Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 2 of 18
Found at i:119146 original size:3 final size:3
Alignment explanation
Indices: 119060--119126 Score: 59
Period size: 3 Copynumber: 22.7 Consensus size: 3
119050 TTAATTTGTG
* * * *
119060 TAT TAA TAT TAT TGT TGT TAT TAT TAT TAT TAT TAT TA- TAT T-T AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
119106 GTAT TAT T-T TATT TAT TAT TA
1 -TAT TAT TAT TA-T TAT TAT TA
119127 ATAAATTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
2 5 0.09
3 43 0.81
4 5 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:119149 original size:29 final size:30
Alignment explanation
Indices: 119129--119185 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
119119 TATTATTAAT
119129 AAATTAAATAAT-ATTATTTTATTAAAAATA
1 AAATT-AATAATAATTATTTTATTAAAAATA
*
119159 AAATTATTAATAATTA-TTT-TTAAAAAT
1 AAATTAATAATAATTATTTTATTAAAAAT
119186 TTTTAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 8 0.32
29 8 0.32
30 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AAATTAATAATAATTATTTTATTAAAAATA
Found at i:122583 original size:23 final size:21
Alignment explanation
Indices: 122557--122601 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
122547 GATTTTTAAA
122557 AATTTTAAATATTAAATATTTAT
1 AATTTTAAA-ATT-AATATTTAT
*
122580 AATTTTAAAATTTATATTTAT
1 AATTTTAAAATTAATATTTAT
122601 A
1 A
122602 TATAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 3 0.14
23 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTTTAAAATTAATATTTAT
Found at i:122605 original size:2 final size:2
Alignment explanation
Indices: 122592--122652 Score: 70
Period size: 2 Copynumber: 31.0 Consensus size: 2
122582 TTTTAAAATT
* * *
122592 TA TA TT TA TA TA TA AA TA TA TA TA TA TA TA TA TA -A TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
122633 TA TA TT TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
122653 ATAAATTTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:124223 original size:29 final size:30
Alignment explanation
Indices: 124185--124251 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 30
124175 TTTATTATAT
124185 TATTTAAATAAATTTTTAT-ATTTGTA-TTG
1 TATTTAAATAAATTTTTATGATTT-TATTTG
*
124214 TGTTTAAATAAATTTTTATGATTTTATTTG
1 TATTTAAATAAATTTTTATGATTTTATTTG
124244 TATTTAAA
1 TATTTAAA
124252 GAAGTTCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 20 0.59
30 14 0.41
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.58
Consensus pattern (30 bp):
TATTTAAATAAATTTTTATGATTTTATTTG
Found at i:124839 original size:13 final size:12
Alignment explanation
Indices: 124821--124867 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
124811 CCTTACGAAG
124821 AAGAAAAGAAAGA
1 AAGAAAAGAAA-A
*
124834 AAGAAAGGAAAAA
1 AAGAAAAG-AAAA
*
124847 AAAAAAAGAAAA
1 AAGAAAAGAAAA
124859 AAGAAAAGA
1 AAGAAAAGA
124868 TCAAGATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 12 0.41
13 14 0.48
14 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAGAAAAGAAAA
Found at i:124854 original size:18 final size:18
Alignment explanation
Indices: 124823--124857 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
124813 TTACGAAGAA
* *
124823 GAAAAGAAAGAAAGAAAG
1 GAAAAAAAAAAAAGAAAG
124841 GAAAAAAAAAAAAGAAA
1 GAAAAAAAAAAAAGAAA
124858 AAAGAAAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAAAAAGAAAG
Found at i:126022 original size:13 final size:13
Alignment explanation
Indices: 126004--126031 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
125994 TTTTCACAAT
126004 TTGTATCGATACA
1 TTGTATCGATACA
126017 TTGTATCGATACA
1 TTGTATCGATACA
126030 TT
1 TT
126032 CAAACATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:128409 original size:51 final size:51
Alignment explanation
Indices: 128354--128497 Score: 175
Period size: 51 Copynumber: 2.8 Consensus size: 51
128344 TCCCGGTTCC
*
128354 ATTTCCAAAACATCAATTTTTCTTAATTGGGGATACTCCAACTCCAATTTT
1 ATTTCCAAAACATCAATTTTTCTCAATTGGGGATACTCCAACTCCAATTTT
* * * * *
128405 ATTT-CAAAAGCATCGA-TTTACTGCAATCGGGGATACTCCAACTTCGATTTT
1 ATTTCCAAAA-CATCAATTTTTCT-CAATTGGGGATACTCCAACTCCAATTTT
* * *
128456 ATTTCTAAAACACCAATTTTTCACAATTGGGGATACTCCAAC
1 ATTTCCAAAACATCAATTTTTCTCAATTGGGGATACTCCAAC
128498 CCCATTATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
50 10 0.13
51 59 0.77
52 8 0.10
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (51 bp):
ATTTCCAAAACATCAATTTTTCTCAATTGGGGATACTCCAACTCCAATTTT
Found at i:128545 original size:28 final size:27
Alignment explanation
Indices: 128485--128554 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 27
128475 TTCACAATTG
128485 GGGATACTCCAACCCCATTATTTCATCA
1 GGGATACTCCAACCCCATTATTTCA-CA
*
128513 GGGATACTCCAACCCCGTTATTTC-CAA
1 GGGATACTCCAACCCCATTATTTCAC-A
*
128540 GAGGATACTTCAACC
1 G-GGATACTCCAACC
128555 TTGGCTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 35 0.92
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (27 bp):
GGGATACTCCAACCCCATTATTTCACA
Found at i:128651 original size:28 final size:28
Alignment explanation
Indices: 128592--128656 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
128582 TTTCATAATC
*
128592 GGGGATACTCCAACCCCGTTATGTCATT
1 GGGGATACTCCAACCCCGTTATGTCATA
* * *
128620 GGGGATACTCCAATCCTGTTATTTTCA-A
1 GGGGATACTCCAACCCCGTTA-TGTCATA
128648 GGGGATACT
1 GGGGATACT
128657 TCGACTCCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATGTCATA
Found at i:128672 original size:108 final size:107
Alignment explanation
Indices: 128435--128744 Score: 354
Period size: 108 Copynumber: 2.9 Consensus size: 107
128425 CTGCAATCGG
* * * *
128435 GGATACTCCAACTTCGATTTTATTTCTAAAACACCAATTTTTCACAATTGGGGATACTCCAACCC
1 GGATACTTCAACCTCGACTTTATATCTAAAACACCAATTTTTCACAATTGGGGATACTCCAACCC
* *
128500 CATTATTTCATCAGGGATACTCCAACCCCGTTATTTCCAAGA
66 CGTTATTTCATCGGGGATACTCCAACCCCGTTATTTCCAAGA
* * * ** * * *
128542 GGATACTTCAACCTTGGCTTTATATCTAAAATATTGATTTTTTCATAATCGGGGATACTCCAACC
1 GGATACTTCAACCTCGACTTTATATCTAAAACA-CCAATTTTTCACAATTGGGGATACTCCAACC
* * * * * *
128607 CCGTTATGTCATTGGGGATACTCCAATCCTGTTATTTTCAAGG
65 CCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTCCAAGA
* * * * *
128650 GGATACTTCGA-CTCCGATTTTATTTCTAAAACACCAATTTCTCACAATTGGAGATACTCCAACC
1 GGATACTTCAACCT-CGACTTTATATCTAAAACACCAATTTTTCACAATTGGGGATACTCCAACC
128714 CCGTTATTTTCA-CGGGGATACTCCAACCCCG
65 CCGTTA-TTTCATCGGGGATACTCCAACCCCG
128745 GCCTTATTTC
Statistics
Matches: 163, Mismatches: 37, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
107 74 0.45
108 89 0.55
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (107 bp):
GGATACTTCAACCTCGACTTTATATCTAAAACACCAATTTTTCACAATTGGGGATACTCCAACCC
CGTTATTTCATCGGGGATACTCCAACCCCGTTATTTCCAAGA
Found at i:128907 original size:79 final size:80
Alignment explanation
Indices: 128621--128910 Score: 274
Period size: 79 Copynumber: 3.7 Consensus size: 80
128611 TATGTCATTG
* * * * *
128621 GGGATACTCCAATCCTGTTATTTTCAAGGGGATACTTCGA-CTCCGATTTTATTTCTAAAACACC
1 GGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCT-CGATTTTATTTCTAAAAGACC
*
128685 AA-TTTCTCACAAT-T
65 AATTTTCTCACAATCA
* * ***
128699 GGAGATACTCCAACCCCGTTATTTTC-ACGGGGATACTCCAACCCCGGCCTTATTTCT-AAAGCA
1 GG-GATACTCCAACCCTGTTATTTTCGA-GGGGATACTCCAACCTCGATTTTATTTCTAAAAG-A
* * *
128762 TCGATTTT-TCACAATCG
63 CCAATTTTCTCACAATCA
* * *
128779 GGGATACTCTAA-CCTCGTTATTTTCGAGGGGATACTCCAATCC-CAATTTTATTTTTAAAAGAC
1 GGGATACTCCAACCCT-GTTATTTTCGAGGGGATACTCCAA-CCTCGATTTTATTTCTAAAAGAC
**
128842 CAATTTTCT-GTAATCA
64 CAATTTTCTCACAATCA
* *
128858 AGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACCTCGATTTTATT
1 GGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATT
128911 CTCAGAATAC
Statistics
Matches: 171, Mismatches: 28, Indels: 25
0.76 0.12 0.11
Matches are distributed among these distances:
78 10 0.06
79 144 0.84
80 17 0.10
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (80 bp):
GGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATTTCTAAAAGACCA
ATTTTCTCACAATCA
Found at i:128927 original size:79 final size:79
Alignment explanation
Indices: 128780--128948 Score: 198
Period size: 79 Copynumber: 2.1 Consensus size: 79
128770 TCACAATCGG
* * * *
128780 GGATACTCTAACCTCGTTATTTTCGAGGGGATACTCCAATCCCAATTTTATTTTTAAAAGACCAA
1 GGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAATCCCAATTTTATTCTCAAAAGACCAA
*
128845 TTTTCTGTAATCAA
66 TTTTCTATAATCAA
* * * *
128859 GGATACTCCAACC-CTGTTATTTCCGAGGGGATACTCCAA-CCTCGATTTTATTCTCAGAATACT
1 GGATACTCCAACCTC-GTTATTTCCGAGGGGATACTCCAATCC-CAATTTTATTCTCAAAAGACC
* *
128922 GATTTTCTATAATCAG
64 AATTTTCTATAATCAA
128938 GTGATACTCCA
1 G-GATACTCCA
128949 GCCCCGTTGT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
78 3 0.04
79 64 0.84
80 9 0.12
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (79 bp):
GGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAATCCCAATTTTATTCTCAAAAGACCAA
TTTTCTATAATCAA
Found at i:131847 original size:51 final size:51
Alignment explanation
Indices: 131717--131848 Score: 174
Period size: 51 Copynumber: 2.6 Consensus size: 51
131707 AAAAATAACA
