Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000417.1 Hibiscus syriacus cultivar Beakdansim tig00000764_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: 2005044
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:7993 original size:33 final size:30
Alignment explanation
Indices: 7955--8019 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
7945 TAAAAAAAAC
7955 AATAATAAAGAAGGATATATAAAATATTATGAA
1 AATAAT-AAGAA-GATATATAAAATATT-TGAA
* *
7988 AATAATAAGTATATATATAAAATATTTGAA
1 AATAATAAGAAGATATATAAAATATTTGAA
8018 AA
1 AA
8020 GAAAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 6 0.20
31 14 0.47
32 4 0.13
33 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (30 bp):
AATAATAAGAAGATATATAAAATATTTGAA
Found at i:8924 original size:12 final size:12
Alignment explanation
Indices: 8907--8931 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8897 TAATAATAAC
8907 ATAATAATTGAA
1 ATAATAATTGAA
8919 ATAATAATTGAA
1 ATAATAATTGAA
8931 A
1 A
8932 CATATCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATAATAATTGAA
Found at i:16364 original size:23 final size:23
Alignment explanation
Indices: 16338--16382 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16328 GACATTATAT
*
16338 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTATACGC
**
16361 GGCACTTTGGTGCATTTATACG
1 GGCACTACGGTGCATTTATACG
16383 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (23 bp):
GGCACTACGGTGCATTTATACGC
Found at i:21482 original size:23 final size:23
Alignment explanation
Indices: 21456--21539 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
21446 TATGGAACTA
21456 CGGTGCATTTCTACGTGGCACTT
1 CGGTGCATTTCTACGTGGCACTT
* * *
21479 CGGTGTAATTCTACGTGGCACTA
1 CGGTGCATTTCTACGTGGCACTT
* *
21502 CGGTGCATTTCTACGCGACACTT
1 CGGTGCATTTCTACGTGGCACTT
*
21525 CGGTGCATTTATACG
1 CGGTGCATTTCTACG
21540 AGCTGTGGTG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
CGGTGCATTTCTACGTGGCACTT
Found at i:27224 original size:6 final size:6
Alignment explanation
Indices: 27179--27221 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
27169 TATCGCATTG
* * *
27179 CTACTG CTACTG CTACTT CTACTT CTACTT CTACTT CCACTT C
1 CTACTT CTACTT CTACTT CTACTT CTACTT CTACTT CTACTT C
27222 CACAGAGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.16, C:0.37, G:0.05, T:0.42
Consensus pattern (6 bp):
CTACTT
Found at i:27710 original size:14 final size:14
Alignment explanation
Indices: 27680--27714 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
27670 GAACGTTCGG
* *
27680 TTATGTTCGTTCGT
1 TTATGTTCATTCAT
27694 TTATGTTCATTCAT
1 TTATGTTCATTCAT
27708 TTATGTT
1 TTATGTT
27715 TAACCCAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.60
Consensus pattern (14 bp):
TTATGTTCATTCAT
Found at i:32753 original size:17 final size:17
Alignment explanation
Indices: 32714--32755 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
32704 ACTCCTCCAA
*
32714 AATAAAAATATAAAATT
1 AATAAATATATAAAATT
*
32731 AGTAAATATATATAAA-T
1 AATAAATATATA-AAATT
32748 AATAAATA
1 AATAAATA
32756 ATTCAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AATAAATATATAAAATT
Found at i:37826 original size:192 final size:192
Alignment explanation
Indices: 37499--37879 Score: 672
Period size: 192 Copynumber: 2.0 Consensus size: 192
37489 CCGATGTTGT
37499 TATCAGAGAATGGTACAGGTGATTAGGGGGTATGTAATTATATTTTGTTTTATATACGAGTCTGA
1 TATCAGAGAATGGTACAGGTGATTAGGGGGTATGTAATTATATTTTGTTTTATATACGAGTCTGA
37564 AAATCTGTTTTATTTCTGCATACTGATAAATCATTTTATAAGTTACATGTTTTAATAAAAGTTTT
66 AAATCTGTTTTATTTCTGCATACTGATAAATCATTTTATAAGTTACATGTTTTAATAAAAGTTTT
* *
37629 AAATTTTCCGCCATTTTTACAGTAGGTCGCTCCGGTGGCCCTAATGTGACACTCCAGACCGA
131 AAATTTTCCGCCATTTTTACAGTAGGTCGCTCCGGTGGCCCTAATGTAAAACTCCAGACCGA
* * *
37691 TATCAGATAATGGTACAGGTGATTAGGGGGTATGTCATTATATTTTGTTTTATATAGGAGTCTGA
1 TATCAGAGAATGGTACAGGTGATTAGGGGGTATGTAATTATATTTTGTTTTATATACGAGTCTGA
*
37756 AAATTTGTTTTATTTCTGCATACTGATAAATCATTTTATAAGTTACATGTTTTAATAAAAGTTTT
66 AAATCTGTTTTATTTCTGCATACTGATAAATCATTTTATAAGTTACATGTTTTAATAAAAGTTTT
* * * *
37821 AAATTTTTCTCCATTTTTATAGTGGGTCGCTCCGGTGGCCCTAATGTAAAACTCCAGAC
131 AAATTTTCCGCCATTTTTACAGTAGGTCGCTCCGGTGGCCCTAATGTAAAACTCCAGAC
37880 TGGATCGGGT
Statistics
Matches: 179, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
192 179 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (192 bp):
TATCAGAGAATGGTACAGGTGATTAGGGGGTATGTAATTATATTTTGTTTTATATACGAGTCTGA
AAATCTGTTTTATTTCTGCATACTGATAAATCATTTTATAAGTTACATGTTTTAATAAAAGTTTT
AAATTTTCCGCCATTTTTACAGTAGGTCGCTCCGGTGGCCCTAATGTAAAACTCCAGACCGA
Found at i:41726 original size:15 final size:15
Alignment explanation
Indices: 41706--41742 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
41696 ATATTTAGCT
*
41706 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
41721 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
41736 GGGCGGG
1 GGGCGGG
41743 TAATATCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:42912 original size:49 final size:49
Alignment explanation
Indices: 42855--42952 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
42845 CATTTCCAGA
*
42855 AGAATTGTTATTGGAAATTCTTATGCATGTGGCCTCTAATTCTTTCACC
1 AGAATTGTTATCGGAAATTCTTATGCATGTGGCCTCTAATTCTTTCACC
42904 AGAATTGTTATCGGAAATTCTTATGCATGTGGCCTCTAATTCTTTCACC
1 AGAATTGTTATCGGAAATTCTTATGCATGTGGCCTCTAATTCTTTCACC
42953 GATTTCGTCG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (49 bp):
AGAATTGTTATCGGAAATTCTTATGCATGTGGCCTCTAATTCTTTCACC
Found at i:53781 original size:21 final size:22
Alignment explanation
Indices: 53752--53807 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
53742 TCCTCTTTTT
* *
53752 TTATTTATATTATATTATT-TA
1 TTATATATATTATATCATTATA
53773 TTATATATATCTTATATCATTATA
1 TTATATATA--TTATATCATTATA
53797 TATATATATAT
1 T-TATATATAT
53808 AGATGTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 8 0.28
23 10 0.34
24 3 0.10
25 8 0.28
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATATATATTATATCATTATA
Found at i:53800 original size:23 final size:23
Alignment explanation
Indices: 53761--53807 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
53751 TTTATTTATA
*
53761 TTATATTATTTATTATATATATC
1 TTATATCATTTATTATATATATC
53784 TTATATCATTATATATATATATAT
1 TTATATCATT-TAT-TATATATAT
53808 AGATGTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 3 0.14
25 9 0.43
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATATCATTTATTATATATATC
Found at i:53862 original size:17 final size:17
Alignment explanation
Indices: 53840--53972 Score: 66
Period size: 17 Copynumber: 8.0 Consensus size: 17
53830 TTACTATGTA
53840 TATATTTTTCTTAATAT
1 TATATTTTTCTTAATAT
**
53857 TATATTTTATACGTTTTTA-
1 TATATTTT-T-C-TTAATAT
53876 TATATATTTTCTTAATAT
1 TATAT-TTTTCTTAATAT
* * **
53894 TCTATTTTTGTTTTTAT
1 TATATTTTTCTTAATAT
* *
53911 T-TATTTAT-AT-ATAT
1 TATATTTTTCTTAATAT
* *
53925 TATATTTTTACTTTATTT
1 TATATTTTT-CTTAATAT
*
53943 TAT-TTTTTC-TACTAT
1 TATATTTTTCTTAATAT
53958 T-T-TTTTTCTTAATAT
1 TATATTTTTCTTAATAT
53973 CATGTATATC
Statistics
Matches: 88, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
14 11 0.12
15 16 0.18
16 7 0.08
17 28 0.32
18 12 0.14
19 7 0.08
20 7 0.08
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.68
Consensus pattern (17 bp):
TATATTTTTCTTAATAT
Found at i:53916 original size:32 final size:36
Alignment explanation
Indices: 53838--53910 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
53828 ATTTACTATG
53838 TATATAT-TTTTCTTAATATTATATTTTATACGTTTT
1 TATATATATTTTCTTAATATTATATTTTATA-GTTTT
*
53874 TATATATATTTTCTTAATATTCTATTTT-T-GTTTT
1 TATATATATTTTCTTAATATTATATTTTATAGTTTT
53908 TAT
1 TAT
53911 TTATTTATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
34 8 0.23
36 8 0.23
37 19 0.54
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (36 bp):
TATATATATTTTCTTAATATTATATTTTATAGTTTT
Found at i:54189 original size:12 final size:12
Alignment explanation
Indices: 54172--54201 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54162 TTCATTTTGT
54172 TTATTTTTATTA
1 TTATTTTTATTA
54184 TTATTTTTATTA
1 TTATTTTTATTA
54196 TT-TTTT
1 TTATTTT
54202 ATGTGCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
TTATTTTTATTA
Found at i:54203 original size:22 final size:22
Alignment explanation
Indices: 54159--54200 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
54149 TTTTAACATT
54159 TTATTCATTTTGTTTATTTTTA
1 TTATTCATTTTGTTTATTTTTA
54181 TTATT-ATTTT-TATTATTTTT
1 TTATTCATTTTGT-TTATTTTT
54201 TATGTGCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.05
21 13 0.68
22 5 0.26
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (22 bp):
TTATTCATTTTGTTTATTTTTA
Found at i:54238 original size:41 final size:41
Alignment explanation
Indices: 54167--54244 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
54157 TTTTATTCAT
* *
54167 TTTGTTTATTTTTATTATTATTTTTATTATTTTTTATGTGC
1 TTTGTTTATTTTTATTATTATTGTTATTATTTATTATGTGC
*
54208 TTTG-TTATTTTCTATTTTTTATTGTT-TTATTTATTAT
1 TTTGTTTATTTT-TA-TTATTATTGTTATTATTTATTAT
54245 TCTCATGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 7 0.22
41 16 0.50
42 9 0.28
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (41 bp):
TTTGTTTATTTTTATTATTATTGTTATTATTTATTATGTGC
Found at i:54241 original size:26 final size:27
Alignment explanation
Indices: 54194--54247 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
54184 TTATTTTTAT
