Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009233.1 Hibiscus syriacus cultivar Beakdansim tig00112852_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: 663203
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 1 of 3
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--98 Score: 144
Period size: 7 Copynumber: 14.0 Consensus size: 7
1 CCGAGCC
1 CCGAGCC
8 CCGAGCCC
1 CCGAG-CC
16 CCGAG-C
1 CCGAGCC
22 CCGAGCC
1 CCGAGCC
29 CCGAGCC
1 CCGAGCC
36 CCGAGCC
1 CCGAGCC
43 CCGAGCC
1 CCGAGCC
50 CCGAGCC
1 CCGAGCC
57 CCGAGCC
1 CCGAGCC
64 CCGAGCC
1 CCGAGCC
*
71 CTGAGCC
1 CCGAGCC
*
78 CTGAGCC
1 CCGAGCC
*
85 CTGAGCC
1 CCGAGCC
*
92 CTGAGCC
1 CCGAGCC
99 TGAGCCCTCA
Statistics
Matches: 88, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
6 6 0.07
7 75 0.85
8 7 0.08
ACGTcount: A:0.14, C:0.53, G:0.29, T:0.04
Consensus pattern (7 bp):
CCGAGCC
Found at i:113 original size:7 final size:7
Alignment explanation
Indices: 103--173 Score: 121
Period size: 7 Copynumber: 10.6 Consensus size: 7
93 TGAGCCTGAG
103 CCCTCAA
1 CCCTCAA
110 CCCTCAA
1 CCCTCAA
117 CCCTCAA
1 CCCTCAA
124 --CTCAA
1 CCCTCAA
129 -CCTCAA
1 CCCTCAA
135 CCCTCAA
1 CCCTCAA
142 CCCTCAA
1 CCCTCAA
149 CCCTCAA
1 CCCTCAA
156 CCCTCAA
1 CCCTCAA
163 CCCTCAA
1 CCCTCAA
170 CCCT
1 CCCT
174 AGACCCTATA
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.08
6 5 0.08
7 52 0.84
ACGTcount: A:0.28, C:0.56, G:0.00, T:0.15
Consensus pattern (7 bp):
CCCTCAA
Found at i:113 original size:20 final size:21
Alignment explanation
Indices: 59--120 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
49 CCCGAGCCCC
* * *
59 GAGCCCCGAGCCCTGAGCCCT
1 GAGCCCTGAGCCCTCAACCCT
* *
80 GAGCCCTGAGCCCT-GAGCCT
1 GAGCCCTGAGCCCTCAACCCT
* *
100 GAGCCCTCAACCCTCAACCCT
1 GAGCCCTGAGCCCTCAACCCT
121 CAACTCAACC
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.13
Consensus pattern (21 bp):
GAGCCCTGAGCCCTCAACCCT
Found at i:179 original size:7 final size:7
Alignment explanation
Indices: 169--463 Score: 376
Period size: 7 Copynumber: 43.6 Consensus size: 7
159 TCAACCCTCA
169 ACCCTAG
1 ACCCTAG
*
176 ACCCTAT
1 ACCCTAG
183 A-CCTAG
1 ACCCTAG
189 A-CCTAG
1 ACCCTAG
195 A-CCTAG
1 ACCCTAG
201 A-CCTAG
1 ACCCTAG
207 ACCCTAG
1 ACCCTAG
214 ACCCTAG
1 ACCCTAG
221 ACCCT--
1 ACCCTAG
*
226 ACCCTAC
1 ACCCTAG
233 A-CCTAG
1 ACCCTAG
239 A-CCTA-
1 ACCCTAG
* *
244 CCCCTAC
1 ACCCTAG
251 ACCCTAG
1 ACCCTAG
*
258 ACCCTAC
1 ACCCTAG
*
265 ACCCTAC
1 ACCCTAG
272 ACCCTAG
1 ACCCTAG
279 ACCCTAG
1 ACCCTAG
286 ACCCTAG
1 ACCCTAG
293 ACCCTAG
1 ACCCTAG
*
300 ACCCTAC
1 ACCCTAG
*
307 ACCCTAC
1 ACCCTAG
314 ACCCTAG
1 ACCCTAG
*
321 ACCCTAC
1 ACCCTAG
328 ACCCTAG
1 ACCCTAG
335 ACCCTAG
1 ACCCTAG
342 ACCCTAG
1 ACCCTAG
349 ACCCTAG
1 ACCCTAG
356 ACCCTAG
1 ACCCTAG
363 ACCCTAG
1 ACCCTAG
370 ACCCTAG
1 ACCCTAG
377 ACCCTAG
1 ACCCTAG
384 ACCCTAG
1 ACCCTAG
391 ACCCTAG
1 ACCCTAG
398 ACCCTAG
1 ACCCTAG
*
405 ACCCTAA
1 ACCCTAG
*
412 ACCCTAA
1 ACCCTAG
*
419 ACCCTAA
1 ACCCTAG
*
426 ACCCTAA
1 ACCCTAG
*
433 ACCCTAA
1 ACCCTAG
*
440 ACCCTAA
1 ACCCTAG
*
447 ACCCTAA
1 ACCCTAG
454 ACCC-AG
1 ACCCTAG
460 ACCC
1 ACCC
464 CGGACCCCGG
Statistics
Matches: 269, Mismatches: 14, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
5 5 0.02
6 41 0.15
7 223 0.83
ACGTcount: A:0.31, C:0.45, G:0.09, T:0.15
Consensus pattern (7 bp):
ACCCTAG
Found at i:476 original size:14 final size:13
Alignment explanation
Indices: 467--497 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
457 CAGACCCCGG
467 ACCCCGGACCCCA
1 ACCCCGGACCCCA
480 AGCCCCGGACCCCA
1 A-CCCCGGACCCCA
494 ACCC
1 ACCC
498 TAGACCCCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.23, C:0.61, G:0.16, T:0.00
Consensus pattern (13 bp):
ACCCCGGACCCCA
Found at i:519 original size:7 final size:7
Alignment explanation
Indices: 509--553 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
499 AGACCCCGGA
509 CCCGAGC
1 CCCGAGC
516 CCCGAGC
1 CCCGAGC
523 CCCGAGC
1 CCCGAGC
530 CCCGAGC
1 CCCGAGC
537 CCCGAGC
1 CCCGAGC
544 CCCGAGC
1 CCCGAGC
551 CCC
1 CCC
554 AAACCCTGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.13, C:0.60, G:0.27, T:0.00
Consensus pattern (7 bp):
CCCGAGC
Found at i:18657 original size:32 final size:32
Alignment explanation
Indices: 18620--18725 Score: 185
Period size: 32 Copynumber: 3.3 Consensus size: 32
18610 CATAATACAA
* * *
18620 AAATCTAATCTCAAGCTACAACAGTTCTTAAT
1 AAATCTAAGCTCAAGCTACAGCAGTTCTTAGT
18652 AAATCTAAGCTCAAGCTACAGCAGTTCTTAGT
1 AAATCTAAGCTCAAGCTACAGCAGTTCTTAGT
18684 AAATCTAAGCTCAAGCTACAGCAGTTCTTAGT
1 AAATCTAAGCTCAAGCTACAGCAGTTCTTAGT
18716 AAATCTAAGC
1 AAATCTAAGC
18726 AATCTTATCT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 71 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (32 bp):
AAATCTAAGCTCAAGCTACAGCAGTTCTTAGT
Found at i:21251 original size:34 final size:34
Alignment explanation
Indices: 21213--21277 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
21203 CGTCACATCC
21213 AGTAAGGCCATGAGCACACAGCCGAGGAACCGGT
1 AGTAAGGCCATGAGCACACAGCCGAGGAACCGGT
*
21247 AGTAAGGCCCTGAGCACACAGCCGAGGAACC
1 AGTAAGGCCATGAGCACACAGCCGAGGAACC
21278 TCCAAGTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.32, C:0.29, G:0.31, T:0.08
Consensus pattern (34 bp):
AGTAAGGCCATGAGCACACAGCCGAGGAACCGGT
Found at i:21392 original size:24 final size:24
Alignment explanation
Indices: 21365--21455 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
21355 CATAATTCAA
21365 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* * * *
21389 GTCATGTATCAGATTAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAG
21413 GTCAA-TATCATATCAGAATCCAG
1 GTCAAGTATCATATCAGAATCCAG
* *
21436 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAAT
21456 TCAAATTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 19 0.34
24 37 0.66
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAG
Found at i:21455 original size:47 final size:48
Alignment explanation
Indices: 21365--21455 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
21355 CATAATTCAA
* **
21365 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATTAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
*
21413 GTCAA-TATCATATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCATATCAGAATCCAGGTCAGGTATCAGAACAGAAT
21456 TCAAATTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:31858 original size:18 final size:19
Alignment explanation
Indices: 31837--31887 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
31827 AAAACACGTA
31837 AAAAGATAAAAAAAT-AAT
1 AAAAGATAAAAAAATGAAT
31855 AAAA-ATAAACAAAATGAAT
1 AAAAGATAAA-AAAATGAAT
*
31874 AAAATGTTAAAAAA
1 AAAA-GATAAAAAA
31888 CAAAAATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 5 0.18
18 9 0.32
19 7 0.25
20 3 0.11
21 4 0.14
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.18
Consensus pattern (19 bp):
AAAAGATAAAAAAATGAAT
Found at i:32102 original size:16 final size:17
Alignment explanation
Indices: 32070--32108 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
32060 TAATATTAAA
32070 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
32087 AAAATAA-AGTAAAAAT
1 AAAATAATAGAAAAAAT
*
32103 ATAATA
1 AAAATA
32109 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:32113 original size:2 final size:2
Alignment explanation
Indices: 32101--32134 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
32091 TAAAGTAAAA
32101 AT AT A- 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 AT AT A
32135 AATAAAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:32280 original size:21 final size:20
Alignment explanation
Indices: 32254--32311 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 20
32244 ACATATTTAT
*
32254 ATATATATAAAATGATATAAG
1 ATATATATAAAAT-AAATAAG
* *
32275 ATATATATAGAATAAATAAT
1 ATATATATAAAATAAATAAG
32295 ATA-ATAT-AAATAAATAA
1 ATATATATAAAATAAATAA
32312 AAAAACAGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 9 0.27
19 4 0.12
20 8 0.24
21 12 0.36
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
ATATATATAAAATAAATAAG
Found at i:32306 original size:18 final size:18
Alignment explanation
Indices: 32275--32311 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
32265 ATGATATAAG
32275 ATATATATAGAATAAATA
1 ATATATATAGAATAAATA
32293 ATATAATATA-AATAAATA
1 ATAT-ATATAGAATAAATA
32311 A
1 A
32312 AAAAACAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
ATATATATAGAATAAATA
Found at i:33671 original size:36 final size:36
Alignment explanation
Indices: 33621--33730 Score: 129
Period size: 36 Copynumber: 3.1 Consensus size: 36
33611 AAAGGTTGAA
33621 GTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAACTT
1 GTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAACTT
33657 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAAC--
1 GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAACTT
* * * * *
