Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold252
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: 304253
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 2
Found at i:199924 original size:74 final size:74
Alignment explanation
Indices: 199803--199950 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
199793 AATTGGGAGT
199803 AGCTAAATCTCACTTTTAATTGATATATTACTGTTCATGTATCACTATTTATCACTGTTCATGTA
1 AGCTAAATCTCACTTTTAATTGATATATTACTGTTCATGTATCACTATTTATCACTGTTCATGTA
199868 TTGATACAG
66 TTGATACAG
199877 AGCTAAATCTCACTTTTAATTGATATATTACTGTTCATGTATCACTATTTATCACTGTTCATGTA
1 AGCTAAATCTCACTTTTAATTGATATATTACTGTTCATGTATCACTATTTATCACTGTTCATGTA
199942 TTGATACAG
66 TTGATACAG
199951 TGTGTCAATA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (74 bp):
AGCTAAATCTCACTTTTAATTGATATATTACTGTTCATGTATCACTATTTATCACTGTTCATGTA
TTGATACAG
Found at i:200062 original size:20 final size:20
Alignment explanation
Indices: 200031--200081 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
200021 CATGTATCAT
* *
200031 ATCGATATATTATGAATTGT
1 ATCGATACATTATGAATTGC
*
200051 ATTGATACATTATGAATTGC
1 ATCGATACATTATGAATTGC
200071 ATCGATACATT
1 ATCGATACATT
200082 GGAGCGTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (20 bp):
ATCGATACATTATGAATTGC
Found at i:205170 original size:20 final size:21
Alignment explanation
Indices: 205126--205179 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
205116 TTTTACAATT
* *
205126 TGTATCAATACAAACAGTAAA
1 TGTATCGATACATACAGTAAA
*
205147 TGTATCGATACATA-AGTGAA
1 TGTATCGATACATACAGTAAA
205167 TGTATCGATACAT
1 TGTATCGATACAT
205180 GCCTAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATACAGTAAA
Found at i:205311 original size:20 final size:21
Alignment explanation
Indices: 205224--205320 Score: 83
Period size: 20 Copynumber: 4.8 Consensus size: 21
205214 TCTAGAAAGG
205224 AAATGTATCGATACA-TAAAT
1 AAATGTATCGATACATTAAAT
* * *
205244 AAATGCATCGATACATTTACT
1 AAATGTATCGATACATTAAAT
*** * *
205265 GTTTGTATTGATACATT-ATT
1 AAATGTATCGATACATTAAAT
* *
205285 CATTGTATCGATACATTAAAT
1 AAATGTATCGATACATTAAAT
205306 -AATGTATCGATACAT
1 AAATGTATCGATACAT
205321 GTAGGCAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
20 44 0.72
21 17 0.28
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.38
Consensus pattern (21 bp):
AAATGTATCGATACATTAAAT
Found at i:210354 original size:22 final size:22
Alignment explanation
Indices: 210321--210372 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
210311 ATGAAAGTAG
*
210321 CAAGCTTG-GAAAATATACCAA
1 CAAGGTTGAGAAAATATACCAA
210342 CAAGGTTGAGAAAATATACCAA
1 CAAGGTTGAGAAAATATACCAA
210364 CAAGGTTGA
1 CAAGGTTGA
210373 CAATGCTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (22 bp):
CAAGGTTGAGAAAATATACCAA
Found at i:211115 original size:31 final size:32
Alignment explanation
Indices: 211052--211128 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
211042 GATACATTAA
* * *
211052 AGAATGTATCAATACATTTGGGTCAAAAACCC
1 AGAATGTATCGATACATTTGAGACAAAAACCC
*
211084 AGAATGTATCGATACATTT-AGACTAAAACCC
1 AGAATGTATCGATACATTTGAGACAAAAACCC
* *
211115 AAAATGTATTGATA
1 AGAATGTATCGATA
211129 TAATGAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 21 0.54
32 18 0.46
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (32 bp):
AGAATGTATCGATACATTTGAGACAAAAACCC
Found at i:217387 original size:155 final size:155
Alignment explanation
Indices: 216994--217393 Score: 333
Period size: 155 Copynumber: 2.6 Consensus size: 155
216984 TGTTAGAGTG
* * * * *
216994 TACCTTTGACGTGAAAGTATCAT-AGTAACCCTAAAGGGCACAAAAATGATATA-AGAGG-ATGA
1 TACCTTTGACGTAAAAGTATC-TCGGTAACCCTAAAGGACACAAAAACGATATAGAAAGGCA--A
** * * * * * * * * * *
217056 ATTTATCCTAAAAGCGTACCCTTGGTATAAAAGTGACCCGGTGATTA---GA-ACTTGGTTCGAA
63 ACCTATCCTAAAAGCATATCTTTGGCATAAAAGTAACTCGATAATTACCTAAGACTTGGTTCAAA
*
217117 GAAAAATTACCAAAATGGCCTTAGGATA
128 GAAAAATTACCAAAATGCCCTTAGGATA
* * * *
217145 TACTTTTGACGTAAAAGTATCTCGGTAACCCTAAAGGACACAAAAATGGTGTAGAAAGGCAAACC
1 TACCTTTGACGTAAAAGTATCTCGGTAACCCTAAAGGACACAAAAACGATATAGAAAGGCAAACC
*
217210 TATCCTAAAAGCATATCTTTGGCTTAAAAGTAACTCGATAATTACCTAAGACTTGGTTCAAAAGA
66 TATCCTAAAAGCATATCTTTGGCATAAAAGTAACTCGATAATTACCTAAGACTTGGTTC-AAAGA
217275 AAAA-TACCAAAAT-CCCTTTAAGG-TA
130 AAAATTACCAAAATGCCC-TT-AGGATA
* * * **
217300 TACCTTTGACGTGAAAGTAT-TGTGGTAATCCTAAAGGACATGAAAACGATATA-AAAGG-ATGA
1 TACCTTTGACGTAAAAGTATCT-CGGTAACCCTAAAGGACACAAAAACGATATAGAAAGGCA--A
* * *
217362 ACCTATTCTAAAGGTATA-CTTTTGGCATAAAA
63 ACCTATCCTAAAAGCATATC-TTTGGCATAAAA
217394 ATGACCCAGT
Statistics
Matches: 201, Mismatches: 34, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
150 1 0.00
151 82 0.41
152 4 0.02
153 2 0.01
154 10 0.05
155 91 0.45
156 11 0.05
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (155 bp):
TACCTTTGACGTAAAAGTATCTCGGTAACCCTAAAGGACACAAAAACGATATAGAAAGGCAAACC
TATCCTAAAAGCATATCTTTGGCATAAAAGTAACTCGATAATTACCTAAGACTTGGTTCAAAGAA
AAATTACCAAAATGCCCTTAGGATA
Found at i:217409 original size:155 final size:155
Alignment explanation
Indices: 217250--217528 Score: 337
Period size: 155 Copynumber: 1.8 Consensus size: 155
217240 TAACTCGATA
* * * **
217250 ATTACCTAAGACTTGGTTCAAAAGAAAAA-TACCAAAATCCCTTTAAGGTATACCTTTGACGTGA
1 ATTACCTAAGACTCGGTT-AAAAGAAAAATTACCAAAATCCCTTTAAGGTATACATTCGACACGA
* * *
217314 AAGTAT-TGTGGTAATCCTAAAGGACATGAAAACGATATAAAAGGATGAACCTATTCTAAAGGTA
65 AAGTATCT-TGATAATCCTAAAGGACACGAAAACGATATAAAAGGATGAACCTATCCTAAAGGTA
217378 TACTTTTGGCATAAAAATGACCCAGTG
129 TACTTTTGGCATAAAAATGACCCAGTG
* * * ** * * *
217405 ATTACTTAAGACTCGGTTTAAGGAAAAATTATTAAAATGCTTTTAGGGTATACATTCGACACGAA
1 ATTACCTAAGACTCGGTTAAAAGAAAAATTACCAAAATCCCTTTAAGGTATACATTCGACACGAA
* * * * *
217470 AGTATCTTGATAATCCTAAATGATACGAAAATGATGTAATAGGATGAACCTATCCTAAA
66 AGTATCTTGATAATCCTAAAGGACACGAAAACGATATAAAAGGATGAACCTATCCTAAA
217529 TGGGCAATTT
Statistics
Matches: 101, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
154 8 0.08
155 92 0.91
156 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (155 bp):
ATTACCTAAGACTCGGTTAAAAGAAAAATTACCAAAATCCCTTTAAGGTATACATTCGACACGAA
AGTATCTTGATAATCCTAAAGGACACGAAAACGATATAAAAGGATGAACCTATCCTAAAGGTATA
CTTTTGGCATAAAAATGACCCAGTG
Found at i:218229 original size:29 final size:30
Alignment explanation
Indices: 218182--218252 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
218172 AGCATGCAAC
**
218182 AAATTTTACAAAAAATACAAATTGGTCTCT
1 AAATTTTACAAAAAATACAAAAAGGTCTCT
* *
218212 AAATTTT-CTAAAATTACAAAAAGGTCTCT
1 AAATTTTACAAAAAATACAAAAAGGTCTCT
*
218241 AAATGTTA-AAAA
1 AAATTTTACAAAA
218253 TACCTAAAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 27 0.79
30 7 0.21
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.32
Consensus pattern (30 bp):
AAATTTTACAAAAAATACAAAAAGGTCTCT
Found at i:218867 original size:12 final size:12
Alignment explanation
Indices: 218842--218875 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
218832 TAGGCTTTTC
*
218842 TTTTTTAAAT-T
1 TTTTTTAATTAT
218853 TTTTTTAATTAT
1 TTTTTTAATTAT
218865 TTTTTTAATTA
1 TTTTTTAATTA
218876 ATTAAGACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTAATTAT
Found at i:219035 original size:5 final size:5
Alignment explanation
Indices: 219025--219051 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
219015 AACTAGTATA
219025 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
219052 GAAATCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:219310 original size:13 final size:13
Alignment explanation
Indices: 219292--219316 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
219282 ATTATAAACT
219292 CAAAAAAATTTGA
1 CAAAAAAATTTGA
219305 CAAAAAAATTTG
1 CAAAAAAATTTG
219317 CGAAGTAGAA
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:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (13 bp):
CAAAAAAATTTGA
Found at i:221792 original size:13 final size:13
Alignment explanation
Indices: 221774--221799 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
221764 CATTTTATGG
221774 TGTATCGATACAT
1 TGTATCGATACAT
221787 TGTATCGATACAT
1 TGTATCGATACAT
221800 ACTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:221796 original size:33 final size:32
Alignment explanation
Indices: 221754--221817 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
221744 TACAAGCCAA
**
221754 TGTATCGATACATTTTATGGTGTATCGATACAT
1 TGTATCGATACATACTAT-GTGTATCGATACAT
*
221787 TGTATCGATACATACTGTGTGTATCGATACA
1 TGTATCGATACATACTATGTGTATCGATACA
221818 AGTTTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATACTATGTGTATCGATACAT
Found at i:221908 original size:13 final size:13
Alignment explanation
Indices: 221890--221914 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
221880 ACAATGCAAC
221890 ATGTATCGATACA
1 ATGTATCGATACA
221903 ATGTATCGATAC
1 ATGTATCGATAC
221915 TGTGCAACAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:221914 original size:33 final size:33
Alignment explanation
Indices: 221872--221937 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
221862 TCTTTTTCAA
