Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007733.1 Hibiscus syriacus cultivar Beakdansim tig00109987_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1979160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:283946 original size:22 final size:22
Alignment explanation
Indices: 283906--283948 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
283896 TTTAATTTTT
*
283906 ATTTAAAAATTAAGGATTTTAA
1 ATTTAAAAATGAAGGATTTTAA
* *
283928 ATTTAAAAATGCAGTATTTTA
1 ATTTAAAAATGAAGGATTTTA
283949 CAGCACAGCT
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:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (22 bp):
ATTTAAAAATGAAGGATTTTAA
Found at i:285058 original size:14 final size:14
Alignment explanation
Indices: 285035--285066 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
285025 CGTTCGTGAA
285035 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
*
285049 CGTTCGGTTATGTT
1 CGTTCAGTTATGTT
285063 CGTT
1 CGTT
285067 TATGTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (14 bp):
CGTTCAGTTATGTT
Found at i:285085 original size:10 final size:10
Alignment explanation
Indices: 285056--285086 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
285046 GTTCGTTCGG
*
285056 TTATGTTCGT
1 TTATGTTCAT
285066 TTATGTTCAT
1 TTATGTTCAT
285076 TTATGTTCAT
1 TTATGTTCAT
285086 T
1 T
285087 CATTTATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.16, C:0.10, G:0.13, T:0.61
Consensus pattern (10 bp):
TTATGTTCAT
Found at i:285094 original size:34 final size:34
Alignment explanation
Indices: 285012--285096 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 34
285002 CATAGGTCTC
*
285012 GTTCGTTCATTTACGTTCGTGAACGTTCAGTTAT
1 GTTCGTTCATTTATGTTCGTGAACGTTCAGTTAT
** ** * *
285046 GTTCGTTCGGTTATGTTCGTTTATGTTCATTTAT
1 GTTCGTTCATTTATGTTCGTGAACGTTCAGTTAT
*
285080 GTTCATTCATTTATGTT
1 GTTCGTTCATTTATGTT
285097 TAACCCAATC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.15, C:0.14, G:0.19, T:0.52
Consensus pattern (34 bp):
GTTCGTTCATTTATGTTCGTGAACGTTCAGTTAT
Found at i:297227 original size:19 final size:19
Alignment explanation
Indices: 297199--297244 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
297189 ATTTTATTCT
*
297199 TATCGTAACGAACTTGGAC
1 TATCGCAACGAACTTGGAC
297218 TATCGCAACGAACTTGGAC
1 TATCGCAACGAACTTGGAC
297237 TATCGCAA
1 TATCGCAA
297245 TGAATTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (19 bp):
TATCGCAACGAACTTGGAC
Found at i:300272 original size:2 final size:2
Alignment explanation
Indices: 300265--300289 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
300255 TTCAGGCTGC
300265 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
300290 GCAAAAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:302319 original size:2 final size:2
Alignment explanation
Indices: 302312--302339 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
302302 TACGATAATC
302312 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
302340 CAGAAAAGCG
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:303527 original size:28 final size:27
Alignment explanation
Indices: 303496--303561 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 27
303486 AAAAAAGTTT
303496 ATATATATATCAAAAAACCGTATAAAAC
1 ATATATATATCAAAAAACCGT-TAAAAC
* * * * *
303524 ATATACAGAACAAAATACCGTTAATAC
1 ATATATATATCAAAAAACCGTTAAAAC
303551 A-A-ATATATCAA
1 ATATATATATCAA
303562 TACAGTAGCA
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
25 6 0.20
26 1 0.03
27 6 0.20
28 17 0.57
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.24
Consensus pattern (27 bp):
ATATATATATCAAAAAACCGTTAAAAC
Found at i:304198 original size:30 final size:28
Alignment explanation
Indices: 304125--304205 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 28
304115 AGACTCAGAA
*
304125 ATCAGATACAGAA-ATATAGAAATTAGAG
1 ATCAGATA-AAAATATATAGAAATTAGAG
* * *
304153 ATCATATCAGAAATATATAGTAAATTAGAT
1 ATCAGAT-AAAAATATATAG-AAATTAGAG
*
304183 ATCAGATAAACAATATTTAGAAA
1 ATCAGATAAA-AATATATAGAAA
304206 ATCAAGTATC
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
28 8 0.19
29 12 0.29
30 22 0.52
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.27
Consensus pattern (28 bp):
ATCAGATAAAAATATATAGAAATTAGAG
Found at i:304422 original size:3 final size:3
Alignment explanation
Indices: 304414--304445 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
304404 TCAAAATCCC
304414 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
304446 CCCCTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:305109 original size:14 final size:14
Alignment explanation
Indices: 305102--305128 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
305092 CGACTGACCC
305102 GACCCGACCCGACT
1 GACCCGACCCGACT
305116 GACCCGACCCGAC
1 GACCCGACCCGAC
305129 CCGACTGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.52, G:0.22, T:0.04
Consensus pattern (14 bp):
GACCCGACCCGACT
Found at i:305114 original size:19 final size:19
Alignment explanation
Indices: 305090--305168 Score: 99
Period size: 19 Copynumber: 4.1 Consensus size: 19
305080 ACCTGGTTCG
305090 CCCGACTGACCCGACCCGA
1 CCCGACTGACCCGACCCGA
305109 CCCGACTGACCCGACCCGA
1 CCCGACTGACCCGACCCGA
305128 CCCGACTGTTGACCCGACCCGA
1 CCCGAC---TGACCCGACCCGA
* *
305150 -CTG-TTGACCCGACCCGA
1 CCCGACTGACCCGACCCGA
305167 CC
1 CC
305169 GTTGACCGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
17 13 0.24
18 1 0.02
19 25 0.46
21 2 0.04
22 13 0.24
ACGTcount: A:0.19, C:0.49, G:0.22, T:0.10
Consensus pattern (19 bp):
CCCGACTGACCCGACCCGA
Found at i:305143 original size:17 final size:17
Alignment explanation
Indices: 305102--305175 Score: 103
Period size: 17 Copynumber: 4.2 Consensus size: 17
305092 CGACTGACCC
**
305102 GACCCGACCCGACTGACCC
1 GACCCGACCCGACTG--TT
305121 GACCCGACCCGACTGTT
1 GACCCGACCCGACTGTT
305138 GACCCGACCCGACTGTT
1 GACCCGACCCGACTGTT
*
305155 GACCCGACCCGACCGTT
1 GACCCGACCCGACTGTT
305172 GACC
1 GACC
305176 GTTGACCGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
17 37 0.71
19 15 0.29
ACGTcount: A:0.19, C:0.46, G:0.23, T:0.12
Consensus pattern (17 bp):
GACCCGACCCGACTGTT
Found at i:305150 original size:5 final size:5
Alignment explanation
Indices: 305097--305133 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
305087 TCGCCCGACT
*
305097 GACCC GACCC GACCC GA-CT GACCC GACCC GACCC GAC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GAC
305134 TGTTGACCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 26 0.90
ACGTcount: A:0.22, C:0.54, G:0.22, T:0.03
Consensus pattern (5 bp):
GACCC
Found at i:306125 original size:63 final size:63
Alignment explanation
Indices: 306057--306180 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
306047 CTAATGTGAC
* * *
306057 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
306119 T
63 T
* *
306120 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
306181 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:306140 original size:32 final size:32
Alignment explanation
Indices: 306057--306180 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
306047 CTAATGTGAC
* * *
306057 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
306087 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
306120 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
306151 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
306181 TCCCTTAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.58
32 20 0.28
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:312389 original size:17 final size:17
Alignment explanation
Indices: 312367--312421 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
312357 CGACTGACCC
312367 GACCCGACCCGACTGTT
1 GACCCGACCCGACTGTT
312384 GACCCGACCCGACTGTT
1 GACCCGACCCGACTGTT
*
312401 GACCCGACCCGACCGTT
1 GACCCGACCCGACTGTT
312418 GACC
1 GACC
312422 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.18, C:0.44, G:0.24, T:0.15
Consensus pattern (17 bp):
GACCCGACCCGACTGTT
Found at i:312389 original size:22 final size:22
Alignment explanation
Indices: 312361--312414 Score: 73
Period size: 17 Copynumber: 2.7 Consensus size: 22
312351 TCGACCCGAC
312361 TGACCCGACCCGACCCGACTGT
1 TGACCCGACCCGACCCGACTGT
312383 T-----GACCCGACCCGACTGT
1 TGACCCGACCCGACCCGACTGT
312400 TGACCCGACCCGACC
1 TGACCCGACCCGACC
312415 GTTGACCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
17 17 0.63
22 10 0.37
ACGTcount: A:0.19, C:0.46, G:0.22, T:0.13
Consensus pattern (22 bp):
TGACCCGACCCGACCCGACTGT
Found at i:313372 original size:63 final size:63
Alignment explanation
Indices: 313304--313427 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
313294 CTAATGTGAC
* * *
313304 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
313366 T
63 T
* *
313367 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
313428 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:313387 original size:32 final size:32
Alignment explanation
Indices: 313304--313427 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
313294 CTAATGTGAC
* * *
313304 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
313334 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
313367 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
