Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001736.1 Hibiscus syriacus cultivar Beakdansim tig00003507_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1778036
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1507078 original size:24 final size:24
Alignment explanation
Indices: 1507044--1507097 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1507034 CTGAAACATC
1507044 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1507068 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1507092 ATCAAA
1 ATCAAA
1507098 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1507941 original size:20 final size:20
Alignment explanation
Indices: 1507916--1508026 Score: 134
Period size: 20 Copynumber: 5.5 Consensus size: 20
1507906 TTGAAATTCA
*
1507916 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
1507936 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
1507956 ACGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
* **
1507976 GAGTTGCGATTATGT-ATTATC
1 GCGTTGCGA-TA-GTCAGAATC
*
1507997 GCGTTGCGATAGTTAGAATC
1 GCGTTGCGATAGTCAGAATC
*
1508017 GTGTTGCGAT
1 GCGTTGCGAT
1508027 TATGTATTGT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 60 0.77
21 14 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:1508002 original size:21 final size:21
Alignment explanation
Indices: 1507973--1508048 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
1507963 GATAGTCAGA
*
1507973 ATCGAGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
1507994 ATCGCGTTGCGA-TA-GTTAGA
1 ATCGCGTTGCGATTATG-TATT
*
1508014 ATCGTGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
*
1508035 GTCGCGTTGCGATT
1 ATCGCGTTGCGATT
1508049 TACATATTCG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.02
20 15 0.34
21 27 0.61
22 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:1508015 original size:41 final size:41
Alignment explanation
Indices: 1507916--1508047 Score: 169
Period size: 41 Copynumber: 3.2 Consensus size: 41
1507906 TTGAAATTCA
* * **
1507916 GCGTTGCGACAGTCAGAATCGCGTTGCGA-TA-GTCAGAATC
1 GCGTTGCGATAGTCAGAATCGAGTTGCGATTATGT-ATTATC
*
1507956 ACGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATTATC
1 GCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATTATC
* * *
1507997 GCGTTGCGATAGTTAGAATCGTGTTGCGATTATGTATTGTC
1 GCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATTATC
1508038 GCGTTGCGAT
1 GCGTTGCGAT
1508048 TTACATATTC
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
40 26 0.32
41 53 0.65
42 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.32
Consensus pattern (41 bp):
GCGTTGCGATAGTCAGAATCGAGTTGCGATTATGTATTATC
Found at i:1508065 original size:41 final size:40
Alignment explanation
Indices: 1507957--1508068 Score: 111
Period size: 41 Copynumber: 2.7 Consensus size: 40
1507947 GTCAGAATCA
* *
1507957 CGTTGCGATAGTCAGAATCG-AGTTGCGATTATGTATTATCG
1 CGTTGCGATA-TTACAATCGCA-TTGCGATTATGTATTATCG
* ** *
1507998 CGTTGCGATAGTTAGAATCGTGTTGCGATTATGTATTGTCG
1 CGTTGCGATA-TTACAATCGCATTGCGATTATGTATTATCG
