Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 118 of 226
Found at i:40194595 original size:83 final size:82
Alignment explanation
Indices: 40194456--40194664 Score: 337
Period size: 83 Copynumber: 2.5 Consensus size: 82
40194446 CTTTTTTGCT
* *
40194456 AAAGTCTGAGCATTAGCGGCGCTTTTCCAAAAAGGTCGCTAAAGGTCTGAGCATTAGCGGCGCTT
1 AAAGTCTGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTAGCGGCGCTT
*
40194521 TTCCAAAAAATGCCGCTA
66 TTCC-AAAAACGCCGCTA
**
40194539 AAAGTCTGAGCATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGGTCTGAGCATTAGCGGCGCTT
1 AAAGTCTGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTAGCGGCGCTT
*
40194604 TTCCATAAACGCCGCTA
66 TTCCAAAAACGCCGCTA
* *
40194621 AAGGTCTGAACATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAG
1 AAAGTCTGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAG
40194665 CCTAGAAAGG
Statistics
Matches: 116, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
82 51 0.44
83 65 0.56
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (82 bp):
AAAGTCTGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGGTCTGAGCATTAGCGGCGCTT
TTCCAAAAACGCCGCTA
Found at i:40194792 original size:40 final size:38
Alignment explanation
Indices: 40194704--40194825 Score: 129
Period size: 40 Copynumber: 3.1 Consensus size: 38
40194694 GGCTTAGGTT
* * *
40194704 TTTTTGCAAA-CGCCGCTAGTGCTCATTTTTAGCGGCG
1 TTTTTGAAAAGCGCCGCTAATGCTGATTTTTAGCGGCG
** *
40194741 TTTTCAAAAAAGCGCCGCTAATGCTGGATCTTTAGCGGCG
1 TTTT-TGAAAAGCGCCGCTAATGCT-GATTTTTAGCGGCG
* *
40194781 ATTTTTGAAAAGTGCCGCTAATACTTGATTTTTAGCGGCG
1 -TTTTTGAAAAGCGCCGCTAATGC-TGATTTTTAGCGGCG
40194821 TTTTT
1 TTTTT
40194826 TATTCAAACG
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
37 4 0.06
38 3 0.04
39 17 0.25
40 40 0.58
41 5 0.07
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (38 bp):
TTTTTGAAAAGCGCCGCTAATGCTGATTTTTAGCGGCG
Found at i:40212609 original size:41 final size:41
Alignment explanation
Indices: 40212496--40212631 Score: 115
Period size: 41 Copynumber: 3.4 Consensus size: 41
40212486 ACCAGTTTGG
* * *
40212496 CACCCAGTGCCTCATC-AGA-TAATGCAAAGTAATAAATTGA
1 CACCCAATGCCTCATCGA-ATTAATCCAAAGTAGTAAATTGA
* * * * *
40212536 CAACCAATGTCTCATCTG--TTAAACC---GGAGTAAATTGG
1 CACCCAATGCCTCATC-GAATTAATCCAAAGTAGTAAATTGA
*
40212573 CACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGA
1 CACCCAATGCCTCATCGAATTAATCCAAAGTAGTAAATTGA
*
40212614 CACCCAATGTCTCATCGA
1 CACCCAATGCCTCATCGA
40212632 CTCGAAGTCG
Statistics
Matches: 72, Mismatches: 16, Indels: 15
0.70 0.16 0.15
Matches are distributed among these distances:
36 1 0.01
37 22 0.31
38 6 0.08
40 17 0.24
41 26 0.36
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (41 bp):
CACCCAATGCCTCATCGAATTAATCCAAAGTAGTAAATTGA
Found at i:40213581 original size:22 final size:22
Alignment explanation
Indices: 40213541--40213598 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
40213531 TTCTTTCCTT
* * * *
40213541 TTTCTATTCTGTTTCGTTTGGC
1 TTTCTTTTTTGTTTCGTTTCGA
*
40213563 TTTCTTTGTTTGTTT-GTTTCTA
1 TTTCTTT-TTTGTTTCGTTTCGA
40213585 TTTCTTTTTTGTTT
1 TTTCTTTTTTGTTT
40213599 TTATTATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 7 0.23
22 17 0.57
23 6 0.20
ACGTcount: A:0.03, C:0.12, G:0.14, T:0.71
Consensus pattern (22 bp):
TTTCTTTTTTGTTTCGTTTCGA
Found at i:40213617 original size:5 final size:5
Alignment explanation
Indices: 40213609--40213642 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
40213599 TTATTATTAT
*
40213609 TATAA TATAA TATGA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA
40213643 TACTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:40213663 original size:9 final size:11
Alignment explanation
Indices: 40213636--40213663 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
40213626 TAATATAATA
40213636 TAATATATACT
1 TAATATATACT
40213647 TAATATATACT
1 TAATATATACT
40213658 TAATAT
1 TAATAT
40213664 TTAAGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATATATACT
Found at i:40223265 original size:7 final size:7
Alignment explanation
Indices: 40223255--40223294 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
40223245 ATTAAAGCAT
*
40223255 GGAAAAT
1 GGAAAAA
40223262 GGAAAAA
1 GGAAAAA
40223269 GGAAAAA
1 GGAAAAA
40223276 GGAAAAA
1 GGAAAAA
40223283 GGAAAAA
1 GGAAAAA
40223290 -GAAAA
1 GGAAAA
40223295 TAAACAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.03
Consensus pattern (7 bp):
GGAAAAA
Found at i:40251341 original size:2 final size:2
Alignment explanation
Indices: 40251334--40251360 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40251324 ACATTACTTG
40251334 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
40251361 TAGGTTTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40252263 original size:2 final size:2
Alignment explanation
Indices: 40252251--40252283 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
40252241 ATTCAATTTT
*
40252251 AC AC CC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
40252284 AAAAACTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:40260114 original size:2 final size:2
Alignment explanation
Indices: 40260103--40260133 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
40260093 GTATGTGAAT
40260103 TA TA -A 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
40260134 ACTATACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:40260579 original size:23 final size:23
Alignment explanation
Indices: 40260553--40260597 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40260543 AATAGATTTG
* *
40260553 AAATCAACAATATACAAATCAAT
1 AAATAAACAATACACAAATCAAT
**
40260576 AAATAAATTATACACAAATCAA
1 AAATAAACAATACACAAATCAA
40260598 CAAAATAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAACAATACACAAATCAAT
Found at i:40260831 original size:23 final size:22
Alignment explanation
Indices: 40260788--40260845 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
40260778 AAAGGGTACC
* *
40260788 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
40260809 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
40260832 TGCATATCATATCT
1 TACAAATCATATCT
40260846 AAGATTGCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:40260862 original size:21 final size:19
Alignment explanation
Indices: 40260824--40260919 Score: 147
Period size: 21 Copynumber: 4.8 Consensus size: 19
40260814 AATCATATCT
40260824 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
40260843 TCTAAGATTGCTTGTATCATA
1 TCTAAGATTGC--ATATCATA
40260864 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
40260883 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
40260904 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
40260920 CTTGAAGATT
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
19 34 0.48
21 37 0.52
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:40260872 original size:40 final size:40
Alignment explanation
Indices: 40260824--40260919 Score: 174
Period size: 40 Copynumber: 2.4 Consensus size: 40
40260814 AATCATATCT
* *
40260824 TCTAAGATTGCATATCATATCTAAGATTGCTTGTATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
40260864 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
40260904 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
40260920 CTTGAAGATT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:40261109 original size:6 final size:6
Alignment explanation
Indices: 40261098--40261132 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
40261088 ACCGCAAAGA
*
40261098 AAATAG AAATAG AAATAG AAATAG GAATAG AAATA
1 AAATAG AAATAG AAATAG AAATAG AAATAG AAATA
40261133 AAGAACACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
AAATAG
Found at i:40265593 original size:6 final size:6
Alignment explanation
Indices: 40265557--40265591 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
40265547 ATCACAAAGA
* *
40265557 AAATAG CAATAG AAATAG AAATAG AAATAA AAATA
1 AAATAG AAATAG AAATAG AAATAG AAATAG AAATA
40265592 AAGAACACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (6 bp):
AAATAG
Found at i:40269068 original size:16 final size:15
Alignment explanation
Indices: 40269047--40269076 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40269037 AATGACAATG
40269047 AATAAATCGTGCAGTA
1 AATAAATCGT-CAGTA
40269063 AATAAATCGTCAGT
1 AATAAATCGTCAGT
40269077 TAATGGTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (15 bp):
AATAAATCGTCAGTA
Found at i:40270482 original size:113 final size:112
Alignment explanation
Indices: 40270278--40270561 Score: 263
Period size: 113 Copynumber: 2.5 Consensus size: 112
40270268 TTTTGGTTTT
* * * ** * *
40270278 GCGCCGCAAAATCTCA-AGA-CAAAACGCATCGTTTTTGTCTTGATGTATACAATAATTAGTGTC
1 GCGCCGCAAAATATCATA-ACCAAAACGCATCG-TTTTGTATCGATGTATATTAGAATTAGTGGC
** * * * * * *
40270341 GATTATGATAAAATGCCGCTAAAGCAAGTATTAGAGGCGCATTGCGGGAA
64 GATTACAAAAAAACGCCGCTAAAACAAGTATTAGAGACGC-TTACGGAAA
* *
40270391 GCGCCGCAAAA-ATCTTAACGAAAACGCATCGTTTTGGTATCGATGTATATTAGAATTAGTGGCG
1 GCGCCGCAAAATATCATAACCAAAACGCATCGTTTT-GTATCGATGTATATTAGAATTAGTGGCG
* * *
40270455 TTTACAAAAAAACGCCAG-TAAAACAAGTCTTAGTGACGCTTACGGAAA
65 ATTACAAAAAAACGCC-GCTAAAACAAGTATTAGAGACGCTTACGGAAA
* **
40270503 GCGCCGCAAAATATGATAACCAAAACGCAGAGTTTTG-ATCGTGATGTATATTAGAATTA
1 GCGCCGCAAAATATCATAACCAAAACGCATCGTTTTGTATC--GATGTATATTAGAATTA
40270562 TGAAGCGCCG
Statistics
Matches: 139, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
111 3 0.02
112 26 0.19
113 109 0.78
114 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (112 bp):
GCGCCGCAAAATATCATAACCAAAACGCATCGTTTTGTATCGATGTATATTAGAATTAGTGGCGA
TTACAAAAAAACGCCGCTAAAACAAGTATTAGAGACGCTTACGGAAA
Found at i:40270624 original size:63 final size:63
Alignment explanation
Indices: 40270501--40270624 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 63
40270491 CGCTTACGGA
* * * * *
40270501 AAGCGCCGCAAAATATGATAACCAAAACGCAGAGTTTTGATCGTGATGTATATTAGAATTATG
1 AAGCGCCGCAAAAAATGATAACCAAAACGCAGAGGTTTGATCGTGATGGATAATACAATTATG
* * *
40270564 AAGCGCCGCAAAAAATGTTAACCAAAACGCAGCGGTTTGGTC-TCGATGGATAATACAATTA
1 AAGCGCCGCAAAAAATGATAACCAAAACGCAGAGGTTTGATCGT-GATGGATAATACAATTA
40270625 GTGGCGTTAG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 1 0.02
63 51 0.98
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (63 bp):
AAGCGCCGCAAAAAATGATAACCAAAACGCAGAGGTTTGATCGTGATGGATAATACAATTATG
Found at i:40270931 original size:229 final size:228
Alignment explanation
Indices: 40270563--40270993 Score: 578
Period size: 229 Copynumber: 1.9 Consensus size: 228
40270553 TTAGAATTAT
* *
40270563 GAAGCGCCGCAAAAAATGTTAACCAAAACGCAGCGGTTTGGTCTCGATGGATAATACAATTAGTG
1 GAAGCGCCGCAAAAAATCTTAACCAAAAAGCAGCGGTTTGGTCTCGATGGATAATACAATTAGTG
* * * * *
40270628 GCGTTAGGGGAAAACGCTGCTAAAGCATAACATTAGCGGCGATTTTCTAGAATCGCCGCAAGATA
66 GCGTTAGGAGAAAACGCCGCTAAAGAATAACATTAGCGGCGATTTTCAAGAAGCGCCGCAAGATA
* * * *
40270693 TGCACACCAAAACGCAGAGTTTGGTGTTGAGGTATATTAGGATTAGTGGCGCTTACTGTAAAACG
131 TGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGACTGGAAAACG
40270758 CCGCTAAAGCGTACTATTAGTGGCGCTTCTCCA
196 CCGCTAAAGCGTACTATTAGTGGCGCTTCTCCA
* ** * * * * * * *
