Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012474.1 Kokia drynarioides strain JFW-HI SEQ_127478, 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: 393988
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 69 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:125 original size:42 final size:42
Alignment explanation
Indices: 78--170 Score: 104
Period size: 42 Copynumber: 2.2 Consensus size: 42
68 TATTTATTTT
* *
78 TTAGAATATTAA-AAAA-TGATTATGATATAATTCCAATATT-AA
1 TTAGAATATTAATAAAATTGAATAT--TAAAATT-CAATATTAAA
*
120 TTAGAATAATAATAAAATTGAATATTAAAATTCAATATTAAA
1 TTAGAATATTAATAAAATTGAATATTAAAATTCAATATTAAA
162 TTA-AATATT
1 TTAGAATATT
171 TTATCCGACC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
41 12 0.27
42 22 0.50
43 4 0.09
44 6 0.14
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (42 bp):
TTAGAATATTAATAAAATTGAATATTAAAATTCAATATTAAA
Found at i:168 original size:12 final size:13
Alignment explanation
Indices: 127--170 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
117 TAATTAGAAT
* *
127 AATAATAAAATTG
1 AATATTAAAATTA
*
140 AATATTAAAATTC
1 AATATTAAAATTA
153 AATATT-AAATTA
1 AATATTAAAATTA
165 AATATT
1 AATATT
171 TTATCCGACC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
AATATTAAAATTA
Found at i:394 original size:24 final size:24
Alignment explanation
Indices: 367--414 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
357 TCTCTTATGT
367 CATGTCAATGACAATATAAAAATG
1 CATGTCAATGACAATATAAAAATG
391 CATGTCAATGACAATATAAAAATG
1 CATGTCAATGACAATATAAAAATG
415 GAATTGGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (24 bp):
CATGTCAATGACAATATAAAAATG
Found at i:6223 original size:14 final size:15
Alignment explanation
Indices: 6201--6229 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6191 TTTTTAAATC
6201 TTTCTTTTTTATTTA
1 TTTCTTTTTTATTTA
6216 TTTC-TTTTTATTTA
1 TTTCTTTTTTATTTA
6230 AGAAACGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTTATTTA
Found at i:10117 original size:6 final size:6
Alignment explanation
Indices: 10106--10143 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
10096 TTCAGTATTT
10106 CTTGCC CTTGCC CTTGCC CTTGCC CTTGCC CTTGCC CT
1 CTTGCC CTTGCC CTTGCC CTTGCC CTTGCC CTTGCC CT
10144 GCCATTCTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.16, T:0.34
Consensus pattern (6 bp):
CTTGCC
Found at i:19394 original size:22 final size:22
Alignment explanation
Indices: 19353--19394 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19343 AAGCACTGTC
* *
19353 AAGCTTTCATCTTCTCCATTGT
1 AAGCCTTCATCTACTCCATTGT
*
19375 AAGCCTTCATCTACTGCATT
1 AAGCCTTCATCTACTCCATT
19395 ACAATCCCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.10, T:0.40
Consensus pattern (22 bp):
AAGCCTTCATCTACTCCATTGT
Found at i:27219 original size:3 final size:3
Alignment explanation
Indices: 27211--27248 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
27201 AAAAGTTGAG
27211 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27249 AGAATTAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:32826 original size:17 final size:17
Alignment explanation
Indices: 32784--32828 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
32774 TTTAAACTCG
*
32784 ATTTATATTTTAAATAA
1 ATTTATTTTTTAAATAA
**
32801 ATTTAATTTTTTATCTAA
1 ATTT-ATTTTTTAAATAA
32819 ATTTATTTTT
1 ATTTATTTTT
32829 CAAACTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTATTTTTTAAATAA
Found at i:43317 original size:57 final size:57
Alignment explanation
Indices: 43255--43370 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
43245 CTCATCAAAT
*
43255 TATAAATACAACTTATGGTATCTACACATTATTTCCATAACACTTCAATAATACTTA
1 TATAAATACAACTTATGGTATCTACAAATTATTTCCATAACACTTCAATAATACTTA
*
43312 TATAAATACAACTTATGGTATCTACAAATTATTTTCATAACACTTCAATAATACTTA
1 TATAAATACAACTTATGGTATCTACAAATTATTTCCATAACACTTCAATAATACTTA
43369 TA
1 TA
43371 ACATAATTGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (57 bp):
TATAAATACAACTTATGGTATCTACAAATTATTTCCATAACACTTCAATAATACTTA
Found at i:43530 original size:18 final size:19
Alignment explanation
Indices: 43515--43555 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
43505 CCCAAAATAT
43515 AAGTCCATTT-CAAAATTCA
1 AAGTCCATTTACAAAATT-A
43534 AAGTCCATTTACAAAAATTA
1 AAGTCCATTTAC-AAAATTA
43554 AA
1 AA
43556 ACTCAAACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.50
20 4 0.20
21 6 0.30
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (19 bp):
AAGTCCATTTACAAAATTA
Found at i:45818 original size:21 final size:21
Alignment explanation
Indices: 45794--45844 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
45784 GGAGTTTTTA
45794 GTATCGGTAGAAGAGTCACTT
1 GTATCGGTAGAAGAGTCACTT
*
45815 GTATCGGTATAAGAGTCACTT
1 GTATCGGTAGAAGAGTCACTT
45836 GTATCGGTA
1 GTATCGGTA
45845 CAAATCTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGAGTCACTT
Found at i:47283 original size:31 final size:29
Alignment explanation
Indices: 47247--47315 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 29
47237 AAGACTAAAT
47247 CCTTTTATTTTTATTT-TTGTTAAAATTTAAC
1 CCTTTTATTTTTATTTCTT-TTAAAA-TT-AC
*
47278 CCTTTTAATTTTATTTCTTTTAAAATTAC
1 CCTTTTATTTTTATTTCTTTTAAAATTAC
47307 CCTTTTATT
1 CCTTTTATT
47316 CCTTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 10 0.29
30 2 0.06
31 21 0.60
32 2 0.06
ACGTcount: A:0.25, C:0.13, G:0.01, T:0.61
Consensus pattern (29 bp):
CCTTTTATTTTTATTTCTTTTAAAATTAC
Found at i:47337 original size:19 final size:20
Alignment explanation
Indices: 47310--47354 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
47300 AAATTACCCT
* *
47310 TTTATTCCTTTTTTAT-TTG
1 TTTAATCCTTTTGTATCTTG
*
47329 TTTAATCCTTTTGTATCTTT
1 TTTAATCCTTTTGTATCTTG
47349 TTTAAT
1 TTTAAT
47355 TAAATCCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTAATCCTTTTGTATCTTG
Found at i:47789 original size:110 final size:110
Alignment explanation
Indices: 47572--47770 Score: 292
Period size: 110 Copynumber: 1.8 Consensus size: 110
47562 TAGTGTTCTT
* * *
47572 TTATTGTAGGGAACTCGAAAAATTGTGCCCTAACATGTTGGGTATGATTTTTTCTTTGAACCTAA
1 TTATTGTAGGGAACTCGAAAAATTGTACCCTAACATGCTAGGTATGATTTTTTCTTTGAACCTAA
*
47637 ATAATTAAGTATCCTATTTAAAATCAATAAATGCTCAATGTTTTG
66 ATAATTAAGCATCCTATTTAAAATCAATAAATGCTCAATGTTTTG
* * * *
47682 TTATTTTAGGGGACTCGAAAAATTGTACCCTAACGTGCTAGGTATGGTTTTTTCTTTGAACCTAA
1 TTATTGTAGGGAACTCGAAAAATTGTACCCTAACATGCTAGGTATGATTTTTTCTTTGAACCTAA
* *
47747 GTATTTGAA-CATCCTATTTAAAAT
66 ATAATT-AAGCATCCTATTTAAAAT
47771 AGATGAATGT
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
110 76 0.97
111 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (110 bp):
TTATTGTAGGGAACTCGAAAAATTGTACCCTAACATGCTAGGTATGATTTTTTCTTTGAACCTAA
ATAATTAAGCATCCTATTTAAAATCAATAAATGCTCAATGTTTTG
Found at i:49837 original size:44 final size:44
Alignment explanation
Indices: 49789--49885 Score: 167
Period size: 44 Copynumber: 2.2 Consensus size: 44
49779 GCTATCTTTA
* *
49789 ATGCTTCTTCCTAAATGGACTCAAGTAAGGTGGAATGAGCAATC
1 ATGCTCCTTCCCAAATGGACTCAAGTAAGGTGGAATGAGCAATC
*
49833 ATGCTCCTTCCCAAATGGACTCAGGTAAGGTGGAATGAGCAATC
1 ATGCTCCTTCCCAAATGGACTCAAGTAAGGTGGAATGAGCAATC
49877 ATGCTCCTT
1 ATGCTCCTT
49886 ACCATATCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (44 bp):
ATGCTCCTTCCCAAATGGACTCAAGTAAGGTGGAATGAGCAATC
Found at i:55629 original size:20 final size:20
Alignment explanation
Indices: 55604--55643 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
55594 TACTTTAGCC
*
55604 ATTTTTATTTTTATTTTAAT
1 ATTTTTATTTTTAATTTAAT
55624 ATTTTTATTTTTAATTTAAT
1 ATTTTTATTTTTAATTTAAT
55644 TGTTACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTTATTTTTAATTTAAT
Found at i:64277 original size:17 final size:18
Alignment explanation
Indices: 64257--64296 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
64247 TTAGTTTTAA
64257 TGCATTTT-TATTATCAT
1 TGCATTTTATATTATCAT
* *
64274 TGCATTTTATTTTGTCAT
1 TGCATTTTATATTATCAT
64292 TGCAT
1 TGCAT
64297 CATTTTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (18 bp):
TGCATTTTATATTATCAT
Found at i:66359 original size:46 final size:46
Alignment explanation
Indices: 66292--66390 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
66282 TCAGTGAACC
* * *
66292 ATTTCCACCCTTTACACTTGATCAGTTTTATATTTCTCGCATTTAA
1 ATTTCCACACTTTACACTTGATCACTTTTATATTTCACGCATTTAA
66338 ATTTCCACACTTTACACTTGATCACTTTTATATTTCACGCATTTAA
1 ATTTCCACACTTTACACTTGATCACTTTTATATTTCACGCATTTAA
66384 ATTTCCA
1 ATTTCCA
66391 TTACTCACAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.44
Consensus pattern (46 bp):
ATTTCCACACTTTACACTTGATCACTTTTATATTTCACGCATTTAA
Found at i:73974 original size:26 final size:26
