148606 AGTGTAATAGTTTTCAGATCTTTCCCCTGATGGTAGTGGATCAGTTGGCAAGGCTTTTGGCGTCT
128 AGTGTAATAGTTTTCAGATCTTTCCCTTGATGCTAGTGGATCCGTTGGCAAGGCTTTTGACGTCT
* * * * *
148671 TGAAATTTGTAATTCCAGGACGGCTCAAGTCTTCTGATTGTCCGAAGACGGCATTTTTGGCACCG
193 CGAAATTTGTAATTCCAGGACGGCTCAAGTCTTCTGGTTGTCCGGAGACGACATTTTTGGCAGCG
* * * * * * * *
148736 GCAGACTCGTACGCTGCCGA-GAAAGAAAGATGA-TTTTAGCAAGTTCAAATACAC--ACACAGA
258 GCAGACTCGTTCACTGCCGAGGACA-ACAGATGATTTTTAGTAAGTT-AAACACACATACGCACA
* * *
148797 GAACAGACAAACATGCCAAGGTTTATGAGTGGAATAATAGGAAACATACTTGGT
321 AAACAGACAAACATGCC-AGGATTATGAGT--AATACTAGGAAACATACTTGGT
* * ** * ** *
148851 GCTAGAGGTTCCTCGACAGTATCGGTCGTCCCCCCAATGTCGACCCTCGGTTGATCTTTCACTAG
1 GCTAGAGGTTCCTCAACAGTATCAGTCGTCTTCCCAAAGTCGACCCTCGGTTGATCTCCCACTAA
* * * *
148916 GGGCGCCTCCAAGCCACTAACAG-CGTTGTTCAATGGATCATTGTGTTTTGTTTCGTAGTTTCCA
66 AGGCGCCTCCAAGCCACTAACAGAC--TGTTCGATGGATCAATGTGTTTTGTCTCGTAGTTTCCA
* * *
148980 GTGTAATAATTTTCAGATCTCTT-CCTTGATGCTAGTGGATCGGTTGGCAAGGCTTTTGAAGTCT
129 GTGTAATAGTTTTCAGATCT-TTCCCTTGATGCTAGTGGATCCGTTGGCAAGGCTTTTGACGTCT
* * * * *
149044 CGAAACTGGTAATTCCAAGACGGCTCAAGTCATCTGGTTGTCCGGAGACGGCATTTTTGGCAGCG
193 CGAAATTTGTAATTCCAGGACGGCTCAAGTCTTCTGGTTGTCCGGAGACGACATTTTTGGCAGCG
* *
149109 GCAGAGTCGTTCACTGCCAAGGACAACAGATGATTTTTAGTAAGTTAAACACACATATGCGCCCA
258 GCAGACTCGTTCACTGCCGAGGACAACAGATGATTTTTAGTAAGTTAAACACACATA--CG--CA
* * * *
149174 CAAAAAAGACAAACATGCCTAGGATTATGCAAGTATTATATTAGGAAACGTACTTGAT
319 CAAAACAGACAAACATGCC-AGGATTATG--AGTA--ATACTAGGAAACATACTTGGT
* * *
149232 CCTAGAGGTTCCTCAACAGTATCAGTCGTCTTCCCAAAGTCAACCCTCGGTTGATCTCTCACTAA
1 GCTAGAGGTTCCTCAACAGTATCAGTCGTCTTCCCAAAGTCGACCCTCGGTTGATCTCCCACTAA
* * * **
149297 AGGTGCCTCTAAGCCACTGACA-AC-GTTCGATGGATCAATGTGGGTTGTCTCGTAGTTTCCAGT
66 AGGCGCCTCCAAGCCACTAACAGACTGTTCGATGGATCAATGTGTTTTGTCTCGTAGTTTCCAGT
* * *
149360 GTAATAATTTTCAGATCTTTCCCTTGATGCTAGTGGATCCGTTGGCAAGGCTTTTGATGCCTCGA
131 GTAATAGTTTTCAGATCTTTCCCTTGATGCTAGTGGATCCGTTGGCAAGGCTTTTGACGTCTCGA
* * * * *
149425 AATTTGTAATTTCAGGACGGCTCAACTCTTCTGGTTGCCCGGAGA-GAACATTTTTGGAAGCGGT
196 AATTTGTAATTCCAGGACGGCTCAAGTCTTCTGGTTGTCCGGAGACG-ACATTTTTGGCAGCGGC
* * **
149489 AGAGTCGTTCACTGCC-AGGAACAACAGATGATTTTTAGCAAGTT-AA-ACACATACGC-C--GT
260 AGACTCGTTCACTGCCGAGG-ACAACAGATGATTTTTAGTAAGTTAAACACACATACGCACAAAA
* *
149548 C-G-C---C--G--AGGATTATGAAAGCAATACTAAGAAACATACTTGGT
324 CAGACAAACATGCCAGGATTATG--AGTAATACTAGGAAACATACTTGGT
* * * *
149589 GCTAGAGGTTCCTCAACAGTATCGGTAGTCTTCCCAAAGTCTACCCTCGGTTGTTCTCCCACTAA
1 GCTAGAGGTTCCTCAACAGTATCAGTCGTCTTCCCAAAGTCGACCCTCGGTTGATCTCCCACTAA
* * * *
149654 AGGCGCCTCCAAACCACTAACAGTACTATTCGGA-GGAT-TATGTTGTTTTGTCTCGTAATTTCC
66 AGGCGCCTCCAAGCCACTAACAG-ACTGTTC-GATGGATCAATG-TGTTTTGTCTCGTAGTTTCC
** * * *
149717 AGTGTTGTAGTTTTCAGATCTTTCCCGTGATGCTAGTGGATCGGTTGGCAAGGCTTTGGACGTCT
