Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 140 of 190
Found at i:41223658 original size:16 final size:17
Alignment explanation
Indices: 41223626--41223659 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41223616 ACTCTAACAT
41223626 GATGTTGAATATCTTTG
1 GATGTTGAATATCTTTG
41223643 GATGTTGAAT-TCTTTG
1 GATGTTGAATATCTTTG
41223659 G
1 G
41223660 GAAATGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.21, C:0.06, G:0.26, T:0.47
Consensus pattern (17 bp):
GATGTTGAATATCTTTG
Found at i:41238951 original size:17 final size:18
Alignment explanation
Indices: 41238923--41238956 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41238913 AGAATTCATC
*
41238923 TTATTATAGATTTAAATA
1 TTATTATAGATTGAAATA
41238941 TTATTAT-GATTGAAAT
1 TTATTATAGATTGAAAT
41238957 TTTTTCGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
TTATTATAGATTGAAATA
Found at i:41239939 original size:151 final size:154
Alignment explanation
Indices: 41239555--41240818 Score: 1643
Period size: 151 Copynumber: 8.3 Consensus size: 154
41239545 TTATATTTGA
* *
41239555 GCCATTTGTTCGTA-TTTTTCCCCGA-ATTTTATTAC-TTT-AAAAAATATACTATTTTTTAATT
1 GCCATTTGTTCGTATTTTTTTCCCGAGATTTTATTACTTTTAAAAAAATATACTATTTTCTAATT
* * * **
41239616 TTCTAATTTTACATTATTTTAGTAGATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTATTT
66 TTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAAT
*
41239681 AAATTAAAAAAAACT-TTATTTCG
131 AAATTTAAAAAAACTCTTATTTCG
* *
41239704 GCCCTTTGTTCGTATTTTTTT-CTG-GATTTTATTAC-TTTAAAAAAATATACTATTTTCTAATT
1 GCCATTTGTTCGTATTTTTTTCCCGAGATTTTATTACTTTTAAAAAAATATACTATTTTCTAATT
* * * * * *
41239766 TTATTATTTTAGATTATTTTAGTACATTATGCTTGAAATTTATTAATTTACTGTATTTTTTAAAT
66 TTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAAT
*
41239831 AAA-TT-AAAAAACTCTTATTTTG
131 AAATTTAAAAAAACTCTTATTTCG
41239853 GCCATTTGTTCGTATTTTTTTCCCGA-ATTTTATTACTTTTAAAAAAATATACTATTTTCTAATT
1 GCCATTTGTTCGTATTTTTTTCCCGAGATTTTATTACTTTTAAAAAAATATACTATTTTCTAATT
41239917 TTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAAT
66 TTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAAT
41239982 AAATTTAAAAAAA-TCCTTATTTCG
131 AAATTTAAAAAAACT-CTTATTTCG
* ** * * *
41240006 ACCATTTGTTCGTATTTTTTTTTCTAGATTTTATTACTTTCAATAAAAATATATTATTTTCTAAT
1 GCCATTTGTTCGTATTTTTTTCCCGAGATTTTATTACTTTTAA-AAAAATATACTATTTTCTAAT
*
41240071 TTTATTATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAA
65 TTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAA
41240136 TAAATTTTAAAAAAAAAAC-CATTATTTCG
130 TAAA-TTT---AAAAAAACTC-TTATTTCG
* * * * *
41240165 GCCCTTTGTACGTA-TTTTTTCCCCATATTTTATTAC-TTT-AAAAAATATAATATTTTCTAATT
1 GCCATTTGTTCGTATTTTTTTCCCGAGATTTTATTACTTTTAAAAAAATATACTATTTTCTAATT
*
41240227 TTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATGTAGTGTGTTTTTTAAAT
66 TTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAAT
* *
41240292 AAATTTAAAAAAACCCATTATTTTG
131 AAATTTAAAAAAACTC-TTATTTCG
* * * * *
41240317 GCCTTTTATTTGTA-TTTTTTCTC-AGATTTTATTAC-TTT-AAAAAATATACTATTTTATAATT
1 GCCATTTGTTCGTATTTTTTTCCCGAGATTTTATTACTTTTAAAAAAATATACTATTTTCTAATT
* * * * *
41240378 TTATTATTTTAGATTATTTTAGTACATTATGCTTGAAATGTATTAATTTACTGTATTTTTTAAAT
66 TTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAAT
*
41240443 AAA-TT--AAAAAC-CATTATTTTG
131 AAATTTAAAAAAACTC-TTATTTCG
* * *
41240464 GCCCTTTGTTTGTATTTCTTTCCCCGA-ATTTTATTACTTTT-AAAAAATATACTATTTTCTAAT
1 GCCATTTGTTCGTATTT-TTTTCCCGAGATTTTATTACTTTTAAAAAAATATACTATTTTCTAAT
* * * *
41240527 TTTATTATTTTACGTTATTTTAGCACATTATGTTTGAAATGTATTCATTTAGTTTATTTTTTAAA
65 TTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAA
*
41240592 TAAATTTAAAAAATC-CTTATTTCG
130 TAAATTTAAAAAAACTCTTATTTCG
* * * * *
41240616 GCCATTTGTTCGTATTTTTTT---TATATTTTATTACTTTCAATAAAAATATATTATTTTATAAT
1 GCCATTTGTTCGTATTTTTTTCCCGAGATTTTATTACTTTTAA-AAAAATATACTATTTTCTAAT
41240678 TTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAA
65 TTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAA
*
41240743 TAAATTTTAAAAAAAACCCTTATTTCG
130 TAAA-TTT-AAAAAAACTCTTATTTCG
* * * *
41240770 GCCCTTTATTCGTATTTTTTTCTCTAGATTTTATTACTTTTAATAAAAA
1 GCCATTTGTTCGTATTTTTTTCCCGAGATTTTATTACTTTTAA-AAAAA
41240819 ACACACTAAA
Statistics
Matches: 991, Mismatches: 89, Indels: 62
0.87 0.08 0.05
Matches are distributed among these distances:
147 22 0.02
148 17 0.02
149 84 0.08
150 186 0.19
151 283 0.29
152 55 0.06
153 49 0.05
154 46 0.05
155 175 0.18
156 4 0.00
157 25 0.03
158 19 0.02
159 26 0.03
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.52
Consensus pattern (154 bp):
GCCATTTGTTCGTATTTTTTTCCCGAGATTTTATTACTTTTAAAAAAATATACTATTTTCTAATT
TTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAAT
AAATTTAAAAAAACTCTTATTTCG
Found at i:41240589 original size:301 final size:303
Alignment explanation
Indices: 41239545--41240817 Score: 1793
Period size: 301 Copynumber: 4.2 Consensus size: 303
41239535 ACCAACATGT
*
41239545 TTATATTTGAGCCATTTGTTCGTA-TTTTTCCCCGAATTTTATTAC-TTTAAAAAATATACTATT
1 TTAT-TTTG-GCCCTTTGTTCGTATTTTTTCCCCGAATTTTATTACTTTTAAAAAATATACTATT
* * * *
41239608 TTTTAATTTTCTAATTTTACATTATTTTAGTAGATTATGTTTGAAATGTATTCATTTAGTGTGTT
64 TTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTT
** * * * *
41239673 TTTTATTTAAA-TTAAAAAAAACTTTATTTCGGCCCTTTGTTCGTATTTTTTTCTGGATTTTATT
129 TTTTAAATAAATTTAAAAAAATCCTTATTTCGGCCATTTGTTCGTATTTTTTTCTAGATTTTATT
*
41239737 ACTTTAA-AAAAATATACTATTTTCTAATTTTATTATTTTAGATTATTTTAGTACATTATGCTTG
194 ACTTTAATAAAAATATACTATTTTATAATTTTATTATTTTAGATTATTTTAGTACATTATGCTTG
*
41239801 AAATTTATTAATTTACTGTATTTTTTAAATAAA-TTAAAAAACTC-
259 AAATGTATTAATTTACTGTATTTTTTAAATAAATTTAAAAAAC-CA
* *
41239845 TTATTTTGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTTAAAAAAATATACTATTT
1 TTATTTTGGCCCTTTGTTCGTATTTTTTCCCCGAATTTTATTACTTTT-AAAAAATATACTATTT
41239910 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTT
65 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTT
*
41239975 TTTAAATAAATTTAAAAAAATCCTTATTTCGACCATTTGTTCGTATTTTTTTTTCTAGATTTTAT
130 TTTAAATAAATTTAAAAAAATCCTTATTTCGGCCATTTGTTCGTA--TTTTTTTCTAGATTTTAT
* * * *
41240040 TACTTTCAATAAAAATATATTATTTTCTAATTTTATTATTTTAAATTATTTTAGTACATTATGTT
193 TACTTT-AATAAAAATATACTATTTTATAATTTTATTATTTTAGATTATTTTAGTACATTATGCT
* * *
41240105 TGAAATGTATTCATTTAGTGTGTTTTTTAAATAAATTTTAAAAAAAAAACCA
257 TGAAATGTATTAATTTACTGTATTTTTTAAATAAA-TTT----AAAAAACCA
* * *
41240157 TTATTTCGGCCCTTTGTACGTATTTTTTCCCC-ATATTTTATTAC-TTTAAAAAATATAATATTT
1 TTATTTTGGCCCTTTGTTCGTATTTTTTCCCCGA-ATTTTATTACTTTTAAAAAATATACTATTT
*
41240220 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATGTAGTGTGTTT
65 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTT
* * * * *
41240285 TTTAAATAAATTTAAAAAAACCCATTATTTTGGCCTTTTATTTGTA-TTTTTTCTCAGATTTTAT
130 TTTAAATAAATTTAAAAAAATCC-TTATTTCGGCCATTTGTTCGTATTTTTTTCT-AGATTTTAT
41240349 TACTTT-A-AAAAATATACTATTTTATAATTTTATTATTTTAGATTATTTTAGTACATTATGCTT
193 TACTTTAATAAAAATATACTATTTTATAATTTTATTATTTTAGATTATTTTAGTACATTATGCTT
41240412 GAAATGTATTAATTTACTGTATTTTTTAAATAAA-TT-AAAAACCA
258 GAAATGTATTAATTTACTGTATTTTTTAAATAAATTTAAAAAACCA
*
41240456 TTATTTTGGCCCTTTGTTTGTATTTCTTTCCCCGAATTTTATTACTTTTAAAAAATATACTATTT
1 TTATTTTGGCCCTTTGTTCGTATTT-TTTCCCCGAATTTTATTACTTTTAAAAAATATACTATTT
* * * *
41240521 TCTAATTTTATTATTTTACGTTATTTTAGCACATTATGTTTGAAATGTATTCATTTAGTTTATTT
65 TCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTT
*
41240586 TTTAAATAAATTT-AAAAAATCCTTATTTCGGCCATTTGTTCGTATTTTTTT-TATATTTTATTA
130 TTTAAATAAATTTAAAAAAATCCTTATTTCGGCCATTTGTTCGTATTTTTTTCTAGATTTTATTA
* * *
41240649 CTTTCAATAAAAATATATTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTG
195 CTTT-AATAAAAATATACTATTTTATAATTTTATTATTTTAGATTATTTTAGTACATTATGCTTG
* * * *
41240714 AAATGTATTCATTTAGTGTGTTTTTTAAATAAATTTTAAAAAAAACCC
259 AAATGTATTAATTTACTGTATTTTTTAAATAAA-TTT--AAAAAACCA
* * * * *
41240762 TTATTTCGGCCCTTTATTCGTATTTTTTTCTCTAGATTTTATTACTTTTAATAAAA
1 TTATTTTGGCCCTTTGTTCGTATTTTTTCCCCGA-ATTTTATTACTTTTAA-AAAA
41240818 AACACACTAA
Statistics
Matches: 875, Mismatches: 66, Indels: 57
0.88 0.07 0.06
Matches are distributed among these distances:
298 28 0.03
299 73 0.08
300 39 0.04
301 261 0.30
302 30 0.03
303 2 0.00
304 25 0.03
305 8 0.01
306 211 0.24
307 5 0.01
308 10 0.01
309 15 0.02
310 101 0.12
311 22 0.03
312 45 0.05
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.52
Consensus pattern (303 bp):
TTATTTTGGCCCTTTGTTCGTATTTTTTCCCCGAATTTTATTACTTTTAAAAAATATACTATTTT
CTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTT
TTAAATAAATTTAAAAAAATCCTTATTTCGGCCATTTGTTCGTATTTTTTTCTAGATTTTATTAC
TTTAATAAAAATATACTATTTTATAATTTTATTATTTTAGATTATTTTAGTACATTATGCTTGAA
ATGTATTAATTTACTGTATTTTTTAAATAAATTTAAAAAACCA
Found at i:41241035 original size:27 final size:25
Alignment explanation
Indices: 41240955--41241027 Score: 92
Period size: 27 Copynumber: 2.8 Consensus size: 25
41240945 AACAAAGAGG
41240955 GGTGCCGCCTGTGACAGTGGCACCATT
1 GGTGCCGCCTGTGACA--GGCACCATT
* *
41240982 GGTGCCACCTCTGCCACAGGCACCATT
1 GGTGCCGCCTGTG--ACAGGCACCATT
41241009 GGTGCCGCCTGTGACAGGC
1 GGTGCCGCCTGTGACAGGC
41241028 CCTCCATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 6 0.15
27 31 0.77
29 3 0.08
ACGTcount: A:0.15, C:0.34, G:0.32, T:0.19
Consensus pattern (25 bp):
GGTGCCGCCTGTGACAGGCACCATT
Found at i:41245673 original size:17 final size:17
Alignment explanation
Indices: 41245651--41245683 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41245641 TTAATCACTT
41245651 TAATATTAAATTTAATC
1 TAATATTAAATTTAATC
41245668 TAATATTAAATTTAAT
1 TAATATTAAATTTAAT
41245684 ATTAAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATATTAAATTTAATC
Found at i:41248573 original size:22 final size:24
Alignment explanation
Indices: 41248523--41248573 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
41248513 TTGCAATGCT
41248523 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
41248548 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
41248569 TTTAT
1 TTTAT
41248574 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:41248749 original size:14 final size:15
Alignment explanation
Indices: 41248727--41248803 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
41248717 CAATCAAACA
41248727 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
41248741 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
41248756 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
41248776 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