Alignment explanation
Indices: 73945--74000 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
73935 TCGTATCAAT
*
73945 TGGATCATGAATATAGATTTAGGGAA
1 TGGATCATGAATATAGATATAGGGAA
73971 TGGATCATGAATATAGATATAGGGAA
1 TGGATCATGAATATAGATATAGGGAA
73997 TGGA
1 TGGA
74001 ACCATCAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.39, C:0.04, G:0.29, T:0.29
Consensus pattern (26 bp):
TGGATCATGAATATAGATATAGGGAA
Found at i:74967 original size:23 final size:24
Alignment explanation
Indices: 74941--74985 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
74931 GCAGAACAGA
74941 AATTAC-TTGAAGAAAAAAAAGAT
1 AATTACGTTGAAGAAAAAAAAGAT
* *
74964 AATTCCGTTGAAGAAATAAAAG
1 AATTACGTTGAAGAAAAAAAAG
74986 TGGGATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.22
Consensus pattern (24 bp):
AATTACGTTGAAGAAAAAAAAGAT
Found at i:80604 original size:153 final size:155
Alignment explanation
Indices: 80404--80713 Score: 536
Period size: 154 Copynumber: 2.0 Consensus size: 155
80394 ATGAAGGAAA
*
80404 AGGGGATAGAGAGCTTACAGAAGGGGTATGGGGATTTGGGGTATGAGAGGAGAATACAAAGGGAT
1 AGGGGATAGAGAGCTTACAGAAGGGGTATGGGGATTTGGGCTATGAGAGGAGAATACAAAGGGAT
* * *
80469 TGAAGTTTCTTTGAGACTG-TAAAAAAAAGGAGAGAAGGAGACGGCAGGGGAAAGGGGAAAA-GG
66 TGAAGTTTCTTTGAGACTGAAAAAAAAAAAGAGAGAAGGAGACGACAGGGGAAA-GGGAAAAGGG
*
80532 AAAAGGGGAAATTTTAGGTAATTTAG
130 AAAAGGGGAAATTTTAGGGAATTTAG
80558 AGGGGATAGAGAGCTTACAGAA-GGGTATGGGGATTTGGGCTATGAGAGGAGAATACAAAGGGAT
1 AGGGGATAGAGAGCTTACAGAAGGGGTATGGGGATTTGGGCTATGAGAGGAGAATACAAAGGGAT
*
80622 TGAAGTTTCTTTGAGATTGAAAAAAAAAAAGAGAGAAGGAGACGACAGGGGAAAGGGAAAAGGGA
66 TGAAGTTTCTTTGAGACTGAAAAAAAAAAAGAGAGAAGGAGACGACAGGGGAAAGGGAAAAGGGA
80687 AAAGGGGAAATTTTAGGGAATTTAG
131 AAAGGGGAAATTTTAGGGAATTTAG
80712 AG
1 AG
80714 ATTTATGATT
Statistics
Matches: 148, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
153 66 0.45
154 82 0.55
ACGTcount: A:0.40, C:0.05, G:0.37, T:0.18
Consensus pattern (155 bp):
AGGGGATAGAGAGCTTACAGAAGGGGTATGGGGATTTGGGCTATGAGAGGAGAATACAAAGGGAT
TGAAGTTTCTTTGAGACTGAAAAAAAAAAAGAGAGAAGGAGACGACAGGGGAAAGGGAAAAGGGA
AAAGGGGAAATTTTAGGGAATTTAG
Found at i:89245 original size:20 final size:21
Alignment explanation
Indices: 89218--89264 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
89208 ATATTAATAA
*
89218 TAAATTTTA-TTTTATTTTTT
1 TAAATTTTAGTTTTAATTTTT
*
89238 TTAATTTTAGTTTTAATTTTT
1 TAAATTTTAGTTTTAATTTTT
89259 TAAATT
1 TAAATT
89265 ATTAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TAAATTTTAGTTTTAATTTTT
Found at i:92346 original size:22 final size:23
Alignment explanation
Indices: 92308--92360 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
92298 TACAATATTC
* *
92308 AAATAATATTAAAAAAGACAGCA
1 AAATAATAGTAAAAAAGACAGAA
* *
92331 AAATAATAGT-AAAAAGGCATAA
1 AAATAATAGTAAAAAAGACAGAA
92353 AAATAATA
1 AAATAATA
92361 TCCAAACAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (23 bp):
AAATAATAGTAAAAAAGACAGAA
Found at i:95803 original size:52 final size:52
Alignment explanation
Indices: 95725--95830 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
95715 AAACACGGTC
95725 TTATTCAAGTAGCCCTTGGGCTCGTTTTCAACTTAATTCATATGGCATCATA
1 TTATTCAAGTAGCCCTTGGGCTCGTTTTCAACTTAATTCATATGGCATCATA
*
95777 TTATTCAAGTAGCCTTTGGGCTCGTTTTCAACTTAATTCATATGGCATCATA
1 TTATTCAAGTAGCCCTTGGGCTCGTTTTCAACTTAATTCATATGGCATCATA
95829 TT
1 TT
95831 CCATATTTAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (52 bp):
TTATTCAAGTAGCCCTTGGGCTCGTTTTCAACTTAATTCATATGGCATCATA
Found at i:97051 original size:41 final size:41
Alignment explanation
Indices: 96994--97087 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
96984 GAATTTTATT
*
96994 TTAACAAGAATTCTAGTCACTCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
97035 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
97076 TTGACAAGAATT
1 TTAACAAGAATT
97088 TTTTACTAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.29
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:102904 original size:16 final size:18
Alignment explanation
Indices: 102865--102898 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
102855 TAAATTTATA
102865 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
102882 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
102899 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:103070 original size:23 final size:24
Alignment explanation
Indices: 103027--103071 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
103017 TTATTAAAAA
103027 TTAAAATAAAATAAAATAAATATT
1 TTAAAATAAAATAAAATAAATATT
103051 TTAAAA-AAAATTAAAA-AAATA
1 TTAAAATAAAA-TAAAATAAATA
103072 ATGTGGACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (24 bp):
TTAAAATAAAATAAAATAAATATT
Found at i:106458 original size:28 final size:26
Alignment explanation
Indices: 106400--106460 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 26
106390 TTTGGTGCCT
* *
106400 AAACATTTTTTTTTTAATTTAGTATTT
1 AAAC-TTTTTTTTTTAATTTAGTACTC
*
106427 AAACTTTTTTTTGTCTAATTTGGTACTC
1 AAACTTTTTTTT-T-TAATTTAGTACTC
106455 AAACTT
1 AAACTT
106461 AACACTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 8 0.28
27 5 0.17
28 16 0.55
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.56
Consensus pattern (26 bp):
AAACTTTTTTTTTTAATTTAGTACTC
Found at i:106478 original size:31 final size:31
Alignment explanation
Indices: 106441--106501 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
106431 TTTTTTTTGT
*
106441 CTAATTTGGTA-CTCAAACTTAACACTTTTTC
1 CTAATTTGATACCT-AAACTTAACACTTTTTC
* *
106472 CTAATTTGATACCTAAACTTGACATTTTTT
1 CTAATTTGATACCTAAACTTAACACTTTTT
106502 TAAAATTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.44
Consensus pattern (31 bp):
CTAATTTGATACCTAAACTTAACACTTTTTC
Found at i:107914 original size:133 final size:133
Alignment explanation
Indices: 107622--108000 Score: 647
Period size: 133 Copynumber: 2.9 Consensus size: 133
107612 AATTTAAATT
* *
107622 CATGTCAATTGCGTTGGTAAAGCATTAAATTTAGCATTTAACTAAAGCTTTATTTTAAAAATTGT
1 CATGTCAATTGCGTTGGTAAAGCATTAAATTTATCACTTAACTAAAGCTTTATTTTAAAAATTGT
* * *
107687 TAATATATTTTATGTACATTTTATTA-CCTCC-C-CTCTCTCTCTCTCTCATTATATATATATAT
66 TAATACATTTTATGTACATTTTATTACCCCCCTCTCTCTCTCTCTCTCTCTTTATATATATATAT
107749 ATA
131 ATA
* *
107752 CATATCAATTGCGTTGGTAAAGCATTAAATTTATCACTTAACCAAAGCTTTATTTTAAAAATTGT
1 CATGTCAATTGCGTTGGTAAAGCATTAAATTTATCACTTAACTAAAGCTTTATTTTAAAAATTGT
107817 TAATACATTTTATGTACATTTTATTACCCCCCTCTCTCTCTCTCTCTCTCTTTATATATATATAT
66 TAATACATTTTATGTACATTTTATTACCCCCCTCTCTCTCTCTCTCTCTCTTTATATATATATAT
107882 ATA
131 ATA
*
107885 CATGTCAATTGCGTTGGTAAAGCATTAAATTTATCACTTAACTAAAGTTTTATTTTAAAAATTGT
1 CATGTCAATTGCGTTGGTAAAGCATTAAATTTATCACTTAACTAAAGCTTTATTTTAAAAATTGT
* *
107950 TAATACATTTTATGCACATTTTATTACCCCTCTCTCTCTCTCTCTCTCTCT
66 TAATACATTTTATGTACATTTTATTACCCCCCTCTCTCTCTCTCTCTCTCT
108001 CTCTCTCTTT
Statistics
Matches: 234, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
130 86 0.37
131 4 0.02
132 1 0.00
133 143 0.61
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (133 bp):
CATGTCAATTGCGTTGGTAAAGCATTAAATTTATCACTTAACTAAAGCTTTATTTTAAAAATTGT
TAATACATTTTATGTACATTTTATTACCCCCCTCTCTCTCTCTCTCTCTCTTTATATATATATAT
ATA
Found at i:107986 original size:2 final size:2
Alignment explanation
Indices: 107979--108008 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
107969 TTTATTACCC
107979 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
108009 TTATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:111506 original size:24 final size:24
Alignment explanation
Indices: 111479--111529 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
111469 AAATTGACTC
* * *
111479 AAACAATTAAACAGAATTTAATTG
1 AAACAAATAAACAAAATTTAACTG
111503 AAACAAATAAACAAAATTTAACTG
1 AAACAAATAAACAAAATTTAACTG
111527 AAA
1 AAA
111530 TATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAAAATTTAACTG
Found at i:123418 original size:26 final size:26
Alignment explanation
Indices: 123372--123445 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
123362 CATTAACTCA
* *
123372 AAAAGAGCTTTTGTGACTGATTTTATT
1 AAAA-AGCCTTTGTGATTGATTTTATT
123399 AAAAAGCCTTTGTGATTGATTTTATT
1 AAAAAGCCTTTGTGATTGATTTTATT
* *
123425 AAAGAGCCTTTGTGGTTGATT
1 AAAAAGCCTTTGTGATTGATT
123446 CCGTAATATG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 39 0.91
27 4 0.09
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.43
Consensus pattern (26 bp):
AAAAAGCCTTTGTGATTGATTTTATT
Found at i:123499 original size:27 final size:27
Alignment explanation
Indices: 123458--123509 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
123448 GTAATATGTG
*
123458 AGCCTTTGTTGCTAACTCTGTTATAAT