40270791 GAAGCGCCGCTAAATTTCTTAACCAAAAATCAGCGTTTTGGTCTTGATGTATACTATAGTTAGTG
1 GAAGCGCCGCAAAAAATCTTAACCAAAAAGCAGCGGTTTGGTCTCGATGGATAATACAATTAGTG
* * **
40270856 GCGCTTATGAGAAAACGCCGCTAAATAATAGTATTAGCGGCGA-TTT-AAGTTAAGCGCCGCAAG
66 GCG-TTAGGAGAAAACGCCGCTAAAGAATAACATTAGCGGCGATTTTCAAG--AAGCGCCGCAAG
*
40270919 ATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGATTGGAAA
128 ATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGACTGGAAA
*
40270984 ATGCCGCTAA
193 ACGCCGCTAA
40270994 TGTATACTAT
Statistics
Matches: 173, Mismatches: 27, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
227 2 0.01
228 59 0.34
229 112 0.65
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (228 bp):
GAAGCGCCGCAAAAAATCTTAACCAAAAAGCAGCGGTTTGGTCTCGATGGATAATACAATTAGTG
GCGTTAGGAGAAAACGCCGCTAAAGAATAACATTAGCGGCGATTTTCAAGAAGCGCCGCAAGATA
TGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGACTGGAAAACG
CCGCTAAAGCGTACTATTAGTGGCGCTTCTCCA
Found at i:40271005 original size:114 final size:113
Alignment explanation
Indices: 40270584--40271008 Score: 373
Period size: 114 Copynumber: 3.7 Consensus size: 113
40270574 AAAAATGTTA
* * * * * *
40270584 ACCAAAACGCAGCGGTTTGGTCTCGATGG-ATAATACAATTAGTGGCG-TTAGGGGAAAACGCTG
1 ACCAAAACGCAG-AGTTTGGTCTTGA-GGTATATTAGAATTAGTGGCGCTTA-TGGAAAACGCCG
* * * * *
40270647 CTAAAGCATAAC-ATTAGCGGCGATTTTCTAGAATCGCCGCAAGATATGCAC
63 CTAATGAAT-ACTATTAGCGGCGATTCTCAAGAAGCGCCGCAAGATATGCAC
* * *
40270698 ACCAAAACGCAGAGTTTGGTGTTGAGGTATATTAGGATTAGTGGCGCTTACTGTAAAACGCCGCT
1 ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTA-TGGAAAACGCCGCT
* ** * * * *
40270763 AAAGCGTACTATTAGTGGCGCTTCTCCAGAAGCGCCGCTAA-AT-TTCTTA-
65 AATGAATACTATTAGCGGCGATTCTCAAGAAGCGCCGC-AAGATATGC--AC
** * * * * *
40270812 ACCAAAAATCAGCGTTTTGGTCTTGATGTATACTATAGTTAGTGGCGCTTATGAGAAAACGCCGC
1 ACCAAAACGCAGAG-TTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATG-GAAAACGCCGC
*
40270877 TAAAT-AATAGTATTAGCGGCGATT-T-AAGTTAAGCGCCGCAAGATATGCAC
64 T-AATGAATACTATTAGCGGCGATTCTCAAG--AAGCGCCGCAAGATATGCAC
* *
40270927 ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGATTGGAAAATGCCGCT
1 ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTA-TGGAAAACGCCGCT
*
40270992 AATGTATACTATTAGCG
65 AATGAATACTATTAGCG
40271009 ACGCGTTTTT
Statistics
Matches: 249, Mismatches: 46, Indels: 32
0.76 0.14 0.10
Matches are distributed among these distances:
112 2 0.01
113 34 0.14
114 127 0.51
115 82 0.33
116 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (113 bp):
ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGGAAAACGCCGCTA
ATGAATACTATTAGCGGCGATTCTCAAGAAGCGCCGCAAGATATGCAC
Found at i:40271122 original size:229 final size:229
Alignment explanation
Indices: 40270620--40271123 Score: 552
Period size: 229 Copynumber: 2.2 Consensus size: 229
40270610 TGGATAATAC
* * * * * *
40270620 AATTAGTGGCG-TTAGGGGAAAACGCTGCTAAAGCATAACATTAGCGGCGATTTTCTAGAATCGC
1 AATTAGTGGCGATTACGAGAAAACGCCGCTAAAGCATAATATTAGCGGCGATTTTCAAGAAGCGC
* * *
40270684 CGCAAGATATGCACACCAAAACGCAGAGTTTGGTGTTGAGGTATATTAGGATTAGTGGCGCTTAC
66 CGCAAGATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGAC
* * * * * * *
40270749 TGTAAAACGCCGCTAAAGCGTACTATTAGTGGCGCTTCTCCAGAAGCGCCGCTAAATTTCTTAAC
131 TGGAAAACGCCGCTAAAGCATACTATTAGCGACGCTTCTCCAGAAGCACCGCTAAATATATTAAC
* *** *
40270814 CAAAAATCAGCGTTTTGGTCTTGATGTATACTAT
196 CAAAAAGCAGCGTTTAAATCTTGATGTATACTAG
* * * ** *
40270848 AGTTAGTGGCGCTTATGAGAAAACGCCGCTAAATAATAGTATTAGCGGCGA-TTT-AAGTTAAGC
1 AATTAGTGGCGATTACGAGAAAACGCCGCTAAAGCATAATATTAGCGGCGATTTTCAAG--AAGC
40270911 GCCGCAAGATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTG
64 GCCGCAAGATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTG
* * * * ** *
40270976 ATTGGAAAATGCCGCTAATGTATACTATTAGCGACGCGTT-TTTAGATGCACCGC-AGAATATAT
129 ACTGGAAAACGCCGCTAAAGCATACTATTAGCGACGC-TTCTCCAGAAGCACCGCTA-AATATAT
* * * *
40271039 TAACCGAAACGCTGCGTTTAAATCTTGATGTATACTGG
192 TAACCAAAAAGCAGCGTTTAAATCTTGATGTATACTAG
* * *
40271077 AATTAGTGGC-ATTCACGATAAATCGCCGCTAAAGCATATTATTAGCG
1 AATTAGTGGCGATT-ACGAGAAAACGCCGCTAAAGCATAATATTAGCG
40271124 ACGCTTTTTG
Statistics
Matches: 226, Mismatches: 44, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
227 2 0.01
228 16 0.07
229 206 0.91
230 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (229 bp):
AATTAGTGGCGATTACGAGAAAACGCCGCTAAAGCATAATATTAGCGGCGATTTTCAAGAAGCGC
CGCAAGATATGCACACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTGAC
TGGAAAACGCCGCTAAAGCATACTATTAGCGACGCTTCTCCAGAAGCACCGCTAAATATATTAAC
CAAAAAGCAGCGTTTAAATCTTGATGTATACTAG
Found at i:40271504 original size:22 final size:22
Alignment explanation
Indices: 40271488--40271542 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
40271478 GGGTTATGGT
*
40271488 GTTTTGGGTTTACGGTTTAGGA
1 GTTTGGGGTTTACGGTTTAGGA
* *
40271510 GTTTGGGGTTTAAGATTTAGG-
1 GTTTGGGGTTTACGGTTTAGGA
40271531 GTTTGGGGTTTA
1 GTTTGGGGTTTA
40271543 GGCTACTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.15, C:0.02, G:0.38, T:0.45
Consensus pattern (22 bp):
GTTTGGGGTTTACGGTTTAGGA
Found at i:40271961 original size:23 final size:24
Alignment explanation
Indices: 40271912--40271975 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
40271902 TATAAGACAT
* *
40271912 TAATTTAATAA-TATAAATAATTTA
1 TAATTT-ATAATTTTAAATAATTGA
40271936 TAATTTATAATTTTAAAT-ATTGA
1 TAATTTATAATTTTAAATAATTGA
40271959 TAATATT-TAAATTTTAA
1 TAAT-TTAT-AATTTTAA
40271976 TGTATGAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 13 0.37
24 22 0.63
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TAATTTATAATTTTAAATAATTGA
Found at i:40272630 original size:44 final size:44
Alignment explanation
Indices: 40272577--40272675 Score: 153
Period size: 44 Copynumber: 2.2 Consensus size: 44
40272567 TTTGAAATTC
* * *
40272577 TTGCGTCCTTCTTGCCCAATTTCTTGAATTCCCAAATCCGTAAA
1 TTGCCTCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAA
*
40272621 TTGCCTCCTTCTTGCCGAATTTCTTGAAATCCCAAATCCCTAAA
1 TTGCCTCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAA
*
40272665 TCGCCTCCTTC
1 TTGCCTCCTTC
40272676 CTCCTTCCAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.21, C:0.33, G:0.10, T:0.35
Consensus pattern (44 bp):
TTGCCTCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAA
Found at i:40274347 original size:35 final size:35
Alignment explanation
Indices: 40274308--40274401 Score: 156
Period size: 35 Copynumber: 2.7 Consensus size: 35
40274298 TAAAGTTATA
40274308 TTTTAAATATTTTATTTTATTTTAATCACGAA-ATT
1 TTTTAAATATTTTATTTTATTTTAATCACGAATA-T
*
40274343 TTTTAAATTTTTTATTTTATTTTAATCACGAATAT
1 TTTTAAATATTTTATTTTATTTTAATCACGAATAT
40274378 TTTTAAATATTTTATTTT-TTTTAA
1 TTTTAAATATTTTATTTTATTTTAA
40274402 AGTTCAAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
34 6 0.11
35 49 0.88
36 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (35 bp):
TTTTAAATATTTTATTTTATTTTAATCACGAATAT
Found at i:40274440 original size:9 final size:9
Alignment explanation
Indices: 40274428--40274493 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
40274418 GTTACGTAAT
40274428 TTACATAAC
1 TTACATAAC
40274437 TTACATAA-
1 TTACATAAC
40274445 TT-CATAAC
1 TTACATAAC
*
40274453 TTACATAAT
1 TTACATAAC
*
40274462 TTAAATTTATA-
1 TTACA--TA-AC
*
40274473 ATACATAAC
1 TTACATAAC
40274482 TTACATAAC
1 TTACATAAC
40274491 TTA
1 TTA
40274494 TTAATATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
7 5 0.11
8 5 0.11
9 30 0.65
11 5 0.11
12 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.39
Consensus pattern (9 bp):
TTACATAAC
Found at i:40274452 original size:16 final size:16
Alignment explanation
Indices: 40274431--40274489 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 16
40274421 ACGTAATTTA
40274431 CATAACTTACATAATT
1 CATAACTTACATAATT
40274447 CATAACTTACATAATT
1 CATAACTTACATAATT
* * *
40274463 --TAAATT-TATAATA
1 CATAACTTACATAATT
40274476 CATAACTTACATAA
1 CATAACTTACATAA
40274490 CTTATTAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 5 0.14
14 5 0.14
15 5 0.14
16 20 0.57
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.37
Consensus pattern (16 bp):
CATAACTTACATAATT
Found at i:40274614 original size:23 final size:22
Alignment explanation
Indices: 40274564--40274627 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
40274554 TTTAAAATTG
40274564 ATACATTACATAACTTACATAAC
1 ATACA-TACATAACTTACATAAC
*
40274587 CTACATACATAAGCTTACAT---
1 ATACATACATAA-CTTACATAAC
*
40274607 ATA-ATACATAACTTATATAAC
1 ATACATACATAACTTACATAAC
40274628 TTAAATTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
18 6 0.18
19 8 0.24
20 2 0.06
22 7 0.21
23 11 0.32
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (22 bp):
ATACATACATAACTTACATAAC
Found at i:40274783 original size:12 final size:12
Alignment explanation
Indices: 40274759--40274822 Score: 101
Period size: 12 Copynumber: 5.3 Consensus size: 12
40274749 AAAAACTTAC
*
40274759 ATAACTTATATA
1 ATAACTTACATA
*
40274771 ATATCTTACATA
1 ATAACTTACATA
40274783 ATAACTTACATA
1 ATAACTTACATA
*
40274795 ATATCTTACATA
1 ATAACTTACATA
40274807 ATAACTTACATA
1 ATAACTTACATA
40274819 ATAA
1 ATAA
40274823 TGCGTACCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 47 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:40274795 original size:24 final size:24
Alignment explanation
Indices: 40274759--40274821 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
40274749 AAAAACTTAC
*
40274759 ATAACTTATATAATATCTTACATA
1 ATAACTTACATAATATCTTACATA
40274783 ATAACTTACATAATATCTTACATA
1 ATAACTTACATAATATCTTACATA
40274807 ATAACTTACATAATA
1 ATAACTTACATAATA
40274822 ATGCGTACCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAACTTACATAATATCTTACATA
Found at i:40274814 original size:119 final size:120
Alignment explanation
Indices: 40274688--40274917 Score: 365
Period size: 119 Copynumber: 1.9 Consensus size: 120
40274678 CACAACTTAC
* *
40274688 ATAACTTAGATAATAATACATACCGTACATAAATTAAATAAGTTACAGAATACACAAAAACAAAA
1 ATAACTTACATAATAATACATACCCTACATAAATTAAATAAGTTACAGAATACACAAAAACAAAA
*
40274753 ACT-TA-CATAACTTATATAATATCTTACATAATAACTTACATAATATCTTACATA
66 A-TGTAGCATAACTTACATAATATCTTACATAATAACTTACATAATATCTTACATA
* * *
40274807 ATAACTTACATAATAATGCGTACCCTACATAAATTAAATAAGTTACATAATACACAAAAACAAAA
1 ATAACTTACATAATAATACATACCCTACATAAATTAAATAAGTTACAGAATACACAAAAACAAAA
**
40274872 ATGTAGTGTAACTTACATAATATCTTACATAATAACTTACATAATA
66 ATGTAGCATAACTTACATAATATCTTACATAATAACTTACATAATA
40274918 ATACATACCG
Statistics
Matches: 101, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
118 1 0.01
119 63 0.62
120 37 0.37
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.30
Consensus pattern (120 bp):
ATAACTTACATAATAATACATACCCTACATAAATTAAATAAGTTACAGAATACACAAAAACAAAA
ATGTAGCATAACTTACATAATATCTTACATAATAACTTACATAATATCTTACATA
Found at i:40274900 original size:12 final size:12
Alignment explanation
Indices: 40274880--40274918 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
40274870 AAATGTAGTG
40274880 TAACTTACATAA
1 TAACTTACATAA
*
40274892 TATCTTACATAA
1 TAACTTACATAA
40274904 TAACTTACATAA
1 TAACTTACATAA
40274916 TAA
1 TAA
40274919 TACATACCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (12 bp):