221872 GTATCGATACAATGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
**
221905 GTATCGATACTGTGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
221938 TAAATGTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (33 bp):
GTATCGATACAATGCAACATGTATCGATACAAT
Found at i:230589 original size:13 final size:13
Alignment explanation
Indices: 230571--230596 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
230561 CATTTTATGG
230571 TGTATCGATACAT
1 TGTATCGATACAT
230584 TGTATCGATACAT
1 TGTATCGATACAT
230597 ACTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:230593 original size:33 final size:32
Alignment explanation
Indices: 230551--230614 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
230541 TACAAGCCAA
**
230551 TGTATCGATACATTTTATGGTGTATCGATACAT
1 TGTATCGATACATACTAT-GTGTATCGATACAT
*
230584 TGTATCGATACATACTGTGTGTATCGATACA
1 TGTATCGATACATACTATGTGTATCGATACA
230615 AGTTTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATACTATGTGTATCGATACAT
Found at i:230694 original size:20 final size:20
Alignment explanation
Indices: 230669--230721 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
230659 TCTTTTTCAA
230669 GTATCGATACAATGCAACAT
1 GTATCGATACAATGCAACAT
**
230689 GTATCGATACTGTGCAACAT
1 GTATCGATACAATGCAACAT
230709 GTATCGATACAAT
1 GTATCGATACAAT
230722 TAAATGTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (20 bp):
GTATCGATACAATGCAACAT
Found at i:234059 original size:59 final size:59
Alignment explanation
Indices: 233993--234108 Score: 216
Period size: 59 Copynumber: 2.0 Consensus size: 59
233983 ATTAAAGAAA
233993 GATAAACTTTTATG-TGAAATTTCTATTCAAATCTAAATCATATTAAGAATTTTTAATAT
1 GATAAACTTTTATGTTG-AATTTCTATTCAAATCTAAATCATATTAAGAATTTTTAATAT
234052 GATAAACTTTTATGTTGAATTTCTATTCAAATCTAAATCATATTAAGAATTTTTAAT
1 GATAAACTTTTATGTTGAATTTCTATTCAAATCTAAATCATATTAAGAATTTTTAAT
234109 CAATTGTATA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 54 0.96
60 2 0.04
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.45
Consensus pattern (59 bp):
GATAAACTTTTATGTTGAATTTCTATTCAAATCTAAATCATATTAAGAATTTTTAATAT
Found at i:236482 original size:14 final size:16
Alignment explanation
Indices: 236451--236487 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
236441 AAATGCTATT
236451 AAAATTTTACATATAA
1 AAAATTTTACATATAA
*
236467 AAAATTTTA-TTA-AA
1 AAAATTTTACATATAA
236481 AAAATTT
1 AAAATTT
236488 AATGAGTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 9 0.45
15 2 0.10
16 9 0.45
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATTTTACATATAA
Found at i:242352 original size:31 final size:31
Alignment explanation
Indices: 242316--242377 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
242306 GATTAATGTA
242316 ACTACATTAGAATGCTATCTCAAATTTTCCT
1 ACTACATTAGAATGCTATCTCAAATTTTCCT
*
242347 ACTACATTAGAATGCTATCTTAAATTTTCCT
1 ACTACATTAGAATGCTATCTCAAATTTTCCT
242378 CCATCTTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (31 bp):
ACTACATTAGAATGCTATCTCAAATTTTCCT
Found at i:242573 original size:2 final size:2
Alignment explanation
Indices: 242566--242598 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
242556 GCTTTTTGTT
*
242566 TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
242599 AAAACAAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:251866 original size:16 final size:15
Alignment explanation
Indices: 251845--251875 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
251835 TAACATTTCC
251845 TCTATTAAAAACTTTT
1 TCTATTAAAAA-TTTT
251861 TCTATTAAAAATTTT
1 TCTATTAAAAATTTT
251876 GAAAGCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (15 bp):
TCTATTAAAAATTTT
Found at i:253899 original size:19 final size:20
Alignment explanation
Indices: 253862--253901 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
253852 TCCCGTGTAA
253862 ATGTATCGATACAATATTTG
1 ATGTATCGATACAATATTTG
253882 ATGTATCGATAC-ATATTTG
1 ATGTATCGATACAATATTTG
253901 A
1 A
253902 AAATATAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACAATATTTG
Found at i:253972 original size:13 final size:13
Alignment explanation
Indices: 253954--253979 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
253944 CAATTTTTTG
253954 TGTATCGATACAT
1 TGTATCGATACAT
253967 TGTATCGATACAT
1 TGTATCGATACAT
253980 ACTTAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:254064 original size:20 final size:20
Alignment explanation
Indices: 254039--254111 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
254029 CAACTTTTTT
254039 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
254059 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
254080 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
254100 ATGTATCGATAC
1 ATGTATCGATAC
254112 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:254077 original size:41 final size:41
Alignment explanation
Indices: 254018--254111 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
254008 CTGCCAAGAA
*
254018 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
254059 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
254100 ATGTATCGATAC
1 ATGTATCGATAC
254112 TTTGAATTGT
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:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:254093 original size:21 final size:21
Alignment explanation
Indices: 254018--254093 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
254008 CTGCCAAGAA
* *
254018 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
254039 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
254059 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
254080 ATGTATCGATACAT
1 ATGTATCGATACAT
254094 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:254804 original size:53 final size:53
Alignment explanation
Indices: 254719--254825 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
254709 CTCCTTTATC
*
254719 TCCCTCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
1 TCCCCCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
254772 TCCCCCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
1 TCCCCCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
254825 T
1 T
254826 TATTTGCACT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.36
Consensus pattern (53 bp):
TCCCCCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
Found at i:256629 original size:13 final size:13
Alignment explanation
Indices: 256611--256649 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
256601 ATAATCACCC
*
256611 TGTATCGATACAG
1 TGTATCGATACAA
256624 TGTATCGATACAA
1 TGTATCGATACAA
256637 TGTATCGATACAA
1 TGTATCGATACAA
256650 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:256660 original size:20 final size:20
Alignment explanation
Indices: 256635--256713 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
256625 GTATCGATAC
256635 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
256655 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
*
256680 GATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
256699 ACATGTATCGATACA
1 A-ATGTATCGATACA
256714 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 3 0.07
23 3 0.07
25 13 0.28
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:258748 original size:15 final size:15
Alignment explanation
Indices: 258728--258758 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
258718 ATTTCGTTTG
*
258728 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
258743 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
258758 G
1 G
258759 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:262765 original size:19 final size:20
Alignment explanation
Indices: 262728--262767 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
262718 TCCCGTGTAA
262728 ATGTATCGATACAATATTTG
1 ATGTATCGATACAATATTTG
262748 ATGTATCGATAC-ATATTTG
1 ATGTATCGATACAATATTTG
262767 A
1 A
262768 AAATATAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACAATATTTG
Found at i:262838 original size:13 final size:13
Alignment explanation
Indices: 262820--262845 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
262810 CAATTTTTTG
262820 TGTATCGATACAT
1 TGTATCGATACAT
262833 TGTATCGATACAT
1 TGTATCGATACAT
262846 ACTTAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:262930 original size:20 final size:20
Alignment explanation
Indices: 262905--262977 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
262895 CAACTTTTTT
262905 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
262925 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
262946 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
262966 ATGTATCGATAC
1 ATGTATCGATAC
262978 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:262943 original size:41 final size:41
Alignment explanation
Indices: 262884--262977 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
262874 CTGCCAAGAA
*
262884 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
262925 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
262966 ATGTATCGATAC
1 ATGTATCGATAC
262978 TTTGAATTGT