41248790 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
41248804 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:41248768 original size:20 final size:20
Alignment explanation
Indices: 41248743--41248782 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41248733 AATATTTTCC
*
41248743 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
41248763 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
41248783 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:41248788 original size:34 final size:35
Alignment explanation
Indices: 41248731--41248797 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
41248721 CAAACACCAG
*
41248731 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
41248766 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
41248798 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:41248804 original size:14 final size:14
Alignment explanation
Indices: 41248766--41248805 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
41248756 ACAGAAAAGT
*
41248766 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
41248780 AAATCATTTTACGG
1 AAAACATTTTACAG
41248794 AAAACATTTTAC
1 AAAACATTTTAC
41248806 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:41250230 original size:28 final size:28
Alignment explanation
Indices: 41250198--41250254 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
41250188 TGAATCAAAT
41250198 GTTCACTTTGAATCTTTTACGGGTTACG
1 GTTCACTTTGAATCTTTTACGGGTTACG
41250226 GTTCACTTTGAATCTTTTACGGGTTACG
1 GTTCACTTTGAATCTTTTACGGGTTACG
41250254 G
1 G
41250255 ACTTGTATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.42
Consensus pattern (28 bp):
GTTCACTTTGAATCTTTTACGGGTTACG
Found at i:41255187 original size:43 final size:43
Alignment explanation
Indices: 41255126--41255213 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
41255116 ATGTTGGTAG
41255126 TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
1 TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
41255169 TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
1 TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
41255212 TC
1 TC
41255214 ATGATGACTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (43 bp):
TCTAAAGTATGCTCGATAACATGAGTTAGGCTCTTGTTTTAAC
Found at i:41259076 original size:19 final size:19
Alignment explanation
Indices: 41259054--41259099 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
41259044 AAAGTTATAG
41259054 AAAAATATAT-AAATTATTA-
1 AAAAATA-ATGAAA-TATTAT
*
41259073 AAAAGTAATGAAATATTAT
1 AAAAATAATGAAATATTAT
41259092 AAAAATAA
1 AAAAATAA
41259100 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAAATAATGAAATATTAT
Found at i:41265694 original size:3 final size:3
Alignment explanation
Indices: 41265686--41265718 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
41265676 TTATTTAAAA
41265686 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41265719 TCATTTTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:41267268 original size:14 final size:14
Alignment explanation
Indices: 41267249--41267276 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41267239 AGTTTCAGTC
41267249 GGCCCAGAATACAA
1 GGCCCAGAATACAA
41267263 GGCCCAGAATACAA
1 GGCCCAGAATACAA
41267277 AATCAGTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.21, T:0.07
Consensus pattern (14 bp):
GGCCCAGAATACAA
Found at i:41268522 original size:22 final size:21
Alignment explanation
Indices: 41268453--41268526 Score: 55
Period size: 22 Copynumber: 3.4 Consensus size: 21
41268443 TTAGTCTTTT
*
41268453 TTTTAATTTTT-TTATTAATTAA
1 TTTTCATTTTTATT-TTAATT-A
* *
41268475 TTTTCATTTTTATTTTGTATTT
1 TTTTCATTTTTATTTT-AATTA
41268497 TTTTC-TTTTTCATATTTAATTA
1 TTTTCATTTTT-AT-TTTAATTA
41268519 TTTT-ATTT
1 TTTTCATTT
41268527 AAATCTATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
21 5 0.12
22 29 0.69
23 8 0.19
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (21 bp):
TTTTCATTTTTATTTTAATTA
Found at i:41268618 original size:20 final size:21
Alignment explanation
Indices: 41268580--41268633 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
41268570 ATACGCATAT
*
41268580 TTATTTTTTAATGTAATGTAG
1 TTATTTTTTAATGTAATGTAA
* *
41268601 TTATTTTTT-ATTTTATGTAA
1 TTATTTTTTAATGTAATGTAA
41268621 TTATTTTTATAAT
1 TTATTTTT-TAAT
41268634 CTATATATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.57
21 10 0.36
22 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (21 bp):
TTATTTTTTAATGTAATGTAA
Found at i:41268678 original size:16 final size:16
Alignment explanation
Indices: 41268635--41268685 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
41268625 TTTTATAATC
*
41268635 TATATATGTATATATA
1 TATATATGTATGTATA
* *
41268651 TTTAT-TCT-TGTATA
1 TATATATGTATGTATA
41268665 TATATATGTATGTATA
1 TATATATGTATGTATA
*
41268681 CATAT
1 TATAT
41268686 TAATATTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 9 0.33
15 4 0.15
16 14 0.52
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (16 bp):
TATATATGTATGTATA
Found at i:41269085 original size:15 final size:15
Alignment explanation
Indices: 41269065--41269094 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41269055 TATGCCATTA
41269065 TTGTATTTATTATTG
1 TTGTATTTATTATTG
*
41269080 TTGTATTTGTTATTG
1 TTGTATTTATTATTG
41269095 CGACATCTAT
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:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (15 bp):
TTGTATTTATTATTG
Found at i:41280987 original size:44 final size:43
Alignment explanation
Indices: 41280936--41281790 Score: 488
Period size: 44 Copynumber: 19.6 Consensus size: 43
41280926 GATCGCATCT
*
41280936 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * * *
41280980 AGTCTTATC-CTCCTGAAGTTGCAGT-AAGGCAGGCTAAAGATGGTA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* *
41281025 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-AGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * * * * *
41281068 TAATCCTATCCCCCTGAGGTTGCAGTGGAGCGGATTAA-AACCTT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A
* * * * * *
41281112 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
41281153 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
41281197 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTAAAGATAGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * *
41281242 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGA-TTA-AAGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * * *
41281285 TAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAA-AATCA
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* * * * * * *
41281328 CAGATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T-CGCATCT
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* * *
41281370 AGTCTTATCTCTCTGAAGTTACAGTGGAGCAGACTAAGTAATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* *
41281414 AGTCTTATCTTCCC-GACGTTGCAGT-GAGGCAGACTGAAGATGGCGA
1 AGTCTTATC-TCCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGC-A
* *
41281460 A-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGA-TTA-AAGCCAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * *
41281502 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA-AACCA
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* * * * * * * *
41281545 CAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGA-TCA-CATCG
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* * * * *
41281588 GGTCTTATCTCCCTGAAATTGTAGTGGAGTAGACTAAGTAAGTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* *
41281632 AGTCTTATC-CTCCTGAAGTTACAGT-GAGACAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAG-CAGACT-AAGA-AGCA
* * * *
41281677 AATCTTATCTACCTGAAGTTGCAGTGGAGCAGATTAA-AACCAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A
* * * ** *
41281720 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGAAG-CA
*
41281766 ATTC-TATCTCCCTGAAGTTGCAGTG
1 AGTCTTATCTCCCTGAAGTTGCAGTG
41281791 AAGCGGGTTA
Statistics
Matches: 637, Mismatches: 115, Indels: 118
0.73 0.13 0.14
Matches are distributed among these distances:
40 43 0.07
41 49 0.08
42 18 0.03
43 43 0.07
44 332 0.52
45 139 0.22
46 13 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
Found at i:41281236 original size:217 final size:217
Alignment explanation
Indices: 41280846--41281788 Score: 1377
Period size: 217 Copynumber: 4.3 Consensus size: 217
41280836 CAGATCAGTG
* * * * * * *
41280846 GCCAATAATCCTATCACCCTGAGGTTGCAATAGAGAGGATTAAAACCTTAAATCTTATATCTCTG
1 GCCAATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACCATAGATCTTATCTCTCTG
* *
41280911 AAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTA
66 AAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
* * *
41280976 AGCAAGTCTTATCCTCCTGAAGTTGCAGTAAGGCAGGCTAAAGATGGTAAATCTTATCTCCCTGA
131 AGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGA
*
41281041 AGTTGCAGTGGAGCAGATTAGA
196 AGTTGCAGTGGAGCAGATTAAA
* * *
41281063 GCCGATAATCCTATCCCCCTGAGGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTG
1 GCCAATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACCATAGATCTTATCTCTCTG
41281128 AAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
66 AAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
*
41281193 AGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATAGCAAATCTTATCTCCCTGA
131 AGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGA
*
41281258 AATTGCAGTGGAGCAGATTAAA
196 AGTTGCAGTGGAGCAGATTAAA
* * *
41281280 GCCGATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTG
1 GCCAATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACCATAGATCTTATCTCTCTG
* * *
41281345 AAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCTCTGAAGTTACAGTGGAGCAGACTAAGTA
66 AAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
* * * * * *
41281410 ATCAAGTCTTATCTTCCCGACGTTGCAGTGAGGCAGACTGAAGATGGCGAATCTTATCTCCCTGA
131 AGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGA
*
41281475 AGTTGCAGTGGAGTAGATTAAA
196 AGTTGCAGTGGAGCAGATTAAA
* * * *
41281497 GCCAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTA
1 GCCAATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACCATAGATCTTATCTCTCTG
* * ** * * *
41281562 AAGTTGCAGTAGAGTAGATCACATCGGGTCTTATCTCCCTGAAATTGTAGTGGAGTAGACTAAGT
66 AAGTTGCAG-AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGT
* * * * *
41281627 AAGTAAGTCTTATCCTCCTGAAGTTACAGTGAGACAGACTGAAGATGGCAAATCTTATCTACCTG