313398 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
313428 TCCCTTAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.58
32 20 0.28
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:315916 original size:10 final size:10
Alignment explanation
Indices: 315903--315952 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
315893 AACACAAACG
315903 AACGAACATA
1 AACGAACATA
*
315913 AACGAACGTA
1 AACGAACATA
* *
315923 AAGGAATATA
1 AACGAACATA
*
315933 AACGAAC--G
1 AACGAACATA
315941 AACGAACATA
1 AACGAACATA
315951 AA
1 AA
315953 ATTAATTGGG
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
8 7 0.23
10 23 0.77
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.10
Consensus pattern (10 bp):
AACGAACATA
Found at i:326309 original size:23 final size:23
Alignment explanation
Indices: 326283--326334 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
326273 ACCAAAAGAT
*
326283 AGAGAAAAATGTG-CAACAAAGGC
1 AGAGAAAAACGTGTC-ACAAAGGC
* *
326306 AGAGATAAACGTGTCATAAAGGC
1 AGAGAAAAACGTGTCACAAAGGC
326329 AGAGAA
1 AGAGAA
326335 CATGTTCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.50, C:0.12, G:0.27, T:0.12
Consensus pattern (23 bp):
AGAGAAAAACGTGTCACAAAGGC
Found at i:329112 original size:182 final size:182
Alignment explanation
Indices: 328781--329228 Score: 722
Period size: 182 Copynumber: 2.5 Consensus size: 182
328771 TCGGTTTGTT
328781 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAA-ATGACAAAACCGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
** * * *
328845 CTATAAATGACAAACAT--GTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATTATAA
66 CTCGAAATGACAAA-ATCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTATTATAA
* * *
328908 GTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATATCGCTAATAAAATG
130 GTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAATG
328961 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
*
329026 CTCGAAATGACAAAATCGGTAAAGAGCTACCGGATATATTGAAAGTGTTGATACTTTATTATAAG
66 CTCGAAATGACAAAATCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTATTATAAG
*
329091 TATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAGTG
131 TATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAATG
* ** *
329143 TCGATACTTTATAAAAATGTATCGATGCATAACAATATAACAGGTAAAAATATGACAAAATAGCT
1 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
* *
329208 CTCGAAATGATAAAACCGGTA
66 CTCGAAATGACAAAATCGGTA
329229 GTAAAAAAGT
Statistics
Matches: 249, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
180 52 0.21
181 26 0.10
182 171 0.69
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
CTCGAAATGACAAAATCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTATTATAAG
TATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAAAATG
Found at i:329369 original size:11 final size:11
Alignment explanation
Indices: 329353--329377 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
329343 CAAAAGAATA
329353 ATTAGTCGTAT
1 ATTAGTCGTAT
329364 ATTAGTCGTAT
1 ATTAGTCGTAT
329375 ATT
1 ATT
329378 CTTATTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (11 bp):
ATTAGTCGTAT
Found at i:329812 original size:23 final size:23
Alignment explanation
Indices: 329786--329833 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
329776 AAATATGTCA
* *
329786 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGATACCTAATATATT
329809 ATATAAGCGATACCTAATATATT
1 ATATAAGCGATACCTAATATATT
329832 AT
1 AT
329834 TGTACTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGATACCTAATATATT
Found at i:330243 original size:5 final size:5
Alignment explanation
Indices: 330235--330700 Score: 541
Period size: 5 Copynumber: 91.6 Consensus size: 5
330225 TGTAGACACA
* * *
330235 TATAT TATAT TATA- TAGTAG TAT-T ATATAT TA-AA TATAT TACA- TAT-T
1 TATAT TATAT TATAT TA-TAT TATAT -TATAT TATAT TATAT TATAT TATAT
*
330282 ATATAT TATAG TAGTA- T-TAT TATAT GTAT-T ATATAT TATATGT TATAT
1 -TATAT TATAT TA-TAT TATAT TATAT -TATAT -TATAT TATA--T TATAT
* * *
330330 TGCATAT ATATAA TATAGT ATATAT TATA- CATATT TATAG TATA- TAGTA-
1 T--ATAT -TATAT TATA-T -TATAT TATAT TATA-T TATAT TATAT TA-TAT
330379 TATAT TAAAGTAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT T--A-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
330427 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
330477 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA- T-TAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
330525 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
330575 TATAT TATA- TATAT TATAT TATAT TATAT TATAT TATA- TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
330623 TATATT ATATAT TATAT TATAT TATAT TATATT ATATAT TATAT TATAT
1 TATA-T -TATAT TATAT TATAT TATAT TATA-T -TATAT TATAT TATAT
330672 T-TAT TATAT TATAT ATATAT ATATAT TAT
1 TATAT TATAT TATAT -TATAT -TATAT TAT
330701 TATCGGTTTT
Statistics
Matches: 412, Mismatches: 12, Indels: 74
0.83 0.02 0.15
Matches are distributed among these distances:
3 4 0.01
4 29 0.07
5 319 0.77
6 33 0.08
7 22 0.05
8 5 0.01
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:330697 original size:10 final size:10
Alignment explanation
Indices: 330234--330697 Score: 262
Period size: 8 Copynumber: 52.8 Consensus size: 10
330224 TTGTAGACAC
330234 ATATAT-TAT
1 ATATATATAT
330243 AT-TATATAGT
1 ATATATATA-T
330253 AGTAT-TATAT
1 A-TATATATAT
*
330263 AT-TAAATAT
1 ATATATATAT
*
330272 AT-TACATAT
1 ATATATATAT
330281 -TATATAT-T
1 ATATATATAT
330289 ATAGTAGTAT-T
1 ATA-TA-TATAT
*
330300 AT-TATATGT
1 ATATATATAT
330309 AT-TATATAT
1 ATATATATAT
*
330318 -TATATGT-T
1 ATATATATAT
**
330326 ATAT-TGCAT
1 ATATATATAT
330335 ATATATA-AT
1 ATATATATAT
330344 ATAGTATATAT
1 ATA-TATATAT
*
330355 -TATACATAT
1 ATATATATAT
*
330364 TTATAGTATAT
1 ATATA-TATAT
330375 AGTATATAT-T
1 A-TATATATAT
*
330385 AAAGTAT-TAT
1 ATA-TATATAT
330395 AT-TATAT-T
1 ATATATATAT
330403 ATAT-TATAT
1 ATATATATAT
330412 -TATAT-TAT
1 ATATATATAT
330420 AT-TATAT-T
1 ATATATATAT
330428 ATAT-TATAT
1 ATATATATAT
330437 -TATAT-TAT
1 ATATATATAT
330445 AT-TATAT-T
1 ATATATATAT
330453 ATAT-TATAT
1 ATATATATAT
330462 -TATAT-TAT
1 ATATATATAT
330470 AT-TATAT-T
1 ATATATATAT
330478 ATAT-TATAT
1 ATATATATAT
330487 -TATAT-TAT
1 ATATATATAT
330495 AT-TATAT-T
1 ATATATATAT
330503 ATAT-TATAT
1 ATATATATAT
330512 -TATAT-TAT
1 ATATATATAT
330520 -TATAT-TAT
1 ATATATATAT
330528 AT-TATAT-T
1 ATATATATAT
330536 ATAT-TATAT
1 ATATATATAT
330545 -TATAT-TAT
1 ATATATATAT
330553 AT-TATAT-T
1 ATATATATAT
330561 ATAT-TATAT
1 ATATATATAT
330570 -TATAT-TAT
1 ATATATATAT
330578 AT-TATATAT
1 ATATATATAT
330587 AT-TATAT-T
1 ATATATATAT
330595 ATAT-TATAT
1 ATATATATAT
330604 -TATAT-TAT
1 ATATATATAT
330612 ATATAT-TAT
1 ATATATATAT
330621 AT-TATAT-T
1 ATATATATAT
330629 ATATAT-TAT
1 ATATATATAT
330638 AT-TATAT-T
1 ATATATATAT
330646 ATAT-TATAT
1 ATATATATAT
330655 -TATATAT-T
1 ATATATATAT
330663 ATAT-TATAT
1 ATATATATAT
*
330672 TTAT-TATAT
1 ATATATATAT
330681 -TATATATAT
1 ATATATATAT
330690 ATATATAT
1 ATATATAT
330698 TATTATCGGT
Statistics
Matches: 370, Mismatches: 13, Indels: 143
0.70 0.02 0.27
Matches are distributed among these distances:
8 167 0.45
9 147 0.40
10 31 0.08
11 20 0.05
12 5 0.01
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (10 bp):
ATATATATAT
Found at i:333091 original size:103 final size:103
Alignment explanation
Indices: 332907--333111 Score: 340
Period size: 103 Copynumber: 2.0 Consensus size: 103
332897 TACGCGATCC
* * * * *
332907 TTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTG
1 TTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATACTTGATCCCTA
332972 GCATATGTATATGATTCTTAAGGAA-TGATATGTGGTCA
66 GCATATGTATATGATTCTTAAGGAAGT-ATATGTGGTCA
333010 TTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATACTTGATCCCTA
1 TTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATACTTGATCCCTA
*
333075 GTATATGTATATGATTCTTAAGGAAGTATATGTGGTC
66 GCATATGTATATGATTCTTAAGGAAGTATATGTGGTC
333112 CTTATGGACA
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 94 0.99
104 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (103 bp):
TTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATACTTGATCCCTA
GCATATGTATATGATTCTTAAGGAAGTATATGTGGTCA
Found at i:333164 original size:23 final size:23
Alignment explanation
Indices: 333131--333198 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
333121 ATTATTATAT
333131 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
333154 GGCACTCCGGTGCAATTCTAGGT
1 GGCACTACGGTGCAATTCTACGC
* * *
333177 GGCACTTCGGTGTAATTATACG
1 GGCACTACGGTGCAATTCTACG
333199 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:333579 original size:16 final size:16
Alignment explanation
Indices: 333528--333580 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
333518 TGTATGTGAT
333528 ATATGTATATGATGTGTG
1 ATATG-ATAT-ATGTGTG
* * **
333546 ATATGATGTGTGCATG
1 ATATGATATATGTGTG
333562 ATATGATATATGTGTG
1 ATATGATATATGTGTG
333578 ATA
1 ATA
333581 GGGGTTATGG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (16 bp):
ATATGATATATGTGTG
Found at i:335571 original size:2 final size:2
Alignment explanation
Indices: 335564--335591 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