54194 TATTTTTTATGTGCTTTGTTATT-TTC
1 TATTTTTTATGTGCTTTGTTATTATTC
* *
54220 TATTTTTTAT-TGTTTTATTTATTATTC
1 TATTTTTTATGTGCTTT-GTTATTATTC
54247 T
1 T
54248 CATGTTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.21
26 15 0.62
27 4 0.17
ACGTcount: A:0.15, C:0.06, G:0.07, T:0.72
Consensus pattern (27 bp):
TATTTTTTATGTGCTTTGTTATTATTC
Found at i:57376 original size:19 final size:19
Alignment explanation
Indices: 57352--57388 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
57342 GGAAAAAGAG
* *
57352 AAAAAAGCAAAGAGAAAAT
1 AAAAAAGAAAAAAGAAAAT
57371 AAAAAAGAAAAAAGAAAA
1 AAAAAAGAAAAAAGAAAA
57389 AAGGAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (19 bp):
AAAAAAGAAAAAAGAAAAT
Found at i:57408 original size:33 final size:34
Alignment explanation
Indices: 57332--57408 Score: 79
Period size: 34 Copynumber: 2.2 Consensus size: 34
57322 AAATTCAATC
57332 AGAACAAAAAGGAAAAAGAGAAAAAAGCAAAGAGA
1 AGAA-AAAAAGGAAAAAGAGAAAAAAGCAAAGAGA
* *
57367 A-AATAAAAAAGAAAAA-AGAAAAAAGGAAA-ATTGA
1 AGAA-AAAAAGGAAAAAGAGAAAAAAGCAAAGA--GA
57401 AGAAAAAA
1 AGAAAAAA
57409 GAAGACAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
32 1 0.03
33 12 0.33
34 20 0.56
35 3 0.08
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.04
Consensus pattern (34 bp):
AGAAAAAAAGGAAAAAGAGAAAAAAGCAAAGAGA
Found at i:57410 original size:7 final size:7
Alignment explanation
Indices: 57337--57411 Score: 55
Period size: 7 Copynumber: 10.3 Consensus size: 7
57327 CAATCAGAAC
*
57337 AAAAAGG
1 AAAAAAG
57344 AAAAAGAG
1 AAAAA-AG
57352 AAAAAAG
1 AAAAAAG
*
57359 --CAAAG
1 AAAAAAG
* *
57364 AGAAAAT
1 AAAAAAG
57371 AAAAAAG
1 AAAAAAG
57378 AAAAAAG
1 AAAAAAG
57385 AAAAAAGG
1 AAAAAA-G
57393 AAAATTGAAG
1 AAAA---AAG
57403 AAAAAAG
1 AAAAAAG
57410 AA
1 AA
57412 GACAAGATGC
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
5 4 0.07
7 33 0.60
8 11 0.20
10 5 0.09
11 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (7 bp):
AAAAAAG
Found at i:57588 original size:69 final size:69
Alignment explanation
Indices: 57469--57606 Score: 188
Period size: 69 Copynumber: 2.0 Consensus size: 69
57459 GATTTAAACT
* *
57469 ATGATATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAATATCATAAAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAAAGCA
57534 TCAA
66 TCAA
* * * * **
57538 ATGAGATTGATCAAGCACAATCATTTCTGAATTACTGCATCAC-TCTACTCGAAGATCATGGAGC
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTC-ACTCGAAGATCATAAAGC
57602 ATCAA
65 ATCAA
57607 GAGAGAGAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 2 0.03
69 58 0.97
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAAAGCA
TCAA
Found at i:58960 original size:37 final size:37
Alignment explanation
Indices: 58919--58990 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
58909 TAAAAAGAAT
* *
58919 ATTTTATCTCGCTTGAGATAGTTT-TCCTTGAAACAAA
1 ATTTTATCTCCCTTGAGACAGTTTCT-CTTGAAACAAA
*
58956 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 ATTTTATCTCCCTTGAGACAGTTTCTCTTGAAACA
58991 TAAACATTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 30 0.97
38 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (37 bp):
ATTTTATCTCCCTTGAGACAGTTTCTCTTGAAACAAA
Found at i:59073 original size:37 final size:37
Alignment explanation
Indices: 59006--59092 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
58996 ATTGAAAACA
** * *
59006 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGCCTCCCTTGAGATAG
59042 TTTCCCTTGAAACAAAATTTTGCCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGCCTCCCTTGAGATAG
*
59079 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
59093 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGCCTCCCTTGAGATAG
Found at i:59155 original size:36 final size:36
Alignment explanation
Indices: 59108--59369 Score: 288
Period size: 36 Copynumber: 7.4 Consensus size: 36
59098 ATTGAAAACA
*
59108 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
59144 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
59180 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** * *
59209 TTTTATTTGAAACAAATTTCGTCTCCCTTAAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * *
59245 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
59282 TTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
59318 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
59354 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
59370 ATCTTTGAAT
Statistics
Matches: 190, Mismatches: 26, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
28 2 0.01
29 18 0.09
30 2 0.01
35 1 0.01
36 135 0.71
37 32 0.17
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:59296 original size:102 final size:101
Alignment explanation
Indices: 58925--59369 Score: 480
Period size: 102 Copynumber: 4.3 Consensus size: 101
58915 GAATATTTTA
* * *
58925 TCTCGCTTGAGATAGTTTTCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
* *
58990 ATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
65 ATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
* * *
59027 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGCCTCCCTTGAGATAGTTTCTCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
59092 ATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
65 ATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
* *
59129 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
* * ** *** *
59194 -AAATATTTGAATATGTTTTATTTGAAACAAATTTCG
66 TAAACA-TTGAAAACATTTCCCTTGAAATAAATTTCG
* * ** * * *
59230 TCTCCCTTAAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
*** * * * *
59295 AATTTTCGTCTCTCTTG-AGACAGTTTCTCTTGAAACAAATTTCG
65 -A---T--AAAC-ATTGAAAACA-TTTCCCTTGAAATAAATTTCG
59339 TCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAA
59370 ATCTTTGAAT
Statistics
Matches: 289, Mismatches: 43, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
100 4 0.01
101 79 0.27
102 157 0.54
103 1 0.00
108 4 0.01
109 44 0.15
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (101 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
TAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
Found at i:59309 original size:21 final size:20
Alignment explanation
Indices: 59284--59348 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
59274 TGAGACAGTT
59284 TCTCTTGAAACAATTTTCGTC
1 TCTCTTGAAACAA-TTTCGTC
* *
59305 TCTCTTGAGAC-A----GTT
1 TCTCTTGAAACAATTTCGTC
59320 TCTCTTGAAACAAATTTCGTC
1 TCTCTTGAAAC-AATTTCGTC
59341 TCTCTTGA
1 TCTCTTGA
59349 GACAGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 12 0.35
17 1 0.03
20 1 0.03
21 20 0.59
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (20 bp):
TCTCTTGAAACAATTTCGTC
Found at i:59357 original size:72 final size:73
Alignment explanation
Indices: 59215--59369 Score: 231
Period size: 73 Copynumber: 2.1 Consensus size: 73
59205 TATGTTTTAT
* * * *
59215 TTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCTCTTGAAACTAAATTTCGTCTCTCTTGAGAC
*
59280 AGTTTCTC
66 AGTTTCCC
* * *
59288 TTGAAACAATTTTCGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTCTCTTGAGAC
1 TTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCTCTTGAAACTAAATTTCGTCTCTCTTGAGAC
59352 AGTTTCCC
66 AGTTTCCC
59360 TTGAAACAAA
1 TTGAAACAAA
59370 ATCTTTGAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 35 0.48
73 38 0.52
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (73 bp):
TTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCTCTTGAAACTAAATTTCGTCTCTCTTGAGAC
AGTTTCCC
Found at i:59387 original size:138 final size:134
Alignment explanation
Indices: 59006--59431 Score: 366
Period size: 138 Copynumber: 3.1 Consensus size: 134
58996 ATTGAAAACA
* * *
59006 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGCCTCCCT
1 TTTCCCTTGAAA-CAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA-TTTG-CTCTCT
* * * *
59071 TGAGATAGTTTCTCTTGAAACATAAA-CATTGAAAACATTTCCCTTGAAATAAATTTCGTCTCTC
62 TGAGATAGTTTCACTTGAAACA-AAATCTTTGAAAACATTTCTCTTGAAATAAATTTTGTCTCTC
59135 TTGAGACAG
126 TTGAGACAG
* *
59144 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA----ATAT-TTGA
1 TTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTGCTCTCTTGA
* * * * * * * *
59204 -ATATGTTTTATTTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCTTTTGGAACTAAGTTTTGT
65 GATA-GTTTCACTTGAAACAAA-ATC-T-T---TGAAAACA-TTTCTCTT-GAAATAAATTTTGT
59268 CTCTCTTGAGACAG
121 CTCTCTTGAGACAG
* *
59282 TTTCTCTTGAAACAATTTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTT
1 TTTCCCTTGAAACAATTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTT-G-CTCTCTT
* * *** * * *
59347 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCTCCT-AAAAAAAATTTGTCTC-CTT
63 GAGATAGTTTCACTTGAAACAAAATCTTTGAAAACATTTCTCTTGAAATAAATTTTGTCTCTC-T
59410 TGAGACAG
127 TGAGACAG
*
59418 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
59432 CAAAATCTTC
Statistics
Matches: 231, Mismatches: 36, Indels: 44
0.74 0.12 0.14
Matches are distributed among these distances:
129 5 0.02
130 16 0.07
131 2 0.01
133 1 0.00
135 1 0.00
136 41 0.18
137 15 0.06
138 120 0.52
139 4 0.02
142 1 0.00
143 1 0.00
144 4 0.02
145 18 0.08
146 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (134 bp):
TTTCCCTTGAAACAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTGCTCTCTTGAG
ATAGTTTCACTTGAAACAAAATCTTTGAAAACATTTCTCTTGAAATAAATTTTGTCTCTCTTGAG
ACAG
Found at i:59420 original size:64 final size:67
Alignment explanation