128 AGTGTAATAGTTTTCAGATCTTTCCCTTGATGCTAGTGGATCCGTTGGCAAGGCTTTTGACGTCT
* * *
149782 CGAAATTGGTTATTCCAGGACGGCTCAAGTCTTCTGGTTGGT-CGGAGACGACATTTTTTGCAGC
193 CGAAATTTGTAATTCCAGGACGGCTCAAGTCTTCTGGTT-GTCCGGAGACGACATTTTTGGCAGC
* * * ** * * * * *
149846 GGCAGACTTGTACACTACCGATAACGATAGAT-AATTTTAGTAGGTTAAAATACACACAGA-G-A
257 GGCAGACTCGTTCACTGCCGAGGACAACAGATGATTTTTAGTAAGTT--AA-ACACACATACGCA
* *
149908 GAAAACAGAAAAACATGCC--------GAG---TACTAGGAAACATACTTGGT
319 CAAAACAGACAAACATGCCAGGATTATGAGTAATACTAGGAAACATACTTGGT
* * *
149950 GCTAGAGGTTCCTCGACAGTATCAGTCGTCTTCCCAAAGTCGACCCTCGGTTGTTCTCCCACTAG
1 GCTAGAGGTTCCTCAACAGTATCAGTCGTCTTCCCAAAGTCGACCCTCGGTTGATCTCCCACTAA
* * * * * *
150015 AGGGGCCTCCAAGCCACTATCAGCGCTGTTCGGTGGATCATTGTGTTTTGTCTCGTAGTTTCCAA
66 AGGCGCCTCCAAGCCACTAACAG-ACTGTTCGATGGATCAATGTGTTTTGTCTCGTAGTTTCCAG
* * * * * * *
150080 TGTTATAGTTTTCAGATCTCTCCCTTGAAGCTATTAGATCCGTCGGCAAGGGTTTTGACGTCTCG
130 TGTAATAGTTTTCAGATCTTTCCCTTGATGCTAGTGGATCCGTTGGCAAGGCTTTTGACGTCTCG
* ** * * *
150145 ACATTTGTAATTCCAGGACGGCTCAAGTCCGCCGGTTGTCCGTAGACGACTTTTTTGGCAGCGGC
195 AAATTTGTAATTCCAGGACGGCTCAAGTCTTCTGGTTGTCCGGAGACGACATTTTTGGCAGCGGC
* * * *
150210 AGACTCGTTCACTGCCGAGAACCACAGATGATTTTCAGTAAGTT-AA-ACGC--A--CACAAAAC
260 AGACTCGTTCACTGCCGAGGACAACAGATGATTTTTAGTAAGTTAAACACACATACGCACAAAAC
* *
150269 AGACAAACATGCCAAGGATGATGAAAAGTAATACTAGGAAACATACATGGT
325 AGACAAACATGCC-AGGATTATG---AGTAATACTAGGAAACATACTTGGT
150320 GCT
1 GCT
150323 CCATGAACTT
Statistics
Matches: 1220, Mismatches: 183, Indels: 138
0.79 0.12 0.09
Matches are distributed among these distances:
355 19 0.02
357 97 0.08
358 1 0.00
359 30 0.02
360 158 0.13
361 264 0.22
362 15 0.01
363 2 0.00
364 10 0.01
365 1 0.00
366 2 0.00
367 3 0.00
368 2 0.00
369 1 0.00
370 106 0.09
371 2 0.00
372 2 0.00
373 163 0.13
374 18 0.01
375 1 0.00
376 7 0.01
377 9 0.01
378 184 0.15
379 27 0.02
381 96 0.08
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (371 bp):
GCTAGAGGTTCCTCAACAGTATCAGTCGTCTTCCCAAAGTCGACCCTCGGTTGATCTCCCACTAA
AGGCGCCTCCAAGCCACTAACAGACTGTTCGATGGATCAATGTGTTTTGTCTCGTAGTTTCCAGT
GTAATAGTTTTCAGATCTTTCCCTTGATGCTAGTGGATCCGTTGGCAAGGCTTTTGACGTCTCGA
AATTTGTAATTCCAGGACGGCTCAAGTCTTCTGGTTGTCCGGAGACGACATTTTTGGCAGCGGCA
GACTCGTTCACTGCCGAGGACAACAGATGATTTTTAGTAAGTTAAACACACATACGCACAAAACA
GACAAACATGCCAGGATTATGAGTAATACTAGGAAACATACTTGGT
Found at i:166639 original size:3 final size:3
Alignment explanation
Indices: 166631--166666 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
166621 ATTTGAAAGA
166631 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
166667 TATTCATATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:172950 original size:36 final size:38
Alignment explanation
Indices: 172876--172952 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 38
172866 TTTAAAAAAA