33692 -TTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
33727 GTTT
1 GTTT
33731 AACGTAGAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
33 3 0.05
34 25 0.40
36 29 0.46
37 6 0.10
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:33703 original size:34 final size:34
Alignment explanation
Indices: 33631--33719 Score: 117
Period size: 34 Copynumber: 2.6 Consensus size: 34
33621 GTTTCAAGGA
* *
33631 AAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAG
1 AAACTGTCTCAAGAGAGACAAAAC-T-TTCCAAAAG
33667 AAACTGTCTCAAGAGAGACAAAAAC-TTCCAAAAG
1 AAACTGTCTCAAGAGAGAC-AAAACTTTCCAAAAG
*
33701 AAACTGTCTCAAGGGAGAC
1 AAACTGTCTCAAGAGAGAC
33720 GAAATTTGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
34 25 0.51
36 19 0.39
37 5 0.10
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (34 bp):
AAACTGTCTCAAGAGAGACAAAACTTTCCAAAAG
Found at i:33938 original size:103 final size:101
Alignment explanation
Indices: 33757--34072 Score: 407
Period size: 103 Copynumber: 3.1 Consensus size: 101
33747 AAATATTTTG
* * *
33757 TTTCAAAGGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTATCTCAATGGAGACAAAATTT
1 TTTC-AAGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
*
33822 TGTTTCAAGGGAACATATCTCAAGAGAGACAAAATTCA
64 TGTTTCAAAGGAACATATCTCAAGAGAGACAAAATTCA
* * *
33860 TTTCAATGGAAATGGTTTTCAATGTTTATGTTTCAAGGGAAACTGTCTCAAGGGAGACAAGATTT
1 TTTCAA-GGAAAT-GTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
**
33925 TGTTTCAAAGGAACCGATCTCAAGAGAGACAAAATTCA
64 TGTTTCAAAGGAACATATCTCAAGAGAGACAAAATTCA
* * * *
33963 TTTCAAGTGAAATGTTTTCAATGTTTATGTTTCAAAAGAAACTATCTCAAGAGAGACAAAACTTA
1 TTTCAAG-GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* * * * * **
34028 GTTCCAAAAGAAAATGTCTCAAGGGAGACAAAATTTG
65 GTTTCAAAGGAACATATCTCAAGAGAGACAAAATTCA
34065 TTTCAAGG
1 TTTCAAGG
34073 GAAACATATT
Statistics
Matches: 185, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
101 1 0.01
102 84 0.45
103 100 0.54
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (101 bp):
TTTCAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTG
TTTCAAAGGAACATATCTCAAGAGAGACAAAATTCA
Found at i:34085 original size:20 final size:21
Alignment explanation
Indices: 34046--34086 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34036 AGAAAATGTC
*
34046 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAAACAAAATTTGTT
*
34067 TCAAGGGAAAC-ATATTTGTT
1 TCAAGGGAAACAAAATTTGTT
34087 GAAAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (21 bp):
TCAAGGGAAACAAAATTTGTT
Found at i:43994 original size:32 final size:33
Alignment explanation
Indices: 43958--44048 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
43948 ATTCCCAAAG
* *
43958 ATGCCCCAATATTCGATGTTGAATCT-AAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAAA
*
43990 ATGCCCCAACATTTGATGTTAAATCTCAAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAAA
*
44023 ATTCCCCAACATTTGATGTTGAATCT
1 ATGCCCCAACATTTGATGTTGAATCT
44049 TTAAAGATGC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 23 0.43
33 30 0.57
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (33 bp):
ATGCCCCAACATTTGATGTTGAATCTCAAAAAA
Found at i:47834 original size:69 final size:69
Alignment explanation
Indices: 47718--47855 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 69
47708 TGTCTCTCTC
* *
47718 TTGATGCTCTATGATCTTCGAGTGGAATGATTCAGTGGTTTAAAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGGAATGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
47783 TCAT
66 TCAT
* **
47787 TTGATGCTCTATGATCTTCGAGT-GAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAAT
1 TTGATGCTCTATGATCTTCGAGTGGAA-TGATTCAGTGATTCAAAAATGATTGTGCTTGATCAAT
47851 CTCAT
65 CTCAT
47856 AGTTTGAATC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 3 0.05
69 60 0.95
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGGAATGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
TCAT
Found at i:47956 original size:13 final size:14
Alignment explanation
Indices: 47927--47977 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
47917 TTTTTCTTCA
47927 ATTTTC-CTTTGTT
1 ATTTTCTCTTTGTT
47940 -TTTTCTCTTT-TT
1 ATTTTCTCTTTGTT
47952 ATTTTCTCTTTGCTT
1 ATTTTCTCTTTG-TT
*
47967 TTTTTCTCTTT
1 ATTTTCTCTTT
47978 TTGTTCTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
15 12 0.36
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (14 bp):
ATTTTCTCTTTGTT
Found at i:47969 original size:26 final size:26
Alignment explanation
Indices: 47927--47979 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
47917 TTTTTCTTCA
47927 ATTTTCCTTTG-TTTTTTCTCTTTTT
1 ATTTTCCTTTGCTTTTTTCTCTTTTT
47952 ATTTTCTCTTTGCTTTTTTTCTCTTTTT
1 ATTTTC-CTTTGC-TTTTTTCTCTTTTT
47980 GTTCTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
28 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (26 bp):
ATTTTCCTTTGCTTTTTTCTCTTTTT
Found at i:51237 original size:16 final size:17
Alignment explanation
Indices: 51205--51243 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
51195 TGATATTAAA
51205 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
51222 AAAATAA-AGTAAAAAT
1 AAAATAATAGAAAAAAT
*
51238 ATAATA
1 AAAATA
51244 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:51382 original size:2 final size:2
Alignment explanation
Indices: 51370--51412 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
51360 TTAATACATC
* *
51370 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA -A GA 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
51411 TA
1 TA
51413 ATAAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:51436 original size:14 final size:15
Alignment explanation
Indices: 51370--51435 Score: 75
Period size: 14 Copynumber: 4.5 Consensus size: 15
51360 TTAATACATC
*
51370 TATACATATATAT-A
1 TATAAATATATATAA
*
51384 TATATATATATAT-A
1 TATAAATATATATAA
51398 TATAAGATATATATAA
1 TATAA-ATATATATAA
*
51414 TAAAAATA-ATATAA
1 TATAAATATATATAA
51428 TATAAATA
1 TATAAATA
51436 AATAAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
14 30 0.65
15 11 0.24
16 5 0.11
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (15 bp):
TATAAATATATATAA
Found at i:51823 original size:21 final size:21
Alignment explanation
Indices: 51788--51847 Score: 93
Period size: 21 Copynumber: 2.8 Consensus size: 21
51778 GTTTACAATA
*
51788 GCTTTGCCTTTGTATTTTTCAT
1 GCTTT-CCTCTGTATTTTTCAT
*
51810 GCTTTCCTCTGTATTTTTCGT
1 GCTTTCCTCTGTATTTTTCAT
51831 GCTTTCCTCTGTATTTT
1 GCTTTCCTCTGTATTTT
51848 GTGTGTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 31 0.86
22 5 0.14
ACGTcount: A:0.07, C:0.22, G:0.13, T:0.58
Consensus pattern (21 bp):
GCTTTCCTCTGTATTTTTCAT
Found at i:53501 original size:17 final size:17
Alignment explanation
Indices: 53479--53527 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
53469 AAATTAAGAG
53479 TTAGTTTGATTAATACA
1 TTAGTTTGATTAATACA
* * *
53496 TTAGTTTAATAAATGCA
1 TTAGTTTGATTAATACA
*
53513 CTAGTTTGATTAATA
1 TTAGTTTGATTAATA
53528 AACTAACTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TTAGTTTGATTAATACA
Found at i:53858 original size:24 final size:25
Alignment explanation
Indices: 53802--53858 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
53792 AAGTAAGGTA
*
53802 GAACTTCATTTGAATCACCCTTAGT
1 GAACTTCATTTGAATCACCATTAGT
53827 GAACTTCATTTGAATCACCATTA-T
1 GAACTTCATTTGAATCACCATTAGT
53851 GAACTTCA
1 GAACTTCA
53859 ATAATTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 9 0.29
25 22 0.71
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (25 bp):
GAACTTCATTTGAATCACCATTAGT
Found at i:56527 original size:15 final size:15
Alignment explanation
Indices: 56507--56549 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
56497 TTAATTAAAC
*
56507 CTCTCTCTTCCCTTT
1 CTCTCTCTTCCCCTT
56522 CTCTCTCTTCCCCTT
1 CTCTCTCTTCCCCTT
* *
56537 CCCCCTCTTCCCC
1 CTCTCTCTTCCCC
56550 GTCACTCTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (15 bp):
CTCTCTCTTCCCCTT
Found at i:57166 original size:16 final size:16
Alignment explanation
Indices: 57147--57177 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
57137 AAATTAGCCA
57147 AGTTTACTATTACAGT
1 AGTTTACTATTACAGT
57163 AGTTTACTATTACAG
1 AGTTTACTATTACAG
57178 ACCATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (16 bp):
AGTTTACTATTACAGT
Found at i:68875 original size:22 final size:24
Alignment explanation
Indices: 68830--68878 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
68820 AAAAATTTTA
*
68830 TTTAAAAATAAAAATCATATATTT
1 TTTAAAAATAAAAATCATAAATTT
*
68854 TTTAAAAA-GAAAA-CATAAATTT
1 TTTAAAAATAAAAATCATAAATTT
68876 TTT
1 TTT
68879 TGAAATAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 4 0.17
24 8 0.35
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (24 bp):
TTTAAAAATAAAAATCATAAATTT
Found at i:68879 original size:24 final size:24
Alignment explanation