Indices: 59318--59482 Score: 189
Period size: 66 Copynumber: 2.5 Consensus size: 67
59308 CTTGAGACAG
* * **
59318 TTTCTCTTGAAAC-AAATTTCGTCT-CTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAA
1 TTTCCCTTAAAACAAAATTT-GTCTCCT-TTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAA
59379 TTTA
64 TTTA
*
59383 TTTCTCC-TAAAA-AAAATTTGTCTCCTTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAAT
1 TTTC-CCTTAAAACAAAATTTGTCTCCTTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAAT
59446 TTA
65 TTA
* *
59449 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGA
1 TTTCCCTTAAAACAAAA-TTTGTCTCCTTTGAGA
59483 TCGTTTTTCA
Statistics
Matches: 85, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
64 21 0.25
65 20 0.24
66 26 0.31
67 4 0.05
68 14 0.16
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (67 bp):
TTTCCCTTAAAACAAAATTTGTCTCCTTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATT
TA
Found at i:60422 original size:110 final size:110
Alignment explanation
Indices: 60220--60423 Score: 257
Period size: 110 Copynumber: 1.9 Consensus size: 110
60210 TCCCAGTTTC
* * * *
60220 AGAGCCAATTTTAACTTCACAGCAGGGGATATTGGACTCAAGACAACACAAGCTCAAATTCATAA
1 AGAGCCAATTTCAACTTCACAGCAGAGGATATTGAACTCAAGACAACACAAGCTCAAATTCACAA
* * * * * *
60285 CGAATGGGCGACTGATTGTCAATAAACAACTTTTCAGTTTCATTT
66 CAAAAGGGAGACTGACTATCAACAAACAACTTTTCAGTTTCATTT
* * *
60330 AGAGTCAATTTCAACTTCACAGC-GAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCACA
1 AGAGCCAATTTCAACTTCACAGCAG-AGGATATTGAACTCAAGACAACACAAGCTCAAATTCACA
* *
60394 GCAAAAGGGAGACTGACTATCAGCAAACAA
65 ACAAAAGGGAGACTGACTATCAACAAACAA
60424 TTTCCAGAGC
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
109 1 0.01
110 77 0.99
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (110 bp):
AGAGCCAATTTCAACTTCACAGCAGAGGATATTGAACTCAAGACAACACAAGCTCAAATTCACAA
CAAAAGGGAGACTGACTATCAACAAACAACTTTTCAGTTTCATTT
Found at i:61918 original size:13 final size:14
Alignment explanation
Indices: 61893--61931 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
61883 ATTCCTTTTT
61893 TTATTTATATTATA
1 TTATTTATATTATA
61907 TTATTT-TATTATA
1 TTATTTATATTATA
61920 TATATCTTATAT
1 T-TAT-TTATAT
61932 CATTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.36
14 9 0.41
15 2 0.09
16 3 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:61929 original size:19 final size:19
Alignment explanation
Indices: 61870--61943 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
61860 TTTTTAATTA
61870 TATTTT-TTACTATAT-TCCT
1 TATTTTATTA-TATATAT-CT
* *
61889 TTTTTTATT-TATATTATAT
1 TATTTTATTATATA-TATCT
61908 TATTTTATTATATATATCT
1 TATTTTATTATATATATCT
* *
61927 TATATCATTATATATAT
1 TATTTTATTATATATAT
61944 ATGTGTGTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 4 0.09
19 34 0.76
20 7 0.16
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTTATTATATATATCT
Found at i:62337 original size:3 final size:3
Alignment explanation
Indices: 62323--62366 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
62313 TTCATTTTGT
*
62323 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
62367 TTACCTGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:73865 original size:22 final size:22
Alignment explanation
Indices: 73834--73903 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
73824 CCTTCTTTTT
* *
73834 TCGCCAGCAGTCACAACCTCCA
1 TCGCCGGCAGTCACAGCCTCCA
*
73856 TCGCCGGCAGTCATAGCCTCCA
1 TCGCCGGCAGTCACAGCCTCCA
* * * *
73878 TCGTCGACAATCACAGCTTCCA
1 TCGCCGGCAGTCACAGCCTCCA
73900 TCGC
1 TCGC
73904 TGGGCGCTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.23, C:0.41, G:0.17, T:0.19
Consensus pattern (22 bp):
TCGCCGGCAGTCACAGCCTCCA
Found at i:77582 original size:18 final size:18
Alignment explanation
Indices: 77559--77593 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
77549 AGGGATTAAC
*
77559 AGTGGTCTTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
77577 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
77594 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:83517 original size:21 final size:22
Alignment explanation
Indices: 83492--83532 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
83482 ATTTAATAAG
83492 TATATTTT-AAAAACTTATTAT
1 TATATTTTCAAAAACTTATTAT
*
83513 TATATTTTCAGAAACTTATT
1 TATATTTTCAAAAACTTATT
83533 TAAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATTTTCAAAAACTTATTAT
Found at i:85068 original size:21 final size:21
Alignment explanation
Indices: 85043--85104 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
85033 ATTATCCAAT
*
85043 AAACTTGACATCCATAATAAC
1 AAACTTGAAATCCATAATAAC
* *
85064 AAACTTGAAATCCATGACAAC
1 AAACTTGAAATCCATAATAAC
85085 AAACTTGAAATCCATAATAA
1 AAACTTGAAATCCATAATAA
85105 TAAATCAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.50, C:0.21, G:0.06, T:0.23
Consensus pattern (21 bp):
AAACTTGAAATCCATAATAAC
Found at i:87436 original size:23 final size:23
Alignment explanation
Indices: 87410--87478 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
87400 CACCACAGCT
*
87410 CATATAAATGCACCGAAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
** *
87433 CATAGATTTGCACCGAAGTGCCG
1 CATAGAAATGCACCGAAGTGCCA
* *
87456 CGTAGAAATGCACCAAAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
87479 TATAAGATGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTGCCA
Found at i:93510 original size:65 final size:63
Alignment explanation
Indices: 93406--93562 Score: 174
Period size: 65 Copynumber: 2.4 Consensus size: 63
93396 GAATAAATTG
* * *
93406 AACATCGAATGCATTATATGCATTCGATGCGCATACCATGCATCGATGCACTCAAG-TTTTTATG
1 AACATCGAATGCATT-TATGCA-TCGATACACATACCATGCATCGATGCACTCAAGCTTGTT-TG
93470 AA
63 -A
**
93472 AACATCGAATGCATTTGATGCATCGATACACA-AGCCATGCATCGATGCACTCGGGCTTGTTTGA
1 AACATCGAATGCATTT-ATGCATCGATACACATA-CCATGCATCGATGCACTCAAGCTTGTTTGA
* *
93536 AACATCGAATGCACTTCATACATCGAT
1 AACATCGAATGCA-TTTATGCATCGAT
93563 GCACTCTTAG
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
64 24 0.30
65 32 0.40
66 24 0.30
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATACACATACCATGCATCGATGCACTCAAGCTTGTTTGA
Found at i:96220 original size:21 final size:20
Alignment explanation
Indices: 96194--96232 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
96184 AAACCATTCA
96194 GGGGGGAATCGGTATCCCTTG
1 GGGGGGAATCGGT-TCCCTTG
96215 GGGGGGAATCGGTTCCCT
1 GGGGGGAATCGGTTCCCT
96233 CTGAGCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.13, C:0.21, G:0.44, T:0.23
Consensus pattern (20 bp):
GGGGGGAATCGGTTCCCTTG
Found at i:96560 original size:28 final size:28
Alignment explanation
Indices: 96528--96584 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
96518 TAAGATTTTG
96528 AAATCAAGTTTTGAAATTACTCCCCCTT
1 AAATCAAGTTTTGAAATTACTCCCCCTT
96556 AAATCAAGTTTTGAAATTACTCCCCCTT
1 AAATCAAGTTTTGAAATTACTCCCCCTT
96584 A
1 A
96585 CTTTAACACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (28 bp):
AAATCAAGTTTTGAAATTACTCCCCCTT
Found at i:98398 original size:2 final size:2
Alignment explanation
Indices: 98391--98442 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
98381 TTGAGAAACA
98391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98433 AT AT AT AT AT
1 AT AT AT AT AT
98443 TCATAACAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105117 original size:15 final size:15
Alignment explanation
Indices: 105097--105134 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
105087 CTTGAAAGTA
105097 AAATCAAAGATTTAC
1 AAATCAAAGATTTAC
105112 AAATCAAAGATTTAC
1 AAATCAAAGATTTAC
105127 AAATCAAA
1 AAATCAAA
105135 CTAGAAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.58, C:0.13, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATCAAAGATTTAC
Found at i:113193 original size:19 final size:20
Alignment explanation
Indices: 113152--113194 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
113142 GATAAATAGG
* *
113152 TATCGATACACTCCTCAATA
1 TATCGATACACTCCTAAAGA
113172 TATCGATACA-TCCTAAAGA
1 TATCGATACACTCCTAAAGA
113191 TATC
1 TATC
113195 CTTCAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (20 bp):
TATCGATACACTCCTAAAGA
Found at i:114709 original size:40 final size:40
Alignment explanation
Indices: 114649--114815 Score: 105
Period size: 40 Copynumber: 4.2 Consensus size: 40
114639 GTGGTGTATA
* *
114649 TATATAAAAACTA-CATTAAAGTAGAGTATTTAGTGGCGTT
1 TATATAAAAAC-ACCACTAAAGTAGAGTATTTAGCGGCGTT
* * *
114689 TATATAAAAACGCCACTAAAGTACGAGTCTTTGGCGGCGTT
1 TATATAAAAACACCACTAAAGTA-GAGTATTTAGCGGCGTT
* * * ** *
114730 TGTGCTTAAAACACCACTAAAGTATTGTATTTAACGGC---
1 TAT-ATAAAAACACCACTAAAGTAGAGTATTTAGCGGCGTT
** * *
114768 -ATAT-AAAATGCTACTAAAGTACGAGTATTTACCGGCGTT
1 TATATAAAAACACCACTAAAGTA-GAGTATTTAGCGGCGTT
*
114807 TGT-TAAAAA
1 TATATAAAAA
114816 AGCGTCGCCA
Statistics
Matches: 95, Mismatches: 23, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
35 14 0.15
36 12 0.13
37 1 0.01
39 1 0.01
40 25 0.26
41 25 0.26
42 17 0.18
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (40 bp):
TATATAAAAACACCACTAAAGTAGAGTATTTAGCGGCGTT
Found at i:116138 original size:31 final size:33
Alignment explanation
Indices: 116103--116173 Score: 110
Period size: 34 Copynumber: 2.2 Consensus size: 33
116093 TCCTTACACT
*
116103 ATTTTAGATTTAC-AAAAAA-TCCATAATTAGA
1 ATTTTAGATTTACAAAAAAAGTCCATAATTAAA
116134 ATTTTAGATTTACAAAAAAAAGTCCATAATTAAA
1 ATTTTAGATTTAC-AAAAAAAGTCCATAATTAAA
116168 ATTTTA