1508039 CGTTGCGAT-TTACATATTCGCATTGCGATT
1 CGTTGCGATATTACA-A-TCGCATTGCGATT
1508069 TTTAGAAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
39 4 0.06
40 1 0.02
41 57 0.92
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (40 bp):
CGTTGCGATATTACAATCGCATTGCGATTATGTATTATCG
Found at i:1508081 original size:22 final size:22
Alignment explanation
Indices: 1508056--1508111 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
1508046 ATTTACATAT
* *
1508056 TCGCATTGCGATTTTTAGAAAA
1 TCGCAATGCGATATTTAGAAAA
* *
1508078 TCGCAACGCGA-ATTTGGAAAA
1 TCGCAATGCGATATTTAGAAAA
1508099 TCGCAATGCGATA
1 TCGCAATGCGATA
1508112 GTCAAAATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (22 bp):
TCGCAATGCGATATTTAGAAAA
Found at i:1508179 original size:19 final size:19
Alignment explanation
Indices: 1508155--1508191 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1508145 TGCGATACTG
*
1508155 GAGATCGCGTTACGATTTA
1 GAGATCGCATTACGATTTA
*
1508174 GAGATCGCATTGCGATTT
1 GAGATCGCATTACGATTT
1508192 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:1509473 original size:18 final size:19
Alignment explanation
Indices: 1509450--1509496 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
1509440 ATGAAAGCCT
*
1509450 TTGAAACTTGTT-AACTTG
1 TTGAAACTTGTTCAACTTC
1509468 TTGAAACTT-TTCAACTTC
1 TTGAAACTTGTTCAACTTC
*
1509486 TTGAAATTTGT
1 TTGAAACTTGT
1509497 GTTTAACCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.08
18 22 0.88
19 1 0.04
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (19 bp):
TTGAAACTTGTTCAACTTC
Found at i:1512216 original size:17 final size:18
Alignment explanation
Indices: 1512182--1512219 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
1512172 TTTTGTTTGT
1512182 ATTTTATTTAAGTATTTA
1 ATTTTATTTAAGTATTTA
*
1512200 ATTTT-TTTAA-TATTTT
1 ATTTTATTTAAGTATTTA
1512216 ATTT
1 ATTT
1512220 AATTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 5 0.26
18 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTTATTTAAGTATTTA
Found at i:1514406 original size:13 final size:12
Alignment explanation
Indices: 1514387--1514436 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
1514377 AATACTTACT
1514387 TTATTTTGTTAA
1 TTATTTTGTTAA
*
1514399 TGTATTTTGGATAA
1 T-TATTTT-GTTAA
1514413 TT-TTTT-TTAA
1 TTATTTTGTTAA
1514423 TTTATTTTGTTAA
1 -TTATTTTGTTAA
1514436 T
1 T
1514437 ATTGTTGGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
10 3 0.10
11 2 0.06
12 10 0.32
13 11 0.35
14 5 0.16
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (12 bp):
TTATTTTGTTAA
Found at i:1516900 original size:16 final size:16
Alignment explanation
Indices: 1516879--1516914 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1516869 ATATTTTTTC
1516879 AAATAATCATAATAAA
1 AAATAATCATAATAAA
*
1516895 AAATAATTATAATAAA
1 AAATAATCATAATAAA
1516911 AAAT
1 AAAT
1516915 TATAACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAATCATAATAAA
Found at i:1519532 original size:18 final size:18
Alignment explanation