130 AAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTG
41281692 AAGTTGCAGTGGAGCAGATTAAA
195 AAGTTGCAGTGGAGCAGATTAAA
* * * * *
41281715 ACCAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA-AT-TCTATCTCCC
1 GCCAATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACC-ATAGATCT-TATCTCTC
41281778 TGAAGTTGCAG
64 TGAAGTTGCAG
41281789 TGAAGCGGGT
Statistics
Matches: 662, Mismatches: 61, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
217 472 0.71
218 188 0.28
219 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (217 bp):
GCCAATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACCATAGATCTTATCTCTCTG
AAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTA
AGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGA
AGTTGCAGTGGAGCAGATTAAA
Found at i:41281266 original size:89 final size:86
Alignment explanation
Indices: 41280936--41281790 Score: 442
Period size: 89 Copynumber: 9.8 Consensus size: 86
41280926 GATCGCATCT
* *
41280936 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACT-AAG-TAAGCAAGTCTTATC-CTCCTGAAG
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAAGAT-A-CAAATCTTATCTC-CCTGAAG
* * * *
41280998 TTGCAGT-AAGGCAGGCTAAAGATGGTA
62 TTGCAGTGGA-GCAGACT-AAGA-AGCA
* * ** * * *
41281025 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-TAGAGCCGATAATCCTATCCCCCTGAGGT
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAAGATAC-A-AATCTTATCTCCCTGAAGT
* * * *
41281088 TGCAGTGGAGCGGATTAA-AACCTT
63 TGCAGTGGAGCAGACTAAGAAGC-A
* * * *
41281112 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCAT-CTAGTCTTATCTCCCTGAAGT
1 AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAAG-ATACAAATCTTATCTCCCTGAAGT
41281172 TGCAGTGGAGCAGACTAAGTAAGCA
63 TGCAGTGGAGCAGACTAAG-AAGCA
*
41281197 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTAAAGATAGCAAATCTTATCTCCCTGAAAT
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGACTAAAGATA-CAAATCTTATCTCCCTGAAGT
*
41281261 TGCAGTGGAGCAGA-TTA-AAGCCGA
63 TGCAGTGGAGCAGACTAAGAAG-C-A
* * * * * * *
41281285 TAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAA-ATCACAGATCTTATCTCTCTGAAGT
1 -AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAAGAT-ACAAATCTTATCTCCCTGAAGT
* * * * * *
41281349 TACAG-AGAGCAGA-T-CGCATCT
63 TGCAGTGGAGCAGACTAAGAAGCA
* * *
41281370 AGTCTTATCTCTCTGAAGTTACAGTGGAGCAGACT-AAG-TAATCAAGTCTTATCTTCCC-GACG
1 AGTCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAAGAT-A-CAAATCTTATC-TCCCTGAAG
*
41281432 TTGCAGT-GAGGCAGACTGAAGATGGCGA
62 TTGCAGTGGA-GCAGACT-AAGA-AGC-A
* * ** *
41281460 A-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCA-ATAATCCTATCTCCCTGAAGTT
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAAGATACA-AATCTTATCTCCCTGAAGTT
* *
41281523 GCAGTGGAGCAGATTAA-AACCA
64 GCAGTGGAGCAGACTAAGAAGCA
* * * * * *** *
41281545 CAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGA-T-CACAT-CGGGTCTTATCTCCCTGAAAT
1 -AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAAGATACAAATCTTATCTCCCTGAAGT
* * *
41281607 TGTAGTGGAGTAGACTAAGTAAGTA
63 TGCAGTGGAGCAGACTAAG-AAGCA
* * * *
41281632 AGTCTTATCCTCCTGAAGTTACAGT-GAGACAGACTGAAGATGGCAAATCTTATCTACCTGAAGT
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGAG-CAGACTAAAGAT-ACAAATCTTATCTCCCTGAAGT
* *
41281696 TGCAGTGGAGCAGATTAA-AACCAA
63 TGCAGTGGAGCAGACTAAGAAGC-A
* * * ** * *
41281720 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATTC-TATCTCCCTGAAGT
1 -AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAAG-ATACAAATCTTATCTCCCTGAAGT
41281784 TGCAGTG
63 TGCAGTG
41281791 AAGCGGGTTA
Statistics
Matches: 588, Mismatches: 117, Indels: 123
0.71 0.14 0.15
Matches are distributed among these distances:
83 5 0.01
84 100 0.17
85 69 0.12
86 20 0.03
87 36 0.06
88 114 0.19
89 229 0.39
90 15 0.03
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (86 bp):
AGTCTTATCTCCTGAAGTTGCAGTGGAGCAGACTAAAGATACAAATCTTATCTCCCTGAAGTTGC
AGTGGAGCAGACTAAGAAGCA
Found at i:41281854 original size:24 final size:24
Alignment explanation
Indices: 41281827--41281873 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
41281817 CTCTCTAGAG
41281827 TTGCAGAGAGCAGATCGCATCTAA
1 TTGCAGAGAGCAGATCGCATCTAA
* *
41281851 TTGCAGAGATCAGATTGCATCTA
1 TTGCAGAGAGCAGATCGCATCTA
41281874 GTCTTTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (24 bp):
TTGCAGAGAGCAGATCGCATCTAA
Found at i:41283942 original size:18 final size:18
Alignment explanation
Indices: 41283901--41283948 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
41283891 TTTAATAGTA
* *
41283901 ATAATAATAATAATAATG
1 ATAATAATAAAAATAATC
* *
41283919 ACAATAATAAAAATTATC
1 ATAATAATAAAAATAATC
*
41283937 ATAATACTAAAA
1 ATAATAATAAAA
41283949 TAACGAACAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.29
Consensus pattern (18 bp):
ATAATAATAAAAATAATC
Found at i:41285684 original size:11 final size:10
Alignment explanation
Indices: 41285658--41285683 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41285648 AGGGGAGAGC
41285658 TTTTTTGAAG
1 TTTTTTGAAG
41285668 TTTTTTGAAG
1 TTTTTTGAAG
41285678 TTTTTT
1 TTTTTT
41285684 TTAAAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (10 bp):
TTTTTTGAAG
Found at i:41286258 original size:20 final size:21
Alignment explanation
Indices: 41286220--41286273 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
41286210 ATACGCATAT
41286220 TTATTTTTTAATGTAATGTAA
1 TTATTTTTTAATGTAATGTAA
* *
41286241 TTATTTTTT-ATTTTATGTAA
1 TTATTTTTTAATGTAATGTAA
41286261 TTATTTTTATAAT
1 TTATTTTT-TAAT
41286274 CTATCTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 17 0.59
21 10 0.34
22 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.65
Consensus pattern (21 bp):
TTATTTTTTAATGTAATGTAA
Found at i:41289725 original size:23 final size:22
Alignment explanation
Indices: 41289693--41289754 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
41289683 GCCCGGCCCG
* *
41289693 TTTTTAATTATAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
41289717 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
41289739 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
41289755 TTGTTATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 16 0.46
23 14 0.40
24 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:41289749 original size:16 final size:16
Alignment explanation
Indices: 41289728--41289784 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
41289718 TTTTATTAAA
*
41289728 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
41289744 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
41289760 ATCAAAATTAATTGTT
1 ATTAAAATTAATTGTT
41289776 ATTAAAATT
1 ATTAAAATT
41289785 CTATCAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:41290035 original size:23 final size:21
Alignment explanation
Indices: 41290009--41290055 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
41289999 AAACTTAAAA
* *
41290009 TAAAACTAAAACTAGTATATTTT
1 TAAAA-TAAAAATA-TATATATT
41290032 TAAAATAAAAATATATATATT
1 TAAAATAAAAATATATATATT
41290053 TAA
1 TAA
41290056 TATATTTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 7 0.32
23 5 0.23
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAATAAAAATATATATATT
Found at i:41290928 original size:6 final size:6
Alignment explanation
Indices: 41290917--41290953 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
41290907 GTTAAGGATG
*
41290917 GGGGAA GGGGAA GGGGAA AGGGAA GGGGAA GGGGAA G
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA G
41290954 AGAAAGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:41290960 original size:18 final size:18
Alignment explanation
Indices: 41290921--41290961 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41290911 AGGATGGGGG
*
41290921 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGA
41290939 AAGGGGAAGGGG-AAGAGA
1 AAGGGGAAGGGGAAAG-GA
41290957 AAGGG
1 AAGGG
41290962 AAGATCGGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGGAAAGGA
Found at i:41292239 original size:16 final size:16
Alignment explanation
Indices: 41292218--41292248 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41292208 TTATAGTCCT
*
41292218 ATTACAGCCTTATTCC
1 ATTACAACCTTATTCC
41292234 ATTACAACCTTATTC
1 ATTACAACCTTATTC
41292249 AATTCTAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACAACCTTATTCC
Found at i:41293230 original size:2 final size:2
Alignment explanation
Indices: 41293223--41293248 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41293213 TGGGTTTTGG
41293223 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
41293249 AATTATCTTT
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):
TA
Found at i:41299040 original size:37 final size:37
Alignment explanation
Indices: 41298990--41299115 Score: 119
Period size: 37 Copynumber: 3.3 Consensus size: 37
41298980 ACACTCGCTA
*
41298990 GATTTAAAATCGCGACTGTCATTTTTACGGTTCAATT
1 GATTTAAGATCGCGACTGTCATTTTTACGGTTCAATT
* * * *
41299027 GATTTAAGATCGCGA-TGTTTGATATTCTAACAGTTCGATT
1 GATTTAAGATCGCGACTG--TCAT-TT-TTACGGTTCAATT
* * * * *
41299067 GATTTAACATCGCAACTGTCATTTTTTCGGTTGACTT
1 GATTTAAGATCGCGACTGTCATTTTTACGGTTCAATT
41299104 GATTTAAGATCG
1 GATTTAAGATCG
41299116 TGACCTTCGA
Statistics
Matches: 69, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
36 2 0.03
37 32 0.46
38 5 0.07
39 5 0.07
40 23 0.33
41 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.40
Consensus pattern (37 bp):
GATTTAAGATCGCGACTGTCATTTTTACGGTTCAATT
Found at i:41299169 original size:77 final size:77
Alignment explanation
Indices: 41298990--41299135 Score: 211
Period size: 77 Copynumber: 1.9 Consensus size: 77
41298980 ACACTCGCTA
* * ** *
41298990 GATTTAAAATCGCGACTGTCATTTTTACGGTTCAATTGATTTAAGATCGCGATGTTTGATATTCT
1 GATTTAACATCGCAACTGTCATTTTTACGGTTCAATTGATTTAAGATCGCGACCTTCGATATTCT
41299055 AACAGTTCGATT
66 AACAGTTCGATT
* * * *
41299067 GATTTAACATCGCAACTGTCATTTTTTCGGTTGACTTGATTTAAGATCGTGACCTTCGATATTCT
1 GATTTAACATCGCAACTGTCATTTTTACGGTTCAATTGATTTAAGATCGCGACCTTCGATATTCT
41299132 AACA
66 AACA
41299136 TTTTGCTTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
77 60 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (77 bp):
GATTTAACATCGCAACTGTCATTTTTACGGTTCAATTGATTTAAGATCGCGACCTTCGATATTCT
AACAGTTCGATT
Found at i:41300409 original size:36 final size:38
Alignment explanation
Indices: 41300362--41300456 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 38
41300352 GTCTCCAAAT
* *
41300362 TCACATTTCAATTCAATTTCACTTTTTCA-CTTTCAA-