335554 CGGTTACGAC
335564 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
335592 TAAAATATCT
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:336544 original size:21 final size:21
Alignment explanation
Indices: 336511--336556 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
336501 TTGATGATTA
*
336511 TTTATTCTCTTAT-TTTTTAT
1 TTTATTCTCTTATCTTTTTAC
*
336531 TTTATTTCTTTTATCTTTTTAC
1 TTTA-TTCTCTTATCTTTTTAC
336553 TTTA
1 TTTA
336557 ATCTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 8 0.36
22 10 0.45
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTATTCTCTTATCTTTTTAC
Found at i:336561 original size:21 final size:20
Alignment explanation
Indices: 336511--336563 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
336501 TTGATGATTA
* *
336511 TTTATTCTCTTATTTTTTAT
1 TTTATTCTTTTATTTTTTAC
336531 TTTATTTCTTTTATCTTTTTAC
1 TTTA-TTCTTTTAT-TTTTTAC
*
336553 TTTAATCTTTT
1 TTTATTCTTTT
336564 TAATTTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 14 0.50
22 10 0.36
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTCTTTTATTTTTTAC
Found at i:339614 original size:99 final size:99
Alignment explanation
Indices: 339502--339799 Score: 564
Period size: 99 Copynumber: 3.0 Consensus size: 99
339492 AATAATATAT
339502 TAAATAATATATATTAATATTAGTGAGTCCACGTTATCTCTACTTTGATTTTTTACTTTTTTTTT
1 TAAATAATATATATTAATATTAGTGAGTCCACGTTATCTCTACTTTGATTTTTTACTTTTTTTTT
339567 TACATTTTATGAATATTTTTAGCAATTGAAAATA
66 TACATTTTATGAATATTTTTAGCAATTGAAAATA
339601 TAAATAATATATATTAATATTAGTGAGTCCACGTTATCTCTACTTTGATTTTTTAC--TTTTTTT
1 TAAATAATATATATTAATATTAGTGAGTCCACGTTATCTCTACTTTGATTTTTTACTTTTTTTTT
339664 TACATTTTATGAATATTTTTAGCAATTGAAAATA
66 TACATTTTATGAATATTTTTAGCAATTGAAAATA
*
339698 TAAATAATATATATTAATATTAGTGAGTCCACGTTATCTCTACTTTGATTTTTTTCTTTTTTTTT
1 TAAATAATATATATTAATATTAGTGAGTCCACGTTATCTCTACTTTGATTTTTTACTTTTTTTTT
*
339763 TACATTTTATGAATATTTTTAGAAATTGAAAATA
66 TACATTTTATGAATATTTTTAGCAATTGAAAATA
339797 TAA
1 TAA
339800 TAAAAAAGTA
Statistics
Matches: 195, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
97 96 0.49
99 99 0.51
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.50
Consensus pattern (99 bp):
TAAATAATATATATTAATATTAGTGAGTCCACGTTATCTCTACTTTGATTTTTTACTTTTTTTTT
TACATTTTATGAATATTTTTAGCAATTGAAAATA
Found at i:341995 original size:82 final size:81
Alignment explanation
Indices: 341858--342007 Score: 246
Period size: 82 Copynumber: 1.8 Consensus size: 81
341848 GAAAAAAAAC
* * * * *
341858 TACATTAAAAGTAAAAGATAATTTCACAAATAATATTTAGATGATGTCAAATACTTTATTATTTA
1 TACATTAAAAGTAAAAGACAATTTCACAAATAACAATTAAATGATGTCAAATACTTTAGTA-TTA
341923 TTTAGATTCGTATCTAA
65 TTTAGATTCGTATCTAA
341940 TACATTAAAAGTAAAAGACAATTTCACAAATAACAATTAAATGATGTCAAATACTTTAGTATTAT
1 TACATTAAAAGTAAAAGACAATTTCACAAATAACAATTAAATGATGTCAAATACTTTAGTATTAT
342005 TTA
66 TTA
342008 TTTTATTTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
81 7 0.11
82 56 0.89
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.37
Consensus pattern (81 bp):
TACATTAAAAGTAAAAGACAATTTCACAAATAACAATTAAATGATGTCAAATACTTTAGTATTAT
TTAGATTCGTATCTAA
Found at i:344227 original size:59 final size:59
Alignment explanation
Indices: 344114--344250 Score: 161
Period size: 59 Copynumber: 2.3 Consensus size: 59
344104 CAACAGACTG
* * * * *
344114 CATATTCGGGATTGCATTAAAGTATAACTAGTGCATATGATGGGTACGATCTTATGTAT
1 CATATTCGGGATTGCACTAAAGTATAACTAGTGCAGATGATAGGCACGACCTTATGTAT
* * *
344173 CATATTCTGGATTGCACTAAAGTATAACTAGTGTAGAT-AGTAGGCACGACCTTATGTGT
1 CATATTCGGGATTGCACTAAAGTATAACTAGTGCAGATGA-TAGGCACGACCTTATGTAT
*
344232 CATACTCGGG-TTAGCACTA
1 CATATTCGGGATT-GCACTA
344251 CGGTACACAT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
58 3 0.05
59 63 0.95
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (59 bp):
CATATTCGGGATTGCACTAAAGTATAACTAGTGCAGATGATAGGCACGACCTTATGTAT
Found at i:347031 original size:13 final size:13
Alignment explanation
Indices: 347013--347037 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
347003 CATGATAGAG
347013 ATCATGCTTGGCT
1 ATCATGCTTGGCT
347026 ATCATGCTTGGC
1 ATCATGCTTGGC
347038 GTGTAGAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (13 bp):
ATCATGCTTGGCT
Found at i:347223 original size:15 final size:17
Alignment explanation
Indices: 347203--347237 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
347193 CTAATGAAAA
347203 TAAAATA-T-TAACTCT
1 TAAAATATTCTAACTCT
347218 TAAAATATTCTAACTCT
1 TAAAATATTCTAACTCT
347235 TAA
1 TAA
347238 TTCTAACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 1 0.06
17 10 0.56
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAATATTCTAACTCT
Found at i:347288 original size:20 final size:22
Alignment explanation
Indices: 347249--347293 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
347239 TCTAACGAAC
*
347249 TAAAAATCCTAATCAATAAATAT
1 TAAAAATCCTAA-CAATAAAAAT
347272 TAAAAATCCT-A-AATAAAAAT
1 TAAAAATCCTAACAATAAAAAT
347292 TA
1 TA
347294 TATGCAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
22 1 0.05
23 10 0.48
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAATCCTAACAATAAAAAT
Found at i:348915 original size:18 final size:21
Alignment explanation
Indices: 348894--348947 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
348884 AAATGCTAAT
348894 AAATAA-AAAAAATAT-AAA-
1 AAATAATAAAAAATATGAAAG
*
348912 AAATAATAATAAATATGAAAG
1 AAATAATAAAAAATATGAAAG
*
348933 AAATAATAAATAATA
1 AAATAATAAAAAATA
348948 AAAGGTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.20
19 8 0.27
20 3 0.10
21 13 0.43
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (21 bp):
AAATAATAAAAAATATGAAAG
Found at i:348938 original size:28 final size:28
Alignment explanation
Indices: 348890--348948 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
348880 AACAAAATGC
348890 TAATAAATAAAAAAAATATAAAAAATAA
1 TAATAAATAAAAAAAATATAAAAAATAA
* * *
348918 TAATAAATATGAAAGAA-ATAATAAATAA
1 TAATAAATA-AAAAAAATATAAAAAATAA
348946 TAA
1 TAA
348949 AAGGTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (28 bp):
TAATAAATAAAAAAAATATAAAAAATAA
Found at i:350134 original size:15 final size:14
Alignment explanation
Indices: 350102--350130 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
350092 CTCAAAAAAC
350102 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
350116 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
350130 A
1 A
350131 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:350213 original size:31 final size:32
Alignment explanation
Indices: 350170--350340 Score: 104
Period size: 31 Copynumber: 5.2 Consensus size: 32
350160 ATATAATACA
**
350170 TATATTTCAAAAATA-TTTTTTAAACTATATAT
1 TATATTTCAAAAA-AGTTTTCAAAACTATATAT
350202 TATATTT-AAAAAAGTTTTCAAAACTATAT-T
1 TATATTTCAAAAAAGTTTTCAAAACTATATAT
* *
350232 ATATAGTTTTC-AAAATGTTTT-AAAAATAT-TA-
1 -TATA--TTTCAAAAAAGTTTTCAAAACTATATAT
* *
350263 TATAAGTTTTAAAAAACGTTTTTAAAACTATATATT
1 TAT-A-TTTCAAAAAA-GTTTTCAAAACTATATA-T
* *
350299 ATATAATTTATTCAAAAATGTTTTTAAAACTATATAT
1 -TAT-A--T-TTCAAAAAAGTTTTCAAAACTATATAT
350336 TATAT
1 TATAT
350341 AAGTTTTTAA
Statistics
Matches: 112, Mismatches: 11, Indels: 31
0.73 0.07 0.20
Matches are distributed among these distances:
30 8 0.07
31 28 0.25
32 19 0.17
33 20 0.18
34 2 0.02
35 1 0.01
36 3 0.03
37 6 0.05
38 18 0.16
39 7 0.06
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (32 bp):
TATATTTCAAAAAAGTTTTCAAAACTATATAT
Found at i:350387 original size:35 final size:35
Alignment explanation
Indices: 350174--350467 Score: 249
Period size: 38 Copynumber: 8.4 Consensus size: 35
350164 AATACATATA
* *
350174 TTTCAAAAATATTTTTTAAACTATATA-T-TATA--
1 TTTCAAAAAT-GTTTTAAAACTATATATTATATAGT
*
350206 TTT-AAAAAAGTTTTCAAAAC--TATATTATATAGT
1 TTTCAAAAATGTTTT-AAAACTATATATTATATAGT
*
350239 TTTC-AAAATGTTTTAAAAATAT-TA-TATA-AGT
1 TTTCAAAAATGTTTTAAAACTATATATTATATAGT
* * *
350270 TTTAAAAAACGTTTTTAAAACTATATATTATATAATT
1 TTTCAAAAATG-TTTTAAAACTATATATTATAT-AGT
350307 TATTCAAAAATGTTTTTAAAACTATATATTATATAAGT
1 T-TTCAAAAATG-TTTTAAAACTATATATTATAT-AGT
* *
350345 TTT-TAAAATGATTTTAAAACTATATGTTATATA-T
1 TTTCAAAAATG-TTTTAAAACTATATATTATATAGT
* *
350379 TTTCTAAAATGTTTTAAAAACTATATGTTATATAGT
1 TTTCAAAAATGTTTT-AAAACTATATATTATATAGT
*
350415 TTTCAAAAAATATTTTAAAAAACTATATATTACCTATA-T
1 TTTC-AAAAATGTTTT--AAAACTATATATTA--TATAGT
350454 TTTC-AAAATGTTTT
1 TTTCAAAAATGTTTT
350468 CTTTTTAAAA
Statistics
Matches: 221, Mismatches: 19, Indels: 39
0.79 0.07 0.14
Matches are distributed among these distances:
29 4 0.02
30 5 0.02
31 19 0.09
32 16 0.07
33 25 0.11
34 11 0.05
35 30 0.14
36 31 0.14
37 23 0.10
38 48 0.22
39 5 0.02
40 4 0.02
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (35 bp):
TTTCAAAAATGTTTTAAAACTATATATTATATAGT
Found at i:350410 original size:109 final size:104
Alignment explanation
Indices: 350195--350467 Score: 288
Period size: 109 Copynumber: 2.6 Consensus size: 104
350185 TTTTTTAAAC
* * *
350195 TATATATTATATTTAAAAAAGTTTTCAAAAC--TATATTATATAGTTTTCAAAATGTTTTAAAAA
1 TATATATT-TATTCAAAAATGTTTTAAAAACTATATATTATATAGTTTTCAAAATGTTTTAAAAA
*
350258 TATTATATAAGTTTTAAAAAACGTTTTTAAAACTATATAT
65 TATTATATAAGTTTTAAAAAACGTTTTAAAAACTATATAT
* *