Indices: 1519509--1519555 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1519499 ATGAAAGCTT
* *
1519509 TTGAAACTTGTTAACTTG
1 TTGAAACTTGTCAACTTC
* *
1519527 TTGAAACATGTCAATTTC
1 TTGAAACTTGTCAACTTC
1519545 TTGAAACTTGT
1 TTGAAACTTGT
1519556 GTTTAATCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (18 bp):
TTGAAACTTGTCAACTTC
Found at i:1523152 original size:84 final size:84
Alignment explanation
Indices: 1523005--1523632 Score: 659
Period size: 84 Copynumber: 7.6 Consensus size: 84
1522995 AAAGTTGAAA
* * * *
1523005 AATTA-CAACACTAGAATATTTATCTTCGATG-TCCTTAACAAGTTGAGAATACAATTTGAGATT
1 AATTAGCAACACTAGAATATTTATCTTCGA-GCTCCTTAGCAAGTTGAGAAGACAACTTGGGATT
* *
1523068 TTTGTCGACAAAAGATCTCT
65 TTTGTCGACAGAAGATCTCC
* * * * *
1523088 AATTAGCAACATTAGAATGTTTAT-TCTCAAGTTCCTTAGCAAGTTGAGAAGATAACTTGGGATT
1 AATTAGCAACACTAGAATATTTATCT-TCGAGCTCCTTAGCAAGTTGAGAAGACAACTTGGGATT
* *
1523152 TTTGTCGACAAAAGATCTCG
65 TTTGTCGACAGAAGATCTCC
** *
1523172 AATTAGCAACA-TTTAATATTTATCTTCGAGCTCCTTAGCAAGTTGAGAAGATAACTTGGGATTA
1 AATTAGCAACACTAGAATATTTATCTTCGAGCTCCTTAGCAAGTTGAGAAGACAACTTGGGATT-
1523236 TTT-TCGACAGAAGATCTCC
65 TTTGTCGACAGAAGATCTCC
* *
1523255 AATTAGCAACACTGGAATATTTATCTTCGAGCTCCTTAGCAAGTTGAGATGACAACTTGGGATTT
1 AATTAGCAACACTAGAATATTTATCTTCGAGCTCCTTAGCAAGTTGAGAAGACAACTTGGGATTT
1523320 TTGTC-ATCAGAAGATCTCC
66 TTGTCGA-CAGAAGATCTCC
* * *
1523339 AGTTAGCAACACTATAATATTTATCTTCGAGCTCCTTAGTAAGTTGAGAAGACAACTTGGGATTT
1 AATTAGCAACACTAGAATATTTATCTTCGAGCTCCTTAGCAAGTTGAGAAGACAACTTGGGATTT
*
1523404 TTGTCAACAGAAGATCTCC
66 TTGTCGACAGAAGATCTCC
* * ** **
1523423 AATTAGCAACACTAGAATATTTATCTT-GAAGCTCCGTAGTAAGTTGAGAAGTTAACTCAGGATT
1 AATTAGCAACACTAGAATATTTATCTTCG-AGCTCCTTAGCAAGTTGAGAAGACAACTTGGGATT
*
1523487 TTTGTTC--C-----A--TAC
65 TTTG-TCGACAGAAGATCTCC
* * * *
1523499 AA-TAGCAACACTAGAATATTTATCCTT-AAGCTCCTTAGTAGGTTGAGAAGTCAATTCTT--GA
1 AATTAGCAACACTAGAATATTTAT-CTTCGAGCTCCTTAGCAAGTTGAGAAGACAA--CTTGGGA
*
1523560 TTTTTATCGGA-AGAAGATCTCC
63 TTTTTGTC-GACAGAAGATCTCC
* * * * * *
1523582 AGTTAGCATCATTAGAATATTTATCTCCGAGCTCATTTGCAAGTTGAGAAG
1 AATTAGCAACACTAGAATATTTATCTTCGAGCTCCTTAGCAAGTTGAGAAG
1523633 TTAATTCAGG
Statistics
Matches: 470, Mismatches: 49, Indels: 51
0.82 0.09 0.09
Matches are distributed among these distances:
74 2 0.00
75 51 0.11
76 7 0.01
77 2 0.00
78 1 0.00
81 1 0.00
83 88 0.19
84 315 0.67
85 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (84 bp):
AATTAGCAACACTAGAATATTTATCTTCGAGCTCCTTAGCAAGTTGAGAAGACAACTTGGGATTT
TTGTCGACAGAAGATCTCC
Found at i:1523295 original size:167 final size:168
Alignment explanation
Indices: 1523005--1523649 Score: 675
Period size: 167 Copynumber: 3.9 Consensus size: 168
1522995 AAAGTTGAAA
* * * * *
1523005 AATTA-CAACACTAGAATATTTATCTTCGATG-TCCTTAACAAGTTGAGAATACAATTTGAGATT
1 AATTAGCAACACTATAATATTTATCTTCGA-GCTCCTTAGCAAGTTGAGAAGACAACTTGGGATT
* * * * * *
1523068 TTTGTCGACAAAAGATCTCTAATTAGCAACATTAGAATGTTTAT-TCTCAAGTTCCTTAGCAAGT
65 TTTGTCGACAGAAGATCTCCAATTAGCAACACTAGAATATTTATCT-TCGAGCTCCTTAGCAAGT
*
1523132 TGAGAAGATAACTTGGGATTTTTGTCGA-CAAAAGATCTCG
