Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009009.1 Hibiscus syriacus cultivar Beakdansim tig00112395_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: 196393
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:452 original size:17 final size:17
Alignment explanation
Indices: 430--480 Score: 86
Period size: 17 Copynumber: 3.0 Consensus size: 17
420 CAACGGTCAA
430 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
447 CGGTCAAC-GGTCGGGT
1 CGGTCAACGGGTCGGGT
463 CGGGTCAACGGGTCGGGT
1 C-GGTCAACGGGTCGGGT
481 AAACGGGTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.28
17 15 0.47
18 8 0.25
ACGTcount: A:0.12, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
CGGTCAACGGGTCGGGT
Found at i:476 original size:13 final size:13
Alignment explanation
Indices: 458--507 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
448 GGTCAACGGT
458 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
471 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
484 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
497 CGGGTCGGGTC
1 CGGGTCGGGTC
508 GGGTTGTGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.14, C:0.22, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:2595 original size:35 final size:35
Alignment explanation
Indices: 2544--2623 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
2534 AAAACAATCA
* *
2544 TCAATTATATTTTAAACCCCAAAATT-CAAAATACT
1 TCAATTACATTCTAAACCCC-AAATTCCAAAATACT
*
2579 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
*
2614 TCGATTACAT
1 TCAATTACAT
2624 GCCCAACCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 5 0.12
35 35 0.88
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATACT
Found at i:3062 original size:148 final size:149
Alignment explanation
Indices: 2785--3233 Score: 681
Period size: 148 Copynumber: 3.0 Consensus size: 149
2775 GGTTAAATAC
* * *
2785 TCAATTCATTTTATAAAATAGTTGACTAGAAATTTTTTCGGTTTGA-GTTTATAAAATTTAAATA
1 TCAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGATGTTTATAAAATTTAAATA
*
2849 AAGTCGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAAAATTTATCATATTAT
66 AAGTCGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTAT
2914 AATATTATTTGATTCTAAT
131 AATATTATTTGATTCTAAT
* *
2933 TCAGTTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTT-ATGTTTATAAAATTTAAATC
1 TCAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGATGTTTATAAAATTTAAATA
*
2997 AAGTCGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTGTCATATTAT
66 AAGTCGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTAT
*
3062 AATATTGTTTGATTCTAAT
131 AATATTATTTGATTCTAAT
* * ** *
3081 TCAATTCAGTTTATAAAATAGTTAACTCAAAAAATTTTCTATTTGAT-TTTAT-AAATTTAAATA
1 TCAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGATGTTTATAAAATTTAAATA
* *
3144 AAGTCAAATTGAATTGAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATAAT
66 AAGTC-----GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCAT
*
3209 ACTATAATATTATTTGATTCTAAT
126 ATTATAATATTATTTGATTCTAAT
3233 T
1 T
3234 TAAATAGTGT
Statistics
Matches: 274, Mismatches: 20, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
147 16 0.06
148 181 0.66
149 2 0.01
152 75 0.27
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (149 bp):
TCAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGATGTTTATAAAATTTAAATA
AAGTCGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTAT
AATATTATTTGATTCTAAT
Found at i:3772 original size:35 final size:35
Alignment explanation
Indices: 3733--3845 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 35
3723 GGGGTTGGAC
*
3733 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGCATTTTGGAATTTGAGGTTTAGA
*
3768 ATGTATTTGAAGCATTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGCATTTTGGAATTTGAGGTTTAGA
* * * * *
3803 ATATAGTTGAAGCATTTTAGAATTCGAGGTTTATA
1 ATGTAATTGAAGCATTTTGGAATTTGAGGTTTAGA
3838 ATGTAATT
1 ATGTAATT
3846 AATGATTGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.32, C:0.03, G:0.23, T:0.42
Consensus pattern (35 bp):
ATGTAATTGAAGCATTTTGGAATTTGAGGTTTAGA
Found at i:9760 original size:2 final size:2
Alignment explanation
Indices: 9753--9782 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9743 AGAATTTATT
9753 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
9783 ATTTTTTAAA
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):
TA
Found at i:15766 original size:23 final size:22
Alignment explanation
Indices: 15718--15770 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
15708 GAATCCTACC
**
15718 ATATATATTATTTTTTATATTT
1 ATATATATTATTTTTTATATGA
15740 ATATAT-TTATGTATTTTATATGA
1 ATATATATTAT-T-TTTTATATGA
15763 ATATATAT
1 ATATATAT
15771 AATACTAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 7 0.27
23 14 0.54
24 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
ATATATATTATTTTTTATATGA
Found at i:19909 original size:14 final size:14
Alignment explanation
Indices: 19877--19916 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
19867 GATACATGTG
19877 TATATTAT-AA-AT
1 TATATTATAAATAT
19889 T-TATTATAAATAT
1 TATATTATAAATAT
*
19902 TATATTATAATTAT
1 TATATTATAAATAT
19916 T
1 T
19917 GGTTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 6 0.25
12 3 0.12
13 3 0.12
14 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATATTATAAATAT
Found at i:28360 original size:233 final size:234
Alignment explanation
Indices: 27929--28370 Score: 701
Period size: 235 Copynumber: 1.9 Consensus size: 234
27919 TCTTCGTTCA
* * *
27929 GAACGCTATCGATGTGTCTAAGCTTCGTGCTTCGGAACTCGAAGAATTTGTCAAAGGTTCCGATT
1 GAACGCTATCGATGTATCTAAGCCTCGTGCTTCGGAACTCAAAGAATTTGTCAAAGGTTCCGATT
* **
27994 TATTCTTATCTATTTCACGAGTCGTTTTGTTTATTTTAGAGTTATGTAGTTTCTGTTTAGTTTTT
66 TATTCTTATCTATTTCACGAGTCG-TTTGTTTATTTTAGAATTATGTAGTTTAGGTTTAGTTTTT
* *
28059 GTTGAATTAGATTAGTTTTAGCAGCTTTAAGAAAAATTATGGAAGATTGAGATGAGATCTGCGCT
130 GTTAAATTAGATTAGTTTTAGCAGCTTTAAGAAAAATTATGGAAGATTGAGATGAGATATGCGCT
28124 TATTCGAAAACTTTCAAACATCTAAGTTATGATTAGTTAT
195 TATTCGAAAACTTTCAAACATCTAAGTTATGATTAGTTAT
* *
28164 GAACGCTATCGATGTATCTAAGCCTCGTGTTTCGGGACTCAAAGAATTTGTCAAAGGTTCCGATT
1 GAACGCTATCGATGTATCTAAGCCTCGTGCTTCGGAACTCAAAGAATTTGTCAAAGGTTCCGATT
* * * *
28229 TCTTCTTATCTATTTCATGATTC-TTT-TTTAGTTTTAGAATTGTGTAGTTTAGGTTTAGTTTTT
66 TATTCTTATCTATTTCACGAGTCGTTTGTTTA-TTTTAGAATTATGTAGTTTAGGTTTAG-TTTT
28292 TGTTAAATTAGATTAGTTTTAGCAGCTTTAAG-AAAATTATGGAAGATTGAGATGAGATATGCGC
129 TGTTAAATTAGATTAGTTTTAGCAGCTTTAAGAAAAATTATGGAAGATTGAGATGAGATATGCGC
*
28356 TTATTCTAAAACTTT
194 TTATTCGAAAACTTT
28371 TGAACTCGTA
Statistics
Matches: 190, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
232 4 0.02
233 71 0.37
234 35 0.18
235 80 0.42
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (234 bp):
GAACGCTATCGATGTATCTAAGCCTCGTGCTTCGGAACTCAAAGAATTTGTCAAAGGTTCCGATT
TATTCTTATCTATTTCACGAGTCGTTTGTTTATTTTAGAATTATGTAGTTTAGGTTTAGTTTTTG
TTAAATTAGATTAGTTTTAGCAGCTTTAAGAAAAATTATGGAAGATTGAGATGAGATATGCGCTT
ATTCGAAAACTTTCAAACATCTAAGTTATGATTAGTTAT
Found at i:37501 original size:95 final size:95
Alignment explanation
Indices: 37334--37525 Score: 287
Period size: 95 Copynumber: 2.0 Consensus size: 95
37324 CAACATTTGA
* * *
37334 GATAATTTTAAAACTAAAAATAGACACATTTAATGAAACAATGGGAGTACATTTTAAGTTTAATA
1 GATAATTTTAAAACTAAAAAGAGACACATTTAATGAAACAATGGGAGTACATTTTAACTATAATA
* *
37399 TGTCATGTTGAATAAATTTTAACTCAATAC
66 TGGCATGTCGAATAAATTTTAACTCAATAC
* * * *
37429 GATAATTTTAAAATTCAAAAGAGACACGTTTAATGAAACAACT-GGAGTACATTTTAACTATAGT