1 AGCCTTTGTTGCTAACTCTGATATAAT
123485 AGCCTTTG-TGACTAACTCTGATATA
1 AGCCTTTGTTG-CTAACTCTGATATA
123510 TGTGAACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (27 bp):
AGCCTTTGTTGCTAACTCTGATATAAT
Found at i:123690 original size:27 final size:26
Alignment explanation
Indices: 123660--123726 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
123650 CCTTTATGGC
*
123660 TATCTTATGAATGGACGCCTTCATGAT
1 TATCTT-TGAATGGACGCCTCCATGAT
* * *
123687 TATCTTCTAAATGGATGCCTCCGTGAT
1 TATCTT-TGAATGGACGCCTCCATGAT
123714 TATCTTTG-ATGGA
1 TATCTTTGAATGGA
123727 GAACACTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 5 0.15
26 1 0.03
27 28 0.82
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (26 bp):
TATCTTTGAATGGACGCCTCCATGAT
Found at i:126334 original size:87 final size:88
Alignment explanation
Indices: 126236--126411 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 88
126226 GAACTTTATC
*
126236 TTGTTATTATAAT-CCAAAAAAAATATTAAAAATAATAAAGAAATAAACAATCAATTTTCTATTT
1 TTGTTACTATAATCCCAAAAAAAATATTAAAAATAATAAAGAAATAAACAATCAATTTTCTATTT
126300 CCACTACAAGAGAAGGGAAGGGT
66 CCACTACAAGAGAAGGGAAGGGT
*
126323 TTGTTACTATAATCCACCAAAAAAAATATTAAAAATAATAAAGAAATAAATAATCAATTTTCTAT
1 TTGTTACTATAAT-C-CCAAAAAAAATATTAAAAATAATAAAGAAATAAACAATCAATTTTCTAT
126388 TTCCACTACAAGAGAAGGGAAGGG
64 TTCCACTACAAGAGAAGGGAAGGG
126412 ATTGATGTTC
Statistics
Matches: 84, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
87 12 0.14
90 72 0.86
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (88 bp):
TTGTTACTATAATCCCAAAAAAAATATTAAAAATAATAAAGAAATAAACAATCAATTTTCTATTT
CCACTACAAGAGAAGGGAAGGGT
Found at i:126654 original size:30 final size:30
Alignment explanation
Indices: 126618--126680 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
126608 TTAATAAAAG
* *
126618 TAAAATTATATTTTAATTTCCTTAAAAA-TA
1 TAAAATTATAATATAATTT-CTTAAAAATTA
* *
126648 TAAAATTTTAATATAATTTTTTAAAAATTA
1 TAAAATTATAATATAATTTCTTAAAAATTA
126678 TAA
1 TAA
126681 TTTTATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAATTATAATATAATTTCTTAAAAATTA
Found at i:126681 original size:22 final size:22
Alignment explanation
Indices: 126649--126713 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
126639 TTAAAAATAT
* * *
126649 AAAATTTTAATATAATTTTTTA
1 AAAATTATAATTTAATTTTGTA
*
126671 AAAATTATAATTTTATTATTGTA
1 AAAATTATAATTTAATT-TTGTA
126694 AAAATTATAATTTAATTTTG
1 AAAATTATAATTTAATTTTG
126714 GCTCTCTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 17 0.46
23 20 0.54
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (22 bp):
AAAATTATAATTTAATTTTGTA
Found at i:132521 original size:26 final size:26
Alignment explanation
Indices: 132492--132561 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 26
132482 TGGAGCCAAA
132492 TTTTTTTTAACTTTTAAAGG-CAATT
1 TTTTTTTTAACTTTTAAAGGCCAATT
* *
132517 TTTTTTTTCAATTTTTAATGGCCCAATT
1 TTTTTTTT-AACTTTTAAAGG-CCAATT
* *
132545 ATTTTTTTAGCTTTTAA
1 TTTTTTTTAACTTTTAA
132562 GGGCTCAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 8 0.22
26 10 0.27
27 7 0.19
28 12 0.32
ACGTcount: A:0.24, C:0.10, G:0.07, T:0.59
Consensus pattern (26 bp):
TTTTTTTTAACTTTTAAAGGCCAATT
Found at i:132609 original size:31 final size:32
Alignment explanation
Indices: 132555--132635 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
132545 ATTTTTTTAG
*
132555 CTTTTAAGGGCTCA-AAAATATTTTTT-TACCAA
1 CTTTTAAGGG-ACATAAAATATTTTTTCT-CCAA
132587 CTTTTAAGGGACATAAAA-ATTTTTTCTCCAA
1 CTTTTAAGGGACATAAAATATTTTTTCTCCAA
* *
132618 CTTTTAAGGAACCTAAAA
1 CTTTTAAGGGACATAAAA
132636 CCCCATTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
31 29 0.66
32 15 0.34
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (32 bp):
CTTTTAAGGGACATAAAATATTTTTTCTCCAA
Found at i:135784 original size:14 final size:15
Alignment explanation
Indices: 135767--135796 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
135757 AATTATTTTG
135767 TTTAAAT-TATAAAA
1 TTTAAATATATAAAA
135781 TTTAAATATATAAAA
1 TTTAAATATATAAAA
135796 T
1 T
135797 CACATGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTAAATATATAAAA
Found at i:136498 original size:23 final size:23
Alignment explanation
Indices: 136467--136535 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
136457 AAGGTAGAAG
*
136467 CGTGCCACAAGGCAGAGAAAAAG
1 CGTGCCACAAGGCAGAGAAAAAA
* * *
136490 TGTGTCACAAGGTAGAGAAAAAA
1 CGTGCCACAAGGCAGAGAAAAAA
*
136513 CGTGCCACAAAGGCAGATAAAAA
1 CGTGCCAC-AAGGCAGAGAAAAA
136536 TTAGAAGAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 25 0.68
24 12 0.32
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (23 bp):
CGTGCCACAAGGCAGAGAAAAAA
Found at i:153450 original size:16 final size:16
Alignment explanation
Indices: 153429--153460 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
153419 AAAAATTTTT
*
153429 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
153445 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
153461 TTTGTAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:160138 original size:37 final size:37
Alignment explanation
Indices: 160097--160174 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
160087 TGTTTCAAAA
* *
160097 TTTACAAAATAGAT-CATATACCTCAAATTTTATAATT
1 TTTACAAAATA-ATCCATAAAACTCAAATTTTATAATT
* *
160134 TTTACAAAATAATCCCTAAAATTCAAATTTTATAATT
1 TTTACAAAATAATCCATAAAACTCAAATTTTATAATT
160171 TTTA
1 TTTA
160175 TGATTTAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 2 0.06
37 34 0.94
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.42
Consensus pattern (37 bp):
TTTACAAAATAATCCATAAAACTCAAATTTTATAATT
Found at i:160503 original size:20 final size:19
Alignment explanation
Indices: 160474--160512 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
160464 AAGTATAGTG
160474 TTTTCAATACTTTAGACAT
1 TTTTCAATACTTTAGACAT
160493 TTTTCCAATACTTTAGACAT
1 TTTT-CAATACTTTAGACAT
160513 CATACTCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (19 bp):
TTTTCAATACTTTAGACAT
Found at i:171901 original size:30 final size:30
Alignment explanation
Indices: 171860--171932 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 30
171850 GTTAATAGTT
* *
171860 GGATCTAAATTTTATA-ATATAAAAAGTGAAG
1 GGAT-TAAATTTTATAGAAAT-AAAAGTAAAG
171891 GGATTAAATTTT-TAGAAATAAAAGTAAAG
1 GGATTAAATTTTATAGAAATAAAAGTAAAG
171920 GGATTAAATTTTA
1 GGATTAAATTTTA
171933 GGCATAATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 23 0.61
30 11 0.29
31 4 0.11
ACGTcount: A:0.48, C:0.01, G:0.16, T:0.34
Consensus pattern (30 bp):
GGATTAAATTTTATAGAAATAAAAGTAAAG
Found at i:173517 original size:11 final size:11
Alignment explanation
Indices: 173501--173535 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
173491 GATAATTATG
173501 ATTTTAAAATA
1 ATTTTAAAATA
173512 ATTTT--AATA
1 ATTTTAAAATA
173521 ATTTTAAAATA
1 ATTTTAAAATA
173532 ATTT
1 ATTT
173536 GTTGACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.41
11 13 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:177203 original size:36 final size:36
Alignment explanation
Indices: 177142--177266 Score: 198
Period size: 36 Copynumber: 3.5 Consensus size: 36
177132 TCGTTATTTG
* * *
177142 TTTTATTCCCTATTGAC-CCTGAGGTCATGATACTCA
1 TTTTACTCCCTATTGACTCAT-AGGTCATGATGCTCA
*
177178 TTCTACTCCCTATTGACTCATAGGTCATGATGCTCA
1 TTTTACTCCCTATTGACTCATAGGTCATGATGCTCA
177214 TTTTACTCCCTATTGACTCATAGGTCATGATGCTCA
1 TTTTACTCCCTATTGACTCATAGGTCATGATGCTCA
177250 TTTTACTCCCTATTGAC
1 TTTTACTCCCTATTGAC
177267 CCGAAGGTCA
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
36 81 0.98
37 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (36 bp):
TTTTACTCCCTATTGACTCATAGGTCATGATGCTCA
Found at i:184592 original size:36 final size:36
Alignment explanation
Indices: 184493--184593 Score: 139
Period size: 36 Copynumber: 2.8 Consensus size: 36
184483 TCGTTATTTG
* * * *
184493 TTTTATTCCCTGTTGACACTAAGGTCACGATTCTCA
1 TTTTATTCCCTGTTGACCCGAAGGTCATGATGCTCA
* * *
184529 TTTTACTCTCTGTTGACCCGTAGGTCATGATGCTCA
1 TTTTATTCCCTGTTGACCCGAAGGTCATGATGCTCA
184565 TTTTATTCCCTGTTGACCCGAAGGTCATG
1 TTTTATTCCCTGTTGACCCGAAGGTCATG
184594 CCTGTTACCA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (36 bp):
TTTTATTCCCTGTTGACCCGAAGGTCATGATGCTCA
Found at i:187291 original size:44 final size:44
Alignment explanation
Indices: 187202--187289 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
187192 TAGTGTCGAG
* * * *
187202 TTAAGAGTTAGAATATGTGGTTAAAATAAGAAGATTAGGAAAAA
1 TTAAGAATTAGAATATGTAGTTAAAATAAGAAAATTAAGAAAAA
*
187246 TTAAGAATTAGAATGTGTAGTCT-AAATAAGAAAAGTTAAGAAAA
1 TTAAGAATTAGAATATGTAGT-TAAAATAAGAAAA-TTAAGAAAA