129 TGAGAAGATAACTTGGGATTTTTGTC-ATCAAAAGATCTCC
* *
1523172 AATTAGCAACA-TTTAATATTTATCTTCGAGCTCCTTAGCAAGTTGAGAAGATAACTTGGGATTA
1 AATTAGCAACACTATAATATTTATCTTCGAGCTCCTTAGCAAGTTGAGAAGACAACTTGGGATT-
*
1523236 TTT-TCGACAGAAGATCTCCAATTAGCAACACTGGAATATTTATCTTCGAGCTCCTTAGCAAGTT
65 TTTGTCGACAGAAGATCTCCAATTAGCAACACTAGAATATTTATCTTCGAGCTCCTTAGCAAGTT
* * *
1523300 GAGATGACAACTTGGGATTTTTGTCATCAGAAGATCTCC
130 GAGAAGATAACTTGGGATTTTTGTCATCAAAAGATCTCC
* *
1523339 AGTTAGCAACACTATAATATTTATCTTCGAGCTCCTTAGTAAGTTGAGAAGACAACTTGGGATTT
1 AATTAGCAACACTATAATATTTATCTTCGAGCTCCTTAGCAAGTTGAGAAGACAACTTGGGATTT
* * *
1523404 TTGTCAACAGAAGATCTCCAATTAGCAACACTAGAATATTTATCTT-GAAGCTCCGTAGTAAGTT
66 TTGTCGACAGAAGATCTCCAATTAGCAACACTAGAATATTTATCTTCG-AGCTCCTTAGCAAGTT
* ** * *
1523468 GAGAAGTTAACTCAGGATTTTTGT--TC----CA--TAC
130 GAGAAGATAACTTGGGATTTTTGTCATCAAAAGATCTCC
* * * * *
1523499 AA-TAGCAACACTAGAATATTTATCCTT-AAGCTCCTTAGTAGGTTGAGAAGTCAATTCTT--GA
1 AATTAGCAACACTATAATATTTAT-CTTCGAGCTCCTTAGCAAGTTGAGAAGACAA--CTTGGGA
* * * * * * *
1523560 TTTTTATCGGA-AGAAGATCTCCAGTTAGCATCATTAGAATATTTATCTCCGAGCTCATTTGCAA
63 TTTTTGTC-GACAGAAGATCTCCAATTAGCAACACTAGAATATTTATCTTCGAGCTCCTTAGCAA
* *
1523624 GTTGAGAAGTTAA-TTCAGGATTTTTG
127 GTTGAGAAGATAACTT-GGGATTTTTG
1523650 GTCACTAAAA
Statistics
Matches: 415, Mismatches: 49, Indels: 36
0.83 0.10 0.07
Matches are distributed among these distances:
158 1 0.00
159 119 0.29
160 8 0.02
161 3 0.01
162 1 0.00
166 4 0.01
167 147 0.35
168 132 0.32
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (168 bp):
AATTAGCAACACTATAATATTTATCTTCGAGCTCCTTAGCAAGTTGAGAAGACAACTTGGGATTT
TTGTCGACAGAAGATCTCCAATTAGCAACACTAGAATATTTATCTTCGAGCTCCTTAGCAAGTTG
AGAAGATAACTTGGGATTTTTGTCATCAAAAGATCTCC
Found at i:1523579 original size:159 final size:159
Alignment explanation
Indices: 1523010--1523693 Score: 532
Period size: 159 Copynumber: 4.2 Consensus size: 159
1523000 TGAAAAATTA
* ** * * *
1523010 CAACACTAGAATATTTAT-CTTCGATG-TCCTTAACAAGTTGAGAATACAATTTGAGATTTTTGT
1 CAACACTAGAATATTTATCCTTC-AAGCTCCTTAGTAAGTTGAGAAGACAACTTG-GATTTTTAT
* * * * * ** *
1523073 CGACAAAAGATCTCTAATTAGCAACATTAGAATGTTTATTCTCAAGTTCCTTAGCAAGTTGAGAA
64 CAACAGAAGATCTCCAATTAGCAACACTAGAATATTTA-TCTTGAGCTCCTTAGCAAGTTGAGAA
* **
1523138 GATAACTTGGGATTTTTG-TCGACAAAAGATCT-CGAATTAG
128 GTTAACTCAGGATTTTTGTTC--C-----A-CTAC-AA-TAG
** * * *
1523178 CAACA-TTTAATATTTAT-CTTCGAGCTCCTTAGCAAGTTGAGAAGATAACTTGGGATTATTT-T
1 CAACACTAGAATATTTATCCTTCAAGCTCCTTAGTAAGTTGAGAAGACAACTT-GGATT-TTTAT
* * *
1523240 CGACAGAAGATCTCCAATTAGCAACACTGGAATATTTATCTTCGAGCTCCTTAGCAAGTTGAGAT
64 CAACAGAAGATCTCCAATTAGCAACACTAGAATATTTATCTT-GAGCTCCTTAGCAAGTTGAGAA
** ** * * *
1523305 GACAACTTGGGATTTTTGTCATCAGAAGATCTCCAGTTAG
128 GTTAACTCAGGATTTTTGT--TC----CA-CTACA-ATAG
* * *
1523345 CAACACTATAATATTTAT-CTTCGAGCTCCTTAGTAAGTTGAGAAGACAACTTGGGATTTTTGTC
1 CAACACTAGAATATTTATCCTTCAAGCTCCTTAGTAAGTTGAGAAGACAACTT-GGATTTTTATC
* *
1523409 AACAGAAGATCTCCAATTAGCAACACTAGAATATTTATCTTGAAGCTCCGTAGTAAGTTGAGAAG