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:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:262959 original size:21 final size:21
Alignment explanation
Indices: 262884--262959 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
262874 CTGCCAAGAA
* *
262884 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
262905 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
262925 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
262946 ATGTATCGATACAT
1 ATGTATCGATACAT
262960 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:265897 original size:71 final size:71
Alignment explanation
Indices: 265781--265954 Score: 314
Period size: 71 Copynumber: 2.5 Consensus size: 71
265771 ATATTCCAAA
265781 GTATCGATACATAGGTATTTGTATCGATACATTAAAGTTGACTTAAGCTACAAAGGTCAAAACCC
1 GTATCGATACATAGGTATTTGTATCGATACATTAAAGTTGACTTAAGCTACAAAGGTCAAAACCC
265846 TTGTAT
66 TTGTAT
265852 GTATCGATACATAGGTATTTGTATCGATACATTAAAGTTGACTTAAGCTACAAAGGTCAAAACCC
1 GTATCGATACATAGGTATTTGTATCGATACATTAAAGTTGACTTAAGCTACAAAGGTCAAAACCC
265917 TTGTAT
66 TTGTAT
* *
265923 GTATCGATACAT-GGCACATTGTATCGATACAT
1 GTATCGATACATAGGTA-TTTGTATCGATACAT
265955 GTTCATTGTA
Statistics
Matches: 100, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
70 3 0.03
71 97 0.97
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (71 bp):
GTATCGATACATAGGTATTTGTATCGATACATTAAAGTTGACTTAAGCTACAAAGGTCAAAACCC
TTGTAT
Found at i:265947 original size:20 final size:20
Alignment explanation
Indices: 265922--265994 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
265912 AACCCTTGTA
265922 TGTATCGATACATGGCACAT
1 TGTATCGATACATGGCACAT
**
265942 TGTATCGATACAT-GTTCAT
1 TGTATCGATACATGGCACAT
* *
265961 TGTATCGATAC-TAGCATAAT
1 TGTATCGATACATGGCA-CAT
265981 TGTATCGATACATG
1 TGTATCGATACATG
265995 AAACTGGCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 1 0.02
19 16 0.36
20 26 0.59
21 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGGCACAT
Found at i:266061 original size:33 final size:33
Alignment explanation
Indices: 266024--266088 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
266014 TACCACTGTT
* * * *
266024 TGTATTGATACATGGCACATTGTATCGATACAA
1 TGTATCGATACATGACAAATTATATCGATACAA
*
266057 TGTATCGATACATGATAAATTATATCGATACA
1 TGTATCGATACATGACAAATTATATCGATACA
266089 TTGCTTCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGACAAATTATATCGATACAA
Found at i:266062 original size:13 final size:13
Alignment explanation
Indices: 266044--266068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
266034 CATGGCACAT
266044 TGTATCGATACAA
1 TGTATCGATACAA
266057 TGTATCGATACA
1 TGTATCGATACA
266069 TGATAAATTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:266894 original size:33 final size:33
Alignment explanation
Indices: 266852--266915 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
266842 TTGGGCATAA
266852 TGTATCGATACAAT-TCTTCATGTATCGATACAC
1 TGTATCGATACAATGTC-TCATGTATCGATACAC
*
266885 TGTATCGATATAATGTCTCATGTATCGATAC
1 TGTATCGATACAATGTCTCATGTATCGATAC
266916 TTTCTCTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (33 bp):
TGTATCGATACAATGTCTCATGTATCGATACAC
Found at i:271539 original size:18 final size:17
Alignment explanation
Indices: 271504--271567 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 17
271494 TCTAATAAGG
271504 AAAGAAATAAGTAAAAGAA
1 AAAGAAA-AA-TAAAAGAA
271523 AAAGAAAAATCAAAAGAA
1 AAAGAAAAAT-AAAAGAA
271541 CAAA-AAAAA-AAAAG-A
1 -AAAGAAAAATAAAAGAA
*
271556 GAAGAAAAATAA
1 AAAGAAAAATAA
271568 GAACATAAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
14 2 0.05
15 6 0.15
16 7 0.17
17 1 0.03
18 14 0.35
19 10 0.25
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAGAAAAATAAAAGAA
Found at i:277959 original size:6 final size:6
Alignment explanation
Indices: 277950--278012 Score: 54
Period size: 6 Copynumber: 10.5 Consensus size: 6
277940 AACTAGAGAT
* * * * * *
277950 GGTGGA GGTGGT GGTGGT GGTGGT GGTGGA GGTGGT GGAGGT GGTGGA
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA
* *
277998 GGAGGA GGAGGA GGT
1 GGTGGA GGTGGA GGT
278013 AGTATCTCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.13, C:0.00, G:0.67, T:0.21
Consensus pattern (6 bp):
GGTGGA
Found at i:277964 original size:3 final size:3
Alignment explanation
Indices: 277949--277996 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
277939 CAACTAGAGA
* * *
277949 TGG TGG AGG TGG TGG TGG TGG TGG TGG TGG AGG TGG TGG AGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
277997 AGGAGGAGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.06, C:0.00, G:0.67, T:0.27
Consensus pattern (3 bp):
TGG
Found at i:278340 original size:16 final size:16
Alignment explanation
Indices: 278319--278350 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
278309 CACATATGAA
278319 GCTACACAAAGACAAG
1 GCTACACAAAGACAAG
278335 GCTACACAAAGACAAG
1 GCTACACAAAGACAAG
278351 CATAAAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.19, T:0.06
Consensus pattern (16 bp):
GCTACACAAAGACAAG
Found at i:279735 original size:18 final size:18
Alignment explanation
Indices: 279701--279735 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
279691 AACTAATAAA
* *
279701 AAAAATCAAAAAGAAAAC
1 AAAAAGCAAAAAAAAAAC
279719 AAAAAGCAAAAAAAAAA
1 AAAAAGCAAAAAAAAAA
279736 GGAAAAAAAG
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:0.83, C:0.09, G:0.06, T:0.03
Consensus pattern (18 bp):
AAAAAGCAAAAAAAAAAC
Found at i:286122 original size:290 final size:290
Alignment explanation
Indices: 285590--286145 Score: 1049
Period size: 290 Copynumber: 1.9 Consensus size: 290
285580 CTAATCAAGC
*
285590 ACAACCAGGACTACATCAAGCACCTGGTCCCTACTACCCGAATGCACCTTACCCAAGCCCAGTCA
1 ACAACCAGGACTACATCAAGCACCTAGTCCCTACTACCCGAATGCACCTTACCCAAGCCCAGTCA
285655 TAATACCCTCTCAGCCAGTGTATGCCGCAACCTATAGCCAATCTTTCGCTATCCCACCATGACCA
66 TAATACCCTCTCAGCCAGTGTATGCCGCAACCTATAGCCAATCTTTCGCTATCCCACCATGACCA
*
285720 CCACGAAATAATCAACCCCGAGCTAACCTAAACGCCAACCCTAATGCCAATAATGTACCAAACAA
131 CCACGAAATAATCAACCCCGAGCTAACCTAAACGCCAACACTAATGCCAATAATGTACCAAACAA
* *
285785 TTCAAGTGCAAATCAGCGAAGGCAGTAGTTCGACCCTATCTCTATGACATATAAAGAGCTTTACC
196 TTCAAGTGCAAATCAGCGAAGGCAGCAGTTCGACCCTATCCCTATGACATATAAAGAGCTTTACC
285850 AGACTTGGTCCCTTCGACCCTATCCCTATG
261 AGACTTGGTCCCTTCGACCCTATCCCTATG
*
285880 ACAACCGGGACTACATCAAGCACCTAGTCCCTACTACCCGAATGCACCTTACCCAAGCCCAGTCA
1 ACAACCAGGACTACATCAAGCACCTAGTCCCTACTACCCGAATGCACCTTACCCAAGCCCAGTCA
*
285945 TAATACCCTCTCAGCCAGTGTATGCCGCAACCTATAGCCCATCTTTCGCTATCCCACCATGACCA
66 TAATACCCTCTCAGCCAGTGTATGCCGCAACCTATAGCCAATCTTTCGCTATCCCACCATGACCA
*
286010 CCACGAAATAATCAACCCCGAGCTAACCTAAATGCCAACACTAATGCCAATAATGTACCAAACAA
131 CCACGAAATAATCAACCCCGAGCTAACCTAAACGCCAACACTAATGCCAATAATGTACCAAACAA
286075 TTCAAGTGCAAATCAGCGAAGGCAGCAGTTCGACCCTATCCCTATGACATATAAAGAGCTTTACC
196 TTCAAGTGCAAATCAGCGAAGGCAGCAGTTCGACCCTATCCCTATGACATATAAAGAGCTTTACC
286140 AGACTT
261 AGACTT
286146 TGCTCCAAAG
Statistics
Matches: 259, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
290 259 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.21
Consensus pattern (290 bp):
ACAACCAGGACTACATCAAGCACCTAGTCCCTACTACCCGAATGCACCTTACCCAAGCCCAGTCA
TAATACCCTCTCAGCCAGTGTATGCCGCAACCTATAGCCAATCTTTCGCTATCCCACCATGACCA
CCACGAAATAATCAACCCCGAGCTAACCTAAACGCCAACACTAATGCCAATAATGTACCAAACAA
TTCAAGTGCAAATCAGCGAAGGCAGCAGTTCGACCCTATCCCTATGACATATAAAGAGCTTTACC
AGACTTGGTCCCTTCGACCCTATCCCTATG
Found at i:287178 original size:22 final size:23
Alignment explanation
Indices: 287141--287184 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
287131 CTTCAAAATG
*
287141 ACAAAAAATGTCAAAAGCAAAAGC
1 ACAAAAAATG-CAAAAGAAAAAGC
287165 ACAAAAAATG-AAAAGAAAAA
1 ACAAAAAATGCAAAAGAAAAA
287185 AGTGCAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
24 10 0.53
ACGTcount: A:0.70, C:0.11, G:0.11, T:0.07
Consensus pattern (23 bp):
ACAAAAAATGCAAAAGAAAAAGC
Found at i:287184 original size:14 final size:16
Alignment explanation
Indices: 287153--287199 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
287143 AAAAAATGTC
287153 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCA-AA
287169 AAAATG-AAAAG-AAA
1 AAAATGCAAAAGCAAA
*
287183 AAAGTGCAAAAGCAAA
1 AAAATGCAAAAGCAAA
287199 A
1 A
287200 TAAAAAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 13 0.48
17 1 0.04
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAATGCAAAAGCAAA
Found at i:288607 original size:27 final size:27
Alignment explanation
Indices: 288503--288929 Score: 631
Period size: 27 Copynumber: 15.6 Consensus size: 27
288493 ACTGTGACCT
*
288503 CTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
288530 CTTTTAGAGTCCACAACTCCGTGGCATC
1 CTTTTA-AGTCCACAACTCCGTGGCACC
* * **
288558 CTTTTAAAGTCCACAATTTCGTGGCATT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
288586 CTTTTAAGTCCACAACTCCGTGGCA-C
1 CTTTTAAGTCCACAACTCCGTGGCACC
288612 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
288640 CTTTTAAAGTTCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
288668 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
288695 CTTTTAAGTCCACCACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * **
288722 CTTTTAAGTCCATAACTCTGTGAAACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
288749 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
288777 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
288805 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
288832 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
288859 CTTTTAAGTCCACAACTCCATGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
288887 CTTTTAAGTTCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
288914 CTTTTTAAGTCCACAA
1 C-TTTTAAGTCCACAA
288930 GGCGGTGGCA
Statistics
Matches: 366, Mismatches: 27, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.01
27 191 0.52
28 169 0.46
29 1 0.00
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:288643 original size:82 final size:82
Alignment explanation
Indices: 288503--288929 Score: 628
Period size: 82 Copynumber: 5.2 Consensus size: 82
288493 ACTGTGACCT
* * *
288503 CTTTAAAGTCCACAACTCCGTGGCACCCTTTTAGAGTCCACAACTCCGTGGCATCCTTTTAAAGT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
* **
288568 CCACAATTTCGTGGCATT
65 CCACAACTTCGTGGCACC
288586 CTTTTAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
* *
288650 TCACAACTCCGTGGCACC
65 CCACAACTTCGTGGCACC
* *
288668 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACCACTCCGTGGCACTCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* **
288732 CATAAC-TCTGTGAAACC
66 CACAACTTC-GTGGCACC
288749 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGT
*
288814 CCACAACTCCGTGGCACC
65 CCACAACTTCGTGGCACC
*
288832 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCATGGCATCCCTTTTAAGT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCA-CCCTTTTAAGT
*
288896 TCACAACTTCGTGGCACC
65 CCACAACTTCGTGGCACC
288914 CTTTTTAAGTCCACAA
1 C-TTTTAAGTCCACAA
288930 GGCGGTGGCA
Statistics
Matches: 313, Mismatches: 24, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
80 1 0.00
81 39 0.12
82 182 0.58
83 90 0.29
84 1 0.00
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (82 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
CACAACTTCGTGGCACC
Found at i:288939 original size:137 final size:136
Alignment explanation
Indices: 288504--288929 Score: 660
Period size: 137 Copynumber: 3.1 Consensus size: 136
288494 CTGTGACCTC
*
288504 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAGAGTCCACAACTCCGTGGCATCCTTTTAAAGTC
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTA-AGTCCACAACTCCGTGGCACCCTTTT-AAGTC
* * *
288569 CACAATTTCGTGGCATTCTTTTAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCG
64 CACAACTCCGTGGCACTCTTTTAAGTCCACAACTCC-TGGCACCCTTTTAAAGTCCACAACTCCG
288633 TGGCACCCT
128 TGGCACCCT
*
288642 TTTAAAGTTCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* * *
288707 CCACTCCGTGGCACTCTTTTAAGTCCATAACT-CTGTGAAACCCTTTTAAAGTCCACAACTCCGT
66 CAACTCCGTGGCACTCTTTTAAGTCCACAACTCCTG-G-CACCCTTTTAAAGTCCACAACTCCGT
288771 GGCACCCT
129 GGCACCCT
288779 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
1 TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
* * *
288844 CAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGGCATCCCTTTT-AAGTTCACAACTTCGT
66 CAACTCCGTGGCACTCTTTTAAGTCCACAACTCC-TGGCA-CCCTTTTAAAGTCCACAACTCCGT
288908 GGCACCCT
129 GGCACCCT
*
288916 TTTTAAGTCCACAA
1 TTTAAAGTCCACAA
288930 GGCGGTGGCA
Statistics
Matches: 266, Mismatches: 16, Indels: 13
0.90 0.05 0.04
Matches are distributed among these distances:
134 2 0.01
135 2 0.01
136 35 0.13
137 185 0.70
138 40 0.15
139 2 0.01
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (136 bp):
TTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
CAACTCCGTGGCACTCTTTTAAGTCCACAACTCCTGGCACCCTTTTAAAGTCCACAACTCCGTGG
CACCCT
Found at i:289014 original size:28 final size:28
Alignment explanation
Indices: 288949--289445 Score: 291
Period size: 32 Copynumber: 16.4 Consensus size: 28
288939 ATTCCCTTCT
*
288949 AAAGCCCACAAGTTAGTGGCA-CATTTTTC
1 AAAGCCCACAAGTCAGTGGCATCA--TTTC
* *
288978 AAAGCCCACAAGTTAGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCATTTC
** *
289006 AAAGTCCACACAAGTTGGTGGCATCCTTTC
1 AAAG-CC-CACAAGTCAGTGGCATCATTTC
*
289036 AAAGCCCACAAGTCAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCATTTC
*
289064 AAAGCCCACAAGTCAGTGGCACCATTTC
1 AAAGCCCACAAGTCAGTGGCATCATTTC
* *
289092 AAAGCCCATAAGTCAGTGGCAACATTTC
1 AAAGCCCACAAGTCAGTGGCATCATTTC
* *
289120 AAAGCCCACACAAATCGGTGGCA-CTATTTC
1 AAAG-CC-CACAAGTCAGTGGCATC-ATTTC
* *
289150 AAAGCCCACACAAGTCGGTGGCAACCCATTTC
1 AAAG-CC-CACAAGTCAGTGGC-A-TCATTTC
* * *
289182 AAAGCCGACACAAGTCGGTGGCAACCCTTTTC
1 AAAGCC--CACAAGTCAGTGGC-A-TCATTTC
289214 AAAGCCCACACAAGTCAGTGGCA-CTATTTC
1 AAAG-CC-CACAAGTCAGTGGCATC-ATTTC
* * *
289244 AAAGCCCACACAAGTCGGTGGCAACCCTTTTC
1 AAAG-CC-CACAAGTCAGTGGC-A-TCATTTC
* *
289276 AAAGCCCACACAAGTCGGTGGCAACCCATTTC
1 AAAG-CC-CACAAGTCAGTGGC-A-TCATTTC
* * *
289308 AAAGCCCACACAAGTCGGTGGCAACCCTTTTC
1 AAAG-CC-CACAAGTCAGTGGC-A-TCATTTC
*
289340 AAAGCCCACACAAGTC-GATGGCAACCCATTTC
1 AAAG-CC-CACAAGTCAG-TGGC-A-TCATTTC
* * *
289372 AAAGCCCACATAAGTCGGTGGTAACCCATTTC
1 AAAGCCCAC--AAGTCAGTGG-CA-TCATTTC
* * *
289404 AAAGCCCACACAAGTCGGTGGCAACCCTTTTC
1 AAAG-CC-CACAAGTCAGTGGC-A-TCATTTC
289436 AAAGCCCACA
1 AAAGCCCACA
289446 CAAGTTGATG
Statistics
Matches: 421, Mismatches: 24, Indels: 45
0.86 0.05 0.09
Matches are distributed among these distances:
28 84 0.20
29 29 0.07
30 95 0.23
31 10 0.02
32 193 0.46
33 7 0.02
34 3 0.01
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCATCATTTC
Found at i:289186 original size:32 final size:32
Alignment explanation
Indices: 289002--289534 Score: 602
Period size: 32 Copynumber: 17.2 Consensus size: 32
288992 AGTGGCATCT
* * *
289002 TTTCAAAGTCCACACAAGTTGGTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
289032 TTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
289060 TTTCAAAG-CC-CACAAGTCAGTGGC-A-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
289088 TTTCAAAG-CC-CATAAGTCAGTGGCAA--CA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
289116 TTTCAAAGCCCACACAAATCGGTGGC-A-CTA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
289146 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
289178 TTTCAAAGCCGACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
289210 TTTCAAAGCCCACACAAGTCAGTGGC-A-CTA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
289240 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
289272 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
289304 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
289336 TTTCAAAGCCCACACAAGTCGATGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
289368 TTTCAAAGCCCACATAAGTCGGTGGTAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
289400 TTTCAAAGCCCACACAAGTCGGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
289432 TTTCAAAGCCCACACAAGTTGATGGGAACCTC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACC-CA
* ** * * *
289464 TTTCAAAAGTCCACAC-TTTCGATGGAAACCCT
1 TTTC-AAAGCCCACACAAGTCGGTGGCAACCCA
* * * * *
289496 TTTAAAAACCCACGCAAGTCAGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
289528 TTTCAAA
1 TTTCAAA
289535 TCACCATTTT
Statistics
Matches: 444, Mismatches: 46, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
27 2 0.00
28 74 0.17
29 6 0.01
30 71 0.16
31 12 0.03
32 268 0.60
33 11 0.02
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:289225 original size:94 final size:92
Alignment explanation
Indices: 289002--289450 Score: 578
Period size: 94 Copynumber: 4.9 Consensus size: 92
288992 AGTGGCATCT
* * * *
289002 TTTCAAAGTCCACACAAGTTGGTGGC-ATCC-TTTCAAAG-CC-CACAAGTCAGTGGCATCCTTT
1 TTTCAAAG-CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCA-CTTTT
*
289063 CAAAG-CC-CACAAGTCAGTGGC-A-CCA
64 CAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
289088 TTTCAAAGCC-CATAAGTCAGTGGCAA--CATTTCAAAGCCCACACAAATCGGTGGCACTATTTC
1 TTTCAAAGCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACT-TTTC
289150 AAAGCCCACACAAGTCGGTGGCAACCCA
65 AAAGCCCACACAAGTCGGTGGCAACCCA
* *
289178 TTTCAAAGCCGACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCAGTGGCACTATTT
1 TTTCAAAGCC-ACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACT-TTT
*
289243 CAAAGCCCACACAAGTCGGTGGCAACCCT
64 CAAAGCCCACACAAGTCGGTGGCAACCCA
289272 TTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTT
1 TTTCAAAG-CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC-A--CTT
*
289337 TTCAAAGCCCACACAAGTCGATGGCAACCCA
62 TTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
289368 TTTCAAAGCCCACATAAGTCGGTGGTAACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCTT
1 TTTCAAAG-CCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGC-A--CTT
289433 TTCAAAGCCCACACAAGT
62 TTCAAAGCCCACACAAGT
289451 TGATGGGAAC
Statistics
Matches: 327, Mismatches: 19, Indels: 24
0.88 0.05 0.06
Matches are distributed among these distances:
83 1 0.00
84 19 0.06
85 6 0.02
86 29 0.09
87 2 0.01
88 13 0.04
89 1 0.00