1 GATAATTTTAAAACTAAAAAGAGACACATTTAATGAAACAA-TGGGAGTACATTTTAACTATAAT
37493 ATGGCATGTCGAATAAATTTTAACTCAATAC
65 ATGGCATGTCGAATAAATTTTAACTCAATAC
37524 GA
1 GA
37526 CGTTACAGCA
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 86 0.99
96 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (95 bp):
GATAATTTTAAAACTAAAAAGAGACACATTTAATGAAACAATGGGAGTACATTTTAACTATAATA
TGGCATGTCGAATAAATTTTAACTCAATAC
Found at i:39819 original size:30 final size:30
Alignment explanation
Indices: 39753--39821 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
39743 CAGAAAACAC
* **
39753 CATGTATAAAATTGAGAATTTTTAAACATT
1 CATGTATGAAATTGAGAATTGGTAAACATT
*
39783 -ATGTATGAAATTGAGAATTCGGTATAC-TT
1 CATGTATGAAATTGAGAATT-GGTAAACATT
39812 CATGTATGAA
1 CATGTATGAA
39822 GGAGGTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (30 bp):
CATGTATGAAATTGAGAATTGGTAAACATT
Found at i:42855 original size:22 final size:22
Alignment explanation
Indices: 42785--42847 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
42775 TAGATTTTAG
42785 GGTT-TAGAGTTATGATTTAAA
1 GGTTATAGAGTTATGATTTAAA
42806 GGTTATAGAGTTATGATTTAAA
1 GGTTATAGAGTTATGATTTAAA
*
42828 GGTTATGGAGTTATGATTTA
1 GGTTATAGAGTTATGATTTA
42848 TGGTTTATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
21 4 0.10
22 36 0.90
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (22 bp):
GGTTATAGAGTTATGATTTAAA
Found at i:51069 original size:5 final size:5
Alignment explanation
Indices: 51051--51111 Score: 54
Period size: 5 Copynumber: 12.6 Consensus size: 5
51041 CCGCCGCCGC
* * * *
51051 CGTC- CGTC- CGTCT CGTCT CGTCT CGTCT CGGCT CGGCT CGGCT CGGCT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT
* *
51099 CGGCT CGGCT CGT
1 CGTCT CGTCT CGT
51112 GGTCGTGGTC
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
4 8 0.15
5 46 0.85
ACGTcount: A:0.00, C:0.41, G:0.31, T:0.28
Consensus pattern (5 bp):
CGTCT
Found at i:51074 original size:10 final size:10
Alignment explanation
Indices: 51062--51110 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
51052 GTCCGTCCGT
*
51062 CTCGTCTCGT
1 CTCGTCTCGG
51072 CTCGTCTCGG
1 CTCGTCTCGG
*
51082 CTCGGCTCGG
1 CTCGTCTCGG
*
51092 CTCGGCTCGG
1 CTCGTCTCGG
*
51102 CTCGGCTCG
1 CTCGTCTCG
51111 TGGTCGTGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.00, C:0.41, G:0.33, T:0.27
Consensus pattern (10 bp):
CTCGTCTCGG
Found at i:51079 original size:15 final size:15
Alignment explanation
Indices: 51059--51110 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
51049 GCCGTCCGTC
* *
51059 CGTCTCGTCTCGTCT
1 CGTCTCGGCTCGGCT
51074 CGTCTCGGCTCGGCT
1 CGTCTCGGCTCGGCT
*
51089 CGGCTCGGCTCGGCT
1 CGTCTCGGCTCGGCT
*
51104 CGGCTCG
1 CGTCTCG
51111 TGGTCGTGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.00, C:0.40, G:0.33, T:0.27
Consensus pattern (15 bp):
CGTCTCGGCTCGGCT
Found at i:51119 original size:6 final size:6
Alignment explanation
Indices: 51108--51246 Score: 206
Period size: 6 Copynumber: 23.2 Consensus size: 6
51098 TCGGCTCGGC
* * *
51108 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* * * * *
51156 TCGAGG TCGAGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
51204 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
51247 AATACGTGTC
Statistics
Matches: 131, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 131 1.00
ACGTcount: A:0.06, C:0.17, G:0.50, T:0.28
Consensus pattern (6 bp):
TCGTGG
Found at i:51549 original size:22 final size:22
Alignment explanation
Indices: 51524--51578 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
51514 TCAGGAGTTA
* *
51524 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
51546 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
51568 CGGGAGTTATA
1 CAGGAGTTATA
51579 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:57133 original size:5 final size:5
Alignment explanation
Indices: 57114--57152 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
57104 GTCCGTCCGT
* * *
57114 CTCGT CTCGT CTCGG CTCGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
57153 TGGTCGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.03, C:0.41, G:0.33, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:57161 original size:6 final size:6
Alignment explanation
Indices: 57150--57228 Score: 140
Period size: 6 Copynumber: 13.2 Consensus size: 6
57140 TCGGCTCGGC
* *
57150 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
57198 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
57229 AATACGTGTC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:57530 original size:22 final size:22
Alignment explanation
Indices: 57505--57559 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
57495 TCAGGAGTTA
* *
57505 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
57527 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
57549 CGGGAGTTATA
1 CAGGAGTTATA
57560 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:65317 original size:23 final size:24
Alignment explanation
Indices: 65268--65318 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
65258 TATTATATTG
*
65268 TATTTTAAAAATTATTAGTTAATA
1 TATTTTAAAAATTATTAGTTAAAA
*
65292 TATTTTAAATATCT-TTA-TTAAAA
1 TATTTTAAAAAT-TATTAGTTAAAA
65315 TATT
1 TATT
65319 ATTATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 14 0.58
25 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TATTTTAAAAATTATTAGTTAAAA
Found at i:65501 original size:22 final size:22
Alignment explanation
Indices: 65459--65523 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
65449 ATATCTTATC
**
65459 TTATTATAATA-TAATTGATATA
1 TTATTATAATATTAA-AAATATA
65481 TTATTATAATATTAAAAATATA
1 TTATTATAATATTAAAAATATA
* * * *
65503 ATATTACATTATTAGAAATAT
1 TTATTATAATATTAAAAATAT
65524 TAATAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
22 33 0.92
23 3 0.08
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (22 bp):
TTATTATAATATTAAAAATATA
Found at i:78593 original size:2 final size:2
Alignment explanation
Indices: 78586--78650 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
78576 TTTGTAACCA
78586 AT AT AT AT -T 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
78627 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
78651 GATGACGGCT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:78795 original size:30 final size:29
Alignment explanation
Indices: 78759--78853 Score: 120
Period size: 30 Copynumber: 3.2 Consensus size: 29
78749 GGGTGAGATT
78759 GGTCGCCATGCAGTCGGAGCGAAGCTTGAA
1 GGTCGCCATGCAGTCGG-GCGAAGCTTGAA
* * *
78789 GGTCGCCATGCACTCAGGGCGAAGATTGTA
1 GGTCGCCATGCAGTC-GGGCGAAGCTTGAA
*
78819 TGTCGCCATGCAGTCGGGGCGAA-CTTGAA
1 GGTCGCCATGCAGTC-GGGCGAAGCTTGAA
78848 GGTCGC
1 GGTCGC
78854 TACTTGAAGG
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
29 9 0.16
30 44 0.80
31 2 0.04
ACGTcount: A:0.21, C:0.24, G:0.36, T:0.19
Consensus pattern (29 bp):
GGTCGCCATGCAGTCGGGCGAAGCTTGAA
Found at i:78860 original size:14 final size:14
Alignment explanation
Indices: 78841--78867 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
78831 GTCGGGGCGA
78841 ACTTGAAGGTCGCT
1 ACTTGAAGGTCGCT
78855 ACTTGAAGGTCGC
1 ACTTGAAGGTCGC
78868 CATGCAGTCG
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:0.22, G:0.30, T:0.26
Consensus pattern (14 bp):
ACTTGAAGGTCGCT
Found at i:79052 original size:34 final size:34
Alignment explanation
Indices: 79003--79082 Score: 133