TAACTTACATAA
Found at i:40275029 original size:9 final size:9
Alignment explanation
Indices: 40275005--40275118 Score: 100
Period size: 9 Copynumber: 13.6 Consensus size: 9
40274995 GTATATAATG
40275005 ACTTACATA
1 ACTTACATA
40275014 A--TACATA
1 ACTTACATA
*
40275021 ATTTACATA
1 ACTTACATA
*
40275030 AGTTACATA
1 ACTTACATA
*
40275039 A--GACATA
1 ACTTACATA
40275046 ACTTACATA
1 ACTTACATA
* *
40275055 AGTTTCATA
1 ACTTACATA
*
40275064 A--TACACA
1 ACTTACATA
*
40275071 ACTTACACA
1 ACTTACATA
*
40275080 ACTTACACA
1 ACTTACATA
40275089 ACTTACATA
1 ACTTACATA
40275098 ACTTACATA
1 ACTTACATA
40275107 A--TACATA
1 ACTTACATA
40275114 ACTTA
1 ACTTA
40275119 TTCCTAAATC
Statistics
Matches: 89, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
7 25 0.28
9 64 0.72
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:40275040 original size:96 final size:96
Alignment explanation
Indices: 40274783--40275020 Score: 356
Period size: 96 Copynumber: 2.5 Consensus size: 96
40274773 ATCTTACATA
* *
40274783 ATAACTTACATAATATCTTACATAATAACTTACATAATAATGCGTACCCTACATAAATTAAATAA
1 ATAACTTACATAATATCTTACATAATAACTTACATAATAATACATACCCTACATAAATTAAATAA
*
40274848 GTTACATAATACACAAAAACAAAAATGTAGT
66 GTTACATAATACACAAAAACAAAAATGTAGC
* *
40274879 GTAACTTACATAATATCTTACATAATAACTTACATAATAATACATACCGTACATAAATTAAATAA
1 ATAACTTACATAATATCTTACATAATAACTTACATAATAATACATACCCTACATAAATTAAATAA
40274944 GTTACATAATACACAAAAACAAAAACT-TA-C
66 GTTACATAATACACAAAAACAAAAA-TGTAGC
* * *
40274974 ATAACTTACATAATATCTTACGTATATAA-TGACTTACATAATACATA
1 ATAACTTACATAATATCTTACATA-ATAACTTACATA-ATAATACATA
40275021 ATTTACATAA
Statistics
Matches: 130, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
95 27 0.21
96 102 0.78
97 1 0.01
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (96 bp):
ATAACTTACATAATATCTTACATAATAACTTACATAATAATACATACCCTACATAAATTAAATAA
GTTACATAATACACAAAAACAAAAATGTAGC
Found at i:40275064 original size:34 final size:32
Alignment explanation
Indices: 40275008--40275118 Score: 93
Period size: 34 Copynumber: 3.3 Consensus size: 32
40274998 TATAATGACT
40275008 TACATAA--TACATAATTTACATAAGTTACATAA
1 TACATAACTTACATAATTT-CATAA-TTACATAA
* *
40275040 GACATAACTTACATAAGTTTCATAA-TACACAA
1 TACATAACTTACATAA-TTTCATAATTACATAA
* * *
40275072 CTTACACAACTTACACAACTTACATAACTTACATAA
1 --TACATAACTTACATAA-TTTCATAA-TTACATAA
40275108 TACATAACTTA
1 TACATAACTTA
40275119 TTCCTAAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
32 12 0.19
34 42 0.67
35 3 0.05
36 6 0.10
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.31
Consensus pattern (32 bp):
TACATAACTTACATAATTTCATAATTACATAA
Found at i:40275113 original size:16 final size:17
Alignment explanation
Indices: 40275007--40275118 Score: 92
Period size: 16 Copynumber: 6.7 Consensus size: 17
40274997 ATATAATGAC
40275007 TTACATAA--TACATAA
1 TTACATAACTTACATAA
*
40275022 TTTACATAAGTTACATAA
1 -TTACATAACTTACATAA
*
40275040 -GACATAACTTACATAA
1 TTACATAACTTACATAA
* *
40275056 GTTTCATAA--TACACAA
1 -TTACATAACTTACATAA
* *
40275072 CTTACACAACTTACACAA
1 -TTACATAACTTACATAA
40275090 CTTACATAACTTACATAA
1 -TTACATAACTTACATAA
40275108 -TACATAACTTA
1 TTACATAACTTA
40275119 TTCCTAAATC
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
16 45 0.56
18 35 0.44
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (17 bp):
TTACATAACTTACATAA
Found at i:40275118 original size:25 final size:25
Alignment explanation
Indices: 40274967--40275114 Score: 122
Period size: 25 Copynumber: 5.8 Consensus size: 25
40274957 CAAAAACAAA
40274967 AACTTACATAACTTACATAATATC-T
1 AACTTACATAACTTACATAATA-CAT
* * *
40274992 TACGTATATAATGACTTACATAATACAT
1 AAC-T-TA-CATAACTTACATAATACAT
* * *
40275020 AATTTACATAAGTTACATAAGACAT
1 AACTTACATAACTTACATAATACAT
* * *
40275045 AACTTACATAAGTTTCATAATACAC
1 AACTTACATAACTTACATAATACAT
* *
40275070 AACTTACACAACTTACACAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
40275097 AACTTACATAA--TACATAA
1 AACTTACATAACTTACATAA
40275115 CTTATTCCTA
Statistics
Matches: 97, Mismatches: 20, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
25 60 0.62
26 3 0.03
27 18 0.19
28 16 0.16
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:40280661 original size:21 final size:20
Alignment explanation
Indices: 40280636--40280704 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 20
40280626 CAACAACTTA
*
40280636 AAGCAGAGGCAGCAGCGAGGG
1 AAGCAGAGGCA-CAGCGAGAG
*
40280657 AAGCAGAGGCTACAACGAGAG
1 AAGCAGAGGC-ACAGCGAGAG
40280678 AAGCAGAGGCCACAGCGAGAG
1 AAGCAGAGG-CACAGCGAGAG
40280699 AAGCAG
1 AAGCAG
40280705 CGATAGAAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 41 0.95
22 2 0.05
ACGTcount: A:0.39, C:0.20, G:0.39, T:0.01
Consensus pattern (20 bp):
AAGCAGAGGCACAGCGAGAG
Found at i:40281255 original size:42 final size:42
Alignment explanation
Indices: 40281160--40281404 Score: 359
Period size: 43 Copynumber: 5.8 Consensus size: 42
40281150 AATAAGCGTA
40281160 GCTAAAGAACACT-A-CTTTTAGCGGCGTTTTCTTCCTAAGCGCC
1 GCTAAAGAACA-TGATC-TTTAGCGGCGTTTT-TTCCTAAGCGCC
*
40281203 GCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCAAGCGCC
1 GCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCTAAGCGCC
*
40281245 GCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCAAGCGCC
1 GCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCTAAGCGCC
*
40281287 GCTAAAGAACATGATCTTTAGCGGCGTTTTCCTCCTAAGCGCC
1 GCTAAAGAACATGATCTTTAGCGGCGTTTT-TTCCTAAGCGCC
* * *
40281330 GCTAAAGAACATGATCTTTAGCGGCGTTTATTTTCTTAGCGCA
1 GCTAAAGAACATGATCTTTAGCGGCGTTT-TTTCCTAAGCGCC
* *
40281373 GCTAAAGAATATGTTCTTTAGCGGCGTTTTTT
1 GCTAAAGAACATGATCTTTAGCGGCGTTTTTT
40281405 TTTGTAAGCG
Statistics
Matches: 189, Mismatches: 9, Indels: 9
0.91 0.04 0.04
Matches are distributed among these distances:
42 87 0.46
43 100 0.53
44 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (42 bp):
GCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCTAAGCGCC
Found at i:40281328 original size:127 final size:128
Alignment explanation
Indices: 40281160--40281404 Score: 388
Period size: 127 Copynumber: 1.9 Consensus size: 128
40281150 AATAAGCGTA
*
40281160 GCTAAAGAACACTACTTTTAGCGGCGTTTTCTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGC
1 GCTAAAGAACACTACTTTTAGCGGCGTTTTCCTCCTAAGCGCCGCTAAAGAACATGATCTTTAGC
*
40281225 GGCGTTT-TTTCCCAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCAAGCGCC
66 GGCGTTTATTTCCCAAGCGCAGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCAAGCGCC
40281287 GCTAAAGAACA-TGA-TCTTTAGCGGCGTTTTCCTCCTAAGCGCCGCTAAAGAACATGATCTTTA
1 GCTAAAGAACACT-ACT-TTTAGCGGCGTTTTCCTCCTAAGCGCCGCTAAAGAACATGATCTTTA
* ** * *
40281350 GCGGCGTTTATTTTCTTAGCGCAGCTAAAGAATATGTTCTTTAGCGGCGTTTTTT
64 GCGGCGTTTATTTCCCAAGCGCAGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
40281405 TTTGTAAGCG
Statistics
Matches: 108, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
126 2 0.02
127 67 0.62
128 39 0.36
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (128 bp):
GCTAAAGAACACTACTTTTAGCGGCGTTTTCCTCCTAAGCGCCGCTAAAGAACATGATCTTTAGC
GGCGTTTATTTCCCAAGCGCAGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCCAAGCGCC
Found at i:40285121 original size:50 final size:51
Alignment explanation
Indices: 40285037--40285135 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 51
40285027 TTTTAGATAC
*
40285037 TGATACATTAACTCTTATGGAGCTTTCAACTAATTTTATACTACCAAATCG
1 TGATACATTAACTCTTATAGAGCTTTCAACTAATTTTATACTACCAAATCG
* * *
40285088 TGATATATTAACTCTT-TAGAGCTTTCGACTAATTTTTTACTACCAAAT
1 TGATACATTAACTCTTATAGAGCTTTCAACTAATTTTATACTACCAAAT
40285136 ATTGTAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 29 0.66
51 15 0.34
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.40
Consensus pattern (51 bp):
TGATACATTAACTCTTATAGAGCTTTCAACTAATTTTATACTACCAAATCG
Found at i:40287368 original size:29 final size:29
Alignment explanation
Indices: 40287309--40287368 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
40287299 GTTTTTTTGT
* * **
40287309 AAAATCAGCCTATTCCTGTAATTTTTCAA
1 AAAATCAGCCTATTCATGTAATTATAAAA
* *
40287338 AAAATCGGTCTATTCATGTAATTATAAAA
1 AAAATCAGCCTATTCATGTAATTATAAAA
40287367 AA
1 AA
40287369 GGGCATTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (29 bp):
AAAATCAGCCTATTCATGTAATTATAAAA
Found at i:40287942 original size:23 final size:23
Alignment explanation
Indices: 40287916--40287960 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
40287906 CTGATAACGT
40287916 GTTATAAAATAATCAAATAAAAC
1 GTTATAAAATAATCAAATAAAAC
40287939 GTTATAAAATAATCAAATAAAA
1 GTTATAAAATAATCAAATAAAA
40287961 GAACACTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.27
Consensus pattern (23 bp):
GTTATAAAATAATCAAATAAAAC
Found at i:40288620 original size:105 final size:105
Alignment explanation
Indices: 40288501--40288714 Score: 419
Period size: 105 Copynumber: 2.0 Consensus size: 105
40288491 TAAAATAGTT
*
40288501 ATAATTATTGTTTTTTAATGTCAATAATATCACATTCAATCCCATATATTTTCCTGAACATGCGA
1 ATAATTATTGTTTTTTAATGTCAATAATATCACATTCAATCCCATATATTTTCCTAAACATGCGA
40288566 ATAACTACAAAAATGTCACATCTTATCAAATATCAATCAA
66 ATAACTACAAAAATGTCACATCTTATCAAATATCAATCAA
40288606 ATAATTATTGTTTTTTAATGTCAATAATATCACATTCAATCCCATATATTTTCCTAAACATGCGA
1 ATAATTATTGTTTTTTAATGTCAATAATATCACATTCAATCCCATATATTTTCCTAAACATGCGA
40288671 ATAACTACAAAAATGTCACATCTTATCAAATATCAATCAA
66 ATAACTACAAAAATGTCACATCTTATCAAATATCAATCAA
40288711 ATAA
1 ATAA
40288715 GATGAAGAGA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 108 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (105 bp):
ATAATTATTGTTTTTTAATGTCAATAATATCACATTCAATCCCATATATTTTCCTAAACATGCGA
ATAACTACAAAAATGTCACATCTTATCAAATATCAATCAA
Found at i:40291388 original size:19 final size:19
Alignment explanation
Indices: 40291364--40291411 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
40291354 CAATAATATC
40291364 ATCTATTCAAACACTTAAA
1 ATCTATTCAAACACTTAAA
40291383 ATCTATTCAAACACTTAAA
1 ATCTATTCAAACACTTAAA
*
40291402 ATCTAATCAA
1 ATCTATTCAA
40291412 TATGCATATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (19 bp):
ATCTATTCAAACACTTAAA
Found at i:40297304 original size:12 final size:11
Alignment explanation
Indices: 40297285--40297319 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
40297275 GGACTTATGG
40297285 TGATGTTTAGT
1 TGATGTTTAGT
40297296 TGAATGTTTAGT
1 TG-ATGTTTAGT
40297308 TGATGATTTAGT
1 TGATG-TTTAGT
40297320 ATGTATAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.23
12 17 0.77
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (11 bp):
TGATGTTTAGT
Found at i:40299071 original size:20 final size:20
Alignment explanation
Indices: 40299048--40299088 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40299038 AAAAAGGTTA
40299048 TTTAGCAAGCAAAACTCCTT
1 TTTAGCAAGCAAAACTCCTT
40299068 TTTAGCAAGCAAAACTCCTT
1 TTTAGCAAGCAAAACTCCTT
40299088 T
1 T
40299089 CATTTTCTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (20 bp):
TTTAGCAAGCAAAACTCCTT
Found at i:40313778 original size:25 final size:25
Alignment explanation
Indices: 40313744--40313794 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
40313734 TACTATTTGT