Indices: 68822--68879 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
68812 GTGATTTTAA
* *
68822 AAATTTTATTTAAAAATAAAAATC
1 AAATTTTTTTTAAAAAGAAAAATC
* *
68846 ATATATTTTTTAAAAAGAAAACAT-
1 AAATTTTTTTTAAAAAGAAAA-ATC
68870 AAATTTTTTT
1 AAATTTTTTT
68880 GAAATAATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (24 bp):
AAATTTTTTTTAAAAAGAAAAATC
Found at i:76268 original size:37 final size:35
Alignment explanation
Indices: 76184--76268 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 35
76174 AAACTTAATG
* *
76184 TTAAATTTTGAATGAGGTATTAAAATGAAATAAACA
1 TTAAATTTT-AATGAGGTACTAAAATGAAATAAAAA
*
76220 CTAAAGTTTTTAATGACGGATACTAAAATGAAATAAAAA
1 TTAAA--TTTTAATGA-GG-TACTAAAATGAAATAAAAA
76259 TTAAATTTTA
1 TTAAATTTTA
76269 GGTAAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
36 4 0.10
37 10 0.24
38 6 0.15
39 21 0.51
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (35 bp):
TTAAATTTTAATGAGGTACTAAAATGAAATAAAAA
Found at i:78049 original size:18 final size:18
Alignment explanation
Indices: 78004--78050 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
77994 CTAATCATAA
78004 TTTTT-TTTCTTTCTATT
1 TTTTTATTTCTTTCTATT
*
78021 TTTTTAATTCTTTCT-TT
1 TTTTTATTTCTTTCTATT
*
78038 TTGTTTGTTTCTT
1 TT-TTTATTTCTT
78051 AGGAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.06, C:0.11, G:0.04, T:0.79
Consensus pattern (18 bp):
TTTTTATTTCTTTCTATT
Found at i:82339 original size:2 final size:2
Alignment explanation
Indices: 82327--82364 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
82317 CTACAAACTA
*
82327 AT AT TT 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
82365 GTTACTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:82601 original size:18 final size:18
Alignment explanation
Indices: 82574--82614 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
82564 ATTAGCGTTA
* *
82574 TTAT-TATTTTTTTTATT
1 TTATATATTTTATTCATT
82591 TTATATATTTTATTCATT
1 TTATATATTTTATTCATT
82609 TTATAT
1 TTATAT
82615 TTACTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATATATTTTATTCATT
Found at i:93911 original size:105 final size:105
Alignment explanation
Indices: 93729--94566 Score: 1276
Period size: 105 Copynumber: 8.0 Consensus size: 105
93719 GGAGGATATC
93729 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* * *
93794 ATTTCGGGGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
93834 ACTCCAGACAATGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTTTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
93899 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
93939 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
*
94004 ATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
94044 ACTCCAGACAACTCAAGTTCAACTTCACGACGAAGGGACCGATGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
*
94109 ATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
94149 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* *
94214 ATTTCAGAGCCAATTTCAACTTTACAGCGAAGGGTATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
94254 ACTCTAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAATAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* *
94319 ATTTCAGAGCCAATTTCAACTTCCCAGTGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
94359 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGATGGTTGTCAAC-A-AAGTT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* *
94420 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAG
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * ** ** *
94459 ACTCGAGACAACACAAGCTCAACTTCAC-AGCGAAGGG-GTGACTGACTGTCAACAAACAATTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGA-CGAAGGGACCG-CTGGTTGTCAAC-AACAACTTC
** * *
94522 CCAATACCAGAACCAATTTCAACTTCACAGCGGAGGATATTGG
63 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
94565 AC
1 AC
94567 GCGGAATAAT
Statistics
Matches: 672, Mismatches: 53, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
99 2 0.00
100 74 0.11
101 1 0.00
102 2 0.00
103 8 0.01
104 2 0.00
105 549 0.82
106 34 0.05
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:95993 original size:13 final size:13
Alignment explanation
Indices: 95975--95999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95965 TTTTGATCCC
95975 CAAATCCAATTTT
1 CAAATCCAATTTT
95988 CAAATCCAATTT
1 CAAATCCAATTT
96000 CCTTTTGATT
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:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (13 bp):
CAAATCCAATTTT
Found at i:96228 original size:2 final size:2
Alignment explanation
Indices: 96205--96246 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
96195 CTACAAACTA
* * *
96205 AT AT TT AT AT AA AT AT AA 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
96247 TACTTTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:96487 original size:9 final size:8
Alignment explanation
Indices: 96461--96502 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 8
96451 ATTAGCGTTA
96461 TTATTATT
1 TTATTATT
*
96469 TTTTTATT
1 TTATTATT
96477 TTATATATT
1 TTAT-TATT
96486 TTATTCATT
1 TTATT-ATT
96495 TTA-TATT
1 TTATTATT
96502 T
1 T
96503 ACTTTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 4 0.13
8 12 0.40
9 14 0.47
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTATT
Found at i:96487 original size:16 final size:18
Alignment explanation
Indices: 96461--96500 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
96451 ATTAGCGTTA
*
96461 TTAT-TATTTT-TTTATT
1 TTATATATTTTATTCATT
96477 TTATATATTTTATTCATT
1 TTATATATTTTATTCATT
96495 TTATAT
1 TTATAT
96501 TTACTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 6 0.29
18 11 0.52
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATATATTTTATTCATT
Found at i:108698 original size:12 final size:12
Alignment explanation
Indices: 108677--108705 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
108667 TTGTCTCGTC
108677 TTCC-TCTAACT
1 TTCCATCTAACT
108688 TTCCATCTAACT
1 TTCCATCTAACT
108700 TTCCAT
1 TTCCAT
108706 ATTCATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (12 bp):
TTCCATCTAACT
Found at i:108933 original size:20 final size:21
Alignment explanation
Indices: 108897--108936 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
108887 ATTTTTGTGA
*
108897 TAAACCGATTAATTCCATTAC
1 TAAACCGATTAAATCCATTAC
108918 TAAACCG-TTAAATCCATTA
1 TAAACCGATTAAATCCATTA
108937 TTAATTACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (21 bp):
TAAACCGATTAAATCCATTAC
Found at i:110308 original size:22 final size:22
Alignment explanation
Indices: 110274--110318 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
110264 ATATAGAGAA
110274 ATATGACACGATTCTTTGGTGT
1 ATATGACACGATTCTTTGGTGT
* * *
110296 ATATGCCATGATTTTTTGGTGT
1 ATATGACACGATTCTTTGGTGT
110318 A
1 A
110319 AGGGTATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (22 bp):
ATATGACACGATTCTTTGGTGT
Found at i:120183 original size:109 final size:109
Alignment explanation
Indices: 119997--120203 Score: 258
Period size: 109 Copynumber: 1.9 Consensus size: 109
119987 AATTATGAAA
* * *
119997 AATATATATTAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTACCTTAAG
1 AATATATATTAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTACCTTAAG
* *
120062 ACAGCTCTTTTCTTCGATATTAAAAAATAAATAATTAAAACAATT
66 ACAGCTCCTTTCTT-AATATTAAAAAATAAATAATTAAAACAATT
* * ***
120107 AATATATAATTTAT-AAA-ATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGTTTTA
1 AATATAT-ATTAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTACCTTA
* *
120170 AGACTG-TCCTTTCTTAATATTGAAAAATAAATAA
64 AGACAGCTCCTTTCTTAATATTAAAAAATAAATAA
120204 ATATTAAAAC
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
108 17 0.20
109 34 0.41
110 27 0.33
111 5 0.06
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (109 bp):
AATATATATTAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTACCTTAAG
ACAGCTCCTTTCTTAATATTAAAAAATAAATAATTAAAACAATT
Found at i:120376 original size:20 final size:20
Alignment explanation
Indices: 120309--120376 Score: 50
Period size: 20 Copynumber: 3.4 Consensus size: 20
120299 TAATAATAGT
*
120309 AATAATAATTAAAAGTA-AACA
1 AATAA-AATTAAAA-TATAATA
* * *
120330 TATAAAATTAACATATAATG
1 AATAAAATTAAAATATAATA
*
120350 AACAAAATTAAAACTAT-ATA
1 AATAAAATTAAAA-TATAATA
120370 AATAAAA
1 AATAAAA
120377 ATTGAAATTA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
19 2 0.06
20 27 0.75
21 7 0.19
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (20 bp):
AATAAAATTAAAATATAATA
Found at i:121618 original size:3 final size:3
Alignment explanation
Indices: 121610--121650 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
121600 GGCCTGTTTG
121610 TAA TAA TAA TAA TAA TAA TATA TAA -AA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA
121651 GAAAATGGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:122240 original size:6 final size:6