* * * * * *
131717 GGGTTGGAGTATCCCCAATTACGAGAAATCAATATTTTGGAAATAAAGCCG
1 GGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAACCG
* * * *
131768 GGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCG
1 GGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAACCG
131819 GGGTTGGAGTATCCCCGATTATGAAAAATT
1 GGGTTGGAGTATCCCCGATTATGAAAAATT
131849 GAGAAACTTA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAACCG
Found at i:134234 original size:21 final size:21
Alignment explanation
Indices: 134210--134251 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
134200 GTATCAATAC
134210 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
134231 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
134252 GGCAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:134300 original size:19 final size:20
Alignment explanation
Indices: 134276--134329 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
134266 AGCGATACAT
*
134276 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTGAA
**
134295 TGTATCGATACATTTACTGAA
1 TGTATCGATACA-AAACTGAA
134316 TGTATCGATACAAA
1 TGTATCGATACAAA
134330 TTATTGAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
TGTATCGATACAAAACTGAA
Found at i:135043 original size:40 final size:42
Alignment explanation
Indices: 134997--135096 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
134987 GTCCCACTTT
* *
134997 TTGAGGACAAAGGAAAAG-A-GAATGAAATAG-GTCTTGCTCC
1 TTGAGGACAAAGGAAAAGAAGGAAAGAAA-AGTGTCCTGCTCC
* * * *
135037 TTGAGGACGAAGGAAGAGAAGGAAAGGAAAGTGTCCTGCTTC
1 TTGAGGACAAAGGAAAAGAAGGAAAGAAAAGTGTCCTGCTCC
135079 TTGAGGACAAAGTGAAAA
1 TTGAGGACAAAG-GAAAA
135097 AGAGTACGTC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
40 16 0.33
41 3 0.06
42 25 0.52
43 4 0.08
ACGTcount: A:0.40, C:0.11, G:0.31, T:0.18
Consensus pattern (42 bp):
TTGAGGACAAAGGAAAAGAAGGAAAGAAAAGTGTCCTGCTCC
Found at i:135418 original size:214 final size:215
Alignment explanation
Indices: 135049--135453 Score: 591
Period size: 214 Copynumber: 1.9 Consensus size: 215
135039 GAGGACGAAG
* *
135049 GAAGAGAAGGAAAGGAAAGTGTCCTGCTTCTTGAGGACAAAGTGAAAAAGAGTACGTCCCATTTT
1 GAAGAGAAGGAAAGGAAAATGTCCTGCTTCTTAAGGACAAAGTGAAAAAGAGTACGTCCCATTTT
* * *
135114 TCGAGGAAAAAGGAAAAAAGGAAGCGAAACACATCATGCTCTTTGAGGACGAAAGAAAGAGGAAA
66 TCGAGGAAAAAGGAAAAAAGGAAACGAAACACATCATGCTCTCTGAGGACAAAAGAAAGAGGAAA
* *
135179 ATAAAGTGCATCCTGCTCTTTGAGGAC-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCA
131 ATAAAGTGCATCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGAGTGGGCTTTGAAAGGCA
135243 TCCTGCTTTTTGAGGACTGA
196 TCCTGCTTTTTGAGGACTGA
* ****
135263 GAAGAGAAGGAAAGGAAAATGTCCTGCTTCTTAAGGACAAGGTGAAAAAGAGTACGTTTTGTTTT
1 GAAGAGAAGGAAAGGAAAATGTCCTGCTTCTTAAGGACAAAGTGAAAAAGAGTACGTCCCATTTT
* * * * *
135328 TCGAGGACAAAGGAAAAAGGGAAACGAAATACGTCCTGCTCTCTGAGGACAAAAGGAAA-AGGAA
66 TCGAGGAAAAAGGAAAAAAGGAAACGAAACACATCATGCTCTCTGAGGACAAAA-GAAAGAGGAA
* * *
135392 AAT-AAGATGCGTCCTACTCTTTGAGGACTACAAAGTGCCACCAACTTGAGTGGGCTTTGAAA
130 AATAAAG-TGCATCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGAGTGGGCTTTGAAA
135454 AGAAAAAGGT
Statistics
Matches: 168, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
213 3 0.02
214 131 0.78
215 34 0.20
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (215 bp):
GAAGAGAAGGAAAGGAAAATGTCCTGCTTCTTAAGGACAAAGTGAAAAAGAGTACGTCCCATTTT
TCGAGGAAAAAGGAAAAAAGGAAACGAAACACATCATGCTCTCTGAGGACAAAAGAAAGAGGAAA
ATAAAGTGCATCCTACTCTTTGAGGACTAAAAAGTGCCACCAACTCGAGTGGGCTTTGAAAGGCA
TCCTGCTTTTTGAGGACTGA
Found at i:135679 original size:43 final size:42
Alignment explanation
Indices: 135618--135812 Score: 182
Period size: 43 Copynumber: 4.5 Consensus size: 42
135608 AAGGAAAAGG
135618 TGTCCTGCTCTTTGAGGACTGAAAGGAAAAGGAAAATAAAGTA
1 TGTCCTGCTCTTTGAGGACT-AAAGGAAAAGGAAAATAAAGTA
* *
135661 TGTCCTACTCTTTGAGGACTAGAAGGGAAAAGAAGGAAATAAAG-A
1 TGTCCTGCTCTTTGAGGACTA-AA-GGAAAAG--GAAAATAAAGTA
* * * *
135706 GCGTCCTACTCTTTGAGGAC-AAAGGAGAAAAGGAAAACGAAA-TG
1 -TGTCCTGCTCTTTGAGGACTAAA-G-GAAAAGGAAAA-TAAAGTA
* *
135750 TGTCCTGCTCTTTGAGGAC-AAAAGAAAGAGGAAAATAAAGTG
1 TGTCCTGCTCTTTGAGGACTAAAGGAAA-AGGAAAATAAAGTA
**
135792 CATCCTGCTCTTTGAGGACTA
1 TGTCCTGCTCTTTGAGGACTA
135813 CAAAGTGCCA
Statistics
Matches: 129, Mismatches: 12, Indels: 22
0.79 0.07 0.13
Matches are distributed among these distances:
41 7 0.05
42 27 0.21
43 46 0.36
44 14 0.11
45 8 0.06
46 27 0.21
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.22
Consensus pattern (42 bp):
TGTCCTGCTCTTTGAGGACTAAAGGAAAAGGAAAATAAAGTA
Found at i:135865 original size:62 final size:58
Alignment explanation
Indices: 135780--135988 Score: 209
Period size: 55 Copynumber: 3.6 Consensus size: 58
135770 AAAGAAAGAG
* * *
135780 GAAAATAAAGTGCATCCTGCTCTTTGAGGACTACAAAGTGCCACCAACTTGAGTGGGCTTT
1 GAAAA-AAAG-GCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTT
* * * ** *
135841 GAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTGGAGGGTGCTATGAACTCGTGTGGGCTTT
1 G--AA-AAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTT
135903 ----AAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT
1 GAAAAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTT
135958 G----AAAGGCGTCCTGCTCTTTGAGGACTAAAGG
1 GAAAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGG
135989 GTGAAAAGAG
Statistics
Matches: 128, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
54 5 0.04
55 74 0.58
61 1 0.01
62 40 0.31
63 6 0.05
64 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (58 bp):
GAAAAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:135937 original size:55 final size:55
Alignment explanation
Indices: 135848--135988 Score: 212
Period size: 55 Copynumber: 2.6 Consensus size: 55
135838 TTTGAAAAGA
* * * **
135848 AAAAGGCGTCCTGCTCTTTGAGGACTGGAGGGTGCTATGAACTCGTGTGGGCTTT
1 AAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTT
*
135903 AAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTT
*
135958 GAAAGGCGTCCTGCTCTTTGAGGACT-AAAGG
1 AAAAGGCGTCCTGCTCTTTGAGGACTGAAAGG
135989 GTGAAAAGAG
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
54 5 0.06
55 74 0.94
ACGTcount: A:0.21, C:0.20, G:0.32, T:0.27
Consensus pattern (55 bp):
AAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTT
Found at i:136065 original size:55 final size:55
Alignment explanation
Indices: 136002--136302 Score: 446
Period size: 55 Copynumber: 5.5 Consensus size: 55
135992 AAAAGAGAGA
*
136002 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
* *
136057 GCATCCTGCTCTTTGAGGACTAGGAA-GTGCCACCAACTCGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTA-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
* * ** * *
136112 GCGTCTTGCTCTTTGAGGACTGGAAAATGCCATCAACTCGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
* *
136167 GCGTCCTACTCTTTGAGGACTAGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAG
1 GCGTCCTGCTCTTTGAGGACTA-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
*
136222 GCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
*
136277 GCGTCCTGCTTTTTGAGGACTA-AAGG
1 GCGTCCTGCTCTTTGAGGACTAGAAGG
136303 GTGAAATGAG
Statistics
Matches: 223, Mismatches: 19, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
54 9 0.04
55 208 0.93
56 6 0.03
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (55 bp):
GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
Found at i:136069 original size:94 final size:94
Alignment explanation
Indices: 135908--136078 Score: 308
Period size: 94 Copynumber: 1.8 Consensus size: 94
135898 GCTTTAAAAG
* *
135908 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCT
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCT
135973 CTTTGAGGACTAAAGGGTGAAAAGAGAGA
66 CTTTGAGGACTAAAGGGTGAAAAGAGAGA
136002 GCGTCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGC
1 GCGTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGC
136066 TCTTTGAGGACTA
65 TCTTTGAGGACTA
136079 GGAAGTGCCA
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
93 1 0.01
94 73 0.99
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (94 bp):
GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCT
CTTTGAGGACTAAAGGGTGAAAAGAGAGA
Found at i:136114 original size:204 final size:205
Alignment explanation
Indices: 135794--136188 Score: 571
Period size: 204 Copynumber: 1.9 Consensus size: 205
135784 ATAAAGTGCA
*
135794 TCCTGCTCTTTGAGGACTACAAAGTGCCACCAACTTGAGTGGGCTTTGAAAAGAAAAAGGCGTCC
1 TCCTGCTCTTTGAGGACTACAAAGTGCCACCAACTTGAGTGGGCTTT------AAAAAGGCATCC
* * **
135859 TGCTCTTTGAGGACTGGAGGGTGCTATGAACTCGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGA
60 TGCTCTTTGAGGACTGGAGAGTGCCACCAACTCGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGA
* * *
135924 GGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAG
125 GGACTGGAAA-ATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTACTCTTTGAGGACTAAAG
135988 GGTGAAAAGAGAGAGCG
189 GGTGAAAAGAGAGAGCG
* * *
136005 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGCATCCTGCTCT
1 TCCTGCTCTTTGAGGACTACAAAGTGCCACCAACTTGAGTGGGCTTTAAAAAGGCATCCTGCTCT
* *