40313744 AGATGTCAGGTGAGTCTTTAAGCTG
1 AGATGTCAGGTGAGTCTTTAAGCTG
40313769 AGATGTCAGGTGAGTCTTTAAGCTG
1 AGATGTCAGGTGAGTCTTTAAGCTG
40313794 A
1 A
40313795 CTCTTGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.31
Consensus pattern (25 bp):
AGATGTCAGGTGAGTCTTTAAGCTG
Found at i:40314260 original size:26 final size:26
Alignment explanation
Indices: 40314231--40314348 Score: 110
Period size: 26 Copynumber: 4.3 Consensus size: 26
40314221 AACATGTCAA
*
40314231 GAAAGAAAGCTTGTGTGGTATAATAT
1 GAAAGAAAGCTTGTGTGGCATAATAT
*
40314257 GAAAGAAAGCATGTGTGGCATAATAT
1 GAAAGAAAGCTTGTGTGGCATAATAT
* *
40314283 GAAGGAAAGCTTGTATGGCGTACCATAATAT
1 GAAAGAAAGCTTGTGT-G-G---CATAATAT
* * * *
40314314 GAAGGAAAGCTTGTATGGCGTAACAT
1 GAAAGAAAGCTTGTGTGGCATAATAT
*
40314340 AAAAGAAAG
1 GAAAGAAAG
40314349 TGTATGTGGC
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
26 50 0.64
27 1 0.01
28 1 0.01
29 1 0.01
30 1 0.01
31 24 0.31
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (26 bp):
GAAAGAAAGCTTGTGTGGCATAATAT
Found at i:40314310 original size:31 final size:31
Alignment explanation
Indices: 40314275--40314341 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
40314265 GCATGTGTGG
*
40314275 CATAATATGAAGGAAAGCTTGTATGGCGTAC
1 CATAATATGAAGGAAAGCTTGTATGGCGTAA
40314306 CATAATATGAAGGAAAGCTTGTATGGCGTAA
1 CATAATATGAAGGAAAGCTTGTATGGCGTAA
40314337 CATAA
1 CATAA
40314342 AAGAAAGTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (31 bp):
CATAATATGAAGGAAAGCTTGTATGGCGTAA
Found at i:40315542 original size:25 final size:25
Alignment explanation
Indices: 40315503--40315555 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
40315493 TCATTAGGGT
* *
40315503 TACCGATTTATAGCTCGTGAGAGCA
1 TACCGATTCACAGCTCGTGAGAGCA
**
40315528 TACCGATTCACAGCTCGTTTGAGCA
1 TACCGATTCACAGCTCGTGAGAGCA
40315553 TAC
1 TAC
40315556 ATGTACATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (25 bp):
TACCGATTCACAGCTCGTGAGAGCA
Found at i:40316324 original size:43 final size:42
Alignment explanation
Indices: 40316262--40316461 Score: 202
Period size: 43 Copynumber: 4.7 Consensus size: 42
40316252 TTTTAGAAAT
* * * * **
40316262 AAACGCTGCTAAAGGTCATGACCTTTAGCGGAACTTATCCCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCAGCGCTT-TCCCAC
* *
40316305 AAACGCCGCTATAGATCATGACTTTTAGCAGCGTTTTTCCCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCAGCG-CTTTCCCAC
* * * * *
40316348 AAACGCAGCTATAGATCATGACTTTTAGCTGCGCTTTTCCTC
1 AAACGCCGCTATAGATCATGACCTTTAGCAGCGCTTTCCCAC
* *
40316390 AAACGCCGCTATAGAACATGAGCTTTAGCAGCGCTTTACCCAC
1 AAACGCCGCTATAGATCATGACCTTTAGCAGCGCTTT-CCCAC
* * * *
40316433 AAACGCCGTTAAAGAACATGATCTTTAGC
1 AAACGCCGCTATAGATCATGACCTTTAGC
40316462 GGCACTTTTA
Statistics
Matches: 132, Mismatches: 23, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 38 0.29
43 92 0.70
44 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (42 bp):
AAACGCCGCTATAGATCATGACCTTTAGCAGCGCTTTCCCAC
Found at i:40316410 original size:42 final size:43
Alignment explanation
Indices: 40316301--40316486 Score: 200
Period size: 43 Copynumber: 4.3 Consensus size: 43
40316291 GGAACTTATC
* * *
40316301 CCACAAACGCCGCTATAGATCATGACTTTTAGCAGCGTTTTTC
1 CCACAAACGCCGCTATAGAACATGACTTTTAGCAGCGCTTTTA
* * *
40316344 CCACAAACGCAGCTATAGATCATGACTTTTAGCTGCGCTTTT-
1 CCACAAACGCCGCTATAGAACATGACTTTTAGCAGCGCTTTTA
*
40316386 CCTCAAACGCCGCTATAGAACATGAGC-TTTAGCAGCGC-TTTA
1 CCACAAACGCCGCTATAGAACATGA-CTTTTAGCAGCGCTTTTA
* * * *
40316428 CCCACAAACGCCGTTAAAGAACATGA-TCTTTAGCGGCACTTTTA
1 -CCACAAACGCCGCTATAGAACATGACT-TTTAGCAGCGCTTTTA
* *
40316472 TCGCAAACGCCGCTA
1 CCACAAACGCCGCTA
40316487 AAAGTATGGT
Statistics
Matches: 122, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
41 3 0.02
42 32 0.26
43 83 0.68
44 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
CCACAAACGCCGCTATAGAACATGACTTTTAGCAGCGCTTTTA
Found at i:40316453 original size:85 final size:86
Alignment explanation
Indices: 40316262--40316486 Score: 240
Period size: 85 Copynumber: 2.6 Consensus size: 86
40316252 TTTTAGAAAT
* ** * * * * * *
40316262 AAACGCTGCTAAAGGTCATGACCTTTAGCGGAACTTATCCCACAAACGCCGCTATAGATCATGAC
1 AAACGCAGCTAAAGAACATGATCTTTAGCGGCACTTTTACCGCAAACGCCGCTATAGAACATGAC
* *
40316327 TTTTAGCAGCGTTTTTCCCAC
66 TTTTAGCAGCGCTTTACCCAC
* * * * *
40316348 AAACGCAGCTATAGATCATGA-CTTTTAGCTGCGCTTTT-CCTCAAACGCCGCTATAGAACATGA
1 AAACGCAGCTAAAGAACATGATC-TTTAGCGGCACTTTTACCGCAAACGCCGCTATAGAACATGA
40316411 GC-TTTAGCAGCGCTTTACCCAC
65 -CTTTTAGCAGCGCTTTACCCAC
* * *
40316433 AAACGCCGTTAAAGAACATGATCTTTAGCGGCACTTTTATCGCAAACGCCGCTA
1 AAACGCAGCTAAAGAACATGATCTTTAGCGGCACTTTTACCGCAAACGCCGCTA
40316487 AAAGTATGGT
Statistics
Matches: 116, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
85 72 0.62
86 44 0.38
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (86 bp):
AAACGCAGCTAAAGAACATGATCTTTAGCGGCACTTTTACCGCAAACGCCGCTATAGAACATGAC
TTTTAGCAGCGCTTTACCCAC
Found at i:40316479 original size:43 final size:43
Alignment explanation
Indices: 40316262--40316488 Score: 158
Period size: 43 Copynumber: 5.3 Consensus size: 43
40316252 TTTTAGAAAT
* ** * * *
40316262 AAACGCTGCTAAAGGTCATGACCTTTAGCGGAAC-TTATCCCAC
1 AAACGCCGCTAAAGAACATGAGCTTTAGCAGCACTTTA-CCCAC
* * ** *
40316305 AAACGCCGCTATAGATCATGA-CTTTTAGCAGCGTTTTTCCCAC
1 AAACGCCGCTAAAGAACATGAGC-TTTAGCAGCACTTTACCCAC
* * * * * * *
40316348 AAACGCAGCTATAGATCATGA-CTTTTAGCTGCGCTTT-TCCTC
1 AAACGCCGCTAAAGAACATGAGC-TTTAGCAGCACTTTACCCAC
* *
40316390 AAACGCCGCTATAGAACATGAGCTTTAGCAGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGAGCTTTAGCAGCACTTTACCCAC
* * * * *
40316433 AAACGCCGTTAAAGAACATGATCTTTAGCGGCACTTTTA-TCGC
1 AAACGCCGCTAAAGAACATGAGCTTTAGCAGCAC-TTTACCCAC
40316476 AAACGCCGCTAAA
1 AAACGCCGCTAAA
40316489 AGTATGGTTC
Statistics
Matches: 153, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
42 36 0.24
43 111 0.73
44 6 0.04
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGAGCTTTAGCAGCACTTTACCCAC
Found at i:40318204 original size:86 final size:87
Alignment explanation
Indices: 40318101--40318292 Score: 287
Period size: 87 Copynumber: 2.2 Consensus size: 87
40318091 CTAAAAAAGA
* * **
40318101 AAATTTTCAATATTTATAACAACTTATATGCAACAAATTAG-CAAAAATAAATGGTTCAAGTTCA
1 AAATTTTCAATTTTTATAACAACTTATATGCAACAAATTAGAAAAAAATAAACAGTTCAAGTTCA
* *
40318165 TGCATTTACCAACAACCAGACT
66 TGCATTCACCAACAACCAGACC
* *
40318187 AAATTTTCAATTTTTATAACAACTTATGTGCAACAAATTAGAAAAAAATCAACAGTTCAAGTTCA
1 AAATTTTCAATTTTTATAACAACTTATATGCAACAAATTAGAAAAAAATAAACAGTTCAAGTTCA
*
40318252 TGCATTCATCAACAACCAGACC
66 TGCATTCACCAACAACCAGACC
*
40318274 AAATTTTCAACTTTTATAA
1 AAATTTTCAATTTTTATAA
40318293 AGTAGAAGGA
Statistics
Matches: 95, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 39 0.41
87 56 0.59
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (87 bp):
AAATTTTCAATTTTTATAACAACTTATATGCAACAAATTAGAAAAAAATAAACAGTTCAAGTTCA
TGCATTCACCAACAACCAGACC
Found at i:40328229 original size:22 final size:24
Alignment explanation
Indices: 40328190--40328244 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
40328180 AGAATAACTT
*
40328190 AGGGAAATTTAGGGGAAACGAAGTT
1 AGGGAAA-TTAGGGGAAACGAAGTC
*
40328215 A-GGAAATT-GGGGAAATGAAGTC
1 AGGGAAATTAGGGGAAACGAAGTC
40328237 AGGGAAAT
1 AGGGAAAT
40328245 CTGACATGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 13 0.48
23 8 0.30
24 5 0.19
25 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.36, T:0.18
Consensus pattern (24 bp):
AGGGAAATTAGGGGAAACGAAGTC
Found at i:40332420 original size:15 final size:15
Alignment explanation
Indices: 40332400--40332430 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40332390 CCAACCTTCA
*
40332400 AATTTTAGGTCAATT
1 AATTTTACGTCAATT
40332415 AATTTTACGTCAATT
1 AATTTTACGTCAATT
40332430 A
1 A
40332431 TACATAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (15 bp):
AATTTTACGTCAATT
Found at i:40336611 original size:15 final size:15
Alignment explanation
Indices: 40336576--40336627 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40336566 TTAAGAATTT
*
40336576 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40336590 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40336604 TATTTAATAATAAT-
1 TATTTAATTATAATA
40336618 TATGTTAATT
1 TAT-TTAATT
40336628 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40336708 original size:59 final size:59
Alignment explanation
Indices: 40336525--40336708 Score: 148
Period size: 59 Copynumber: 3.1 Consensus size: 59
40336515 TATAGTATCA
* *
40336525 TATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAGAATTTTATTAAAT
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTATTTATTAAGAATTTTATTAAAT
* * * * * * * *
40336584 TATA-TAT--TTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-CAGTAT
1 TATATTATGATTTGAGTA-AAT-TCATATAAGAAT-ATTAT-TT-ATTAAGAATTTTATTA-AAT
40336643 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTT-TTAAGAATTTTATTAAAT
1 --TATATTATGATTTGAGTAAATTCATATAAGAATATT-ATTTATTAAGAATTTTATTAAAT
40336704 TATAT
1 TATAT
40336709 ATTTTAATTA
Statistics
Matches: 92, Mismatches: 18, Indels: 30
0.66 0.13 0.21
Matches are distributed among these distances:
56 6 0.07
57 10 0.11
58 9 0.10
59 19 0.21
60 7 0.08
61 12 0.13
62 10 0.11
63 13 0.14
64 6 0.07
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (59 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATTATTTATTAAGAATTTTATTAAAT
Found at i:40336726 original size:16 final size:16
Alignment explanation
Indices: 40336705--40336746 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40336695 TTATTAAATT
*
40336705 ATATATTTTAATTATA
1 ATATATTTTAATAATA
40336721 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
40336736 AT-TATGTTTAA
1 ATATAT-TTTAA
40336747 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:40336731 original size:15 final size:15
Alignment explanation
Indices: 40336696--40336737 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40336686 TTAAGAATTT
*
40336696 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40336710 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40336724 TATTTAATAATAAT
1 TATTTAATTATAAT
40336738 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40336731 original size:120 final size:120
Alignment explanation
Indices: 40336513--40336743 Score: 419
Period size: 120 Copynumber: 1.9 Consensus size: 120
40336503 NNNATAGTTA
* *
40336513 TTTATAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAGAATTTTA
1 TTTACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTAATTTATTAAGAATTTTA
40336578 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAT
66 TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAT
*
40336633 TTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTT-TTAAGAATTTT
1 TTTACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAAT-TTAATTTATTAAGAATTTT
40336697 ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
65 ATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
40336744 TAAATATGAT
Statistics
Matches: 107, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
120 101 0.94
121 6 0.06
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
TTTACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTAATTTATTAAGAATTTTA
TTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATAT
Found at i:40336857 original size:154 final size:154
Alignment explanation
Indices: 40336680--40336990 Score: 568
Period size: 154 Copynumber: 2.0 Consensus size: 154
40336670 ATAAGAATAT
* *
40336680 TAATTTTTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
40336745 AAATATGATTAAATTATTTATTATTGATATTAATCTTATTAAAATTTAAATAATAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAATCTTATTAAAATTTAAATAACAATAACAATAA
40336810 TAATTTACCAAAACAAATTTATGC
131 TAATTTACCAAAACAAATTTATGC
40336834 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
40336899 AAATATGATTAAATTATTTATTATTGATAATAATCTTATTAAAATTTAAATAACAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAATCTTATTAAAATTTAAATAACAATAACAATAA
* *
40336964 TCATTTACCAAAACAAATTTCTGC
131 TAATTTACCAAAACAAATTTATGC
40336988 TAA
1 TAA
40336991 GGGTATTCTA
Statistics
Matches: 151, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
154 151 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (154 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATCTTATTAAAATTTAAATAACAATAACAATAA
TAATTTACCAAAACAAATTTATGC
Found at i:40336874 original size:18 final size:17
Alignment explanation
Indices: 40336846--40336880 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40336836 ATTATTAAGA
*
40336846 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40336863 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40336881 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40336914 original size:75 final size:75
Alignment explanation
Indices: 40336681--40336916 Score: 203
Period size: 75 Copynumber: 3.1 Consensus size: 75
40336671 TAAGAATATT
* *
40336681 AATTTTTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
40336746 AATATGATTA
66 AATATGATTA
* ** * * * * * * *
40336756 AATTATTTATTATTGATATTAATCTTATTAAAATTTAAATAATAATA-A--CAATAATAATT-TA
1 AATTATTAAGAATT-TTATTAA-ATTA-TATATTTTAATTAA-AATATATTTAATAATAATTATG
*** * *
40336817 CCAAAACA-AATTTA
62 TTTAAATATGA-TTA
40336831 TGCTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG
1 ----AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG
40336896 TTTAAATATGATTA
62 TTTAAATATGATTA
40336910 AATTATT
1 AATTATT
40336917 TATTATTGAT
Statistics
Matches: 115, Mismatches: 32, Indels: 28
0.66 0.18 0.16
Matches are distributed among these distances:
74 1 0.01
75 29 0.25
76 28 0.24
77 6 0.05
78 27 0.23
79 23 0.20
80 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (75 bp):
AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTA
Found at i:40337131 original size:16 final size:16
Alignment explanation
Indices: 40337110--40337148 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40337100 TTGATTTGCT
*
40337110 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
40337126 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
40337142 ATTACAC
1 ATTACAC
40337149 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:40337149 original size:16 final size:16
Alignment explanation
Indices: 40337123--40337179 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
40337113 ACACAGCTTT
* *
40337123 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
40337139 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
40337155 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
40337171 TCCAATACA
1 TCCAATACA
40337180 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:40337803 original size:14 final size:14
Alignment explanation
Indices: 40337786--40337968 Score: 70
Period size: 14 Copynumber: 12.9 Consensus size: 14
40337776 CTAGTTAATC
40337786 TAAACCCTAAACCA
1 TAAACCCTAAACCA
* *
40337800 TAAA-CTTAAACCC
1 TAAACCCTAAACCA
*
40337813 TAAAACCCTTAACACA
1 T-AAACCCTAAAC-CA
*
40337829 T-AACCTCTAAACCT
1 TAAACC-CTAAACCA
* * *
40337843 TAAACCC-CAGCCTT
1 TAAACCCTAAACC-A
*
40337857 TAAACCATAAACCA
1 TAAACCCTAAACCA
* * * *
40337871 TAAATCATAACCCC
1 TAAACCCTAAACCA
* *
40337885 TAAACTCATAATCCA
1 TAAAC-CCTAAACCA
*
40337900 TAAACCTTAAA--A
1 TAAACCCTAAACCA
*
40337912 TAGTAACTCCTAAACCT
1 TA--AAC-CCTAAACCA
* *
40337929 TAAACTCTAAACAA
1 TAAACCCTAAACCA
*
40337943 TATACCCTAAACCA
1 TAAACCCTAAACCA
* *
40337957 AAAACCTTAAAC
1 TAAACCCTAAAC
40337969 TATAGTGATA
Statistics
Matches: 124, Mismatches: 32, Indels: 26
0.68 0.18 0.14
Matches are distributed among these distances:
12 3 0.02
13 11 0.09
14 69 0.56
15 37 0.30
16 2 0.02
17 2 0.02
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:40337847 original size:29 final size:28
Alignment explanation
Indices: 40337786--40337849 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
40337776 CTAGTTAATC
40337786 TAAACCCTAAACCATAAACTTAAACCCT
1 TAAACCCTAAACCATAAACTTAAACCCT
* * *
40337814 AAAACCCTTAACACATAACCTCTAAA-CCT
1 TAAACCCTAAAC-CATAAACT-TAAACCCT
40337843 TAAACCC
1 TAAACCC
40337850 CAGCCTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 10 0.33
29 16 0.53
30 4 0.13
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.20
Consensus pattern (28 bp):
TAAACCCTAAACCATAAACTTAAACCCT
Found at i:40337867 original size:7 final size:7
Alignment explanation
Indices: 40337857--40337910 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
40337847 CCCCAGCCTT
40337857 TAAACCA
1 TAAACCA
40337864 TAAACCA
1 TAAACCA
*
40337871 TAAATCA
1 TAAACCA
* *
40337878 TAACCCC
1 TAAACCA
40337885 TAAACTCA
1 TAAAC-CA
*
40337893 TAATCCA
1 TAAACCA
*
40337900 TAAACCT
1 TAAACCA
40337907 TAAA
1 TAAA
40337911 ATAGTAACTC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:40337910 original size:22 final size:23
Alignment explanation
Indices: 40337885--40337935 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
40337875 TCATAACCCC
40337885 TAAACTCA-TAA-TCCATAAACCT
1 TAAACTCAGTAACTCC-TAAACCT
*
40337907 TAAAAT-AGTAACTCCTAAACCT
1 TAAACTCAGTAACTCCTAAACCT
40337929 TAAACTC
1 TAAACTC
40337936 TAAACAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 1 0.04
22 20 0.83
23 3 0.12
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.27
Consensus pattern (23 bp):
TAAACTCAGTAACTCCTAAACCT
Found at i:40338412 original size:82 final size:80
Alignment explanation
Indices: 40338276--40338538 Score: 255
Period size: 82 Copynumber: 3.2 Consensus size: 80
40338266 AATATTTTTT
* ** *
40338276 GCGGCGCTTTTTGAAAACGTCGCT-AAAATAGAGCATTAGCGGCGCTTTTCCAAAAATGCCGCTA
1 GCGGCGCTTTTTAAAAACGTCGCTAAAAATAGAGCATTAGCAACGCTTTTCCAAAAACGCCGCTA
*
40338340 AAGACCTCGAGCA-CTA
66 AAG-CCCCGAGCATC-A
*
40338356 GCGGCGCTTTTTAAAAGACGCCGCTAAAAATAGAGCATTAGCAACGCTTCTT-CAAAAACGCCGC
1 GCGGCGCTTTTTAAAA-ACGTCGCTAAAAATAGAGCATTAGCAACGCTT-TTCCAAAAACGCCGC
40338420 TAAAGCCCCGAGCATCA
64 TAAAGCCCCGAGCATCA
* * **** *** * *
40338437 GCGACACTTTTTCAAAAACGTCGCTAAAGCCCCGAGCATTAGCGGTGCTTTTTCAAAAACACCGC
1 GCGGCGCTTTTT-AAAAACGTCGCTAAA-AATAGAGCATTAGCAACGCTTTTCCAAAAACGCCGC
* *
40338502 TAAATCCCC-ATGCATTA
64 TAAAGCCCCGA-GCATCA
40338519 GCGGCGCTTTTTCAAAAACG
1 GCGGCGCTTTTT-AAAAACG
40338539 CCACTAAATC
Statistics
Matches: 154, Mismatches: 21, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
80 15 0.10
81 39 0.25
82 98 0.64
83 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (80 bp):
GCGGCGCTTTTTAAAAACGTCGCTAAAAATAGAGCATTAGCAACGCTTTTCCAAAAACGCCGCTA
AAGCCCCGAGCATCA
Found at i:40338451 original size:41 final size:41
Alignment explanation
Indices: 40338306--40338633 Score: 333
Period size: 41 Copynumber: 8.0 Consensus size: 41
40338296 CGCTAAAATA
* * *
40338306 GAGCATTAGCGGCGCTTTTCCAAAAATGCCGCTAAAGACCTC
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAG-CCCC
* ****
40338348 GAGCACTAGCGGCGCTTTTT-AAAAGACGCCGCTAAA-AATA
1 GAGCATTAGCGGCGCTTTTTCAAAA-ACGCCGCTAAAGCCCC
** *
40338388 GAGCATTAGCAACGCTTCTTCAAAAACGCCGCTAAAGCCCC
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCC
* * * *
40338429 GAGCATCAGCGACACTTTTTCAAAAACGTCGCTAAAGCCCC
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCC
* * *
40338470 GAGCATTAGCGGTGCTTTTTCAAAAACACCGCTAAATCCCC
1 GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCC
* *
40338511 -ATGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAATCCCC
1 GA-GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCC
* *
40338552 -ATGCATTAGCGGCTCTTTTTCAAAAACGCCGCTAAATCCCC
1 GA-GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCC
* * * * *
40338593 -ATGCCTTAGCGACGCTTTTTGAAAAATGCCACTAAAGCCCC
1 GA-GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCC
40338634 TAAAACACAA
Statistics
Matches: 244, Mismatches: 38, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
40 29 0.12
41 187 0.77
42 28 0.11
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (41 bp):
GAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCC
Found at i:40347286 original size:29 final size:29
Alignment explanation
Indices: 40347253--40347308 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
40347243 TACTACCTTC
*
40347253 ATGAATCATAGCTTGTTTAGACTAATGCT
1 ATGAACCATAGCTTGTTTAGACTAATGCT
40347282 ATGAACCATAGCTTGTTTAGACTAATG
1 ATGAACCATAGCTTGTTTAGACTAATG
40347309 TTACATTCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (29 bp):
ATGAACCATAGCTTGTTTAGACTAATGCT
Found at i:40349917 original size:87 final size:86
Alignment explanation
Indices: 40349756--40349917 Score: 202
Period size: 87 Copynumber: 1.9 Consensus size: 86
40349746 TTATTAAAAT
* *
40349756 ATTTATTTTATTATTAATTTCACTACTATTTTAATTATAACTATTTTAAGCTTTGTAATGTATTT
1 ATTTAGTTTATTATTAATTTCACTACTATTTTAATTATAACTATTTTAA-CTTTGTAATCTATTT
*
40349821 TAAATTTGTTAATTTTCGCCTA
65 TAAACTTGTTAATTTTCGCCTA
* * * * *
40349843 ATTTAGTTTATTGTTAATTTTACTATTATTTTAATTGTAATTATTTTAA-TATT-TAATCTATTT
1 ATTTAGTTTATTATTAATTTCACTACTATTTTAATTATAACTATTTTAACT-TTGTAATCTATTT
40349906 AGTAAACTTGTT
65 --TAAACTTGTT
40349918 TTATTTTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
85 10 0.16
86 2 0.03
87 52 0.81
ACGTcount: A:0.30, C:0.07, G:0.06, T:0.57
Consensus pattern (86 bp):
ATTTAGTTTATTATTAATTTCACTACTATTTTAATTATAACTATTTTAACTTTGTAATCTATTTT
AAACTTGTTAATTTTCGCCTA
Found at i:40353337 original size:23 final size:22
Alignment explanation
Indices: 40353303--40353352 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
40353293 AATTATGTTT
*
40353303 ATTAATTATTAA-TTATTATAAA
1 ATTATTTATTAATTTATT-TAAA
40353325 ATTATTTATTTAATTTATTTAAA
1 ATTATTTA-TTAATTTATTTAAA
40353348 ATTAT
1 ATTAT
40353353 AAAATATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
23 13 0.52
24 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTATTTATTAATTTATTTAAA
Found at i:40353343 original size:31 final size:30
Alignment explanation
Indices: 40353300--40353368 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
40353290 TTTAATTATG
*
40353300 TTTATTAATTA-TTAATTATTATAAAAT-TA
1 TTTATTAATTATTTAA-AATTATAAAATATA
40353329 TTTATTTAATTTATTTAAAATTATAAAATATA
1 TTTA-TTAA-TTATTTAAAATTATAAAATATA
40353361 TTT-TTAAT
1 TTTATTAAT
40353369 CTATATTAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
29 5 0.14
30 8 0.23
31 13 0.37
32 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTATTAATTATTTAAAATTATAAAATATA