1 TCACAATTCAATTCAATTTCACTTTTCCATCTTTCAAG
* *
41300398 TCACAATTCAATTCAAAATTCACTTTTCCATTTTTCAAG
1 TCACAATTCAATTC-AATTTCACTTTTCCATCTTTCAAG
*
41300437 TCATTATATTCAATTCAATT
1 TCA-CA-ATTCAATTCAATT
41300457 CCAGACATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 13 0.27
37 13 0.27
38 6 0.12
39 3 0.06
40 4 0.08
41 9 0.19
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (38 bp):
TCACAATTCAATTCAATTTCACTTTTCCATCTTTCAAG
Found at i:41303320 original size:42 final size:42
Alignment explanation
Indices: 41303256--41303353 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
41303246 GATCTCGGTA
* * *
41303256 TCGCACACCTAGTGCCTATTATTCAACATTGTCATTTTAATT
1 TCGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAATT
* *
41303298 TCGCACACTTAGTGCCCGTTATTCAACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAATT
41303340 TCGCACACTTAGTG
1 TCGCACACTTAGTG
41303354 TCATTCCTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAATT
Found at i:41303468 original size:2 final size:2
Alignment explanation
Indices: 41303461--41303490 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41303451 ATTCAGCTAC
41303461 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
41303491 TTGCATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41308403 original size:20 final size:19
Alignment explanation
Indices: 41308364--41308402 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41308354 TATTTTAAAA
41308364 TATTTGTACATTTTAATTT
1 TATTTGTACATTTTAATTT
*
41308383 TATTATGTATATTTT-ATTT
1 TATT-TGTACATTTTAATTT
41308402 T
1 T
41308403 TTTCTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (19 bp):
TATTTGTACATTTTAATTT
Found at i:41314764 original size:31 final size:29
Alignment explanation
Indices: 41314729--41314833 Score: 110
Period size: 31 Copynumber: 3.6 Consensus size: 29
41314719 GACATAAGTA
41314729 TAAATATG-GAAAAGTTTCGTGGCATAAATTG
1 TAAATATGCGAAAAGTTT-GTGGCAT-AA-TG
*
41314760 TAAATATGCGAAAAG-TTATGGCATAA-G
1 TAAATATGCGAAAAGTTTGTGGCATAATG
* *
41314787 TAAATATGCAAAAAGTTTTGTGGCATAAGTA
1 TAAATATGCGAAAAG-TTTGTGGCATAA-TG
41314818 TAAATATG-GAAAAGTT
1 TAAATATGCGAAAAGTT
41314834 GAAGTGAAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
27 15 0.23
29 14 0.22
30 11 0.17
31 18 0.28
32 6 0.09
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (29 bp):
TAAATATGCGAAAAGTTTGTGGCATAATG
Found at i:41314793 original size:27 final size:27
Alignment explanation
Indices: 41314759--41314833 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
41314749 GGCATAAATT
41314759 GTAAATATGCGAAAAGTTATGGCATAA
1 GTAAATATGCGAAAAGTTATGGCATAA
* *
41314786 GTAAATATGCAAAAAGTTTTGTGGCATAA
1 GTAAATATGCGAAAAG--TTATGGCATAA
41314815 GTATAAATATG-GAAAAGTT
1 G--TAAATATGCGAAAAGTT
41314834 GAAGTGAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 15 0.37
28 2 0.05
29 11 0.27
30 5 0.12
31 8 0.20
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.29
Consensus pattern (27 bp):
GTAAATATGCGAAAAGTTATGGCATAA
Found at i:41315120 original size:11 final size:11
Alignment explanation
Indices: 41315106--41315147 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
41315096 TAAATATTAC
41315106 TTTATTAATAT
1 TTTATTAATAT
*
41315117 TTTAATGAGATAT
1 TTT-ATTA-ATAT
41315130 TTTATTAATAT
1 TTTATTAATAT
41315141 TTTATTA
1 TTTATTA
41315148 TAAATAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.52
12 6 0.22
13 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TTTATTAATAT
Found at i:41334372 original size:17 final size:18
Alignment explanation
Indices: 41334330--41334372 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
41334320 TTAATATGGT
*
41334330 TATATATAAAATTATAAA
1 TATATATTAAATTATAAA
41334348 TA-ATTATTAAA-TATAAA
1 TATA-TATTAAATTATAAA
41334365 TATATATT
1 TATATATT
41334373 TAAAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATATTAAATTATAAA
Found at i:41334779 original size:33 final size:31
Alignment explanation
Indices: 41334749--41334811 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
41334739 ACCAAAAATT
41334749 TATTTTAAAAATTAAAATTAAAATTAAAAAAAG
1 TATTTTAAAAA-T-AAATTAAAATTAAAAAAAG
**
41334782 TATTTTAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATAAATTAAAATTAAAAAAA
41334812 ATTTAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 16 0.57
32 1 0.04
33 11 0.39
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (31 bp):
TATTTTAAAAATAAATTAAAATTAAAAAAAG
Found at i:41334808 original size:17 final size:17
Alignment explanation
Indices: 41334786--41334819 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41334776 AAAAAGTATT
* *
41334786 TTAAAAATATTTTAAAA
1 TTAAAAAAAATTTAAAA
41334803 TTAAAAAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
41334820 AGTATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAAATTTAAAA
Found at i:41334820 original size:29 final size:30
Alignment explanation
Indices: 41334766--41334831 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
41334756 AAAATTAAAA
*
41334766 TTAAAATTAAAAAAAGTATTTTAAAAATATT
1 TTAAAATTAAAAAAAG-ATTTAAAAAATATT
*
41334797 TTAAAATTAAAAAAA-ATTTAAAAAGTATT
1 TTAAAATTAAAAAAAGATTTAAAAAATATT
41334826 TTAAAA
1 TTAAAA
41334832 GAATTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 18 0.55
31 15 0.45
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (30 bp):
TTAAAATTAAAAAAAGATTTAAAAAATATT
Found at i:41334850 original size:30 final size:29
Alignment explanation
Indices: 41334809--41334872 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
41334799 AAAATTAAAA
*
41334809 AAAATTTAAAAAGTATTT-TAAAAGAATTTT
1 AAAA-TTAAAAA-AATTTATAAAAGAATTTT
*
41334839 AAAATTAAAAAAATTTAATAAAAGTATTTT
1 AAAATTAAAAAAATTT-ATAAAAGAATTTT
41334869 AAAA
1 AAAA
41334873 GTATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.13
29 7 0.23
30 19 0.63
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAATTAAAAAAATTTATAAAAGAATTTT
Found at i:41334893 original size:41 final size:40
Alignment explanation
Indices: 41334749--41334893 Score: 202
Period size: 41 Copynumber: 3.5 Consensus size: 40
41334739 ACCAAAAATT
* *
41334749 TATTTTAAAAATTAAAATTAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAA--AAAATTTAAAAAAGTATTTTAAAAG
41334793 TATTTTAAAATTAAAAAAAATTT-AAAAAGTATTTTAAAAG
1 TATTTTAAAATT-AAAAAAATTTAAAAAAGTATTTTAAAAG
*
41334833 AATTTTAAAATTAAAAAAATTTAATAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAATTTAA-AAAAGTATTTTAAAAG
41334874 TATTTTAAAATTAAAAAAAT
1 TATTTTAAAATTAAAAAAAT
41334894 AAAAAATAAT
Statistics
Matches: 95, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
39 10 0.11
40 28 0.29
41 41 0.43
43 10 0.11
44 6 0.06
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAG
Found at i:41336907 original size:17 final size:17
Alignment explanation
Indices: 41336885--41336920 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
41336875 CGATTGCATG
41336885 TTTCTATTGCTGTTTAT
1 TTTCTATTGCTGTTTAT
41336902 TTTCTATTGCTGTTTAT
1 TTTCTATTGCTGTTTAT
41336919 TT
1 TT
41336921 CCCTTTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTCTATTGCTGTTTAT
Found at i:41337311 original size:32 final size:34
Alignment explanation
Indices: 41337248--41337311 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
41337238 TCTAATAATT
* *
41337248 TCACTATTATAAAACTATTTTCCTTAAAAGAATG
1 TCACTATTATAAAACCATTCTCCTTAAAAGAATG
41337282 TCAC-ATTATAAAACCATTCT-CTTAAAAGAA
1 TCACTATTATAAAACCATTCTCCTTAAAAGAA
41337312 AATCGAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 10 0.36
33 14 0.50
34 4 0.14
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (34 bp):
TCACTATTATAAAACCATTCTCCTTAAAAGAATG
Found at i:41338108 original size:22 final size:21
Alignment explanation
Indices: 41338094--41338150 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 21
41338084 TTGTATTGAT
41338094 ATTGTTCTTGATTTGTTCTGAA
1 ATTGTT-TTGATTTGTTCTGAA
41338116 ATTGTTTTGA-TTGTCTGCTGGAA
1 ATTGTTTTGATTTGT-T-CT-GAA
41338139 ATTGTTTTGATT
1 ATTGTTTTGATT
41338151 GTCTGCTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.13
21 5 0.16
22 8 0.26
23 13 0.42
24 1 0.03
ACGTcount: A:0.18, C:0.07, G:0.21, T:0.54
Consensus pattern (21 bp):
ATTGTTTTGATTTGTTCTGAA
Found at i:41338141 original size:23 final size:23
Alignment explanation
Indices: 41338113--41338165 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
41338103 GATTTGTTCT
41338113 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
41338136 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
41338159 GAAATTG
1 GAAATTG
41338166 AATTTGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.45
Consensus pattern (23 bp):
GAAATTGTTTTGATTGTCTGCTG
Found at i:41339464 original size:48 final size:48
Alignment explanation
Indices: 41339352--41339727 Score: 698
Period size: 48 Copynumber: 7.8 Consensus size: 48
41339342 AAATAATAAC
*
41339352 ATCAATAATTAAAATAAGGACTTTAATATTTCATTAAAATAAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAAT-AAGGACTA
41339401 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
41339449 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
*
41339497 ATCAATATTTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
41339545 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
* *
41339593 ATCAATAATTAAAATAAGAACTTTAATATTTCATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
41339641 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
*
41339689 ATCAATATTTAAAATAAGGACTTTAATATTTTATTAAAA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAA
41339728 ATCAAGAAAT
Statistics
Matches: 319, Mismatches: 8, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
48 280 0.88
49 39 0.12
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.36
Consensus pattern (48 bp):
ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
Found at i:41343235 original size:92 final size:91
Alignment explanation
Indices: 41343078--41343286 Score: 269
Period size: 92 Copynumber: 2.3 Consensus size: 91
41343068 TTGATTTTAG
* * * *
41343078 TAAATTAATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
* *
41343143 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
*
41343170 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
41343234 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
41343262 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
41343287 GTTATAATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 70 0.68
93 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:41343249 original size:24 final size:25