136069 TTGAGGACTAGGA-AGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCTTGCTCTTTGAGGACT
66 TTGAGGACT-GGAGAGTGCCACCAACTCGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACT
*
136133 GGAAAATGCCATCAACTCGTGTGGGCTTTGAAAGGCGTCCTACTCTTTGAGGACTA
130 GGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTACTCTTTGAGGACTA
136189 GGAAGTGCCA
Statistics
Matches: 168, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
204 117 0.70
205 7 0.04
211 44 0.26
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (205 bp):
TCCTGCTCTTTGAGGACTACAAAGTGCCACCAACTTGAGTGGGCTTTAAAAAGGCATCCTGCTCT
TTGAGGACTGGAGAGTGCCACCAACTCGTGTGGGCTTTAAAAGGCGTCCTGCTCTTTGAGGACTG
GAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTACTCTTTGAGGACTAAAGGGTGAAA
AGAGAGAGCG
Found at i:136467 original size:62 final size:63
Alignment explanation
Indices: 136318--136527 Score: 304
Period size: 62 Copynumber: 3.4 Consensus size: 63
136308 ATGAGAGAGC
* * * *
136318 GTCCTACTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAGAGGT
1 GTCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAAGAAAAAAGGT
* * *
136379 GTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTAGGCTTTAAAAAGAAAAAAGGC
1 GTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAAGAAAAAAGGT
*
136441 GTCTTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTAGGCTTTAAAAAGAAAAAAGGT
1 GTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAAGAAAAAAGGT
136503 GTCCTGCTCTTTGAGGACTGGAAGG
1 GTCCTGCTCTTTGAGGACTGGAAGG
136528 GCTAAAAGTG
Statistics
Matches: 133, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
59 2 0.02
60 22 0.17
61 23 0.17
62 81 0.61
63 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (63 bp):
GTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAAGAAAAAAGGT
Found at i:142651 original size:52 final size:52
Alignment explanation
Indices: 142503--142631 Score: 258
Period size: 52 Copynumber: 2.5 Consensus size: 52
142493 CGAAATATGA
142503 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
142555 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
142607 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
142632 AAGATCAGTG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 77 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:142731 original size:19 final size:18
Alignment explanation
Indices: 142707--142769 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
142697 TAGCTTACAT
142707 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
142726 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
142739 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
142758 TGTATCGATACA
1 TGTATCGATACA
142770 TTGTATTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:142743 original size:32 final size:32
Alignment explanation
Indices: 142702--142799 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
142692 GGCAGTAGCT
*
142702 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
142734 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
142766 TACATTGTATTGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
142799 T
1 T
142800 GCAAATCGTT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 51 0.81
33 12 0.19
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:142744 original size:13 final size:13
Alignment explanation
Indices: 142726--142782 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
142716 ACAAAACTTA
142726 TGTATCGATACAT
1 TGTATCGATACAT
142739 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
142757 ATGTATCGATACAT
1 -TGTATCGATACAT
*
142771 TGTATTGATACA
1 TGTATCGATACA
142783 ACACTTTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:146499 original size:79 final size:79
Alignment explanation
Indices: 146342--146534 Score: 201
Period size: 79 Copynumber: 2.4 Consensus size: 79
146332 TGAAAATTTT
* * * * * ** *
146342 AATATTTTGGAGATAATAA-CGGGTTTGGAGTGTCCCCTTGAAAATAATGAGGTTGGAGTATCCC
1 AATATTTAGGAAATAA-AACCGGGATTGGAGTATCCTCTCAAAAATAACGAGGTTGGAGTATCCC
** *
146406 CGGTTGTGACAAATC
65 CAATTATGACAAATC
* *
146421 AATGA-TTAGGAAATAAAATCGGGATTGGAGTATCCTCTCAAAAATAACGGGGTTGGAGTATCCC
1 AAT-ATTTAGGAAATAAAACCGGGATTGGAGTATCCTCTCAAAAATAACGAGGTTGGAGTATCCC
*
146485 CAATTATGAGAAATC
65 CAATTATGACAAATC
* * *
146500 AATATTTTGGAAATAAAGCCGGGGTTGGAGTATCC
1 AATATTTAGGAAATAAAACCGGGATTGGAGTATCC
146535 CCGATTGTGG
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
78 3 0.03
79 90 0.96
80 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (79 bp):
AATATTTAGGAAATAAAACCGGGATTGGAGTATCCTCTCAAAAATAACGAGGTTGGAGTATCCCC
AATTATGACAAATC
Found at i:146601 original size:51 final size:51
Alignment explanation
Indices: 146470--146601 Score: 183
Period size: 51 Copynumber: 2.6 Consensus size: 51
146460 AAAAATAACG
* * * * * *
146470 GGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCG
1 GGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAACCA
* * *
146521 GGGTTGGAGTATCCCCGATTGTGGAAAATTAATGTTTTAGAAATAAAACCA
1 GGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAACCA
146572 GGGTTGGAGTATCCCCGATTATGAAAAATT
1 GGGTTGGAGTATCCCCGATTATGAAAAATT
146602 GAGAAACTTA
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAACCA
Found at i:148963 original size:13 final size:13
Alignment explanation
Indices: 148945--148969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
148935 ACAAAGATCG
148945 ATGTATCGATACA
1 ATGTATCGATACA
148958 ATGTATCGATAC
1 ATGTATCGATAC
148970 TTTTCCTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:148981 original size:21 final size:21
Alignment explanation
Indices: 148957--148998 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
148947 GTATCGATAC
*
148957 AATGTATCGATACTTTTCCTT
1 AATGTATCGATACATTTCCTT
148978 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
148999 GGCAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:158052 original size:79 final size:77
Alignment explanation
Indices: 157949--158153 Score: 241
Period size: 79 Copynumber: 2.6 Consensus size: 77
157939 GATAATAACG
* * * *
157949 GGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGA-T
1 GGGTTGGAGTATCCCCTTG-AAATAACGGGATTGGAGTATCCCCGATTATGAAAAATCAAT-ATT
158013 TAGGAAATAAAATC
64 TAGGAAATAAAATC
* * *
158027 GGGATTGGAGTATCCCCTTAGAAATAACGGGTTTGGAGTATCCCCAATTATGAGAAATCAATATT
1 GGG-TTGGAGTATCCCCTT-GAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATCAATATT
* *
158092 TTGGAAATAAAGTC
64 TAGGAAATAAAATC
* **
158106 GAGGTTGGAGTATCCCCTCGGAGGTAACGGGATTGGAGTATCCCCGAT
1 G-GGTTGGAGTATCCCCT-TGAAATAACGGGATTGGAGTATCCCCGAT
158154 GAAATAACGA
Statistics
Matches: 109, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
78 4 0.04
79 102 0.94
80 3 0.03
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (77 bp):
GGGTTGGAGTATCCCCTTGAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATCAATATTTA
GGAAATAAAATC
Found at i:158137 original size:107 final size:107
Alignment explanation
Indices: 158026--158229 Score: 272
Period size: 107 Copynumber: 1.9 Consensus size: 107
158016 GAAATAAAAT
* *
158026 CGGGATTGGAGTATCCCC-TTAGAAATAACG-GGTTTGGAGTATCCCCAATTATGAGAAA-TCAA
1 CGGGATTGGAGTATCCCCGAT-GAAATAACGAGG-TTGGAGTATCCCCAATTATGAAAAACT-AA
* *
158088 TATTTTGGAAATAAAGTC-GAGGTTGGAGTATCCCCTCGGAGGTAA
63 TATTTTGGAAATAAAATCGGA-GTTGGAATATCCCCTCGGAGGTAA
* * * *
158133 CGGGATTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCAATTGTGAAAAACTAGTGT
1 CGGGATTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAACTAATAT
158198 TTTGGAAATAAAATCGGAGTTGGAATATCCCC
66 TTTGGAAATAAAATCGGAGTTGGAATATCCCC
158230 GATTGTGGAG
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
107 79 0.93
108 6 0.07
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (107 bp):
CGGGATTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAACTAATAT
TTTGGAAATAAAATCGGAGTTGGAATATCCCCTCGGAGGTAA
Found at i:158235 original size:51 final size:51
Alignment explanation
Indices: 158165--158261 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 51
158155 AAATAACGAG
* * *
158165 GTTGGAGTATCCTCAATTGTGAAAAACTAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAATATCCCCAATTGTGAAAAACTAGTGTTTTAGAAATAAAATCGGA
* * * * *
158216 GTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAA
1 GTTGGAATATCCCCAATTGTGAAAAACTAGTGTTTTAGAAATAAAA
158262 CCGAGGTTCG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 38 1.00
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32
Consensus pattern (51 bp):
GTTGGAATATCCCCAATTGTGAAAAACTAGTGTTTTAGAAATAAAATCGGA
Found at i:158306 original size:79 final size:80
Alignment explanation
Indices: 158216--158391 Score: 219
Period size: 80 Copynumber: 2.2 Consensus size: 80
158206 TAAAATCGGA
* * * * * *
158216 GTTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAA-CCGAGGTTCGAGTATTCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCCGAGGTTCGAGTATCCC
*
158280 CTCGAGAATAATGGC
66 CTCGAAAATAATGGC
* * * * *
158295 GTTGGAGTATCCTCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGGTTGGAGTGTCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCCGAGGTTCGAGTATCCC
*
158360 CTCGAAAATAATGGG
66 CTCGAAAATAATGGC
*
158375 GTTGGAGTATCTCCGAT
1 GTTGGAGTATCCCCGAT
158392 GATTAACGGG
Statistics
Matches: 81, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
79 40 0.49
80 41 0.51
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (80 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCCGAGGTTCGAGTATCCC
CTCGAAAATAATGGC
Found at i:158549 original size:51 final size:51
Alignment explanation
Indices: 158398--158584 Score: 239
Period size: 51 Copynumber: 3.6 Consensus size: 51
158388 CGATGATTAA
* * *
158398 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTGAAAATAAAAC
** * * * *
158450 CGAAGTTGGAGTATCCTCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGAAAATAAAAC
* * * *
158502 CGGGGTCGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAAC
158553 CGGGGTTGGAGTATCCCCGATTATGAAAAATT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATT
158585 GAGAAACTTA
Statistics
Matches: 114, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
51 54 0.47
52 50 0.44
53 10 0.09
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAAC
Found at i:161847 original size:42 final size:43
Alignment explanation
Indices: 161792--161892 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
161782 CCGTTTTTTT
* * * * *
161792 AGGATAAAGGAAAAAAGGAAACGAAA-TACGTCTTGCTCTCTG
1 AGGACAAAAGAAAAAAGGAAAAGAAAGTACATCCTGCTCTCTG
* * *
161834 AGGACAAAAG-AAAAAGGAAAATAAAGTGCATCCTGCTCTTTG
1 AGGACAAAAGAAAAAAGGAAAAGAAAGTACATCCTGCTCTCTG
*
161876 AGGACAAAAGAGAAAAG
1 AGGACAAAAGAAAAAAG
161893 AAGGGAAGGA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
41 13 0.27
42 30 0.62
43 5 0.10
ACGTcount: A:0.48, C:0.13, G:0.24, T:0.16
Consensus pattern (43 bp):
AGGACAAAAGAAAAAAGGAAAAGAAAGTACATCCTGCTCTCTG
Found at i:162138 original size:60 final size:59
Alignment explanation
Indices: 161909--162162 Score: 277
Period size: 61 Copynumber: 4.3 Consensus size: 59
161899 AGGAAGTGTG
* * * **
161909 TCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTCAAAAG--AAGGCA
* * * *
161970 TCCTGCCCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCCAAAAGAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT--CAAAAGAAGGCA
* * *
162031 TCCTACACTTTGAAGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGGAGAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTCAAA---AGAAGGCA
* *
162092 TCCTGCTCTTTGAGGACTG-AAAGTGCCACTAGCTTGTGTGGGCTTT---AA-AAGGCA
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTCAAAAGAAGGCA
162146 TCCTGCTCTTTGAGGAC
1 TCCTGCTCTTTGAGGAC
162163 AAAAAGGCGA
Statistics
Matches: 168, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
54 23 0.14
55 1 0.01
58 4 0.02
60 25 0.15
61 110 0.65
63 5 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTCAAAAGAAGGCA
Found at i:162523 original size:116 final size:114
Alignment explanation
Indices: 162177--162608 Score: 492
Period size: 116 Copynumber: 3.8 Consensus size: 114
162167 AGGCGAAAGG
* * * * *
162177 AGAGAGCGTCCTACTCTTTAAGGTCTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGA
1 AGAG-GCGTCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTTAAAA-GAAA
*
162241 AGGCGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA
63 AGGCGTCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT--A
* *
162296 AGAAAAGGCGTCCTCCTCTTTGAGGACTGGAAAATGCCACCCACTTGTGTGGGCTTT----G-AA
1 AG---AGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAA
* *
162356 AGGCATCCTGCTCTTTGAGGACTGAAAAATGCCACTAACTTGTGTGGGCTTTA
63 AGGCGTCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTA
* *
162409 AGAGGCGTCCTGCTCTCTGAGGACTGGAAAATGCCACCAACCTGTGTGGGCTTTAAAAAGAAAAG
1 AGAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAG
* * *
162474 GTGTCCTGCTCTTTGAGGATTAGAAAATGCCACCAACTCGTGTGGGCTTTA
65 GCGTCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTA
* * *
162525 AAAGGAGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAG
1 AGAGGCGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAG
*
162584 GCGTCCTGCTCTTTGAAGACTGAAA
65 GCGTCCTGCTCTTTGAGGACTGAAA
162609 GGTGAAAGGA
Statistics
Matches: 274, Mismatches: 26, Indels: 36
0.82 0.08 0.11
Matches are distributed among these distances:
109 4 0.01
110 70 0.26
111 1 0.00
113 3 0.01
114 1 0.00
115 53 0.19
116 93 0.34
117 1 0.00
119 2 0.01
120 2 0.01
121 42 0.15
122 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (114 bp):
AGAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG
CGTCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTA
Found at i:162538 original size:171 final size:171
Alignment explanation
Indices: 162209--162605 Score: 566
Period size: 171 Copynumber: 2.3 Consensus size: 171
162199 GTCTAGGAAG
*
162209 TGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTACTCTTTGAGGACTGGAAAATGCC
1 TGCCACCAACTTGTGTGGGCTTT--AA--AG-AGGCGTCCTGCTCTTTGAGGACTGGAAAATGCC
* * * *
162274 ACCAACTTGTGTGGGCTTTGAAAGAAAAGGCGTCCTCCTCTTTGAGGACTGGAAAATGCCACCCA
61 ACCAACCTGTGTGGGCTTTAAAAGAAAAGGCGTCCTCCTCTTTGAGGACTAGAAAATGCCACCAA
* *
162339 CTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTGAAAAA
126 CTCGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTGAAAAA
* *
162385 TGCCACTAACTTGTGTGGGCTTT-AAGAGGCGTCCTGCTCTCTGAGGACTGGAAAATGCCACCAA
1 TGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAA
* * *
162449 CCTGTGTGGGCTTTAAAAAGAAAAGGTGTCCTGCTCTTTGAGGATTAGAAAATGCCACCAACTCG
66 CCTGTGTGGGCTTT-AAAAGAAAAGGCGTCCTCCTCTTTGAGGACTAGAAAATGCCACCAACTCG
**
162514 TGTGGGCTTTAAAAGG-AGTCCTGCTCTTTGAGGACTGAAAGG
130 TGTGGGCTTTAAAAGGCA-TCCTGCTCTTTGAGGACTGAAAAA
* *
162556 TGCCACCAACTTGTGTGGGCTTTGAA-AGGCGTCCTGCTCTTTGAAGACTG
1 TGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCTTTGAGGACTG
162606 AAAGGTGAAA
Statistics
Matches: 201, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
170 50 0.25
171 126 0.63
172 2 0.01
173 1 0.00
176 22 0.11
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (171 bp):
TGCCACCAACTTGTGTGGGCTTTAAAGAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAA
CCTGTGTGGGCTTTAAAAGAAAAGGCGTCCTCCTCTTTGAGGACTAGAAAATGCCACCAACTCGT
GTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGACTGAAAAA
Found at i:162612 original size:55 final size:55
Alignment explanation
Indices: 162182--162605 Score: 467
Period size: 55 Copynumber: 7.4 Consensus size: 55
162172 AAAGGAGAGA
* * * *
162182 GCGTCCTACTCTTTAAGGTCTAGG-AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAG
1 GCGTCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTT-----GA-AAG
*
162243 GCGTCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAG
* *
162303 GCGTCCTCCTCTTTGAGGACTGGAAAATGCCACCCACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* * *
162358 GCATCCTGCTCTTTGAGGACTGAAAAATGCCACTAACTTGTGTGGGCTTT-AAGAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AG
* *
162413 GCGTCCTGCTCTCTGAGGACTGGAAAATGCCACCAACCTGTGTGGGCTTTAAAAAGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAG
* * * * *
162474 GTGTCCTGCTCTTTGAGGATTAGAAAATGCCACCAACTCGTGTGGGCTTTAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
* *
162529 GAGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAG
*
162584 GCGTCCTGCTCTTTGAAGACTG
1 GCGTCCTGCTCTTTGAGGACTG
162606 AAAGGTGAAA
Statistics
Matches: 320, Mismatches: 31, Indels: 29
0.84 0.08 0.08
Matches are distributed among these distances:
54 6 0.02
55 164 0.51
56 1 0.00
60 56 0.17
61 91 0.28
62 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (55 bp):
GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
Found at i:166388 original size:52 final size:52
Alignment explanation
Indices: 166309--166437 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
166299 GGAAATATGA
*
166309 AAATTTGCCTGCATGTATCGATTCATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
166361 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
166413 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
166438 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:166448 original size:52 final size:51
Alignment explanation
Indices: 166309--166457 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 51
166299 GGAAATATGA
*
166309 AAATTTGCCTGCATGTATCGATTCATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
166361 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
166413 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
166458 ATGTATCGAT
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 89 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:166464 original size:13 final size:13
Alignment explanation
Indices: 166446--166470 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
166436 CAAAGATCAG
166446 TGTATCGATACAA
1 TGTATCGATACAA
166459 TGTATCGATACA
1 TGTATCGATACA
166471 TTTGGGTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:166537 original size:19 final size:18
Alignment explanation
Indices: 166513--166610 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
166503 TAGCTTACAT
166513 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
166532 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