350298 TATATAATTTATTCAAAAATGTTTTTAAAACTATATATTATATAAGTTTTTAAAATGATTTTAAA
1 TATAT-ATTTATTCAAAAATGTTTTAAAAACTATATATTATAT-AGTTTTCAAAATG-TTTTAAA
** * *
350363 ACTATATGT-TATATA-TTTTCTAAAATGTTTTAAAAACTATATGT
63 A--ATAT-TATATA-AGTTTTAAAAAACGTTTTAAAAACTATATAT
* *
350407 TATATAGTT-TTCAAAAAATATTTTAAAAAACTATATATTACCTATA-TTTTCAAAATGTTTT
1 TATATATTTATTC-AAAAATGTTTT-AAAAACTATATATTA--TATAGTTTTCAAAATGTTTT
350468 CTTTTTAAAA
Statistics
Matches: 144, Mismatches: 13, Indels: 21
0.81 0.07 0.12
Matches are distributed among these distances:
103 24 0.17
104 3 0.02
105 10 0.07
106 12 0.08
107 11 0.08
108 17 0.12
109 61 0.42
110 3 0.02
111 3 0.02
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (104 bp):
TATATATTTATTCAAAAATGTTTTAAAAACTATATATTATATAGTTTTCAAAATGTTTTAAAAAT
ATTATATAAGTTTTAAAAAACGTTTTAAAAACTATATAT
Found at i:351354 original size:165 final size:165
Alignment explanation
Indices: 351155--351900 Score: 1375
Period size: 165 Copynumber: 4.5 Consensus size: 165
351145 TGATCCCGGA
* *
351155 GGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGC
1 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
351220 GGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
66 GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
351285 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
131 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
351320 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
351385 GTAGTCGAACTCGAAGGTTTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
66 GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
351450 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
131 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
351485 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
351550 GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
66 GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
351615 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
131 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
*
351650 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTAGGAGCTGAGC
1 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
351715 GTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
66 GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
* * * ***
351780 TTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
131 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
*
351815 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
1 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
351880 GTAGTCGAACTCGAAGGTCTT
66 GTAGTCGAACTCGAAGGTCTT
351901 GGTGGCAGGA
Statistics
Matches: 565, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
165 565 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (165 bp):
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
Found at i:355235 original size:19 final size:20
Alignment explanation
Indices: 355211--355253 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
355201 AGTTAATGTG
355211 AATGCAAAGAAAATAA-CAA
1 AATGCAAAGAAAATAAGCAA
355230 AATGCAAAGAAAATAAGCAA
1 AATGCAAAGAAAATAAGCAA
355250 AATG
1 AATG
355254 TATAAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.65, C:0.09, G:0.14, T:0.12
Consensus pattern (20 bp):
AATGCAAAGAAAATAAGCAA
Found at i:358186 original size:15 final size:14
Alignment explanation
Indices: 358154--358182 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
358144 CTCAAAAAAC
358154 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
358168 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
358182 A
1 A
358183 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:358259 original size:32 final size:33
Alignment explanation
Indices: 358221--358492 Score: 163
Period size: 33 Copynumber: 8.0 Consensus size: 33
358211 TATATAATAC
*
358221 ATATATTTCAAAAATATTTTTTAAACTATATAT
1 ATATATTTCAAAAATATTTTTAAAACTATATAT
*
358254 -TATATTT-AAAAA-AGTTTTCAAAACTATAT-T
1 ATATATTTCAAAAATA-TTTTTAAAACTATATAT
* *
358284 ATATAGTTTTC-AAAAT-GTTTTAAAAATAT-TAT
1 ATATA--TTTCAAAAATATTTTTAAAACTATATAT
*
358316 ATA-AGTTTTAAAAA-ACGTTTTTAAAACTATATAT
1 ATATA-TTTCAAAAATA--TTTTTAAAACTATATAT
*
358350 ATATAATTTATTCAAAAATGTTTTTAAAACTATATAT
1 ATAT-A--T-TTCAAAAATATTTTTAAAACTATATAT
**
358387 A-ATAAGTTTTTAAAATGA--TTTAAAACTATATGTTAT
1 ATAT-A-TTTCAAAAAT-ATTTTTAAAACTATA---TAT
* * * *
358423 ATATATTTCTAAAATGTTTTAAAAACTATATGT
1 ATATATTTCAAAAATATTTTTAAAACTATATAT
*
358456 ATATAGTTTTCAAAAAATATTTTAAAAAACTATATAT
1 ATATA--TTTC-AAAAATATTTT-TAAAACTATATAT
358493 TACCCATATT
Statistics
Matches: 188, Mismatches: 23, Indels: 52
0.71 0.09 0.20
Matches are distributed among these distances:
30 5 0.03
31 28 0.15
32 21 0.11
33 37 0.20
34 13 0.07
35 14 0.07
36 30 0.16
37 33 0.18
38 7 0.04
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (33 bp):
ATATATTTCAAAAATATTTTTAAAACTATATAT
Found at i:368601 original size:391 final size:391
Alignment explanation
Indices: 367879--368637 Score: 1175
Period size: 391 Copynumber: 1.9 Consensus size: 391
367869 TCTGATAATG
*
367879 TTTTTTCACACTTCATTATGTGGCAAGCAATCAAGATTCAAGAGCCCAAGAAATTACTATCTTGA
1 TTTTTTCACACATCATTATGTGGCAAGCAATCAAGATTCAAGAGCCCAAGAAATTACTATCTTGA
* * *
367944 TAACATATTGAAAACTAGGGTAAAGTACACGGATGATCTCCCAACAATAAGATATTGCTTTGTTG
66 TAACATATTGAAAACTAGGGTAAAATACACAGATGATCTCCCAACAATAAGATATTGCTTTATTG
* *
368009 AGTCTCTCGACTATTAAAATTTACAAAATAATTTCTTGATTGTAGAACATTTTTTTTTGAGTCCC
131 AGTCTCTCAACTATTAAAAATTACAAAATAATTTCTTGATTGTAGAACA-TTTTTTTTGAGTCCC
* * * * *
368074 TGAACTATTAAAAGTTATAAAATGGTCACTCAACTATTCATATGCTCCAAACACGTCCTTTTCTG
195 AGAACTATTAAAAGTTATAAAATGGTCACTCAACTATTCATATACTCCAAACACATCATTTTATG
* *
368139 TTAAAAATTTAATGACAGTTTGAGCTAGACGTTAATTGCCGACTGTAATAAGATAAAATTTGATC
260 TTAAAAAGTTAAAGACAGTTTGAGCTAGACGTTAATTGCCGACTGTAATAAGATAAAATTTGATC
* * * * *
368204 TCAAAATCTCAAATGATTATCATATCTCATTCAACGGGTTAATGTCCAATTCAAGTTGACATCAT
325 TCAAAATCTCAAACGATAATCATACCTCAGTCAACAGGTTAATGTCCAATTCAAGTTGACATCAT
368269 TT
390 TT
* *
368271 TTTTTTCACACATCATTATGTGGCAAGCAATCAAGATTCAAGAGCCCAAGAAAATTACTCTCTTT
1 TTTTTTCACACATCATTATGTGGCAAGCAATCAAGATTCAAGAGCCCAAG-AAATTACTATCTTG
*
368336 ATAACATATTGAAAACTAGGGTAAAATACACAGATGATC-CCCAAACAATAGGATATTGCTTTAT
65 ATAACATATTGAAAACTAGGGTAAAATACACAGATGATCTCCC-AACAATAAGATATTGCTTTAT
** *
368400 TGAGTCTCTCAACTATTAAAAATTACAAAATGGTTTCTTGATTGTAGGACA-TTTTTTTGAGTCC
129 TGAGTCTCTCAACTATTAAAAATTACAAAATAATTTCTTGATTGTAGAACATTTTTTTTGAGT-C
* * *
368464 CCAG-ACTATTAAAAGTTATAAAATGGTCATTCGATTATTCATATACTCCAAACACATCATTTTA
193 CCAGAACTATTAAAAGTTATAAAATGGTCACTCAACTATTCATATACTCCAAACACATCATTTTA
* *
368528 TGTTAAAAAGTTAACAG-TAGTTTGAGCTAGACGTTAATTGCCGACTGTAATATGATAAAATTTG
258 TGTTAAAAAGTTAA-AGACAGTTTGAGCTAGACGTTAATTGCCGACTGTAATAAGATAAAATTTG
*
368592 ATCTCAAAATCTCAAACGATAATTATACCTCAGTCAACAGGTTAAT
322 ATCTCAAAATCTCAAACGATAATCATACCTCAGTCAACAGGTTAAT
368638 ATGAAGCTCA
Statistics
Matches: 333, Mismatches: 30, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
391 162 0.49
392 57 0.17
393 114 0.34
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (391 bp):
TTTTTTCACACATCATTATGTGGCAAGCAATCAAGATTCAAGAGCCCAAGAAATTACTATCTTGA
TAACATATTGAAAACTAGGGTAAAATACACAGATGATCTCCCAACAATAAGATATTGCTTTATTG
AGTCTCTCAACTATTAAAAATTACAAAATAATTTCTTGATTGTAGAACATTTTTTTTGAGTCCCA
GAACTATTAAAAGTTATAAAATGGTCACTCAACTATTCATATACTCCAAACACATCATTTTATGT
TAAAAAGTTAAAGACAGTTTGAGCTAGACGTTAATTGCCGACTGTAATAAGATAAAATTTGATCT
CAAAATCTCAAACGATAATCATACCTCAGTCAACAGGTTAATGTCCAATTCAAGTTGACATCATT
T
Found at i:370933 original size:11 final size:10
Alignment explanation
Indices: 370907--370932 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
370897 TATTATTTTT
370907 AAAAAATGTA
1 AAAAAATGTA
370917 AAAAAATGTA
1 AAAAAATGTA
370927 AAAAAA
1 AAAAAA
370933 AAATTATATT
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (10 bp):
AAAAAATGTA
Found at i:372754 original size:19 final size:20
Alignment explanation
Indices: 372726--372764 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
372716 GTTTTCAAAG
372726 TTTTGGG-TTTATTTTTAAA
1 TTTTGGGTTTTATTTTTAAA
* *
372745 TTTTGTGTTTTCTTTTTAAA
1 TTTTGGGTTTTATTTTTAAA
372765 AAAAATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.67
Consensus pattern (20 bp):
TTTTGGGTTTTATTTTTAAA
Found at i:372928 original size:29 final size:30
Alignment explanation
Indices: 372885--372941 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
372875 ATGATTAACG
372885 AAATGAAACGTTAGACACCAAACTGGAACA
1 AAATGAAACGTTAGACACCAAACTGGAACA
* * *
372915 AAAT-AAATGTTAGACACTAAAGTGGAA
1 AAATGAAACGTTAGACACCAAACTGGAA
372942 AAAGGGACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.51, C:0.14, G:0.18, T:0.18
Consensus pattern (30 bp):
AAATGAAACGTTAGACACCAAACTGGAACA
Found at i:373834 original size:15 final size:16
Alignment explanation
Indices: 373814--373845 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
373804 GTTATAGAGG
373814 TTTTCTTCTT-TTTCT
1 TTTTCTTCTTCTTTCT
373829 TTTTCTTCTTCTTTCT
1 TTTTCTTCTTCTTTCT
373845 T
1 T
373846 CTCCTTCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTCTTCTTCTTTCT
Found at i:374950 original size:10 final size:9
Alignment explanation
Indices: 374924--374948 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
374914 TTATTATTTT