1 ATTTTA
116174 TATGAAGTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
31 13 0.36
33 6 0.17
34 17 0.47
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (33 bp):
ATTTTAGATTTACAAAAAAAGTCCATAATTAAA
Found at i:117434 original size:39 final size:40
Alignment explanation
Indices: 117391--117474 Score: 91
Period size: 39 Copynumber: 2.1 Consensus size: 40
117381 AGCTAAATAT
* * * *
117391 GAAGACT-CTACAATTGCATGGCGTCTTTAGGCAAATGAA
1 GAAGACTCCTACAACTGCATGACATCTTCAGGCAAATGAA
* * *
117430 GAAGA-TCCTACGACTGCATGATATGTTCAGGCAAATGAA
1 GAAGACTCCTACAACTGCATGACATCTTCAGGCAAATGAA
117469 GAAGAC
1 GAAGAC
117475 CCAGGAGTGC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
38 1 0.03
39 35 0.97
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.23
Consensus pattern (40 bp):
GAAGACTCCTACAACTGCATGACATCTTCAGGCAAATGAA
Found at i:117963 original size:19 final size:19
Alignment explanation
Indices: 117939--117980 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
117929 CAATCCATAT
117939 AATGTATGGCACATGGTAA
1 AATGTATGGCACATGGTAA
117958 AATGTATGGCACATGGTAA
1 AATGTATGGCACATGGTAA
117977 AATG
1 AATG
117981 CATGTCTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (19 bp):
AATGTATGGCACATGGTAA
Found at i:120732 original size:42 final size:42
Alignment explanation
Indices: 120611--120735 Score: 205
Period size: 42 Copynumber: 3.0 Consensus size: 42
120601 CAATCGAATC
** *
120611 ATTAGGTGAATCATTGGAATTTCCAATATTATTATTAAAAGT
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAGAAGT
*
120653 ATTAGGTGAATCATTGAAATTTCCAATAGGATTATTAGAAGT
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAGAAGT
*
120695 ATTAGGTGAATCATTGGAATTTCCAATCGGATTATTAGAAG
1 ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAGAAG
120736 GTTTAACCGG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (42 bp):
ATTAGGTGAATCATTGGAATTTCCAATAGGATTATTAGAAGT
Found at i:120892 original size:28 final size:28
Alignment explanation
Indices: 120860--120918 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
120850 ACATATTTAA
*
120860 AAGTAATCAATAAAACAAATATAGTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
*
120888 AAGTAAACAATAAAACAAATATATTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
120916 AAG
1 AAG
120919 GAAAGATACA
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:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (28 bp):
AAGTAAACAATAAAACAAATATAGTAGC
Found at i:121283 original size:28 final size:28
Alignment explanation
Indices: 121251--121305 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
121241 ATACTAAGTT
121251 TGCCGACTAAACATG-AAAGAAATGAGTG
1 TGCCGACTAAACATGCAAA-AAATGAGTG
121279 TGCCGACTAAACATGCAAAAAATGAGT
1 TGCCGACTAAACATGCAAAAAATGAGT
121306 AAGTTGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (28 bp):
TGCCGACTAAACATGCAAAAAATGAGTG
Found at i:130428 original size:23 final size:21
Alignment explanation
Indices: 130388--130431 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
130378 TATAATTAAT
*
130388 AAAATTTAAATAACTAAAATA
1 AAAATTTAAATAAATAAAATA
130409 AAAATATTAAAATAAATAAAATA
1 AAAAT-TT-AAATAAATAAAATA
130432 TCAAATAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 2 0.10
23 13 0.65
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAATTTAAATAAATAAAATA
Found at i:140837 original size:2 final size:2
Alignment explanation
Indices: 140830--140872 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
140820 TCATAAAATT
140830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
140872 T
1 T
140873 TTACAAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:141834 original size:15 final size:16
Alignment explanation
Indices: 141814--141846 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
141804 AAAATACAAC
141814 ATTCTCAG-TAATCTT
1 ATTCTCAGATAATCTT
*
141829 ATTCTCTGATAATCTT
1 ATTCTCAGATAATCTT
141845 AT
1 AT
141847 ATTATCATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.48
Consensus pattern (16 bp):
ATTCTCAGATAATCTT
Found at i:144303 original size:21 final size:22
Alignment explanation
Indices: 144279--144325 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
144269 ACTTTGACTA
144279 TCGCATTGCGA-TAGTCCAAGT
1 TCGCATTGCGATTAGTCCAAGT
* *
144300 TCGCGTTGCGATTTATTCCAAGT
1 TCGCATTGCGA-TTAGTCCAAGT
144323 TCG
1 TCG
144326 TTGTGATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
23 12 0.55
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (22 bp):
TCGCATTGCGATTAGTCCAAGT
Found at i:149011 original size:20 final size:22
Alignment explanation
Indices: 148966--149023 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
148956 GCATGGGTAG
148966 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
148990 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
149010 TGTATCGATGCACT
1 TGCATCGATGCACT
149024 TCAAAGGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:149723 original size:24 final size:24
Alignment explanation
Indices: 149693--149748 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
149683 TAGAAGTTCG
*
149693 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAACTCA
149717 ATTGAAGCCTAAAATTTGAACTCA
1 ATTGAAGCCTAAAATTTGAACTCA
149741 ATTGAAGC
1 ATTGAAGC
149749 GAAAGAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAACTCA
Found at i:151596 original size:23 final size:23
Alignment explanation
Indices: 151570--151633 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
151560 GGACATTATA
*
151570 TGGCACTACGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
151593 TGGCACTTCAGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
151616 CGGCACTTCGGTGCATTT
1 TGGCACTTCGGTGCATTT
151634 ACATGAGCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.16, C:0.27, G:0.25, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:167489 original size:15 final size:16
Alignment explanation
Indices: 167458--167490 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
167448 TTCTTACTCT
167458 TTCAACATTTGAATCA
1 TTCAACATTTGAATCA
*
167474 TTCAATATTT-AATCA
1 TTCAACATTTGAATCA
167489 TT
1 TT
167491 TAAAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (16 bp):
TTCAACATTTGAATCA
Found at i:176403 original size:12 final size:13
Alignment explanation
Indices: 176377--176401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
176367 TAGTCACTAA
176377 AATTTAATTTTTT
1 AATTTAATTTTTT
176390 AATTTAATTTTT
1 AATTTAATTTTT
176402 AAACCATAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
AATTTAATTTTTT
Found at i:181848 original size:25 final size:25
Alignment explanation
Indices: 181820--181869 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
181810 CAAATATACG
181820 AGCCGAGATCGAATATTGTTGAACT
1 AGCCGAGATCGAATATTGTTGAACT
181845 AGCCGAGATCGAATATTGTTGAACT
1 AGCCGAGATCGAATATTGTTGAACT
181870 GTACTCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (25 bp):
AGCCGAGATCGAATATTGTTGAACT
Found at i:182061 original size:14 final size:14
Alignment explanation
Indices: 182042--182111 Score: 104
Period size: 14 Copynumber: 5.0 Consensus size: 14
182032 AACTCAATTT
182042 AAGCTCGATTCAAG
1 AAGCTCGATTCAAG
182056 AAGCTCGATTCAAG
1 AAGCTCGATTCAAG
182070 AAGCTCGATTCAAG
1 AAGCTCGATTCAAG
* *
182084 AAACTCAATTCAAG
1 AAGCTCGATTCAAG
* *
182098 AAACTCAATTCAAG
1 AAGCTCGATTCAAG
182112 CTCAACAGGT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 54 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (14 bp):
AAGCTCGATTCAAG
Found at i:183870 original size:14 final size:14
Alignment explanation
Indices: 183851--183956 Score: 54
Period size: 14 Copynumber: 7.6 Consensus size: 14
183841 ATGTGTATAA
183851 CTTAAACCCTAAAC
1 CTTAAACCCTAAAC
*
183865 CTTAAA-CCTGAA-
1 CTTAAACCCTAAAC
* **
183877 TTATAAACCAAAAAC
1 CT-TAAACCCTAAAC
* * * * *
183892 CCTATACCTTATAT
1 CTTAAACCCTAAAC
* *
183906 CTAAAACACTAAAC
1 CTTAAACCCTAAAC
* *
183920 CATAAACCATAAAAC
1 CTTAAACCCT-AAAC
183935 CTTAAACCCTAAAC
1 CTTAAACCCTAAAC
*
183949 CCTAAACC
1 CTTAAACC
183957 TTATTACACA
Statistics
Matches: 62, Mismatches: 26, Indels: 8
0.65 0.27 0.08
Matches are distributed among these distances:
12 1 0.02
13 9 0.15
14 40 0.65
15 12 0.19
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (14 bp):
CTTAAACCCTAAAC
Found at i:183932 original size:22 final size:22
Alignment explanation
Indices: 183907--183959 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
183897 ACCTTATATC
183907 TAAAACAC-TAAACCATAAACCA
1 TAAAAC-CTTAAACCATAAACCA
* *
183929 TAAAACCTTAAACCCTAAACCC
1 TAAAACCTTAAACCATAAACCA
183951 T-AAACCTTA
1 TAAAACCTTA
183960 TTACACAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (22 bp):
TAAAACCTTAAACCATAAACCA
Found at i:185519 original size:18 final size:17
Alignment explanation
Indices: 185465--185513 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
185455 TTGGACCCTT
* *
185465 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
185483 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
185501 AGTGCATTCGATG
1 AGTGCA-TCGATG
185514 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:185622 original size:64 final size:64
Alignment explanation
Indices: 185486--185622 Score: 163
Period size: 64 Copynumber: 2.1 Consensus size: 64
185476 GCACTAAGAG
* * ***
185486 TGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCAAA
* *
185550 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCAT-G-AA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGCAA
185612 A
64 A
185613 TGCATTCGAT
1 TGCA-TCGAT
185623 ATTCAATTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
63 4 0.06
64 33 0.52
65 23 0.37
66 3 0.05
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCAAA
Found at i:185654 original size:45 final size:46
Alignment explanation
Indices: 185547--185654 Score: 125
Period size: 46 Copynumber: 2.4 Consensus size: 46
185537 GATGCATGGC
* *
185547 TGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCA
1 TGGTGCATCGATGCATGAAATGCATTCGA-GTATTCATAAAAT-CTCA
**
185595 --GTGCATCGATGCATGAAATGCATTCGA-TATTCAATTTAAT-TCA
1 TGGTGCATCGATGCATGAAATGCATTCGAGTATTC-ATAAAATCTCA
185638 TGGTGCATCGATGCATG
1 TGGTGCATCGATGCATG
185655 GATTGGTGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
43 3 0.06
44 4 0.08
45 20 0.38
46 26 0.49
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (46 bp):
TGGTGCATCGATGCATGAAATGCATTCGAGTATTCATAAAATCTCA
Found at i:186125 original size:2 final size:2
Alignment explanation
Indices: 186118--186148 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
186108 TAGCAATTGA
186118 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
186149 GCTTAAGCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:190260 original size:22 final size:21
Alignment explanation
Indices: 190218--190257 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
190208 GAGTTTATTT
190218 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
190239 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
190258 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:192000 original size:23 final size:23
Alignment explanation
Indices: 191974--192060 Score: 138
Period size: 23 Copynumber: 3.8 Consensus size: 23
191964 CAGCTCATAT
*
191974 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGGAGTGCCACGTAG
*
191997 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCACGTAG
*
192020 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCACGTAG
*
192043 AATTGCACCGTAGTGCCA
1 AATTGCACCGGAGTGCCA
192061 TATAATAATG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.25, C:0.26, G:0.30, T:0.18
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCACGTAG
Found at i:192247 original size:102 final size:103
Alignment explanation
Indices: 192071--192292 Score: 428
Period size: 102 Copynumber: 2.2 Consensus size: 103
192061 TATAATAATG
*
192071 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCATTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
192136 CACCAGACTTCACACA-GTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
192173 TCCCGAAGGACCACATATCACTCATTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCATTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
192238 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
192276 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
192293 GACCCTCGAA
Statistics
Matches: 118, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
102 80 0.68
103 38 0.32
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
TCCCGAAGGACCACATATCACTCATTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:193139 original size:64 final size:62
Alignment explanation
Indices: 193071--193254 Score: 223
Period size: 64 Copynumber: 2.9 Consensus size: 62
193061 CATAAAATGT
*
193071 ATTCGATGTTGTATTATTACTGGGTTGCATCGATGCA-TACCTTATGCATCGATGCACTAATTGC
1 ATTCGATGTT-TATTATTAATGGG-TGCATCGATGCACTACCTTATGCATCGATGCAC-AATTGC
*
193135 ATTCGATGTTTCCTTATTAATGGGATGCATCGATGCACTA-CTTATGCATCGATGCACAATTGC
1 ATTCGATGTTT-ATTATTAATGGG-TGCATCGATGCACTACCTTATGCATCGATGCACAATTGC
* * *
193198 ATTCGATGTATTTATT-TTAAAAGAGTGCATCGATGCACTACC-AATGCATCGATGCAC
1 ATTCGATG--TTTATTATT-AATGGGTGCATCGATGCACTACCTTATGCATCGATGCAC
193255 CTTCAAACAA
Statistics
Matches: 107, Mismatches: 7, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
63 46 0.43
64 56 0.52
65 5 0.05
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (62 bp):
ATTCGATGTTTATTATTAATGGGTGCATCGATGCACTACCTTATGCATCGATGCACAATTGC
Found at i:193228 original size:63 final size:64
Alignment explanation
Indices: 193032--193254 Score: 217
Period size: 64 Copynumber: 3.5 Consensus size: 64
193022 TAATGAAGGT
* * * * * ** *
193032 ATGCATTGATGCACTACTGA-GCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCATTATTAAAGA
193094 G
64 G
* * * *
193095 TTGCATCGATGCA-TACCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACTA-CTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAAAGAG
*
193159 ATGCATCGATGCACTACTTATGCATCGATGCAC-AATTGCATTCGATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCATTATTAAAGAG
**
193221 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
193255 CTTCAAACAA
Statistics
Matches: 138, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
62 4 0.03
63 64 0.46
64 67 0.49
65 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:195027 original size:18 final size:17
Alignment explanation
Indices: 194973--195021 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
194963 TTGGACCCTT
* *
194973 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
194991 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
195009 AGTGCATTCGATG
1 AGTGCA-TCGATG
195022 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:195079 original size:64 final size:66
Alignment explanation
Indices: 194993--195130 Score: 201
Period size: 64 Copynumber: 2.1 Consensus size: 66
194983 TGCACTAAGA
* *
194993 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCAGAGTGCATCGATACATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCCACAGTGCATCGATACATGGAT
195055 TG
65 TG
* * *
195057 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATACATGGATT
195122 G
66 G
195123 GTGCATCG
1 GTGCATCG
195131 GGGATCACTT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
64 28 0.42
65 24 0.36
66 14 0.21
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (66 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATACATGGATT
G
Found at i:197132 original size:17 final size:19
Alignment explanation
Indices: 197071--197120 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
197061 TTGGACCCTT
* *
197071 AGTGCATCGGTCCAATAAG
1 AGTGCATCGGTGCACTAAG
197090 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
197109 AGTGCATCGGTG
1 AGTGCATCGGTG
197121 TATCAAGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:197190 original size:64 final size:65
Alignment explanation
Indices: 197110--197263 Score: 170
Period size: 65 Copynumber: 2.4 Consensus size: 65
197100 TGCACTAAGA
* * * ** * *
197110 GTGCATCGGTGTATCAAGTGCATTTGATG-TTTCA-AAATAGCCAGAGTGCATCGATGTATGGCT
1 GTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAA-AGCCACAGTGCATCGATGCATGG-T
*
197173 -G
64 AC
* *
197174 GTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAC
1 GTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGTAC
*
197239 GTGCATCGATGCATGAAATGCATTC
1 GTGCATCGATGCATCAAATGCATTC
197264 GATATTCAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 25 0.33
65 48 0.63
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGTAC
Found at i:197308 original size:65 final size:63
Alignment explanation
Indices: 197154--197316 Score: 168
Period size: 65 Copynumber: 2.5 Consensus size: 63
197144 AAATAGCCAG
* * *
197154 AGTGCATCGATGTATGGCTGGTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAAATCCTC
1 AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCAA-GTATTCATAAAAT-CTC
** * * **
197219 AGTGCATCGATGCATGGTACGTGCATCGATGCATGAAATGCATTCGA-TATTCAATTTAAT-TC
1 AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCAAGTATTC-ATAAAATCTC
*
197281 ATGGTGCATCGATGCATGGATTGGTGCATCGGTGCA
1 A--GTGCATCGATGCATGG-TTGGTGCATCGATGCA
197317 CCACTCTGAA
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
62 3 0.04
63 4 0.05
64 21 0.26
65 54 0.66
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCAAGTATTCATAAAATCTC
Found at i:199969 original size:23 final size:22
Alignment explanation
Indices: 199943--200020 Score: 86
Period size: 21 Copynumber: 3.5 Consensus size: 22
199933 CCCGACGGAA
199943 GCATCGATGCACATTCAAGGCGT
1 GCATCGATGCACATTCAAGG-GT
* * *
199966 GCATCGGTGCACCTTC-ATGGT
1 GCATCGATGCACATTCAAGGGT
* *
199987 GTATCGATGCACATTCAAGGAT
1 GCATCGATGCACATTCAAGGGT
*
200009 ACATCGATGCAC
1 GCATCGATGCAC
200021 TGTTAGGTGT
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
21 15 0.34
22 15 0.34
23 14 0.32
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (22 bp):
GCATCGATGCACATTCAAGGGT
Found at i:199997 original size:21 final size:20
Alignment explanation
Indices: 199943--200039 Score: 70
Period size: 21 Copynumber: 4.5 Consensus size: 20
199933 CCCGACGGAA
199943 GCATCGATGCACATTCAAGGCGT
1 GCATCGATGCACATTC-A-G-GT
* *
199966 GCATCGGTGCACCTTCATGGT
1 GCATCGATGCACATTCA-GGT
*
199987 GTATCGATGCACATTCAAGGAT
1 GCATCGATGCACATTC-AGG-T
* *
200009 ACATCGATGCAC-TGTTAGGT
1 GCATCGATGCACAT-TCAGGT
*
200029 GTATCGATGCA
1 GCATCGATGCA
200040 TGAAGCACAA
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
20 10 0.17
21 21 0.35
22 15 0.25
23 14 0.23
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.27
Consensus pattern (20 bp):
GCATCGATGCACATTCAGGT
Found at i:203885 original size:20 final size:21
Alignment explanation
Indices: 203846--203886 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
203836 GAGTTTATTT
203846 TCATTTTTCAATTTTGAAAAA