Alignment explanation
Indices: 41343214--41343261 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
41343204 TTATGAAATT
41343214 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
41343238 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
41343262 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:41343457 original size:16 final size:16
Alignment explanation
Indices: 41343436--41343477 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41343426 TTATTAAATT
*
41343436 ATATATTTTAATTATA
1 ATATATTTTAATAATA
41343452 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
41343467 AT-TATGTTTAA
1 ATATAT-TTTAA
41343478 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:41343462 original size:15 final size:15
Alignment explanation
Indices: 41343427--41343468 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41343417 TTAAGAATTT
*
41343427 TATTAAATTAT-ATA
1 TATTTAATTATAATA
41343441 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
41343455 TATTTAATAATAAT
1 TATTTAATTATAAT
41343469 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:41343608 original size:18 final size:17
Alignment explanation
Indices: 41343580--41343614 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41343570 ATTATTAAGA
*
41343580 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41343597 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41343615 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:41343718 original size:157 final size:157
Alignment explanation
Indices: 41343411--41343727 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
41343401 ATAAGAATAT
*
41343411 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* * *
41343476 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACGA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
41343541 TAATAATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
41343568 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
41343633 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
41343698 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
41343725 TAA
1 TAA
41343728 GGGTATTCTA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:41343874 original size:16 final size:16
Alignment explanation
Indices: 41343850--41343917 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
41343840 GATTTGCTAT
* *
41343850 TACAGCTCTAATTCAA
1 TACACCTCTAATCCAA
41343866 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
41343882 TAAACCTCTAATCCAA
1 TACACCTCTAATCCAA
41343898 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
41343914 TACA
1 TACA
41343918 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.40, C:0.32, G:0.01, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:41350473 original size:261 final size:261
Alignment explanation
Indices: 41350009--41350486 Score: 642
Period size: 261 Copynumber: 1.8 Consensus size: 261
41349999 ACCAACTCAG
* ** *
41350009 TTAAAATGTATAAAAATATAAAATAAAACTTTAATAAAGTGGTAAATTAAATGTTTTACTAATGT
1 TTAAAATATATAAAAATATAAAATAAAACTTTAATAAAGTGGTAAATTAAAAATTTTACTAATGC
* * * * * * ** *
41350074 AGTTGACGTGGGTTCAAATCCCAATATATGTATATTTTTATTGGATTTGTTTTAAAGTGAAAAGA
66 AATTGACGTAGGTTCAAATACCAATATATGCATAGTTTTAATCAATTTGTTTTAAAGTGAAAAAA
** * *
41350139 CTAAAATACTCTTGAATAACATTACTTATTTTAATTACGAAAGGGCATTCTCGTAACTTCCTAAC
131 CTAAAATACTCTCAAATAACATTACTTATTTTAATTACGAAAGGACATTCTCATAACTTCCTAAC
*
41350204 TGAGTTGGTGACCCTGTTGAGGGTTACATAAACTCGATTAGAGATAATAAGGCGTGCATAATAAA
196 TGAGTTGGTGACCCAGTTGAGGGTTACATAAACTCGATTAGAGATAATAAGGCGTGCATAATAAA
41350269 A
261 A
* * * *
41350270 TTAAAATATATAAAAATATCAAAATAAAATTTTAGTTGAA-TGGTAAATTAAAAATTTTATTAAT
1 TTAAAATATATAAAAATAT-AAAATAAAACTTTA-ATAAAGTGGTAAATTAAAAATTTTACTAAT
* *
41350334 GCAATTGATGTAGGTTTAAATACCAATATATGCAT-GTTTTAATCAACTTT-TTTTAAAGTGAAA
64 GCAATTGACGTAGGTTCAAATACCAATATATGCATAGTTTTAATCAA-TTTGTTTTAAAGTGAAA
* *
41350397 AAACTAAAATA-TCCTCAAATAATATTACTTATTTTAATTAC-AGAAGGACATTCTCATAAGTTC
128 AAACTAAAATACT-CTCAAATAACATTACTTATTTTAATTACGA-AAGGACATTCTCATAACTTC
41350460 CTAACTGAGTTGGTGACCCAGTTGAGG
191 CTAACTGAGTTGGTGACCCAGTTGAGG
41350487 ATGACACCAA
Statistics
Matches: 186, Mismatches: 26, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
260 2 0.01
261 116 0.62
262 65 0.35
263 3 0.02
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (261 bp):
TTAAAATATATAAAAATATAAAATAAAACTTTAATAAAGTGGTAAATTAAAAATTTTACTAATGC
AATTGACGTAGGTTCAAATACCAATATATGCATAGTTTTAATCAATTTGTTTTAAAGTGAAAAAA
CTAAAATACTCTCAAATAACATTACTTATTTTAATTACGAAAGGACATTCTCATAACTTCCTAAC
TGAGTTGGTGACCCAGTTGAGGGTTACATAAACTCGATTAGAGATAATAAGGCGTGCATAATAAA
A
Found at i:41350822 original size:308 final size:295
Alignment explanation
Indices: 41350257--41351047 Score: 813
Period size: 308 Copynumber: 2.6 Consensus size: 295
41350247 ATAATAAGGC
* * *
41350257 GTGCATAATAAAATTAAAATATATAAAAATATCAAAATAAAATTTTAGTTGAATGGTAAATTAAA
1 GTGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAATTTTAGTTGAGTGGTAAATTAAA
* * * * *
41350322 AATTTTATTAATGCAATTGATGTAGGTTTAAATACCAATATATGCATGTTTTAATCAACTTTTTT
66 AGTTTTATTAATGCAATTGGTGTGGGTTCAAATACCAATATATGCATATTTTAATCAAC-TTTTT
* * *
41350387 TAAAGTGAAAAAACTAAAATATCCTCAAATAATATTACTTATTTTAATTACAGAAGGACATTCTC
130 TAAAGTGAAAAAACTAAAATACCCTCAAATAATATTACTTATTTCAATTACAAAAGGACATTCTC
* * *
41350452 ATAAGTTCCTAACTGAGTTGGTGACCCAGTTGAGGATGACACCAACTCAATTAGGAGTTTTATTA
195 ATAACTTCCTAACTAAGTTGGTGACCCAGTTGAGGATGACACCAACTCAATAAGGAGTTTTATTA
*
41350517 ATAGTGTGTATATATATATACAAATACA-CAACCAATAAAGTTCATGGAGT
260 ATA----G--TATATATATACAAAT-CATCAA--AATAAA----A--AAGT
* *
41350567 GTGCATAATAAAATTAAAATGTATAAAAATATTAAAGTAAAACTTTAGATT-AGTGGTAAATTAA
1 GTGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAATTTTAG-TTGAGTGGTAAATTAA
* * ** * * * * **
41350631 ATGTTCTAAAAATGCAATTGGTGTGGGTTCAAATATC-ATCATGTGTATATTTTTATTGA-TTTT
65 AAGTTTTATTAATGCAATTGGTGTGGGTTCAAATACCAAT-ATATGCATATTTTAATCAACTTTT
*** *
41350694 TTAAAGTGAAAATGTTAAAATACCCTCGAATAATATTACTTATTTCAATTACAAAAGGACATTCT
129 TTAAAGTGAAAAAACTAAAATACCCTCAAATAATATTACTTATTTCAATTACAAAAGGACATTCT
* * * * * * *
41350759 CGTAACTTCCTAACTAAGTTGGTGACCCGGTTGAGGGTGACGCCAACTTAGTCAATG-GTTTTAT
194 CATAACTTCCTAACTAAGTTGGTGACCCAGTTGAGGATGACACCAACTCAAT-AAGGAGTTTTAT
* ** *
41350823 TAATAGTATATATATACAACTCATGGAGATAAAAAAGT
258 TAATAGTATATATATACAAATCATCAAAATAAAAAAGT
* **
41350861 GTGCATAATAAAGTTAAAATGTATAAAAATATTAAAATAAAATTTTAGTTGAGTGAAAAATTAAA
1 GTGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAATTTTAGTTGAGTGGTAAATTAAA
* * ** ****
41350926 AGTTTTATTAATGCAATTGGTGTGGGTTCAAAT-CCTACTGTATGCATATTTTTTTTGTTTTTTT
66 AGTTTTATTAATGCAATTGGTGTGGGTTCAAATACC-AATATATGCATA-TTTTAAT-CAACTTT
* * * *
41350990 TTTAAAGTGAAAAAACTAAAATATCTTCAAATAATATTAATTATATT-AATTACGAAAG
128 TTTAAAGTGAAAAAACTAAAATACCCTCAAATAATATTACTTAT-TTCAATTACAAAAG
41351048 AGTATTCTCG
Statistics
Matches: 403, Mismatches: 67, Indels: 35
0.80 0.13 0.07
Matches are distributed among these distances:
293 3 0.01
294 95 0.24
295 7 0.02
296 2 0.00
297 50 0.12
298 2 0.00
300 5 0.01
301 2 0.00
302 15 0.04
304 1 0.00
308 118 0.29
309 4 0.01
310 97 0.24
311 2 0.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (295 bp):
GTGCATAATAAAATTAAAATGTATAAAAATATTAAAATAAAATTTTAGTTGAGTGGTAAATTAAA
AGTTTTATTAATGCAATTGGTGTGGGTTCAAATACCAATATATGCATATTTTAATCAACTTTTTT
AAAGTGAAAAAACTAAAATACCCTCAAATAATATTACTTATTTCAATTACAAAAGGACATTCTCA
TAACTTCCTAACTAAGTTGGTGACCCAGTTGAGGATGACACCAACTCAATAAGGAGTTTTATTAA
TAGTATATATATACAAATCATCAAAATAAAAAAGT
Found at i:41351671 original size:16 final size:17
Alignment explanation
Indices: 41351640--41351672 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41351630 CATTTCATAA
*
41351640 ATTTTTATAATATTAAT
1 ATTTTAATAATATTAAT
41351657 ATTTTAATAAT-TTAAT
1 ATTTTAATAATATTAAT
41351673 TCCCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTAATAATATTAAT
Found at i:41353027 original size:18 final size:18
Alignment explanation
Indices: 41353000--41353037 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41352990 ACTCCAAGGC
41353000 GACGACGAAGATGAAGAT
1 GACGACGAAGATGAAGAT
* *
41353018 GACGATGAAGATGGAGAT
1 GACGACGAAGATGAAGAT
41353036 GA
1 GA
41353038 TGAAGATGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.37, T:0.13
Consensus pattern (18 bp):
GACGACGAAGATGAAGAT
Found at i:41376336 original size:22 final size:22
Alignment explanation
Indices: 41376311--41376353 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41376301 TATGTATGTC
* *
41376311 ATATTTAAATTTATTTTGATTT
1 ATATCTAAATATATTTTGATTT
*
41376333 ATATCTAGATATATTTTGATT
1 ATATCTAAATATATTTTGATT
41376354 ACCACTCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (22 bp):
ATATCTAAATATATTTTGATTT
Found at i:41378825 original size:20 final size:20
Alignment explanation
Indices: 41378802--41378869 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
41378792 CCTTGATCCT
*
41378802 TGTCTAAATACAACGAATCG
1 TGTCTCAATACAACGAATCG
* *** *
41378822 TGTCTCAAGACCTTG-ATCCT
1 TGTCTCAATACAACGAAT-CG
41378842 TGTCTCAATACAACGAATCG
1 TGTCTCAATACAACGAATCG
41378862 TGTCTCAA
1 TGTCTCAA
41378870 GACCTTGGAT
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (20 bp):
TGTCTCAATACAACGAATCG
Found at i:41378837 original size:40 final size:40
Alignment explanation
Indices: 41378789--41378876 Score: 167
Period size: 40 Copynumber: 2.2 Consensus size: 40
41378779 CTATGTCTGG
41378789 AGACCTTGATCCTTGTCTAAATACAACGAATCGTGTCTCA
1 AGACCTTGATCCTTGTCTAAATACAACGAATCGTGTCTCA
*
41378829 AGACCTTGATCCTTGTCTCAATACAACGAATCGTGTCTCA
1 AGACCTTGATCCTTGTCTAAATACAACGAATCGTGTCTCA
41378869 AGACCTTG
1 AGACCTTG
41378877 GATCGAATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (40 bp):
AGACCTTGATCCTTGTCTAAATACAACGAATCGTGTCTCA
Found at i:41378881 original size:20 final size:20
Alignment explanation
Indices: 41378818--41378881 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
41378808 AATACAACGA
41378818 ATCGTGTCTCAAGACCTT-G
1 ATCGTGTCTCAAGACCTTGG
* * *** *
41378837 ATCCTTGTCTCAATACAACGA
1 AT-CGTGTCTCAAGACCTTGG
41378858 ATCGTGTCTCAAGACCTTGG
1 ATCGTGTCTCAAGACCTTGG
41378878 ATCG
1 ATCG
41378882 AATTTGATTG
Statistics
Matches: 31, Mismatches: 12, Indels: 3
0.67 0.26 0.07
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (20 bp):
ATCGTGTCTCAAGACCTTGG
Found at i:41379744 original size:40 final size:39
Alignment explanation
Indices: 41379624--41379754 Score: 124
Period size: 40 Copynumber: 3.3 Consensus size: 39