Alignment explanation
Indices: 122198--122238 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
122188 CATGTAAAAT
* * *
122198 TATTAA TATTAA TATTAA TATTAA AATTAA AATTAT TATTA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTA
122239 TTTAGCTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
TATTAA
Found at i:127718 original size:17 final size:18
Alignment explanation
Indices: 127696--127729 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
127686 TTATAAAAAC
127696 TTTAAAT-TTTCATATAA
1 TTTAAATATTTCATATAA
*
127713 TTTAAATATTTTATATA
1 TTTAAATATTTCATATA
127730 TGTTATAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAATATTTCATATAA
Found at i:129232 original size:19 final size:19
Alignment explanation
Indices: 129216--129252 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
129206 ATAATGATCG
129216 AATTATATAAAAATGATAA
1 AATTATATAAAAATGATAA
* *
129235 AATTATGTTAAAATGATA
1 AATTATATAAAAATGATA
129253 TTTTAATTAA
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:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (19 bp):
AATTATATAAAAATGATAA
Found at i:131243 original size:20 final size:20
Alignment explanation
Indices: 131218--131266 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
131208 CATAGCTTTG
131218 CTAAGCTTTCAATCATATTC
1 CTAAGCTTTCAATCATATTC
131238 CTAAGCTTTCAATCATATTC
1 CTAAGCTTTCAATCATATTC
131258 CTAAGCTTT
1 CTAAGCTTT
131267 GCTAAGCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (20 bp):
CTAAGCTTTCAATCATATTC
Found at i:133648 original size:39 final size:39
Alignment explanation
Indices: 133574--133751 Score: 115
Period size: 39 Copynumber: 4.3 Consensus size: 39
133564 AAGGACATGC
* * *
133574 GTAAGGACTTATCCTGTGCACAAAGCCGAGAAGCCTGCG
1 GTAAGGACTTACCCTGAGCAAAAAGCCGAGAAGCCTGCG
**
133613 GTAAGGACTTACCCTGAGCAAAAAGTTGAGGAGCCTGGAGCCTGCG
1 GTAAGGACTTACCCTGAGCAAAAAGCCGA-GA------AGCCTGCG
* * * * **
133659 GTAAGGACTTATCCTAAGCACAAAGCCGAGGAGCCCACG
1 GTAAGGACTTACCCTGAGCAAAAAGCCGAGAAGCCTGCG
* * * *
133698 GTAAGGACTTACCTTGGGCACAAAA-CCGAGGAGTCAGCGGCG
1 GTAAGGACTTACCCTGAGCA-AAAAGCCGAGAAG-C--CTGCG
133740 GTAAGGACTTAC
1 GTAAGGACTTAC
133752 AAGTCATAGA
Statistics
Matches: 108, Mismatches: 20, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
39 54 0.50
40 6 0.06
42 15 0.14
45 1 0.01
46 32 0.30
ACGTcount: A:0.30, C:0.24, G:0.30, T:0.16
Consensus pattern (39 bp):
GTAAGGACTTACCCTGAGCAAAAAGCCGAGAAGCCTGCG
Found at i:133690 original size:46 final size:46
Alignment explanation
Indices: 133605--133693 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
133595 AAAGCCGAGA
* **
133605 AGCCTGCGGTAAGGACTTACCCTGAGCAAAAAGTTGAGGAGCCTGG
1 AGCCTGCGGTAAGGACTTACCCTAAGCAAAAAGCCGAGGAGCCTGG
* *
133651 AGCCTGCGGTAAGGACTTATCCTAAGCACAAAGCCGAGGAGCC
1 AGCCTGCGGTAAGGACTTACCCTAAGCAAAAAGCCGAGGAGCC
133694 CACGGTAAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.29, C:0.25, G:0.30, T:0.16
Consensus pattern (46 bp):
AGCCTGCGGTAAGGACTTACCCTAAGCAAAAAGCCGAGGAGCCTGG
Found at i:133729 original size:85 final size:85
Alignment explanation
Indices: 133574--133730 Score: 217
Period size: 85 Copynumber: 1.8 Consensus size: 85
133564 AAGGACATGC
** ** *
133574 GTAAGGACTTATCCTGTGCACAAAGCCGAGAAGCCTGCGGTAAGGACTTACCCTGAGCAAAAAGT
1 GTAAGGACTTATCCTAAGCACAAAGCCGAGAAGCCCACGGTAAGGACTTACCCTGAGCAAAAAGC
*
133639 TGAGGAGCCTGGAGCCTGCG
66 CGAGGAGCCTGGAGCCTGCG
* * *
133659 GTAAGGACTTATCCTAAGCACAAAGCCGAGGAGCCCACGGTAAGGACTTACCTTGGGCACAAAA-
1 GTAAGGACTTATCCTAAGCACAAAGCCGAGAAGCCCACGGTAAGGACTTACCCTGAGCA-AAAAG
133723 CCGAGGAG
65 CCGAGGAG
133731 TCAGCGGCGG
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 58 0.94
86 4 0.06
ACGTcount: A:0.31, C:0.24, G:0.29, T:0.16
Consensus pattern (85 bp):
GTAAGGACTTATCCTAAGCACAAAGCCGAGAAGCCCACGGTAAGGACTTACCCTGAGCAAAAAGC
CGAGGAGCCTGGAGCCTGCG
Found at i:155792 original size:17 final size:15
Alignment explanation
Indices: 155769--155809 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
155759 AATCAAGTAG
155769 TTTTAAAATATATATT
1 TTTTAAAATATA-ATT
*
155785 TTTATAAAATTTAATT
1 TTT-TAAAATATAATT
155801 TTTTAAAAT
1 TTTTAAAAT
155810 GTTTAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 9 0.39
17 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTAAAATATAATT
Found at i:156254 original size:24 final size:24
Alignment explanation
Indices: 156205--156254 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
156195 CACGAACGAC
*
156205 TATTAGAGATGAATAAAGAATGAT
1 TATTAGAGATGAATAAAGAATAAT
* * *
156229 TATTAGTGATGAATGAAGATTAAT
1 TATTAGAGATGAATAAAGAATAAT
156253 TA
1 TA
156255 ATAACTATGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (24 bp):
TATTAGAGATGAATAAAGAATAAT
Found at i:157179 original size:18 final size:17
Alignment explanation
Indices: 157137--157184 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
157127 GATTGTTAAT
*
157137 GGTGAGAAAGAAAAGGA
1 GGTGAGGAAGAAAAGGA
157154 GGTGGAGGAAGAAAAGGA
1 GGT-GAGGAAGAAAAGGA
157172 GGATGAGG-AGAAA
1 GG-TGAGGAAGAAA
157185 GTTGTGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 8 0.29
18 19 0.68
19 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.46, T:0.06
Consensus pattern (17 bp):
GGTGAGGAAGAAAAGGA
Found at i:164539 original size:59 final size:59
Alignment explanation
Indices: 164466--164577 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 59
164456 GCACTAACCA
* *
164466 TATTCTCTTCCATGCAAACTAATGAAGGTTATTATAAGTATAGACAATTGAATGAACTG
1 TATTCTCTCCCATGCAAACTAATGAAGGTAATTATAAGTATAGACAATTGAATGAACTG
* *
164525 TATTCTCTCCCATGCAAACTAATGAAGGTAATTGTTAGTATAGACAATTGAAT
1 TATTCTCTCCCATGCAAACTAATGAAGGTAATTATAAGTATAGACAATTGAAT
164578 TTGTTAAAGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (59 bp):
TATTCTCTCCCATGCAAACTAATGAAGGTAATTATAAGTATAGACAATTGAATGAACTG
Found at i:166264 original size:103 final size:103
Alignment explanation
Indices: 166085--166312 Score: 438
Period size: 103 Copynumber: 2.2 Consensus size: 103
166075 CGTAACATAA
*
166085 AATTTTGTGTCTGTTTTTAATGTACTATGTATACTCTTTAAGATTTTCGATAGTTAGGGAAGAGA
1 AATTTTGTGTCCGTTTTTAATGTACTATGTATACTCTTTAAGATTTTCGATAGTTAGGGAAGAGA
166150 AAATTCAGACCAAAAGATAATGTTTATGTTGATATTCC
66 AAATTCAGACCAAAAGATAATGTTTATGTTGATATTCC
*
166188 AATTTTGTGTCCGTTTTTAATGTACTATGTATACTCTTTAAGATTTTCGATATTTAGGGAAGAGA
1 AATTTTGTGTCCGTTTTTAATGTACTATGTATACTCTTTAAGATTTTCGATAGTTAGGGAAGAGA
166253 AAATTCAGACCAAAAGATAATGTTTATGTTGATATTCC
66 AAATTCAGACCAAAAGATAATGTTTATGTTGATATTCC
166291 AATTTTGTGTCCGTTTTTAATG
1 AATTTTGTGTCCGTTTTTAATG
166313 GCTAACGACG
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 123 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (103 bp):
AATTTTGTGTCCGTTTTTAATGTACTATGTATACTCTTTAAGATTTTCGATAGTTAGGGAAGAGA
AAATTCAGACCAAAAGATAATGTTTATGTTGATATTCC
Found at i:177337 original size:30 final size:28
Alignment explanation
Indices: 177259--177396 Score: 100
Period size: 29 Copynumber: 4.7 Consensus size: 28
177249 TGAAAAATTG
* *
177259 AATACTTTAGGTACATATTTTGACAAAAA
1 AATACTTTAGATACTTATTTTGA-AAAAA
* * * *
177288 AATATTTTGGGTA-TCTATTTTGACCAAAA
1 AATACTTTAGATACT-TATTTTGA-AAAAA
*
177317 AATAACTTTAGATACTTATTTTGAATAAA
1 AAT-ACTTTAGATACTTATTTTGAAAAAA
* **
177346 AATACGTTAGATACTTA-AATGAAAAATATA
1 AATACTTTAGATACTTATTTTG-AAAA-A-A
177376 ATATACTTTAGATACTTATTT
1 A-ATACTTTAGATACTTATTT
177397 GTTATATAGG
Statistics
Matches: 85, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
27 2 0.02
28 16 0.19
29 34 0.40
30 17 0.20
31 16 0.19
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (28 bp):
AATACTTTAGATACTTATTTTGAAAAAA
Found at i:178027 original size:59 final size:56
Alignment explanation
Indices: 177948--178081 Score: 144
Period size: 59 Copynumber: 2.3 Consensus size: 56
177938 GTAACATCTA
* * * *
177948 TCAAATTTAGGTACCAAATT-GAATAAAAAAATACAGGTACAGCATTATGAAAAAAACTG
1 TCAAATTCAGGTACTAAATTGGAA-AAAAAAACACAAGTACAGCATTA-G--AAAAACTG
* * * *
178007 TCAAATTCATGTACTAAATTGGAAAGAAAAACACAAGTACCGCATTAGAAAAAGTG
1 TCAAATTCAGGTACTAAATTGGAAAAAAAAACACAAGTACAGCATTAGAAAAACTG
*
178063 TCAAAATCAGGTACTAAAT
1 TCAAATTCAGGTACTAAAT
178082 GATGCATTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
56 24 0.38
58 1 0.02
59 36 0.56
60 3 0.05
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.23
Consensus pattern (56 bp):
TCAAATTCAGGTACTAAATTGGAAAAAAAAACACAAGTACAGCATTAGAAAAACTG
Found at i:182384 original size:86 final size:86
Alignment explanation
Indices: 182236--182409 Score: 303
Period size: 86 Copynumber: 2.0 Consensus size: 86
182226 GAGAAAATAT
* ** * *
182236 CTACCATAGAAGCCAATTCCAAGTTGGACCAATTGACGGTTGATAAAATAGAATAATGTCAGAGT
1 CTACCATAGAAGCCAATCCCAAGTTGGACCAATTGACGGCAGATAAAATAGAATAATATCAGAGC
182301 TCGAGAACTATTTATTTTGAA
66 TCGAGAACTATTTATTTTGAA
182322 CTACCATAGAAGCCAATCCCAAGTTGGACCAATTGACGGCAGATAAAATAGAATAATATCAGAGC