1 TCATTTTTCAATTTTGAAAAA
203867 TCATTTTT-ATATTTT-AAAAA
1 TCATTTTTCA-ATTTTGAAAAA
203887 CAATTTCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAAAA
Found at i:205888 original size:19 final size:19
Alignment explanation
Indices: 205864--205915 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
205854 AATAGCCAGA
205864 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
205883 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
205902 GTGCATCGATGCAT
1 GTGCATCGATGCAT
205916 CAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.21, G:0.35, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTG
Found at i:205951 original size:84 final size:83
Alignment explanation
Indices: 205827--205981 Score: 206
Period size: 84 Copynumber: 1.8 Consensus size: 83
205817 GCACTAAAAG
* * *
205827 TGCATCAAGTGTATTCGATGTTTCAAAAATAGCCAGAGTGCATCGATGCATGGCT-GGTGCATCG
1 TGCATCAAATGCATTCGATGTTTCAAAAATA-CCACAGTGCATCGATGCATGG-TAGGTGCATCG
205891 ATGCATGGCTGGTGCATCGA
64 ATGCATGGCTGGTGCATCGA
* * *
205911 TGCATCAAATGCATTCGATGTTTTCATAAAAT-CCTCAGTGCATCGGTGCATGGTATGTGCATCG
1 TGCATCAAATGCATTCGATG-TTTCA-AAAATACCACAGTGCATCGATGCATGGTAGGTGCATCG
205975 ATGCATG
64 ATGCATG
205982 AAATGCATTC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
83 1 0.02
84 51 0.82
85 5 0.08
86 5 0.08
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (83 bp):
TGCATCAAATGCATTCGATGTTTCAAAAATACCACAGTGCATCGATGCATGGTAGGTGCATCGAT
GCATGGCTGGTGCATCGA
Found at i:205953 original size:65 final size:62
Alignment explanation
Indices: 205882--206047 Score: 183
Period size: 65 Copynumber: 2.6 Consensus size: 62
205872 ATGCATGGCT
205882 GGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCT
1 GGTGCATCGATGCATGG-TGGTGCATCGATGCATCAAATGCATTCGATG--TTCAATAAAAT--T
205946 CA
61 CA
* * * **
205948 -GTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCA
1 GGTGCATCGATGCATGGT-GGTGCATCGATGCATCAAATGCATTCGATGTTCAATAAAATTCA
*
206010 TGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 -GGTGCATCGATGCATGG--TGGTGCATCGATGCATCA
206048 CTCTGAAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 21 0.25
65 57 0.67
66 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (62 bp):
GGTGCATCGATGCATGGTGGTGCATCGATGCATCAAATGCATTCGATGTTCAATAAAATTCA
Found at i:208120 original size:3 final size:3
Alignment explanation
Indices: 208112--208142 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
208102 CGAGTAAAGT
208112 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
208143 AAATACGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:215142 original size:24 final size:24
Alignment explanation
Indices: 215091--215142 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
215081 GTCGAAGCAT
* *
215091 ATGAAGATGCTCACCAGCCAGCCA
1 ATGAAGAGGCTCACCAGCCAACCA
* *
215115 ATGAAGAGGTTCACCAGCCAACCG
1 ATGAAGAGGCTCACCAGCCAACCA
215139 ATGA
1 ATGA
215143 GGAAGAACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.29, G:0.23, T:0.13
Consensus pattern (24 bp):
ATGAAGAGGCTCACCAGCCAACCA
Found at i:219327 original size:726 final size:722
Alignment explanation
Indices: 217935--220094 Score: 3593
Period size: 726 Copynumber: 3.0 Consensus size: 722
217925 AGACATTTCC
* * *
217935 ATCCAATTTGTCACAGCATATCTATTTGCTACCATATTACCATCATTCCATTTCCACAACATCCA
1 ATCCAATTTGCCACAACATATCCATTTGCTACCATATTACCATCATTCCATTTCCACAACATCCA
* *
218000 TCTCATCTTGCTACATCATTATCATTTGTACATACTATTAGTAACTTTACTTAGGTGACAGAGTA
66 TCTCATCTTGCTACATCATTATCATTTGTACATACCATAAGTAACTTTACTTAGGTGACAGAGTA
* *
218065 AAGTGTTTTGATCGAACTTATCAATTTCCTCCAATCCCTGTGGAGGCGATACTCACTTATAATTG
131 AAGTGTTTTGATCGAACTTATCAATTTCCTCCAATCCATGTGGAGGCGATACTCACTTATCATTG
*
218130 TATTACTTATTTGATTGTGTATACTTGCACATATTTCTGCACCCATATATAGTACTAACACAGCG
196 TATTACTTATTCGATTGTGTATACTTGCACATATTTCTGCACCCATATATAGTACTAACACAGCG
218195 CGGACACCTACCATTTGCTTGGCCATGGCTTTTTGACCTGTAAGCAAATTTTCGAACTCAACAAG
261 CGGACACCTACCATTTGCTTGGCCATGGCTTTTTGACCTGTAAGCAAATTTTCGAACTCAACAAG
* *
218260 CGAGTGTTGTGTCAGCCATCCCTATACAGCGGCAACAAACCCTCGATAGTCGGGTCTCAAACCAT
326 CGAGTGTTGTGTCGGCCATCCCTGTACAGCGGCAACAAACCCTCGATAGTCGGGTCTCAAACCAT
* *
218325 AGATAATTATTCTTTTTATCCTGGCTTCCCCAATAGCAGTTGTCGGATCTAATTCTAAAATTTCG
391 AGATAATTATTCTTTTTATCCTGGCTTCCCCAATAGCAGCTGTCGGATCTAATTCTGAAATTTCG
* *
218390 TGGCATATCACCTTCACCTTGTGAAAGTATTGGGCAACCGCCATGTCGCATTGCGCCATTGATAG
456 CGGCATATCGCCTTCACCTTGTGAAAGTATTGGGCAACCGCCATGTCGCATTGCGCCATTGATAG
*
218455 AAGTTCATTCTCGAGAAGTTGCAATTATGTATTGTTCCTCTTTGAAAAGAGTGTAGCAAAGGTGT
521 AAGTTCATTCTCGAGAAGTTGCAATTATGTATTGTTCCTCTTCGAAAAGAGTGTAGCAAAGGTGT
* *
218520 CTCATGATTTCTTCAGTGATTTAGCATCCCGAATATTCTCCAATATTTCTTCTTCTATTGTGGTC
586 CTCATGCTTTCTTCAGTGATTTAGCATCCCGAATATGCTCCAATATTTCTTCTTCTATTGTGGTC
* *
218585 TTTAAAGCAAACATTGCTTTGGCTACCTTAATTTTCCACTTTCGCAAGACACCGTTAGCATTTTC
651 TTTAAAGCAAACATTGCTTTGCCTACTTTAATTTTCCACTTTCGCAAGACACCGTTAGCA-TTTC
218650 TGCTGCCAGTT
715 -GCTGCC--TT
*
218661 ATCCAATTTGCCACAACATATCCATTTGCTACCATATTACCATCATTTCATTTCCACAACATCCA
1 ATCCAATTTGCCACAACATATCCATTTGCTACCATATTACCATCATTCCATTTCCACAACATCCA
*
218726 TCTCATCTTGCTACATCATTATCATTTGTACATACCATAAGTAACTTTACTTAGGTGACAAAGTA
66 TCTCATCTTGCTACATCATTATCATTTGTACATACCATAAGTAACTTTACTTAGGTGACAGAGTA
*
218791 AAGTGTTTTGATCGAACTTATCAATTTCCTCCAATCCATATGGAGGCGATACTCACTTATCATTG
131 AAGTGTTTTGATCGAACTTATCAATTTCCTCCAATCCATGTGGAGGCGATACTCACTTATCATTG
218856 TATTACTTATTCGATTGTGTATACTTGCACATATTTCTGCACCCATATATAGTACTAACACAGCG
196 TATTACTTATTCGATTGTGTATACTTGCACATATTTCTGCACCCATATATAGTACTAACACAGCG
* * *
218921 CGGACACCTACCATTTGCTTTGCCATGGCTTTTTGACATGTAAGCATATTTTCGAACTCAACAAG
261 CGGACACCTACCATTTGCTTGGCCATGGCTTTTTGACCTGTAAGCAAATTTTCGAACTCAACAAG
*
218986 CGAGTGTTGTGTCGGCCATCCCTGTACAGCGGCAACAAACCCTCGATAGTCGGGGCTCAAACCAT
326 CGAGTGTTGTGTCGGCCATCCCTGTACAGCGGCAACAAACCCTCGATAGTCGGGTCTCAAACCAT
* * *
219051 GGATAATTATTCTTTTTATCATGGCTTCCCCAATAGTAGCTGTCGGATCTAATTCTGAAATTTCG
391 AGATAATTATTCTTTTTATCCTGGCTTCCCCAATAGCAGCTGTCGGATCTAATTCTGAAATTTCG
* *
219116 CGGCATATCGCCTTCACCTTGTGAAAGTATTGGGCAACCGCCATGTTGCATTACGCCATTGATAG
456 CGGCATATCGCCTTCACCTTGTGAAAGTATTGGGCAACCGCCATGTCGCATTGCGCCATTGATAG
* *
219181 AAGTTCATTCTCGAGAAGTTGCAATTGTGTATTGTTCCTCTTCGAAAAGAGTGTAGCAAATGTGT
521 AAGTTCATTCTCGAGAAGTTGCAATTATGTATTGTTCCTCTTCGAAAAGAGTGTAGCAAAGGTGT
*
219246 CTCATGCTTTCTTCAGTGATTTAGCATCCCGAATATGCTCTAATATTTCTTCTTCTATTGTGGTC
586 CTCATGCTTTCTTCAGTGATTTAGCATCCCGAATATGCTCCAATATTTCTTCTTCTATTGTGGTC
*
219311 TTTAAAGCAAACATTGCTTTGCCTACTTTAATTTTCCACTTTCGCAAGATACCGTTAGCA-----
651 TTTAAAGCAAACATTGCTTTGCCTACTTTAATTTTCCACTTTCGCAAGACACCGTTAGCATTTCG
219371 -T---TT
716 CTGCCTT
219374 -TCCAATTTGCCACAACATATCCATTTGCTACCATATTACCATCATTCCATTTCCACAACATCCA
1 ATCCAATTTGCCACAACATATCCATTTGCTACCATATTACCATCATTCCATTTCCACAACATCCA
* * *
219438 TCTCATCTTGCCACATCATTACCATTTGTACATACCATCAGTAACTTTACTTAGGTGACAGAGTA
66 TCTCATCTTGCTACATCATTATCATTTGTACATACCATAAGTAACTTTACTTAGGTGACAGAGTA
* * *
219503 AAGTGCTTTGATCGAACTTATCAATTTCCTCCAATCCTTGTGGAGGCAATACTCACTTATCATTG
131 AAGTGTTTTGATCGAACTTATCAATTTCCTCCAATCCATGTGGAGGCGATACTCACTTATCATTG
* *
219568 TATTACTTATTCGATTGTGTATACTTGCACATATTTTTGCACCCATATATAGTACTCACACAGCG
196 TATTACTTATTCGATTGTGTATACTTGCACATATTTCTGCACCCATATATAGTACTAACACAGCG
* * *
219633 CGGACACCTACAATTTGCTTGGCCATGGCTTTTTGACCTGTATGCAAATTTTCGAACTCAACAAT
261 CGGACACCTACCATTTGCTTGGCCATGGCTTTTTGACCTGTAAGCAAATTTTCGAACTCAACAAG
* * * * * *
219698 CGAGTGTTGTATCGGTCATCCCTGTACAGTGACAACAAACCCTTGATAGTCGGGTATCAAACCAT
326 CGAGTGTTGTGTCGGCCATCCCTGTACAGCGGCAACAAACCCTCGATAGTCGGGTCTCAAACCAT
* * **
219763 AGACAATTATTCTTTTTATCCTAGCTTCCCCAATAGCAGCTGTCGGATCTAATTCTGAAATTTTA
391 AGATAATTATTCTTTTTATCCTGGCTTCCCCAATAGCAGCTGTCGGATCTAATTCTGAAATTTCG
* *
219828 CGGCATATCGCCTTCACCTTGTAAAAGTATTGGGCAACCCCCATGTCGCATTGCGCCATTGATAG
456 CGGCATATCGCCTTCACCTTGTGAAAGTATTGGGCAACCGCCATGTCGCATTGCGCCATTGATAG
* * * *
219893 AAGTTCATTCTCGAGAAGTTACAATTTTGTATCGTTCCTCTTCGAAAAGAGTGTAGCGAAGGTGT
521 AAGTTCATTCTCGAGAAGTTGCAATTATGTATTGTTCCTCTTCGAAAAGAGTGTAGCAAAGGTGT
* * *
219958 CCCATGCTTCCTTCAGTGATTTAGCATCCCGAATATGCTCCAACATTTCTTCTTCTATTGTGGTC
586 CTCATGCTTTCTTCAGTGATTTAGCATCCCGAATATGCTCCAATATTTCTTCTTCTATTGTGGTC
* *
220023 TTTAAAGCAAACATTGCTTTGCCTATTTTAATTTTCCACTTTCACAAGACACCGTTAGCATCTTC
651 TTTAAAGCAAACATTGCTTTGCCTACTTTAATTTTCCACTTTCGCAAGACACCGTTAGCAT-TT-
220088 CGCTGCC
714 CGCTGCC
220095 GGTTGTGTAA
Statistics
Matches: 1341, Mismatches: 82, Indels: 25
0.93 0.06 0.02
Matches are distributed among these distances:
712 662 0.49
713 2 0.00
718 1 0.00
720 1 0.00
726 675 0.50
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.34
Consensus pattern (722 bp):
ATCCAATTTGCCACAACATATCCATTTGCTACCATATTACCATCATTCCATTTCCACAACATCCA
TCTCATCTTGCTACATCATTATCATTTGTACATACCATAAGTAACTTTACTTAGGTGACAGAGTA
AAGTGTTTTGATCGAACTTATCAATTTCCTCCAATCCATGTGGAGGCGATACTCACTTATCATTG
TATTACTTATTCGATTGTGTATACTTGCACATATTTCTGCACCCATATATAGTACTAACACAGCG
CGGACACCTACCATTTGCTTGGCCATGGCTTTTTGACCTGTAAGCAAATTTTCGAACTCAACAAG
CGAGTGTTGTGTCGGCCATCCCTGTACAGCGGCAACAAACCCTCGATAGTCGGGTCTCAAACCAT
AGATAATTATTCTTTTTATCCTGGCTTCCCCAATAGCAGCTGTCGGATCTAATTCTGAAATTTCG
CGGCATATCGCCTTCACCTTGTGAAAGTATTGGGCAACCGCCATGTCGCATTGCGCCATTGATAG
AAGTTCATTCTCGAGAAGTTGCAATTATGTATTGTTCCTCTTCGAAAAGAGTGTAGCAAAGGTGT
CTCATGCTTTCTTCAGTGATTTAGCATCCCGAATATGCTCCAATATTTCTTCTTCTATTGTGGTC
TTTAAAGCAAACATTGCTTTGCCTACTTTAATTTTCCACTTTCGCAAGACACCGTTAGCATTTCG
CTGCCTT
Found at i:220722 original size:76 final size:76