90 13 0.04
92 14 0.04
94 113 0.35
95 3 0.01
96 111 0.34
97 2 0.01
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.19
Consensus pattern (92 bp):
TTTCAAAGCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCGGTGGCACTTTTCA
AAGCCCACACAAGTCGGTGGCAACCCA
Found at i:290810 original size:20 final size:20
Alignment explanation
Indices: 290767--290813 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
290757 GGTAAGAAAG
* * * *
290767 AAAGAAAGAAGATGAAGAAG
1 AAAGAAAGAACAAGAAAAAA
290787 AAAGAAAGAACAAGAAAAAA
1 AAAGAAAGAACAAGAAAAAA
290807 AAAGAAA
1 AAAGAAA
290814 AAAATATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.74, C:0.02, G:0.21, T:0.02
Consensus pattern (20 bp):
AAAGAAAGAACAAGAAAAAA
Found at i:293664 original size:16 final size:15
Alignment explanation
Indices: 293631--293660 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
293621 TTTTTTAATA
293631 AAATTAAAAAAATTT
1 AAATTAAAAAAATTT
*
293646 AAATTAAATAAATTT
1 AAATTAAAAAAATTT
293661 TAAAAAATAG
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAAAAAAATTT
Found at i:294290 original size:71 final size:72
Alignment explanation
Indices: 294195--294463 Score: 250
Period size: 71 Copynumber: 3.8 Consensus size: 72
294185 TATAGTTATG
*
294195 AGTTTAAAT-TTTAAAG-TATAATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTGGTTTG
1 AGTTTAAATATTT-AAGTTATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTGGTTTG
*
294258 ATTAGACA
65 ATTATACA
* * * * * **
294266 AGTTTAAATATTT-AGTTATTATTTATTTTTATTCGTGAAAGTTTAAATTTGTTTTTTAAG-AAG
1 AGTTTAAATATTTAAGTTATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTT-GGTTTG
294329 ATTATACA
65 ATTATACA
* * * * * * * *
294337 AG-TTAAATTTTTTAAAG-TATAATATA-TTTTATTTATAGAAGTTTAAATCT-GTTTTTGGTTT
1 AGTTTAAA-TATTT-AAGTTATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTGGTTT
*
294398 AATTATA-A
64 GATTATACA
* *
294406 GAATTTAAATATTTAAGTTATTATTTATTTTTATTTGTAAAAATTTTAATTTATTTTT
1 -AGTTTAAATATTTAAGTTATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTT
294464 ATTTATAAAA
Statistics
Matches: 154, Mismatches: 32, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
69 5 0.03
70 30 0.19
71 102 0.66
72 15 0.10
73 2 0.01
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (72 bp):
AGTTTAAATATTTAAGTTATTATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTGGTTTGA
TTATACA
Found at i:294392 original size:142 final size:143
Alignment explanation
Indices: 294203--294463 Score: 357
Period size: 142 Copynumber: 1.8 Consensus size: 143
294193 TGAGTTTAAA
* * * *
294203 TTTTAAAGTATAATTTATTTTTATTTGTAAAAATTTAAATTTATTTTTTGGTTTGATTAGACA-A
1 TTTTAAAGTATAATATATTTTTATTTATAAAAATTTAAATCTA-TTTTTGGTTTAATTAGA-AGA
* * * *
294267 GTTTAAATATTT-AGTTATTATTTATTTTTATTCGTGAAAGTTTAAATTTGTTTTTTAAGAAGAT
64 ATTTAAATATTTAAGTTATTATTTATTTTTATTCGTAAAAATTTAAATTTATTTTTTAAGAAGAT
294331 TATACAAGTTAAATT
129 TATACAAGTTAAATT
* * * *
294346 TTTTAAAGTATAATATA-TTTTATTTATAGAAGTTTAAATCTGTTTTTGGTTTAATTATAAGAAT
1 TTTTAAAGTATAATATATTTTTATTTATAAAAATTTAAATCTATTTTTGGTTTAATTAGAAGAAT
* *
294410 TTAAATATTTAAGTTATTATTTATTTTTATTTGTAAAAATTTTAATTTATTTTT
66 TTAAATATTTAAGTTATTATTTATTTTTATTCGTAAAAATTTAAATTTATTTTT
294464 ATTTATAAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
140 1 0.01
141 27 0.26
142 58 0.57
143 16 0.16
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (143 bp):
TTTTAAAGTATAATATATTTTTATTTATAAAAATTTAAATCTATTTTTGGTTTAATTAGAAGAAT
TTAAATATTTAAGTTATTATTTATTTTTATTCGTAAAAATTTAAATTTATTTTTTAAGAAGATTA
TACAAGTTAAATT
Found at i:294790 original size:72 final size:73
Alignment explanation
Indices: 294483--295537 Score: 636
Period size: 71 Copynumber: 14.7 Consensus size: 73
294473 ATCACACCAG
* * * * * * * *
294483 AAAACAAATTTAAAGTTATACAAATAAAAATAAAATCATATCTT-GAAATTTTAAACTCATATAA
1 AAAAGAAATTTAAACTTTTACAAATAAAAAT-AAATAATACCTTAAAAAATTTAAACTCGTATAA
*
294547 TAAT-TCCTAA
65 TCATAT-C-AA
* *
294557 AAAATAAATTTAAACTTTTAC-AATAAAAATAAAAATAAAAATACTTTAAAAAATTTTAAACTTC
1 AAAAGAAATTTAAACTTTTACAAATAAAAAT--AAAT---AATACCTTAAAAAA-TTTAAAC-TC
* * *
294621 -CATAAT-AAAACAAA
59 GTATAATCATATC-AA
* * * *
294635 AAAACAAATTTAAAGTTTTACAAAT-AAAAT-CAT-AT--CTT--AAAATTTAAAACTCATATAA
1 AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACCTTAAAAAATTT-AAACTCGTATAA
*
294693 TCATACCAGA
65 TCATATCA-A
* *** * * *
294703 GAAACG-AATTTAAACTTTTATGGATAGAAATAAGTTATACCTTAAAAAATTTAAACTCGTATAA
1 -AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACCTTAAAAAATTTAAACTCGTATAA
*
294767 TCATA-CAC
65 TCATATCAA
* *
294775 AAAAGAAATTTAAACTTTTACAAATAAAGATAAACAATACCTT-AAAAATTTAAACTCGTATAAT
1 AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACCTTAAAAAATTTAAACTCGTATAAT
* * *
294839 TAAACCAA
66 CATATCAA
* * * * *
294847 AGAACAAATTTAAACTTTAAC-AA-AAAAATAAATTATACCTTAAAAAATTTAAA-TTGTATAAT
1 AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACCTTAAAAAATTTAAACTCGTATAAT
*
294909 CATATTGAA
66 CATA-TCAA
* *** *
294918 AAAAGAAATTTAAACTTCTACAAATAAAAATAAA-AATGTTTTAAAAAATTTAAACTCGTCTAAT
1 AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACCTTAAAAAATTTAAACTCGTATAAT
294982 CGA-ATCAA
66 C-ATATCAA
* * * *
294990 AAAACAAATTT-AA-TGTTTACAAATAAAAATAAATCATA-CTTTAAAAATTTAAACTCGTATTA
1 AAAAGAAATTTAAACT-TTTACAAATAAAAATAAATAATACCTTAAAAAATTTAAACTCGTATAA
295052 TCATACTCAA
65 TCATA-TCAA
* *
295062 AAAATAAATTTAAACTTCTACAAATAAAAATAAA-AATACCTTTTAAAAAA-TTAAA-TACGTAT
1 AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACC--TTAAAAAATTTAAACT-CGTAT
* *
295124 AATCA-AACTAG
63 AATCATATC-AA
* * ** * * ** *
295135 GAAACAAATTTAATGTTCTACAAATAAAAATAAATTATTTCTT--AAAATTTAAACTCATATAAT
1 AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACCTTAAAAAATTTAAACTCGTATAAT
* *
295198 CGTA-CTA
66 CATATCAA
* * * * *
295205 AAAATAAATTTAAACTTATACAAAT---AATCAATAATATCTT-AAAAATTTAAACTCGTTTAAT
1 AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACCTTAAAAAATTTAAACTCGTATAAT
* *
295266 AATACCTAA
66 CATATC-AA
* ** * * * * * * *
295275 AAAA-AAATTCAATGTTCTACAAAT-AAAATAAATTATATCGT-AAAAATTTTATCTTGTATAAT
1 AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACCTTAAAAAATTTAAACTCGTATAAT
295337 --TAT-AA
66 CATATCAA
* * * * ** **
295342 CAAA-AAATTT-AACTTCTA-TAATAGAAATAAATTGTACCGTTAAAAAATTTAAACTTATATAA
1 AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACC-TTAAAAAATTTAAACTCGTATAA
* *
295404 TTATACCCAA
65 TCATA-TCAA
* * * * * *
295414 AAAA-CAATTTAAACTTATACAAACAAAGATCAATAATA-CTT-AAAAATTTAAACTTGTAATAA
1 AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACCTTAAAAAATTTAAACTCGT-ATAA
*
295476 TCAAATCAA
65 TCATATCAA
** * * * *
295485 AAACTAAATTTAAACTTTAACAAACAAAAATAAATTATACCTTAAAAATTTTA
1 AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACCTTAAAAAATTTA
295538 CTTTTATTGC
Statistics
Matches: 769, Mismatches: 150, Indels: 124
0.74 0.14 0.12
Matches are distributed among these distances:
65 3 0.00
66 23 0.03
67 37 0.05
68 57 0.07
69 28 0.04
70 59 0.08
71 169 0.22
72 151 0.20
73 96 0.12
74 77 0.10
75 16 0.02
77 5 0.01
78 31 0.04
79 15 0.02
80 2 0.00
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.32
Consensus pattern (73 bp):
AAAAGAAATTTAAACTTTTACAAATAAAAATAAATAATACCTTAAAAAATTTAAACTCGTATAAT
CATATCAA
Found at i:295954 original size:73 final size:71
Alignment explanation
Indices: 295856--296106 Score: 228
Period size: 71 Copynumber: 3.5 Consensus size: 71
295846 TTTTATGAGT
* *
295856 AAAAAA-AACTTAAATTTTTATAAATAAAAATAAATAATAACTTAAATATTTAAACAATTATAAT
1 AAAAAATAACTTAAACTTTTACAAATAAAAATAAATAATAACTTAAATATTTAAAC--TTAT-AT
*
295920 CATCAAACC
63 AATCAAACC
* *
295929 AAAAACAT-ACTT-AACTTTTACAAAT-AAAATAAATTAT-ACTTTAAAAAATTTAAACTTATAT
1 AAAAA-ATAACTTAAACTTTTACAAATAAAAATAAATAATAAC-TT-AAATATTTAAACTTATAT
* *
295990 AATCATACT
63 AATCAAACC
* * * * * *
295999 TAAAAATAATTTAAAC-TTTCCATGAATAAAAACAAATAATAAC-TAAATATTTAAACTTGTCTA
1 AAAAAATAACTTAAACTTTTACA--AATAAAAATAAATAATAACTTAAATATTTAAACTTATATA
*
296062 ATCAAACT
64 ATCAAACC
* *
296070 AAAAAATAAATTTAAACTTCTACAAATAAAAATAAAT
1 AAAAAAT-AACTTAAACTTTTACAAATAAAAATAAAT
296107 TATACTTTAA
Statistics
Matches: 146, Mismatches: 20, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
69 2 0.01
70 20 0.14
71 50 0.34
72 26 0.18
73 41 0.28
74 7 0.05
ACGTcount: A:0.56, C:0.11, G:0.01, T:0.32
Consensus pattern (71 bp):
AAAAAATAACTTAAACTTTTACAAATAAAAATAAATAATAACTTAAATATTTAAACTTATATAAT
CAAACC
Found at i:296481 original size:71 final size:72
Alignment explanation
Indices: 296382--296911 Score: 460
Period size: 73 Copynumber: 7.4 Consensus size: 72
296372 TCAACAGTTT
* * * *
296382 TACAAATAAAAAGAAATAATACCTTAAAAATTTAAACTCGTATCATCATACCTAAAAAATAAAAT
1 TACAAATAAAAATAAAT-ATATCTTAAAAATTTAAACTCGTATAATCATACCTAAAAAATAAATT
*
296447 TACACTTC
65 TAAACTTC
* ** * * *
296455 TACAAATAAAAATAAA-ATACCTTAAAAAAATTTAAAC-AATATAATCA-AACTAGAAAATAAGT
1 TACAAATAAAAATAAATATATCTT--AAAAATTTAAACTCGTATAATCATACCTAAAAAATAAAT
**
296517 TTAATTTTC
64 TTAAACTTC
* * *
296526 GACAAATAAAAATAAATTATATCTTAAAAATATAAACTCGTATAATCATACCCAAAAAATAAATT
1 TACAAATAAAAATAAA-TATATCTTAAAAATTTAAACTCGTATAATCATACCTAAAAAATAAATT