Period size: 34 Copynumber: 2.3 Consensus size: 34
78993 AATTCAGCAC
*
79003 TAATTAAAGTAAAATTTGGGCATTATTTGCACCAA
1 TAATT-AACTAAAATTTGGGCATTATTTGCACCAA
*
79038 TAATTAACTAAAATTTTGGCATTATTTGCACCAA
1 TAATTAACTAAAATTTGGGCATTATTTGCACCAA
79072 TAATTAACTAA
1 TAATTAACTAA
79083 GTTCCAGACT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
34 38 0.88
35 5 0.12
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.36
Consensus pattern (34 bp):
TAATTAACTAAAATTTGGGCATTATTTGCACCAA
Found at i:79513 original size:11 final size:11
Alignment explanation
Indices: 79492--79537 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 11
79482 AAGAAAGGGA
79492 GAAGAAGGAAAG
1 GAAGAA-GAAAG
79504 GAAGAAGAAAGG
1 GAAGAAGAAA-G
79516 AAGAAGAAGAAAG
1 --GAAGAAGAAAG
79529 GAAGAAGAA
1 GAAGAAGAA
79538 GACCGGGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 13 0.42
12 7 0.23
13 1 0.03
14 10 0.32
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (11 bp):
GAAGAAGAAAG
Found at i:79523 original size:14 final size:14
Alignment explanation
Indices: 79477--79539 Score: 78
Period size: 14 Copynumber: 4.6 Consensus size: 14
79467 GTACGGTTAT
*
79477 GAAGAAAGAAAGGGA
1 GAAG-AAGAAAGGAA
79492 GAAGAAGGAAA-G--
1 GAAGAA-GAAAGGAA
79504 GAAGAAGAAAGGAA
1 GAAGAAGAAAGGAA
79518 GAAGAAGAAAGGAA
1 GAAGAAGAAAGGAA
79532 GAAGAAGA
1 GAAGAAGA
79540 CCGGGTAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.09
12 7 0.16
14 25 0.57
15 8 0.18
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (14 bp):
GAAGAAGAAAGGAA
Found at i:80954 original size:14 final size:13
Alignment explanation
Indices: 80931--80964 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
80921 ATTCTCTATT
80931 TTAATATAAAATA
1 TTAATATAAAATA
80944 TTAATTATAAAATA
1 TTAA-TATAAAATA
*
80958 TTTATAT
1 TTAATAT
80965 TTATTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TTAATATAAAATA
Found at i:80970 original size:20 final size:19
Alignment explanation
Indices: 80941--80978 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
80931 TTAATATAAA
80941 ATATTAATTATAAAATATTT
1 ATATTAATTA-AAAATATTT
*
80961 ATATTTATTAAAAATATT
1 ATATTAATTAAAAATATT
80979 GAACAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATTAATTAAAAATATTT
Found at i:82198 original size:17 final size:15
Alignment explanation
Indices: 82176--82215 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
82166 GTTGCAAATG
82176 TTAAATATTATTAAAA
1 TTAAATATTA-TAAAA
*
82192 CTTAAATATTATAATA
1 -TTAAATATTATAAAA
82208 TTAAATAT
1 TTAAATAT
82216 GCATGTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATTATAAAA
Found at i:85745 original size:18 final size:15
Alignment explanation
Indices: 85707--85760 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
85697 TTTACCCGGT
*
85707 CTTCTTCTCCCTCCTTT
1 CTTCTTCTCCCT--TTC
*
85724 CTTCTTCTTCCTTTC
1 CTTCTTCTCCCTTTC
85739 CTTCTTCTCCCTTTC
1 CTTCTTCTCCCTTTC
85754 CTTCTTC
1 CTTCTTC
85761 ATAACCGTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 23 0.68
17 11 0.32
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (15 bp):
CTTCTTCTCCCTTTC
Found at i:86193 original size:34 final size:34
Alignment explanation
Indices: 86153--86233 Score: 135
Period size: 34 Copynumber: 2.4 Consensus size: 34
86143 ACGTCTGGAA
*
86153 TTTAGTTAATTATTGGTGTAAATAATGCCAAAAT
1 TTTAGTTAATTATTGGTGCAAATAATGCCAAAAT
86187 TTTAGTTAATTATTGGTGCAAATAATGCCAAAAT
1 TTTAGTTAATTATTGGTGCAAATAATGCCAAAAT
*
86221 TTTACTTTAATTA
1 TTTA-GTTAATTA
86234 GTGCTGAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 37 0.84
35 7 0.16
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.43
Consensus pattern (34 bp):
TTTAGTTAATTATTGGTGCAAATAATGCCAAAAT
Found at i:86430 original size:29 final size:29
Alignment explanation
Indices: 86353--86490 Score: 145
Period size: 29 Copynumber: 4.8 Consensus size: 29
86343 ACCTATAAGG
86353 TCGCCCCGACTGCATGGCGACCTTCAAG-
1 TCGCCCCGACTGCATGGCGACCTTCAAGT
*** **
86381 TAATCTGGACTGCATGGCGACCTTCAAGT
1 TCGCCCCGACTGCATGGCGACCTTCAAGT
* * * *
86410 TCGCCTCGACTGCATGGCGACATACAATCT
1 TCGCCCCGACTGCATGGCGACCTTCAA-GT
*
86440 TCG-CCCGAGTGCATGGCGACCTTCAAGCT
1 TCGCCCCGACTGCATGGCGACCTTCAAG-T
*
86469 TCGCCCCGACTGCATGTCGACC
1 TCGCCCCGACTGCATGGCGACC
86491 AATCTTACTC
Statistics
Matches: 87, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
28 23 0.26
29 44 0.51
30 20 0.23
ACGTcount: A:0.20, C:0.35, G:0.24, T:0.22
Consensus pattern (29 bp):
TCGCCCCGACTGCATGGCGACCTTCAAGT
Found at i:87171 original size:40 final size:40
Alignment explanation
Indices: 87123--87200 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
87113 TTAACATGAA
87123 GGATAAAAGAATTATTTCTATTCTTTGAGGTCTTAAATCC
1 GGATAAAAGAATTATTTCTATTCTTTGAGGTCTTAAATCC
*
87163 GGATAAAAGAATTATTTCTATTCTTTGGGGTCTTAAAT
1 GGATAAAAGAATTATTTCTATTCTTTGAGGTCTTAAAT
87201 TCGAATGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (40 bp):
GGATAAAAGAATTATTTCTATTCTTTGAGGTCTTAAATCC
Found at i:87664 original size:35 final size:35
Alignment explanation
Indices: 87618--87713 Score: 140
Period size: 35 Copynumber: 2.7 Consensus size: 35
87608 AACATAATCA
* *
87618 TCAATTACATTCTAAACCCCAAATTCTAAAATGCT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
*
87653 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
*
87688 TCAATTACATGTC-CAACCCCAAATTC
1 TCAATTACAT-TCTAAACCCCAAATTC
87714 ATAATACATT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 53 0.96
36 2 0.04
ACGTcount: A:0.40, C:0.28, G:0.02, T:0.30
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATACT
Found at i:88154 original size:147 final size:147
Alignment explanation
Indices: 87879--88166 Score: 490
Period size: 147 Copynumber: 2.0 Consensus size: 147
87869 TACACAATTC
* *
87879 AGTTTATAAAATAGTTGACTCAAAATTTTTTTTATTTGAGTTTATAAAATTTAAATTAAGTCGAA
1 AGTTTATAAAATAGTTGACTCAAAATTTTTTTGATTTGAGTTTATAAAATTTAAATCAAGTCGAA
* *
87944 TTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATATAATATTATT
66 TTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATATATAATATTATT
88009 TGATTCTAATTCAGTTT
131 TGATTCTAATTCAGTTT
*
88026 AGTTTATAAAATAGTTGACTC-GAATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAA-TCGA
1 AGTTTATAAAATAGTTGACTCAAAATTTTTTT-GATTTGAGTTTATAAAATTTAAATCAAGTCGA
*
88089 ATTGAATTGAATTTTTGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATATTA
65 ATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATA-TATAATATTA
88154 TTTGATTCTAATT
129 TTTGATTCTAATT
88167 TAAATAGTTT
Statistics
Matches: 133, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
146 64 0.48
147 69 0.52
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (147 bp):
AGTTTATAAAATAGTTGACTCAAAATTTTTTTGATTTGAGTTTATAAAATTTAAATCAAGTCGAA
TTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATATATAATATTATT
TGATTCTAATTCAGTTT
Found at i:88175 original size:146 final size:147
Alignment explanation
Indices: 87879--88176 Score: 476
Period size: 146 Copynumber: 2.0 Consensus size: 147
87869 TACACAATTC
* *
87879 AGTTTATAAAATAGTTGACTCAAAATTTTTTTTATTTGAGTTTATAAAATTTAAATTAAGTCGAA
1 AGTTTATAAAATAGTTGACTCAAAATTTTTTTGATTTGAGTTTATAAAATTTAAATCAAGTCGAA
* *
87944 TTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATATAATATTATT
66 TTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATATATAATATTATT
**
88009 TGATTCTAATTCAGTTT
131 TGATTCTAATTCAGAAT
*
88026 AGTTTATAAAATAGTTGACTC-GAATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAA-TCGA
1 AGTTTATAAAATAGTTGACTCAAAATTTTTTT-GATTTGAGTTTATAAAATTTAAATCAAGTCGA