172876 AATTGACAATTGTAATAAAAGGATCGATCCTTTAAGGG
1 AATTGACAATTGTAATAAAAGGATCGATCCTTTAAGGG
172914 AATTGAC-ATTGTAATAAAAGGATCG-TCCTTTAAGGG
1 AATTGACAATTGTAATAAAAGGATCGATCCTTTAAGGG
172950 AAT
1 AAT
172953 GGGTTGATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 14 0.36
37 18 0.46
38 7 0.18
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (38 bp):
AATTGACAATTGTAATAAAAGGATCGATCCTTTAAGGG
Found at i:184235 original size:31 final size:31
Alignment explanation
Indices: 184183--184268 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
184173 TGATTTTGGA
* * *
184183 AAAAATGAAAGTTTAGATACTAAAATAGACT
1 AAAACTGATAGTTTAGGTACTAAAATAGACT
184214 AAAACTGATAGTTTAGGTACTAAAATAGACT
1 AAAACTGATAGTTTAGGTACTAAAATAGACT
184245 AAAACTGATAGTTTAGGTACTAAA
1 AAAACTGATAGTTTAGGTACTAAA
184269 TGTATAGTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (31 bp):
AAAACTGATAGTTTAGGTACTAAAATAGACT
Found at i:189313 original size:14 final size:14
Alignment explanation
Indices: 189296--189323 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
189286 ATCATAACAA
189296 AATTATATAACTAT
1 AATTATATAACTAT
189310 AATTATATAACTAT
1 AATTATATAACTAT
189324 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:189845 original size:259 final size:262
Alignment explanation
Indices: 189384--189908 Score: 966
Period size: 259 Copynumber: 2.0 Consensus size: 262
189374 TTTTTTTTGA
189384 GTTCAAGCCTTTTTGAGTTCAAGTTTCAATATTATATTTCGAGTTTGAGTTAAACTTGATAATTT
1 GTTCAAGCCTTTTTGAGTTCAAGTTTCAATATTATATTTCGAGTTTGAGTTAAACTTGATAATTT
189449 TTAGCTTGTGAGTTTGAGTTGAGTTGAGCTTACTTTTAAAGTTTTCAAATTCGAGTCAAGCTCAG
66 TTAGCTTGTGAGTTTGAGTTGAGTTGAGCTTACTTTTAAAGTTTTCAAATTCGAGTCAAGCTCAG
189514 CAATACTCGAGTTCGACTTGGCTCGTTTAACAAACGACGTTGTTTAGTTTAATTTTTTTTTAAAA
131 CAATACTCGAGTTCGACTTGGCTCGTTTAACAAACGACGTTGTTTAGTTTAATTTTTTTTTAAAA
*
189579 AAAC-AAAATCTCTGTTTTTCCCGGTTTTTTTCGGTTTTCAGCCGGTCCGGTTCGAACGGTTTAG
196 AAACAAAAATCTCTGTTTTTCCCGGTTTTTTTCGGTTTTCAGCCGGTCCGGTTCGAACGGTTCAG
189643 CG
261 CG
*
189645 GTTCAAGCCTTTTTGAGTTCAAGTTTCAATA-T-TATTTCGAGTTTGAGTTGAACTTGATAATTT
1 GTTCAAGCCTTTTTGAGTTCAAGTTTCAATATTATATTTCGAGTTTGAGTTAAACTTGATAATTT
*
189708 TTAGCTTGTGAGTTTGAGTTGAGTTGAGCTTACTTTTAAAGTTTTCAAATTCGAGTCGAGCTCAG
66 TTAGCTTGTGAGTTTGAGTTGAGTTGAGCTTACTTTTAAAGTTTTCAAATTCGAGTCAAGCTCAG
* * * *
189773 CAATACTTGAGTTCGGCTTGGCTCGTTTAACAAACGACGTTGTTTGGTTTAATTTTTTTTTTAAA
131 CAATACTCGAGTTCGACTTGGCTCGTTTAACAAACGACGTTGTTTAGTTTAATTTTTTTTTAAAA
189838 AAACAAAAATCTCTGTTTTTCCCGGTTTTTTTCGGTTTTCAGCCGGTCCGGTTCGAACGGTTCAG
196 AAACAAAAATCTCTGTTTTTCCCGGTTTTTTTCGGTTTTCAGCCGGTCCGGTTCGAACGGTTCAG
189903 CG
261 CG
189905 GTTC
1 GTTC
189909 TGGCCGGTTC
Statistics
Matches: 256, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
259 159 0.62
260 66 0.26
261 31 0.12
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (262 bp):