166545 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
166564 TGTATCGATTC--A--T-
1 TGTATCGATACAAACTTA
166577 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
166597 TGTATCGATACAAA
1 TGTATCGATACAAA
166611 TCGTTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 23 0.36
20 13 0.20
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:166549 original size:32 final size:32
Alignment explanation
Indices: 166508--166608 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
166498 GGCAGTAGCT
*
166508 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
166540 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
166572 TTCATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
166605 TACA
1 TACA
166609 AATCGTTGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 51 0.78
33 14 0.22
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:166550 original size:13 final size:13
Alignment explanation
Indices: 166532--166588 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
166522 ACAAAACTTA
166532 TGTATCGATACAT
1 TGTATCGATACAT
166545 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
*
166563 ATGTATCGATTCAT
1 -TGTATCGATACAT
166577 TGTATCGATACA
1 TGTATCGATACA
166589 ACACTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
14 1 0.03
16 5 0.14
18 1 0.03
19 9 0.25
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:173229 original size:13 final size:13
Alignment explanation
Indices: 173211--173235 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173201 CATAAAGTAT
173211 TGTATCGATACAA
1 TGTATCGATACAA
173224 TGTATCGATACA
1 TGTATCGATACA
173236 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:173233 original size:33 final size:33
Alignment explanation
Indices: 173191--173257 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
173181 TTCAACGATT
173191 TGTATCGATACATAAAGTATTGTATCGATACAA
1 TGTATCGATACATAAAGTATTGTATCGATACAA
*** *
173224 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTATTGTATCGATACAA
173257 T
1 T
173258 TCAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTATTGTATCGATACAA
Found at i:173316 original size:13 final size:13
Alignment explanation
Indices: 173298--173322 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
173288 ATCACTTAAA
173298 TGTATCGATACAT
1 TGTATCGATACAT
173311 TGTATCGATACA
1 TGTATCGATACA
173323 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:173387 original size:52 final size:52
Alignment explanation
Indices: 173331--173459 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
173321 CACTGATCTT
173331 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
* **
173383 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
173435 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
173460 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
Found at i:187295 original size:1 final size:1
Alignment explanation
Indices: 187289--187369 Score: 90
Period size: 1 Copynumber: 81.0 Consensus size: 1
187279 CGTCCTCCAC
* * * * * * *
187289 AAAAAAAACAAAAAAAACAAAAAAAACAAAAAAAAACAAAAAAAACAAAAAAAAACAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
187354 AAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAA
187370 GGTCCGGATG
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:187304 original size:10 final size:9
Alignment explanation
Indices: 187287--187369 Score: 132
Period size: 9 Copynumber: 9.1 Consensus size: 9
187277 GGCGTCCTCC
187287 ACAAAAAAA
1 ACAAAAAAA
187296 ACAAAAAAA
1 ACAAAAAAA
187305 ACAAAAAAA
1 ACAAAAAAA
187314 ACAAAAAAAA
1 AC-AAAAAAA
187324 ACAAAAAAA
1 ACAAAAAAA
187333 ACAAAAAAA
1 ACAAAAAAA
*
187342 A-ACAAAAA
1 ACAAAAAAA
187350 ACAAAAAAAA
1 AC-AAAAAAA
187360 ACAAAAAAA
1 ACAAAAAAA
187369 A
1 A
187370 GGTCCGGATG
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
8 7 0.10
9 45 0.65
10 17 0.25
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (9 bp):
ACAAAAAAA
Found at i:187311 original size:19 final size:19
Alignment explanation
Indices: 187287--187369 Score: 145
Period size: 19 Copynumber: 4.5 Consensus size: 19
187277 GGCGTCCTCC
187287 ACAAAAAAAAC-AAAAAAA
1 ACAAAAAAAACAAAAAAAA
187305 ACAAAAAAAACAAAAAAAA
1 ACAAAAAAAACAAAAAAAA
187324 ACAAAAAAAACAAAAAAAA
1 ACAAAAAAAACAAAAAAAA
187343 AC--AAAAAACAAAAAAAA
1 ACAAAAAAAACAAAAAAAA
187360 ACAAAAAAAA
1 ACAAAAAAAA
187370 GGTCCGGATG
Statistics
Matches: 62, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.27
18 11 0.18
19 34 0.55
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (19 bp):
ACAAAAAAAACAAAAAAAA
Found at i:188817 original size:29 final size:30
Alignment explanation
Indices: 188747--188834 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 30
188737 CCTCACCCTT
* * *
188747 CAAAGCCCACAAATCAGTGGCACCCTTTTC
1 CAAAGCCCACAACTCCGTGGCACTCTTTTC
* * *
188777 CGAAGCCCACAAGTCGGTGGCA-TCTTTTC
1 CAAAGCCCACAACTCCGTGGCACTCTTTTC
* *
188806 CAAAGTCTACAACTCCGTGGCACTCTTTT
1 CAAAGCCCACAACTCCGTGGCACTCTTTT
188835 TCTTTTGTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
29 23 0.48
30 25 0.52
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (30 bp):
CAAAGCCCACAACTCCGTGGCACTCTTTTC
Found at i:188854 original size:35 final size:34
Alignment explanation
Indices: 188814--188886 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 34
188804 TCCAAAGTCT
* * *
188814 ACAACTCCGTGGCACTCTTTTTCTTTTGTAAGCTC
1 ACAACTCCATAGCACTCTTTTTCTTTT-TAAGCCC
*
188849 ACAACTCTATAGCACTCTTTTTCTTTTTAAGCCC
1 ACAACTCCATAGCACTCTTTTTCTTTTTAAGCCC
188883 ACAA
1 ACAA
188887 GTTAGTGGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.38
Consensus pattern (34 bp):
ACAACTCCATAGCACTCTTTTTCTTTTTAAGCCC
Found at i:188903 original size:34 final size:34
Alignment explanation
Indices: 188822--188932 Score: 97
Period size: 30 Copynumber: 3.4 Consensus size: 34
188812 CTACAACTCC
* * *
188822 GTGGCACTCTTTTTCTTTTGTAAGCTCACAACTCTA
1 GTGGCACCCTTTTTCTTTT-TAAGCCCACAAGT-TA
* *
188858 -TAGCACTCTTTTTCTTTTTAAGCCCACAAGTTA
1 GTGGCACCCTTTTTCTTTTTAAGCCCACAAGTTA
**
188891 GTGGCACCC-TTTTC---AAAAGCCCACAAGTTA
1 GTGGCACCCTTTTTCTTTTTAAGCCCACAAGTTA
*
188921 GTGGCAACCTTT
1 GTGGCACCCTTT
188933 AAAAGCCCAC
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
30 22 0.34
31 2 0.03
33 7 0.11
34 17 0.26
35 17 0.26
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.36
Consensus pattern (34 bp):
GTGGCACCCTTTTTCTTTTTAAGCCCACAAGTTA
Found at i:188911 original size:30 final size:29
Alignment explanation
Indices: 188877--189000 Score: 148
Period size: 28 Copynumber: 4.3 Consensus size: 29
188867 TTTTCTTTTT
*
188877 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTTAGTGGCAACC-TTTCAA
188907 AAGCCCACAAGTTAGTGGCAACCTTT-AA
1 AAGCCCACAAGTTAGTGGCAACCTTTCAA
* *
188935 AAGCCCACAAGTCAGTAGCAACC-TTCAA
1 AAGCCCACAAGTTAGTGGCAACCTTTCAA
* *
188963 AAGCACACAAGTT-GAT-GCAAACCTCTCAA
1 AAGCCCACAAGTTAG-TGGC-AACCTTTCAA
188992 AAGCCCACA
1 AAGCCCACA
189001 CAAGTTGGTG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
27 5 0.06
28 41 0.49
29 15 0.18
30 22 0.27
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.18
Consensus pattern (29 bp):
AAGCCCACAAGTTAGTGGCAACCTTTCAA
Found at i:189178 original size:43 final size:43
Alignment explanation
Indices: 189117--189205 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 43
189107 CACCTTCATA
**
189117 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCACC
1 TTTAAGTCCAATACAGCTGACCTTGAATCAGCACATTGGCACC
* *
189160 TTTAAGTCCAATACAGCTGGCCTTGAATCAGCATATTGGCACC
1 TTTAAGTCCAATACAGCTGACCTTGAATCAGCACATTGGCACC
189203 TTT
1 TTT
189206 TCCATCTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (43 bp):
TTTAAGTCCAATACAGCTGACCTTGAATCAGCACATTGGCACC
Found at i:189203 original size:92 final size:94
Alignment explanation
Indices: 189066--189249 Score: 275
Period size: 92 Copynumber: 2.0 Consensus size: 94
189056 TGGCACCTTG
*
189066 CCTTTAAGTCCAATATCGTTGGCCTTAAATCAGCATATTGGCACC-TT-CATATTTAAGTCCAAT
1 CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTCCATATTTAAGTCCAAT
189129 GTAGCTGACCTTGAATCAGCACATTGGCA
66 GTAGCTGACCTTGAATCAGCACATTGGCA
* * *
189158 CCTTTAAGTCCAATA-CAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCA
1 CCTTTAAGTCCAATATC-GCTGGCCTTAAATCAGCATATTGGCACC-TTTCCATATTTAAGTCCA
* *
189222 ATGTAGCTGGCCTTGAATCAGTACATTG
64 ATGTAGCTGACCTTGAATCAGCACATTG
189250 ACATCATTTT
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
91 1 0.01
92 41 0.50
94 2 0.02
95 38 0.46
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (94 bp):
CCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTCCATATTTAAGTCCAAT
GTAGCTGACCTTGAATCAGCACATTGGCA
Found at i:189237 original size:52 final size:53
Alignment explanation
Indices: 189159--189312 Score: 166
Period size: 52 Copynumber: 2.9 Consensus size: 53
189149 ACATTGGCAC
*
189159 CTTTAAGTCCAATACAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * * * *
189211 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGTACATTGACATCATTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-CTTTTCTCAT