41379614 TTTGGATTAA
* * *
41379624 AAACGCCGCAAAAGGTAAAGTATTAGCG-GTATTTTTGCAT
1 AAACGCCGCAAAAAGTAAAGCAATAGCGCGT-TTTTT-CAT
* * ** *
41379664 AAATGCCAC-AAAAGATAAAGCAATAGCGGCAATTTCTCAT
1 AAACGCCGCAAAAAG-TAAAGCAATAGC-GCGTTTTTTCAT
41379704 AAACGCCGCAAAAAGTAAAGCAATAGCGACGTTTTTTCAT
1 AAACGCCGCAAAAAGTAAAGCAATAGCG-CGTTTTTTCAT
41379744 -AACGCCGCAAA
1 AAACGCCGCAAA
41379755 TTTTTTCTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 11
0.75 0.13 0.11
Matches are distributed among these distances:
39 16 0.22
40 47 0.64
41 10 0.14
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.21
Consensus pattern (39 bp):
AAACGCCGCAAAAAGTAAAGCAATAGCGCGTTTTTTCAT
Found at i:41381993 original size:2 final size:2
Alignment explanation
Indices: 41381988--41382015 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41381978 TATCCAATGC
41381988 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
41382016 TTATCTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41382322 original size:181 final size:174
Alignment explanation
Indices: 41382015--41382365 Score: 470
Period size: 181 Copynumber: 2.0 Consensus size: 174
41382005 TATATATATA
** * * *
41382015 TTTATCTATTTAAGGAGCTTTCTGCGACTGATATTTTTTTCAGCTTGCACATGTGTCTTGTGAGC
1 TTTATCTATTTAACCAGCTTTCTGCAACTGAAATTTTTTTCAGCTTGCACACGTGTCTTGTGAGC
* * * *
41382080 ACTTGAATTCATCAAAAGACATTACAGAAGAAATTCTTTTATCATGTTCTTGGTTGCATCACCTA
66 ACATGAATTCATCAAAAGACATTACAAAAGAAATTCTTTTATCATGTTCTCGGTAGCATCACCTA
* * * *
41382145 TTAAGGAAACATATATTTCCTTAGTATGTCTCTCAATAAGGCATTTCT
131 TTAA-G-AA-A-ACATTTCATTAGCATGTCTCTCAATAAAGCATTTCT
* *
41382193 TTTATCTATTTAACCAGCTTTCTGCAAGT-AAATTTTTCCTTCATCTTGCAGGCACGTGTCTTGT
1 TTTATCTATTTAACCAGCTTTCTGCAACTGAAATTTTT--TTCAGCTTGCA--CACGTGTCTTGT
* *
41382257 GAGTACATGAATTCATCTAAAGACATTACAAAAGAAATTCTTTTATCATGTTCTCGGTAGCATCA
62 GAGCACATGAATTCATCAAAAGACATTACAAAAGAAATTCTTTTATCATGTTCTCGGTAGCATCA
41382322 CCTATTAAGAAAACATTTCATTAGCATGTCTCTCAATAAAGCAT
127 CCTATTAAGAAAACATTTCATTAGCATGTCTCTCAATAAAGCAT
41382366 CTTTTTTTGG
Statistics
Matches: 152, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
177 35 0.23
178 26 0.17
179 12 0.08
180 1 0.01
181 78 0.51
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (174 bp):
TTTATCTATTTAACCAGCTTTCTGCAACTGAAATTTTTTTCAGCTTGCACACGTGTCTTGTGAGC
ACATGAATTCATCAAAAGACATTACAAAAGAAATTCTTTTATCATGTTCTCGGTAGCATCACCTA
TTAAGAAAACATTTCATTAGCATGTCTCTCAATAAAGCATTTCT
Found at i:41384397 original size:22 final size:21
Alignment explanation
Indices: 41384367--41384426 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
41384357 ACACTCCATG
41384367 ATGCACACAAGTGCCAAATATAA
1 ATGC-CACAAGTGCCAAATA-AA
* *
41384390 ATGCCACAAGCGCC-AATAGA
1 ATGCCACAAGTGCCAAATAAA
*
41384410 ATGTACACAAGTGCCAA
1 ATG-CCACAAGTGCCAA
41384427 TCTTCCTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 4 0.13
21 13 0.42
22 10 0.32
23 4 0.13
ACGTcount: A:0.43, C:0.25, G:0.17, T:0.15
Consensus pattern (21 bp):
ATGCCACAAGTGCCAAATAAA
Found at i:41393522 original size:22 final size:22
Alignment explanation
Indices: 41393494--41393537 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41393484 AACATGAGAA
* *
41393494 GGAAAAGATTCATATAGGTCAT
1 GGAAAAGATTCACATAAGTCAT
*
41393516 GGAAAAGCTTCACATAAGTCAT
1 GGAAAAGATTCACATAAGTCAT
41393538 CCTTTGGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (22 bp):
GGAAAAGATTCACATAAGTCAT
Found at i:41403210 original size:177 final size:178
Alignment explanation
Indices: 41402890--41403254 Score: 524
Period size: 177 Copynumber: 2.1 Consensus size: 178
41402880 TTGAATTACT
* *
41402890 CAATTTAGTCCTTAAAATCAGGACAAACATAACTTTCAATTTAAAGCCTCGAATTAAAATCTCAT
1 CAATTTAGTCCTTAAAATCAGGACAAACATAACTTTCAATTTAAAGCCTCGAATTAAAATCTAAC
* * * * *
41402955 TTCACCAAAACTCATTAGGGACCCTCTATTTTGTATCCCTACCAAATATATTTGACAATTTTGTA
66 TTCACCAAAACTCATTAAGGACCATCTATTTTGTATCCCTACAAAAAATATATGACAATTTTGTA
*
41403020 TTTTATTCAATTTGGTCCCTAATATATGAAACTAACAATTAAG-TTGTA
131 TTTTATTCAATTTGGTCCCTAATATACGAAACTAACAATTAAGCTT-TA
** **
41403068 CAATTTAGTACC-TAAAATTGGGACATGCATAACTTTCAATTTAAAGCCTCGAATTAAAATCTAA
1 CAATTTAGT-CCTTAAAATCAGGACAAACATAACTTTCAATTTAAAGCCTCGAATTAAAATCTAA
*
41403132 CTTCACC-AAACTCATTAAGGATCATCTATTTTGTATCCCTACAAAAAA-ATAATGACAATTTT-
65 CTTCACCAAAACTCATTAAGGACCATCTATTTTGTATCCCTACAAAAAATAT-ATGACAATTTTG
* *
41403194 TCATTTTATTCAATTTGGTCTCTAATATACGAAACTAACAATTAGGCTTTA
129 T-ATTTTATTCAATTTGGTCCCTAATATACGAAACTAACAATTAAGCTTTA
41403245 CAATTTAGTC
1 CAATTTAGTC
41403255 ATTTTCTTAA
Statistics
Matches: 168, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
176 4 0.02
177 98 0.58
178 64 0.38
179 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (178 bp):
CAATTTAGTCCTTAAAATCAGGACAAACATAACTTTCAATTTAAAGCCTCGAATTAAAATCTAAC
TTCACCAAAACTCATTAAGGACCATCTATTTTGTATCCCTACAAAAAATATATGACAATTTTGTA
TTTTATTCAATTTGGTCCCTAATATACGAAACTAACAATTAAGCTTTA
Found at i:41403496 original size:3 final size:3
Alignment explanation
Indices: 41403483--41403512 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
41403473 ACGGAGGTGA
*
41403483 AAG ATG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41403513 TTTCATCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:41405070 original size:144 final size:143
Alignment explanation
Indices: 41404806--41405096 Score: 510
Period size: 144 Copynumber: 2.0 Consensus size: 143
41404796 TTATTTAGAC
* *
41404806 CTTTAGTCCATTTCTTTGCTTGTAATGACTTTTCATCCTTTTAGTTTAATGTATTTTAGTTTCTT
1 CTTTAGTCCATTTCTTTGCTTGTAATGACTTTTCAACCTTTTAGTTTAATGTATTTTAATTTCTT
* *
41404871 TTAATTTAATCTGTTAAAGACTTCAACTTTTATGTTTCTTCTTCTCTATTTTGTTGTTGGATACC
66 TTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTCTTCTCTATTTTGTTGTTGGATACC
41404936 TCTCATTACTTTT
131 TCTCATTACTTTT
*
41404949 CTTTGAGTCCATTTCTTTGCTTGTACTGACTTTTCAACCTTTTAGTTTAATGTATTTTAATTTCT
1 CTTT-AGTCCATTTCTTTGCTTGTAATGACTTTTCAACCTTTTAGTTTAATGTATTTTAATTTCT
*
41405014 TTTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTGTTCTCTATTTTGTTGTTGGATAC
65 TTTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTCTTCTCTATTTTGTTGTTGGATAC
*
41405079 CTCTGATTACTTTT
130 CTCTCATTACTTTT
41405093 CTTT
1 CTTT
41405097 TCTGTTTTCT
Statistics
Matches: 140, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
143 4 0.03
144 136 0.97
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (143 bp):
CTTTAGTCCATTTCTTTGCTTGTAATGACTTTTCAACCTTTTAGTTTAATGTATTTTAATTTCTT
TTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTCTTCTCTATTTTGTTGTTGGATACC
TCTCATTACTTTT
Found at i:41405610 original size:33 final size:33
Alignment explanation
Indices: 41405573--41405639 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
41405563 TTTCATAACT
41405573 TTGCACGTTGTACAATTTAGTCCTCGATAGCTA
1 TTGCACGTTGTACAATTTAGTCCTCGATAGCTA
41405606 TTGCACGTTGTACAATTTAGTCCTCGATAGCTA
1 TTGCACGTTGTACAATTTAGTCCTCGATAGCTA
41405639 T
1 T
41405640 CTCGTAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (33 bp):
TTGCACGTTGTACAATTTAGTCCTCGATAGCTA
Found at i:41406485 original size:24 final size:24
Alignment explanation
Indices: 41406399--41406485 Score: 66
Period size: 24 Copynumber: 3.6 Consensus size: 24
41406389 GGCTTAGAAT
**
41406399 TAGTCTTAAAATTACCCTTTAGGAC
1 TAGTCTTAAAATTAAAC-TTAGGAC
* * ** ** *
41406424 TAGTTTTAGAATTAGGCTTACAAT
1 TAGTCTTAAAATTAAACTTAGGAC
* *
41406448 TAGTCTCAATATTAAACTTAGGAC
1 TAGTCTTAAAATTAAACTTAGGAC
41406472 TAGTCTTAAAATTA
1 TAGTCTTAAAATTA
41406486 GGTCTAGGAT
Statistics
Matches: 44, Mismatches: 18, Indels: 1
0.70 0.29 0.02
Matches are distributed among these distances:
24 31 0.70
25 13 0.30
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (24 bp):
TAGTCTTAAAATTAAACTTAGGAC
Found at i:41406531 original size:13 final size:13
Alignment explanation
Indices: 41406515--41406565 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
41406505 GAACTTAATT
41406515 TTAGAACTTAGGA
1 TTAGAACTTAGGA
* *
41406528 TTAG-ACTTAAGC
1 TTAGAACTTAGGA
* *
41406540 TAAGAGCTTAGGA
1 TTAGAACTTAGGA
*
41406553 TTAGGACTTAGGA
1 TTAGAACTTAGGA
41406566 CTTAAAACTC
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (13 bp):
TTAGAACTTAGGA
Found at i:41408153 original size:22 final size:22
Alignment explanation
Indices: 41408125--41408166 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
41408115 GTAGTTAAGT
41408125 GACCATATGTCTCAAGACATAG
1 GACCATATGTCTCAAGACATAG
41408147 GACCATATGTCTCAAGACAT
1 GACCATATGTCTCAAGACAT
41408167 GAAAGTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (22 bp):
GACCATATGTCTCAAGACATAG
Found at i:41409503 original size:19 final size:20
Alignment explanation
Indices: 41409479--41409532 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
41409469 GCAATTAAGC
41409479 CTAGAAATTTTGGTATAGG-
1 CTAGAAATTTTGGTATAGGA
* *
41409498 CTAGAAATTTTAGTATCGGA
1 CTAGAAATTTTGGTATAGGA
*
41409518 TTA-AAATTTTGGTAT
1 CTAGAAATTTTGGTAT
41409533 TGCTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 28 0.93
20 2 0.07
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (20 bp):
CTAGAAATTTTGGTATAGGA
Found at i:41415395 original size:21 final size:21
Alignment explanation
Indices: 41415352--41415465 Score: 113
Period size: 21 Copynumber: 5.5 Consensus size: 21
41415342 TCGAAAACTG
* * *
41415352 AACAGAAGCTCATGATAGCTA
1 AACAGAAGCTCATAAGAGTTA
41415373 AACAGAAGCTCATAAGAGTTA
1 AACAGAAGCTCATAAGAGTTA
* * * * *
41415394 AATAGAAACACATAAGGGTTG
1 AACAGAAGCTCATAAGAGTTA
* *
41415415 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGTTA
* *
41415436 AACAGAAACTCATAA-AGTTG
1 AACAGAAGCTCATAAGAGTTA
41415456 AACAGAAGCT
1 AACAGAAGCT
41415466 TGTGAGAGCT
Statistics
Matches: 73, Mismatches: 20, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
20 12 0.16
21 61 0.84
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGTTA
Found at i:41415474 original size:41 final size:42
Alignment explanation
Indices: 41415373--41415522 Score: 140
Period size: 42 Copynumber: 3.6 Consensus size: 42
41415363 ATGATAGCTA
* * * *
41415373 AACAGAAGCTCATAAGAGTTAAATAGAAACACATAAGGGTTG
1 AACAGAAGCTCGTAAGAGCTAAACAGAAACACATAAGAGTTG
*
41415415 AACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAA-AGTTG
1 AACAGAAGCTCGTAAGAGCTAAACAGAAACACATAAGAGTTG
* * * * **** * *
41415456 AACAGAAGCTTGTGAGAGCTGAACAAAAATTTGTATGAGTTA
1 AACAGAAGCTCGTAAGAGCTAAACAGAAACACATAAGAGTTG
* *
41415498 AACGGAAGCTCGTAAGAGCTTAACA
1 AACAGAAGCTCGTAAGAGCTAAACA
41415523 TAAAGTAAAA
Statistics