GTTCAAGCCTTTTTGAGTTCAAGTTTCAATATTATATTTCGAGTTTGAGTTAAACTTGATAATTT
TTAGCTTGTGAGTTTGAGTTGAGTTGAGCTTACTTTTAAAGTTTTCAAATTCGAGTCAAGCTCAG
CAATACTCGAGTTCGACTTGGCTCGTTTAACAAACGACGTTGTTTAGTTTAATTTTTTTTTAAAA
AAACAAAAATCTCTGTTTTTCCCGGTTTTTTTCGGTTTTCAGCCGGTCCGGTTCGAACGGTTCAG
CG
Found at i:190129 original size:15 final size:15
Alignment explanation
Indices: 190111--190141 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
190101 AAATTCTAAA
190111 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
190126 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
190141 T
1 T
190142 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:190883 original size:30 final size:30
Alignment explanation
Indices: 190847--190979 Score: 221
Period size: 30 Copynumber: 4.4 Consensus size: 30
190837 TCCGAAGGAC
190847 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
190877 CTATCCAGAGGCCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
190907 CTATCCAGAGATCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
190937 CTATCCATAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
190967 CTGTCCATAGGTC
1 CTATCCAGAGGTC
190980 CCGAAGAACC
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 97 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:190996 original size:30 final size:30
Alignment explanation
Indices: 190847--191006 Score: 176
Period size: 30 Copynumber: 5.3 Consensus size: 30
190837 TCCGAAGGAC
* *
190847 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCACAAAGATCCTCGGTAA
* * *
190877 CTATCCAGAGGCCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCACAAAGATCCTCGGTAA
* * *
190907 CTATCCAGAGATCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCACAAAGATCCTCGGTAA
*
190937 CTATCCATAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCACAAAGATCCTCGGTAA
* * * * *
190967 CTGTCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCATAGGTCACAAAGATCCTCGGT-AA
*
190998 CTATTCATA
1 CTATCCATA
191007 TGTTCCTTAA
Statistics
Matches: 116, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 107 0.92
31 9 0.08
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCATAGGTCACAAAGATCCTCGGTAA
Found at i:203039 original size:37 final size:37
Alignment explanation
Indices: 202996--203114 Score: 90
Period size: 37 Copynumber: 3.3 Consensus size: 37
202986 AATTCACTTA
202996 TTAAAAGATCATAAAAGCACATAAGCGTTACGACAAC
1 TTAAAAGATCATAAAAGCACATAAGCGTTACGACAAC
* * * * **
203033 TTAAAAGGTCATCATATG-ATCCTAA---TT-C-ACTTC
1 TTAAAAGATCAT-AAAAGCA-CATAAGCGTTACGACAAC
* *
203066 TTAAAAGGTCAT-AAAGCACATATGCGTTACGACAAC
1 TTAAAAGATCATAAAAGCACATAAGCGTTACGACAAC
203102 TTAAAAAGATCAT
1 TT-AAAAGATCAT
203115 CATATGATCC
Statistics
Matches: 60, Mismatches: 13, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
31 5 0.08
32 1 0.02
33 15 0.25
34 3 0.05