* * * * * *
189266 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
189313 ATCACTTTTC
Statistics
Matches: 80, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
52 36 0.45
53 4 0.05
54 5 0.06
55 35 0.44
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:190133 original size:13 final size:13
Alignment explanation
Indices: 190115--190139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
190105 CATAAAGTGT
190115 TGTATCGATACAA
1 TGTATCGATACAA
190128 TGTATCGATACA
1 TGTATCGATACA
190140 TTTTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:190220 original size:13 final size:13
Alignment explanation
Indices: 190202--190226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
190192 ATCACTTAAA
190202 TGTATCGATACAT
1 TGTATCGATACAT
190215 TGTATCGATACA
1 TGTATCGATACA
190227 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:193407 original size:13 final size:13
Alignment explanation
Indices: 193389--193413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
193379 CGTTGCGACA
193389 GTATCGATACATT
1 GTATCGATACATT
193402 GTATCGATACAT
1 GTATCGATACAT
193414 ATTTTGTGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:193527 original size:20 final size:20
Alignment explanation
Indices: 193483--193538 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
193473 ACATCTTTTT
*
193483 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
193503 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
* *
193522 TTATGTATCAATACTTT
1 -CATGTATCGATACTTT
193539 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:195519 original size:21 final size:20
Alignment explanation
Indices: 195490--195532 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
195480 GACTAGTGTG
* *
195490 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
195511 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
195531 GG
1 GG
195533 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:195981 original size:13 final size:13
Alignment explanation
Indices: 195963--196000 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
195953 ATAATCCCCC
195963 TGTATCGATACAG
1 TGTATCGATACAG
*
195976 TGTATCGATACAT
1 TGTATCGATACAG
195989 TGTATCGATACA
1 TGTATCGATACA
196001 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:198109 original size:15 final size:15
Alignment explanation
Indices: 198073--198110 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
198063 TTCATTAATT
* *
198073 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
198088 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
198103 TCATTTTG
1 TCATTTTG
198111 GATATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:199940 original size:21 final size:21
Alignment explanation
Indices: 199911--199955 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
199901 AAATTTTTAT
*
199911 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
199931 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
199953 TTT
1 TTT
199956 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:201872 original size:32 final size:30
Alignment explanation
Indices: 201836--201894 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
201826 GAAATCAAAT
201836 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
201868 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
201895 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:202193 original size:13 final size:13
Alignment explanation
Indices: 202175--202200 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
202165 AATTTTTTTG
202175 TGTATCGATACAT
1 TGTATCGATACAT
202188 TGTATCGATACAT
1 TGTATCGATACAT
202201 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:202211 original size:32 final size:34
Alignment explanation
Indices: 202154--202218 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
202144 TATAAGCCAA
*
202154 TGTATCGATACAATTTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTATTTTGTGTATCGATACAT
202188 TGTATCGATAC-A-TATTTTGTGTATCGATACA
1 TGTATCGATACAATTATTTTGTGTATCGATACA
202219 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 18 0.60
33 1 0.03
34 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (34 bp):
TGTATCGATACAATTATTTTGTGTATCGATACAT
Found at i:203916 original size:20 final size:21
Alignment explanation
Indices: 203893--203933 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
203883 CATTTCATAC
203893 ATGTATCGAT-ACATTCACTT
1 ATGTATCGATAACATTCACTT
*
203913 ATGTATTGATAAACATTCACT
1 ATGTATCGAT-AACATTCACT
203934 AATTGTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (21 bp):
ATGTATCGATAACATTCACTT
Found at i:204967 original size:33 final size:32
Alignment explanation
Indices: 204924--204992 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 32
204914 TGTACTACCA
* *
204924 TTTATAAAAATATTAT-TTTTTTTATAAATTTTT
1 TTTAAAAAAATATT-TCTTTTTTT-TAAATTTTG
* *
204957 TTTAAAAAAATCTTTCTTTTTTTTTAATTTTG
1 TTTAAAAAAATATTTCTTTTTTTTAAATTTTG
204989 TTTA
1 TTTA
204993 TCATATTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (32 bp):
TTTAAAAAAATATTTCTTTTTTTTAAATTTTG
Found at i:205596 original size:21 final size:21
Alignment explanation
Indices: 205561--205634 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
205551 TATTGGTACG
* * *
205561 TATAGATTTATATTTGATATAA
1 TATAAATTAATATTTAAT-TAA
205583 T-TAAATTAATATTTAATTAA
1 TATAAATTAATATTTAATTAA
* *
205603 TATATATTAATTTATATTAATTGA
1 TATAAATTAA--TAT-TTAATTAA
205627 TATAAATT
1 TATAAATT
205635 TTTTTATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.10
21 20 0.48
22 1 0.02
23 3 0.07
24 14 0.33
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
TATAAATTAATATTTAATTAA
Found at i:205624 original size:10 final size:10
Alignment explanation
Indices: 205593--205635 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
205583 TTAAATTAAT
205593 ATTTA-ATTA
1 ATTTATATTA
*
205602 ATATATATTA
1 ATTTATATTA
205612 ATTTATATTA
1 ATTTATATTA
* *
205622 ATTGATATAA
1 ATTTATATTA
205632 ATTT
1 ATTT
205636 TTTTATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 4 0.14
10 24 0.86
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
ATTTATATTA
Found at i:205640 original size:24 final size:24
Alignment explanation
Indices: 205566--205643 Score: 65
Period size: 24 Copynumber: 3.3 Consensus size: 24
205556 GTACGTATAG
*
205566 ATTTATATTTGATATAAT-TAAATTA
1 ATTTATA-TTAAT-TAATATAAATTA
*
205591 A--TAT-TTAATTAATATATATTA
1 ATTTATATTAATTAATATAAATTA
* *
205612 ATTTATATTAATTGATATAAATTT
1 ATTTATATTAATTAATATAAATTA
*
205636 TTTTATAT
1 ATTTATAT
205644 ATTTTTTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
20 4 0.09
21 11 0.26
23 6 0.14
24 21 0.49
25 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (24 bp):
ATTTATATTAATTAATATAAATTA
Found at i:205657 original size:24 final size:24
Alignment explanation
Indices: 205630--205686 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
205620 TAATTGATAT
*
205630 AAATTTTTTTATATATTTTTTAAA
1 AAATTTTTTTATATAATTTTTAAA
** *
205654 AAA-TTACTTATTTAATTTTTAAA
1 AAATTTTTTTATATAATTTTTAAA
205677 ATAATTTTTT
1 A-AATTTTTT
205687 AATTTTTTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
23 17 0.68
24 5 0.20
25 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
AAATTTTTTTATATAATTTTTAAA
Found at i:205853 original size:22 final size:21
Alignment explanation
Indices: 205828--205869 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
205818 GATTTTTAAA
205828 AATTTAAAAATTAAATATTTAT
1 AATTTAAAAATT-AATATTTAT
* *
205850 AATTTTAAAATTTATATTTA
1 AATTTAAAAATTAATATTTA
205870 CATATGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTTAAAAATTAATATTTAT
Found at i:209727 original size:20 final size:22
Alignment explanation
Indices: 209678--209728 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
209668 ACTTTATCGA
*
209678 TATTAAAATAATTTTTTAATAT
1 TATTAAAATTATTTTTTAATAT
209700 TATT--AATTATTTTTT-AT-T
1 TATTAAAATTATTTTTTAATAT
209718 TATTAAAATTA
1 TATTAAAATTA
209729 AAAGTATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 5 0.19
19 2 0.08
20 15 0.58
22 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTAAAATTATTTTTTAATAT
Found at i:211296 original size:2 final size:2
Alignment explanation
Indices: 211289--211324 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
211279 CGATGATAAT
211289 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
211325 ATTGGTGAGA
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):
TA
Found at i:212461 original size:20 final size:20
Alignment explanation
Indices: 212419--212464 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
212409 CTACCATTGT
*
212419 TTGTATCGATACATGGTACA
1 TTGTATCGATACATGATACA
212439 TTGTATCGATACATGATGA-A
1 TTGTATCGATACATGAT-ACA
212459 TTGTAT
1 TTGTAT
212465 TGAAACATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATACA
Found at i:220550 original size:20 final size:20
Alignment explanation
Indices: 220525--220574 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
220515 CTACCACTGT
220525 TTGTATCGATACATG-GTACA
1 TTGTATCGATACATGAGTA-A