1 CTACCATAGAAGCCAATCCCAAGTTGGACCAATTGACGGCAGATAAAATAGAATAATATCAGAGC
182387 TCGAGAACTATTTATTTTGAA
66 TCGAGAACTATTTATTTTGAA
182408 CT
1 CT
182410 CTTTGATTAG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (86 bp):
CTACCATAGAAGCCAATCCCAAGTTGGACCAATTGACGGCAGATAAAATAGAATAATATCAGAGC
TCGAGAACTATTTATTTTGAA
Found at i:192632 original size:12 final size:12
Alignment explanation
Indices: 192615--192641 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
192605 TAGATATTAT
192615 TTTGAATTTAGA
1 TTTGAATTTAGA
192627 TTTGAATTTAGA
1 TTTGAATTTAGA
192639 TTT
1 TTT
192642 TTTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (12 bp):
TTTGAATTTAGA
Found at i:192643 original size:26 final size:24
Alignment explanation
Indices: 192614--192675 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
192604 TTAGATATTA
*
192614 TTTTGAATTTAGATTTGAATTTAGAT
1 TTTTGAATTTA-ATTT-AATATAGAT
* *
192640 TTTTTAATTTAATTTAATATATAT
1 TTTTGAATTTAATTTAATATAGAT
*
192664 TTTT-ATTTTAAT
1 TTTTGAATTTAAT
192676 CTACGTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 7 0.22
24 11 0.34
25 4 0.12
26 10 0.31
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTTGAATTTAATTTAATATAGAT
Found at i:208598 original size:24 final size:25
Alignment explanation
Indices: 208568--208616 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
208558 ATTGTTAATG
208568 AATAAGGTAA-GTTTTTCATTCTAT
1 AATAAGGTAAGGTTTTTCATTCTAT
*
208592 AATAAGGTAATGGTTTTTTATTCTA
1 AATAAGGTAA-GGTTTTTCATTCTA
208617 AACTAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
26 12 0.55
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (25 bp):
AATAAGGTAAGGTTTTTCATTCTAT
Found at i:217119 original size:59 final size:60
Alignment explanation
Indices: 217023--217154 Score: 164
Period size: 59 Copynumber: 2.2 Consensus size: 60
217013 AATTTAGGGT
217023 AAAGTATAC-AAATGGTCCCTCGACTATAGGATATTGCTTTATTGAGTCACC-CAACTAATA
1 AAAGT-TACAAAATGGTCCCTCGACTATAGGATATTGCTTTATTGAGTC-CCTCAACTAATA
* * ** *
217083 AAAGTTACAAAATGGT-TCTCGACTATAGGA-AGTTGCTTTGTTGAGTCCCTTGACTATTA
1 AAAGTTACAAAATGGTCCCTCGACTATAGGATA-TTGCTTTATTGAGTCCCTCAACTAATA
217142 AAAGTTACAAAAT
1 AAAGTTACAAAAT
217155 AGTCACTCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
58 3 0.05
59 49 0.77
60 12 0.19
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCTCGACTATAGGATATTGCTTTATTGAGTCCCTCAACTAATA
Found at i:217449 original size:60 final size:60
Alignment explanation
Indices: 217383--217515 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 60
217373 TCGAGTGACT
* * * *
217383 ATTTTGTAACTTTTAATAGTCGATGGACTT-AATGAAA-CAACT-TTCTATAGTTAGGGGACC
1 ATTTTGTAACTTTTAATAGTCAAGGGA-TTCAAT-AAAGCAA-TATCCTATAGTTAAGGGACC
*
217443 ATTTTGTTACTTTTAATAGTCAAGGGATTCAATAAAGCAATATCCTATAGTTAAGGGACC
1 ATTTTGTAACTTTTAATAGTCAAGGGATTCAATAAAGCAATATCCTATAGTTAAGGGACC
217503 A-TTTGTATACTTT
1 ATTTTGTA-ACTTT
217516 ACCCTAAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
59 11 0.17
60 52 0.83
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTCAAGGGATTCAATAAAGCAATATCCTATAGTTAAGGGACC
Found at i:217690 original size:176 final size:176
Alignment explanation
Indices: 217382--217704 Score: 493
Period size: 176 Copynumber: 1.8 Consensus size: 176
217372 GTCGAGTGAC
* *
217382 TATTTTGTAACTTTTAATAGTCGATGGACTTAATGAAACAACTTTCTATAGTTAGGGGACCATTT
1 TATTTTGTAACTTTTAATAGTCGAGGGACTCAATGAAACAACTTTCTATAGTTAGGGGACCATTT
* * * * *
217447 TGTTACTTTTAATAGTCAAGGGATTCAATAAAGCAATATCCTATAGTTAAGGGACCATTTGTATA
66 TGTTAATTTTAATAGTCAAGAGACTCAAAAAAGCAATATCCTATAGTCAAGGGACCATTTGTATA
*
217512 CTTTACCCTAAATTTTAAATATTAAATTATGAGATATATAAATAAA
131 CTTTACCCTAAAATTTAAATATTAAATTATGAGATATATAAATAAA
* *
217558 TATTTTGTAACTTTTAATAGTCGAGGGACTCAATGAAGCAACTTTCTATAGTTGGGGGACCATTT
1 TATTTTGTAACTTTTAATAGTCGAGGGACTCAATGAAACAACTTTCTATAGTTAGGGGACCATTT
* * * ** * *
217623 TGTTAATTTTAATAGTTAAGAGACTCAAAAAAGTAATATCTTATAGTCGGGGGACCGTTTTTATA
66 TGTTAATTTTAATAGTCAAGAGACTCAAAAAAGCAATATCCTATAGTCAAGGGACCATTTGTATA
217688 CTTTACCCTAAAATTTA
131 CTTTACCCTAAAATTTA
217705 TAATCCGGGT
Statistics
Matches: 130, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
176 130 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (176 bp):
TATTTTGTAACTTTTAATAGTCGAGGGACTCAATGAAACAACTTTCTATAGTTAGGGGACCATTT
TGTTAATTTTAATAGTCAAGAGACTCAAAAAAGCAATATCCTATAGTCAAGGGACCATTTGTATA
CTTTACCCTAAAATTTAAATATTAAATTATGAGATATATAAATAAA
Found at i:221366 original size:31 final size:31
Alignment explanation
Indices: 221326--221384 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
221316 GAACGGTCCT
*
221326 TAATGTTATCGAT-TAGTTCGATTTTAGTATC
1 TAATATTATCGATCT-GTTCGATTTTAGTATC
*
221357 TAATATTATCGATCTGTTTGATTTTAGT
1 TAATATTATCGATCTGTTCGATTTTAGT
221385 CCCTTACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.51
Consensus pattern (31 bp):
TAATATTATCGATCTGTTCGATTTTAGTATC
Found at i:224557 original size:13 final size:13
Alignment explanation
Indices: 224539--224595 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
224529 TCAGTATATG
224539 TTCATTCGTTATA
1 TTCATTCGTTATA
*
224552 TTCATTCATT-TA
1 TTCATTCGTTATA
* *
224564 -T-ATCCGTATATG
1 TTCATTCGT-TATA
224576 TTCATTCGTTATA
1 TTCATTCGTTATA
224589 TTCATTC
1 TTCATTC
224596 ATTTATGTCC
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
10 4 0.12
11 2 0.06
12 3 0.09
13 20 0.59
14 5 0.15
ACGTcount: A:0.23, C:0.18, G:0.07, T:0.53
Consensus pattern (13 bp):
TTCATTCGTTATA
Found at i:224561 original size:37 final size:37
Alignment explanation
Indices: 224505--224615 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
224495 CGGTAATCCG
* * *
224505 TTCGTTTATGTTCGTTCATTTATGTCAGTATATGTTCA
1 TTCG-TTATATTCATTCATTTATGTCCGTATATGTTCA
*
224543 TTCGTTATATTCATTCATTTATATCCGTATATGTTCA
1 TTCGTTATATTCATTCATTTATGTCCGTATATGTTCA
*
224580 TTCGTTATATTCATTCATTTATGTCCGTGTATGTTC
1 TTCGTTATATTCATTCATTTATGTCCGTATATGTTC
224616 GTTTATATTC
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
37 63 0.94
38 4 0.06
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (37 bp):
TTCGTTATATTCATTCATTTATGTCCGTATATGTTCA
Found at i:224794 original size:23 final size:23
Alignment explanation
Indices: 224759--224820 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
224749 ACTTAAATAA
224759 TTTAT-TTTCATTTATTGTGTTCG
1 TTTATGTTT-ATTTATTGTGTTCG
*
224782 TTTATGTTTATTTATTGTGTTTG
1 TTTATGTTTATTTATTGTGTTCG
*
224805 TTTACGTTTATTTATT
1 TTTATGTTTATTTATT
224821 ATATTTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 33 0.92
24 3 0.08
ACGTcount: A:0.15, C:0.05, G:0.13, T:0.68
Consensus pattern (23 bp):
TTTATGTTTATTTATTGTGTTCG
Found at i:224827 original size:23 final size:23
Alignment explanation
Indices: 224781--224832 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
224771 TATTGTGTTC
* * *
224781 GTTTATGTTTATTTATTGTGTTT
1 GTTTACGTTTATTTATTATATTT
224804 GTTTACGTTTATTTATTATATTT
1 GTTTACGTTTATTTATTATATTT
224827 GTTTAC
1 GTTTAC
224833 ATATGCTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.04, G:0.13, T:0.65
Consensus pattern (23 bp):
GTTTACGTTTATTTATTATATTT
Found at i:225605 original size:38 final size:38
Alignment explanation
Indices: 225563--225635 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
225553 CAGAAATTTC
* *
225563 TAGAATTAGGACTCAGGAAAGGATAGTCTAATTACTTA
1 TAGAATTAGAACTCAGGAAAGAATAGTCTAATTACTTA
* * *
225601 TAGAATTAGAACTCGGGAAATAATAGTCTACTTAC
1 TAGAATTAGAACTCAGGAAAGAATAGTCTAATTAC
225636 AAGGTAGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (38 bp):
TAGAATTAGAACTCAGGAAAGAATAGTCTAATTACTTA
Found at i:228735 original size:30 final size:31
Alignment explanation
Indices: 228688--228755 Score: 120
Period size: 30 Copynumber: 2.2 Consensus size: 31
228678 TTAACATGCT
*
228688 ATGCTAATGAGTAATGACCACGAAGCTTAAC
1 ATGCTAATGACTAATGACCACGAAGCTTAAC
228719 ATGCTAATG-CTAATGACCACGAAGCTTAAC
1 ATGCTAATGACTAATGACCACGAAGCTTAAC
228749 ATGCTAA
1 ATGCTAA
228756 AATCTTGAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 27 0.75
31 9 0.25
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (31 bp):
ATGCTAATGACTAATGACCACGAAGCTTAAC
Found at i:228794 original size:18 final size:18
Alignment explanation
Indices: 228768--228810 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
228758 TCTTGAGCGC
*
228768 AACTTTTCTGATTACCAA
1 AACTATTCTGATTACCAA
228786 AACTATTCTGATTACCAA
1 AACTATTCTGATTACCAA
228804 AACTATT
1 AACTATT
228811 AACATCAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (18 bp):
AACTATTCTGATTACCAA
Found at i:240267 original size:18 final size:18
Alignment explanation
Indices: 240234--240268 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
240224 AAAATCGGTT
* *
240234 AATTAACCGAATTTATTG
1 AATTAACCAAAATTATTG
240252 AATTAACCAAAATTATT
1 AATTAACCAAAATTATT
240269 AAATATTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTAACCAAAATTATTG
Found at i:254101 original size:40 final size:40
Alignment explanation
Indices: 254002--254101 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
253992 ATCAAAGTTA
* *
254002 AAGGACCACAAAGTAAAAAATAGTAATTATTACCAAAATT
1 AAGGACCACGAAGTAAAAAATAGTAATCATTACCAAAATT
* * * *
254042 AAGGACTACTG-TGTTAAAAATAGTTATCATTACCAAAATT
1 AAGGACCAC-GAAGTAAAAAATAGTAATCATTACCAAAATT
254082 AAGGACCACGAAGTAAAAAA
1 AAGGACCACGAAGTAAAAAA
254102 ATGAAAAAGG
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
39 1 0.02
40 48 0.98
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (40 bp):
AAGGACCACGAAGTAAAAAATAGTAATCATTACCAAAATT
Found at i:255327 original size:7 final size:7
Alignment explanation
Indices: 255315--255349 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
255305 AAATGGAGAA
255315 GACGAAG
1 GACGAAG
255322 GACGAAG
1 GACGAAG
255329 GACGAAG
1 GACGAAG
255336 GACGAAG
1 GACGAAG
255343 GACGAAG
1 GACGAAG
255350 AAATGACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.43, T:0.00
Consensus pattern (7 bp):
GACGAAG
Found at i:255693 original size:12 final size:12
Alignment explanation
Indices: 255665--255699 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
255655 TGTTGGGTTA
255665 GTTTTTGTCAAC
1 GTTTTTGTCAAC
255677 G-TTTTGTCAAC
1 GTTTTTGTCAAC
255688 GTTTTTGTCAAC
1 GTTTTTGTCAAC
255700 CCTAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (12 bp):
GTTTTTGTCAAC
Found at i:259295 original size:19 final size:19
Alignment explanation
Indices: 259271--259310 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
259261 TAAGTAGATT
259271 TCCTTAAATTCATTCGATC
1 TCCTTAAATTCATTCGATC
259290 TCCTTAAATTCATTCGATC
1 TCCTTAAATTCATTCGATC
259309 TC
1 TC
259311 GAGTATCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.05, T:0.42
Consensus pattern (19 bp):
TCCTTAAATTCATTCGATC
Found at i:260894 original size:3 final size:3
Alignment explanation
Indices: 260888--260918 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
260878 TTATTAGGAA
260888 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
260919 ATTGTGTAAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:261086 original size:16 final size:16
Alignment explanation
Indices: 261065--261097 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
261055 CGACGAACGG
261065 TGATGAACACCACTAA
1 TGATGAACACCACTAA
*
261081 TGATGAACACCATTAA
1 TGATGAACACCACTAA
261097 T
1 T
261098 TTAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.24
Consensus pattern (16 bp):
TGATGAACACCACTAA
Found at i:263047 original size:2 final size:2
Alignment explanation
Indices: 263040--263065 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
263030 ACGGTATTTA
263040 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
263066 TAGTTGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:267025 original size:3 final size:3
Alignment explanation
Indices: 267017--267054 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
267007 TCATAGCGCT
267017 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
267055 GTTTTTTTTG
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:269904 original size:2 final size:2
Alignment explanation
Indices: 269867--269891 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
269857 TATCACATAA
269867 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 A
269892 CACACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:271782 original size:29 final size:30
Alignment explanation
Indices: 271720--271801 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 30
271710 TAACCTTATT
*
271720 CTGATTCTGTATGTGATTATAT-CCTAGTC
1 CTGATTCTGTATGAGATTATATCCCTAGTC
* * *
271749 TTGATTTTGTATGAGATTATATCCCT-TTC
1 CTGATTCTGTATGAGATTATATCCCTAGTC
* *
271778 CTGATTCTGCAT-AGATCATATCCC
1 CTGATTCTGTATGAGATTATATCCC
271802 CGTCCTATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
28 11 0.25
29 30 0.68
30 3 0.07
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.44
Consensus pattern (30 bp):
CTGATTCTGTATGAGATTATATCCCTAGTC
Found at i:274808 original size:42 final size:41
Alignment explanation
Indices: 274749--274872 Score: 151
Period size: 42 Copynumber: 3.0 Consensus size: 41
274739 TTTAATCCTT
*
274749 TGGATTTCTGCTTCCGTAGCGTCCATATCTTTCATGAATTTC
1 TGGATTTCTGCTTCCGTAGCATCCATATCTTTCAT-AATTTC
* *
274791 TGGATTTCAGCTTCCGTAGCAAT-CATATCTTCCATAAATTTC
1 TGGATTTCTGCTTCCGTAGC-ATCCATATCTTTCAT-AATTTC
* * * *
274833 TGGATTTCTGCTTCAGGAGCACCCGTATCTTTCATAATTT
1 TGGATTTCTGCTTCCGTAGCATCCATATCTTTCATAATTT
274873 TTTGGAGTTC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 6 0.09
42 63 0.90
43 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (41 bp):
TGGATTTCTGCTTCCGTAGCATCCATATCTTTCATAATTTC
Found at i:275551 original size:32 final size:32
Alignment explanation
Indices: 275505--275573 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
275495 TTCAGATCAA
*
275505 AAATAGAAAGGAAC-AGACAAGTCAACAGCGCC
1 AAATAGAAAGGAACAAG-CAAGTCAACAGCACC
* *
275537 AAATTGAAAGGAACAAGCAAGTCAACGGCACC
1 AAATAGAAAGGAACAAGCAAGTCAACAGCACC
275569 AAATA
1 AAATA
275574 TCTTCCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.09
Consensus pattern (32 bp):
AAATAGAAAGGAACAAGCAAGTCAACAGCACC
Found at i:282704 original size:34 final size:34
Alignment explanation
Indices: 282661--282763 Score: 206
Period size: 34 Copynumber: 3.0 Consensus size: 34
282651 TCACTAGAGT
282661 TATGCGAACTTTTCAATTTTGGTTGGCTATGGAA
1 TATGCGAACTTTTCAATTTTGGTTGGCTATGGAA
282695 TATGCGAACTTTTCAATTTTGGTTGGCTATGGAA
1 TATGCGAACTTTTCAATTTTGGTTGGCTATGGAA
282729 TATGCGAACTTTTCAATTTTGGTTGGCTATGGAA
1 TATGCGAACTTTTCAATTTTGGTTGGCTATGGAA
282763 T
1 T
282764 TGTATATACA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (34 bp):
TATGCGAACTTTTCAATTTTGGTTGGCTATGGAA
Found at i:283080 original size:23 final size:23
Alignment explanation
Indices: 283028--283082 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
283018 AATTTTAATA
*
283028 AAAATATTAATTATTAACATATTT
1 AAAATA-TATTTATTAACATATTT
*
283052 AAAATATATTTATTAATAT-TTT
1 AAAATATATTTATTAACATATTT
283074 AATAATATA
1 AA-AATATA
283083 ATATAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 5 0.18
23 17 0.61
24 6 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATATATTTATTAACATATTT
Found at i:284384 original size:7 final size:8
Alignment explanation
Indices: 284360--284387 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
284350 TCAATTTGAA
284360 TTGAATTT
1 TTGAATTT
284368 TTGAATTT
1 TTGAATTT
284376 TTGAATTT
1 TTGAATTT
284384 TTGA
1 TTGA
284388 GTTACTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (8 bp):
TTGAATTT
Found at i:284807 original size:158 final size:157
Alignment explanation
Indices: 284500--284865 Score: 479
Period size: 158 Copynumber: 2.3 Consensus size: 157
284490 TTTATTAAAA
* *
284500 TTGAACCACAAGCTCCTAAACCATAGTATAATACATGTGTACTTTAAATTCCTCTTTTTGATAAA
1 TTGAACCACATGCTCCTAAACCATAGTAGAATACATGTGTACTTT-AATTCCTCTTTTTGATAAA
*
284565 AATATTTTATTTTTCAATTTAGTCCTTAAATTTGTTATAATCTCCTTATTTCTTCAATTCGTCAT
65 AATATTTTATTTTTCAATTTAGTCCTTAAATTTGTTATAATCTCCTTATTCCTTCAATTCGTCAT
*
284630 TTATTTTAAATATA-TTTTTTACCAAAT
130 TTATTTCAAATATATTTTTTTACCAAAT
* **
284657 TTTAGTCACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAAC
1 TTGAACCACATGCTCCTAAACCATAGTAGAATACATGTGTACTTT-AATTCCTCTTTTTGATAA-
* * * * *
284722 AAATTTTTTATTTTTCAATTTAGTCCTTCAATTT-TTCATAATCTCCTTATTCCTTTAATTTGTG
64 AAATATTTTATTTTTCAATTTAGTCCTTAAATTTGTT-ATAATCTCCTTATTCCTTCAATTCGTC
* *
284786 ATTTATTTCAAGTCA-CTTTTTTTACCAAAT
128 ATTTATTTCAAAT-ATATTTTTTTACCAAAT
* * * *
284816 TTGAACCACATGCTCATATACCACAATAGAATAC-TCGTGTAACTTTAATT
1 TTGAACCACATGCTCCTAAACCATAGTAGAATACAT-GTGT-ACTTTAATT
284866 TTTTTAACTA
Statistics
Matches: 181, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
157 60 0.33
158 67 0.37
159 49 0.27
160 5 0.03
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (157 bp):
TTGAACCACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTAATTCCTCTTTTTGATAAAA
ATATTTTATTTTTCAATTTAGTCCTTAAATTTGTTATAATCTCCTTATTCCTTCAATTCGTCATT
TATTTCAAATATATTTTTTTACCAAAT
Found at i:284894 original size:158 final size:157
Alignment explanation
Indices: 284486--284865 Score: 394
Period size: 157 Copynumber: 2.4 Consensus size: 157
284476 TTTTAAGTCA
** * * * * * * *
284486 ATTTTTTATTAAAATTGAACCACAAGCTCCTAAACCATAGTATAATACATGTGTACTTTAAATTC
1 ATTTTTTACCAAATTTGAACCACATGCTCATAAACCACAATAGAATACATGTGTACTTTCAATT-
* *
284551 CTCTTTTTGATAA-AAA-TATTTTATTTTTCAATTTAGTCCTTAAATTTGTTATAATCTCCTTAT
65 CTCTTTTTAATAACAAATTA-TCTATTTTTCAATTTAGTCCTTAAATTTGTTATAATCTCCTTAT
* *
284614 TTCTTCAATTCGTCATTTATTTTAAATAT
129 TCCTTCAATTCGTCATTTATTTCAAATAT
* ** * * *
284643 ATTTTTTACCAAATTTTAGTCACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTC
1 ATTTTTTACCAAATTTGAACCACATGCTCATAAACCACAATAGAATACATGTGTACTTTCAATT-
* * * *