65 AACAGAAGATCTCCAATTAGCAACACTAGAATATTTATCTTG-AGCTCCTTAGCAAGTTGAGAAG
1523474 TTAACTCAGGATTTTTGTTCCA-TACAATAG
129 TTAACTCAGGATTTTTGTTCCACTACAATAG
* *
1523504 CAACACTAGAATATTTATCCTT-AAGCTCCTTAGTAGGTTGAGAAGTCAATTCTT-GATTTTTAT
1 CAACACTAGAATATTTATCCTTCAAGCTCCTTAGTAAGTTGAGAAGACAA--CTTGGATTTTTAT
* * * * * * *
1523567 CGGA-AGAAGATCTCCAGTTAGCATCATTAGAATATTTATCTCCGAGCTCATTTGCAAGTTGAGA
64 C-AACAGAAGATCTCCAATTAGCAACACTAGAATATTTATCT-TGAGCTCCTTAGCAAGTTGAGA
* * * *
1523631 AGTTAATTCAGGATTTTTGGT-CACTAAAATCG
127 AGTTAACTCAGGATTTTTGTTCCACTACAATAG
* *
1523663 CAGCACTAGAATATTTAT-CTTCAAACTCCTT
1 CAACACTAGAATATTTATCCTTCAAGCTCCTT
1523694 GACAAGTCGA
Statistics
Matches: 439, Mismatches: 56, Indels: 51
0.80 0.10 0.09
Matches are distributed among these distances:
158 5 0.01
159 153 0.35
160 8 0.02
161 3 0.01
162 1 0.00
166 6 0.01
167 127 0.29
168 133 0.30
170 2 0.00
172 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (159 bp):
CAACACTAGAATATTTATCCTTCAAGCTCCTTAGTAAGTTGAGAAGACAACTTGGATTTTTATCA
ACAGAAGATCTCCAATTAGCAACACTAGAATATTTATCTTGAGCTCCTTAGCAAGTTGAGAAGTT
AACTCAGGATTTTTGTTCCACTACAATAG
Found at i:1523868 original size:2 final size:2
Alignment explanation
Indices: 1523861--1523895 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1523851 AACGCAGAGT
1523861 TA TA TA TA 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 TA TA TA TA T
1523896 GCATAAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1524316 original size:2 final size:2
Alignment explanation
Indices: 1524309--1524339 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1524299 TGGTGGTTAC
1524309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1524340 GGGATGAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1525012 original size:3 final size:3
Alignment explanation
Indices: 1524956--1524994 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1524946 TTCGTCCCGC
* *
1524956 TAT TAT TAT TAT TAT TAT TATT TAA TAT TAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA
1524995 CTGCTACAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1533373 original size:134 final size:133
Alignment explanation
Indices: 1532999--1533545 Score: 657
Period size: 134 Copynumber: 4.1 Consensus size: 133
1532989 TGGGTGTTCC
* * ** * * *
1532999 AGATATAATTTTACCTCAAGAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTA
1 AGATATGATTTTCCCTCAAGAAGAAGCAGAACAAATCCTTCTATTTCAAGATTTGATATTCCCTG
* * *
1533064 AGTAACAGTGGAACAAGTTTGCCTCGATTCAATCTTCCATAAAGAACAGTGAAATGAATCAATAT
66 AGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTAAAGAACAGTG-AATGAATCAACAT
*
1533129 TTCC
130 TTCT
* * * * * * *
1533133 AGGTATGATTTTTCCTCAACAAGAAGCATAATATATCCCTCTCTCA-CTCAAGATTTGATATTCC
1 AGATATGATTTTCCCTCAAGAAGAAGCAGAACAAAT-CCT-TCT-ATTTCAAGATTTGATATTCC
* * *
1533197 CTGAGTAACAGTGGAACAAGTCTGCCTTGATTCAATATTCCCTAAAGAACAATAGAATGAATCAA
63 CTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTAAAGAACAGT-GAATGAATCAA
1533262 CATTTCT
127 CATTTCT
* * *
1533269 AGATTTGATTTTCCCTCAAGAAGAAGAAAAACAAATCCTTCTATTTCAAGATTTGATATTCCCTG