35 3 0.05
36 5 0.08
37 21 0.35
38 7 0.12
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (37 bp):
TTAAAAGATCATAAAAGCACATAAGCGTTACGACAAC
Found at i:203070 original size:70 final size:70
Alignment explanation
Indices: 202848--203125 Score: 396
Period size: 72 Copynumber: 3.9 Consensus size: 70
202838 AAACCGAATA
* * *
202848 ACTTCTTAAAAGATCATAAAAGCACATAAGCTTTACGACAACTTAGAAAAATCATCGTATGATCC
1 ACTTCTTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTA-AAAGATCATCATATGATCC
***
202913 TAACAG
65 TAATTC
* * *
202919 ACTTCTTAAAAGATCAATTAAAGCACACAAACGTTACGACAACTTAAACAGATCATCATATGATC
1 ACTTCTTAAAAGATC-ATAAAAGCACATAAGCGTTACGACAACTTAAA-AGATCATCATATGATC
202984 CTAATTC
64 CTAATTC
* *
202991 ACTTATTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAAAAGGTCATCATATGATCCT
1 ACTTCTTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAAAAGATCATCATATGATCCT
203056 AATTC
66 AATTC
* *
203061 ACTTCTTAAAAGGTCAT-AAAGCACATATGCGTTACGACAACTTAAAAAGATCATCATATGATCC
1 ACTTCTTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTT-AAAAGATCATCATATGATCC
203125 T
65 T
203126 CATTGAATGC
Statistics
Matches: 186, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
69 25 0.13
70 57 0.31
71 46 0.25
72 58 0.31
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (70 bp):
ACTTCTTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAAAAGATCATCATATGATCCT
AATTC
Found at i:203125 original size:140 final size:143
Alignment explanation
Indices: 202848--203125 Score: 418
Period size: 140 Copynumber: 2.0 Consensus size: 143
202838 AAACCGAATA
* * *
202848 ACTTCTTAAAAGATCATAAAAGCACATAAGCTTTACGACAACTTAGAAAAATCATCGTATGATCC
1 ACTTATTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAGAAAAATCATCATATGATCC
* *
202913 TAACAGACTTCTTAAAAGATCAATTAAAGCACACAAACGTTACGACAACTTAAACAGATCATCAT
66 TAACACACTTCTTAAAAGATCAATTAAAGCACACAAACGTTACGACAACTTAAAAAGATCATCAT
202978 ATGATCCTAATTC
131 ATGATCCTAATTC
**
202991 ACTTATTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTA-AAAGGTCATCATATGATCC
1 ACTTATTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAGAAAAATCATCATATGATCC
** * * **
203055 TAATTCACTTCTTAAAAGGTC-A-TAAAGCACATATGCGTTACGACAACTTAAAAAGATCATCAT
66 TAACACACTTCTTAAAAGATCAATTAAAGCACACAAACGTTACGACAACTTAAAAAGATCATCAT
203118 ATGATCCT
131 ATGATCCT
203126 CATTGAATGC
Statistics
Matches: 122, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
140 45 0.37
141 1 0.01
142 33 0.27
143 43 0.35
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (143 bp):
ACTTATTAAAAGATCATAAAAGCACATAAGCGTTACGACAACTTAGAAAAATCATCATATGATCC
TAACACACTTCTTAAAAGATCAATTAAAGCACACAAACGTTACGACAACTTAAAAAGATCATCAT
ATGATCCTAATTC
Found at i:207224 original size:264 final size:265
Alignment explanation
Indices: 206907--208072 Score: 1605
Period size: 264 Copynumber: 4.4 Consensus size: 265