*
88089 ATTGAATTGAATTTTTGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATATTA
65 ATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATA-TATAATATTA
*
88154 TTTGATTCTAATTTA-AAT
129 TTTGATTCTAATTCAGAAT
88172 AGTTT
1 AGTTT
88177 TTTAACCATA
Statistics
Matches: 140, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
146 70 0.50
147 70 0.50
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (147 bp):
AGTTTATAAAATAGTTGACTCAAAATTTTTTTGATTTGAGTTTATAAAATTTAAATCAAGTCGAA
TTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATATATAATATTATT
TGATTCTAATTCAGAAT
Found at i:88745 original size:35 final size:35
Alignment explanation
Indices: 88706--88779 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
88696 TTGGGTATTA
*
88706 AATTGAAGTATTTTGGAATTT-GAGGTTTAGAATGT
1 AATTGAAGTATTTTGAAATTTAGA-GTTTAGAATGT
88741 AATTGAAGTATTTTGAAATTTAGAGTTTAGAATGT
1 AATTGAAGTATTTTGAAATTTAGAGTTTAGAATGT
88776 AATT
1 AATT
88780 TATGACTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
35 35 0.95
36 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (35 bp):
AATTGAAGTATTTTGAAATTTAGAGTTTAGAATGT
Found at i:100497 original size:27 final size:27
Alignment explanation
Indices: 100445--100500 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
100435 ACCTGACTTG
* **
100445 AAAATTATATATCTTCCACATGACTCC
1 AAAAATATATATCTTCCACACAACTCC
*
100472 AAAAATATATATCTTCCACCCAACTCC
1 AAAAATATATATCTTCCACACAACTCC
100499 AA
1 AA
100501 TTTAAATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.29, G:0.02, T:0.29
Consensus pattern (27 bp):
AAAAATATATATCTTCCACACAACTCC
Found at i:101690 original size:2 final size:2
Alignment explanation
Indices: 101683--101729 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
101673 TGAAGGATTG
101683 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
101725 AT AT A
1 AT AT A
101730 ATTAAGAAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:104705 original size:15 final size:15
Alignment explanation
Indices: 104680--104751 Score: 101
Period size: 15 Copynumber: 4.9 Consensus size: 15
104670 TGGTTTTCCA
104680 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
104695 GAATTTGAATTACTG
1 GAAAATGAATTACTG
104710 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
104725 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
104739 GAAAATGAATTAC
1 GAAAATGAATTAC
104752 ATTTCTGTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.25
15 36 0.75
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:104749 original size:29 final size:30
Alignment explanation
Indices: 104680--104751 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
104670 TGGTTTTCCA
104680 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
104710 GAAAATGAATTACTGGAATTTGAATT-CTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
104739 GAAAATGAATTAC
1 GAAAATGAATTAC
104752 ATTTCTGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (30 bp):
GAAAATGAATTACTGGAATTTGAATTACTG
Found at i:104757 original size:20 final size:20
Alignment explanation
Indices: 104734--104803 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
104724 GGAATTTGAA
104734 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
104754 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
104774 TTCTGAAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
104794 TTCTGGAAAA
1 TTCTGGAAAA
104804 CATCTGGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:105035 original size:31 final size:28
Alignment explanation
Indices: 104969--105072 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 28
104959 ATTTACTAAA
*
104969 ATATTATTGAAATATATAAATAATATTAT
1 ATATTATT-AAATATATAAAAAATATTAT
104998 -TCATTATTAAATATATAAAAAAATTTATTAT
1 AT-ATTATTAAATATAT-AAAAAA--TATTAT
105029 ATATTATTAAA-ATA-AAATATAATATCT-T
1 ATATTATTAAATATATAAA-A-AATAT-TAT
105057 ATATTATTATAATATA
1 ATATTATTA-AATATA
105073 ATTGATTATT
Statistics
Matches: 64, Mismatches: 1, Indels: 19
0.76 0.01 0.23
Matches are distributed among these distances:
28 25 0.39
29 15 0.23
30 8 0.12
31 15 0.23
32 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (28 bp):
ATATTATTAAATATATAAAAAATATTAT
Found at i:105086 original size:28 final size:28
Alignment explanation
Indices: 105022--105116 Score: 75
Period size: 28 Copynumber: 3.2 Consensus size: 28
105012 ATAAAAAAAT
*
105022 TTATTATATATTATTAAAATAAAATATA
1 TTATTTTATATTATTAAAATAAAATATA
* * * *
105050 ATATCTTATATTATTATAATATAAT-TGA
1 TTATTTTATATTATTAAAATAAAATAT-A
105078 TTATTTTATATAATATTAAAAATATAATATTATA
1 TTATTTTATAT--TATT-AAAATA-AA-A-TATA
105112 TTATT
1 TTATT
105117 ATAAATATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
27 1 0.02
28 30 0.60
30 4 0.08
31 5 0.10
32 1 0.02
33 1 0.02
34 7 0.14
35 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
TTATTTTATATTATTAAAATAAAATATA
Found at i:105111 original size:22 final size:23
Alignment explanation
Indices: 105086--105129 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
105076 GATTATTTTA
105086 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
105108 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
105130 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:105134 original size:22 final size:22
Alignment explanation
Indices: 105090--105146 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
105080 ATTTTATATA
* *
105090 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
105111 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
105133 ATATTTTAAATATT
1 ATATTATAAATATT
105147 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:105145 original size:52 final size:50
Alignment explanation
Indices: 105027--105146 Score: 122
Period size: 54 Copynumber: 2.3 Consensus size: 50
105017 AAAATTTATT
**
105027 ATATATTATTAAA-A-TAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAATATAATA-CTTATATTATTATAATATAATAA
105077 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATT-AAAATATAATACTTATATTATTAT-AATA-TAATAA
105131 ATATATTTTAAATATT
1 ATATATTTTAAATATT
105147 TTAATAATTA
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
49 3 0.05
50 6 0.10
51 2 0.03
52 19 0.32
53 7 0.12
54 20 0.34
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (50 bp):
ATATATTTTAAATATTAAAATATAATACTTATATTATTATAATATAATAA
Found at i:105394 original size:42 final size:42
Alignment explanation
Indices: 105335--105454 Score: 204
Period size: 42 Copynumber: 2.9 Consensus size: 42
105325 ATTAATTACA
* *
105335 TTCCGTAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
105377 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
105419 TTCCGGAAAACGAATTACATGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
105455 TTCGGGAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:105931 original size:60 final size:60
Alignment explanation
Indices: 105859--106005 Score: 179
Period size: 60 Copynumber: 2.5 Consensus size: 60
105849 ATTACATTAA
* * * * * *
105859 ACATCCTCAAACTATGACTCTCATTCTAAAT-TAGTTCTTAAACTTTTGAATATTCTAATT
1 ACATCCTTAAACTATGACTCTCATTCTAAATCT-GTCCCTAAACTTCTGAACATTCCAATT
* *
105919 TCATCCTTAAACTATGACTCTCATTCTAAATCTGTCCCTAAACTTCTGAGCATTCCAATT
1 ACATCCTTAAACTATGACTCTCATTCTAAATCTGTCCCTAAACTTCTGAACATTCCAATT
* * *
105979 ACACCCCTAAACTATGACCCTCATTCT
1 ACATCCTTAAACTATGACTCTCATTCT
106006 GTATTAAGTC
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 73 0.99
61 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (60 bp):