284708 CTCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTT-TTCATAATCTCCTTAT
65 CTCTTTTTAATAACAAATTATCTATTTTTCAATTTAGTCCTTAAATTTGTT-ATAATCTCCTTAT
* * * *
284772 TCCTTTAATTTGTGATTTATTTCAAGTCACT
129 TCCTTCAATTCGTCATTTATTTCAAAT-A-T
*
284803 -TTTTTTACCAAATTTGAACCACATGCTCATATACCACAATAGAATAC-TCGTGTAACTTT-AAT
1 ATTTTTTACCAAATTTGAACCACATGCTCATAAACCACAATAGAATACAT-GTGT-ACTTTCAAT
284865 T
64 T
284866 TTTTTAACTA
Statistics
Matches: 192, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
157 71 0.37
158 65 0.34
159 50 0.26
160 6 0.03
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.46
Consensus pattern (157 bp):
ATTTTTTACCAAATTTGAACCACATGCTCATAAACCACAATAGAATACATGTGTACTTTCAATTC
TCTTTTTAATAACAAATTATCTATTTTTCAATTTAGTCCTTAAATTTGTTATAATCTCCTTATTC
CTTCAATTCGTCATTTATTTCAAATAT
Found at i:285070 original size:20 final size:21
Alignment explanation
Indices: 285031--285096 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 21
285021 TTCTTTAAAA
285031 TATAATATTATGAATATATTT
1 TATAATATTATGAATATATTT
* *
285052 TATAATTTTA-GATTATATTT
1 TATAATATTATGAATATATTT
* *
285072 GAT-ATATTA--AATA-ATAT
1 TATAATATTATGAATATATTT
285089 TATAATAT
1 TATAATAT
285097 GAAAGAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
17 5 0.14
18 7 0.19
19 5 0.14
20 11 0.30
21 9 0.24
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (21 bp):
TATAATATTATGAATATATTT
Found at i:292448 original size:24 final size:24
Alignment explanation
Indices: 292411--292459 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
292401 AAATGCATAA
292411 AAAGAAGAACTCCATGTCTGTTTT
1 AAAGAAGAACTCCATGTCTGTTTT
* *
292435 AAAGAGGAATTCCATGTCTGTTTT
1 AAAGAAGAACTCCATGTCTGTTTT
292459 A
1 A
292460 CCTTTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (24 bp):
AAAGAAGAACTCCATGTCTGTTTT
Found at i:295251 original size:16 final size:16
Alignment explanation
Indices: 295223--295255 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
295213 ATTAAAGTAT
295223 TATTTTATCTTTTAAA
1 TATTTTATCTTTTAAA
295239 TATTTATAT-TTTTAAA
1 TATTT-TATCTTTTAAA
295255 T
1 T
295256 GATGAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTTATCTTTTAAA
Found at i:296633 original size:24 final size:24
Alignment explanation
Indices: 296601--296649 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
296591 AGAAATAAGG
296601 CTTCAAAGGAACTTCAGACAGACC
1 CTTCAAAGGAACTTCAGACAGACC
296625 CTTCAAAGGAACTTCAGACAGACC
1 CTTCAAAGGAACTTCAGACAGACC
296649 C
1 C
296650 AAGGCAGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.31, G:0.16, T:0.16
Consensus pattern (24 bp):
CTTCAAAGGAACTTCAGACAGACC
Found at i:297961 original size:116 final size:114
Alignment explanation
Indices: 297759--297987 Score: 352
Period size: 116 Copynumber: 2.0 Consensus size: 114
297749 TTCTACTCAT
* * *
297759 TTCACAAAGTTATTTCCAGGTAATGAAAATTAAATAACTACTAATCAAAAGTGTGTTAATTCAGT
1 TTCACAAAGTTATTTCCAGGAAATGAAAATTAAATAAATACTAATCAAAAGTGCGTTAATTCAGT
*
297824 CCGATCTACTCATTTCACAGAATCAACCGAATACGACAACTA-TTTTGG
66 CAGATCTACTCATTTCACAGAATCAACCGAATACGACAACTAGTTTTGG
* *
297872 TTCACAAATTTATTTGCAGGAAATGAAAAAAATTAAATAAATACTAATCAAAAGTGCGTTAATTC
1 TTCACAAAGTTATTTCCAGGAAATG---AAAATTAAATAAATACTAATCAAAAGTGCGTTAATTC
* *
297937 AGTCAGATCTACTCATTTCTCAGAATCAACCGAATACGAGAACTAGTTTTG
63 AGTCAGATCTACTCATTTCACAGAATCAACCGAATACGACAACTAGTTTTG
297988 TTCTTCATGA
Statistics
Matches: 104, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
113 22 0.21
116 77 0.74
117 5 0.05
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.31
Consensus pattern (114 bp):
TTCACAAAGTTATTTCCAGGAAATGAAAATTAAATAAATACTAATCAAAAGTGCGTTAATTCAGT
CAGATCTACTCATTTCACAGAATCAACCGAATACGACAACTAGTTTTGG
Found at i:299920 original size:90 final size:89
Alignment explanation
Indices: 299767--299985 Score: 330
Period size: 90 Copynumber: 2.4 Consensus size: 89
299757 TGTTCACTAA
* **
299767 TACTTCTACAACATAGAAGAGAATGAAGTTTCAAACATGCTTAAACATGCAATATCTTTCGATTT
1 TACTTCTACAACATAGAAGAGAACGAAGTTT-AAACATGCTTAAACACACAATATCTTTCGATTT
*
299832 AAAGATAGAGAAAGATCTTACCAAT
65 AAAGATAGAAAAAGATCTTACCAAT
*
299857 TACTTCTACAACATAGAAGAGAACGAGAGTTTAAACATGCTTAATCACACAATATCTTTCGATTT
1 TACTTCTACAACATAGAAGAGAACGA-AGTTTAAACATGCTTAAACACACAATATCTTTCGATTT
* *
299922 ATAGATGGAAAAAGATCTTACCAAT
65 AAAGATAGAAAAAGATCTTACCAAT
* *
299947 TACTTCTACAACAAAGAAGAGAACGAAGGTTCAAACATG
1 TACTTCTACAACATAGAAGAGAACGAA-GTTTAAACATG
299986 TTGATGAGAC
Statistics
Matches: 118, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
89 1 0.01
90 112 0.95
91 5 0.04
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.27
Consensus pattern (89 bp):
TACTTCTACAACATAGAAGAGAACGAAGTTTAAACATGCTTAAACACACAATATCTTTCGATTTA
AAGATAGAAAAAGATCTTACCAAT
Found at i:317748 original size:66 final size:64
Alignment explanation
Indices: 317642--317804 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 64
317632 TGGTTGAAGG
* *
317642 TGCATCGATGCATAAGGAGTGCATCAATGCA-CTCATTTAAATTAAATGAACATCGAAT-GCCAT
1 TGCATCGATGCATAAGGAGTGCATCGATGCACCTCA-TTAAAATAAA--AACATCGAATAG-CAT
317705 TAA
62 TAA
* * *
317708 TGCATCGATGCATAAGGAGTGCATCGATGCACCTGC-TTAAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCACCT-CATTAAAATAAAAACATCGAATAGCATTAA
* *
317772 TGCACCGATGCAT-GGGTAGTGCATCGATGCACC
1 TGCATCGATGCATAAGG-AGTGCATCGATGCACC
317805 CGTCAAGTGA
Statistics
Matches: 86, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
63 2 0.02
64 42 0.49
65 1 0.01
66 38 0.44
67 2 0.02
68 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (64 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCACCTCATTAAAATAAAAACATCGAATAGCATTAA
Found at i:319037 original size:16 final size:16
Alignment explanation
Indices: 319016--319054 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
319006 GATATGAAAT
319016 ATATGGTTACACATAC
1 ATATGGTTACACATAC
319032 ATATGGTTACACATAC
1 ATATGGTTACACATAC
319048 ATATGGT
1 ATATGGT
319055 ATGTGACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (16 bp):
ATATGGTTACACATAC
Found at i:319197 original size:22 final size:22
Alignment explanation
Indices: 319172--319311 Score: 217
Period size: 22 Copynumber: 6.4 Consensus size: 22
319162 ATATTAGTCT
*
319172 TTCGGGACGTATCCAGTGGTTC
1 TTCGGGACGTATCCAGTGGTCC
* *
319194 TTCGAGACGTATCCAATGGTCC
1 TTCGGGACGTATCCAGTGGTCC
319216 TTCGGGACGTATCCAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
*
319238 TTCGGGACGTATCCAATGGTCC
1 TTCGGGACGTATCCAGTGGTCC
* *
319260 TTCGGGACATATCTAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
*
319282 TTCGGGACGTATCTAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
319304 TTCGGGAC
1 TTCGGGAC
319312 ATAGCAGTCC
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 108 1.00
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.29
Consensus pattern (22 bp):
TTCGGGACGTATCCAGTGGTCC
Found at i:322505 original size:32 final size:32
Alignment explanation
Indices: 322454--322548 Score: 100
Period size: 32 Copynumber: 3.0 Consensus size: 32
322444 TGTGTGTTAA
* * * *
322454 ATAGTAGTATCAGTGTTGCATTTAGATAATGC
1 ATAGTAGAATCAATATTGCATTCAGATAATGC
322486 ATAGTAGAATCAATATTGCATTCAGATAATGC
1 ATAGTAGAATCAATATTGCATTCAGATAATGC
* ** * * *
322518 ACAACAGAGTCAGTATTGAATTCAGATAATG
1 ATAGTAGAATCAATATTGCATTCAGATAATG
322549 TTCAACATGG
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.32
Consensus pattern (32 bp):
ATAGTAGAATCAATATTGCATTCAGATAATGC
Found at i:322555 original size:32 final size:31
Alignment explanation
Indices: 322499--322613 Score: 110
Period size: 32 Copynumber: 3.6 Consensus size: 31
322489 GTAGAATCAA
* *
322499 TATTGCATTCAGATAATGCACAACAGAGTCAG
1 TATTGAATTCAGATAATG-TCAACAGAGTCAG
*
322531 TATTGAATTCAGATAATGTTCAACATG-GTTAG
1 TATTGAATTCAGATAATG-TCAACA-GAGTCAG
*
322563 TATTGCATTCAGATAATG-CATAGCAGAGTCAG
1 TATTGAATTCAGATAATGTCA-A-CAGAGTCAG
*
322595 TATTGCAA-TCAGACAATGT
1 TATTG-AATTCAGATAATGT
322614 AGAGTAGCGC
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
30 2 0.03
31 2 0.03
32 63 0.91
33 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (31 bp):
TATTGAATTCAGATAATGTCAACAGAGTCAG
Found at i:327229 original size:117 final size:117
Alignment explanation
Indices: 327023--327259 Score: 474
Period size: 117 Copynumber: 2.0 Consensus size: 117
327013 ACACCAATGT
327023 GTACGGCGGGTTCTTAGGCGCTAAACATGCCGCCCGTGTCATGATCCCGGCGAAGAAAGGCTGCA
1 GTACGGCGGGTTCTTAGGCGCTAAACATGCCGCCCGTGTCATGATCCCGGCGAAGAAAGGCTGCA
327088 TTCTTTTCACCGCTAGTGTGTTGTCGGTGTTGGGCGGTTTCTCTGAGCATCC
66 TTCTTTTCACCGCTAGTGTGTTGTCGGTGTTGGGCGGTTTCTCTGAGCATCC
327140 GTACGGCGGGTTCTTAGGCGCTAAACATGCCGCCCGTGTCATGATCCCGGCGAAGAAAGGCTGCA
1 GTACGGCGGGTTCTTAGGCGCTAAACATGCCGCCCGTGTCATGATCCCGGCGAAGAAAGGCTGCA
327205 TTCTTTTCACCGCTAGTGTGTTGTCGGTGTTGGGCGGTTTCTCTGAGCATCC
66 TTCTTTTCACCGCTAGTGTGTTGTCGGTGTTGGGCGGTTTCTCTGAGCATCC
327257 GTA
1 GTA
327260 TGTGGCGTCG
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 120 1.00