Matches: 89, Mismatches: 18, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
41 32 0.36
42 57 0.64
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTAAACAGAAACACATAAGAGTTG
Found at i:41415480 original size:21 final size:20
Alignment explanation
Indices: 41415413--41415480 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
41415403 ACATAAGGGT
41415413 TGAACAGAAGCTCGTAAGAGC
1 TGAACAGAAGCTCGT-AGAGC
* * * * *
41415434 TAAACAGAAACTCATAAAGT
1 TGAACAGAAGCTCGTAGAGC
*
41415454 TGAACAGAAGCTTGTGAGAGC
1 TGAACAGAAGCTCGT-AGAGC
41415475 TGAACA
1 TGAACA
41415481 AAAATTTGTA
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.18
Consensus pattern (20 bp):
TGAACAGAAGCTCGTAGAGC
Found at i:41417694 original size:18 final size:18
Alignment explanation
Indices: 41417671--41417718 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
41417661 AAAAAGCCTA
*
41417671 ACACAATATTTTTTTTTG
1 ACACAATATTTTTTTCTG
*
41417689 ACACAAT-TTTTTATCTG
1 ACACAATATTTTTTTCTG
41417706 ACA-AATATTTTTT
1 ACACAATATTTTTT
41417719 AAAATTTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 3 0.12
17 16 0.62
18 7 0.27
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.52
Consensus pattern (18 bp):
ACACAATATTTTTTTCTG
Found at i:41427431 original size:28 final size:29
Alignment explanation
Indices: 41427378--41427433 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
41427368 TAAATATTGA
*
41427378 AATTTATGATTTAAAATAAATTAATAATAT
1 AATTTAT-ATTTAAAATAAATAAATAATAT
41427408 AATTTAT-TTTAAATATAAA-AAATAAT
1 AATTTATATTTAAA-ATAAATAAATAAT
41427434 TTTTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 12 0.50
29 5 0.21
30 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (29 bp):
AATTTATATTTAAAATAAATAAATAATAT
Found at i:41428720 original size:14 final size:15
Alignment explanation
Indices: 41428703--41428740 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
41428693 TTTATTTTTT
41428703 ATTAATTATAAAA-A
1 ATTAATTATAAAATA
* *
41428717 ATTAATTTTAAAATT
1 ATTAATTATAAAATA
41428732 ATTAATTAT
1 ATTAATTAT
41428741 TATCATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAATTATAAAATA
Found at i:41428786 original size:19 final size:18
Alignment explanation
Indices: 41428742--41428788 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
41428732 ATTAATTATT
41428742 ATCATATTT-TAAATAAA
1 ATCATATTTATAAATAAA
*
41428759 ATCATATTTATATATAAA
1 ATCATATTTATAAATAAA
*
41428777 AGTTATATTTAT
1 A-TCATATTTAT
41428789 TTAATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 9 0.35
18 8 0.31
19 9 0.35
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (18 bp):
ATCATATTTATAAATAAA
Found at i:41428789 original size:23 final size:21
Alignment explanation
Indices: 41428763--41428811 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
41428753 AATAAAATCA
*
41428763 TATTTATATATAAAAGTTATATT
1 TATTTATAT-TAAAAATT-TATT
41428786 TATTTA-ATTAAAAATTTATT
1 TATTTATATTAAAAATTTATT
41428806 T-TTTAT
1 TATTTAT
41428812 TTTTAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 5 0.21
21 7 0.29
22 2 0.08
23 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TATTTATATTAAAAATTTATT
Found at i:41430533 original size:26 final size:26
Alignment explanation
Indices: 41430494--41430567 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
41430484 AGATTAGTTG
*
41430494 AAAACTATAAAAAAAATTATTAT-TATA
1 AAAATTAT-AAAAAAATTATTATGTA-A
* * **
41430521 AAAATTATTAAAAAATCAAAATGGTAA
1 AAAATTATAAAAAAATTATTAT-GTAA
41430548 AAAATTATAAAAAAATTATT
1 AAAATTATAAAAAAATTATT
41430568 TGAATTTTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
26 10 0.28
27 24 0.67
28 2 0.06
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (26 bp):
AAAATTATAAAAAAATTATTATGTAA
Found at i:41438177 original size:3 final size:3
Alignment explanation
Indices: 41438169--41438208 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
41438159 CAAAAAGGAA
41438169 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
41438209 TTATTATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:41448135 original size:28 final size:26
Alignment explanation
Indices: 41448089--41448151 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 26
41448079 ATTTTATTTC
41448089 TCAAAAACACTGCTAAACACCAAACTTT
1 TCAAAAACACTGCTAAACA--AAACTTT
* * *
41448117 TCAAAAACACTTCTCAACAATACTTT
1 TCAAAAACACTGCTAAACAAAACTTT
*
41448143 TCAAGAACA
1 TCAAAAACA
41448152 TTGTTACCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 14 0.45
28 17 0.55
ACGTcount: A:0.46, C:0.27, G:0.03, T:0.24
Consensus pattern (26 bp):
TCAAAAACACTGCTAAACAAAACTTT
Found at i:41458460 original size:23 final size:23
Alignment explanation
Indices: 41458416--41458460 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
41458406 TTTATTAAAA
* * *
41458416 ATAATGAAATTATAAATGAATAC
1 ATAATAAAATTACAAATAAATAC
*
41458439 ATAATAAAATTACATATAAATA
1 ATAATAAAATTACAAATAAATA
41458461 TCTTAAAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (23 bp):
ATAATAAAATTACAAATAAATAC
Found at i:41463899 original size:16 final size:16
Alignment explanation
Indices: 41463878--41463910 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41463868 ACTATTGATG
41463878 CTACTCATAACATTAA
1 CTACTCATAACATTAA
41463894 CTACTCATAACATTAA
1 CTACTCATAACATTAA
41463910 C
1 C
41463911 CAAGTTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.30
Consensus pattern (16 bp):
CTACTCATAACATTAA
Found at i:41476007 original size:17 final size:17
Alignment explanation
Indices: 41475965--41476008 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
41475955 AATATTAAAA
41475965 AATATTTTTATACTTTT
1 AATATTTTTATACTTTT
* *
41475982 AATAATTTTATATTTTT
1 AATATTTTTATACTTTT
41475999 AGA-ATTTTTA
1 A-ATATTTTTA
41476009 AAATTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
AATATTTTTATACTTTT
Found at i:41477715 original size:22 final size:22
Alignment explanation
Indices: 41477689--41477736 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
41477679 AATTATGATC
*
41477689 ATTACTTTAATTGCACT-ATTTA
1 ATTACTATAATT-CACTGATTTA
*
41477711 ATTACTATAATTCATTGATTTA
1 ATTACTATAATTCACTGATTTA
41477733 ATTA
1 ATTA
41477737 TTAATTTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTACTATAATTCACTGATTTA
Found at i:41479938 original size:20 final size:21
Alignment explanation
Indices: 41479899--41479939 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
41479889 GTAATTATAT
*
41479899 TAATTAAATGAAATAAAAATA
1 TAATTAAATGAAACAAAAATA
*
41479920 TAATTAACT-AAACAAAAATA
1 TAATTAAATGAAACAAAAATA
41479940 ATTACACATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
TAATTAAATGAAACAAAAATA
Found at i:41480769 original size:15 final size:15
Alignment explanation
Indices: 41480744--41480778 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41480734 GACTCTATTT
*
41480744 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
41480758 TAATTAATATTAAGA
1 TAATTAATATTAAGA
41480773 TAATTA
1 TAATTA
41480779 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:41482266 original size:66 final size:66
Alignment explanation
Indices: 41482196--41482328 Score: 187
Period size: 66 Copynumber: 2.0 Consensus size: 66
41482186 GCTTAGGTAC
* *
41482196 AAACTTTGCTCTAAAAACATGTTCCTCTCGATGAACAAAATAAGTGCTCTC-TCTAATTTGTACA
1 AAACTTTGCTCTAAAAACATATTCCTCTCGATAAACAAAATAAGTGCTC-CATCTAATTTGTACA
41482260 CA
65 CA
* * * * *
41482262 AAACTTTGGTCTAAATACATATTTCTTTCGATAAACAAAATAAGTGCTCCATTTAATTTGTACAC
1 AAACTTTGCTCTAAAAACATATTCCTCTCGATAAACAAAATAAGTGCTCCATCTAATTTGTACAC
41482327 A
66 A
41482328 A
1 A
41482329 TTAAATAAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 1 0.02
66 58 0.98
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.34
Consensus pattern (66 bp):
AAACTTTGCTCTAAAAACATATTCCTCTCGATAAACAAAATAAGTGCTCCATCTAATTTGTACAC
A
Found at i:41490404 original size:19 final size:19
Alignment explanation
Indices: 41490380--41490424 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
41490370 AGGAATTAGG
41490380 AAATTTTGAACTAATCTTC
1 AAATTTTGAACTAATCTTC
41490399 AAATTTTGAACTAATCTTC
1 AAATTTTGAACTAATCTTC
41490418 AAATTTT
1 AAATTTT
41490425 TCAGGAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44
Consensus pattern (19 bp):
AAATTTTGAACTAATCTTC
Found at i:41496120 original size:34 final size:32
Alignment explanation
Indices: 41495999--41496128 Score: 127
Period size: 34 Copynumber: 3.9 Consensus size: 32
41495989 TTTTTAAAAA
* *
41495999 TAAATCAGGGTTTATAGTTTTT-TAAAATTAAT
1 TAAATTAGGGTTTA-AGTTTTTAAAAAATTAAT
* *
41496031 TAAATTAGGTTTTAAGGGTTTTAAATAAATTAAT
1 TAAATTAGGGTTTAA-GTTTTTAAA-AAATTAAT
* *
41496065 TAAATTAAGGTCTAGAGTTTTTAAGAAAATTAAT
1 TAAATTAGGGTTTA-AGTTTTTAA-AAAATTAAT
* *
41496099 TAAATTAGGGTTTAATTTTTTTAAACAATT
1 TAAATTAGGGTTTAA-GTTTTTAAAAAATT
41496129 TTGTGTTTAG
Statistics
Matches: 80, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
31 1 0.01
32 17 0.21
33 7 0.09
34 53 0.66
35 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (32 bp):
TAAATTAGGGTTTAAGTTTTTAAAAAATTAAT
Found at i:41496364 original size:126 final size:126
Alignment explanation
Indices: 41496215--41496862 Score: 847
Period size: 126 Copynumber: 5.2 Consensus size: 126
41496205 TTTGTTTTTT
* * * * * *
41496215 TTTTTCTATAGTAGTTTCAGAAAAATTAATTTTGAGAAGACGATTCTTAAAAAATAGTGTCGAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAA
* * * *
41496280 ATGCTAT-AAGTAAGATGCACTATCAACAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
66 ACGCT-TCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
* *
41496341 TTTTTCTACAGTTGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAA
* * *
41496406 AAGCTTCAAGCAAGATGCATTGTCAGCAAAATTACTGAAAAATGCTCCCACGTAGACGCTC
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
** * * * *
41496467 TTTTTCTATGGTAGTTCTTGAAAAAATGATTTTGAGAAGACAATTCTGAAAAATTAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAA
* * * * *
41496532 ACGCTTCAAGCAAGATGCACTGTCAGTAAAAATACTGAAAAATGCTCCCACATGGACGCTC
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
*
41496593 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGAC-AGTTCTGAAAAAATAGTGTC-AA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGA-TTCTGAAAAAATAGTGTCAAA
* * * * *
41496656 AACGCTTCAAACAGGATGCATTGTCAGCAAAATTATTG-AAAAAGCTCCTACGTAGACGCTC
65 AACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
* * * *
41496717 TTTTTGTACAATAGTTCCTGAAAAAATAATATTT-AGAAGACGGTTCTGAAAAAATAGTGTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAAT-TTTGAGAAGACGATTCTGAAAAAATAGTGTCAAA