206897 AAAAGCTCTC
* * * * * *
206907 TTTGTTACTGTGTGAAAACGTTAGATCATGTCACTATCTAGTCAAATTATAACGATCTTATTTAT
1 TTTGTTACTGAGTGAAAATGTTAGATCATGTTATTATCAAGTCAAACTATAACGATCTTATTTAT
*
206972 TGTATTTATTCGACCTCAATGATTGTTGTTTATAGACATGTAACACGTGTTATGAAAATTGAAAT
66 TGTATTTATTCGACCTCAATGATTGTTGTTTATAGACATCTAACACGTGTTATGAAAATTGAAAT
* *
207037 GTACATGAGAAACTATACTGATAAATATTGTTGTCGTTTACTATGACATCAATAATTTAATTTAT
131 GTACATGAGAAACTATACTGATAAATATTGTTGTCGTTTACTGTGACATCAATAATTTAATCTAT
* *
207102 CAATC-AAAAAATTCTAAAATGATTGGATCTGTTGTAATAAATGGAGTTCACGCGCTTGACAAAG
196 CAATCGAAAGAATTCTAAAATGATTGGATCTGTTGTAATAAATGGAGTTCACACGCTTGACAAAG
207166 TTATT
261 TTATT
* *
207171 TTTGTTATTGAGTGAAAATGTTAGATCATGTTATTATCAAATCAAACTATAACGATCTTATTTAT
1 TTTGTTACTGAGTGAAAATGTTAGATCATGTTATTATCAAGTCAAACTATAACGATCTTATTTAT
* * *
207236 TGTATTTATTCGACTTCAATGATTGTTGTTTACATACATCTAACACGTGTTATGAAAATTGAAAT
66 TGTATTTATTCGACCTCAATGATTGTTGTTTATAGACATCTAACACGTGTTATGAAAATTGAAAT
* *
207301 GTACATGTGAAACTATACTGATAAATATTGTTGTCGTTTAATGTGACATCAATAATTTAATCTAT
131 GTACATGAGAAACTATACTGATAAATATTGTTGTCGTTTACTGTGACATCAATAATTTAATCTAT
**
207366 CAATCGAAAGAATTCTAAAATGATTGGATCTGTTGTAATAAATGGAGTTCACATACTTGACAAAG
196 CAATCGAAAGAATTCTAAAATGATTGGATCTGTTGTAATAAATGGAGTTCACACGCTTGACAAAG
207431 TTATT
261 TTATT
* **
207436 TTTGTTACTGAGTGAAAACGTTAGATCATGTTATTATCAAGTCAAACTATAACGATAATATTTAT
1 TTTGTTACTGAGTGAAAATGTTAGATCATGTTATTATCAAGTCAAACTATAACGATCTTATTTAT
* **
207501 TGTATTTATTCGACCTCAATGATTGTTATTTATAGACATGAAACACGTGTTATG-AAATTGAAAT
66 TGTATTTATTCGACCTCAATGATTGTTGTTTATAGACATCTAACACGTGTTATGAAAATTGAAAT
* * * * * * *
207565 GTATATGTA-AAACTATATTGATAAATATTGTTGTCGTTTATTGTGACGTCAATGATTTGATTTA
131 GTACATG-AGAAACTATACTGATAAATATTGTTGTCGTTTACTGTGACATCAATAATTTAATCTA
* * *
207629 TCAATCGAAAGAATTCTAAAATGATTGGATCTATTGTAATAACTGGAGTTC-CTACGCTTGAGAA
195 TCAATCGAAAGAATTCTAAAATGATTGGATCTGTTGTAATAAATGGAGTTCAC-ACGCTTGACAA
207693 AGTTATT
259 AGTTATT
* *
207700 TTTGTTACTGAGTGAAAATGTTAGATCACGTTATCATCAAGTCAAACTATAACGATCTTATTTAT
1 TTTGTTACTGAGTGAAAATGTTAGATCATGTTATTATCAAGTCAAACTATAACGATCTTATTTAT
*** * *
207765 TGTATTTATTCGACCTCAATGATTGTTGTTTACCTATATCTAACACGTGTTATGAAAATTAAAAT
66 TGTATTTATTCGACCTCAATGATTGTTGTTTATAGACATCTAACACGTGTTATGAAAATTGAAAT
* * * * *
207830 GTACATGTGAAATTGTACTGATAAATATTGTTGTTGTTTACTGTAACATCAATAATTTAATCTAT
131 GTACATGAGAAACTATACTGATAAATATTGTTGTCGTTTACTGTGACATCAATAATTTAATCTAT
* * * ** * *
207895 CAATCGAAAGAGTTCTAAAAATAAATGGATCTGTTGTAATAACCGGAGTT----CGCTTTAGAAA
196 CAATCGAAAGAATTCT-AAAATGATTGGATCTGTTGTAATAAATGGAGTTCACACGCTTGACAAA
* *
207956 GTTCTC
260 GTTATT
* * * * * *
207962 TTTGTTACTGAGTGAAAATGTTAGATCATGTTATCACCAA-ACAAAATTATAATGATCTTATTTG
1 TTTGTTACTGAGTGAAAATGTTAGATCATGTTATTATCAAGTC-AAACTATAACGATCTTATTTA
* * * * * *
208026 TTTTATTTATTCAACTTAAATGATTGTT-TTTGTAGACATATAACACG