374924 TAAAAAATG
1 TAAAAAATG
374933 TAAAAAATG
1 TAAAAAATG
374942 TAAAAAA
1 TAAAAAA
374949 ATTATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (9 bp):
TAAAAAATG
Found at i:376803 original size:20 final size:20
Alignment explanation
Indices: 376759--376796 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
376749 GAAATGAAGG
376759 TTTTTAAAGTTTTGGGTTTA
1 TTTTTAAAGTTTTGGGTTTA
*
376779 TTTTTAAA-TTTTGTGTTT
1 TTTTTAAAGTTTTGGGTTT
376797 TCTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.18, C:0.00, G:0.16, T:0.66
Consensus pattern (20 bp):
TTTTTAAAGTTTTGGGTTTA
Found at i:376947 original size:29 final size:30
Alignment explanation
Indices: 376892--376948 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
376882 ATGATTAACG
376892 AAATGAAACGTTAGACACCAAACTGGAACA
1 AAATGAAACGTTAGACACCAAACTGGAACA
* * *
376922 AAAT-AAATGTTAGACACTAAAGTGGAA
1 AAATGAAACGTTAGACACCAAACTGGAA
376949 AAAGGGTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.51, C:0.14, G:0.18, T:0.18
Consensus pattern (30 bp):
AAATGAAACGTTAGACACCAAACTGGAACA
Found at i:377838 original size:15 final size:16
Alignment explanation
Indices: 377818--377857 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
377808 GTTATAGAGG
377818 TTTTCTTCTTTTT-CT
1 TTTTCTTCTTTTTCCT
377833 TTTTCTT-TTTTTCCT
1 TTTTCTTCTTTTTCCT
377848 TCTTTCTTCT
1 T-TTTCTTCT
377858 CCTTCAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.23
15 10 0.45
16 6 0.27
17 1 0.05
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTCTTCTTTTTCCT
Found at i:378842 original size:61 final size:61
Alignment explanation
Indices: 378714--378842 Score: 145
Period size: 61 Copynumber: 2.1 Consensus size: 61
378704 ATAGTCGGGT
* * * * *
378714 GACCA-TTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAATAACATCCTATAGTTGGTG
1 GACCATTTTTATAACTTTTAATAGTCAAGAGACTCAACAAAATAACATCATATAATCGGTG
* * * * *
378774 GATCATTTTTATAACTTTTAATAGTCAAGGGACTCAATAAAGTAATATCATATAATCGAG-G
1 GACCATTTTTATAACTTTTAATAGTCAAGAGACTCAACAAAATAACATCATATAATCG-GTG
378835 GACCATTT
1 GACCATTT
378843 GTGTATTTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
60 4 0.07
61 51 0.91
62 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (61 bp):
GACCATTTTTATAACTTTTAATAGTCAAGAGACTCAACAAAATAACATCATATAATCGGTG
Found at i:388659 original size:10 final size:10
Alignment explanation
Indices: 388611--388660 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
388601 TATATTACTA
*
388611 ATTTAATTTA
1 ATTTAATTTT
388621 ATTTAATTTT
1 ATTTAATTTT
* *
388631 GTTTGATTTT
1 ATTTAATTTT
388641 ATTT-A-TTT
1 ATTTAATTTT
*
388649 ATTTTATTTT
1 ATTTAATTTT
388659 AT
1 AT
388661 AAAATGCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 7 0.21
9 2 0.06
10 25 0.74
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (10 bp):
ATTTAATTTT
Found at i:400486 original size:10 final size:10
Alignment explanation
Indices: 400473--400505 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
400463 AAAAAAACCC
400473 AAAATTTTCA
1 AAAATTTTCA
400483 AAAATTTTCA
1 AAAATTTTCA
400493 AAAATTTT-A
1 AAAATTTTCA
400502 AAAA
1 AAAA
400506 CCTCCCCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATTTTCA
Found at i:403932 original size:22 final size:21
Alignment explanation
Indices: 403897--403937 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
403887 GTTGTGGCCG
*
403897 TTTTTAGCCGTTGGTGATGTT
1 TTTTTAGCCGTTGGGGATGTT
*
403918 TTTTTAGCTGTTTGGGGATG
1 TTTTTAGCCG-TTGGGGATG
403938 AAAACTCTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.07, G:0.32, T:0.51
Consensus pattern (21 bp):
TTTTTAGCCGTTGGGGATGTT
Found at i:404125 original size:18 final size:18
Alignment explanation
Indices: 404102--404145 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
404092 ATACAAAGTA
*
404102 GTATCGGTACCCTTTTGG
1 GTATCGGTACCCCTTTGG
* *
404120 GTATCGATACCCCTTTGT
1 GTATCGGTACCCCTTTGG
404138 GTATCGGT
1 GTATCGGT
404146 GTAACACCCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.39
Consensus pattern (18 bp):
GTATCGGTACCCCTTTGG
Found at i:404963 original size:23 final size:23
Alignment explanation
Indices: 404929--404997 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
404919 CACCACAGCT
*
404929 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
404952 CGTAGAATTGCACC-ATAGTGCCG
1 CGTAGAAATGCACCGA-AGTGCCA
*
404975 CGTAGAAATGCATCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
404998 TATAAGGTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:405501 original size:2 final size:2
Alignment explanation
Indices: 405496--405547 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
405486 TATCTTATTC
405496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
405538 AT AT AT AT AT
1 AT AT AT AT AT
405548 CTGCAAATAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:407378 original size:31 final size:31
Alignment explanation
Indices: 407340--407404 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
407330 AGAGTCGAGG
*
407340 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
407371 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
407402 GTT
1 GTT
407405 ACCGAGGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:407485 original size:29 final size:30
Alignment explanation
Indices: 407390--407491 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
407380 GGTTCTTCGG
* *
407390 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
407420 GACCTCTTGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
407450 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
407479 GACCTCTGGATAG
1 GACCTCTGGATAG
407492 GTCCTTCGGG
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
29 21 0.32
30 45 0.68
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:410595 original size:21 final size:23
Alignment explanation
Indices: 410571--410618 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
410561 CTTGAGATAA
410571 TTTATTTGA-ACATTTT-AAGAT
1 TTTATTTGATACATTTTGAAGAT
**
410592 TTTATTTGATTTATTTTGAAGAT
1 TTTATTTGATACATTTTGAAGAT
410615 TTTA
1 TTTA
410619 ATGTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 5 0.22
23 9 0.39
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.58
Consensus pattern (23 bp):
TTTATTTGATACATTTTGAAGAT
Found at i:410626 original size:23 final size:22
Alignment explanation
Indices: 410582--410628 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
410572 TTATTTGAAC
*
410582 ATTTTAAGATTTTATTTGATTT
1 ATTTTAAGATTTTATGTGATTT
410604 ATTTTGAAGATTTTAATGT-ATTT
1 ATTTT-AAGATTTT-ATGTGATTT
410627 AT
1 AT
410629 GATATGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 14 0.64
24 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (22 bp):
ATTTTAAGATTTTATGTGATTT
Found at i:412618 original size:90 final size:90
Alignment explanation
Indices: 412460--412640 Score: 292
Period size: 90 Copynumber: 2.0 Consensus size: 90
412450 AATGGAGAGA
* **
412460 GGACGTCAAATCCAATCCTGAGAAAAGAGAATGAGTATTACAAAGGCAGATAAAACTAGTCTTGA
1 GGACATCAAATCCAATCCTGAGAAAAGAGAATGAGTATTACAAAGGCAGATAAAACTAGTCACGA
412525 TTTCATACGAATAGTAGAAGACTAT
66 TTTCATACGAATAGTAGAAGACTAT
* * *
412550 GGACATCAAATCCAA-CCTTGAGAAAATAGAATGAGTATTATAAAGGTAGATAAAACTAGTCACG
1 GGACATCAAATCCAATCC-TGAGAAAAGAGAATGAGTATTACAAAGGCAGATAAAACTAGTCACG
412614 ATTTCATACGAATAGTAGAAGACTAT
65 ATTTCATACGAATAGTAGAAGACTAT
412640 G
1 G
412641 TTAAAGTATA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 2 0.02
90 82 0.98
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (90 bp):
GGACATCAAATCCAATCCTGAGAAAAGAGAATGAGTATTACAAAGGCAGATAAAACTAGTCACGA
TTTCATACGAATAGTAGAAGACTAT
Found at i:418724 original size:21 final size:21
Alignment explanation
Indices: 418700--418757 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
418690 ATGTAATTAT
*
418700 TTGGAACATATATGTGGTTCA
1 TTGGAACATATATGTGGTCCA
* * *
418721 TTGGAACACATATTTGGTCCT
1 TTGGAACATATATGTGGTCCA
**
418742 TTGGAGTATATATGTG
1 TTGGAACATATATGTG
418758 ATCCTTAAGG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (21 bp):
TTGGAACATATATGTGGTCCA
Found at i:418762 original size:21 final size:22
Alignment explanation
Indices: 418744--418833 Score: 67
Period size: 21 Copynumber: 4.1 Consensus size: 22
418734 TTGGTCCTTT
418744 GGAGTATATATGTGATCCTTAA
1 GGAGTATATATGTGATCCTTAA
* * * *
418766 GGAGAATTATATGTGGTCATTTA
1 GGAGTA-TATATGTGATCCTTAA
** * *
418789 -GAACATATATATGATCCTTCA
1 GGAGTATATATGTGATCCTTAA
* *
418810 GGA-TATATATGTGGTCCTTCA
1 GGAGTATATATGTGATCCTTAA
418831 GGA
1 GGA
418834 AAAGTTCTAT
Statistics
Matches: 53, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
21 30 0.57
22 10 0.19
23 13 0.25
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (22 bp):
GGAGTATATATGTGATCCTTAA
Found at i:418807 original size:65 final size:65
Alignment explanation
Indices: 418708--418833 Score: 157
Period size: 65 Copynumber: 1.9 Consensus size: 65
418698 ATTTGGAACA
* * * *
418708 TATATGTGGTTCATTGGAACACATATTTGGTCCTT-TGGAGTATATATGTGATCCTTAAGGAGAA
1 TATATGTGGTTCATTAGAACACATATATGATCCTTCAGGA-TATATATGTGATCCTTAAGGAGAA
418772 T
65 T
* * *
418773 TATATGTGG-TCATTTAGAACATATATATGATCCTTCAGGATATATATGTGGTCCTTCAGGA
1 TATATGTGGTTCA-TTAGAACACATATATGATCCTTCAGGATATATATGTGATCCTTAAGGA