ACATCCTTAAACTATGACTCTCATTCTAAATCTGTCCCTAAACTTCTGAACATTCCAATT
Found at i:106356 original size:60 final size:59
Alignment explanation
Indices: 106224--106385 Score: 159
Period size: 60 Copynumber: 2.7 Consensus size: 59
106214 GATGCTATTG
* * * * * *
106224 GAATATTCAAAAGTTAT-AGGACTAGTTTGAAATG-AAGATAATAGTTTAGGGATAAATTA
1 GAATATTCAAAAGTT-TGAGGACCAATTTAAAATGAAAG-TCATAATTTAGAGATAAATTA
* * * *
106283 GAATATTCAAAAGTTT-AGGGATCAATTTAGATTGAGAGTCATAATTTAGAGATGAAATTA
1 GAATATTCAAAAGTTTGA-GGACCAATTTAAAATGAAAGTCATAATTTAGAGAT-AAATTA
* *
106343 GAATGTTTAAAAGTTTGAGGACCAATTTAAAATGAAAGTCATA
1 GAATATTCAAAAGTTTGAGGACCAATTTAAAATGAAAGTCATA
106386 GTTTGAAGAT
Statistics
Matches: 83, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
58 2 0.02
59 37 0.45
60 43 0.52
61 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (59 bp):
GAATATTCAAAAGTTTGAGGACCAATTTAAAATGAAAGTCATAATTTAGAGATAAATTA
Found at i:107307 original size:31 final size:31
Alignment explanation
Indices: 107271--107344 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
107261 AAACTACTTA
*
107271 TTTAGTATCTAAACTATTAATTTTGATTTAT
1 TTTAGTATCTAAACTATCAATTTTGATTTAT
* * *
107302 TTTAGTATTTAAATTATCAGTTTTGATTTAT
1 TTTAGTATCTAAACTATCAATTTTGATTTAT
107333 TTTAGTATCTAA
1 TTTAGTATCTAA
107345 TTTTGTAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.55
Consensus pattern (31 bp):
TTTAGTATCTAAACTATCAATTTTGATTTAT
Found at i:107416 original size:14 final size:14
Alignment explanation
Indices: 107394--107426 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
107384 CATTTTAATA
*
107394 CTTACTGTTAAAAC
1 CTTAATGTTAAAAC
107408 CTTAATGTTAAAAC
1 CTTAATGTTAAAAC
107422 CTTAA
1 CTTAA
107427 CTCGTTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.36
Consensus pattern (14 bp):
CTTAATGTTAAAAC
Found at i:108915 original size:20 final size:20
Alignment explanation
Indices: 108890--108929 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
108880 GTTAAGGCCC
*
108890 CTAATTTTTTCAATCTCACT
1 CTAATTTTTCCAATCTCACT
*
108910 CTAATTTTTCCAGTCTCACT
1 CTAATTTTTCCAATCTCACT
108930 TTTTAGCTTT
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:0.23, C:0.28, G:0.03, T:0.47
Consensus pattern (20 bp):
CTAATTTTTCCAATCTCACT
Found at i:109020 original size:43 final size:41
Alignment explanation
Indices: 108910--109301 Score: 299
Period size: 42 Copynumber: 9.2 Consensus size: 41
108900 CAATCTCACT
* *
108910 CTAATTTTTCCAGTCTCACTTTTTAGC-TTTATAATTGAAGCC
1 CTAATTTTT-CAATCTCACTTTTTA-CATTTATAATTGAGGCC
* *
108952 CTTAATTTTTTTCAATTTCACTTTTTACATTTATAATCGAGGCTC
1 C-TAA--TTTTTCAATCTCACTTTTTACATTTATAATTGAGGC-C
108997 CTGAATTTTTCAATCTCACTTTTTACATTTATAATTGAGGTCC
1 CT-AATTTTTCAATCTCACTTTTTACATTTATAATTGAGG-CC
* * * * * *
109040 CAAAATTTTCTATCTCACTTTCTACTTTTATAATTGAAGCC
1 CTAATTTTTCAATCTCACTTTTTACATTTATAATTGAGGCC
* * * * *
109081 TCTATTGTTTTAATATCTC-C-TTTTACCTTTATAATCGAGGTTC
1 -CTAAT-TTTTCA-ATCTCACTTTTTACATTTATAATTGAGG-CC
* * *
109124 CTAATTTTTTCAAT-TCCACCTTTTACCTTTATAATTGAAGCC
1 CTAA-TTTTTCAATCT-CACTTTTTACATTTATAATTGAGGCC
* * * *
109166 TCTAATTTTTTTTAATCTAACATTTTACACTTATAATTGAGGCC
1 -CTAA--TTTTTCAATCTCACTTTTTACATTTATAATTGAGGCC
* *
109210 CTTAATTTTTCAAACTCACTTTTTACCTTTATAATTGAGGTCC
1 C-TAATTTTTCAATCTCACTTTTTACATTTATAATTGAGG-CC
** ** *
109253 CTAATTTTTTCAATCAAACTTTTT-TTTTTATAATTTAGGACC
1 CTAA-TTTTTCAATCTCACTTTTTACATTTATAATTGAGG-CC
109295 CTAATTT
1 CTAATTT
109302 AATAATTTTT
Statistics
Matches: 283, Mismatches: 46, Indels: 43
0.76 0.12 0.12
Matches are distributed among these distances:
40 1 0.00
41 8 0.03
42 111 0.39
43 88 0.31
44 65 0.23
45 10 0.04
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (41 bp):
CTAATTTTTCAATCTCACTTTTTACATTTATAATTGAGGCC
Found at i:109070 original size:129 final size:128
Alignment explanation
Indices: 108923--109276 Score: 352
Period size: 129 Copynumber: 2.7 Consensus size: 128
108913 ATTTTTCCAG
* *
108923 TCTCACTTTTTAGCTTTATAATTGAAGCCCTTAATTTTTTTCAATTTCACTTTTTACATTTATAA
1 TCTCAC-TTTTA-CTTTATAATTGAAGCCCTTAATTTTTTTCAATATCACTTTTTACCTTTATAA
*
108988 TCGAGGCTCCTGAA-TTTTTCAATCTCACTTTTTACATTTATAATTGAGGTCC-C-AAAATTTTC
64 TCGAGG-TCCT-AATTTTTTCAATCTCACTTTTTACATTTATAATTGAAG-CCTCTAAAATTTTC
109050 T-A
126 TAA
* * *
109052 TCTCACTTTCTACTTTTATAATTGAAG-CCTCT-ATTGTTTT-AATATCTCCTTTTACCTTTATA
1 TCTCACTTT-TAC-TTTATAATTGAAGCCCT-TAATTTTTTTCAATATCACTTTTTACCTTTATA
* * ** *
109114 ATCGAGGTTCCTAATTTTTTCAAT-TCCACCTTTTACCTTTATAATTGAAGCCTCTAATTTTTTT
63 ATCGAGG-TCCTAATTTTTTCAATCT-CACTTTTTACATTTATAATTGAAGCCTCTAAAATTTTC
109178 TAA
126 TAA
* * *
109181 TCTAACATTTTACACTTATAATTGAGGCCCTTAA--TTTTTCAA-ACTCACTTTTTACCTTTATA
1 TCTCAC-TTTTAC-TTTATAATTGAAGCCCTTAATTTTTTTCAATA-TCACTTTTTACCTTTATA
* **
109243 ATTGAGGTCCCTAATTTTTTCAATCAAACTTTTT
63 ATCGAGGT-CCTAATTTTTTCAATCTCACTTTTT
109277 TTTTTATAAT
Statistics
Matches: 187, Mismatches: 23, Indels: 30
0.78 0.10 0.12
Matches are distributed among these distances:
126 5 0.03
127 60 0.32
128 27 0.14
129 88 0.47
130 7 0.04
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (128 bp):
TCTCACTTTTACTTTATAATTGAAGCCCTTAATTTTTTTCAATATCACTTTTTACCTTTATAATC
GAGGTCCTAATTTTTTCAATCTCACTTTTTACATTTATAATTGAAGCCTCTAAAATTTTCTAA
Found at i:109104 original size:85 final size:83
Alignment explanation
Indices: 108959--109247 Score: 248
Period size: 85 Copynumber: 3.4 Consensus size: 83
108949 GCCCTTAATT
* * * * *
108959 TTTTTCAATTTCACTTTTTACATTTATAATCG-AGGCTCCTGAA-T-TTTTCAATCTCACTTTTT
1 TTTTTCAATCTCAC-TTTTACCTTTATAATTGAAGCCT-CT-AATTGTTTTAAATCTC-C-TTTT
109021 ACATTTATAATTGAGGTCCCAAA
61 ACATTTATAATTGAGGTCCCAAA
* * * *
109044 ATTTTCTATCTCACTTTCTACTTTTATAATTGAAGCCTCT-ATTGTTTTAATATCTCCTTTTACC
1 TTTTTCAATCTCACTTT-TACCTTTATAATTGAAGCCTCTAATTGTTTTAA-ATCTCCTTTTACA
* * *
109108 TTTATAATCGAGGTTCCTAAT
64 TTTATAATTGAGG-TCCCAAA
* * *
109129 TTTTTCAAT-TCCACCTTTTACCTTTATAATTGAAGCCTCTAATTTTTTTTAATCTAACATTTTA
1 TTTTTCAATCT-CA-CTTTTACCTTTATAATTGAAGCCTCTAATTGTTTTAAATCT--CCTTTTA
* *
109193 CACTTATAATTGAGG-CCCTTAA
62 CATTTATAATTGAGGTCCC-AAA
*
109215 TTTTTCAAACTCACTTTTTACCTTTATAATTGA
1 TTTTTCAATCTCAC-TTTTACCTTTATAATTGA
109248 GGTCCCTAAT
Statistics
Matches: 166, Mismatches: 24, Indels: 27
0.76 0.11 0.12
Matches are distributed among these distances:
83 1 0.01
84 23 0.14
85 73 0.44
86 50 0.30
87 19 0.11
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (83 bp):
TTTTTCAATCTCACTTTTACCTTTATAATTGAAGCCTCTAATTGTTTTAAATCTCCTTTTACATT
TATAATTGAGGTCCCAAA
Found at i:109155 original size:127 final size:129
Alignment explanation
Indices: 108923--109161 Score: 319
Period size: 127 Copynumber: 1.9 Consensus size: 129
108913 ATTTTTCCAG
* * * *
108923 TCTCACTTTTTAGCTTTATAATTGAAGCCCTTAATTTTTTTCAATTTCACTTTTTACATTTATAA
1 TCTCACTTTCTAGCTTTATAATTGAAGCCCTTAATTGTTTTCAATATCACCTTTTACATTTATAA
*
108988 TCGAGGCTCCTGAATTTTTCAATCTCACTTTTTACATTTATAATTGAGGTCCCAAAATTTTCTA
66 TCGAGGCTCCTGAATTTTTCAATCTCACCTTTTACATTTATAATTGAGGTCCCAAAATTTTCTA
* *
109052 TCTCACTTTCTA-CTTTTATAATTGAAG-CCTCT-ATTGTTTT-AATATCTCCTTTTACCTTTAT
1 TCTCACTTTCTAGC-TTTATAATTGAAGCCCT-TAATTGTTTTCAATATCACCTTTTACATTTAT
* *
109113 AATCGAGGTTCCT-AATTTTTTCAAT-TCCACCTTTTACCTTTATAATTGA
64 AATCGAGGCTCCTGAA-TTTTTCAATCT-CACCTTTTACATTTATAATTGA
109162 AGCCTCTAAT
Statistics
Matches: 97, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
126 3 0.03
127 58 0.60
128 11 0.11
129 25 0.26
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (129 bp):
TCTCACTTTCTAGCTTTATAATTGAAGCCCTTAATTGTTTTCAATATCACCTTTTACATTTATAA