187290 TTCAAGGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 28 0.76
45 9 0.24
ACGTcount: A:0.51, C:0.01, G:0.20, T:0.27
Consensus pattern (44 bp):
TTAAGAATTAGAATATGTAGTTAAAATAAGAAAATTAAGAAAAA
Found at i:189041 original size:6 final size:6
Alignment explanation
Indices: 189030--189068 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
189020 TGATCAAAAT
* * *
189030 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
189069 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:191306 original size:3 final size:3
Alignment explanation
Indices: 191298--191325 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
191288 ATTTAAAGGT
191298 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
191326 AAAACCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:196783 original size:30 final size:29
Alignment explanation
Indices: 196749--196814 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
196739 GTGATTTCTG
196749 AAAATTGAATC-AAATCAAAATTTAATATAT
1 AAAATTGAA-CAAAATCAAAATTT-ATATAT
*
196779 AAAATTGCACAAAATCAAAATTTATATAT
1 AAAATTGAACAAAATCAAAATTTATATAT
*
196808 AACATTG
1 AAAATTG
196815 CACATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 13 0.39
30 20 0.61
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAATTGAACAAAATCAAAATTTATATAT
Found at i:196806 original size:29 final size:30
Alignment explanation
Indices: 196760--196818 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
196750 AAATTGAATC
196760 AAATCAAAATTTAATATATAAAATTGCACA
1 AAATCAAAATTTAATATATAAAATTGCACA
*
196790 AAATCAAAATTT-ATATATAACATTGCACA
1 AAATCAAAATTTAATATATAAAATTGCACA
196819 TTAAATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTAATATATAAAATTGCACA
Found at i:196837 original size:31 final size:29
Alignment explanation
Indices: 196760--196839 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
196750 AAATTGAATC
*
196760 AAATCAAAATTTAATATATAAAATTGCACA
1 AAATCAAAA-TTCATATATAAAATTGCACA
* *
196790 AAATCAAAATTTATATATAACATTGCACA
1 AAATCAAAATTCATATATAAAATTGCACA
* *
196819 TTAAATTAAAGTTCATATATA
1 --AAATCAAAATTCATATATA
196840 GTTTTGATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 18 0.42
30 9 0.21
31 16 0.37
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.34
Consensus pattern (29 bp):
AAATCAAAATTCATATATAAAATTGCACA
Found at i:202667 original size:41 final size:41
Alignment explanation
Indices: 202610--202693 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
202600 TCGTTACTTC
202610 TAAAAGTGAAGAAGAATGAGATGCAGAAGCATTCTTTGTAG
1 TAAAAGTGAAGAAGAATGAGATGCAGAAGCATTCTTTGTAG
*
202651 TAAAAGTGAAGAAGAATGGGATGCAGAAGCATTCTTTGTAG
1 TAAAAGTGAAGAAGAATGAGATGCAGAAGCATTCTTTGTAG
202692 TA
1 TA
202694 GAAGAGGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.25
Consensus pattern (41 bp):
TAAAAGTGAAGAAGAATGAGATGCAGAAGCATTCTTTGTAG
Found at i:204888 original size:59 final size:59
Alignment explanation
Indices: 204825--204952 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 59
204815 GTTTTAGTTA
* * * *
204825 CATTTATGTTGTGTTTCATTTTGGAGACCTAGTGGTGAGGTCCAATC-TTAATTTAATTT
1 CATTTATGTTGTATTTCATTTTAGAGACCTAGTGATAAGGTCC-ATCTTTAATTTAATTT
** * * *
204884 CATTTATGTTGTATTTCATTTTAGAGGGCTAGTTATAAGGTTCATCTTTATTTTAATTT
1 CATTTATGTTGTATTTCATTTTAGAGACCTAGTGATAAGGTCCATCTTTAATTTAATTT
204943 CATTTATGTT
1 CATTTATGTT
204953 TTATGTTGCA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 3 0.05
59 56 0.95
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50
Consensus pattern (59 bp):
CATTTATGTTGTATTTCATTTTAGAGACCTAGTGATAAGGTCCATCTTTAATTTAATTT
Found at i:204990 original size:67 final size:66
Alignment explanation
Indices: 204886--205019 Score: 189
Period size: 67 Copynumber: 2.0 Consensus size: 66
204876 TTTAATTTCA
* * * * *
204886 TTTATGTTGTATTTCATTTTAGAGGGCTAGTTATAAGGTTCATCTT-TATTTTAATTTCATTTAT
1 TTTATGTTGCATTTCATTTTAGAGGCCTAGTTATAAGG-TCAACTTCTACTTTAATTTCATTGAT
204950 GT
65 GT
*
204952 TTTATGTTGCATTTCATTTTTAGAGGCCTAGTTGTAAGGTCAACTTCTACTTTAATTTCATTGAT
1 TTTATGTTGCATTTCA-TTTTAGAGGCCTAGTTATAAGGTCAACTTCTACTTTAATTTCATTGAT
205017 GT
65 GT
205019 T
1 T
205020 GCATTTTATT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
66 21 0.35
67 39 0.65
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.51
Consensus pattern (66 bp):
TTTATGTTGCATTTCATTTTAGAGGCCTAGTTATAAGGTCAACTTCTACTTTAATTTCATTGATG
T
Found at i:205069 original size:59 final size:59
Alignment explanation
Indices: 205005--205262 Score: 211
Period size: 59 Copynumber: 4.4 Consensus size: 59
204995 CTTCTACTTT
* * * * *
205005 AATTTCATTGATGTTGCATTTTATTTCAAAAGCTTAACTGTGAGGTCCATTTTTGTTTC
1 AATTTCATTTATGTTGCATTTCATTTCAAAAGCCTAATTGTGAGATCCATTTTTGTTTC
* * * * * *
205064 AATTTCAATTATG-TGACATTTCATTTCAAAGGCCTAGTTGTAAGATTCATTTTTGTTTT
1 AATTTCATTTATGTTG-CATTTCATTTCAAAAGCCTAATTGTGAGATCCATTTTTGTTTC
* * * * **
205123 TATTTTATTTATGTTGCCTTTCATTTC-AAAGCCCTAATTATGAGATCCATTTTCATTTC
1 AATTTCATTTATGTTGCATTTCATTTCAAAAG-CCTAATTGTGAGATCCATTTTTGTTTC
*** * * * * *
205182 AATTTCATTTATG-TGACATTTCATTTTTGATGCCTAGTTGTGAAAT-TATTTTCGTTTC
1 AATTTCATTTATGTTG-CATTTCATTTCAAAAGCCTAATTGTGAGATCCATTTTTGTTTC
* *
205240 AATTTCAATT-TGTTACATTTCAT
1 AATTTCATTTATGTTGCATTTCAT
205263 ATTAGAGGCC
Statistics
Matches: 157, Mismatches: 36, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
57 10 0.06
58 27 0.17
59 116 0.74
60 4 0.03
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (59 bp):
AATTTCATTTATGTTGCATTTCATTTCAAAAGCCTAATTGTGAGATCCATTTTTGTTTC
Found at i:205217 original size:118 final size:118
Alignment explanation
Indices: 204952--205262 Score: 303
Period size: 118 Copynumber: 2.6 Consensus size: 118
204942 TCATTTATGT
* * * **
204952 TTTATGTTG-CATTTCATTTTTAGAGGCCTAGTTGTAAG-GTCAACTTCTACTTTAATTTCATTG
1 TTTATG-TGACATTTCATTTTT-GAGGCCTAGTTGTAAGATTC-ATTTTTGTTTTAATTTCATTG
* * * * **
205015 ATGTTGCATTTTATTTCAAAAGCTTAACTGTGAGGTCCATTTTTGTTTCAATTTCA
63 ATGTTGCATTTCATTTCAAAAGCCTAACTATGAGATCCATTTTCATTTCAATTTCA
* *** * * *
205071 ATTATGTGACATTTCATTTCAAAGGCCTAGTTGTAAGATTCATTTTTGTTTTTATTTTATTTATG
1 TTTATGTGACATTTCATTTTTGAGGCCTAGTTGTAAGATTCATTTTTGTTTTAATTTCATTGATG
* *
205136 TTGCCTTTCATTTC-AAAGCCCTAATTATGAGATCCATTTTCATTTCAATTTCA
66 TTGCATTTCATTTCAAAAG-CCTAACTATGAGATCCATTTTCATTTCAATTTCA
* * *
205189 TTTATGTGACATTTCATTTTTGATGCCTAGTTGTGAA-ATT-ATTTTCGTTTCAATTTCAATT--
1 TTTATGTGACATTTCATTTTTGAGGCCTAGTTGT-AAGATTCATTTTTGTTTTAATTTC-ATTGA
*
205250 TGTTACATTTCAT
64 TGTTGCATTTCAT
205263 ATTAGAGGCC
Statistics
Matches: 156, Mismatches: 31, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
116 11 0.07
117 17 0.11
118 109 0.70
119 19 0.12
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.49
Consensus pattern (118 bp):
TTTATGTGACATTTCATTTTTGAGGCCTAGTTGTAAGATTCATTTTTGTTTTAATTTCATTGATG
TTGCATTTCATTTCAAAAGCCTAACTATGAGATCCATTTTCATTTCAATTTCA
Found at i:208828 original size:18 final size:18
Alignment explanation
Indices: 208782--208830 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
208772 GGTCCTATCC
*
208782 ATTAGATTTTTAG-TTTAA
1 ATTAGA-TTTTAGAATTAA
*
208800 ATTGGATTTTAGAATTAA
1 ATTAGATTTTAGAATTAA
208818 ATTAGATTTTAGA
1 ATTAGATTTTAGA
208831 TTTTTCAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (18 bp):
ATTAGATTTTAGAATTAA
Found at i:208904 original size:42 final size:44
Alignment explanation
Indices: 208814--208907 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 44
208804 GATTTTAGAA
*
208814 TTAAATTAGATTTTAGATTTTTCAAGTCATAGTTAGATTTTAGTT
1 TTAAATTAGATTTTAGATTTTTCAAGTCA-AGTTAGATTTAAGTT
* *
208859 TTAAATTAGATTTTATATTTTT-AATTC-AGTTAGATTATAAG-T
1 TTAAATTAGATTTTAGATTTTTCAAGTCAAGTTAGATT-TAAGTT
208901 TTAAATT
1 TTAAATT
208908 CTAGGTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
42 17 0.38
43 3 0.07
44 4 0.09
45 21 0.47
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (44 bp):
TTAAATTAGATTTTAGATTTTTCAAGTCAAGTTAGATTTAAGTT
Found at i:208967 original size:17 final size:17
Alignment explanation
Indices: 208945--208981 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
208935 TATTTCAGAC
* *
208945 TTTTAAGTTTAATTAGA
1 TTTTAAGCTTAACTAGA
208962 TTTTAAGCTTAACTAGA
1 TTTTAAGCTTAACTAGA
208979 TTT
1 TTT
208982 CTAATAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (17 bp):
TTTTAAGCTTAACTAGA
Found at i:212373 original size:15 final size:15
Alignment explanation
Indices: 212349--212378 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
212339 TTTGATTCTT
*
212349 AAAAATTAAAAATTA
1 AAAAACTAAAAATTA
212364 AAAAACTAAAAATTA
1 AAAAACTAAAAATTA
212379 TTTAAAAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAACTAAAAATTA
Found at i:212423 original size:19 final size:19
Alignment explanation