418834 AAAGTTCTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 3 0.06
65 46 0.88
66 3 0.06
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (65 bp):
TATATGTGGTTCATTAGAACACATATATGATCCTTCAGGATATATATGTGATCCTTAAGGAGAAT
Found at i:424068 original size:12 final size:13
Alignment explanation
Indices: 424043--424067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
424033 TTATACTCAT
424043 TTTATTCAAAAAA
1 TTTATTCAAAAAA
424056 TTTATTCAAAAA
1 TTTATTCAAAAA
424068 TGAATAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TTTATTCAAAAAA
Found at i:434441 original size:3 final size:3
Alignment explanation
Indices: 434433--434472 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
434423 TTAATCTGAG
434433 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
434473 CAAGAGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:456594 original size:51 final size:51
Alignment explanation
Indices: 456514--456615 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 51
456504 ATTAGATTTA
* * * *
456514 GTTGAATCTAGCGTCGTCTCCTTTCGATTTGTTGACGGGTTTGTAATTTCC
1 GTTGAATCTAGCGTCGTATCCTTTAGATTTGTTGACGGATTTGCAATTTCC
*
456565 GTTGAATCTAGCGTCGTATCCTTTAGATTTGTTGATGGATTTGCAATTTCC
1 GTTGAATCTAGCGTCGTATCCTTTAGATTTGTTGACGGATTTGCAATTTCC
456616 TATGGAAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.43
Consensus pattern (51 bp):
GTTGAATCTAGCGTCGTATCCTTTAGATTTGTTGACGGATTTGCAATTTCC
Found at i:465545 original size:17 final size:17
Alignment explanation
Indices: 465511--465549 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
465501 ATGGTATTTT
* *
465511 AAAAT-TTATTTTTTTA
1 AAAATATTATATTTATA
465527 AAAATATTATATTTATA
1 AAAATATTATATTTATA
465544 AAAATA
1 AAAATA
465550 CCCTAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAATATTATATTTATA
Found at i:469285 original size:60 final size:59
Alignment explanation
Indices: 469162--469285 Score: 133
Period size: 60 Copynumber: 2.1 Consensus size: 59
469152 TGGTCTCCTG
* * ** *
469162 ACTATAGATGTTACTTTATTAAGTCTCTCGACTATTAAAAGTTACAAAATGGTTCTTCG
1 ACTATAGATGTTACTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATAGTTCCCCC
* * * * *
469221 ACTATAGAATGTTGCTTTGTTGAGTCCCTCGACTATTAGAAGTTATAAAATAG-TCACCCC
1 ACTATAG-ATGTTACTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATAGTTC-CCCC
469281 ACTAT
1 ACTAT
469286 TCATTATATT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
59 9 0.17
60 44 0.83
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (59 bp):
ACTATAGATGTTACTTTATTAAGTCCCTCGACTATTAAAAGTTACAAAATAGTTCCCCC
Found at i:470262 original size:3 final size:3
Alignment explanation
Indices: 470254--470282 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
470244 CTCGATTAAG
470254 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
470283 GGGTAAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:471213 original size:14 final size:14
Alignment explanation
Indices: 471196--471226 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
471186 AATATTATTT
471196 AAAAATTAAAATTA
1 AAAAATTAAAATTA
471210 AAAAATTAAAATTA
1 AAAAATTAAAATTA
471224 AAA
1 AAA
471227 TTATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATTAAAATTA
Found at i:478213 original size:17 final size:17
Alignment explanation
Indices: 478183--478228 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
478173 AAATTCATAA
*
478183 AAAC-TTTATGAAATTT
1 AAACTTTTATTAAATTT
478199 AAACTTTTATTAAATTT
1 AAACTTTTATTAAATTT
478216 AAACTTTTATTAA
1 AAACTTTTATTAA
478229 TACAAAAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 4 0.14
17 24 0.86
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (17 bp):
AAACTTTTATTAAATTT
Found at i:478820 original size:31 final size:31
Alignment explanation
Indices: 478755--478842 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 31
478745 GAATGACCTA
** * * *
478755 TCCATATGTTTCGAAGAACATAGAT-ATCTG
1 TCCATATGTCCCGAAGGACATAGGTAAACTG
* *
478785 TCCATATGTCCCTAAGGGCATAGGTAAACTG
1 TCCATATGTCCCGAAGGACATAGGTAAACTG
478816 TCCATATGTCCCGAAGGACATAGGTAA
1 TCCATATGTCCCGAAGGACATAGGTAA
478843 CCCTGACTCT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
30 19 0.40
31 29 0.60
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (31 bp):
TCCATATGTCCCGAAGGACATAGGTAAACTG
Found at i:480321 original size:24 final size:20
Alignment explanation
Indices: 480294--480351 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
480284 GCATGGGTAG
480294 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
480318 TGCATCAATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
480338 TGCATCGATGCACT
1 TGCATCGATGCACT
480352 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:488926 original size:22 final size:22
Alignment explanation
Indices: 488898--488944 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
488888 AGTAAATTTG
488898 AATTTGTTTCTAAATTGTTGGA
1 AATTTGTTTCTAAATTGTTGGA
488920 AATTTGTTTCTAAATTGTTGGA
1 AATTTGTTTCTAAATTGTTGGA
488942 AAT
1 AAT
488945 AATATACTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.49
Consensus pattern (22 bp):
AATTTGTTTCTAAATTGTTGGA
Found at i:504164 original size:27 final size:28
Alignment explanation
Indices: 504121--504178 Score: 100
Period size: 27 Copynumber: 2.1 Consensus size: 28
504111 TTAAGCATGA
*
504121 ATAAATTTAGGGATAGATGTATGATTTT
1 ATAAATTCAGGGATAGATGTATGATTTT
504149 ATAAATTCA-GGATAGATGTATGATTTT
1 ATAAATTCAGGGATAGATGTATGATTTT
504176 ATA
1 ATA
504179 TTAGAGGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 21 0.72
28 8 0.28
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.41
Consensus pattern (28 bp):
ATAAATTCAGGGATAGATGTATGATTTT
Found at i:510216 original size:213 final size:213
Alignment explanation
Indices: 509845--510274 Score: 727
Period size: 213 Copynumber: 2.0 Consensus size: 213
509835 TGTTGGTTTG
*
509845 CTCATAAATGGCCACTTTAGCATGCATGAATCAAAAGAAAGAACATTAATCGAAATTAACCGATA
1 CTCATAAATGGCCACTTTAGCATGCATGAATCAAAAGAAAGAACATTAATCGAAATTAACCGACA
*
509910 TTATTTTCTGGTCGAAAACATTCGAATCCTCTAGGCTAAAATCATGTTCATTGCTATAAGCTTGT
66 TTATTTTCTGGTCGAAAAAATTCGAATCCTCTAGGCTAAAATCATGTTCATTGCTATAAGCTTGT
* *
509975 TATGCAATTATCAGTTTTAGTCATTCATGATTGCTGCATCTGAAAATGTGGTTTGCTGATAAC-C
131 TATGCAATTATCAGTTTCAGTCATTCATGATTGCTGCAGCTGAAAATGTGGTTTGCTGATAACTC
510039 AATTTTGATCCAATGGATT
196 -ATTTTGATCCAATGGATT
**
510058 CTCATAAATGGCCACTTTAGCATGCATGAATCAAAAGAAAGAACATTAATCGAAATTAATGGACA
1 CTCATAAATGGCCACTTTAGCATGCATGAATCAAAAGAAAGAACATTAATCGAAATTAACCGACA
* * *
510123 TTATTTTCTGGTCGAAAAAATTCGAATCCTCTTGGCTAAGATCATGTTCATTGCTATCAGCTTGT
66 TTATTTTCTGGTCGAAAAAATTCGAATCCTCTAGGCTAAAATCATGTTCATTGCTATAAGCTTGT
* * * *
510188 TATGCAATTGTCAGTTTCAGTTATTCATGATTGCTGCAGCTGAAAATGTGGTTTGTTGATATCTC
131 TATGCAATTATCAGTTTCAGTCATTCATGATTGCTGCAGCTGAAAATGTGGTTTGCTGATAACTC
510253 ATTTTGATCCAATGGATT
196 ATTTTGATCCAATGGATT
510271 CTCA
1 CTCA
510275 GGCAAAAAGA
Statistics
Matches: 203, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
213 202 1.00
214 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (213 bp):
CTCATAAATGGCCACTTTAGCATGCATGAATCAAAAGAAAGAACATTAATCGAAATTAACCGACA
TTATTTTCTGGTCGAAAAAATTCGAATCCTCTAGGCTAAAATCATGTTCATTGCTATAAGCTTGT
TATGCAATTATCAGTTTCAGTCATTCATGATTGCTGCAGCTGAAAATGTGGTTTGCTGATAACTC
ATTTTGATCCAATGGATT
Found at i:526730 original size:17 final size:17
Alignment explanation
Indices: 526708--526772 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
526698 ACAGATTACA
526708 TCCTTCGGGATGACAGG
1 TCCTTCGGGATGACAGG
*
526725 TCCTTCGGGA-CACAGATG
1 TCCTTCGGGATGACAG--G
*
526743 ACATCCTTCGGGATGATAGG
1 ---TCCTTCGGGATGACAGG
526763 TCCTTCGGGA
1 TCCTTCGGGA
526773 CATTTATACG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
16 4 0.10
17 20 0.51
18 1 0.03
20 1 0.03
21 10 0.26
22 3 0.08
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.25
Consensus pattern (17 bp):
TCCTTCGGGATGACAGG
Found at i:526735 original size:38 final size:38
Alignment explanation
Indices: 526679--526774 Score: 165
Period size: 38 Copynumber: 2.5 Consensus size: 38
526669 TATAAGACAT
* *
526679 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
526717 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
526755 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
526775 TTTATACGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:526751 original size:21 final size:21
Alignment explanation
Indices: 526687--526755 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
526677 ATATGATAGG
* *
526687 TCCTACGGGACACAGATTACA
1 TCCTTCGGGACACAGATGACA
*
526708 TCCTTCGGGATGACAG--G---
1 TCCTTCGGGA-CACAGATGACA
526725 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
526746 TCCTTCGGGA
1 TCCTTCGGGA
526756 TGATAGGTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (21 bp):
TCCTTCGGGACACAGATGACA
Found at i:532941 original size:17 final size:17
Alignment explanation
Indices: 532919--532983 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
532909 ACAGATTACA
532919 TCCTTCGGGATGACAGG
1 TCCTTCGGGATGACAGG
*
532936 TCCTTCGGGA-CACAGATG
1 TCCTTCGGGATGACAG--G
*
532954 ACATCCTTCGGGATGATAGG
1 ---TCCTTCGGGATGACAGG
532974 TCCTTCGGGA
1 TCCTTCGGGA
532984 CATTTATACG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