1 AGATATGATTTTCCCTCAAGAAGAAGCAGAACAAATCCTTCTATTTCAAGATTTGATATTCCCTG
* * *
1533334 AGTAACAGTGGAACAAGTCTACCTCGATTAAATCCTCCCTAAAGAACAGTGGAATGAATCAACAT
66 AGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTAAAGAACAGT-GAATGAATCAACAT
1533399 TTCT
130 TTCT
* * * * *
1533403 AGATATGATTTTCCCTCAAAAAGAAGCGGAACATATCATTCTCTTTCAAGATTTGATATTCCCTG
1 AGATATGATTTTCCCTCAAGAAGAAGCAGAACAAATCCTTCTATTTCAAGATTTGATATTCCCTG
* * * * *
1533468 AGTAACAGTGGAACAAGTATGCCTTGATTCAATATTCCC-AGAAGAACGGTGGAATGAGTCAACA
66 AGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTA-AAGAACAGT-GAATGAATCAACA
1533532 TTTCT
129 TTTCT
* *
1533537 TGATCTGAT
1 AGATATGAT
1533546 CTACCCTGAA
Statistics
Matches: 353, Mismatches: 54, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
133 2 0.01
134 235 0.67
135 5 0.01
136 110 0.31
137 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (133 bp):
AGATATGATTTTCCCTCAAGAAGAAGCAGAACAAATCCTTCTATTTCAAGATTTGATATTCCCTG
AGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTAAAGAACAGTGAATGAATCAACATT
TCT
Found at i:1536149 original size:9 final size:8
Alignment explanation
Indices: 1536137--1536212 Score: 50
Period size: 9 Copynumber: 9.2 Consensus size: 8
1536127 AATATTTTAT
1536137 ATATAATTA
1 ATATAA-TA
*
1536146 ATATAAAA
1 ATATAATA
1536154 ATATAA-A
1 ATATAATA
*
1536161 ATATTATA
1 ATATAATA
1536169 TATATAATTA
1 -ATATAA-TA
*
1536179 ATATAAAAA
1 ATAT-AATA
1536188 ATATAA-A
1 ATATAATA
*
1536195 ATATTAT-
1 ATATAATA
1536202 ATATATATA
1 ATATA-ATA
1536211 AT
1 AT
1536213 CGGGGCGGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
7 16 0.30
8 12 0.22
9 22 0.41
10 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:1536162 original size:33 final size:34
Alignment explanation
Indices: 1536125--1536208 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
1536115 CTGGAACCCA
*
1536125 AAAATATTTTATATATAATTAATAT-AAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
1536158 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
1536192 AAAATATTATATATATA
1 AAAATATTATATATATA
1536209 TAATCGGGGC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 24 0.49
34 25 0.51
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:1537151 original size:18 final size:18
Alignment explanation
Indices: 1537128--1537163 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1537118 GTTCTTAAGG
1537128 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1537146 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1537164 TTCTACACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1543279 original size:21 final size:20
Alignment explanation
Indices: 1543236--1543286 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1543226 ATATATGTTT
**
1543236 TATGAACAGT-AAAATACGG
1 TATGAACAGTAAAAATACCA
1543255 TATGAACAGTAAATAATACCA
1 TATGAACAGTAAA-AATACCA
*
1543276 TATGAATAGTA
1 TATGAACAGTA
1543287 GTGAACAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 10 0.37
20 2 0.07
21 15 0.56
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (20 bp):