* * * * * * *
41496781 AATGCTTCAAGTAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACACTC
65 AACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
41496843 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
41496863 CTTGGCCTTA
Statistics
Matches: 457, Mismatches: 59, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
124 70 0.15
125 73 0.16
126 314 0.69
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAA
ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
Found at i:41518205 original size:19 final size:18
Alignment explanation
Indices: 41518178--41518213 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41518168 GTTTAGCAAT
41518178 GCTTAAAAAAACACTTTTG
1 GCTT-AAAAAACACTTTTG
*
41518197 GCTTGAAAAACACTTTT
1 GCTTAAAAAACACTTTT
41518214 TGAAAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
GCTTAAAAAACACTTTTG
Found at i:41518974 original size:13 final size:13
Alignment explanation
Indices: 41518958--41519036 Score: 54
Period size: 13 Copynumber: 6.2 Consensus size: 13
41518948 TTATTTTTCC
41518958 AAAGCACTTTTTA
1 AAAGCACTTTTTA
*
41518971 AAAG--CTTTTCA
1 AAAGCACTTTTTA
** * *
41518982 AAAATACTTCTAA
1 AAAGCACTTTTTA
* **
41518995 AAATCACTTTTCC
1 AAAGCACTTTTTA
41519008 AAAGCACTTTTTA
1 AAAGCACTTTTTA
* *
41519021 AAAACACTTCTTA
1 AAAGCACTTTTTA
41519034 AAA
1 AAA
41519037 ACAATGCTAA
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
11 9 0.18
13 41 0.82
ACGTcount: A:0.43, C:0.19, G:0.04, T:0.34
Consensus pattern (13 bp):
AAAGCACTTTTTA
Found at i:41518990 original size:50 final size:50
Alignment explanation
Indices: 41518927--41519023 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
41518917 AAACCAAATA
* * * *
41518927 TTTCAAAAGTACTTCTCAAAATTATTTTTCCAAAGCACTTTTTAAAAGCT
1 TTTCAAAAATACTTCTAAAAATCACTTTTCCAAAGCACTTTTTAAAAGCT
41518977 TTTCAAAAATACTTCTAAAAATCACTTTTCCAAAGCACTTTTTAAAA
1 TTTCAAAAATACTTCTAAAAATCACTTTTCCAAAGCACTTTTTAAAA
41519024 ACACTTCTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (50 bp):
TTTCAAAAATACTTCTAAAAATCACTTTTCCAAAGCACTTTTTAAAAGCT
Found at i:41519824 original size:22 final size:22
Alignment explanation
Indices: 41519798--41519847 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
41519788 ATTGGGTTGA
* *
41519798 CGTTGTGACGTTGAGGGTTCCT
1 CGTTGCGACGTCGAGGGTTCCT
41519820 CGTTGCGACGTCGAGGGTTCCT
1 CGTTGCGACGTCGAGGGTTCCT
41519842 CGTTGC
1 CGTTGC
41519848 AACATACTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.08, C:0.24, G:0.36, T:0.32
Consensus pattern (22 bp):
CGTTGCGACGTCGAGGGTTCCT
Found at i:41524637 original size:16 final size:16
Alignment explanation
Indices: 41524588--41524640 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
41524578 AAAGAAATTT
*
41524588 AAAAATAAAATATTCA
1 AAAAATAATATATTCA
* *
41524604 AAAAATAATA-AGT-G
1 AAAAATAATATATTCA
*
41524618 AAAAATGATATATTCA
1 AAAAATAATATATTCA
41524634 AAAAATA
1 AAAAATA
41524641 CTATGTCAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
14 9 0.32
15 4 0.14
16 15 0.54
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.25
Consensus pattern (16 bp):
AAAAATAATATATTCA
Found at i:41527732 original size:46 final size:46
Alignment explanation
Indices: 41527625--41527830 Score: 337
Period size: 46 Copynumber: 4.5 Consensus size: 46
41527615 CATACGATCT
* *
41527625 CTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
41527668 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
41527714 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
41527760 CTTATCACTTTGTCAGTTGATCAGATAAGTGTAGCTAAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
41527806 CTTATCACTTTGTCACTAGATCAGA
1 CTTATCACTTTGTCACTTGATCAGA
41527831 AGTACTCAAA
Statistics
Matches: 151, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
43 8 0.05
44 5 0.03
45 20 0.13
46 118 0.78
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
Found at i:41527939 original size:19 final size:21
Alignment explanation
Indices: 41527899--41527945 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
41527889 TTTTATTTTC
41527899 ATTTCATCAATAAATATATAT
1 ATTTCATCAATAAATATATAT
*
41527920 ATTTCATC-ATACAT-TATAT
1 ATTTCATCAATAAATATATAT
*
41527939 AATTCAT
1 ATTTCAT
41527946 GAAATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 5 0.21
21 8 0.33
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTCATCAATAAATATATAT
Found at i:41529985 original size:13 final size:13
Alignment explanation
Indices: 41529967--41529996 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41529957 AAAAAATTCT
41529967 AAAATTATGATAA
1 AAAATTATGATAA
*
41529980 AAAATTATTATAA
1 AAAATTATGATAA
41529993 AAAA
1 AAAA
41529997 CTAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AAAATTATGATAA
Found at i:41536099 original size:22 final size:21
Alignment explanation
Indices: 41536074--41536124 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
41536064 ATTAATTAAC
41536074 AATTGTATAAATTTACTTTTAT
1 AATTGTATAAA-TTACTTTTAT
* *
41536096 AATTTTATAAATTGCTTTTAT
1 AATTGTATAAATTACTTTTAT
*
41536117 -GTTGTATA
1 AATTGTATA
41536125 TCTTCAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 6 0.24
21 9 0.36
22 10 0.40
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (21 bp):
AATTGTATAAATTACTTTTAT
Found at i:41537597 original size:2 final size:2
Alignment explanation
Indices: 41537590--41537616 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41537580 TTAGAAAGTA
41537590 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 A
41537617 CTTCTGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41540882 original size:41 final size:41
Alignment explanation
Indices: 41540820--41540910 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
41540810 CCATTTAGAG
*
41540820 TCAGATTCAGCCACTTCTACAATCCTAAAAGGTCCTAACAA
1 TCAGGTTCAGCCACTTCTACAATCCTAAAAGGTCCTAACAA
41540861 TCAGGTTCAGCCACTTCTACAATCCTAAAAGGTCCTAACAA
1 TCAGGTTCAGCCACTTCTACAATCCTAAAAGGTCCTAACAA
41540902 TCAGGTTCA
1 TCAGGTTCA
41540911 ATTAGGTTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.25
Consensus pattern (41 bp):
TCAGGTTCAGCCACTTCTACAATCCTAAAAGGTCCTAACAA
Found at i:41544503 original size:2 final size:2
Alignment explanation
Indices: 41544496--41544545 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
41544486 CTAAGAATTT
41544496 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
41544538 GA GA GA GA
1 GA GA GA GA
41544546 ATGAGTAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41550334 original size:45 final size:45
Alignment explanation
Indices: 41550283--41550386 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
41550273 TCTAATTTAT
**
41550283 ATTACAAAGTTTGTTCCAAGTTTGTTCCAACATGTGCCAATTAAA
1 ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACCTGCCAATTAAA
* * *
41550328 ATTACAAAGTTTGTTCCAAGTTTGTTTCAACACCTGTCATTTAAA
1 ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACCTGCCAATTAAA
41550373 ATTACAAAGTTTGT
1 ATTACAAAGTTTGT
41550387 ATTTTTGCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (45 bp):
ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACCTGCCAATTAAA
Found at i:41571964 original size:44 final size:44
Alignment explanation
Indices: 41571914--41572049 Score: 121
Period size: 44 Copynumber: 3.1 Consensus size: 44
41571904 AAATTCTAGC
*
41571914 CTTGTCTCCCTGAGTGGCAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTCCCTGAGTGGCAGTGGAGTAGGTTGAAAATAACAGAT
* * * *** * * * * *
41571958 CTTGTCTACCTGTATTGACAGCAAAGTAGATCGAAGATACCAG-C
1 CTTGTCTCCCTG-AGTGGCAGTGGAGTAGGTTGAAAATAACAGAT
* **
41572002 CTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAACAGAT
1 CTTGTCTCCCTGAGTGGCAGTGGAGTAGGTTGAAAATAACAGAT
41572046 CTTG
1 CTTG
41572050 CCTTCCTGTA
Statistics
Matches: 65, Mismatches: 25, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
43 19 0.29
44 25 0.38
45 21 0.32
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (44 bp):
CTTGTCTCCCTGAGTGGCAGTGGAGTAGGTTGAAAATAACAGAT
Found at i:41572077 original size:88 final size:88
Alignment explanation
Indices: 41571911--41572082 Score: 238
Period size: 88 Copynumber: 2.0 Consensus size: 88
41571901 GTGAAATTCT
* ** * * *
41571911 AGCCTTGTCTCCCTGAGTGGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTACCTGTATTGA
1 AGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAACAGATCTTGCCTACCTGTATAGA
*
41571976 CAGCAAAGTAGATCGAAGATACC
66 CAGCAAAGCAGATCGAAGATACC
*
41571999 AGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAACAGATCTTGCCTTCCTGTACTAG
1 AGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAACAGATCTTGCCTACCTGTA-TAG
**
41572064 -CAGTGAAGCAGATCGAAGA
65 ACAGCAAAGCAGATCGAAGA
41572083 CATTAGTCTT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 71 0.97
89 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (88 bp):
AGCCTTGTCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATAACAGATCTTGCCTACCTGTATAGA
CAGCAAAGCAGATCGAAGATACC
Found at i:41572151 original size:50 final size:50
Alignment explanation
Indices: 41572089--41572206 Score: 157
Period size: 50 Copynumber: 2.4 Consensus size: 50
41572079 AAGACATTAG
* *
41572089 TCTTATCGCCCTGACATTGCAATGGAA-AAGATTGAAGCCACAACGGTGAA
1 TCTTATCTCCCTGACATTGCAA-CGAAGAAGATTGAAGCCACAACGGTGAA
* * * *
41572139 TCTTATTTCCCTGACGTTGCAACGAAGCAGATTGAAGCCACGACGGTGAA
1 TCTTATCTCCCTGACATTGCAACGAAGAAGATTGAAGCCACAACGGTGAA
*
41572189 TCTTATCTCCCTGGCATT
1 TCTTATCTCCCTGACATT
41572207 AAGGCCTGGA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 3 0.05
50 55 0.95
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (50 bp):
TCTTATCTCCCTGACATTGCAACGAAGAAGATTGAAGCCACAACGGTGAA
Found at i:41572636 original size:45 final size:44
Alignment explanation
Indices: 41572527--41572687 Score: 162
Period size: 45 Copynumber: 3.6 Consensus size: 44
41572517 GATCGCATCT
* * ** *
41572527 AGTCTTATCTCCTTGAAGTTGCAGAGGAGTAGA-CTGAGTAAGTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAG-A
* *
41572571 GGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAGCG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAG-A
** * *
41572616 AGTCTTATCTCCCTGAAGTTGCAGTGGACCAAACTCAAGAAAGTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAG-A
* * *
41572661 AGTCTTATCCCCCTGAAATTGAAGTGG
1 AGTCTTATCTCCCTGAAGTTGCAGTGG
41572688 GGCAAACTAA
Statistics
Matches: 98, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
44 30 0.31
45 68 0.69
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAGA
Done.