16 4 0.10
17 20 0.51
18 1 0.03
20 1 0.03
21 10 0.26
22 3 0.08
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.25
Consensus pattern (17 bp):
TCCTTCGGGATGACAGG
Found at i:532946 original size:38 final size:38
Alignment explanation
Indices: 532890--532985 Score: 165
Period size: 38 Copynumber: 2.5 Consensus size: 38
532880 TATAAGACAT
* *
532890 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
532928 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
532966 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
532986 TTTATACGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:532962 original size:21 final size:21
Alignment explanation
Indices: 532898--532966 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
532888 ATATGATAGG
* *
532898 TCCTACGGGACACAGATTACA
1 TCCTTCGGGACACAGATGACA
*
532919 TCCTTCGGGATGACAG--G---
1 TCCTTCGGGA-CACAGATGACA
532936 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
532957 TCCTTCGGGA
1 TCCTTCGGGA
532967 TGATAGGTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (21 bp):
TCCTTCGGGACACAGATGACA
Found at i:535470 original size:13 final size:15
Alignment explanation
Indices: 535452--535521 Score: 67
Period size: 15 Copynumber: 4.9 Consensus size: 15
535442 AAATATGTTA
535452 TAATTAT-TT-TATT
1 TAATTATATTATATT
*
535465 TAA-T-TACTATATT
1 TAATTATATTATATT
*
535478 TATTTATATTATATT
1 TAATTATATTATATT
*
535493 TATTTATATTATATT
1 TAATTATATTATATT
* *
535508 TAATAATAATATAT
1 TAATTATATTATAT
535522 ATATATATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
11 1 0.02
12 2 0.04
13 9 0.19
14 1 0.02
15 34 0.72
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (15 bp):
TAATTATATTATATT
Found at i:535487 original size:28 final size:26
Alignment explanation
Indices: 535472--535542 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 26
535462 ATTTAATTAC
535472 TATATT-TATTTATATTATATTTATT
1 TATATTATATTTATATTATATTTATT
* * *
535497 TATATTATATTTAATAATAATATATATA
1 TATATTATATTT-AT-ATTATATTTATT
*
535525 TATATATATATATATATT
1 TATAT-TATATTTATATT
535543 TGTTATTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
25 6 0.16
26 5 0.14
27 4 0.11
28 16 0.43
29 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TATATTATATTTATATTATATTTATT
Found at i:535531 original size:10 final size:10
Alignment explanation
Indices: 535472--535541 Score: 60
Period size: 10 Copynumber: 7.5 Consensus size: 10
535462 ATTTAATTAC
* *
535472 TATATTTATT
1 TATATATATA
535482 TATAT-TATA
1 TATATATATA
* *
535491 TTTATTTATA
1 TATATATATA
*
535501 T-TATATTTA
1 TATATATATA
535510 -ATA-ATA-A
1 TATATATATA
535517 TATATATATA
1 TATATATATA
535527 TATATATATA
1 TATATATATA
535537 TATAT
1 TATAT
535542 TTGTTATTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
7 1 0.02
8 5 0.10
9 18 0.36
10 26 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATATATA
Found at i:535538 original size:6 final size:6
Alignment explanation
Indices: 535472--535541 Score: 60
Period size: 6 Copynumber: 12.5 Consensus size: 6
535462 ATTTAATTAC
* * * * *
535472 TATATT TATTTA TAT-TA TATTTA TTTATA T-TATA TTTA-A TA-ATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
535516 -ATATA TATATA TATATA TATATA TAT
1 TATATA TATATA TATATA TATATA TAT
535542 TTGTTATTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
4 2 0.04
5 16 0.30
6 36 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TATATA
Found at i:537306 original size:4 final size:4
Alignment explanation
Indices: 537297--537325 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
537287 GGTCCAAATT
537297 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
537326 ACGTTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:539334 original size:4 final size:4
Alignment explanation
Indices: 539325--539356 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
539315 TTCATCCATT
539325 TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
539357 AGCAGATGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:550931 original size:3 final size:3
Alignment explanation
Indices: 550923--550949 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
550913 TCTACTTGTC
550923 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
550950 TACCCTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:556755 original size:239 final size:236
Alignment explanation
Indices: 556510--557007 Score: 852
Period size: 239 Copynumber: 2.1 Consensus size: 236
556500 GTTGCAAGGG
* * *
556510 TGGGGAACTTTGTGGTGAATTCCTCAAGCGTGGCGCAACCGGAGCTACAAGATAGCGAGTAAAAG
1 TGGGGAATTTTGTGGAGAATTCCTCAAGCGTGGCGCAACCGGAGCTACAAGATAGAGAGTAAAAG
* **
556575 AAGCAGTGTTAGAATCAAAGTCGGTTTTAAATCTATCAGGAAATGACTCATCAATTATCAAACTT
66 AAGCAGTGTTAGAATCAAAGTCGGTTTTAAATCTATCAGG-AATGACTCATCAATGATCAAACCG
556640 CTGAATATATACCTGGAGCACTTGGCTCCAGAACAGGGGCCTTATTGTTAGATGAATTTCCTTCA
130 CTG-ATATATACCTGGAGCACTTGGCTCCAGAACAGGGGCCTTATTGTTAGATGAATTTCCTTCA
556705 TTGACAGTTGGGGGGAAAGCGCTTGACCTACTGGAATTAATGAC
194 TTGACAGTT-GGGGGAAAGCGCTTGACCTACTGGAATTAATGAC
**
556749 TGGGGAATTTTGTGGAGAATTCCTCAATTGTGGCGCAACCGGAGCTACAAGATAGAGAGTAAAAG
1 TGGGGAATTTTGTGGAGAATTCCTCAAGCGTGGCGCAACCGGAGCTACAAGATAGAGAGTAAAAG
* *
556814 AAGCAGTGTTAGAATCAAAGTTGGTTTTAAATCTATCAGGAATGACTCGTCAATGATCAAACCGC
66 AAGCAGTGTTAGAATCAAAGTCGGTTTTAAATCTATCAGGAATGACTCATCAATGATCAAACCGC
*
556879 TGATATATACCTGGAGCACTTGGCTCCAGAACAGGGGCCTTATTGTTAGATGAATTTCCTTCGTT
131 TGATATATACCTGGAGCACTTGGCTCCAGAACAGGGGCCTTATTGTTAGATGAATTTCCTTCATT
* *
556944 GTCAGTTGGGGGAAAGCGCTTGACCTACTGGAGTTAATGAC
196 GACAGTTGGGGGAAAGCGCTTGACCTACTGGAATTAATGAC
556985 TGGGGAATTTTGTGGAGAATTCC
1 TGGGGAATTTTGTGGAGAATTCC
557008 GCAACGGTGG
Statistics
Matches: 246, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
236 56 0.23
237 68 0.28
238 23 0.09
239 99 0.40
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (236 bp):
TGGGGAATTTTGTGGAGAATTCCTCAAGCGTGGCGCAACCGGAGCTACAAGATAGAGAGTAAAAG
AAGCAGTGTTAGAATCAAAGTCGGTTTTAAATCTATCAGGAATGACTCATCAATGATCAAACCGC
TGATATATACCTGGAGCACTTGGCTCCAGAACAGGGGCCTTATTGTTAGATGAATTTCCTTCATT
GACAGTTGGGGGAAAGCGCTTGACCTACTGGAATTAATGAC
Found at i:557713 original size:102 final size:102
Alignment explanation
Indices: 557537--557928 Score: 624
Period size: 102 Copynumber: 3.8 Consensus size: 102
557527 CGGAGGTGGT
* * * * * *
557537 GGAGATGGTGGCAACACCAATGGAGTACTTGGTGCAAAGGATGGCAAATGTTCTTCAATAGGGAA
1 GGAGATGGTGGCAACACCACTGGAATACTTGGAGCCAACGATGGTAAATGTTCTTCAATAGGGAA
* *
557602 TGGTGGCGGAGCTGTATTTCGGGTTCGCTCGGATGGA
66 TGGTGGCGGAGCTGTATTTTGGGTTCGCACGGATGGA
* * *
557639 GGAGATGGT-GCTAACACCACTGGAAAACTTGGAGCCAAGGATGGTAAATTTTCTTCAATAGGGA
1 GGAGATGGTGGC-AACACCACTGGAATACTTGGAGCCAACGATGGTAAATGTTCTTCAATAGGGA
* * *
557703 ATGGTGGCGGAGATGTATTTTGGGTTCGCGCGGACGGA
65 ATGGTGGCGGAGCTGTATTTTGGGTTCGCACGGATGGA
*
557741 GGAGATGGTGGCAACACCACTGGAATACTAGGAGCCAACGATGGTAAATGTTCTTCAATAGGGAA
1 GGAGATGGTGGCAACACCACTGGAATACTTGGAGCCAACGATGGTAAATGTTCTTCAATAGGGAA
*
557806 TGGCGGCGGAGCTGTATTTTGGGTTCGCACGGATGGA
66 TGGTGGCGGAGCTGTATTTTGGGTTCGCACGGATGGA
557843 GGAGATGGTGGCAACACCACTGGAATACTTGGAGCCAACGATGGTAAATGTTCTTCAATAGGGAA
1 GGAGATGGTGGCAACACCACTGGAATACTTGGAGCCAACGATGGTAAATGTTCTTCAATAGGGAA
557908 TGGTGGCGGAGCTGTATTTTG
66 TGGTGGCGGAGCTGTATTTTG
557929 CGGCGTCGGT
Statistics
Matches: 267, Mismatches: 21, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
101 2 0.01
102 263 0.99
103 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.34, T:0.24
Consensus pattern (102 bp):
GGAGATGGTGGCAACACCACTGGAATACTTGGAGCCAACGATGGTAAATGTTCTTCAATAGGGAA
TGGTGGCGGAGCTGTATTTTGGGTTCGCACGGATGGA
Found at i:562482 original size:40 final size:40
Alignment explanation
Indices: 562429--562515 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
562419 TCAAAACCGT
*
562429 TAAATTTTGAACGG-GTGTACTAAAATGAAACAAAAAAAC
1 TAAATTTTGAACGGAGAGTACTAAAATGAAACAAAAAAAC
* *
562468 TAAAGTTTTTAACGGTACGAGTACTAAAATG-AA-ATAAAAAC
1 TAAA-TTTTGAACGG-A-GAGTACTAAAATGAAACAAAAAAAC
562509 TAAATTT
1 TAAATTT
562516 GAAATAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
39 4 0.10
40 12 0.29
41 11 0.27
42 2 0.05
43 12 0.29
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (40 bp):
TAAATTTTGAACGGAGAGTACTAAAATGAAACAAAAAAAC
Found at i:562512 original size:17 final size:18
Alignment explanation
Indices: 562490--562531 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
562480 CGGTACGAGT
562490 ACTAAA-ATGAAATAAAA
1 ACTAAATATGAAATAAAA
*
562507 ACTAAATTTGAAATAAAA
1 ACTAAATATGAAATAAAA
562525 ACTAAAT
1 ACTAAAT
562532 TTTAGGTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.24
Consensus pattern (18 bp):
ACTAAATATGAAATAAAA
Found at i:562520 original size:18 final size:18
Alignment explanation
Indices: 562497--562533 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
562487 AGTACTAAAA
562497 TGAAATAAAAACTAAATT
1 TGAAATAAAAACTAAATT
562515 TGAAATAAAAACTAAATT
1 TGAAATAAAAACTAAATT
562533 T
1 T
562534 TAGGTAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (18 bp):
TGAAATAAAAACTAAATT
Found at i:565480 original size:2 final size:2
Alignment explanation
Indices: 565473--565522 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
565463 ATGACCAAAT
565473 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