*
296591 TAAACTTA
65 TAAACTTC
* * * *
296599 TACAAATAAAGATCAATAATATCTTAAAAATTTAAACTCTTATAATAATACCTAAAAAATAAATT
1 TACAAATAAAAATAAAT-ATATCTTAAAAATTTAAACTCGTATAATCATACCTAAAAAATAAATT
** *
296664 TAATGTTT
65 TAAACTTC
* * * * *
296672 TACAAAGAAATATAAATTATATCTTATAAAGTTT-ACCTCGCAT-ATCATA-C---AAAA-AAA-
1 TACAAATAAAAATAAA-TATATCTTA-AAAATTTAAACTCGTATAATCATACCTAAAAAATAAAT
296729 TTAAACTTC
64 TTAAACTTC
* * * *
296738 TA-TAATAAAAATAAATATATTTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTA
1 TACAAATAAAAATAAATATATCTTAAAAATTTAAACTCGTATAATCATACCTAAAAAATAAATTT
296802 AAACGTTC
66 AAAC-TTC
* * * * * * * * *
296810 -ATAAACAAAGATCAATATATCTTAAAAATTTATACTTGTGTAATCAAATC-AAAAAAT-AATTT
1 TACAAATAAAAATAAATATATCTTAAAAATTTAAACTCGTATAATCATACCTAAAAAATAAATTT
* *
296872 AAATTTT
66 AAACTTC
* *
296879 TACAAATAAAAATAAATTATACCTCAAAAATTT
1 TACAAATAAAAATAAA-TATATCTTAAAAATTT
296912 TACTTTTATT
Statistics
Matches: 365, Mismatches: 71, Indels: 44
0.76 0.15 0.09
Matches are distributed among these distances:
63 6 0.02
64 15 0.04
65 16 0.04
66 9 0.02
67 3 0.01
68 4 0.01
69 6 0.02
70 21 0.06
71 78 0.21
72 62 0.17
73 138 0.38
74 7 0.02
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.32
Consensus pattern (72 bp):
TACAAATAAAAATAAATATATCTTAAAAATTTAAACTCGTATAATCATACCTAAAAAATAAATTT
AAACTTC
Found at i:296497 original size:144 final size:145
Alignment explanation
Indices: 296324--296636 Score: 374
Period size: 144 Copynumber: 2.2 Consensus size: 145
296314 TTTTACAATA
* *
296324 AAAATACTTTAAAAAAA-TTAAACTTATATAATCAAA-TCAGAAACA-AA-TTCAACAGTTTT-A
1 AAAATACCTTAAAAAAATTTAAACTAATATAATCAAACT-AGAAA-ATAAGTT-AA-A-TTTTCA
* * *
296384 CAAATAAAAAGAAATAATACCTTAAAAATTTAAACTCGTATCATCATACCTAAAAAATAAAATTA
61 CAAATAAAAAGAAATAATACCTTAAAAATATAAACTCGTATAATCATACCCAAAAAATAAAATTA
* *
296449 CACTTCTACAAATAAAAAT-
126 AACTTATACAAATAAAAATC
*
296468 AAAATACCTTAAAAAAATTTAAAC-AATATAATCAAACTAGAAAATAAGTTTAATTTTCGACAAA
1 AAAATACCTTAAAAAAATTTAAACTAATATAATCAAACTAGAAAATAAGTTAAATTTTC-ACAAA
* * * *
296532 TAAAAATAAATTATATCTTAAAAATATAAACTCGTATAATCATACCCAAAAAATAAATTTAAACT
65 TAAAAAGAAATAATACCTTAAAAATATAAACTCGTATAATCATACCCAAAAAATAAAATTAAACT
*
296597 TATACAAATAAAGATC
130 TATACAAATAAAAATC
*
296613 AATAATATCTT--AAAAATTTAAACT
1 AA-AATACCTTAAAAAAATTTAAACT
296637 CTTATAATAA
Statistics
Matches: 146, Mismatches: 14, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
142 4 0.03
143 2 0.01
144 122 0.84
145 11 0.08
146 7 0.05
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (145 bp):
AAAATACCTTAAAAAAATTTAAACTAATATAATCAAACTAGAAAATAAGTTAAATTTTCACAAAT
AAAAAGAAATAATACCTTAAAAATATAAACTCGTATAATCATACCCAAAAAATAAAATTAAACTT
ATACAAATAAAAATC
Found at i:296683 original size:144 final size:144
Alignment explanation
Indices: 296383--296800 Score: 386
Period size: 144 Copynumber: 2.9 Consensus size: 144
296373 CAACAGTTTT
* * * *
296383 ACAAAT-AAAA-AGAAATAATACCTTAAAAATTTAAACTCGTATCATCATACCTAAAAAATAAAA
1 ACAAATAAAAATATAAATTATATCTTAAAAA-TTAAACTCGTAT-ATCATACCCAAAAAAT-AAA
* * *
296446 TTACACTTCTACAAATAAAAATAA-AATACCTTAAAAAAATTTAAAC-AATATAATCAA-A-CTA
63 TTAAACTTCTACAAATAAAAATAATAATATCTT--AAAAATTTAAACTCATATAAT-AATACCTA
* *
296507 GAAAATAAGTTTAATTTTCG
125 AAAAATAAATTTAATTTTCG
296527 ACAAAT-AAAA-ATAAATTATATCTTAAAAATATAAACTCGTATAATCATACCCAAAAAATAAAT
1 ACAAATAAAAATATAAATTATATCTTAAAAAT-TAAACTCGTAT-ATCATACCCAAAAAATAAA-
* * *
296590 TTAAACTTATACAAATAAAGATCAATAATATCTTAAAAATTTAAACTCTTATAATAATACCTAAA
63 TTAAACTTCTACAAATAAAAAT-AATAATATCTTAAAAATTTAAACTCATATAATAATACCTAAA
*
296655 AAATAAATTTAATGTTT-T
127 AAATAAATTTAAT-TTTCG
* * * * *
296673 AC-AA-AGAAATATAAATTATATCTTATAAAGTTTACCTCGCATATCATA--C--AAAA-AAATT
1 ACAAATAAAAATATAAATTATATCTTA-AAAATTAAACTCGTATATCATACCCAAAAAATAAATT
* * * * *
296731 AAACTTCTA-TAATAAAAATAA-ATATATTTTAAAAATTTAAACTCGTATAATCATACCCAAAAA
65 AAACTTCTACAAATAAAAATAATA-ATATCTTAAAAATTTAAACTCATATAATAATACCTAAAAA
296794 ATAAATT
129 ATAAATT
296801 AAAACGTTCA
Statistics
Matches: 236, Mismatches: 26, Indels: 31
0.81 0.09 0.11
Matches are distributed among these distances:
136 1 0.00
137 45 0.19
138 8 0.03
139 10 0.04
140 3 0.01
141 4 0.02
143 5 0.02
144 85 0.36
145 20 0.08
146 48 0.20
147 7 0.03
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.31
Consensus pattern (144 bp):
ACAAATAAAAATATAAATTATATCTTAAAAATTAAACTCGTATATCATACCCAAAAAATAAATTA
AACTTCTACAAATAAAAATAATAATATCTTAAAAATTTAAACTCATATAATAATACCTAAAAAAT
AAATTTAATTTTCG
Found at i:297192 original size:106 final size:108
Alignment explanation
Indices: 296906--297167 Score: 417
Period size: 108 Copynumber: 2.5 Consensus size: 108
296896 TATACCTCAA
* * * *
296906 AAATTTTACTTTTATTACATTAATGCAATCAAACTATATTTTACTTTTGTTTCTTAAACTACA-A
1 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTTCATTTATTTCTTAAAC-A-ATA
* *
296970 AAATAAATTTT-ACTTTATTTGCATTAATGTATTGTTGTTGAAAT
64 AAATAAATTTTAATTTTATTTGCATTAATGTATTGTTATTGAAAT
297014 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTTCATTTATTTCTTAAACAATAAA
1 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTTCATTTATTTCTTAAACAATAAA
297079 ATAAATTTTAATTTTA-TTGCA-TAATGTATTGTTATTGAAAT
66 ATAAATTTTAATTTTATTTGCATTAATGTATTGTTATTGAAAT
297120 AAATTTTACTTTTATTGCATTAATGCAATC-AACTATATTTTTCATTTA
1 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTTCATTTA
297168 GTTATGTTAA
Statistics
Matches: 146, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
105 18 0.12
106 50 0.34
107 18 0.12
108 60 0.41
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (108 bp):
AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTTCATTTATTTCTTAAACAATAAA
ATAAATTTTAATTTTATTTGCATTAATGTATTGTTATTGAAAT
Found at i:297685 original size:71 final size:71
Alignment explanation
Indices: 297556--297691 Score: 163
Period size: 71 Copynumber: 1.9 Consensus size: 71
297546 TTTAAACGCT
* * *
297556 TATAATTAAACCAAAAAACAGATTTAAACTTTTACAATAAAATAAATTATACTTTAAAAAATTTA
1 TATAATTAAACCAAAAAACAAAATTAAACTTTTACAATAAAATAAATTATACTCTAAAAAATTTA
297621 AATTAG
66 AATTAG
* *
297627 TATAATTAAATCAAAAAA-ATAAATTAAA-TTTTGAACAA-AAATATAAATTATAC-CTAAAAAT
1 TATAATTAAACCAAAAAACA-AAATTAAACTTTT--ACAATAAA-ATAAATTATACTCTAAAAAA
297688 TTTA
62 TTTA
297692 CTTTTATTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
70 5 0.09
71 36 0.64
72 15 0.27
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (71 bp):
TATAATTAAACCAAAAAACAAAATTAAACTTTTACAATAAAATAAATTATACTCTAAAAAATTTA
AATTAG
Found at i:298178 original size:671 final size:666
Alignment explanation
Indices: 297014--298286 Score: 1726
Period size: 670 Copynumber: 1.9 Consensus size: 666
297004 TTGTTGAAAT
* * *
297014 AAATTTTACTTTTATTGCATTAATGCAATCAAACTATATTTTTCATTTATTTCTTAAACAATAAA
1 AAATTTTACTTTTATTACAATAATGCAATCAAAC-ATATTTTACATTTATTTCTTAAACAATAAA
*
297079 ATAAATTTTAATTTTATTGCATAATGTATTGTTATTGAAATAAATTTTACTTTTATTGCATTAAT
65 ATAAATTTTAATTTTATTGAATAATGTATTGTTATTGAAATAAATTTTACTTTTATTGCATTAAT
* **
297144 GCAATCAACTATATTTTTCATTTAGTTATGTTAATAGTTTTTCTAATTTGAATTTGTAGATAGCA
130 GCAATCAACTATATTTTACATTTAGTTATGTTAATAGTTTTTCTAATTTGAATTTGTAGATAAAA
** *
297209 ATAAATTTAAATTTTTACAAATAAAAATGGGTTGTTTATTATTGTTGTTGAAATAAGTATTATTT
195 ATAAATTTAAATTTTTACAAATAAAAATGAATAGTTTATTATTGTTGTTGAAATAAGTATTATTT
*
297274 ATATAATTTACCTTTTAAATTTTACTTTATTGTTGTTTGAAATAAGTTATTATTTATTTATTACA
260 ATATAATCTACCTTTTAAATTTTACTTTATTGTTGTTTGAAATAAGTTATTATTTATTTATTACA
* *
297339 TTAATGCGTTTTATTTTTAGTGCAATCAAACTATTAAAATAAATTTTGCATTTAATTGCATTGAA
325 TTAATGCATTTTACTTTTAGTGCAATCAAACTATTAAAATAAATTTTGCATTTAATTGCATTGAA
*
297404 TATATTTTGGTTGAAATAAATTTTACTTTTATTCATTAATGCAACCAAACTATTTTTATTTATTT
390 TATATTTTGGTTGAAATAAATTTTACTTTTATTCATTAATGCAACCAAACTATTTTTATTTACTT
* *
297469 CTTAAAATAGTTTTTGGTGTTGATTTATGAGTAAAATAAA-TTTAACTTTTAAAAATAAAAATAA
455 CTTAAAATAGTTTTTGGTGTTAATTTATGAGTAAAATAAATTTTAA-ATTTAAAAATAAAAA-AA
* * * * *
297533 ATAATAACTT-ATATTTAAACGCTTATAATTAAAC-CAAAAAACAGATTTAAACT-TTTAC-AAT
518 AT-ATAACTTAATATTGAAACGC---GAATCAAACAAAAAAAACAAATTTAAA-TATTTACAAAT
297594 AAAATAAATTATACTTTAAAAAATTTAAATTAGTATAATTAAATCAAAAAAATAAATTAAATTTT
578 AAAAT-AATTATACTTTAAAAAATTTAAATTAGTATAATTAAATCAAAAAAATAAATTAAATTTT
297659 GAACAAAAATATAAATTATACCTAA
642 GAACAAAAATATAAATTATACCTAA
*
297684 AAATTTTACTTTTATTACAAT-ATGCAATATCAAAC-TATTTTACTTTTATTTCTTAAACTACA-
1 AAATTTTACTTTTATTACAATAATGC-A-ATCAAACATATTTTACATTTATTTCTTAAAC-A-AT
* * *
297746 AAAATAAATTTTACTTTTATTATAATAATGTATTGTTGTTGAAATAAATTTTACTTTTATTGCAT
62 AAAATAAATTTTAATTTTATT-GAATAATGTATTGTTATTGAAATAAATTTTACTTTTATTGCAT
* * * * *
297811 TAATGCAATCAAATTATATTTTACTTTTATTTAT-TTAATAGTTTTTCTGATTT-CATTT-TATG
126 TAATGCAATC-AACTATATTTTACATTTAGTTATGTTAATAGTTTTTCTAATTTGAATTTGTA-G
** *
297873 CATAAAAATAAATTTAAATTTTTATGAAT-AAAAT-AATAGTTTATTATTGTTGTTGAAAATATG
189 -ATAAAAATAAATTTAAATTTTTACAAATAAAAATGAATAGTTTATTATTGTTGTTG-AAATAAG
*
297936 TTATTATTTATATAATCTACC-TTTAAATTTTACTTTTATTGTTG-TTGAAATAAGTTCTTATTT
252 -TATTATTTATATAATCTACCTTTTAAATTTTAC-TTTATTGTTGTTTGAAATAAGTTATTATTT
* * *
297999 ATTTATTGCATTAATGTATTTTACTTTTATTGCAATCAAACTATTAAAATAAA-TTTGCATTT-A