Found at i:40353649 original size:16 final size:17
Alignment explanation
Indices: 40353624--40353661 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
40353614 TAATGTAAAT
*
40353624 AATA-ATATTAAG-TTA
1 AATATATATTAAGAATA
40353639 AATATATATTAAGAATA
1 AATATATATTAAGAATA
40353656 AATATA
1 AATATA
40353662 AAATTGTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 8 0.40
17 8 0.40
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (17 bp):
AATATATATTAAGAATA
Found at i:40353945 original size:17 final size:16
Alignment explanation
Indices: 40353910--40353939 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40353900 GATGAGTCAT
40353910 ATTTATATTTTAATAA
1 ATTTATATTTTAATAA
40353926 ATTTA-ATTTTAATA
1 ATTTATATTTTAATA
40353940 TAAATTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTATATTTTAATAA
Found at i:40357828 original size:15 final size:12
Alignment explanation
Indices: 40357803--40357847 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 12
40357793 TAAAATATAT
40357803 ATATATATATAAA
1 ATATAT-TATAAA
40357816 ATACCTATGTATAAA
1 ATA--TAT-TATAAA
40357831 ATATATTATAAA
1 ATATATTATAAA
40357843 ATATA
1 ATATA
40357848 AAGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 11 0.38
13 6 0.21
15 12 0.41
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (12 bp):
ATATATTATAAA
Found at i:40358209 original size:3 final size:3
Alignment explanation
Indices: 40358187--40358234 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
40358177 AAAATAAAAC
* * * *
40358187 TAA TAA TATT TAA TAG TAA TAA TAA TAA TAA TAA TAA TTA TCA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40358233 TA
1 TA
40358235 CAAAAATAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
3 35 0.95
4 2 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:40359575 original size:5 final size:5
Alignment explanation
Indices: 40359565--40359596 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
40359555 ACGCTTCTCG
40359565 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CT
1 CTTCT CTTCT CTTCT CTTCT CTTCT CTTCT CT
40359597 ACTACCTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
CTTCT
Found at i:40360019 original size:129 final size:129
Alignment explanation
Indices: 40359884--40360268 Score: 680
Period size: 129 Copynumber: 3.0 Consensus size: 129
40359874 AAACCTGATG
40359884 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
*
40359949 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCCGTAATCTCAGGGAGATAAGATCTGACA
66 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACA
* *
40360013 CGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCATTGTAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
*
40360078 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTTAGGGAGATAAGATCTGACA
66 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACA
* * *
40360142 CGATCTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTTTTTTAATCTGCTCCACTGTAATCT
1 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
* * *
40360207 CAGGGAGATAGGATTACTAGCTTCAATCTACTCCACTGTAATCTCAAGGAGATAAGATCTGA
66 CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
40360269 AATTCTTCGG
Statistics
Matches: 243, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 243 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (129 bp):
CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCT
CAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACA
Found at i:40360308 original size:46 final size:46
Alignment explanation
Indices: 40359934--40360963 Score: 470
Period size: 44 Copynumber: 23.6 Consensus size: 46
40359924 ATTTTAATCC
* * *
40359934 GCTCCACTGTAATCTCAGGGAGATAGGAT-T-AC-TAGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACAT-TCTTCGATCT
* *
40359978 GCTCCGCCGTAATCTCAGGGAGATAAGATCTGACA-----CGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCT
* * * * ** * *
40360019 ACTCTACTGTAA-CTTTAGAGAGATAAGATCCT-TTATT-TT-AATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGAT-CTGACATTCTTCGATCT
* * * *
40360063 GCTCCATTGTAATCTCAGGGAGATAGGAT-T-AC-TAGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACAT-TCTTCGATCT
* *
40360107 GCTCCGCTGTAATCTTAGGGAGATAAGATCTGACA-----CGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCT
* * * * * * **
40360148 ACTCTACTGTAA-CTTCAGAGAGATAAAATC---CTTTTTTTTAATCT
1 GCTCCACTGTAATC-TCAGGGAGATAAGATCTGAC-ATTCTTCGATCT
* * *
40360192 GCTCCACTGTAATCTCAGGGAGATAGGAT-T-AC-TAGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACAT-TCTTCGATCT
* * * *
40360236 ACTCCACTGTAATCTCAAGGAGATAAGATCTGAAATTCTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCT
* * * *
40360282 GTTCCACTGTAATCTCAGGGAAATAAGACCTG--A---TGCGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCT
* * * * ** *
40360323 ACTCTATTGTAA-CTTCAGAGAGATAAGATCCT-TTATT-TT-AATCT
1 GCTCCACTGTAATC-TCAGGGAGATAAGAT-CTGACATTCTTCGATCT
* *
40360367 GCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACCA-TCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGA-CATTCTTCGATCT
*
40360411 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCT
* * * *
40360457 GTTCCACTGTAATCTCAGGGAAATAAGACCTG--A--C-GCGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCT
** ** * * * *
40360498 ATTCTGCTGTAA-CTTCAGAGAGATAAGATCCT-TCATT-TT-AATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGAT-CTGACATTCTTCGATCT
* * *
40360542 ACTCCACTGTAATCTCAGGGAGATAGGAT-T-AC-TATCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACAT-TCTTCGATCT
* *
40360586 GCTCCGCTATAATCTCAGGGAGATAAGATCTGACA-----CGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCT
* * * ** * *
40360627 ACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTATT-TT-AATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGAT-CTGACATTCTTCGATCT
* *
40360671 GCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACCA-TCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGA-CATTCTTCGATCT
* * *
40360715 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCT
* * * * *
40360761 GTTCCACTGTAATCTCAGGGAAATAAGACCTG--A--C-GCGATTT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCT
* * * * * * *
40360802 ACTCTACTGTAA-CTTCAGAGAGATATGATCATTG--GTT-TT-AATCC
1 GCTCCACTGTAATC-TCAGGGAGATAAGATC--TGACATTCTTCGATCT
* * *
40360846 GCTCCACTGTAATCTCAGGGAGATAGGAT-T-AC-TAGCTTCAATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGACAT-TCTTCGATCT
* *
40360890 GCTCCGCTGTAATCTCAGGAAGATAAGATCTG-CAATTCTTC-AGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATCTGAC-ATTCTTCGA-TCT
40360936 GCTCCACTGTAATCTCAGGGAGATAAGA
1 GCTCCACTGTAATCTCAGGGAGATAAGA
40360964 CCTGTATAAT
Statistics
Matches: 740, Mismatches: 159, Indels: 172
0.69 0.15 0.16
Matches are distributed among these distances:
38 1 0.00
40 6 0.01
41 164 0.22
42 18 0.02
43 17 0.02
44 363 0.49
45 20 0.03
46 149 0.20
47 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (46 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCT
Found at i:40360345 original size:304 final size:300
Alignment explanation
Indices: 40359872--40360921 Score: 1178
Period size: 304 Copynumber: 3.5 Consensus size: 300
40359862 CACAGGGAGG
* * * * * * * *
40359872 TAAAACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCT
1 TAAAACCTGACGCAATCTACTCCACTGTAACTTCAGAGAGATAAGATACTTCACTTCAATCCACT
* * * * * *
40359937 CCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCCGTAATCTCAGGGAGAT
66 CCACTGTAATCTCAAGGAGATAAGATTAATATCTTCAATCTGCTCCACTGTAATCTCAGGGAGAT
*
40360002 AAGATCTGACACGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTC
131 AAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTC
* * * ** *
40360067 CATTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTTAGGGAGATA
196 CACTGTAATCTCAGGGAGATAGGATTACCATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATA
* *
40360132 AGATCTGACA-CGATCTACTCTACTGTAA-CTTCAGAGAGA
261 AGATCTGACATCGATCTACTCCACTGTAATC-TCAGAGAAA
***** * * *
40360171 TAAAATCCTTTTTTTTAATCTGCTCCACTGTAA-TCTCAGGGAGATAGGATTAC-T-AGCTTCAA
1 TAAAA-CC--TGACGCAATCTACTCCACTGTAACT-TCAGAGAGATAAGA-TACTTCA-CTTCAA
* ** *
40360233 TCTACTCCACTGTAATCTCAAGGAGATAAGATCTGAA-ATTCTTCGGTCTGTTCCACTGTAATCT
60 TCCACTCCACTGTAATCTCAAGGAGATAAGAT-T-AATA-TCTTCAATCTGCTCCACTGTAATCT
* * ** *
40360297 CAGGGAAATAAGACCTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTTTATTTT
122 CAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTT
*
40360362 AATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACCATCTTTGATCTGCTCCGCTGTAATCTC
187 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACCATCTTTGATCTGCTCCGCTGTAATCTC
** *
40360427 AGGGAGATAAGATCTGACATTCTTCGATCTGTTCCACTGTAATCTCAGGGAAA
252 AGGGAGATAAGATCTGACA----TCGATCTACTCCACTGTAATCTCAGAGAAA
* * * ** * * *
40360480 TAAGACCTGACGCGATCTATTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCACT
1 TAAAACCTGACGCAATCTACTCCACTGTAACTTCAGAGAGATAAGATACTTCACTTCAATCCACT
* * * * *
40360545 CCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTATAATCTCAGGGAGAT
66 CCACTGTAATCTCAAGGAGATAAGATTAATATCTTCAATCTGCTCCACTGTAATCTCAGGGAGAT
40360610 AAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTC
131 AAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTC
40360675 CACTGTAATCTCAGGGAGATAGGATTACCATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATA
196 CACTGTAATCTCAGGGAGATAGGATTACCATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATA
* * ** *
40360740 AGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAA
261 AGATCTG--A--CATCGATCTACTCCACTGTAATCTCAGAGAAA
* * * * * *** * *
40360784 TAAGACCTGACGCGATTTACTCTACTGTAACTTCAGAGAGATATGAT-CATTGGTTTTAATCCGC
1 TAAAACCTGACGCAATCTACTCCACTGTAACTTCAGAGAGATAAGATAC-TTCACTTCAATCCAC
* * * * * *
40360848 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGAAGA
65 TCCACTGTAATCTCAAGGAGATAAGATTAATATCTTCAATCTGCTCCACTGTAATCTCAGGGAGA
40360913 TAAGATCTG
130 TAAGATCTG
40360922 CAATTCTTCA
Statistics
Matches: 643, Mismatches: 84, Indels: 43
0.84 0.11 0.06
Matches are distributed among these distances:
299 5 0.01
300 2 0.00
301 2 0.00
302 61 0.09
303 5 0.01
304 472 0.73
305 4 0.01
306 60 0.09
307 2 0.00
308 3 0.00
309 26 0.04
310 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (300 bp):
TAAAACCTGACGCAATCTACTCCACTGTAACTTCAGAGAGATAAGATACTTCACTTCAATCCACT
CCACTGTAATCTCAAGGAGATAAGATTAATATCTTCAATCTGCTCCACTGTAATCTCAGGGAGAT
AAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTC
CACTGTAATCTCAGGGAGATAGGATTACCATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATA
AGATCTGACATCGATCTACTCCACTGTAATCTCAGAGAAA
Found at i:40360619 original size:129 final size:128
Alignment explanation
Indices: 40360412--40360747 Score: 501
Period size: 129 Copynumber: 2.6 Consensus size: 128
40360402 CTTTGATCTG
* * * *
40360412 CTCCGCTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCTGTTCCACTGTAATCTCAGGG
1 CTCCACTGTAATCTCAGGGAGATAGGAT-T-ACA-TCTTCGATCTGCTCCGCTGTAATCTCAGGG
* * * * *
40360477 AAATAAGACCTGACGCGATCTATTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCC
63 AGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCC
40360542 A
128 A
* *