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.28
Consensus pattern (117 bp):
GTACGGCGGGTTCTTAGGCGCTAAACATGCCGCCCGTGTCATGATCCCGGCGAAGAAAGGCTGCA
TTCTTTTCACCGCTAGTGTGTTGTCGGTGTTGGGCGGTTTCTCTGAGCATCC
Found at i:329467 original size:60 final size:59
Alignment explanation
Indices: 329325--329468 Score: 139
Period size: 60 Copynumber: 2.4 Consensus size: 59
329315 TTGTACTATA
* ** *** *
329325 CATCCTCAAACTATGAATCTCATTTTAAATTGGTCCTTGAACTTTTGAACATTCTAATTC
1 CATCCTCAAACTAT-AACCTCATTTTAAATCAGTCCCCAAACTTTTGAACATTCTAAATC
* * *
329385 TATCCAT-AAA-TGATGACTCTCATTTTAAATCAGTCCCCAAAGTTTTGAACATTCTAAATC
1 CATCC-TCAAACT-ATAAC-CTCATTTTAAATCAGTCCCCAAACTTTTGAACATTCTAAATC
329445 CATCCTCAAACTATAAGCCTCATT
1 CATCCTCAAACTATAA-CCTCATT
329469 CTATATTGAA
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
59 3 0.05
60 60 0.91
61 3 0.05
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.36
Consensus pattern (59 bp):
CATCCTCAAACTATAACCTCATTTTAAATCAGTCCCCAAACTTTTGAACATTCTAAATC
Found at i:329602 original size:31 final size:31
Alignment explanation
Indices: 329567--329668 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 31
329557 TTTAAGGACC
*
329567 AATTTAGAATGATGGTCATAGTTTGGGGATG
1 AATTTAGAATGATGGTCATAGTTTGAGGATG
* * * * *
329598 AATTT-GAAT--TGTTCAAAAGTTTAAAGACG
1 AATTTAGAATGATGGTC-ATAGTTTGAGGATG
* *
329627 AGTTTAGAATGATGGTCATAATTTGAGGATG
1 AATTTAGAATGATGGTCATAGTTTGAGGATG
329658 AATTTAGAATG
1 AATTTAGAATG
329669 TTTAAAAGTT
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
28 4 0.08
29 13 0.25
30 8 0.15
31 24 0.45
32 4 0.08
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (31 bp):
AATTTAGAATGATGGTCATAGTTTGAGGATG
Found at i:329633 original size:60 final size:60
Alignment explanation
Indices: 329541--329698 Score: 212
Period size: 60 Copynumber: 2.6 Consensus size: 60
329531 GGGGAAGTTA
* * *
329541 TTAGAATGTTCAAAAGTTTAAGGACCAATTTAGAATGATGGTCATAGTTTGGGGATGAAT
1 TTAGAATGTTCAAAAGTTTAAAGACCAATTTAGAATGATGGTCATAATTTGAGGATGAAT
* *
329601 TT-GAATTGTTCAAAAGTTTAAAGACGAGTTTAGAATGATGGTCATAATTTGAGGATGAAT
1 TTAGAA-TGTTCAAAAGTTTAAAGACCAATTTAGAATGATGGTCATAATTTGAGGATGAAT
* * *
329661 TTAGAATGTTTAAAAGTTT-GAGAACCAATTTAAAATGA
1 TTAGAATGTTCAAAAGTTTAAAG-ACCAATTTAGAATGA
329699 GAGATATAGT
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
59 5 0.06
60 77 0.91
61 3 0.04
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (60 bp):
TTAGAATGTTCAAAAGTTTAAAGACCAATTTAGAATGATGGTCATAATTTGAGGATGAAT
Found at i:330832 original size:33 final size:33
Alignment explanation
Indices: 330790--330878 Score: 169
Period size: 33 Copynumber: 2.7 Consensus size: 33
330780 TTAAGGGGAC
330790 TTCTTAATAGTCACCGACAAATACAAGAGAGCT
1 TTCTTAATAGTCACCGACAAATACAAGAGAGCT
*
330823 TTCTTAATAGTCACCGACAAATACAATAGAGCT
1 TTCTTAATAGTCACCGACAAATACAAGAGAGCT
330856 TTCTTAATAGTCACCGACAAATA
1 TTCTTAATAGTCACCGACAAATA
330879 GGGTTGTAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.27
Consensus pattern (33 bp):
TTCTTAATAGTCACCGACAAATACAAGAGAGCT
Found at i:332718 original size:4 final size:4
Alignment explanation
Indices: 332711--332745 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
332701 TATATATATA
332711 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
332746 ATACATGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:333335 original size:4 final size:4
Alignment explanation
Indices: 333323--333390 Score: 75
Period size: 4 Copynumber: 17.2 Consensus size: 4
333313 CACACATATA
* * * *
333323 TATG CATG TATG TATG TATG TATG TATA TATG TA-G TATG TATG TCTT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
333370 TATG AATG TATG CATG TATG T
1 TATG TATG TATG TATG TATG T
333391 TATTTCAATT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
3 3 0.06
4 48 0.94
ACGTcount: A:0.26, C:0.04, G:0.22, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:333687 original size:31 final size:31
Alignment explanation
Indices: 333642--333712 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
333632 TATTTTTTCT
* *
333642 TTTAATTTGGCTCTCCAACTCAGAAAATAAA
1 TTTAATGTGACTCTCCAACTCAGAAAATAAA
*
333673 TTTAATGTGACTCTCTAACTCAGAAAATAAA
1 TTTAATGTGACTCTCCAACTCAGAAAATAAA
* *
333704 CTCAATGTG
1 TTTAATGTG
333713 GCCATTCGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (31 bp):
TTTAATGTGACTCTCCAACTCAGAAAATAAA
Found at i:335032 original size:247 final size:247
Alignment explanation
Indices: 334596--335089 Score: 963
Period size: 247 Copynumber: 2.0 Consensus size: 247
334586 AACATGAAGT
334596 TAGCCGATGATATGATCAAAATTCTTCTGATTGTTAAATTAAGATTCAAATTTTAATGTTGTGGC
1 TAGCCGATGATATGATCAAAATTCTTCTGATTGTTAAATTAAGATTCAAATTTTAATGTTGTGGC
*
334661 TTGAACATAATTACCTAAGTGGTTAAAGAATGGTTGTTGTTTCTAGAGGTTATGGATTCGAGCTC
66 TTGAACATAATTACCTAAGTGGTTAAAGAATGGTTGTTGTTTCTAGAGGTCATGGATTCGAGCTC
334726 CATCGACAGCAACAAGGAAATTGAACGTTTATTGTCAAATAGTTGAGAGTATTTAGAATAGATAT
131 CATCGACAGCAACAAGGAAATTGAACGTTTATTGTCAAATAGTTGAGAGTATTTAGAATAGATAT
334791 TACTTTATAATCGCCTTAGCTTAATCAAAAAAATTAATGTTATAAATA-AAAA
196 TACTTTATAATCGCCTTAGCTTAAT-AAAAAAATTAATGTTATAAATACAAAA
334843 TAGCCGATGATATGATCAAAATTCTTCTGATTGTTAAATTAAGATTCAAATTTTAATGTTGTGGC
1 TAGCCGATGATATGATCAAAATTCTTCTGATTGTTAAATTAAGATTCAAATTTTAATGTTGTGGC
334908 TTGAACATAATTACCTAAGTGGTTAAAGAATGGTTGTTGTTTCTAGAGGTCATGGATTCGAGCTC
66 TTGAACATAATTACCTAAGTGGTTAAAGAATGGTTGTTGTTTCTAGAGGTCATGGATTCGAGCTC
334973 CATCGACAGCAACAAGGAAATTGAACGTTTATTGTCAAATAGTTGAGAGTATTTAGAATAGATAT
131 CATCGACAGCAACAAGGAAATTGAACGTTTATTGTCAAATAGTTGAGAGTATTTAGAATAGATAT
335038 TACTTTATAATCGCCTTAGCTTAATAAAAAAATTAATGTTATAAATACAAAA
196 TACTTTATAATCGCCTTAGCTTAATAAAAAAATTAATGTTATAAATACAAAA
335090 AATTAAATTA
Statistics
Matches: 245, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
246 22 0.09
247 223 0.91
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (247 bp):
TAGCCGATGATATGATCAAAATTCTTCTGATTGTTAAATTAAGATTCAAATTTTAATGTTGTGGC
TTGAACATAATTACCTAAGTGGTTAAAGAATGGTTGTTGTTTCTAGAGGTCATGGATTCGAGCTC
CATCGACAGCAACAAGGAAATTGAACGTTTATTGTCAAATAGTTGAGAGTATTTAGAATAGATAT
TACTTTATAATCGCCTTAGCTTAATAAAAAAATTAATGTTATAAATACAAAA
Found at i:336056 original size:25 final size:25
Alignment explanation
Indices: 336027--336102 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
336017 AGCAAACCTT
*
336027 ACCCTAAACCACTTTAACCTACACA
1 ACCCTAAACCACTTTAACCTACAAA
** * *
336052 ACCCTTGACCACTCTCACCTTA-AAA
1 ACCCTAAACCACTTTAACC-TACAAA
*
336077 ACCCTAAATCACTTTAACCTACAAA
1 ACCCTAAACCACTTTAACCTACAAA
336102 A
1 A
336103 TCTTTCATCA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
24 2 0.05
25 35 0.90
26 2 0.05
ACGTcount: A:0.39, C:0.37, G:0.01, T:0.22
Consensus pattern (25 bp):
ACCCTAAACCACTTTAACCTACAAA
Found at i:336093 original size:50 final size:51
Alignment explanation
Indices: 336027--336148 Score: 147
Period size: 50 Copynumber: 2.4 Consensus size: 51
336017 AGCAAACCTT
* * *
336027 ACCCTAAACCACTTTAACCTACACAACCCTTGACCACTCTCACCTTAA-AA
1 ACCCTAAATCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAACAA
* * * * * *
336077 ACCCTAAATCACTTTAACCTACAAAATCTTTCATCACTTTCACTTTAACGA
1 ACCCTAAATCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAACAA
*
336128 ACCCTATATCACTTTAACCTA
1 ACCCTAAATCACTTTAACCTA
336149 AAATCACTCC
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 40 0.66
51 21 0.34
ACGTcount: A:0.35, C:0.34, G:0.02, T:0.29
Consensus pattern (51 bp):
ACCCTAAATCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAACAA
Found at i:336415 original size:50 final size:50
Alignment explanation
Indices: 336361--336457 Score: 151
Period size: 50 Copynumber: 1.9 Consensus size: 50
336351 CTTGAAACAC
336361 TCTTTCCACCGT-GACACCACACCAGCTAGAAGGCGCTTCCCCTGAAACGT
1 TCTTTCCACCGTAG-CACCACACCAGCTAGAAGGCGCTTCCCCTGAAACGT
* * *
336411 TCTTTCCATCGTAGCACCACACCAGCTGGAAGGCGTTTCCCCTGAAA
1 TCTTTCCACCGTAGCACCACACCAGCTAGAAGGCGCTTCCCCTGAAA
336458 TGCTCCTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 42 0.98
51 1 0.02
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.22
Consensus pattern (50 bp):
TCTTTCCACCGTAGCACCACACCAGCTAGAAGGCGCTTCCCCTGAAACGT
Found at i:336924 original size:28 final size:29
Alignment explanation
Indices: 336866--336927 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
336856 ATACGGGATT
*
336866 TGGTACATATACTTTGACAATGCTTAATG
1 TGGTACATATAATTTGACAATGCTTAATG
336895 TGGTACATATAATTTGA-AATGGC-TAATG
1 TGGTACATATAATTTGACAAT-GCTTAATG
336923 TGGTA
1 TGGTA
336928 TCTGTACTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (29 bp):
TGGTACATATAATTTGACAATGCTTAATG
Found at i:337525 original size:2 final size:2
Alignment explanation
Indices: 337518--337546 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
337508 TAATTTTGAC
337518 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 A
337547 GTATTTGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.