*
220545 TTGTATCGATACATGATTAA
1 TTGTATCGATACATGAGTAA
220565 TTGTATCGAT
1 TTGTATCGAT
220575 GCATTGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (20 bp):
TTGTATCGATACATGAGTAA
Found at i:221387 original size:27 final size:27
Alignment explanation
Indices: 221356--221407 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
221346 TTACATATTT
* *
221356 GTATTTCAAATATACAAATTCATTATC
1 GTATTACAAATATACAAATACATTATC
221383 GTATTACAAATATACAAATACATTA
1 GTATTACAAATATACAAATACATTA
221408 CCAAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (27 bp):
GTATTACAAATATACAAATACATTATC
Found at i:221470 original size:19 final size:18
Alignment explanation
Indices: 221448--221495 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
221438 AAATGTAGTA
221448 TTACATAAA-TTTATGATAT
1 TTACATAAATTTTAT-A-AT
221467 TTACATAAAGTTTTATAAT
1 TTACATAAA-TTTTATAAT
221486 TTACA-AAATT
1 TTACATAAATT
221496 ATATTAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 2 0.07
18 3 0.11
19 16 0.59
20 1 0.04
21 5 0.19
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (18 bp):
TTACATAAATTTTATAAT
Found at i:221775 original size:20 final size:19
Alignment explanation
Indices: 221750--221808 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
221740 TGCATAAGAT
*
221750 TTACATAGAACATTATCATA
1 TTACATAAAACATTATC-TA
221770 TTACATAAAATCATTA-CTA
1 TTACATAAAA-CATTATCTA
*
221789 TTTCTATAAAACATTATCTA
1 TTAC-ATAAAACATTATCTA
221809 AGATTTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 10 0.29
20 19 0.56
21 5 0.15
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (19 bp):
TTACATAAAACATTATCTA
Found at i:222986 original size:15 final size:15
Alignment explanation
Indices: 222968--223015 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
222958 AACTAATCTC
222968 TTTAAATTTTAAAAA
1 TTTAAATTTTAAAAA
*
222983 TTTATATTTTAAAAGA
1 TTTAAATTTTAAAA-A
*
222999 ATT-AATTTT-AAAA
1 TTTAAATTTTAAAAA
223012 TTTA
1 TTTA
223016 CGTAAAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
13 3 0.11
14 3 0.11
15 18 0.67
16 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TTTAAATTTTAAAAA
Found at i:225188 original size:30 final size:30
Alignment explanation
Indices: 225154--225232 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 30
225144 CTTTTAGGAT
225154 AAGTAATTTTGACACAAATACCTT-TAACAC
1 AAGTAATTTTGACACAAATA-CTTCTAACAC
* * * * *
225184 AAGTACTTTTAACATAAATACTTCTAGCAT
1 AAGTAATTTTGACACAAATACTTCTAACAC
*
225214 AAAT-ATTTTGACACAAATA
1 AAGTAATTTTGACACAAATA
225233 TTTTGGTATA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.33
Consensus pattern (30 bp):
AAGTAATTTTGACACAAATACTTCTAACAC
Found at i:225205 original size:15 final size:15
Alignment explanation
Indices: 225160--225236 Score: 68
Period size: 15 Copynumber: 5.3 Consensus size: 15
225150 GGATAAGTAA
*
225160 TTTTGACACAAATAC
1 TTTTAACACAAATAC
* *
225175 CTTTAACACAAGTAC
1 TTTTAACACAAATAC
*
225190 TTTTAACATAAATAC
1 TTTTAACACAAATAC
* * *
225205 TTCTAGCATAAATA-
1 TTTTAACACAAATAC
*
225219 TTTTGACACAAATA-
1 TTTTAACACAAATAC
225233 TTTT
1 TTTT
225237 GGTATAAGTA
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
14 14 0.28
15 36 0.72
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (15 bp):
TTTTAACACAAATAC
Found at i:227055 original size:2 final size:2
Alignment explanation
Indices: 227050--227074 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
227040 ACACACACAC
227050 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
227075 GTTTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:228123 original size:14 final size:15
Alignment explanation
Indices: 228106--228140 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
228096 AGTTTAAAAA
228106 AATATTTTTAT-ATT
1 AATATTTTTATAATT
228120 AATATTTTTATAATT
1 AATATTTTTATAATT
228135 AA-ATTT
1 AATATTT
228141 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATATTTTTATAATT
Found at i:228923 original size:20 final size:19
Alignment explanation
Indices: 228876--228930 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
228866 AATATTGATA
*
228876 CATTGTATCGATACATGCT
1 CATTGTATCGATACATACT
* *
228895 CACTGTATCTATACATACT
1 CATTGTATCGATACATACT
228914 CAATTGTATCGATACAT
1 C-ATTGTATCGATACAT
228931 GAAACTGACA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:228985 original size:20 final size:20
Alignment explanation
Indices: 228960--229012 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
228950 TTATGTGAAA
** *
228960 TGTATCGATACATGGGGCAT
1 TGTATCGATACATGAAGAAT
228980 TGTATCGATACATGAAGAAT
1 TGTATCGATACATGAAGAAT
*
229000 TTTATCGATACAT
1 TGTATCGATACAT
229013 TATGCCCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAT
Found at i:233750 original size:16 final size:15
Alignment explanation
Indices: 233725--233755 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
233715 AAGGGTTTTC
233725 AAAAATTTTAATAGA
1 AAAAATTTTAATAGA
233740 AAAAGATTTTAATAGA
1 AAAA-ATTTTAATAGA
233756 GGAAATGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (15 bp):
AAAAATTTTAATAGA
Found at i:237640 original size:33 final size:33
Alignment explanation
Indices: 237585--237648 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
237575 CTCTAGAAAG
*
237585 TATCGATACATATCTAGATGTATCGATACATTA
1 TATCGATACATATCTAGATGTATCAATACATTA
237618 TATCGATACATA-CTCA-ATTGTATCAATACAT
1 TATCGATACATATCT-AGA-TGTATCAATACAT
237649 AAAACTGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (33 bp):
TATCGATACATATCTAGATGTATCAATACATTA
Found at i:237897 original size:21 final size:21
Alignment explanation
Indices: 237873--237929 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
237863 AATTTATCCA
237873 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
237894 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
237915 AATGTATCGATACAT
1 AATGTATCGATACAT
237930 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:238009 original size:19 final size:19
Alignment explanation
Indices: 237985--238052 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
237975 AATTCAACAA
237985 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
238004 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
238019 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
238036 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
238053 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:238024 original size:13 final size:13
Alignment explanation
Indices: 238006--238030 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
237996 ACATAAGTTT
238006 TGTATCGATACAA
1 TGTATCGATACAA
238019 TGTATCGATACA
1 TGTATCGATACA
238031 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:238028 original size:32 final size:32
Alignment explanation
Indices: 237987--238049 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
237977 TTCAACAATT
*
237987 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
238019 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
238050 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:238110 original size:13 final size:13
Alignment explanation
Indices: 238092--238117 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
238082 CATTTTTCTG
238092 TGTATCGATACAT
1 TGTATCGATACAT
238105 TGTATCGATACAT
1 TGTATCGATACAT
238118 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:238114 original size:33 final size:33
Alignment explanation
Indices: 238072--238138 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
238062 GCCAAGGAAA
***
238072 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
238105 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
238138 T
1 T
238139 TGGAAATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:240475 original size:51 final size:53
Alignment explanation
Indices: 240411--240541 Score: 169
Period size: 51 Copynumber: 2.5 Consensus size: 53
240401 AGTTTCTCAA
* * * *
240411 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
240462 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
240516 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
240542 CCCGTTACTT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
50 2 0.03
51 33 0.49
53 9 0.13
54 20 0.30
55 3 0.04
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:253068 original size:8 final size:8
Alignment explanation
Indices: 253046--253118 Score: 60
Period size: 8 Copynumber: 8.9 Consensus size: 8
253036 CCTTCTCTTC
253046 AAAAAAA-
1 AAAAAAAG
253053 AAACAAAAG
1 AAA-AAAAG
253062 AAAAAAAG
1 AAAAAAAG
*
253070 AAAAAAAAAC
1 --AAAAAAAG
*
253080 AAAAAAAC
1 AAAAAAAG
253088 AAAACAAAG
1 AAAA-AAAG
*
253097 AAAAAGAG
1 AAAAAAAG
*
253105 -AGAAAAG
1 AAAAAAAG
253112 AAAAAAA
1 AAAAAAA
253119 CCTACTTAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
7 8 0.15
8 29 0.54
9 10 0.19
10 7 0.13
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:253073 original size:23 final size:23
Alignment explanation
Indices: 253047--253101 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
253037 CTTCTCTTCA
*
253047 AAAAAAAAACAAAAGAAA-AAAAG
1 AAAAAAAAACAAAA-AAACAAAAC