40360543 CTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTATAATCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAGATAGGATTAC-ATCTTCGATCTGCTCCGCTGTAATCTCAGGGAG
* *
40360608 ATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
65 ATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCA
*
40360672 CTCCACTGTAATCTCAGGGAGATAGGATTACCATCTTTGATCTGCTCCGCTGTAATCTCAGGGAG
1 CTCCACTGTAATCTCAGGGAGATAGGATTA-CATCTTCGATCTGCTCCGCTGTAATCTCAGGGAG
40360737 ATAAGATCTGA
65 ATAAGATCTGA
40360748 AATTCTTCGG
Statistics
Matches: 187, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
129 158 0.84
130 3 0.02
131 26 0.14
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (128 bp):
CTCCACTGTAATCTCAGGGAGATAGGATTACATCTTCGATCTGCTCCGCTGTAATCTCAGGGAGA
TAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCA
Found at i:40360619 original size:175 final size:175
Alignment explanation
Indices: 40360070--40360620 Score: 820
Period size: 175 Copynumber: 3.2 Consensus size: 175
40360060 TCCGCTCCAT
* * * * * * *
40360070 TGTAATCTCAGGGAGATAGGAT-T-AC-TAGCTTCAATCTGCTCCGCTGTAATCTTAGGGAGATA
1 TGTAATCTCAGGGAGATAAGATCTGACAT-TCTTCGATCTGTTCCACTGTAATCTCAGGGAAATA
* * * *
40360132 AGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTTTTTTAATCTGCTCC
65 AGACCTGACGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCC
* * *
40360197 ACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCAC
130 ACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGC
* * *
40360243 TGTAATCTCAAGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAA
1 TGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCTGTTCCACTGTAATCTCAGGGAAATAA
* *
40360308 GACCTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCA
66 GACCTGACGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCA
* **
40360373 CTGTAATCTCAGGGAGATAGGATTACCATCTTTGATCTGCTCCGC
131 CTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGC
40360418 TGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCTGTTCCACTGTAATCTCAGGGAAATAA
1 TGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCTGTTCCACTGTAATCTCAGGGAAATAA
* * * **
40360483 GACCTGACGCGATCTATTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCACTCCA
66 GACCTGACGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCA
40360548 CTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGC
131 CTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGC
*
40360593 TATAATCTCAGGGAGATAAGATCTGACA
1 TGTAATCTCAGGGAGATAAGATCTGACA
40360621 CGATCTACTC
Statistics
Matches: 339, Mismatches: 36, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
173 20 0.06
174 1 0.00
175 317 0.94
176 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (175 bp):
TGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCTGTTCCACTGTAATCTCAGGGAAATAA
GACCTGACGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCA
CTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGC
Found at i:40360776 original size:175 final size:174
Alignment explanation
Indices: 40360543--40360967 Score: 620
Period size: 175 Copynumber: 2.4 Consensus size: 174
40360533 TTTTAATCCA
* * * * * *
40360543 CTCCACTGTAATCTCAGGGAGATAGGAT-T-ACTATCTTCAATCTGCTCCGCTATAATCTCAGGG
1 CTCCGCTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTCAGTCTGCTCCACTGTAATCTCAGGG
* * *
40360606 AGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
65 AGATAAGACCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTGATTTTAATCC
* **
40360671 GCTCCACTGTAATCTCAGGGAGATAGGATTACCATCTTTGATCTG
130 GCTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTG
* *
40360716 CTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGG
1 CTCCGCTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCAGTCTGCTCCACTGTAATCTCAGGG
* * * * *
40360781 AAATAAGACCTGACGCGATTTACTCTACTGTAACTTCAGAGAGATATGATCATTGGTTTTAATCC
65 AGATAAGACCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTGATTTTAATCC
*
40360846 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
130 GCTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTG
*
40360891 CTCCGCTGTAATCTCAGGAAGATAAGATCTGCAATTCTTCAGTCTGCTCCACTGTAATCTCAGGG
1 CTCCGCTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCAGTCTGCTCCACTGTAATCTCAGGG
40360956 AGATAAGACCTG
65 AGATAAGACCTG
40360968 TATAATGAAC
Statistics
Matches: 224, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
173 26 0.12
174 1 0.00
175 195 0.87
176 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (174 bp):
CTCCGCTGTAATCTCAGGGAGATAAGATCTGAATTCTTCAGTCTGCTCCACTGTAATCTCAGGGA
GATAAGACCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTGATTTTAATCCG
CTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTG
Found at i:40360892 original size:479 final size:478
Alignment explanation
Indices: 40359929--40360967 Score: 1627
Period size: 479 Copynumber: 2.2 Consensus size: 478
40359919 CCTTTATTTT
* * * * * *
40359929 AATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-T-AC-TAGCTTCAATCTGCTCCGCCGTAAT
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACAT-TCTTC-ATCTGCTCCACTGTAAT
* * *
40359991 CTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATT
64 CTCAGGGAGATAAGACCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATT
* * *
40360056 TTAATCCGCTCCATTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATC
129 TTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTATAATC
* *
40360121 TTAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTTTTT
194 TCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTATTT
* *
40360186 TAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCACTGTAATCT
259 TAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTACTCCACTGTAATCT
*
40360251 CAAGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGAT
324 CAAGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGAC
* * * *
40360316 GCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATC
389 GCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTGATTTTAATCCGCTCCACTGTAATC
* *
40360381 TCAGGGAGATAGGATTACCATCTTT
454 TCAGGGAGATAGGATTACCAGCTTC
* *
40360406 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACATTCTTCGATCTGTTCCACTGTAATC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACATTCTTC-ATCTGCTCCACTGTAATC
* * * *
40360471 TCAGGGAAATAAGACCTGACGCGATCTATTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTT
65 TCAGGGAGATAAGACCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTT
*
40360536 TAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTATAATCT
130 TAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTATAATCT
*
40360601 CAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTT
195 CAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTATTTT
* ** * *
40360666 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACCATCTTTGATCTGCTCCGCTGTAATCTC
260 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTACTCCACTGTAATCTC
*
40360731 AGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGACG
325 AAGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGACG
* * *
40360796 CGATTTACTCTACTGTAACTTCAGAGAGATATGATCATTGGTTTTAATCCGCTCCACTGTAATCT
390 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTGATTTTAATCCGCTCCACTGTAATCT
*
40360861 CAGGGAGATAGGATTACTAGCTTC
455 CAGGGAGATAGGATTACCAGCTTC
*
40360885 AATCTGCTCCGCTGTAATCTCAGGAAGATAAGATCTG-CAATTCTTCAGTCTGCTCCACTGTAAT
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAC-ATTCTTCA-TCTGCTCCACTGTAAT
40360949 CTCAGGGAGATAAGACCTG
64 CTCAGGGAGATAAGACCTG
40360968 TATAATGAAC
Statistics
Matches: 511, Mismatches: 46, Indels: 8
0.90 0.08 0.01
Matches are distributed among these distances:
477 30 0.06
478 3 0.01
479 477 0.93
480 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (478 bp):
AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACATTCTTCATCTGCTCCACTGTAATCT
CAGGGAGATAAGACCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTT
AATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTATAATCTC
AGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTATTTTA
ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAATCTACTCCACTGTAATCTCA
AGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGACGC
GATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTGATTTTAATCCGCTCCACTGTAATCTC
AGGGAGATAGGATTACCAGCTTC
Found at i:40362129 original size:8 final size:8
Alignment explanation
Indices: 40362127--40362165 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 8
40362117 CTTTTTCATT
40362127 TTTTTTCA
1 TTTTTTCA
40362135 -TTTTTCA
1 TTTTTTCA
40362142 TTTTTTCA
1 TTTTTTCA
40362150 TTTTTTTCA
1 -TTTTTTCA
40362159 TCTTTTT
1 T-TTTTT
40362166 TTTTACTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.25
8 8 0.29
9 13 0.46
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTTCA
Found at i:40362136 original size:24 final size:24
Alignment explanation
Indices: 40362109--40362164 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
40362099 TTAGCCTCTC
40362109 CATTTTT-ACTTTTTCATTTTTTTT
1 CATTTTTCACTTTTTCA-TTTTTTT
*
40362133 CATTTTTCATTTTTTCATTTTTTT
1 CATTTTTCACTTTTTCATTTTTTT
40362157 CATCTTTT
1 CAT-TTTT
40362165 TTTTTACTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.73
Consensus pattern (24 bp):
CATTTTTCACTTTTTCATTTTTTT
Found at i:40362138 original size:9 final size:9
Alignment explanation
Indices: 40362118--40362166 Score: 59
Period size: 10 Copynumber: 5.6 Consensus size: 9
40362108 CCATTTTTAC
40362118 TTTTTCATTT
1 TTTTTCA-TT
40362128 TTTTTCA--
1 TTTTTCATT
40362135 TTTTTCA-T
1 TTTTTCATT
40362143 TTTTTCATT
1 TTTTTCATT
40362152 TTTTTCATCT
1 TTTTTCAT-T
40362162 TTTTT
1 TTTTT
40362167 TTTACTTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.19
8 7 0.19
9 9 0.25
10 13 0.36
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTCATT
Found at i:40362155 original size:17 final size:17
Alignment explanation
Indices: 40362118--40362166 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
40362108 CCATTTTTAC
40362118 TTTTTCATTTTTTTTCA-
1 TTTTTCA-TTTTTTTCAT
40362135 TTTTTCA-TTTTTTCATT
1 TTTTTCATTTTTTTCA-T
40362152 TTTTTCATCTTTTTT
1 TTTTTCAT-TTTTTT
40362167 TTTACTTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 8 0.29
17 14 0.50
19 6 0.21
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTCATTTTTTTCAT
Found at i:40362995 original size:6 final size:6
Alignment explanation
Indices: 40362984--40363020 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
40362974 TGACCTCTCA
40362984 TTTTTC TTTTTC TTTTTC TTTTTTC TTTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC -TTTTTC -TTTTTC TTTTT
40363021 TTTCCTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:40363000 original size:7 final size:7
Alignment explanation
Indices: 40362984--40363021 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
40362974 TGACCTCTCA
40362984 TTTTTC-
1 TTTTTCT
40362990 TTTTTC-
1 TTTTTCT
40362996 TTTTTCT
1 TTTTTCT
40363003 TTTTTCT
1 TTTTTCT
40363010 TTTTTCT
1 TTTTTCT
40363017 TTTTT
1 TTTTT
40363022 TTCCTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 12 0.39
7 19 0.61
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTCT
Found at i:40363083 original size:9 final size:9