Alignment explanation
Indices: 220596--220747 Score: 277
Period size: 76 Copynumber: 2.0 Consensus size: 76
220586 TCTAAACCAC
*
220596 TCATTAAAATAACCACAAAATAATTTAAACCATTGAAATTAAAAATGAGAAAAATATCTAATTTT
1 TCATTAAAATAACCACAAAATAATTTAAACCATTGAAATTAAAAATGAGAAAAATATATAATTTT
220661 TACCTAACTAA
66 TACCTAACTAA
* *
220672 TCATTAAAATGACCACAAAATAATTTAAACCATTGAAATTAAAAATGAGAAAAATATATATTTTT
1 TCATTAAAATAACCACAAAATAATTTAAACCATTGAAATTAAAAATGAGAAAAATATATAATTTT
220737 TACCTAACTAA
66 TACCTAACTAA
220748 ATTGATGTAA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (76 bp):
TCATTAAAATAACCACAAAATAATTTAAACCATTGAAATTAAAAATGAGAAAAATATATAATTTT
TACCTAACTAA
Found at i:221666 original size:21 final size:21
Alignment explanation
Indices: 221623--221666 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
221613 TTTAAGTGTT
***
221623 TTTTAAATATATTTTTTTTAA
1 TTTTAAATATATTTTTAAAAA
*
221644 TTTTATATATATTTTTAAAAA
1 TTTTAAATATATTTTTAAAAA
221665 TT
1 TT
221667 ATCAGATTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTAAATATATTTTTAAAAA
Found at i:230462 original size:25 final size:25
Alignment explanation
Indices: 230434--230504 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
230424 TATTTAAATG
*
230434 ATATTAAATATTTAATACTTTATAT
1 ATATTTAATATTTAATACTTTATAT
* *
230459 ATATTTTAGTATTTTATA-TTTATAT
1 ATA-TTTAATATTTAATACTTTATAT
230484 ATATTTAATATTTTAATACTT
1 ATATTTAATA-TTTAATACTT
230505 AATCAAATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
24 6 0.16
25 19 0.50
26 13 0.34
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (25 bp):
ATATTTAATATTTAATACTTTATAT
Found at i:230673 original size:2 final size:2
Alignment explanation
Indices: 230562--230661 Score: 52
Period size: 2 Copynumber: 51.5 Consensus size: 2
230552 TCTAATAATT
*
230562 TA TA TA T- TA -A TA TA TA CTA -A TA CA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* ** * * *
230601 TA TA TA CA CG TA TA TG TA TA CTA TC TA CT- TA TA CTA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA
230643 -A T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
230662 GATTAGTATA
Statistics
Matches: 75, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
1 7 0.09
2 61 0.81
3 7 0.09
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:237383 original size:4 final size:4
Alignment explanation
Indices: 237376--237401 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
237366 TTTTACCCAT
237376 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
237402 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:237386 original size:9 final size:10
Alignment explanation
Indices: 237381--237443 Score: 71
Period size: 9 Copynumber: 6.5 Consensus size: 10
237371 CCCATTTTAT
237381 TTATTTATTTA
1 TTATTTA-TTA
237392 TTTATTTATTA
1 -TTATTTATTA
237403 TTA-TTATTA
1 TTATTTATTA
237412 TTA-TTATTA
1 TTATTTATTA
*
237421 TTATATA-TA
1 TTATTTATTA
237430 TTA-TTATTA
1 TTATTTATTA
237439 TTATT
1 TTATT
237444 AAAAAATAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
8 2 0.04
9 28 0.61
10 6 0.13
11 3 0.07
12 7 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTTATTA
Found at i:237405 original size:3 final size:3
Alignment explanation
Indices: 237397--237444 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
237387 ATTTATTTAT
237397 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
237442 TTA
1 TTA
237445 AAAAATAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:238468 original size:2 final size:2
Alignment explanation
Indices: 238461--238490 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
238451 CCTTATCATC
238461 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
238491 TTTTAGGTAA
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:238707 original size:13 final size:13
Alignment explanation
Indices: 238651--238755 Score: 58
Period size: 12 Copynumber: 8.0 Consensus size: 13
238641 TTCAAATTTC
*
238651 ATTTTTGATT-TT
1 ATTTTTAATTATT
* *
238663 TTTTTTAATATTTT
1 ATTTTTAAT-TATT
238677 ATATTTTAA-TACTAT
1 AT-TTTTAATTA-T-T
238692 ATTTTTAATTATT
1 ATTTTTAATTATT
**
238705 ATTTGCAA-TATT
1 ATTTTTAATTATT
*
238717 ATTTTATTATTATT
1 ATTTT-TAATTATT
238731 ACTTTTT-ATTATT
1 A-TTTTTAATTATT
*
238744 ATTCTT-ATTATT
1 ATTTTTAATTATT
238756 TATATAAATA
Statistics
Matches: 74, Mismatches: 10, Indels: 18
0.73 0.10 0.18
Matches are distributed among these distances:
12 25 0.34
13 17 0.23
14 17 0.23
15 15 0.20
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (13 bp):
ATTTTTAATTATT
Found at i:238719 original size:3 final size:3
Alignment explanation
Indices: 238713--238755 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
238703 TTATTTGCAA
* *
238713 TAT TAT T-T TAT TAT TAT TACT TTT TAT TAT TAT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
238756 TATATAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:238739 original size:16 final size:15
Alignment explanation
Indices: 238718--238755 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
238708 TGCAATATTA
238718 TTTTATTATTATTACT
1 TTTTATTATTATT-CT
238734 TTTTATTATTATTCT
1 TTTTATTATTATTCT
*
238749 TATTATT
1 TTTTATT
238756 TATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTATTATTATTCT
Found at i:238758 original size:16 final size:15
Alignment explanation
Indices: 238713--238755 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 15
238703 TTATTTGCAA
238713 TATTATT-TTATTAT
1 TATTATTCTTATTAT
*
238727 TATTA--CTTTTTAT
1 TATTATTCTTATTAT
238740 TATTATTCTTATTAT
1 TATTATTCTTATTAT
238755 T
1 T
238756 TATATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 5 0.21
15 8 0.33
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTCTTATTAT
Found at i:238977 original size:19 final size:19
Alignment explanation
Indices: 238953--238989 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
238943 TTTTTAAATC
238953 ATATATTAATTATTTAATT
1 ATATATTAATTATTTAATT
* *
238972 ATATATTTATTTTTTAAT
1 ATATATTAATTATTTAAT
238990 ATTGAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATATTAATTATTTAATT
Found at i:241244 original size:27 final size:27
Alignment explanation
Indices: 241208--241267 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
241198 CATTCACATA
241208 TTTACATTTGCATTTACATTTGCATTT
1 TTTACATTTGCATTTACATTTGCATTT
* * *
241235 TTTACGTTTGTATTTACATTTTCA-TT
1 TTTACATTTGCATTTACATTTGCATTT
241261 TTTACAT
1 TTTACAT
241268 AATTACATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTACATTTGCATTTACATTTGCATTT
Found at i:241261 original size:12 final size:12
Alignment explanation
Indices: 241207--241234 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
241197 ACATTCACAT
241207 ATTTACATTTGC
1 ATTTACATTTGC
241219 ATTTACATTTGC
1 ATTTACATTTGC
241231 ATTT
1 ATTT
241235 TTTACGTTTG
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:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:246223 original size:114 final size:114
Alignment explanation
Indices: 246023--246246 Score: 421
Period size: 114 Copynumber: 2.0 Consensus size: 114
246013 GTGCCACGTT
*
246023 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
*
246088 ATTTGGTAGGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 ATTTGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTG
*
246137 CTCATAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
246202 ATTTGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
66 ATTTGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
246247 CTGTATGATC
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 107 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
ATTTGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTG
Found at i:248416 original size:54 final size:54
Alignment explanation
Indices: 248334--248482 Score: 217
Period size: 54 Copynumber: 2.8 Consensus size: 54
248324 TTGGCAGAAG
*
248334 CCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAACAAAAA
1 CCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATATGAACAAAAA
* * *
248388 CCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATATGAGCAGAAG
1 CCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATATGAACAAAAA
* * * * *
248442 CTACAAGAAAGGATGAATGCGCTGTCAAATGTTTTACGAAC
1 CCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
248483 CTGCTATTCT
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 86 1.00
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (54 bp):
CCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAACATATGAACAAAAA
Found at i:248878 original size:22 final size:22
Alignment explanation
Indices: 248849--248903 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
248839 ATCTACACTC
248849 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
248871 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
248893 TTCAAAGATGA
1 TTCAAAGATGA
248904 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:249659 original size:113 final size:113
Alignment explanation
Indices: 249311--249982 Score: 952
Period size: 113 Copynumber: 5.9 Consensus size: 113
249301 GATTCAAATC
249311 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* ** *
249376 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
249424 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
249488 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
*
249536 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