TATGAACAGTAAAAATACCA
Found at i:1544275 original size:21 final size:21
Alignment explanation
Indices: 1544251--1544290 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1544241 ATCCCTTAGA
1544251 ACCACTGTATTATCCCGAATG
1 ACCACTGTATTATCCCGAATG
*
1544272 ACCACTGTATTGTCCCGAA
1 ACCACTGTATTATCCCGAA
1544291 GGACTTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (21 bp):
ACCACTGTATTATCCCGAATG
Found at i:1544389 original size:18 final size:17
Alignment explanation
Indices: 1544362--1544395 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1544352 ACATGGGCAT
*
1544362 TATCATTTGTTCATTTCA
1 TATCACTTGTTC-TTTCA
1544380 TATCACTTGTTCTTTC
1 TATCACTTGTTCTTTC
1544396 TCTTCTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.56
Consensus pattern (17 bp):
TATCACTTGTTCTTTCA
Found at i:1549671 original size:21 final size:22
Alignment explanation
Indices: 1549633--1549674 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1549623 ATTATAATAG
*
1549633 GGGAATCGATTCCCCTGCTACA
1 GGGAATCGATTACCCTGCTACA
1549655 GGGAATCGA-TACCCTGCTAC
1 GGGAATCGATTACCCTGCTAC
1549675 TCTACTGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (22 bp):
GGGAATCGATTACCCTGCTACA
Found at i:1550545 original size:21 final size:21
Alignment explanation
Indices: 1550521--1550561 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1550511 ATGAAATTTT
1550521 TCCTGAAGGACCACTGTATTA
1 TCCTGAAGGACCACTGTATTA
1550542 TCCTGAAGGACCACTGTATT
1 TCCTGAAGGACCACTGTATT
1550562 GTCCCAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (21 bp):
TCCTGAAGGACCACTGTATTA
Found at i:1550574 original size:21 final size:21
Alignment explanation
Indices: 1550526--1550574 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1550516 ATTTTTCCTG
**
1550526 AAGGACCACTGTATTATCCTG
1 AAGGACCACTGTATTATCCCA
*
1550547 AAGGACCACTGTATTGTCCCA
1 AAGGACCACTGTATTATCCCA
*
1550568 AATGACC
1 AAGGACC
1550575 TATGAAACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (21 bp):
AAGGACCACTGTATTATCCCA
Found at i:1551424 original size:20 final size:20
Alignment explanation
Indices: 1551399--1551436 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1551389 TTTTCTTTAG
1551399 GGGGGAATC-GATACCCCCCA
1 GGGGGAATCTG-TACCCCCCA
1551419 GGGGGAATCTGTACCCCC
1 GGGGGAATCTGTACCCCC
1551437 TGCATAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.21, C:0.34, G:0.32, T:0.13
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCCA
Found at i:1552250 original size:23 final size:23
Alignment explanation
Indices: 1552217--1552260 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1552207 GAGTAGAGGG
*
1552217 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGCGGTCCTTCGAGACAAT
*
1552240 TCTACGTGGTCCTTCGAGACA
1 TCTACGCGGTCCTTCGAGACA
1552261 TATATGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.30, G:0.25, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGAGACAAT
Found at i:1552392 original size:18 final size:18
Alignment explanation
Indices: 1552369--1552403 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1552359 TATGTGATAT