Alignment explanation
Indices: 40363063--40363112 Score: 93
Period size: 9 Copynumber: 5.7 Consensus size: 9
40363053 TTTGTTTTTC
40363063 TTTTTTGA-
1 TTTTTTGAT
40363071 TTTTTTGAT
1 TTTTTTGAT
40363080 TTTTTTGAT
1 TTTTTTGAT
40363089 TTTTTTGAT
1 TTTTTTGAT
40363098 TTTTTTGAT
1 TTTTTTGAT
40363107 TTTTTT
1 TTTTTT
40363113 TTGAGTCTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
8 8 0.20
9 33 0.80
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.80
Consensus pattern (9 bp):
TTTTTTGAT
Found at i:40368820 original size:24 final size:24
Alignment explanation
Indices: 40368787--40368833 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
40368777 ATTTGTAAAT
40368787 GGGCTAATTGGGTTTAGTTTGTTG
1 GGGCTAATTGGGTTTAGTTTGTTG
*
40368811 GGGCTGATTGGGTTTAGTTTGTT
1 GGGCTAATTGGGTTTAGTTTGTT
40368834 TGGGTTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.11, C:0.04, G:0.38, T:0.47
Consensus pattern (24 bp):
GGGCTAATTGGGTTTAGTTTGTTG
Found at i:40368967 original size:27 final size:28
Alignment explanation
Indices: 40368895--40368967 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
40368885 TGGGTTGTAC
40368895 AAACATATTAAAATG-ATGTAATAAGCTA
1 AAACATATT-AAATGCATGTAATAAGCTA
* *
40368923 AAACAAATT-AATGTCATGTACTAA-CTA
1 AAACATATTAAATG-CATGTAATAAGCTA
*
40368950 AGACATATTAAATGCATG
1 AAACATATTAAATGCATG
40368968 CATGAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.11
27 14 0.37
28 20 0.53
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (28 bp):
AAACATATTAAATGCATGTAATAAGCTA
Found at i:40371811 original size:15 final size:16
Alignment explanation
Indices: 40371791--40371825 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
40371781 TCTCGCATTG
40371791 TTTTTCTTTT-TCATC
1 TTTTTCTTTTCTCATC
40371806 TTTTTCTTTTCTCATC
1 TTTTTCTTTTCTCATC
40371822 TTTT
1 TTTT
40371826 CACTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTCTTTTCTCATC
Found at i:40371815 original size:20 final size:20
Alignment explanation
Indices: 40371792--40371896 Score: 59
Period size: 20 Copynumber: 5.5 Consensus size: 20
40371782 CTCGCATTGT
40371792 TTTTCTTTTTCATCTTTTTC
1 TTTTCTTTTTCATCTTTTTC
40371812 TTTTC----TCATC-TTTTC
1 TTTTCTTTTTCATCTTTTTC
* *
40371827 ACTTTC-TTTT-ATTATTTTTC
1 -TTTTCTTTTTCA-TCTTTTTC
*
40371847 CTTTCTTTTTC-TCATTTTTC
1 TTTTCTTTTTCATC-TTTTTC
40371867 TTTTCTTTTGT-AT-TTTCATTC
1 TTTTCTTTT-TCATCTTT--TTC
40371888 TTTTCTTTT
1 TTTTCTTTT
40371897 CTCTCATTTG
Statistics
Matches: 68, Mismatches: 4, Indels: 25
0.70 0.04 0.26
Matches are distributed among these distances:
15 5 0.07
16 9 0.13
18 1 0.01
19 11 0.16
20 28 0.41
21 14 0.21
ACGTcount: A:0.08, C:0.19, G:0.01, T:0.72
Consensus pattern (20 bp):
TTTTCTTTTTCATCTTTTTC
Found at i:40371850 original size:19 final size:18
Alignment explanation
Indices: 40371808--40371882 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 18
40371798 TTTTCATCTT
*
40371808 TTTCTTTTCTCATCTTTTCAC
1 TTTCTTTT-TTAT-TTTTC-C
40371829 TTTCTTTTATTATTTTTCC
1 TTTCTTTT-TTATTTTTCC
*
40371848 TTTCTTTTTCTCATTTTTCT
1 TTTCTTTTT-T-ATTTTTCC
*
40371868 TTTCTTTTGTATTTT
1 TTTCTTTTTTATTTT
40371883 CATTCTTTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 6 0.12
19 11 0.23
20 20 0.42
21 11 0.23
ACGTcount: A:0.08, C:0.19, G:0.01, T:0.72
Consensus pattern (18 bp):
TTTCTTTTTTATTTTTCC
Found at i:40371866 original size:15 final size:14
Alignment explanation
Indices: 40371791--40371870 Score: 53
Period size: 15 Copynumber: 5.7 Consensus size: 14
40371781 TCTCGCATTG
40371791 TTTTTCTTTTTCATC
1 TTTTTCTTTTTC-TC
40371806 TTTTTC-TTTTCTC
1 TTTTTCTTTTTCTC
**
40371819 ATCTTTTCACTTTCT-
1 -T-TTTTCTTTTTCTC
*
40371834 TTTATTATTTTTC-C
1 TTT-TTCTTTTTCTC
40371848 --TTTCTTTTTCTC
1 TTTTTCTTTTTCTC
40371860 ATTTTTCTTTT
1 -TTTTTCTTTT
40371871 CTTTTGTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
11 8 0.16
12 2 0.04
13 4 0.08
14 13 0.25
15 19 0.37
16 5 0.10
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTCTTTTTCTC
Found at i:40371893 original size:41 final size:40
Alignment explanation
Indices: 40371798--40371905 Score: 107
Period size: 41 Copynumber: 2.6 Consensus size: 40
40371788 TTGTTTTTCT
40371798 TTTTCA-TCTTTT-TCTTTTCTCATCTTTTCACTTTCTTTTA
1 TTTTCATTCTTTTCT-TTTTCTCAT-TTTTCACTTTCTTTTA
* * *
40371838 TTATT-TTTCCTTTCTTTTTCTCATTTTTC-TTTTCTTTTGTA
1 TT-TTCATTCTTTTCTTTTTCTCATTTTTCACTTTC-TTT-TA
40371879 TTTTCATTCTTTTCTTTTCTCTCATTT
1 TTTTCATTCTTTTCTTTT-TCTCATTT
40371906 GATCTACAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
39 4 0.07
40 12 0.21
41 31 0.55
42 9 0.16
ACGTcount: A:0.08, C:0.20, G:0.01, T:0.70
Consensus pattern (40 bp):
TTTTCATTCTTTTCTTTTTCTCATTTTTCACTTTCTTTTA
Found at i:40388572 original size:12 final size:12
Alignment explanation
Indices: 40388552--40388584 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
40388542 TTTGCACTAA
40388552 ATTAATTTTT-T
1 ATTAATTTTTCT
40388563 ATTAATTTTTCT
1 ATTAATTTTTCT
40388575 ATTCAATTTT
1 ATT-AATTTT
40388585 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 4 0.20
13 6 0.30
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTAATTTTTCT
Found at i:40392416 original size:34 final size:34
Alignment explanation
Indices: 40392373--40392438 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
40392363 AGAATTTAGA
* *
40392373 ATCAGAAGCATATCATTCAGTCTTATTTACATAC
1 ATCACAAGCATATCATTCAGTCTTATTCACATAC
40392407 ATCACAAGCATATCATTCAGTCTTATTCACAT
1 ATCACAAGCATATCATTCAGTCTTATTCACAT
40392439 GCATTCTCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (34 bp):
ATCACAAGCATATCATTCAGTCTTATTCACATAC
Found at i:40399086 original size:37 final size:38
Alignment explanation
Indices: 40399006--40399097 Score: 107
Period size: 38 Copynumber: 2.4 Consensus size: 38
40398996 ACCAGAATGG
* *
40399006 CACCCAGTGCCTCATCGGATAGTTCGAAGCAAAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAGCAAAGTTGA
* *
40399044 CACCCAGTGTCTCATCGGCAAAG-CCGAAG-AAAGTTGT
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGCAAAGTTGA
* *
40399081 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
40399098 AAACTATCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
37 21 0.46
38 22 0.48
39 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGCAAAGTTGA
Found at i:40399310 original size:23 final size:24
Alignment explanation
Indices: 40399266--40399311 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
40399256 TTTCTCACAT
* **
40399266 TTTCAATTCAATTATTTTTCCACC
1 TTTCAATTCAATAATTAATCCACC
40399290 TTTCAA-TCAATAATTAATCCAC
1 TTTCAATTCAATAATTAATCCAC
40399312 AAATTCACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTCAATTCAATAATTAATCCACC
Found at i:40399458 original size:3 final size:3
Alignment explanation
Indices: 40399450--40399484 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
40399440 TAATTCTCAC
40399450 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
40399485 CTTACCTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:40399796 original size:10 final size:10
Alignment explanation
Indices: 40399760--40399805 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
40399750 TGTTTCTTTC
40399760 TTTC-TTTTA
1 TTTCATTTTA
40399769 TTTCATTTGT-
1 TTTCATTT-TA
40399779 TTTC-TTTTA
1 TTTCATTTTA
40399788 TTTCATTTTA
1 TTTCATTTTA
40399798 TTTCATTT
1 TTTCATTT
40399806 ACTTTATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 1 0.03
9 11 0.33
10 20 0.61
11 1 0.03
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (10 bp):
TTTCATTTTA
Found at i:40400296 original size:9 final size:9
Alignment explanation
Indices: 40400282--40400323 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
40400272 TGAATAAATA
40400282 ATAATAATT
1 ATAATAATT
40400291 ATAATAATT
1 ATAATAATT
40400300 AT-ATAGA-T
1 ATAATA-ATT
*
40400308 ATAATATTT
1 ATAATAATT
40400317 ATAATAA
1 ATAATAA
40400324 CTTGAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 6 0.21
9 22 0.79
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
ATAATAATT
Found at i:40404971 original size:13 final size:13
Alignment explanation
Indices: 40404953--40404979 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40404943 ATTTCCATAT
40404953 GGGGTGGCCACAC
1 GGGGTGGCCACAC
40404966 GGGGTGGCCACAC
1 GGGGTGGCCACAC
40404979 G
1 G
40404980 CCCATGTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.30, G:0.48, T:0.07
Consensus pattern (13 bp):
GGGGTGGCCACAC
Found at i:40406069 original size:17 final size:18
Alignment explanation
Indices: 40406038--40406087 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
40406028 GGAACATTCA
40406038 ATTTTTATTAATTTAGCCAT
1 ATTTTTATT--TTTAGCCAT
**
40406058 -TTTTTATTTTTA-TTAT
1 ATTTTTATTTTTAGCCAT
40406074 ATTTTTATTTTTAG
1 ATTTTTATTTTTAG
40406088 TTTAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 2 0.08
17 16 0.62
19 8 0.31
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.68
Consensus pattern (18 bp):
ATTTTTATTTTTAGCCAT
Found at i:40406096 original size:17 final size:17
Alignment explanation
Indices: 40406059--40406096 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
40406049 TTTAGCCATT
*
40406059 TTTTATTTTTATTATAT
1 TTTTATTTTTATTATAA
40406076 TTTTATTTTTAGTT-TAA
1 TTTTATTTTTA-TTATAA
40406093 TTTT
1 TTTT
40406097 TGCATTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTATTTTTATTATAA
Found at i:40410340 original size:6 final size:6
Alignment explanation
Indices: 40410329--40410357 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40410319 TCCATGTCAT
40410329 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
40410358 CTGCTCGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:40411233 original size:11 final size:10
Alignment explanation
Indices: 40411219--40411246 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
40411209 TAAAAAAAAC
40411219 AAAAAAATTG
1 AAAAAAATTG
40411229 AAAAAAATTG
1 AAAAAAATTG
40411239 AAAAAAAT
1 AAAAAAAT
40411247 ACAACACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:40414577 original size:25 final size:25
Alignment explanation
Indices: 40414548--40414611 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
40414538 TAAGAGCTAT
*
40414548 TAACGGAAAGCTTGTAAGAACAATA
1 TAACGGGAAGCTTGTAAGAACAATA
*
40414573 TAACGGGAATCTTGTAAGAACAATA
1 TAACGGGAAGCTTGTAAGAACAATA
40414598 TAACGGGAAGCTTG
1 TAACGGGAAGCTTG
40414612 AGATGGCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.22
Consensus pattern (25 bp):
TAACGGGAAGCTTGTAAGAACAATA
Found at i:40424522 original size:4 final size:4
Alignment explanation
Indices: 40424515--40424539 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
40424505 TATATATATA
40424515 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
40424540 TAAAAGTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:40427420 original size:12 final size:10
Alignment explanation
Indices: 40427393--40427424 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
40427383 ATTTATTAAC
40427393 AAACACATTA
1 AAACACATTA
40427403 AAACACATTA
1 AAACACATTA
*
40427413 AAACACACTA
1 AAACACATTA
40427423 AA
1 AA
40427425 TAAGCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (10 bp):
AAACACATTA
Done.