249601 AGAAGAAGTTCATAATGAAAAGAATTTGTTCAACCTTTTGTTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * ** *
249649 CATCATTTGATGGATCAACATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 CATCATTTGATGGATCAGCTTTTCCA--GAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
* *
249714 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-ATTTTCGCTTGAATT
64 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTTGAATT
** * * **** * *
249764 CATCATTCAATGGATCAGCATTGCCAGGGCGAGTTCATAATGAGAAGAACTCATCTAAAGAAAGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
249829 AGAATAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
* * * * * *
249877 CATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
** * *
249942 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACATTTTGC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
249983 ATGACTCTAT
Statistics
Matches: 510, Mismatches: 44, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
112 107 0.21
113 297 0.58
114 8 0.02
115 98 0.19
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
Found at i:249801 original size:228 final size:225
Alignment explanation
Indices: 249311--249982 Score: 961
Period size: 228 Copynumber: 3.0 Consensus size: 225
249301 GATTCAAATC
* * * *
249311 CATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTAATGGATCAGCATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
249376 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCATTTGATGGATCA
* * *
249441 GCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAATTCATAATGA
131 ACTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGA
* * *
249506 GAAGAATTTGTTCAACCTTTTGTTTGAATT
196 GAAGAACTTGTTCAACATTTTGCTTGAATT
* * *
249536 CATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTAATGGATCAGCATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
249601 AGAAGAAGTTCATAATGAAAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCATTTGATGGATCA
* **
249666 ACATCCCCAGTGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
131 ACTTTTCCA--GAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAA
249731 TGAGAAGAACTTGTTCAA-ATTTTCGCTTGAATT
193 TGAGAAGAACTTGTTCAACATTTT-GCTTGAATT
**** * *
249764 CATCA-TTCAATGGATCAGCATTGCCAGGGCGAGTTCATAATGAGAAGAACTCATCTAAAGAAAG
1 CATCACTT-AATGGATCAGCATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * * *
249828 AAGAATAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCGAATTCATCACTCGATGGATC
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCATTTGATGGATC
*
249893 AACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAAT
130 AACTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAGAAGAAGTTCATAAT
* *
249958 GAGAAGAGCTTGTTCGACATTTTGC
194 GAGAAGAACTTGTTCAACATTTTGC
249983 ATGACTCTAT
Statistics
Matches: 402, Mismatches: 38, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
225 128 0.32
226 68 0.17
227 48 0.12
228 158 0.39
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (225 bp):
CATCACTTAATGGATCAGCATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAATTCATCATTTGATGGATCA
ACTTTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACATTTTGCTTGAATT
Found at i:250084 original size:17 final size:17
Alignment explanation
Indices: 250026--250084 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
250016 CAACATTTCC
*
250026 AGAAGGAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
250043 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
250061 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
250079 AGAAGA
1 AGAAGA
250085 GCTTGTTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 3 0.09
17 15 0.45
18 2 0.06
19 10 0.30
20 3 0.09
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:250334 original size:3 final size:3
Alignment explanation
Indices: 250328--250372 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
250318 CATTTTTTTT
250328 TTA TTA TTA TTA TTA TTA TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
250373 AAAAATAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:250926 original size:19 final size:19
Alignment explanation
Indices: 250902--250945 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
250892 AGAAAGAAAC
250902 TCACCGGAGCCTTCACACG
1 TCACCGGAGCCTTCACACG
250921 TCACCGGAGCCTTCACACG
1 TCACCGGAGCCTTCACACG
250940 TCACCG
1 TCACCG
250946 AAAACCTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.16
Consensus pattern (19 bp):
TCACCGGAGCCTTCACACG
Found at i:251640 original size:13 final size:13
Alignment explanation
Indices: 251584--251688 Score: 67
Period size: 12 Copynumber: 8.0 Consensus size: 13
251574 TTCAAATTTC
*
251584 ATTTTTGATTATT
1 ATTTTTAATTATT
*
251597 -TTTTTAATATTTT
1 ATTTTTAAT-TATT
251610 ATATTTTAA-TACTAT
1 AT-TTTTAATTA-T-T
251625 ATTTTTAATTATT
1 ATTTTTAATTATT
**
251638 ATTTGCAA-TATT
1 ATTTTTAATTATT
*
251650 ATTTTATTATTATT
1 ATTTT-TAATTATT
251664 ACTTTTT-ATTATT
1 A-TTTTTAATTATT
*
251677 ATTCTT-ATTATT
1 ATTTTTAATTATT
251689 TATATAAATA
Statistics
Matches: 74, Mismatches: 9, Indels: 19
0.73 0.09 0.19
Matches are distributed among these distances:
12 25 0.34
13 19 0.26
14 15 0.20
15 15 0.20
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (13 bp):
ATTTTTAATTATT
Found at i:251652 original size:3 final size:3
Alignment explanation
Indices: 251646--251688 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
251636 TTATTTGCAA
* *
251646 TAT TAT T-T TAT TAT TAT TACT TTT TAT TAT TAT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
251689 TATATAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:251672 original size:16 final size:15
Alignment explanation
Indices: 251651--251688 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
251641 TGCAATATTA
251651 TTTTATTATTATTACT
1 TTTTATTATTATT-CT
251667 TTTTATTATTATTCT
1 TTTTATTATTATTCT
*
251682 TATTATT
1 TTTTATT
251689 TATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTATTATTATTCT
Found at i:251691 original size:16 final size:15
Alignment explanation
Indices: 251646--251688 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 15
251636 TTATTTGCAA
251646 TATTATT-TTATTAT
1 TATTATTCTTATTAT
*
251660 TATTA--CTTTTTAT
1 TATTATTCTTATTAT
251673 TATTATTCTTATTAT
1 TATTATTCTTATTAT
251688 T
1 T
251689 TATATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 5 0.21
15 8 0.33
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTCTTATTAT
Found at i:251712 original size:18 final size:16
Alignment explanation
Indices: 251689--251723 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
251679 TCTTATTATT
251689 TATATA-AATAAATATA
1 TATATATAATAAATA-A
251705 TATATATAATAAATAA
1 TATATATAATAAATAA
251721 TAT
1 TAT
251724 TTTTTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATATAATAAATAA
Found at i:251912 original size:20 final size:19
Alignment explanation
Indices: 251875--251924 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
251865 TAAATATCCT
*
251875 ATTTTTTAAATCATATATTA
1 ATTTTTT-AATTATATATTA
*
251895 ATTATTTTAATTATATATTT
1 ATT-TTTTAATTATATATTA
251915 ATTTTTTAAT
1 ATTTTTTAAT
251925 ATTGAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 16 0.59
21 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTTAATTATATATTA
Found at i:252014 original size:119 final size:120
Alignment explanation
Indices: 251774--252020 Score: 290
Period size: 119 Copynumber: 2.1 Consensus size: 120
251764 TTTAATAATC
* *
251774 ATATTTTAATATATATTTATTTATTTTTCAATATTAAGAAAGGACAGTCTTAAAACAACTAGATG
1 ATATTTTAATATATA-TTATTTATTTTTCAATATTAAGAAAAGACAGTCTTAAAACAACTAGAAG
* *
251839 TCAATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTTTAAATCATATATTA
65 TCAATTTTCTGATATTTCTAAATAAATAAATATCCTATTTTATAAATCATATATTA
* ** ** *
251895 ATTATTTTAAT-TATA-TATTTATTTTTTAATATTGAAGAAAAGAGTTGT-TTAAGGCACCTAGA
1 A-TATTTTAATATATATTATTTATTTTTCAATATT-AAGAAAAGA-CAGTCTTAAAACAACTAGA
**
251957 AGTC-ATTTTCTGATATTTCTAAATAAATAAATATTTTA-TTTATAAAT-ATATAAATTA
63 AGTCAATTTTCTGATATTTCTAAATAAATAAATATCCTATTTTATAAATCATAT--ATTA
252014 ATATTTT
1 ATATTTT
252021 TCCATAATTA
Statistics
Matches: 109, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
117 4 0.04
118 14 0.13
119 53 0.49
120 22 0.20
121 7 0.06
122 9 0.08
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (120 bp):
ATATTTTAATATATATTATTTATTTTTCAATATTAAGAAAAGACAGTCTTAAAACAACTAGAAGT
CAATTTTCTGATATTTCTAAATAAATAAATATCCTATTTTATAAATCATATATTA
Found at i:254817 original size:2 final size:2
Alignment explanation
Indices: 254810--254853 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
254800 TGAAATTGCA
254810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
254852 AT
1 AT
254854 CACTGTTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:256123 original size:64 final size:64
Alignment explanation
Indices: 256063--256183 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
256053 TAAAATCGGA
256063 TACAGGTCA-AGTCAGGTAAATTTGACACCAGATCCAGATCGGGTTCAGGTCAGGTCAAATCAG
1 TACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCGGGTTCAGGTCAGGTCAAATCAG
* * * ** **
256126 TTCGGGTTATTTTCAGGTTGATTTGACACCAGATCCAGATCGGGTTCAGGTCAGGTCA
1 TACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCGGGTTCAGGTCAGGTCA
256184 TTTTCAGTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 6 0.12
64 44 0.88
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (64 bp):
TACAGGTCATAGTCAGGTAAATTTGACACCAGATCCAGATCGGGTTCAGGTCAGGTCAAATCAG
Done.