Indices: 212399--212441 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
212389 TATTTCTTGG
212399 TAAAATACATA-AAATTTTA
1 TAAAATACATACAAA-TTTA
*
212418 TAAAATATATACAAATTTA
1 TAAAATACATACAAATTTA
212437 TAAAA
1 TAAAA
212442 GAGTATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAATACATACAAATTTA
Found at i:213038 original size:18 final size:20
Alignment explanation
Indices: 213012--213049 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
213002 ATTATGAGTT
213012 TTTAGAAAA-TA-TATTTTA
1 TTTAGAAAATTATTATTTTA
*
213030 TTTATAAAATTATTATTTTA
1 TTTAGAAAATTATTATTTTA
213050 ATAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTAGAAAATTATTATTTTA
Found at i:215151 original size:2 final size:2
Alignment explanation
Indices: 215144--215169 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
215134 ATATACAGAA
215144 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
215170 CAAGTATCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:216116 original size:3 final size:3
Alignment explanation
Indices: 216108--216136 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
216098 GAAATGGAAC
216108 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
216137 ATGAATAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:228783 original size:39 final size:39
Alignment explanation
Indices: 228739--228816 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
228729 GATTGCTTGT
228739 ATAATAAAAAGAATACACCATCAATGTATCAAATGTTAA
1 ATAATAAAAAGAATACACCATCAATGTATCAAATGTTAA
* * * *
228778 ATAATAAAAAGAGTAGACTATCAGTGTATCAAATGTTAA
1 ATAATAAAAAGAATACACCATCAATGTATCAAATGTTAA
228817 TCTTAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (39 bp):
ATAATAAAAAGAATACACCATCAATGTATCAAATGTTAA
Found at i:248235 original size:5 final size:5
Alignment explanation
Indices: 248218--248252 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
248208 AAATAAAAGA
* *
248218 AAATC AAATT AAACT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT
248253 CTTAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (5 bp):
AAATT
Found at i:249583 original size:30 final size:29
Alignment explanation
Indices: 249520--249584 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
249510 ATACTAACGT
* ** *
249520 AAGTGATTAAAATGTAACATTTCAAACAT
1 AAGTGACTAAAATGTAACATAGCAAACAA
*
249549 AAGTGACTAAAATGTAACCTGAGCAAACAA
1 AAGTGACTAAAATGTAACAT-AGCAAACAA
249579 AAGTGA
1 AAGTGA
249585 TTATTTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.23
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATAGCAAACAA
Found at i:266014 original size:57 final size:57
Alignment explanation
Indices: 265907--266350 Score: 516
Period size: 57 Copynumber: 7.8 Consensus size: 57
265897 AAGATGATTT
** ** * *
265907 ACCTCTTTAAGATGAAAATGAT-GTCACACCTCCTTAAGATGGACTTTATATAATTA
1 ACCTCTTTAAGGCGAAGTTGATAGTCACACCTCTTTAAGATGGACTTTATATAATTC
* * *
265963 ACCTCTTTAAGGCGAAGTTAATAGTCACACCTCTTTAACATAGG-CTCTATATAATTC
1 ACCTCTTTAAGGCGAAGTTGATAGTCACACCTCTTTAAGAT-GGACTTTATATAATTC
* * * *
266020 ACCTCTTTAAGGTGAAGTTAATAGTCACACCTTTTTAAGATGGACTTTATATAGTTC
1 ACCTCTTTAAGGCGAAGTTGATAGTCACACCTCTTTAAGATGGACTTTATATAATTC
*** * * *
266077 ACCT-TTTAAGTTAAAGTTGATAATCACACCTCCTTAAGATGGACTTTATACAATTC
1 ACCTCTTTAAGGCGAAGTTGATAGTCACACCTCTTTAAGATGGACTTTATATAATTC
* * * *
266133 ACGTCTTTAAGGCGAAGTTGATAATCATACCTCCTTAAGATGGACTTTATATAATTC
1 ACCTCTTTAAGGCGAAGTTGATAGTCACACCTCTTTAAGATGGACTTTATATAATTC
* ** * ** * * *
266190 ATCTCTTTGTGGCAAAACTGATAATCACACCTCTTTAATATGGACTTTATACAATTC
1 ACCTCTTTAAGGCGAAGTTGATAGTCACACCTCTTTAAGATGGACTTTATATAATTC
** * * *
266247 ACCTCTTTAAGGAAAAATTGATAGTCACACCTCTTTAAAATGGACTTTATATAGTTC
1 ACCTCTTTAAGGCGAAGTTGATAGTCACACCTCTTTAAGATGGACTTTATATAATTC
*
266304 ACCTCTTTAAGGTGAAGTTGATAGTCACACCTCTTTAAGATGGACTT
1 ACCTCTTTAAGGCGAAGTTGATAGTCACACCTCTTTAAGATGGACTT
266351 ATCCACTTGT
Statistics
Matches: 332, Mismatches: 52, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
56 66 0.20
57 264 0.80
58 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (57 bp):
ACCTCTTTAAGGCGAAGTTGATAGTCACACCTCTTTAAGATGGACTTTATATAATTC
Found at i:266083 original size:28 final size:29
Alignment explanation
Indices: 265933--266350 Score: 113
Period size: 28 Copynumber: 14.7 Consensus size: 29
265923 AATGATGTCA
* *
265933 CACCTCCTTAAGATGGACTTTATATAATT
1 CACCTCTTTAAGATGGACTTTATATAGTT
* ** *
265962 AACCTCTTTAAG--GCGAAGTTA-ATAGTCA
1 CACCTCTTTAAGATG-GACTTTATATAGT-T
* * *
265990 CACCTCTTTAACATAGG-CTCTATATAATT
1 CACCTCTTTAAGAT-GGACTTTATATAGTT
* ** *
266019 CACCTCTTTAAGGT-GAAGTTA-ATAGTCA
1 CACCTCTTTAAGATGGACTTTATATAGT-T
*
266047 CACCTTTTTAAGATGGACTTTATATAGTT
1 CACCTCTTTAAGATGGACTTTATATAGTT
* ** * * *
266076 CACCT-TTTAAGTTAAAGTTGATA-A-TCA
1 CACCTCTTTAAGATGGACTTTATATAGT-T
* * *
266103 CACCTCCTTAAGATGGACTTTATACAATT
1 CACCTCTTTAAGATGGACTTTATATAGTT
* ** * * *
266132 CACGTCTTTAAGGCGAAGTTGATA-A--T
1 CACCTCTTTAAGATGGACTTTATATAGTT
* *
266158 CATACCTCCTTAAGATGGACTTTATATAATT
1 C--ACCTCTTTAAGATGGACTTTATATAGTT
* *** * *
266189 CATCTCTTT--G-TGG-CAAAACTGATAATCA
1 CACCTCTTTAAGATGGACTTTA-T-ATAGT-T
* * *
266217 CACCTCTTTAATATGGACTTTATACAATT
1 CACCTCTTTAAGATGGACTTTATATAGTT
* ** * *
266246 CACCTCTTTAAG--GAAAAATT-GATAGTCA
1 CACCTCTTTAAGATG-GACTTTATATAGT-T
*
266274 CACCTCTTTAAAATGGACTTTATATAGTT
1 CACCTCTTTAAGATGGACTTTATATAGTT
* ** * *
266303 CACCTCTTTAAGGT-GAAGTT-GATAGTCA
1 CACCTCTTTAAGATGGACTTTATATAGT-T
266331 CACCTCTTTAAGATGGACTT
1 CACCTCTTTAAGATGGACTT
266351 ATCCACTTGT
Statistics
Matches: 268, Mismatches: 88, Indels: 66
0.64 0.21 0.16
Matches are distributed among these distances:
25 2 0.01
26 7 0.03
27 31 0.12
28 110 0.41
29 88 0.33
30 21 0.08
31 7 0.03
32 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (29 bp):
CACCTCTTTAAGATGGACTTTATATAGTT
Found at i:268524 original size:108 final size:108
Alignment explanation
Indices: 268335--268539 Score: 401
Period size: 108 Copynumber: 1.9 Consensus size: 108
268325 ATAAATGATA
268335 TTTTAGGTTATGAAAGCACATGTTAAATTATGGTGGCTTGTTGGACAATTCATGTTTAGTGTATG
1 TTTTAGGTTATGAAAGCACATGTTAAATTATGGTGGCTTGTTGGACAATTCATGTTTAGTGTATG
268400 TCTTGTTTACCAAGGAATTTTGACACACACGGTCGTGTGTATG
66 TCTTGTTTACCAAGGAATTTTGACACACACGGTCGTGTGTATG
*
268443 TTTTAGGTTATGAAAGTACATGTTAAATTATGGTGGCTTGTTGGACAATTCATGTTTAGTGTATG
1 TTTTAGGTTATGAAAGCACATGTTAAATTATGGTGGCTTGTTGGACAATTCATGTTTAGTGTATG
268508 TCTTGTTTACCAAGGAATTTTGACACACACGG
66 TCTTGTTTACCAAGGAATTTTGACACACACGG
268540 CCTGTGACAC
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 96 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (108 bp):
TTTTAGGTTATGAAAGCACATGTTAAATTATGGTGGCTTGTTGGACAATTCATGTTTAGTGTATG
TCTTGTTTACCAAGGAATTTTGACACACACGGTCGTGTGTATG
Found at i:279034 original size:25 final size:25
Alignment explanation
Indices: 278936--279028 Score: 134
Period size: 25 Copynumber: 3.7 Consensus size: 25
278926 TAATTGAAAA
**
278936 CTGGCTCGTAAGAGTAATATTCTGT
1 CTGGCTCGTAAGAGCGATATTCTGT
*
278961 CTGGCTCATAAGAGCGATATTCTGT
1 CTGGCTCGTAAGAGCGATATTCTGT
278986 CTGGCTCGTAAGAGCGATAATT-TGT
1 CTGGCTCGTAAGAGCGAT-ATTCTGT
*
279011 CTAGCTCGTAAGAGCGAT
1 CTGGCTCGTAAGAGCGAT
279029 GTTTTGATTG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
25 59 0.95
26 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (25 bp):
CTGGCTCGTAAGAGCGATATTCTGT
Found at i:286337 original size:17 final size:17
Alignment explanation
Indices: 286315--286362 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 17
286305 ATAGGTAATC
286315 GAATTGATCATTTGATA
1 GAATTGATCATTTGATA
286332 GAATTGA--A-TTGATA
1 GAATTGATCATTTGATA
286346 GAATTGATCATTTGATA
1 GAATTGATCATTTGATA
286363 AAATCTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 13 0.46
15 1 0.04
16 1 0.04
17 13 0.46
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.40
Consensus pattern (17 bp):
GAATTGATCATTTGATA
Found at i:288946 original size:18 final size:18
Alignment explanation
Indices: 288914--288950 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
288904 TAAAATCGAA
288914 TTAATCGATTGAATTGAT
1 TTAATCGATTGAATTGAT
288932 TTAATTCGATT-AATTGAT
1 TTAA-TCGATTGAATTGAT
288950 T
1 T
288951 GATTAATCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (18 bp):
TTAATCGATTGAATTGAT
Found at i:293439 original size:3 final size:3
Alignment explanation
Indices: 293431--293467 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
293421 GATTCCTTTT
293431 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 T
293468 GTTTTTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:293599 original size:14 final size:15
Alignment explanation
Indices: 293565--293602 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