565515 TA TA TA TA
1 TA TA TA TA
565523 GTTGAGACCC
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:569186 original size:12 final size:12
Alignment explanation
Indices: 569169--569219 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
569159 TTCAAAGAGG
569169 TTTTATATTTAA
1 TTTTATATTTAA
569181 TTTTATA-TTATA
1 TTTTATATTTA-A
*
569193 TTTGAT-TTTAA
1 TTTTATATTTAA
569204 TTTTA-ATATTAA
1 TTTTATAT-TTAA
569216 TTTT
1 TTTT
569220 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:569257 original size:26 final size:27
Alignment explanation
Indices: 569202--569279 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
569192 ATTTGATTTT
*
569202 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
569227 AATTA-AATATTAATTTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
*
569253 TATTATAGATATTAA--TTTTAATATTA
1 AATTATA-ATATTAATTTTTTAATATTA
569279 A
1 A
569280 TTTTTTTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 16 0.35
25 5 0.11
26 17 0.37
27 1 0.02
28 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:569278 original size:12 final size:12
Alignment explanation
Indices: 569177--569283 Score: 78
Period size: 12 Copynumber: 8.7 Consensus size: 12
569167 GGTTTTATAT
569177 TTAATTTT-ATA
1 TTAATTTTAATA
* *
569188 TT-ATATTTGATT
1 TTAAT-TTTAATA
569200 TTAATTTTAATA
1 TTAATTTTAATA
569212 TTAATTTTTTAA-A
1 TTAA--TTTTAATA
* *
569225 -TAAATTAAATA
1 TTAATTTTAATA
569236 TTAATTTTTTAATA
1 TTAA--TTTTAATA
*
569250 TTATATTATAGATA
1 TTA-ATTTTA-ATA
569264 TTAATTTTAATA
1 TTAATTTTAATA
569276 TTAATTTT
1 TTAATTTT
569284 TTTAAATAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
10 6 0.08
11 6 0.08
12 30 0.39
13 12 0.16
14 21 0.28
15 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:569279 original size:64 final size:63
Alignment explanation
Indices: 569181--569312 Score: 223
Period size: 65 Copynumber: 2.1 Consensus size: 63
569171 TTATATTTAA
*
569181 TTTT-ATATTATATTTGATTTTAATTTTAATATTAA-TTTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTTGATATTAATTTTAATATTAATTTTTTTAAATAAATTAAATATTAATT
569242 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATT-T-GATATTAATTTTAATATTAATTTTTTTAAATAAATTAAATATTAATT
569307 TTTTAA
1 TTTTAA
569313 ATAAATTAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
61 4 0.06
62 10 0.15
63 1 0.02
64 19 0.29
65 32 0.48
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (63 bp):
TTTTAATATTATATTTGATATTAATTTTAATATTAATTTTTTTAAATAAATTAAATATTAATT
Found at i:569308 original size:24 final size:25
Alignment explanation
Indices: 569272--569337 Score: 116
Period size: 24 Copynumber: 2.7 Consensus size: 25
569262 TATTAATTTT
*
569272 AATATTAATTTTTTTAAATAAATTA
1 AATATTAAGTTTTTTAAATAAATTA
569297 AATATTAA-TTTTTTAAATAAATTA
1 AATATTAAGTTTTTTAAATAAATTA
569321 AATATTAAGTTTTTTAA
1 AATATTAAGTTTTTTAA
569338 TATTATATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 24 0.60
25 16 0.40
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
AATATTAAGTTTTTTAAATAAATTA
Found at i:569426 original size:20 final size:19
Alignment explanation
Indices: 569343--569427 Score: 59
Period size: 19 Copynumber: 4.3 Consensus size: 19
569333 TTTAATATTA
* *
569343 TATTATATATATATATATATT
1 TATTTTATATAT-TAT-TAAT
*
569364 TAATTTTATATCA-TATAAAT
1 T-ATTTTATAT-ATTATTAAT
569384 TATTTTATATATTATTAA-
1 TATTTTATATATTATTAAT
*
569402 AATTTTATAT-TTATTTTAAT
1 TATTTTATATATTA--TTAAT
569422 TATTTT
1 TATTTT
569428 GATTTAAGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
17 3 0.06
18 10 0.19
19 18 0.35
20 8 0.15
21 4 0.08
22 8 0.15
23 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTATATATTATTAAT
Found at i:569928 original size:31 final size:31
Alignment explanation
Indices: 569891--569950 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
569881 TAGTTGTATG
* *
569891 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
569922 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
569951 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:573502 original size:12 final size:12
Alignment explanation
Indices: 573474--573547 Score: 85
Period size: 12 Copynumber: 6.9 Consensus size: 12
573464 GAGAGAAGTG
573474 GAACGAGAAG-A
1 GAACGAGAAGCA
573485 G-A-GAGAAGCA
1 GAACGAGAAGCA
573495 GAACGAGAAG-A
1 GAACGAGAAGCA
573506 G-A-GAGAAGCA
1 GAACGAGAAGCA
573516 GAACGAGAAG-A
1 GAACGAGAAGCA
573527 G-A-GAGAAGCA
1 GAACGAGAAGCA
573537 GAACGAGAAGC
1 GAACGAGAAGC
573548 GAGAGAAGCT
Statistics
Matches: 54, Mismatches: 0, Indels: 17
0.76 0.00 0.24
Matches are distributed among these distances:
9 18 0.33
10 9 0.17
11 8 0.15
12 19 0.35
ACGTcount: A:0.51, C:0.11, G:0.38, T:0.00
Consensus pattern (12 bp):
GAACGAGAAGCA
Found at i:573566 original size:42 final size:42
Alignment explanation
Indices: 573459--573589 Score: 160
Period size: 42 Copynumber: 3.1 Consensus size: 42
573449 AGCACAAGTC
* **
573459 GAAGTGAGAGAAGTGGAACGAGAAGAGAGAGAAGCAGAACGA
1 GAAGCGAGAGAAGCAGAACGAGAAGAGAGAGAAGCAGAACGA
*
573501 GAAGAGAGAGAAGCAGAACGAGAAGAGAGAGAAGCAGAACGA
1 GAAGCGAGAGAAGCAGAACGAGAAGAGAGAGAAGCAGAACGA
* *
573543 GAAGCGAGAGAAGCTGAGA-GAGAAGTA-AGAGAAACAGAGA-GA
1 GAAGCGAGAGAAGCAGA-ACGAGAAG-AGAGAGAAGCAGA-ACGA
573585 GAAGC
1 GAAGC
573590 AACATTATCA
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
42 77 0.96
43 3 0.04
ACGTcount: A:0.50, C:0.08, G:0.39, T:0.03
Consensus pattern (42 bp):
GAAGCGAGAGAAGCAGAACGAGAAGAGAGAGAAGCAGAACGA
Found at i:573566 original size:63 final size:63
Alignment explanation
Indices: 573459--573588 Score: 158
Period size: 63 Copynumber: 2.1 Consensus size: 63
573449 AGCACAAGTC
* ** *
573459 GAAGTGAGAGAAGTGGAACGAGAAGAGAGAGAAGCAGAACGAGAAG-AGAGAGAAGCAGA-ACGA
1 GAAGAGAGAGAAGCAGAACGAGAAGAGAGAGAAGCAGAACGAGAAGTA-AGAGAAACAGAGA-GA
* *
573522 GAAGAGAGAGAAGCAGAACGAGAAGCGAGAGAAGCTGAGA-GAGAAGTAAGAGAAACAGAGAGA
1 GAAGAGAGAGAAGCAGAACGAGAAGAGAGAGAAGCAGA-ACGAGAAGTAAGAGAAACAGAGAGA
573585 GAAG
1 GAAG
573589 CAACATTATC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
63 55 0.95
64 3 0.05
ACGTcount: A:0.50, C:0.08, G:0.39, T:0.03
Consensus pattern (63 bp):
GAAGAGAGAGAAGCAGAACGAGAAGAGAGAGAAGCAGAACGAGAAGTAAGAGAAACAGAGAGA
Found at i:573575 original size:21 final size:21
Alignment explanation
Indices: 573459--573556 Score: 160
Period size: 21 Copynumber: 4.7 Consensus size: 21
573449 AGCACAAGTC
* **
573459 GAAGTGAGAGAAGTGGAACGA
1 GAAGAGAGAGAAGCAGAACGA
573480 GAAGAGAGAGAAGCAGAACGA
1 GAAGAGAGAGAAGCAGAACGA
573501 GAAGAGAGAGAAGCAGAACGA
1 GAAGAGAGAGAAGCAGAACGA
573522 GAAGAGAGAGAAGCAGAACGA
1 GAAGAGAGAGAAGCAGAACGA
*
573543 GAAGCGAGAGAAGC
1 GAAGAGAGAGAAGC
573557 TGAGAGAGAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.49, C:0.09, G:0.40, T:0.02
Consensus pattern (21 bp):
GAAGAGAGAGAAGCAGAACGA
Found at i:573762 original size:28 final size:28
Alignment explanation
Indices: 573720--573791 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
573710 TTATTCTAGT
* * *
573720 TGTTAAACTATATTACATTTCACTTT-AA
1 TGTTGAACTACATTACATCTC-CTTTAAA
* *
573748 TGTTGAACTACATTAAATCTCTTTTAAA
1 TGTTGAACTACATTACATCTCCTTTAAA
*
573776 TGTTGAGCTACATTAC
1 TGTTGAACTACATTAC
573792 TTGAATATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 3 0.08
28 33 0.92
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.43
Consensus pattern (28 bp):
TGTTGAACTACATTACATCTCCTTTAAA
Found at i:574381 original size:22 final size:22
Alignment explanation
Indices: 574356--574427 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 22
574346 CTTAAATTCA
574356 TAAAAT-TTTATATATATTAACT
1 TAAAATATTT-TATATATTAACT
574378 TAAAAATATTTT-TATATTAACT
1 T-AAAATATTTTATATATTAACT
574400 TATTAAATATATTT-TATTATTAACT
1 TA--AAATAT-TTTATA-TATTAACT
574425 TAA
1 TAA
574428 TTTAAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
21 1 0.02
22 12 0.27
23 13 0.30
24 8 0.18
25 10 0.23
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAAATATTTTATATATTAACT
Found at i:574388 original size:25 final size:24
Alignment explanation
Indices: 574360--574442 Score: 80
Period size: 22 Copynumber: 3.2 Consensus size: 24
574350 AATTCATAAA
574360 ATTTTATATATATTAACTTAAAAAT
1 ATTTTAT-TATATTAACTTAAAAAT
574385 A-TTT-TTATATTAACTTATTAAATAT
1 ATTTTATTATATTAACTTA--AAA-AT
*
574410 ATTTTATTATTAACTTAATTTAAAAAT
1 ATTTTATTA-T-A-TTAACTTAAAAAT
574437 ATTTTA
1 ATTTTA
574443 ATTTTATTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
22 12 0.24
23 1 0.02
24 6 0.12
25 4 0.08
26 3 0.06
27 11 0.22
28 4 0.08
29 1 0.02
30 7 0.14
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTTTATTATATTAACTTAAAAAT
Found at i:574470 original size:52 final size:52
Alignment explanation
Indices: 574372--574471 Score: 121
Period size: 52 Copynumber: 1.9 Consensus size: 52
574362 TTTATATATA
* *
574372 TTAACTTAAAAATATTTTTATATTAACTTATTAAATATATTTTATTATTAAC
1 TTAACTTAAAAATATTTTAATATTAACTTATTAAATATATTATATTATTAAC
* * ** *
574424 TTAATTTAAAAATATTTTAATTTTATTTTCATTATATATA-TATATTAT
1 TTAACTTAAAAATATTTTAATATTAACTT-ATTAAATATATTATATTAT
574472 GTTAAAATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 31 0.77
53 9 0.22
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (52 bp):
TTAACTTAAAAATATTTTAATATTAACTTATTAAATATATTATATTATTAAC
Done.