TCGAGGCTCCTGAATTTTTCAATCTCACCTTTTACATTTATAATTGAGGTCCCAAAATTTTCTA
Found at i:111534 original size:2 final size:2
Alignment explanation
Indices: 111527--111562 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
111517 CTAATGTTTA
111527 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
111563 TGATTTTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:117949 original size:60 final size:60
Alignment explanation
Indices: 117862--118013 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
117852 TTAAATTGGT
* * **
117862 TCCT-AAATTTTTAAACATTTCAATTTCATCCTTAAACAATGA-CTATCATTCAAAATTAG
1 TCCTCAAACTTTTGAACATTTCAATTTCATCCCCAAACAATGATCT-TCATTCAAAATTAG
* * *
117921 TCCTCAAACTTTTGAACATTTCATTTTCATCCCCAAACTATGATCTTCATTCTAAATTAG
1 TCCTCAAACTTTTGAACATTTCAATTTCATCCCCAAACAATGATCTTCATTCAAAATTAG
* * *
117981 TCC-CTAAACTTTTTGAATATTTTAATTTTATCC
1 TCCTC-AAAC-TTTTGAACATTTCAATTTCATCC
118014 TAAATTATAC
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 5 0.06
60 52 0.67
61 21 0.27
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (60 bp):
TCCTCAAACTTTTGAACATTTCAATTTCATCCCCAAACAATGATCTTCATTCAAAATTAG
Found at i:118212 original size:60 final size:60
Alignment explanation
Indices: 118139--118321 Score: 160
Period size: 60 Copynumber: 3.1 Consensus size: 60
118129 ATTTGGATAA
* * * * *
118139 TTTGGGGATGAAATTGGAAGAC-CTAAAAGTTCAGGGA-TCAATTTAGAATGAGATTTATAG
1 TTTGAGGATGAAATTGGAAGACTC-AAAAGTTCAAGGACT-AATTTAGAATGAGAGTCAAAG
* * * *
118199 TTTGTGGATGAAATTGGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCAAAG
1 TTTGAGGATGAAATTGGAAGACTCAAAAGTTCAAGGACTAATTTAGAATGAGAGTCAAAG
* * * * * *
118259 TTTGAGGATG-AATTGAAATG-TTTAAAAG-TCTAAGGACTAATTTAAAATGGGAGTCATAG
1 TTTGAGGATGAAATTGGAA-GACTCAAAAGTTC-AAGGACTAATTTAGAATGAGAGTCAAAG
118318 TTTG
1 TTTG
118322 GTGACATATG
Statistics
Matches: 103, Mismatches: 16, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
58 1 0.01
59 43 0.42
60 57 0.55
61 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (60 bp):
TTTGAGGATGAAATTGGAAGACTCAAAAGTTCAAGGACTAATTTAGAATGAGAGTCAAAG
Found at i:118302 original size:59 final size:60
Alignment explanation
Indices: 118178--118321 Score: 191
Period size: 59 Copynumber: 2.4 Consensus size: 60
118168 TTCAGGGATC
* * * * *
118178 AATTTAGAATGAGATTTATAGTTTGTGGATGAAATTGGAATATTCAAAAGTTTAAGGACT
1 AATTTAGAATGAGAGTCATAGTTTGAGGATGAAATTGAAATATTCAAAAGTCTAAGGACT
* * *
118238 AATTTAGAATGAGAGTCAAAGTTTGAGGATG-AATTGAAATGTTTAAAAGTCTAAGGACT
1 AATTTAGAATGAGAGTCATAGTTTGAGGATGAAATTGAAATATTCAAAAGTCTAAGGACT
* *
118297 AATTTAAAATGGGAGTCATAGTTTG
1 AATTTAGAATGAGAGTCATAGTTTG
118322 GTGACATATG
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 46 0.63
60 27 0.37
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (60 bp):
AATTTAGAATGAGAGTCATAGTTTGAGGATGAAATTGAAATATTCAAAAGTCTAAGGACT
Found at i:123235 original size:14 final size:14
Alignment explanation
Indices: 123218--123283 Score: 73
Period size: 14 Copynumber: 4.6 Consensus size: 14
123208 ACTTAAACCA
*
123218 TAAACTCTAAATCT
1 TAAACTCTAAATTT
123232 TAAA-TCTTAAATTT
1 TAAACTC-TAAATTT
123246 TAAACTCTAAATTT
1 TAAACTCTAAATTT
*
123260 TAAA-TCCTAAACTT
1 TAAACT-CTAAATTT
123274 TAAACCTCTA
1 TAAA-CTCTA
123284 TCCGACTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 3 0.07
14 36 0.80
15 5 0.11
16 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAACTCTAAATTT
Found at i:123242 original size:21 final size:21
Alignment explanation
Indices: 123224--123277 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
123214 ACCATAAACT
*
123224 CTAAA-TCTTAAATCTTAAATT
1 CTAAACTC-TAAATCTTAAATC
* *
123245 TTAAACTCTAAATTTTAAATC
1 CTAAACTCTAAATCTTAAATC
*
123266 CTAAACTTTAAA
1 CTAAACTCTAAA
123278 CCTCTATCCG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (21 bp):
CTAAACTCTAAATCTTAAATC
Found at i:123249 original size:28 final size:28
Alignment explanation
Indices: 123218--123283 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
123208 ACTTAAACCA
* *
123218 TAAACTCTAAATCTTAAATCTTAAATTT
1 TAAACTCTAAATCTTAAATCCTAAACTT
*
123246 TAAACTCTAAATTTTAAATCCTAAACTT
1 TAAACTCTAAATCTTAAATCCTAAACTT
123274 TAAACCTCTA
1 TAAA-CTCTA
123284 TCCGACTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 29 0.85
29 5 0.15
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (28 bp):
TAAACTCTAAATCTTAAATCCTAAACTT
Found at i:125252 original size:35 final size:35
Alignment explanation
Indices: 125198--125269 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
125188 TAAGAAATAA
*
125198 ATTTACGGGCTCTGCTTTTAATTTAATATATTAAT
1 ATTTACGGGCCCTGCTTTTAATTTAATATATTAAT
* * *
125233 ATTTATGGGCCCTGGTTTTAATTTAGTATATTAAT
1 ATTTACGGGCCCTGCTTTTAATTTAATATATTAAT
125268 AT
1 AT
125270 AATTTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.49
Consensus pattern (35 bp):
ATTTACGGGCCCTGCTTTTAATTTAATATATTAAT
Found at i:125818 original size:3 final size:3
Alignment explanation
Indices: 125810--125846 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
125800 GCCATGTCAT
125810 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
125847 TTTTTAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:133731 original size:3 final size:3
Alignment explanation
Indices: 133725--133837 Score: 181
Period size: 3 Copynumber: 37.7 Consensus size: 3
133715 TTTTTATCCA
* *
133725 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
133773 TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
133821 CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
133838 AATATATTAA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 102 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:133854 original size:13 final size:13
Alignment explanation
Indices: 133836--133871 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
133826 TTATTATTAT
133836 TAAATATATTAAA
1 TAAATATATTAAA
*
133849 TAAATATATAAAA
1 TAAATATATTAAA
133862 TAAATA-ATTA
1 TAAATATATTA
133872 CAGACCAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 3 0.14
13 18 0.86
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAATATATTAAA
Found at i:135070 original size:22 final size:21
Alignment explanation
Indices: 135031--135073 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
135021 AGTATTTTTC
**
135031 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
135052 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
135074 ATATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:137440 original size:14 final size:14
Alignment explanation
Indices: 137402--137455 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
137392 ATTTTAAATA
*
137402 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
137416 TTTTACATTTGCAT
1 ATTTACATTTGCAT
137430 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
137445 CTTTGCATTTG
1 ATTTACATTTG
137456 TACTGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:143198 original size:94 final size:94
Alignment explanation
Indices: 143037--143226 Score: 301
Period size: 94 Copynumber: 2.0 Consensus size: 94
143027 TAAGGAGACC
* *
143037 CAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACC
1 CAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAAACCACAAAACC
*
143102 AATCATTGAATTTGGAAGATAAATGTGCT
66 AATCATTGAATTTGAAAGATAAATGTGCT
*
143131 CAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATG-AACCCCAAAAAC
1 CAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAAACCAC-AAAAC
* * *
143195 CAATCATTGGATTTGAAAGATGAATTTGCT