293555 ATTTATCTCA
* *
293565 ATTTATATTTTAATT
1 ATTTATATTTAAAAT
293580 ATTTATATTTAAAAT
1 ATTTATATTTAAAAT
293595 A-TTATATT
1 ATTTATATT
293603 CTAGTCACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTATATTTAAAAT
Found at i:298415 original size:42 final size:42
Alignment explanation
Indices: 298367--298515 Score: 149
Period size: 42 Copynumber: 3.5 Consensus size: 42
298357 GTAGTATTGT
** * * *
298367 TTCGGTATATTTGATGATGTAGTTACGTGCCAGTATGTTTTC
1 TTCGGTATATCCGATGATGCACTTACGTGCAAGTATGTTTTC
* *
298409 TTCGGTATATCCGATGATGCACTTACGTGTAAGTATGTTTTT
1 TTCGGTATATCCGATGATGCACTTACGTGCAAGTATGTTTTC
* * * * *
298451 TTTGGTACATCCAATGATGCACTTACATGTC-AGTATGATTGT-
1 TTCGGTATATCCGATGATGCACTTACGTG-CAAGTATG-TTTTC
*
298493 TTCGGTTTATCCGATGATGCACT
1 TTCGGTATATCCGATGATGCACT
298516 ATGCACGTAA
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
42 85 0.97
43 3 0.03
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (42 bp):
TTCGGTATATCCGATGATGCACTTACGTGCAAGTATGTTTTC
Found at i:300007 original size:30 final size:30
Alignment explanation
Indices: 299973--300031 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
299963 GATTAATGAG
299973 TTAATATATATATATATT-TGACAT-ATATAA
1 TTAATATA-ATAT-TATTATGACATAATATAA
*
300003 TTAATATAATATTTTTATGACATAATATA
1 TTAATATAATATTATTATGACATAATATA
300032 TTCGCATCGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 3 0.12
29 10 0.38
30 13 0.50
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (30 bp):
TTAATATAATATTATTATGACATAATATAA
Found at i:300746 original size:29 final size:28
Alignment explanation
Indices: 300700--300786 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 28
300690 GTCAACAAAT
* * * *
300700 AATTTTAAAACTAATAAAATTATTTTTTA
1 AATTATAAAATTATTAAAATTA-TTTTAA
300729 AATTATAAAATTATTAAAATTATTTTAA
1 AATTATAAAATTATTAAAATTATTTTAA
*
300757 AATTAATTTAAAATTATT-AAATAATTTTAA
1 AATT-A--TAAAATTATTAAAATTATTTTAA
300787 TTTTCAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
28 9 0.18
29 20 0.40
30 11 0.22
31 10 0.20
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTATAAAATTATTAAAATTATTTTAA
Found at i:300756 original size:11 final size:11
Alignment explanation
Indices: 300714--300774 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
300704 TTAAAACTAA
300714 TAAAATTATTTT
1 TAAAATTA-TTT
*
300726 TTAAATTA---
1 TAAAATTATTT
300734 TAAAATTA--T
1 TAAAATTATTT
300743 TAAAATTATTT
1 TAAAATTATTT
*
300754 TAAAATTAATT
1 TAAAATTATTT
300765 TAAAATTATT
1 TAAAATTATT
300775 AAATAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 7 0.17
9 8 0.19
11 20 0.48
12 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:300770 original size:22 final size:20
Alignment explanation
Indices: 300696--300786 Score: 73
Period size: 20 Copynumber: 4.6 Consensus size: 20
300686 CCACGTCAAC
* * *
300696 AAATAATTTTAAAACTAATA
1 AAATTATTTTAAAATTATTA
*
300716 AAATTATTTTTTAAATTA-TA
1 AAATTA-TTTTAAAATTATTA
300736 AAATTA--TTAAAATTATTTTA
1 AAATTATTTTAAAATTA--TTA
*
300756 AAATTAATTTAAAATTATT-
1 AAATTATTTTAAAATTATTA
*
300775 AAATAATTTTAA
1 AAATTATTTTAA
300787 TTTTCAATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
17 8 0.14
19 10 0.17
20 23 0.39
21 9 0.15
22 9 0.15
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:300796 original size:31 final size:31
Alignment explanation
Indices: 300724--300796 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
300714 TAAAATTATT
*
300724 TTTTAAATTATAAAATTATTAAAATTATTTTAA
1 TTTT-AATT-TAAAATTATTAAAATAATTTTAA
**
300757 AATTAATTTAAAATTATT-AAATAATTTTAA
1 TTTTAATTTAAAATTATTAAAATAATTTTAA
300787 TTTTCAATTT
1 TTTT-AATTT
300797 CATCTTCTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 13 0.38
31 15 0.44
32 4 0.12
33 2 0.06
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
TTTTAATTTAAAATTATTAAAATAATTTTAA
Found at i:301059 original size:98 final size:98
Alignment explanation
Indices: 300903--301094 Score: 314
Period size: 98 Copynumber: 2.0 Consensus size: 98
300893 GAACCAAACC
* * * *
300903 ATGGCTACTTCTCTACTTGGATTTTGAATCAAACCATGGCTTCTTCTTCTTTCGTCACTCTCTTA
1 ATGGCTACTTCTCCACTTGGATTTTGAATCAAACCATCGCTTCTTCTTCTTCCATCACTCTCTTA
*
300968 ACCTTTCAAGGTTCTCTATTTTAATCTCATAACT
66 ACC-TTCAAGGTTCTCTATTTCAATCTCATAACT
*
301002 ATGGCTACTTTTCCACTT-GATTTTGAATCAAACCATCGCTTCTTCTTCTTCCATCACTCTCTTA
1 ATGGCTACTTCTCCACTTGGATTTTGAATCAAACCATCGCTTCTTCTTCTTCCATCACTCTCTTA
301066 ACCTTCAAGGTTCTCTATTTCAATCTCAT
66 ACCTTCAAGGTTCTCTATTTCAATCTCAT
301095 TTCTTAGAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
97 25 0.29
98 46 0.53
99 16 0.18
ACGTcount: A:0.21, C:0.27, G:0.09, T:0.43
Consensus pattern (98 bp):
ATGGCTACTTCTCCACTTGGATTTTGAATCAAACCATCGCTTCTTCTTCTTCCATCACTCTCTTA
ACCTTCAAGGTTCTCTATTTCAATCTCATAACT
Found at i:301744 original size:11 final size:11
Alignment explanation
Indices: 301728--301798 Score: 64
Period size: 11 Copynumber: 6.9 Consensus size: 11
301718 TATATTTTAA
301728 AAAATAATTTT
1 AAAATAATTTT
301739 AAAATAATTTT
1 AAAATAATTTT
301750 -AAA-AATTTT
1 AAAATAATTTT
* *
301759 -ATAT-TTTTAT
1 AAAATAATTT-T
301769 AAAATAATTTT
1 AAAATAATTTT
301780 --AATAATTTT
1 AAAATAATTTT
*
301789 AAAATTATTT
1 AAAATAATTT
301799 ATTGACGTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
9 20 0.41
10 4 0.08
11 22 0.45
12 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:301759 original size:40 final size:41
Alignment explanation
Indices: 301698--301792 Score: 144
Period size: 39 Copynumber: 2.4 Consensus size: 41
301688 GATTAAAATA
*
301698 TTAAAATAA-TTTAATAATTTTATA-TTTTAAAAAATAATT
1 TTAAAATAATTTTAAAAATTTTATATTTTTAAAAAATAATT
*
301737 TTAAAATAATTTTAAAAATTTTATATTTTTATAAAATAATT
1 TTAAAATAATTTTAAAAATTTTATATTTTTAAAAAATAATT
301778 TT--AATAATTTTAAAA
1 TTAAAATAATTTTAAAA
301793 TTATTTATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
39 22 0.42
40 14 0.27
41 16 0.31
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (41 bp):
TTAAAATAATTTTAAAAATTTTATATTTTTAAAAAATAATT
Found at i:301793 original size:20 final size:19
Alignment explanation
Indices: 301710--301798 Score: 67
Period size: 20 Copynumber: 4.4 Consensus size: 19
301700 AAAATAATTT
301710 AATAATTTTAT-ATTTTAAAA
1 AATAATTTTATAATTTT--AA
301730 AATAATTTTAAAATAATTTT-A
1 AATAATTTT---ATAATTTTAA
*
301751 AA-AATTTTATATTTTTATAA
1 AATAATTTTATA-ATTT-TAA
301771 AATAATTTTAATAATTTTAA
1 AATAATTTT-ATAATTTTAA
*
301791 AATTATTT
1 AATAATTT
301799 ATTGACGTGA
Statistics
Matches: 57, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
17 3 0.05
18 3 0.05
19 1 0.02
20 28 0.49
21 12 0.21
22 3 0.05
23 2 0.04
24 5 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATAATTTTATAATTTTAA
Found at i:306138 original size:16 final size:18
Alignment explanation
Indices: 306117--306152 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
306107 CCAACAATGT
306117 TTCAAAAAAT-TAA-AAA
1 TTCAAAAAATGTAATAAA
306133 TTCAAAAAATGTAATAAA
1 TTCAAAAAATGTAATAAA
306151 TT
1 TT
306153 TAAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (18 bp):
TTCAAAAAATGTAATAAA
Found at i:306165 original size:24 final size:25
Alignment explanation
Indices: 306138--306185 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
306128 AAAAATTCAA
* * *
306138 AAAATGTAATAAATTTAAA-TATAT
1 AAAATATAAAAAATTCAAAGTATAT
306162 AAAATATAAAAAATTCAAAGTATA
1 AAAATATAAAAAATTCAAAGTATA
306186 ATGACAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (25 bp):
AAAATATAAAAAATTCAAAGTATAT
Found at i:306227 original size:21 final size:21
Alignment explanation
Indices: 306201--306247 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
306191 AAACTTAACT
306201 TTTAACGTT-TATATTTGTCAA
1 TTTAAC-TTCTATATTTGTCAA
*
306222 TTTAACTTCTATATTTTTCAA
1 TTTAACTTCTATATTTGTCAA
*
306243 GTTAA
1 TTTAA
306248 ATTTAACCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.53
Consensus pattern (21 bp):
TTTAACTTCTATATTTGTCAA
Found at i:306875 original size:28 final size:27
Alignment explanation
Indices: 306823--306876 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
306813 AAATATTTAT
* *
306823 TTAAAATTACAAAAATGGTTAAAATTA
1 TTAAAAATACAAAAATAGTTAAAATTA
306850 TTAAAAATAGCAAAAA-AGTTATAAATT
1 TTAAAAATA-CAAAAATAGTTA-AAATT
306877 TGCCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.31
Consensus pattern (27 bp):
TTAAAAATACAAAAATAGTTAAAATTA
Found at i:308377 original size:58 final size:57
Alignment explanation
Indices: 308309--308445 Score: 204
Period size: 58 Copynumber: 2.4 Consensus size: 57
308299 AATTATTGTT
*
308309 ATTAAATTTTAATAAAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
1 ATTAAATTTTAATATAATTATTATTAAATATAATTTAAT-AAAATAATAAATAATTTA