315 ATTTATTACATTAATGCATTTTACTTTTAGTGCAATCAAACTATTAAAATAAATTTTGCATTTAA
* * *
298062 TTGCATT-AATGTATTGTT-GTTGAAA-AAA-TTTACTTTTATTGCATTAATGTAATCAAACTAT
380 TTGCATTGAATATATT-TTGGTTGAAATAAATTTTACTTTTATT-CATTAATGCAACCAAACTAT
* *
298123 ATTTTGCTTTTACTTCTTACAATAGTTTTCTGGT-TTAATTTTATGAGTAAAAATAAATTTTAAA
443 -TTTT--ATTTACTTCTTAAAATAGTTTT-TGGTGTTAA-TTTATGAGT-AAAATAAATTTTAAA
** *
298187 TTTATGAATAAAAAAAATATAACTTAAATATTGAAACGCGAATCAAACAAAAAAAATAAATTTAA
502 TTTAAAAATAAAAAAAATATAACTT-AATATTGAAACGCGAATCAAACAAAAAAAACAAATTTAA
298252 ATATTTACAAATAAAATAATTATACTTTAAAAAAT
566 ATATTTACAAATAAAATAATTATACTTTAAAAAAT
298287 GAAACTTGTA
Statistics
Matches: 533, Mismatches: 45, Indels: 51
0.85 0.07 0.08
Matches are distributed among these distances:
665 12 0.02
666 21 0.04
667 18 0.03
668 18 0.03
669 120 0.23
670 160 0.30
671 160 0.30
672 24 0.05
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (666 bp):
AAATTTTACTTTTATTACAATAATGCAATCAAACATATTTTACATTTATTTCTTAAACAATAAAA
TAAATTTTAATTTTATTGAATAATGTATTGTTATTGAAATAAATTTTACTTTTATTGCATTAATG
CAATCAACTATATTTTACATTTAGTTATGTTAATAGTTTTTCTAATTTGAATTTGTAGATAAAAA
TAAATTTAAATTTTTACAAATAAAAATGAATAGTTTATTATTGTTGTTGAAATAAGTATTATTTA
TATAATCTACCTTTTAAATTTTACTTTATTGTTGTTTGAAATAAGTTATTATTTATTTATTACAT
TAATGCATTTTACTTTTAGTGCAATCAAACTATTAAAATAAATTTTGCATTTAATTGCATTGAAT
ATATTTTGGTTGAAATAAATTTTACTTTTATTCATTAATGCAACCAAACTATTTTTATTTACTTC
TTAAAATAGTTTTTGGTGTTAATTTATGAGTAAAATAAATTTTAAATTTAAAAATAAAAAAAATA
TAACTTAATATTGAAACGCGAATCAAACAAAAAAAACAAATTTAAATATTTACAAATAAAATAAT
TATACTTTAAAAAATTTAAATTAGTATAATTAAATCAAAAAAATAAATTAAATTTTGAACAAAAA
TATAAATTATACCTAA
Found at i:298190 original size:25 final size:24
Alignment explanation
Indices: 298156--298204 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
298146 AGTTTTCTGG
* *
298156 TTTAATTTTATGAGTAAAAATAAAT
1 TTTAAATTTATGAATAAAAA-AAAT
298181 TTTAAATTTATGAATAAAAAAAAT
1 TTTAAATTTATGAATAAAAAAAAT
298205 ATAACTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (24 bp):
TTTAAATTTATGAATAAAAAAAAT
Found at i:298337 original size:137 final size:137
Alignment explanation
Indices: 298170--298422 Score: 320
Period size: 137 Copynumber: 1.8 Consensus size: 137
298160 ATTTTATGAG
* *
298170 TAAAAATAAATTTTAAATTTATGAATAAAAA-AAATATAACTTAAATATTGAAAC-G-CGAATCA
1 TAAAAATAAATTTTAAATTTATAAATAAAAATAAAAATAAC-TAAATATTGAAACTGTCGAATCA
* *
298232 AACAAAAAAAATAAATTTAAA-TATTTACAAATAAAAT-AATTATACTTTAAAAAATGAAACTTG
65 AAC--AAAAAATAAATTTAAAGT-TATA-AAATAAAATAAATTAGACTTTAAAAAATGAAACTTG
298295 TATAATCACATT
126 TATAATCACATT
* * * *
298307 TAAAAATAAA-TTTAAACTTTGTAAATAAAAATAAAAATAACTAAATATTTAAACTTGTCTAATT
1 TAAAAATAAATTTTAAA-TTTATAAATAAAAATAAAAATAACTAAATATTGAAAC-TGTCGAATC
*
298371 AAACTAAAAATAAATTTAAAGTTATAAAATAAAATAAATTAGACTTTAAAAA
64 AAACAAAAAATAAATTTAAAGTTATAAAATAAAATAAATTAGACTTTAAAAA
298423 TTTAAACCAT
Statistics
Matches: 100, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
136 6 0.06
137 43 0.43
138 41 0.41
139 2 0.02
140 8 0.08
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (137 bp):
TAAAAATAAATTTTAAATTTATAAATAAAAATAAAAATAACTAAATATTGAAACTGTCGAATCAA
ACAAAAAATAAATTTAAAGTTATAAAATAAAATAAATTAGACTTTAAAAAATGAAACTTGTATAA
TCACATT
Found at i:298606 original size:23 final size:23
Alignment explanation
Indices: 298580--298647 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
298570 CTTACAAACA
298580 AAAAATAAATTATACTTTAAAAT
1 AAAAATAAATTATACTTTAAAAT
* *
298603 -AAAACAAATTAAAACTTTACAAAT
1 AAAAATAAATT-ATACTTTA-AAAT
*
298627 AAAAATAAA-AATACTTTAAAA
1 AAAAATAAATTATACTTTAAAA
298648 AATTTAAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 12 0.32
23 14 0.38
24 4 0.11
25 7 0.19
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAATAAATTATACTTTAAAAT
Found at i:298829 original size:144 final size:143
Alignment explanation
Indices: 298608--298872 Score: 322
Period size: 143 Copynumber: 1.8 Consensus size: 143
298598 AAAATAAAAC
*
298608 AAATTAAAACTTTACAAATAAAAATAAAAATACTTTAAAAAATTTAAATCATATAAGTAAATCAG
1 AAATTAAAACTTTACAAATAAAAATAAAAATACTTAAAAAAATTTAAATCATATAAGTAAATCAG
* * *
298673 AAAACAAATTTAAAATTTTATAGATAAAAATAAAATAATACCTTAAAAAT-TAAACTTGTATTAT
66 AAAACAAATTTAAAATTCTACAAATAAAAATAAAAT-ATACCTTAAAAATATAAACTTGTATTAT
298737 CATATCCAAAAATT
130 CATATCCAAAAATT
* * *
298751 AAATTTAAACTTCTAC-AATAAAAA-AAAAATACCTTAAAAAAATTTAAATACGTATAATTAAA-
1 AAATTAAAACTT-TACAAATAAAAATAAAAATA-CTTAAAAAAATTTAAAT-CATATAAGTAAAT
* * ** ** * *
298813 CTAGAGAATAGTTTTAATGTTCTACAAATAAAAATAAACTATATCTTAAAAATATAAACT
63 C-AGAAAACAAATTTAAAATTCTACAAATAAAAATAAAATATACCTTAAAAATATAAACT
298873 CCTACAACCA
Statistics
Matches: 102, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
142 7 0.07
143 48 0.47
144 47 0.46
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (143 bp):
AAATTAAAACTTTACAAATAAAAATAAAAATACTTAAAAAAATTTAAATCATATAAGTAAATCAG
AAAACAAATTTAAAATTCTACAAATAAAAATAAAATATACCTTAAAAATATAAACTTGTATTATC
ATATCCAAAAATT
Found at i:299018 original size:71 final size:72
Alignment explanation
Indices: 298603--299215 Score: 375
Period size: 72 Copynumber: 8.7 Consensus size: 72
298593 ACTTTAAAAT
* * * *
298603 AAAACAAATTAAAACTT-TACAAATAAAAATAAA-AATA-CTTTAAAAAATTTAAA-TCATATAA
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATTATATC-TT-AAAAATTTAAACTCGTATAA
*
298664 GTAA-ATC-A
64 -TAATACCTA
* * * * * * * * *
298672 GAAAACAAATTTAAAATTTTATAGATAAAAATAAAATAATACCTTAAAAA-TTAAACTTGTATTA
1 -AAAATAAATTTAAACTTCTACAAATAAAAAT-AAATTATATCTTAAAAATTTAAACTCGTATAA
*
298736 TCATATCC-A
64 TAATA-CCTA
* *
298745 AAAATTAAATTTAAACTTCTAC-AATAAAAA-AAA-AATACCTTAAAAAAATTTAAA-TACGTAT
1 AAAA-TAAATTTAAACTTCTACAAATAAAAATAAATTATATCTT--AAAAATTTAAACT-CGTAT
298806 AATTAA-A-CTA
62 AA-TAATACCTA
* ** ** * * * * *
298816 GAGAATAGTTTTAATGTTCTACAAATAAAAATAAACTATATCTTAAAAATATAAACTCCTACAAC
1 -AAAATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAAT
* *
298881 CATACCCA
65 AATACCTA
* * * * * *
298889 AAAAAAAATTTAAACTTCGACAAATTAAAGTCAATAATATCTTAAAAATTTAAACTCGTATAATA
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAATA
298954 ATACCTA
66 ATACCTA
** * * * * *
298961 AAAATAAATTTAATGTTTTAC-AATAAAAATAAATTATATCTTATAAATTTTATCTCGTATAATC
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAATA
*
299025 ATAGC--
66 ATACCTA
* * *
299030 AAAA-GAATTTAAACTTCT-C--AT-AGAATAAATTATA-CTTTAAAAA-TTAAACTCATATAAT
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATTATATC-TTAAAAATTTAAACTCGTATAAT
299088 AAT-CCTTA
65 AATACC-TA
* * * * * *
299096 AAAATAAATTTAAACTTCTA-TAATAAAGATCAATAATATCTT-AAAATTTAAATTTGTATAATC
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAAT-
* *
299159 AA-ATCAA
65 AATACCTA
* * *
299166 AAAATAAATTTAAATTTTTACAAATAAAAATAAA-TATACCTTAAAAATTT
1 AAAATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTT
299216 TACTTTTATT
Statistics
Matches: 417, Mismatches: 90, Indels: 71
0.72 0.16 0.12
Matches are distributed among these distances:
63 1 0.00
64 15 0.04
65 18 0.04
66 6 0.01
67 14 0.03
68 10 0.02
69 18 0.04
70 67 0.16
71 99 0.24
72 133 0.32
73 29 0.07
74 7 0.02
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.33
Consensus pattern (72 bp):
AAAATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAATA
ATACCTA
Found at i:299773 original size:70 final size:69
Alignment explanation
Indices: 299634--299894 Score: 227
Period size: 71 Copynumber: 3.8 Consensus size: 69
299624 ATTTTATTGT
** * *
299634 AAAAATAAATTT-AAATT-TATGAATAAAA-AAA-TA-ACTTAAATATTGAAACGCTT-ATAATC
1 AAAAATAAATTTAAAATTATACAAATAAAATAAATTATACTTAAAAATTTAAA--CTTGATAATC
299693 AAAC-TA
64 -AACTTA
299699 AAAAATAAATTTAAACATT-TACAAATAAAATAAATTATACTTAAAAAATTTAAACTTGATAATC
1 AAAAATAAATTTAAA-ATTATACAAATAAAATAAATTATACTT-AAAAATTTAAACTTGATAATC
299763 ATACTTA
64 A-ACTTA
* * * * * * *
299770 AAAAATAAATTTAAACTTCTGCAAA-AAAATAAATAATAAC-TAAATATTTAAACTTGTCTAATT
1 AAAAATAAATTTAAAATTATACAAATAAAATAAATTAT-ACTTAAAAATTTAAACTTG-ATAATC
*
299833 AAATTA
64 AACTTA
* * * *
299839 AAAAATAAATTTAAAGTTATACTAATAAAAATAAATTACACTTTAAAATTTAAACT
1 AAAAATAAATTTAAAATTATACAAAT-AAAATAAATTATACTTAAAAATTTAAACT
299895 CAAAATCACT
Statistics
Matches: 162, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
65 12 0.07
66 2 0.01
67 12 0.07
68 3 0.02
69 45 0.28
70 33 0.20
71 55 0.34
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (69 bp):
AAAAATAAATTTAAAATTATACAAATAAAATAAATTATACTTAAAAATTTAAACTTGATAATCAA
CTTA
Found at i:299851 original size:32 final size:32
Alignment explanation
Indices: 299744--299873 Score: 84
Period size: 32 Copynumber: 3.9 Consensus size: 32
299734 TATACTTAAA
* * *
299744 AAATTTAAACTTG-ATAATCATACTTAAAAAAT
1 AAATTTAAACTTGTCTAAT-AAAATTAAAAAAT
* * *
299776 AAATTTAAACTTCTGC-AAAAAAATAAATAATAACT
1 AAATTTAAACTTGT-CTAATAAAATTAA-AA-AA-T
*
299811 AAATATTTAAACTTGTCTAATTAAATTAAAAAAT
1 -AA-ATTTAAACTTGTCTAATAAAATTAAAAAAT
* * *
299845 AAATTTAAAGTTATACTAATAAAAATAAA
1 AAATTTAAACTTGT-CTAATAAAATTAAA
299874 TTACACTTTA
Statistics
Matches: 75, Mismatches: 14, Indels: 17
0.71 0.13 0.16
Matches are distributed among these distances:
32 27 0.36
33 18 0.24
34 3 0.04
35 3 0.04
36 5 0.07
37 19 0.25