65 TTGTATTTATTCGACCTCAATGATTGTTGTTTATAGACATCTAACACG
208073 GGATAGAGAA
Statistics
Matches: 802, Mismatches: 93, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
261 14 0.02
262 94 0.12
263 1 0.00
264 420 0.52
265 244 0.30
266 29 0.04
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (265 bp):
TTTGTTACTGAGTGAAAATGTTAGATCATGTTATTATCAAGTCAAACTATAACGATCTTATTTAT
TGTATTTATTCGACCTCAATGATTGTTGTTTATAGACATCTAACACGTGTTATGAAAATTGAAAT
GTACATGAGAAACTATACTGATAAATATTGTTGTCGTTTACTGTGACATCAATAATTTAATCTAT
CAATCGAAAGAATTCTAAAATGATTGGATCTGTTGTAATAAATGGAGTTCACACGCTTGACAAAG
TTATT
Found at i:207808 original size:529 final size:526
Alignment explanation
Indices: 206905--207995 Score: 1695
Period size: 529 Copynumber: 2.1 Consensus size: 526
206895 GAAAAAGCTC
* * * * * **
206905 TCTTTGTTACTGTGTGAAAACGTTAGATCATGTCACTATCTAGTCAAATTATAACGATCTTATTT
1 TCTTTGTTACTGAGTGAAAACGTTAGATCATGTTATTATCAAGTCAAACTATAACGATAATATTT
* *
206970 ATTGTATTTATTCGACCTCAATGATTGTTGTTTATAGACATGTAACACGTGTTATGAAAATTGAA
66 ATTGTATTTATTCGACCTCAATGATTGTTATTTATAGACATGAAACACGTGTTATGAAAATTGAA
207035 ATGTACATGAGAAACTATACTGATAAATATTGTTGTCGTTTACTATGACATCAATAATTTAATTT
131 ATGTACATGAGAAACTATACTGATAAATATTGTTGTCGTTTACTATGACATCAATAATTTAATTT
* *
207100 ATCAATCAAAAAATTCTAAAATGATTGGATCTGTTGTAATAAATGGAGTTCACGCGCTTGACAAA
196 ATCAATCAAAAAATTCTAAAATGATTGGATCTATTGTAATAAATGGAGTTCACACGCTTGACAAA
* * *
207165 GTTATTTTTGTTATTGAGTGAAAATGTTAGATCATGTTATTATCAAATCAAACTATAACGATCTT
261 GTTATTTTTGTTACTGAGTGAAAATGTTAGATCACGTTATCATCAAATCAAACTATAACGATCTT
*
207230 ATTTATTGTATTTATTCGACTTCAATGATTGTTGTTTACATACATCTAACACGTGTTATGAAAAT
326 ATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTACATACATCTAACACGTGTTATGAAAAT
* *
207295 TGAAATGTACATGTGAAACTATACTGATAAATATTGTTGTCGTTTAATGTGACATCAATAATTTA
391 TAAAATGTACATGTGAAACTATACTGATAAATATTGTTGTCGTTTAATGTAACATCAATAATTTA
* * *
207360 ATCTATCAATCGAAAGAATTCT-AAAATGATTGGATCTGTTGTAATAAATGGAGTTCACATACTT
456 ATCTATCAATCGAAAGAATTCTAAAAATAAATGGATCTGTTGTAATAAACGGAGTTCAC-T--TT
207424 GACAAAGTTA
518 -ACAAAGTTA
*
207434 TTTTTGTTACTGAGTGAAAACGTTAGATCATGTTATTATCAAGTCAAACTATAACGATAATATTT
1 TCTTTGTTACTGAGTGAAAACGTTAGATCATGTTATTATCAAGTCAAACTATAACGATAATATTT
207499 ATTGTATTTATTCGACCTCAATGATTGTTATTTATAGACATGAAACACGTGTTATG-AAATTGAA
66 ATTGTATTTATTCGACCTCAATGATTGTTATTTATAGACATGAAACACGTGTTATGAAAATTGAA
* * * * * * *
207563 ATGTATATGTA-AAACTATATTGATAAATATTGTTGTCGTTTATTGTGACGTCAATGATTTGATT
131 ATGTACATG-AGAAACTATACTGATAAATATTGTTGTCGTTTACTATGACATCAATAATTTAATT
* * *
207627 TATCAATCGAAAGAATTCTAAAATGATTGGATCTATTGTAATAACTGGAGTTC-CTACGCTTGAG
195 TATCAATC-AAAAAATTCTAAAATGATTGGATCTATTGTAATAAATGGAGTTCAC-ACGCTTGAC
*
207691 AAAGTTATTTTTGTTACTGAGTGAAAATGTTAGATCACGTTATCATCAAGTCAAACTATAACGAT
258 AAAGTTATTTTTGTTACTGAGTGAAAATGTTAGATCACGTTATCATCAAATCAAACTATAACGAT
* *