* * *
308367 ATTATATTTTAACATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTA
1 ATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTA
308424 A-TAACATTTTTAATATAATTAT
1 ATTAA-A-TTTTAATATAATTAT
308446 ATTTTTAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.03
57 19 0.27
58 50 0.70
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (57 bp):
ATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTA
Found at i:308393 original size:26 final size:26
Alignment explanation
Indices: 308364--308445 Score: 56
Period size: 29 Copynumber: 2.9 Consensus size: 26
308354 AATAAATAAT
* *
308364 TTAATTATATTTTAACATAATTATTA
1 TTAAATATATTTTAAAATAATTATTA
*
308390 TTAAATATAATTTAATAAAATAATATATAA
1 TTAAATAT-ATTT--TAAAATAAT-TATTA
* * *
308420 TTTAATAACATTTTTAATATAATTAT
1 TTAAAT-ATA-TTTTAAAATAATTAT
308446 ATTTTTAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
26 7 0.16
27 4 0.09
28 3 0.07
29 16 0.36
30 10 0.23
31 4 0.09
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TTAAATATATTTTAAAATAATTATTA
Found at i:308442 original size:17 final size:17
Alignment explanation
Indices: 308417--308455 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
308407 AAATAATATA
*
308417 TAATTTAATAACATTTT
1 TAATATAATAACATTTT
* *
308434 TAATATAATTATATTTT
1 TAATATAATAACATTTT
308451 TAATA
1 TAATA
308456 CTCGCGCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATATAATAACATTTT
Found at i:319736 original size:140 final size:140
Alignment explanation
Indices: 319488--319756 Score: 461
Period size: 140 Copynumber: 1.9 Consensus size: 140
319478 TCTTGCTCTT
*
319488 TATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCGAAATG
1 TATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAATG
*
319553 TTCAATATAATTCACATGGCAAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATATT
66 TTCAATATAATTCACATGGCAAAAAGCATTTATTTATTTATTTCCAACCACCAAATATGCATATT
319618 AATATATATA
131 AATATATATA
* *
319628 TATATATATA-AATTCAAATCTTTCATTAATCTTTTGTATTCAACTCATTTCAACAATCCAAAAT
1 TATATATA-ACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
*
319692 GTTCAATATAATTCAC-TGGACAAAAAGTATTTATTTATTTATTTCCAACCACCAAATATGCATA
65 GTTCAATATAATTCACATGG-CAAAAAGCATTTATTTATTTATTTCCAACCACCAAATATGCATA
319756 T
129 T
319757 ATATATTTAA
Statistics
Matches: 122, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
139 3 0.02
140 118 0.97
141 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (140 bp):
TATATATAACAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAATG
TTCAATATAATTCACATGGCAAAAAGCATTTATTTATTTATTTCCAACCACCAAATATGCATATT
AATATATATA
Found at i:320873 original size:30 final size:29
Alignment explanation
Indices: 320839--321023 Score: 133
Period size: 30 Copynumber: 6.3 Consensus size: 29
320829 AAAATTATGT
**
320839 TTTGACCTCTAAATTTTTTAAAAATTCAAA
1 TTTGACC-CTAAATTTTCCAAAAATTCAAA
*
320869 TTTGACCTTAAATTTTCCAAAAAATT-AAA
1 TTTGACCCTAAATTTTCC-AAAAATTCAAA
* * *
320898 TTT-ATCCCCCAAATTTTTCAAAAATTTCAAT
1 TTTGA--CCCTAAATTTTCCAAAAA-TTCAAA
* * *
320929 TTTAACCCCAAGTTTTCCAAAAATTCAAA
1 TTTGACCCTAAATTTTCCAAAAATTCAAA
** *
320958 TTTGACCCTTAAATTTTATAAAAATT-GAA
1 TTTGACCC-TAAATTTTCCAAAAATTCAAA
* * * * *
320987 TTTAACCCAAAATTTCCCAAAATTTCCAA
1 TTTGACCCTAAATTTTCCAAAAATTCAAA
*
321016 TTTAACCC
1 TTTGACCC
321024 CTGGTGCTTC
Statistics
Matches: 124, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
28 13 0.10
29 50 0.40
30 55 0.44
31 5 0.04
32 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (29 bp):
TTTGACCCTAAATTTTCCAAAAATTCAAA
Found at i:323202 original size:29 final size:29
Alignment explanation
Indices: 323095--323302 Score: 93
Period size: 29 Copynumber: 7.2 Consensus size: 29
323085 TCTCTGAAAG
*
323095 GAAATACCTTTGTGGCGATCTTTGTTAAA
1 GAAATACCTTTGTGGCTATCTTTGTTAAA
* * *** *
323124 GAAGTGCCTCCATGG-TAATGTTTG-TAAA
1 GAAATACCTTTGTGGCT-ATCTTTGTTAAA
* * * *
323152 GGAAACACCTTTATAGCAATCTTTGTTAAA
1 -GAAATACCTTTGTGGCTATCTTTGTTAAA
* * * *
323182 GAAATGCCTCTGTGGCTATCTCT-TCAAA
1 GAAATACCTTTGTGGCTATCTTTGTTAAA
** * *
323210 GTAAACGCCTTTGT-GTTGATCTCTGTTAAA
1 G-AAATACCTTTGTGGCT-ATCTTTGTTAAA
* * ** * *
323240 GAAATACCTCTATAACAATCTCTG-TAAA
1 GAAATACCTTTGTGGCTATCTTTGTTAAA
* *
323268 GGAAACACTTTTGTGGCTATCTTTGTTAAA
1 -GAAATACCTTTGTGGCTATCTTTGTTAAA
323298 GAAAT
1 GAAAT
323303 CTCTGTTAAA
Statistics
Matches: 126, Mismatches: 43, Indels: 20
0.67 0.23 0.11
Matches are distributed among these distances:
28 15 0.12
29 98 0.78
30 13 0.10
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (29 bp):
GAAATACCTTTGTGGCTATCTTTGTTAAA
Found at i:323261 original size:58 final size:58
Alignment explanation
Indices: 323083--323302 Score: 194
Period size: 58 Copynumber: 3.8 Consensus size: 58
323073 TTTTGTGGCA
* * * * * ***
323083 AATCTCTG-AAAGGAAATACCTTTGTGGCGATCTTTGTTAAAGAAGTGCCTCCATGGT
1 AATCTCTGTAAAGGAAACACCTTTGTGGCTATCTTTGTTAAAGAAATACCTCTATAAC
* * * * * * * **
323140 AATGTTTGTAAAGGAAACACCTTTATAGCAATCTTTGTTAAAGAAATGCCTCTGTGGC
1 AATCTCTGTAAAGGAAACACCTTTGTGGCTATCTTTGTTAAAGAAATACCTCTATAAC
* * * * *
323198 TATCTCT-TCAAAGTAAACGCCTTTGT-GTTGATCTCTGTTAAAGAAATACCTCTATAAC
1 AATCTCTGT-AAAGGAAACACCTTTGTGGCT-ATCTTTGTTAAAGAAATACCTCTATAAC
*
323256 AATCTCTGTAAAGGAAACACTTTTGTGGCTATCTTTGTTAAAGAAAT
1 AATCTCTGTAAAGGAAACACCTTTGTGGCTATCTTTGTTAAAGAAAT
323303 CTCTGTTAAA
Statistics
Matches: 129, Mismatches: 29, Indels: 9
0.77 0.17 0.05
Matches are distributed among these distances:
57 8 0.06
58 118 0.91
59 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (58 bp):
AATCTCTGTAAAGGAAACACCTTTGTGGCTATCTTTGTTAAAGAAATACCTCTATAAC
Found at i:323309 original size:15 final size:15
Alignment explanation
Indices: 323286--323336 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
323276 TTTTGTGGCT
*
323286 ATCTTTGTTAAAGAA
1 ATCTCTGTTAAAGAA
323301 ATCTCTGTTAAAGAA
1 ATCTCTGTTAAAGAA
323316 ATCTCTGTTAAAGAA
1 ATCTCTGTTAAAGAA
323331 ATCTCT
1 ATCTCT
323337 ATGACAATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (15 bp):
ATCTCTGTTAAAGAA
Found at i:329097 original size:31 final size:30
Alignment explanation
Indices: 329033--329097 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
329023 GCTTTATTTT
* *
329033 AAAATTATTTTTTGACCTCTAAATTTTCTA
1 AAAATTATTTTTTGACCTCTAAATTTCCAA
*
329063 AAAATTATATTTTTGTCC-CTAAACTTTCCAA
1 AAAATTAT-TTTTTGACCTCTAAA-TTTCCAA
329094 AAAA
1 AAAA
329098 CCAAATTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.43
Consensus pattern (30 bp):
AAAATTATTTTTTGACCTCTAAATTTCCAA
Found at i:329193 original size:30 final size:30
Alignment explanation
Indices: 329043--329197 Score: 140
Period size: 29 Copynumber: 5.2 Consensus size: 30
329033 AAAATTATTT
* * *
329043 TTTGACCTCTAAATTTTCTAAAAATT-ATATT
1 TTTGACCCCTAAACTTTCTAAAAATTCA-A-A
* * **
329074 TTTG-TCCCTAAACTTTCCAAAAAACCAAA
1 TTTGACCCCTAAACTTTCTAAAAATTCAAA
* **
329103 TTTGACCTC-AAACTTTCTAAAAATTTGAA
1 TTTGACCCCTAAACTTTCTAAAAATTCAAA
**
329132 TTTGACCCCT-AACTTTCTAAAAATTTTAA
1 TTTGACCCCTAAACTTTCTAAAAATTCAAA
329161 TTTGACCCCTAAACTTT-TCAAAAATTCAAA
1 TTTGACCCCTAAACTTTCT-AAAAATTCAAA
329191 TTTGACC
1 TTTGACC
329198 TAGTTTTAAT
Statistics
Matches: 101, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
29 56 0.55
30 40 0.40
31 5 0.05
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.38
Consensus pattern (30 bp):
TTTGACCCCTAAACTTTCTAAAAATTCAAA
Found at i:329441 original size:30 final size:29
Alignment explanation
Indices: 329388--329608 Score: 195
Period size: 30 Copynumber: 7.6 Consensus size: 29
329378 GCTTTATTTT
* * *
329388 AAAATTGGTTTTGA-CCATAAACTTTCCA
1 AAAATTTGATTTGACCCCTAAACTTTCCA
*
329416 AAAATTATGTTTTGACCCCTAAACTTTCCA
1 AAAATT-TGATTTGACCCCTAAACTTTCCA
**
329446 AAAATTCAAATTTGACCCC-AAAC-TTCCA
1 AAAATT-TGATTTGACCCCTAAACTTTCCA
*
329474 AAAATTTGAATTTGACCCC--AACTTTCTA
1 AAAATTTG-ATTTGACCCCTAAACTTTCCA
* ** *
329502 AAAATTCTAATTTGACCATTGAAC-TTCC-
1 AAAATT-TGATTTGACCCCTAAACTTTCCA
* *
329530 AAAATTTCGAATTTGACCCCTTAACTTTCTA
1 AAAATTT-G-ATTTGACCCCTAAACTTTCCA
329561 AAAATTTTGATTTGACCCCTAAACTTTCCA
1 AAAA-TTTGATTTGACCCCTAAACTTTCCA
*
329591 AAAATTTAAATTTGACCC
1 AAAATTT-GATTTGACCC
329609 GATTTTAATG
Statistics
Matches: 159, Mismatches: 21, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
27 4 0.03
28 51 0.32
29 30 0.19
30 66 0.42
31 5 0.03
32 3 0.02
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (29 bp):
AAAATTTGATTTGACCCCTAAACTTTCCA
Found at i:333919 original size:30 final size:31
Alignment explanation
Indices: 333850--333922 Score: 82
Period size: 33 Copynumber: 2.4 Consensus size: 31
333840 ATATAATCTA
333850 ATTAAAAT-TTTTAAATAATTAATATTAATT
1 ATTAAAATATTTTAAATAATTAATATTAATT