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (32 bp):
AAATTTAAACTTGTCTAATAAAATTAAAAAAT
Found at i:300647 original size:29 final size:28
Alignment explanation
Indices: 300591--300651 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
300581 AAGATAGCTT
* *
300591 AAAAATTTAAACTTGTATAATTAAAATA
1 AAAAATTTAAACTTGTACAAATAAAATA
* *
300619 AAAAATTTAAATTTTTACAAATACAAATA
1 AAAAATTTAAACTTGTACAAATA-AAATA
300648 AAAA
1 AAAA
300652 TAAATTAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (28 bp):
AAAAATTTAAACTTGTACAAATAAAATA
Found at i:301216 original size:68 final size:69
Alignment explanation
Indices: 301144--301379 Score: 198
Period size: 68 Copynumber: 3.4 Consensus size: 69
301134 TTTTATGAGT
* *
301144 AAAAATAAA-TTAAACTTTTACGAATAAATAATAATAACTTAAATATTTAAACACTTATAATAAA
1 AAAAATAAATTTAAACTTTTACAAATAAATAATAATAACTTAAATATTTAAACACTTATAATCAA
*
301208 ACCA
66 ATCA
* * * * * **
301212 AAAAACAAATTTAAACTTTTACAAATAAAATAA-ATTATATTTAAAAAAGTTAAACTTTTATAAT
1 AAAAATAAATTTAAACTTTTACAAAT-AAATAATAATA-ACTT-AAATATTTAAACACTTATAAT
*** *
301276 CTTTTTA
63 CAAATCA
* *
301283 AAAAATAAATTTAAACGTTCACGAAA-AACA-AATAATAAC-TAAATATTT-AA-ACTTATCTAA
1 AAAAATAAATTTAAACTTTTAC-AAATAA-ATAATAATAACTTAAATATTTAAACACTTA--TAA
301343 TCAAATCA
62 TCAAATCA
* *
301351 AAAAATAAATTCAAACTTCTACAAATAAA
1 AAAAATAAATTTAAACTTTTACAAATAAA
301380 AGTAAATTAT
Statistics
Matches: 127, Mismatches: 31, Indels: 21
0.71 0.17 0.12
Matches are distributed among these distances:
66 3 0.02
67 6 0.05
68 41 0.32
69 19 0.15
70 14 0.11
71 41 0.32
72 3 0.02
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.32
Consensus pattern (69 bp):
AAAAATAAATTTAAACTTTTACAAATAAATAATAATAACTTAAATATTTAAACACTTATAATCAA
ATCA
Found at i:301326 original size:139 final size:139
Alignment explanation
Indices: 301144--301407 Score: 365
Period size: 139 Copynumber: 1.9 Consensus size: 139
301134 TTTTATGAGT
* * *
301144 AAAAATAAATTAAACTTTTACGAATAAATAATAATAACTTAAATATTTAAACACTTA-TAATAAA
1 AAAAATAAATTAAACGTTCACGAATAAAAAATAATAACTTAAATATTT-AA-ACTTACTAATAAA
* * *
301208 ACCAAAAAACAAATTTAAACTTTTACAAATAAAA-TAAATTATATTTAAAAAAGTTAAACTTTTA
64 ACCAAAAAACAAATTCAAACTTCTACAAATAAAAGTAAATTATACTTAAAAAAGTTAAACTTTTA
301272 TAATCTTTTTA
129 TAATCTTTTTA
*
301283 AAAAATAAATTTAAACGTTCACGAA-AAACAAATAATAAC-TAAATATTTAAACTTATCTAATCA
1 AAAAATAAA-TTAAACGTTCACGAATAAA-AAATAATAACTTAAATATTTAAACTTA-CTAATAA
* * *
301346 AATCAAAAAATAAATTCAAACTTCTACAAATAAAAGTAAATTATACTTAAAAAATTTAAACT
63 AACCAAAAAACAAATTCAAACTTCTACAAATAAAAGTAAATTATACTTAAAAAAGTTAAACT
301408 CCTAACTATA
Statistics
Matches: 110, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
137 5 0.05
138 2 0.02
139 57 0.52
140 46 0.42
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (139 bp):
AAAAATAAATTAAACGTTCACGAATAAAAAATAATAACTTAAATATTTAAACTTACTAATAAAAC
CAAAAAACAAATTCAAACTTCTACAAATAAAAGTAAATTATACTTAAAAAAGTTAAACTTTTATA
ATCTTTTTA
Found at i:301606 original size:19 final size:19
Alignment explanation
Indices: 301582--301646 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
301572 TTTAAAATAA
301582 AATAAATTTAAACTTCTAT
1 AATAAATTTAAACTTCTAT
* * * * *
301601 AATAAAATAAAAATACTTT
1 AATAAATTTAAACTTCTAT
*
301620 AATAAATTTGAAC-TCATAT
1 AATAAATTTAAACTTC-TAT
301639 AATCAAAT
1 AAT-AAAT
301647 CAGAAAATAA
Statistics
Matches: 33, Mismatches: 11, Indels: 3
0.70 0.23 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.85
20 4 0.12
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (19 bp):
AATAAATTTAAACTTCTAT
Found at i:301609 original size:24 final size:22
Alignment explanation
Indices: 301553--301611 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 22
301543 CTAATCTTAC
*
301553 AAATAAAAATAAATTATACTTTA
1 AAAT-AAAATAAATTAAACTTTA
301576 AAATAAAATAAATTTAAACTTCTA
1 AAATAAAATAAA-TTAAACTT-TA
*
301600 TAATAAAATAAA
1 AAATAAAATAAA
301612 AATACTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 8 0.25
23 11 0.34
24 13 0.41
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATAAAATAAATTAAACTTTA
Found at i:301624 original size:22 final size:23
Alignment explanation
Indices: 301558--301624 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
301548 CTTACAAATA
*
301558 AAAATAAATTATACTTTAA-AAT
1 AAAATAAATAATACTTTAATAAT
301580 AAAATAAATTTAA-ACTTCT-ATAAT
1 AAAATAAA--TAATACTT-TAATAAT
301604 AAAATAAA-AATACTTTAATAA
1 AAAATAAATAATACTTTAATAA
301625 ATTTGAACTC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
21 3 0.08
22 16 0.42
23 5 0.13
24 14 0.37
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAATAAATAATACTTTAATAAT
Found at i:301892 original size:72 final size:72
Alignment explanation
Indices: 301580--302159 Score: 365
Period size: 72 Copynumber: 8.2 Consensus size: 72
301570 ACTTTAAAAT
* * * *
301580 AAAATAAATTTAAACTTCTA-TAATAAA-ATAAA-AATA-CTTTAATAAATTTGAACTCATATAA
1 AAAATAAATTTAAACTTCTACAAATAAAGATAAATTATATC-TTAA-AAATTTAAACTCGTATAA
* *
301641 TCAAATC-A
64 TCATACCTA
* * * * * *
301649 GAAAATAAATTTAAAGTTTTACAAATAAAAATAAATCATGTCTTAAAAATTTAAACTTGTATTAA
1 -AAAATAAATTTAAACTTCTACAAATAAAGATAAATTATATCTTAAAAATTTAAACTCGTA-TAA
*
301714 T-ATA-CAA
64 TCATACCTA
* * * * *
301721 AAAAAATAATTTAAATTTCCAAAAAAATAAA-ATAAA--ATAACTTAAAAAAATTTAAA-TACGT
1 AAAATA-AATTTAAACTT-C-TACAAATAAAGATAAATTATATCTT--AAAAATTTAAACT-CGT
*
301782 ATAATCA-AACTA
60 ATAATCATACCTA
* * *** * * *
301794 GAAAACAAGTTTATTGTTCCAAAAATAAAGATAAATTATATCTTAAAAATTTAAACTC-CATAAT
1 -AAAATAAATTTAAACTTCTACAAATAAAGATAAATTATATCTTAAAAATTTAAACTCGTATAAT
*
301858 TATACCTA
65 CATACCTA
* ** * *
301866 AAAATAAATTTAAAACTTATACAAATAGTGAT-AATAATATCTTAAACATTTAAACTCGTATAAT
1 AAAATAAATTT-AAACTTCTACAAATAAAGATAAATTATATCTTAAAAATTTAAACTCGTATAAT
* *
301930 AAAACCTA
65 CATACCTA
* ** * * *
301938 AAAAGCAAATTTAATGTTCTACAAATAAAAATAAATTA-ATCTTAAAAATTTTATCTCGTATAAT
1 AAAA-TAAATTTAAACTTCTACAAATAAAGATAAATTATATCTTAAAAATTTAAACTCGTATAAT
302002 CATA-C--
65 CATACCTA
* * *
302007 -AAA-AAA-TTAAACTTTTA-TAATAGAA-ATAAATTATA-CTTCAAAAAATTAAACTCGTATAA
1 AAAATAAATTTAAACTTCTACAAATA-AAGATAAATTATATCTT-AAAAATTTAAACTCGTATAA
*
302066 TCATATCTAA
64 TCATACCT-A
* * *
302076 AAAATAAATTTAAACTTCTACAAATAAAGATTAATAATATCTT-AAAA-TTAAACTTGTATAATC
1 AAAATAAATTTAAACTTCTACAAATAAAGATAAATTATATCTTAAAAATTTAAACTCGTATAATC
302139 A-A--TA
66 ATACCTA
302143 AAAA-AATATTTAAACTT
1 AAAATAA-ATTTAAACTT
302160 TACCATAACA
Statistics
Matches: 404, Mismatches: 68, Indels: 79
0.73 0.12 0.14
Matches are distributed among these distances:
64 15 0.04
65 33 0.08
66 6 0.01
67 15 0.04
68 4 0.01
70 22 0.05
71 84 0.21
72 140 0.35
73 62 0.15
74 23 0.06
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (72 bp):
AAAATAAATTTAAACTTCTACAAATAAAGATAAATTATATCTTAAAAATTTAAACTCGTATAATC
ATACCTA
Found at i:302338 original size:35 final size:34
Alignment explanation
Indices: 302295--302385 Score: 105
Period size: 33 Copynumber: 2.7 Consensus size: 34
302285 CTGTTGAAAT
* *
302295 AAATTTTACTTTTATTGCATTAACGCAATCA-AAC
1 AAATTTTACTTTTATTGCATTAA-ACAATAACAAC
* **
302329 TATATTTTACTTTTATT-TTTTAAACAATAACAAC
1 -AAATTTTACTTTTATTGCATTAAACAATAACAAC
302363 AAATTTTACTTTTATTGCATTAA
1 AAATTTTACTTTTATTGCATTAA
302386 TGTATTGTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
33 20 0.43
34 11 0.24
35 15 0.33
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.46
Consensus pattern (34 bp):
AAATTTTACTTTTATTGCATTAAACAATAACAAC
Found at i:302424 original size:107 final size:105
Alignment explanation
Indices: 302190--302453 Score: 302
Period size: 107 Copynumber: 2.5 Consensus size: 105
302180 TTTACCTTAA
* * * *
302190 AAATATTACTTTTATTGCATTAATGTAAT-TAACTA-ATATATACTTTTATTTCTTAACTATAAA
1 AAAT-TTACTTTTATTGCATTAATGCAATCAAACTATAT-TTTACTTTTATTTCTTAACAATAAA
*
302253 AATAAAATTTTCTTTTATGAATAATGTATTGCCTGTTGAAAT
64 AATAAAATTTTCTTTTATGAATAATGTATTGCCTATTGAAAT
* * *
302295 AAATTTTACTTTTATTGCATTAACGCAATCAAACTATATTTTACTTTTATTTTTTAAACAATAAC
1 AAA-TTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACTTTTATTTCTT-AACAATAAA
* * *
302360 AA-CAAATTTTACTTTTATTGCATTAATGTATTG-TTATTGAAAT
64 AATAAAATTTT-CTTTTA-TG-AATAATGTATTGCCTATTGAAAT
* * * *
302403 AAATTTACTTTTATTGTATTAATGCAATCAAACAATATTTTCCATTTATTT
1 AAATTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACTTTTATTT
302454 ATTTTAATAG
Statistics
Matches: 136, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
105 25 0.18
106 27 0.20
107 60 0.44
108 13 0.10
109 11 0.08
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (105 bp):
AAATTTACTTTTATTGCATTAATGCAATCAAACTATATTTTACTTTTATTTCTTAACAATAAAAA
TAAAATTTTCTTTTATGAATAATGTATTGCCTATTGAAAT
Found at i:303032 original size:25 final size:24
Alignment explanation
Indices: 302986--303042 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
302976 TTATCTAATC
302986 AAAATAAAATAAATTTAAACTTCTA
1 AAAATAAAATAAATTTAAACTT-TA
* *
303011 CAAATAAAAGTAAA-TTATACTTTA
1 AAAATAAAA-TAAATTTAAACTTTA
303035 AAAATAAA
1 AAAATAAA
303043 CTCATAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 9 0.32
25 15 0.54
26 4 0.14
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (24 bp):
AAAATAAAATAAATTTAAACTTTA
Done.