65 CAATCATTGAATTTGAAAGATAAATGTGCT
143225 CA
1 CA
143227 TAGTAGAAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
93 5 0.06
94 83 0.94
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (94 bp):
CAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAAACCACAAAACC
AATCATTGAATTTGAAAGATAAATGTGCT
Found at i:145947 original size:22 final size:23
Alignment explanation
Indices: 145896--145949 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
145886 ATCTACACTC
*
145896 TTCAAAGATGATAGATTCTCTTT
1 TTCAAAGATGACAGATTCTCTTT
*
145919 TTAAAAGATGACAGATTCTC-TT
1 TTCAAAGATGACAGATTCTCTTT
145941 TTCAAAGAT
1 TTCAAAGAT
145950 AAAAACTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (23 bp):
TTCAAAGATGACAGATTCTCTTT
Found at i:146777 original size:113 final size:113
Alignment explanation
Indices: 146391--147481 Score: 1557
Period size: 113 Copynumber: 9.7 Consensus size: 113
146381 TACCAGTTCG
* *
146391 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * *
146456 AA-CTTTTCGCTTGAATTCATCATTCGAT-GATTCAG-TTTTCCAGAGGA
66 AACCTTTT-GCCTGAATTCATCATTTGATGGA-TCAGCTTTTCCAGAGAA
* * *
146503 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * *
146568 AACATTTTG-CTCAAATCTATCATTCGATGGATCAGCATTTCCAGAGTTAG
66 AACCTTTTGCCTGAATTC-ATCATTTGATGGATCAGCTTTTCCAGAG--AA
*
146618 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * *** * ** * **
146683 AACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAA
66 AACCTTTTGCCTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAA
*
146731 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * **
146796 AACCTTTTCCCTGAATTCATCACTTGATGAATTATTTTTTCCAGAGAA
66 AACCTTTTGCCTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAA
*
146844 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * *
146909 AACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAA
66 AACCTTTTGCCTGAATTCATC-ATTTGATGGATCAGCTTTTCCAGAGAA
* * *
146958 AGTTCACAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCACAATAAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * *
147023 AACC-TTTG-CTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAA
66 AACCTTTTGCCT-GAATTCATCATTTGATGGATCAGCTTTTCCAGAGAA
147070 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
147135 AACCTTTTACCTGAATTCATCATTTGATGGATCATCTTTTCCAGAGAA
66 AACCTTTTGCCTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAA
147183 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
147248 AACCTTTTACCTGAATTCATCATTTGATGGATCAACTTTTCCAGAGAA
66 AACCTTTTGCCTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAA
147296 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * *
147361 AACTTTTTACCTGAATTCATCAATTGATGGATTATCTTTTCCAGAG-A
66 AACCTTTTGCCTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAA
* * *
147408 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAATTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
147473 AACCTTTTG
66 AACCTTTTG
147482 AATGACTCTA
Statistics
Matches: 888, Mismatches: 80, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
111 5 0.01
112 239 0.27
113 458 0.52
114 91 0.10
115 90 0.10
116 5 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCCTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAA
Found at i:147802 original size:3 final size:3
Alignment explanation
Indices: 147796--147903 Score: 198
Period size: 3 Copynumber: 36.0 Consensus size: 3
147786 ATTTTTTTTT
147796 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
147844 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
147892 TTA TTA TTA TTA
1 TTA TTA TTA TTA
147904 AATATATATT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 101 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:147930 original size:14 final size:15
Alignment explanation
Indices: 147902--147936 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
147892 TTATTATTAT
147902 TAAATATATATTAAA
1 TAAATATATATTAAA
147917 TAAATATATA-TAAA
1 TAAATATATATTAAA
147931 TAAATA
1 TAAATA
147937 ATTACAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:148396 original size:22 final size:22
Alignment explanation
Indices: 148345--148386 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
148335 CCCCAACCTG
148345 AAAAAAAGGGAGAGACAGAAAA
1 AAAAAAAGGGAGAGACAGAAAA
148367 AAAAAAAGGGAGAGACAGAA
1 AAAAAAAGGGAGAGACAGAA
148387 TCGAAGAAAG
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:0.67, C:0.05, G:0.29, T:0.00
Consensus pattern (22 bp):
AAAAAAAGGGAGAGACAGAAAA
Found at i:151526 original size:18 final size:21
Alignment explanation
Indices: 151505--151543 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
151495 TTGTAAGGTA
151505 ATTT-TTTTA-ATAT-ATTAT
1 ATTTATTTTATATATGATTAT
151523 ATTTATTTTATATATGATTAT
1 ATTTATTTTATATATGATTAT
151544 TTGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 4 0.22
21 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (21 bp):
ATTTATTTTATATATGATTAT
Found at i:152650 original size:23 final size:24
Alignment explanation
Indices: 152622--152682 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
152612 AAGAACGAAC
*
152622 ATAAACGAACATAAATTAACAC-A
1 ATAAACGAACATAAATGAACACAA
* *
152645 ATAAACGAACGTTAATGAACACAA
1 ATAAACGAACATAAATGAACACAA
*
152669 ACAAACGAACATAA
1 ATAAACGAACATAA
152683 TAAATGAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
23 19 0.61
24 12 0.39
ACGTcount: A:0.59, C:0.18, G:0.08, T:0.15
Consensus pattern (24 bp):
ATAAACGAACATAAATGAACACAA
Found at i:152888 original size:14 final size:14
Alignment explanation
Indices: 152868--152901 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
152858 GATTGAGAAA
152868 AACATAAATGAACG
1 AACATAAATGAACG
*
152882 TACATAAATGAACG
1 AACATAAATGAACG
152896 AACATA
1 AACATA
152902 TTACCGAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.12, T:0.18
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:153576 original size:3 final size:3
Alignment explanation
Indices: 153568--153593 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
153558 TACATGAAAT
153568 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
153594 TAATATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:153725 original size:16 final size:18
Alignment explanation
Indices: 153696--153732 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
153686 ATAATAATAA
153696 TAAAATATTATTTAT-TT
1 TAAAATATTATTTATATT
*
153713 TAAATTATT-TTTATATT
1 TAAAATATTATTTATATT
153730 TAA
1 TAA
153733 TATGCCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TAAAATATTATTTATATT
Found at i:164344 original size:34 final size:34
Alignment explanation
Indices: 164301--164365 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
164291 AAGCTGAAAA
164301 ACTTAGTTTTCGAGAAAAACAATACATAAGCTAG
1 ACTTAGTTTTCGAGAAAAACAATACATAAGCTAG
* *
164335 ACTTTGTTTTCGAGAAAAAGAATACATAAGC
1 ACTTAGTTTTCGAGAAAAACAATACATAAGC
164366 AGATGGTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (34 bp):
ACTTAGTTTTCGAGAAAAACAATACATAAGCTAG
Found at i:167015 original size:23 final size:23
Alignment explanation
Indices: 166989--167039 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
166979 TTAAACGGAT
166989 ATGTTGGCAAATGTTAAATAAAC
1 ATGTTGGCAAATGTTAAATAAAC
* **
167012 ATGTTTGTGAATGTTAAATAAAC
1 ATGTTGGCAAATGTTAAATAAAC
167035 ATGTT
1 ATGTT
167040 TGCTAAACGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (23 bp):
ATGTTGGCAAATGTTAAATAAAC
Found at i:167040 original size:23 final size:23