333880 ACTTAAAAATATTTTAAATTAA-TAAT-TT-ATAT
1 A-TT-AAAATATTTTAAA-TAATTAATATTAAT-T
333912 ATTAAAATATT
1 ATTAAAATATT
333923 AACAATAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
30 9 0.24
31 6 0.16
32 9 0.24
33 11 0.29
34 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (31 bp):
ATTAAAATATTTTAAATAATTAATATTAATT
Found at i:342857 original size:27 final size:26
Alignment explanation
Indices: 342826--342913 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
342816 GACAAGAAGT
342826 ATTAATAATTATTTAAAAATTATAAAA
1 ATTAATAA-TATTTAAAAATTATAAAA
* *
342853 ATTAA-AATATGATAAAAATT-TATAA
1 ATTAATAATAT-TTAAAAATTATAAAA
342878 ATGCTAATAAT-TTTAATAAA-TATATAAA
1 AT--TAATAATATTTAA-AAATTATA-AAA
342906 ATTAATAA
1 ATTAATAA
342914 AAAAGCACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
25 9 0.18
26 20 0.40
27 14 0.28
28 7 0.14
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (26 bp):
ATTAATAATATTTAAAAATTATAAAA
Found at i:342867 original size:17 final size:16
Alignment explanation
Indices: 342838--342872 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
342828 TAATAATTAT
*
342838 TTAAAAATTATAAAAA
1 TTAAAAATGATAAAAA
342854 TTAAAATATGATAAAAA
1 TTAAAA-ATGATAAAAA
342871 TT
1 TT
342873 TATAAATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
TTAAAAATGATAAAAA
Found at i:344464 original size:2 final size:2
Alignment explanation
Indices: 344459--344490 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
344449 ATTGCCGCAA
344459 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
344491 TTCCCTCTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:349069 original size:5 final size:5
Alignment explanation
Indices: 349050--349099 Score: 55
Period size: 5 Copynumber: 10.0 Consensus size: 5
349040 CATACCAGAA
* * ** *
349050 CATAT CTTAT CATAT GATAT CATAT CATAT CGGAT CATAT CATAT TATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
349100 AACGTCCTAC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (5 bp):
CATAT
Found at i:349544 original size:68 final size:68
Alignment explanation
Indices: 349466--349601 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 68
349456 AGCTTATCAA
* *
349466 AACAAATAACAAAATATATATAACACACATGATTTACATAATAATCATACTTAACTCACGTACCT
1 AACAAATAACAAAATATATATAACACACATGATTTACAGAATAAACATACTTAACTCACGTACCT
349531 ACT
66 ACT
*
349534 AACAAATAACAAAATATATATAACACACATGATTTATAGAATAAACATACTTAACTCACGTACCT
1 AACAAATAACAAAATATATATAACACACATGATTTACAGAATAAACATACTTAACTCACGTACCT
349599 ACT
66 ACT
349602 TATAGCAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (68 bp):
AACAAATAACAAAATATATATAACACACATGATTTACAGAATAAACATACTTAACTCACGTACCT
ACT
Found at i:352473 original size:21 final size:20
Alignment explanation
Indices: 352441--352479 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
352431 ATTTAAAGAA
* *
352441 TAATACTACTCATTTATTAT
1 TAATACAACTCAATTATTAT
352461 TAATACAATCTCAATTATT
1 TAATACAA-CTCAATTATT
352480 CATCAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATACAACTCAATTATTAT
Found at i:353229 original size:15 final size:13
Alignment explanation
Indices: 353203--353250 Score: 62
Period size: 12 Copynumber: 3.5 Consensus size: 13
353193 CAGGACAATT
353203 TTTTCTTCCTCTTC
1 TTTTCTT-CTCTTC
353217 ATTTTCATTCTCTTC
1 -TTTTC-TTCTCTTC
353232 TTTTCTT-TCTTC
1 TTTTCTTCTCTTC
353244 TTTTCTT
1 TTTTCTT
353251 TTTTCTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.38
13 2 0.06
14 5 0.16
15 11 0.34
16 2 0.06
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTCTTCTCTTC
Found at i:353244 original size:12 final size:12
Alignment explanation
Indices: 353212--353262 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
353202 TTTTTCTTCC
353212 TCTTCATTTTCATT
1 TCTTC-TTTTC-TT
353226 CTCTTCTTTTCTT
1 -TCTTCTTTTCTT
353239 TCTTCTTTTCTT
1 TCTTCTTTTCTT
*
353251 TTTTCTTCTTCT
1 TCTTCTT-TTCT
353263 AGTTCAATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
12 18 0.53
13 6 0.18
14 5 0.15
15 5 0.15
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (12 bp):
TCTTCTTTTCTT
Found at i:353255 original size:15 final size:16
Alignment explanation
Indices: 353218--353260 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
353208 TTCCTCTTCA
*
353218 TTTTCATTCTCTTCTTT
1 TTTTC-TTCTTTTCTTT
353235 TCTTTCTTCTTTTC-TT
1 T-TTTCTTCTTTTCTTT
353251 TTTTCTTCTT
1 TTTTCTTCTT
353261 CTAGTTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 3 0.12
17 8 0.33
18 4 0.17
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTCTTCTTTTCTTT
Found at i:359352 original size:18 final size:18
Alignment explanation
Indices: 359331--359373 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
359321 ATATGGTTGT
359331 ATCTGATTATATGACTGC
1 ATCTGATTATATGACTGC
* * * *
359349 ATCTAAATATGTGATTGC
1 ATCTGATTATATGACTGC
359367 ATCTGAT
1 ATCTGAT
359374 CAAGTTGCAC
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (18 bp):
ATCTGATTATATGACTGC
Found at i:361849 original size:72 final size:73
Alignment explanation
Indices: 361758--361949 Score: 210
Period size: 73 Copynumber: 2.6 Consensus size: 73
361748 AGAAACAATT
* * * ** * *
361758 AGTTACAC-GACCTGGACACACGGACGTGTGCCGGACTGTGTGGACATTCTG-TTTGTG-AAATA
1 AGTTACACAG-CCTGGACACACGGGCGTGTGCCAGACCGTGTACACATACCGTTTTGTGTAAA-A
361820 AAAAACAGTG
64 AAAAACAGTG
** * * * *
361830 AGTTACATGGGCTGGACACACGGGCGTGTGCCAGACCGTGTACCCATACCGTTTTGTGTGAACAA
1 AGTTACACAGCCTGGACACACGGGCGTGTGCCAGACCGTGTACACATACCGTTTTGTGTAAAAAA
361895 AAACAGTG
66 AAACAGTG
*
361903 AGTTACACAGCCTGGACACACGGGCGTGTGCCAGATCGTGTGACACA
1 AGTTACACAGCCTGGACACACGGGCGTGTGCCAGACCGTGT-ACACA
361950 CACGACCTAA
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
72 39 0.39
73 54 0.55
74 6 0.06
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (73 bp):
AGTTACACAGCCTGGACACACGGGCGTGTGCCAGACCGTGTACACATACCGTTTTGTGTAAAAAA
AAACAGTG
Found at i:362100 original size:39 final size:39
Alignment explanation
Indices: 362046--362171 Score: 171
Period size: 39 Copynumber: 3.2 Consensus size: 39
362036 CTAAACTGGT
*
362046 AGTGACACTGTAAACATTACAATATGCTACTGAACTAGA
1 AGTGACACTGTAAACATTACAATACGCTACTGAACTAGA
* * * *
362085 AGTGACATTGTAAACACTACAATACGCTACTGAACTGGT
1 AGTGACACTGTAAACATTACAATACGCTACTGAACTAGA
* * * *
362124 AGTGACACTGTAAACATTGCAATACACTACTGTACTAGC
1 AGTGACACTGTAAACATTACAATACGCTACTGAACTAGA
362163 AGTGACACT
1 AGTGACACT
362172 AAAAACACTG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (39 bp):
AGTGACACTGTAAACATTACAATACGCTACTGAACTAGA
Found at i:362178 original size:78 final size:78
Alignment explanation
Indices: 362034--362180 Score: 213
Period size: 78 Copynumber: 1.9 Consensus size: 78
362024 GTTATCAATT
** * **
362034 TACTAAACTGGTAGTGACACTGTAAACATTACAATATGCTACTGAACTAGAAGTGACATTGTAAA
1 TACTAAACTGGTAGTGACACTGTAAACATTACAATACACTACTGAACTAGAAGTGACACTAAAAA
362099 CACTACAATACGC
66 CACTACAATACGC
* * * *
362112 TACTGAACTGGTAGTGACACTGTAAACATTGCAATACACTACTGTACTAGCAGTGACACTAAAAA
1 TACTAAACTGGTAGTGACACTGTAAACATTACAATACACTACTGAACTAGAAGTGACACTAAAAA
362177 CACT
66 CACT
362181 GCAAAGAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 60 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (78 bp):
TACTAAACTGGTAGTGACACTGTAAACATTACAATACACTACTGAACTAGAAGTGACACTAAAAA
CACTACAATACGC
Found at i:362184 original size:39 final size:39
Alignment explanation
Indices: 362046--362257 Score: 162
Period size: 39 Copynumber: 5.5 Consensus size: 39
362036 CTAAACTGGT
* * **
362046 AGTGACACTGTAAACATTACAATATGCTACTGAACTAGA
1 AGTGACACTGTAAACACTGCAATACACTACTGAACTAGA
* * * * *
362085 AGTGACATTGTAAACACTACAATACGCTACTGAACTGGT
1 AGTGACACTGTAAACACTGCAATACACTACTGAACTAGA
* * *
362124 AGTGACACTGTAAACATTGCAATACACTACTGTACTAGC
1 AGTGACACTGTAAACACTGCAATACACTACTGAACTAGA
** * * *
362163 AGTGACACTAAAAACACTGCAA-AGAAATACTGAGCT-GA
1 AGTGACACTGTAAACACTGCAATA-CACTACTGAACTAGA
* * ** * *
362201 CCGTGACACTGTAAACACTG-AGTACTGTACT-AAATAGGT
1 -AGTGACACTGTAAACACTGCAATACACTACTGAACTA-GA
362240 AGTGACACTGTAAACACT
1 AGTGACACTGTAAACACT
362258 ACCAGATCGA
Statistics
Matches: 137, Mismatches: 31, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
37 2 0.01
38 24 0.18
39 111 0.81
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (39 bp):
AGTGACACTGTAAACACTGCAATACACTACTGAACTAGA
Found at i:363211 original size:22 final size:21
Alignment explanation
Indices: 363192--363231 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
363182 TTTAATATAA
363192 TTATATAATATTAAA-AATAT
1 TTATATAATATTAAATAATAT
*
363212 TTTTATAATATTAAATAATA
1 TTATATAATATTAAATAATA
363232 ACCAATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATATAATATTAAATAATAT
Done.