253070 AAAAAAAAACAAAAAAACAAAAC
1 AAAAAAAAACAAAAAAACAAAAC
*
253093 AAAGAAAAA
1 AAAAAAAAA
253102 GAGAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 3 0.10
23 26 0.90
ACGTcount: A:0.87, C:0.07, G:0.05, T:0.00
Consensus pattern (23 bp):
AAAAAAAAACAAAAAAACAAAAC
Found at i:253085 original size:35 final size:38
Alignment explanation
Indices: 253046--253116 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 38
253036 CCTTCTCTTC
253046 AAAAAA-AAAACAAAAGAAAAA-A-AGAAAA-AAAAACA
1 AAAAAACAAAAC-AAAGAAAAAGAGAGAAAAGAAAAACA
253081 AAAAAACAAAACAAAGAAAAAGAGAGAAAAGAAAAA
1 AAAAAACAAAACAAAGAAAAAGAGAGAAAAGAAAAA
253117 AACCTACTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
35 15 0.47
36 6 0.19
37 6 0.19
38 5 0.16
ACGTcount: A:0.85, C:0.06, G:0.10, T:0.00
Consensus pattern (38 bp):
AAAAAACAAAACAAAGAAAAAGAGAGAAAAGAAAAACA
Found at i:254285 original size:59 final size:59
Alignment explanation
Indices: 254105--254693 Score: 751
Period size: 59 Copynumber: 10.1 Consensus size: 59
254095 AGCAGGACAC
* * **
254105 CTTTTAAAGCCCACACAAGATGATGGCA-CTTCCAAGTCCTCAAAGAGCAGGACGCCTTCCC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C-AGTCCTCAAAGAGCAGGACGCCTT-TT
** *
254166 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCGGGACGCCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
254226 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAACGGGACACCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTT
* *
254285 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGATGCCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTT
*
254344 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
254403 CTTTTAAAGCCCACCCGAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTT
*
254462 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACC-TTT
1 CTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGCCTTTT
** *
254522 C----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC-TTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTTT
** * *
254577 C----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAGAGAGCAGGACACC---T
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTTT
* *
254630 C--TTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGATGCCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTT
254687 CTTTTAA
1 CTTTTAA
254694 TTTTTTTTCA
Statistics
Matches: 483, Mismatches: 33, Indels: 26
0.89 0.06 0.05
Matches are distributed among these distances:
53 2 0.00
54 21 0.04
55 125 0.26
57 2 0.00
59 204 0.42
60 55 0.11
61 71 0.15
62 1 0.00
63 2 0.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (59 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:254577 original size:27 final size:27
Alignment explanation
Indices: 254489--254577 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 27
254479 AAGTTGGTGG
254489 CACCTTT-CAGTCCTCAAAGAGCAGGA
1 CACCTTTCCAGTCCTCAAAGAGCAGGA
* * * * **
254515 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC-CAGTCCTCA-AAG-AGCAGGA
*
254544 CA-TTTTCCAGTCCTCAAAGAGCAGGA
1 CACCTTTCCAGTCCTCAAAGAGCAGGA
254570 CACCTTTC
1 CACCTTTC
254578 AAAGCCCACA
Statistics
Matches: 43, Mismatches: 14, Indels: 11
0.63 0.21 0.16
Matches are distributed among these distances:
25 3 0.07
26 12 0.28
27 10 0.23
28 10 0.23
29 5 0.12
30 3 0.07
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.22
Consensus pattern (27 bp):
CACCTTTCCAGTCCTCAAAGAGCAGGA
Found at i:255690 original size:51 final size:53
Alignment explanation
Indices: 255626--255756 Score: 160
Period size: 51 Copynumber: 2.5 Consensus size: 53
255616 AGTTTCTCAA
* * * *
255626 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* * *
255677 TT-TTCTATAATCGGAGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
255731 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
255757 CCCGTTACTT
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
50 2 0.03
51 32 0.49
53 9 0.14
54 19 0.29
55 3 0.05
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:258591 original size:12 final size:12
Alignment explanation
Indices: 258559--258593 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
258549 TATTTAAGGT
258559 ATTATATAAATA
1 ATTATATAAATA
* *
258571 ATGACATAAATA
1 ATTATATAAATA
258583 ATTATATAAAT
1 ATTATATAAAT
258594 TTTTTTATGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (12 bp):
ATTATATAAATA
Found at i:259990 original size:16 final size:16
Alignment explanation
Indices: 259962--260005 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
259952 GTGAATAAAA
259962 TATAAAAATAATAAATT
1 TATAAAAA-AATAAATT
* * *
259979 TTTTAAAAAATATATT
1 TATAAAAAAATAAATT
259995 TATAAAAAAAT
1 TATAAAAAAAT
260006 CTAAAAAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TATAAAAAAATAAATT
Found at i:260233 original size:20 final size:19
Alignment explanation
Indices: 260188--260333 Score: 72
Period size: 20 Copynumber: 7.6 Consensus size: 19
260178 AATAATTTTT
260188 ATATTTATATTATATTT-AA
1 ATATTTATATT-TATTTAAA
260207 ATATTTA-ATTTTATTTAAA
1 ATATTTATA-TTTATTTAAA
*
260226 ATATTTTATATTTATATAAA
1 ATA-TTTATATTTATTTAAA
* * *
260246 ATTATATATATATAATTTATA
1 A-TATTTATAT-TTATTTAAA
* * * *
260267 TTATATATATATAATT-AA
1 ATATTTATATTTATTTAAA
*
260285 ATATTATATATATAATTT---
1 ATATT-TATAT-TTATTTAAA
**
260303 ATA-TTATATAAATTTTAAA
1 ATATTTATATTTA-TTTAAA
260322 ATATTTATATTT
1 ATATTTATATTT
260334 CAATTATTTT
Statistics
Matches: 96, Mismatches: 18, Indels: 25
0.69 0.13 0.18
Matches are distributed among these distances:
15 2 0.02
16 8 0.08
17 1 0.01
18 13 0.14
19 25 0.26
20 38 0.40
21 9 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTTATATTTATTTAAA
Found at i:260253 original size:2 final size:2
Alignment explanation
Indices: 260248--260312 Score: 54
Period size: 2 Copynumber: 36.0 Consensus size: 2
260238 TATATAAAAT
* *
260248 TA TA TA TA TA TA -A TT TA TA T- TA TA TA TA TA TA -A T- TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
260286 TA T- TA TA TA TA TA -A TT TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
260313 AATTTTAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
1 7 0.14
2 43 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:260257 original size:14 final size:14
Alignment explanation
Indices: 260238--260314 Score: 56
Period size: 14 Copynumber: 5.6 Consensus size: 14
260228 ATTTTATATT
260238 TATATAAAATTATA
1 TATATAAAATTATA
*
260252 TATATATAATT-TA
1 TATATAAAATTATA
*
260265 TAT-T-ATA-TATA
1 TATATAAAATTATA
260276 TATAATTAAATATTATA
1 TAT-A-TAAA-ATTATA
*
260293 TATAT-AATTTATA
1 TATATAAAATTATA
260306 TTATATAAA
1 -TATATAAA
260315 TTTTAAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
10 1 0.02
11 6 0.12
12 1 0.02
13 10 0.20
14 18 0.37
15 4 0.08
16 2 0.04
17 7 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATATAAAATTATA
Found at i:260319 original size:16 final size:17
Alignment explanation
Indices: 260174--260319 Score: 87
Period size: 16 Copynumber: 8.8 Consensus size: 17
260164 TAATAAATAG
260174 ATATAATAATTTTTATATT
1 ATAT-ATAA-TTTTATATT
*
260193 -TATATTATATTTA-A--
1 ATATATAAT-TTTATATT
*
260207 ATATTTAATTTTAT-TT
1 ATATATAATTTTATATT
*
260223 A-AAAT-ATTTTATATT
1 ATATATAATTTTATATT
**
260238 -TATATAAAATTATA-T
1 ATATATAATTTTATATT
260253 ATATATAATTTATATTATAT
1 ATATATAATTT-TA-TAT-T
**
260273 ATATATAATTAAATATT
1 ATATATAATTTTATATT
*
260290 ATATATATAATTTATATT
1 ATATATA-ATTTTATATT
260308 ATATA-AATTTTA
1 ATATATAATTTTA
260320 AAATATTTAT
Statistics
Matches: 97, Mismatches: 16, Indels: 31
0.67 0.11 0.22
Matches are distributed among these distances:
14 11 0.11
15 14 0.14
16 22 0.23
17 18 0.19
18 20 0.21
19 1 0.01
20 11 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATAATTTTATATT
Found at i:268042 original size:17 final size:17
Alignment explanation
Indices: 268022--268069 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
268012 TCTAAAATTT
268022 GATTTTTTGA-ATTAATA
1 GATTTTTTGATATT-ATA
*
268039 GATTTTTAGATATTATA
1 GATTTTTTGATATTATA
* *
268056 TATTTTTTAATATT
1 GATTTTTTGATATT
268070 TATTTTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 23 0.88
18 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (17 bp):
GATTTTTTGATATTATA
Found at i:270922 original size:17 final size:17
Alignment explanation
Indices: 270883--270925 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
270873 TGTTAACTTC
*
270883 AAATTT-AATTACATAA
1 AAATTTAAATTACAAAA
**
270899 ATTTTTAAATTACAAAA
1 AAATTTAAATTACAAAA
270916 AAATTTAAAT
1 AAATTTAAAT
270926 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTTAAATTACAAAA
Found at i:272370 original size:16 final size:17
Alignment explanation
Indices: 272343--272384 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
272333 ATTTTTAAAT
272343 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
272358 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
272375 AAATTTTATT
1 AAATTTTATT
272385 AAAACCTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 7 0.30
16 6 0.26
17 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Done.