Alignment explanation
Indices: 166998--167041 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
166988 TATGTTGGCA
166998 AATGTTAAATAAACATGTTTGTG
1 AATGTTAAATAAACATGTTTGTG
167021 AATGTTAAATAAACATGTTTG
1 AATGTTAAATAAACATGTTTG
167042 CTAAACGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.39
Consensus pattern (23 bp):
AATGTTAAATAAACATGTTTGTG
Found at i:167131 original size:23 final size:22
Alignment explanation
Indices: 167113--167163 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
167103 ACAAATATCA
167113 ATGTTGGCGAATGTTAAATGAAC
1 ATGTTGGCGAATGTTAAAT-AAC
* *
167136 ATGTTTGTGAATGTTAAATAAAC
1 ATGTTGGCGAATGTTAAAT-AAC
167159 ATGTT
1 ATGTT
167164 CGTTAAACGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (22 bp):
ATGTTGGCGAATGTTAAATAAC
Found at i:167216 original size:124 final size:124
Alignment explanation
Indices: 166989--167237 Score: 435
Period size: 124 Copynumber: 2.0 Consensus size: 124
166979 TTAAACGGAT
*
166989 ATGTTGGCAAATGTTAAATAAACATGTTTGTGAATGTTAAATAAACATGTTTGCTAAACGAATAT
1 ATGTTGGCAAATGTTAAATAAACATGTTTGTGAATGTTAAATAAACATGTTCGCTAAACGAATAT
* *
167054 GTTTGTGAACGCTAAATGAATTAACACGAATAATTTTAAAAATAAATAAACAAATATCA
66 GTTTGTGAACGCTAAATGAATTAACACGAACAACTTTAAAAATAAATAAACAAATATCA
* * *
167113 ATGTTGGCGAATGTTAAATGAACATGTTTGTGAATGTTAAATAAACATGTTCGTTAAACGAATAT
1 ATGTTGGCAAATGTTAAATAAACATGTTTGTGAATGTTAAATAAACATGTTCGCTAAACGAATAT
*
167178 GTTTGTGAACGCTAAATGAATTAATACGAACAACTTTAAAAATAAATAAACAAATATCA
66 GTTTGTGAACGCTAAATGAATTAACACGAACAACTTTAAAAATAAATAAACAAATATCA
167237 A
1 A
167238 CTGAACATGA
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 118 1.00
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (124 bp):
ATGTTGGCAAATGTTAAATAAACATGTTTGTGAATGTTAAATAAACATGTTCGCTAAACGAATAT
GTTTGTGAACGCTAAATGAATTAACACGAACAACTTTAAAAATAAATAAACAAATATCA
Found at i:170592 original size:142 final size:144
Alignment explanation
Indices: 170335--170657 Score: 551
Period size: 142 Copynumber: 2.2 Consensus size: 144
170325 GTCAATTCAG
*
170335 ATTCCATTTCCATGTGGGATGTTTAATGTTTTAACTAAGTTGGATCTAAGCATTGACTTGGTGCC
1 ATTCCATTTCCATGTGGGATGTTTAATGTTTTAACTAAGTTGGATCTAAGCATTAACTTGGTGCC
* *
170400 TGTAATTGAACATGGAGGAGCTTCATCACATGAGTCATGGCCCTCTA-CTTCTTCTTCTTATTCC
66 TGTAAATGAACATGGAGGAGCATCATCACATGAGTCATGGCCCTCTATCTTCTTCTTCTTATTCC
170464 ACCACAAATTAAAT
131 ACCACAAATTAAAT
170478 ATTCCATTTCCATGTGGGATGTTTAATGTTTTAACTAAGTT-GATCTAAGCATTAACTTGGTGCC
1 ATTCCATTTCCATGTGGGATGTTTAATGTTTTAACTAAGTTGGATCTAAGCATTAACTTGGTGCC
* *
170542 TGTAAATGAACATGTAGGAGCATCGTCACATGAGTCATGGCCCTCTACTTCTTCTTCTTCTTATT
66 TGTAAATGAACATGGAGGAGCATCATCACATGAGTCATGGCCCTCTA--TCTTCTTCTTCTTATT
170607 CCACCACAAATTAAAT
129 CCACCACAAATTAAAT
* *
170623 ATTCCATTTCCATGTGGGATGTTTCATGCTTTAAC
1 ATTCCATTTCCATGTGGGATGTTTAATGTTTTAAC
170658 CAATTTTATA
Statistics
Matches: 170, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
142 65 0.38
143 41 0.24
145 64 0.38
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (144 bp):
ATTCCATTTCCATGTGGGATGTTTAATGTTTTAACTAAGTTGGATCTAAGCATTAACTTGGTGCC
TGTAAATGAACATGGAGGAGCATCATCACATGAGTCATGGCCCTCTATCTTCTTCTTCTTATTCC
ACCACAAATTAAAT
Found at i:170721 original size:145 final size:142
Alignment explanation
Indices: 170335--170660 Score: 456
Period size: 145 Copynumber: 2.3 Consensus size: 142
170325 GTCAATTCAG
* * * *
170335 ATTCCATTTCCATGTGGGATGTTTAATGTTTTAACTAAGTTGGATCTAAGCATTGACTTGGTGCC
1 ATTCCATTTCCATGTGGGATGTTTAATGCTTTAACCAAGTT-GATATAAGCATTAACTTGGTGCC
* * * * *
170400 TGTAATTGAACATGGAGGAGCTTCA-TCACATGAGTCATGGCCCTCTACTTCTTCTTCTTATTCC
65 AGTAAATGAAAATGTAGGAGCAT-AGTCACATGAGTCATGGCCCTCTACTTCTTCTTCTTATTCC
170464 ACCACAAATTAAAT
129 ACCACAAATTAAAT
* * * *
170478 ATTCCATTTCCATGTGGGATGTTTAATGTTTTAACTAAGTTGATCTAAGCATTAACTTGGTGCCT
1 ATTCCATTTCCATGTGGGATGTTTAATGCTTTAACCAAGTTGATATAAGCATTAACTTGGTGCCA
* *
170543 GTAAATGAACATGTAGGAGCATCGTCACATGAGTCATGGCCCTCTACTTCTTCTTCTTCTTATTC
66 GTAAATGAAAATGTAGGAGCATAGTCACATGAGTCATGGCCCTCTA---CTTCTTCTTCTTATTC
170608 CACCACAAATTAAAT
128 CACCACAAATTAAAT
*
170623 ATTCCATTTCCATGTGGGATGTTTCATGCTTTAACCAA
1 ATTCCATTTCCATGTGGGATGTTTAATGCTTTAACCAA
170661 TTTTATAATG
Statistics
Matches: 171, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
142 64 0.37
143 41 0.24
145 66 0.39
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (142 bp):
ATTCCATTTCCATGTGGGATGTTTAATGCTTTAACCAAGTTGATATAAGCATTAACTTGGTGCCA
GTAAATGAAAATGTAGGAGCATAGTCACATGAGTCATGGCCCTCTACTTCTTCTTCTTATTCCAC
CACAAATTAAAT
Found at i:183303 original size:15 final size:15
Alignment explanation
Indices: 183280--183314 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
183270 TTGAATTGGG
*
183280 TTTGTGTTGCGTCAT
1 TTTGGGTTGCGTCAT
*
183295 TTTGGGTTGGGTCAT
1 TTTGGGTTGCGTCAT
183310 TTTGG
1 TTTGG
183315 TTCTAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.09, G:0.34, T:0.51
Consensus pattern (15 bp):
TTTGGGTTGCGTCAT
Found at i:184628 original size:24 final size:23
Alignment explanation
Indices: 184558--184648 Score: 69
Period size: 24 Copynumber: 3.8 Consensus size: 23
184548 ATATTAATAT
* *
184558 AATAT-TTTAATATCATTTTGTCAA
1 AATATATTTATTAT-ATTTT-TAAA
* *
184582 AATATTATTTATTAAAATATTTAAA
1 AATA-TATTTATT-ATATTTTTAAA
*
184607 AATATATTTATTAGTATTTTTAAT
1 AATATATTTATTA-TATTTTTAAA
*
184631 AATATA-ATATTATATTTT
1 AATATATTTATTATATTTT
184649 ATAATATTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
22 6 0.11
23 6 0.11
24 25 0.45
25 8 0.15
26 9 0.16
27 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
AATATATTTATTATATTTTTAAA
Found at i:184653 original size:23 final size:22
Alignment explanation
Indices: 184601--184667 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 22
184591 TATTAAAATA
* *
184601 TTTAAAAATATATTTATTAGTATT
1 TTTAATAATATA-ATATTA-TATT
184625 TTTAATAATATAATATTATATT
1 TTTAATAATATAATATTATATT
* *
184647 TTATAATATTATAATAATATA
1 TT-TAATAATATAATATTATA
184668 CTCAATTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 6 0.16
23 21 0.55
24 11 0.29
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
TTTAATAATATAATATTATATT
Found at i:184665 original size:31 final size:31
Alignment explanation
Indices: 184627--184716 Score: 87
Period size: 31 Copynumber: 2.9 Consensus size: 31
184617 TTAGTATTTT
*
184627 TAATAATATAATATTATATTTTATAATATTA
1 TAATAATATAATATTATATTTTATAATAATA
*
184658 TAATAATATACTCAATTATA--TTATAATAATA
1 TAATAATATAAT--ATTATATTTTATAATAATA
* *
184689 TAA-AATATTATAGTTTTATTTTAGTAAT
1 TAATAATATAATA-TTATATTTTA-TAAT
184717 CTCTAAAAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
28 1 0.02
29 4 0.08
30 6 0.12
31 27 0.56
32 4 0.08
33 6 0.12
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (31 bp):
TAATAATATAATATTATATTTTATAATAATA
Found at i:184698 original size:23 final size:23
Alignment explanation
Indices: 184652--184700 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
184642 ATATTTTATA
**
184652 ATATTATAATAATATACTCAATT
1 ATATTATAATAATATACAAAATT
184675 ATATTATAATAATATA-AAATATT
1 ATATTATAATAATATACAAA-ATT
184698 ATA
1 ATA
184701 GTTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATTATAATAATATACAAAATT
Found at i:190324 original size:10 final size:10
Alignment explanation
Indices: 190309--190333 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
190299 TTCATCTCTG
190309 TTTATGTATT
1 TTTATGTATT
190319 TTTATGTATT
1 TTTATGTATT
190329 TTTAT
1 TTTAT
190334 ACTTTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (10 bp):
TTTATGTATT
Done.