207756 CTTATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTACCTATATCTAACACGTGTTATGAA
323 CTTATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTACATACATCTAACACGTGTTATGAA
* * * *
207821 AATTAAAATGTACATGTGAAATTGTACTGATAAATATTGTTGTTGTTTACTGTAACATCAATAAT
388 AATTAAAATGTACATGTGAAACTATACTGATAAATATTGTTGTCGTTTAATGTAACATCAATAAT
* * *
207886 TTAATCTATCAATCGAAAGAGTTCTAAAAATAAATGGATCTGTTGTAATAACCGGAGTTCGCTTT
453 TTAATCTATCAATCGAAAGAATTCTAAAAATAAATGGATCTGTTGTAATAAACGGAGTTCACTTT
* *
207951 AGAAAGTTC
518 ACAAAGTTA
*
207960 TCTTTGTTACTGAGTGAAAATGTTAGATCATGTTAT
1 TCTTTGTTACTGAGTGAAAACGTTAGATCATGTTAT
207996 CACCAAACAA
Statistics
Matches: 513, Mismatches: 45, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
526 41 0.08
527 2 0.00
528 72 0.14
529 367 0.72
530 31 0.06
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (526 bp):
TCTTTGTTACTGAGTGAAAACGTTAGATCATGTTATTATCAAGTCAAACTATAACGATAATATTT
ATTGTATTTATTCGACCTCAATGATTGTTATTTATAGACATGAAACACGTGTTATGAAAATTGAA
ATGTACATGAGAAACTATACTGATAAATATTGTTGTCGTTTACTATGACATCAATAATTTAATTT
ATCAATCAAAAAATTCTAAAATGATTGGATCTATTGTAATAAATGGAGTTCACACGCTTGACAAA
GTTATTTTTGTTACTGAGTGAAAATGTTAGATCACGTTATCATCAAATCAAACTATAACGATCTT
ATTTATTGTATTTATTCGACCTCAATGATTGTTGTTTACATACATCTAACACGTGTTATGAAAAT
TAAAATGTACATGTGAAACTATACTGATAAATATTGTTGTCGTTTAATGTAACATCAATAATTTA
ATCTATCAATCGAAAGAATTCTAAAAATAAATGGATCTGTTGTAATAAACGGAGTTCACTTTACA
AAGTTA
Found at i:210518 original size:21 final size:21
Alignment explanation
Indices: 210494--210553 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
210484 AACTTTGAAA
210494 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
210515 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
210529 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
210550 AAAT
1 AAAT
210554 ATTTCTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:210532 original size:35 final size:36
Alignment explanation
Indices: 210459--210604 Score: 169
Period size: 35 Copynumber: 4.2 Consensus size: 36
210449 TGAAAGTATT
** *
210459 AAAATGGTTTTC-AAGTTTGGTAACCA--ACTTTGAA
1 AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTG-A
*
210493 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG-
1 AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTGA
210528 AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTGA
1 AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTGA
* * *
210564 AAAATAGTTTTTCAAAGTTTGGTAGAT-TTT-GTTGA
1 AAAAT-GGTTTTCAAAGTTTGGTAAATATTTCTTTGA
210599 AAAATG
1 AAAATG
210605 ATAATGGGAT
Statistics
Matches: 99, Mismatches: 8, Indels: 10
0.85 0.07 0.09
Matches are distributed among these distances:
34 13 0.13
35 54 0.55
36 8 0.08
37 24 0.24
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (36 bp):
AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTGA
Done.