1552369 GTGGTCCTTCGGAACATA
1 GTGGTCCTTCGGAACATA
*
1552387 GTGGTCCTTCGGGACAT
1 GTGGTCCTTCGGAACAT
1552404 TTCTACGCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGAACATA
Found at i:1554138 original size:15 final size:15
Alignment explanation
Indices: 1554118--1554146 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1554108 TTTTTATCTT
1554118 TTAAAATTATTTTAC
1 TTAAAATTATTTTAC
1554133 TTAAAATTATTTTA
1 TTAAAATTATTTTA
1554147 AAAGATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAAATTATTTTAC
Found at i:1555564 original size:2 final size:2
Alignment explanation
Indices: 1555559--1555637 Score: 131
Period size: 2 Copynumber: 39.5 Consensus size: 2
1555549 ACCACACATT
* * *
1555559 TA TA TA TT TA TG TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1555601 TA TA TA TA TA 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 TA TA TA TA TA T
1555638 TTATTTATTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1556906 original size:2 final size:2
Alignment explanation
Indices: 1556899--1556923 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1556889 ATTCTATCAT
1556899 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1556924 TTCTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1567018 original size:15 final size:15
Alignment explanation
Indices: 1566998--1567040 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
1566988 TCCTAAGTTG
1566998 AAAAAAGAAAAAAAC
1 AAAAAAGAAAAAAAC
*
1567013 AAAAAAGGAAAAAAC
1 AAAAAAGAAAAAAAC
1567028 AAAAAAGAGAAAA
1 AAAAAAGA-AAAA
1567041 GCGTTTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.84, C:0.05, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAC
Found at i:1567094 original size:8 final size:8
Alignment explanation
Indices: 1567081--1567121 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
1567071 CTAAATTGAA
1567081 AAAAAAAG
1 AAAAAAAG
1567089 AAAAAAAG
1 AAAAAAAG
1567097 --AAAAAG
1 AAAAAAAG
*
1567103 AACAAAAG
1 AAAAAAAG
1567111 -AAAAAAG
1 AAAAAAAG
1567118 AAAA
1 AAAA
1567122 TAGGGTGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
6 6 0.21
7 6 0.21
8 16 0.57
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1567116 original size:15 final size:15
Alignment explanation
Indices: 1567082--1567121 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
1567072 TAAATTGAAA
1567082 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
*
1567097 -AAAAAGAACAAAAG
1 AAAAAAGAAAAAAAG
1567111 AAAAAAGAAAA
1 AAAAAAGAAAA
1567122 TAGGGTGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:1568356 original size:106 final size:106
Alignment explanation
Indices: 1568197--1568882 Score: 975
Period size: 106 Copynumber: 6.5 Consensus size: 106
1568187 ACGAAGGGGC
* *
1568197 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGTTATTGGACTCAAGACAGCACAAGCT
1 TTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCT
*
1568262 CAACTTCACGGCGAAGGGGCGGA-TGACTGTTAACAAATAAT
66 CAACTTCACGGCGAAGGGGC-GACTGACTGTCAACAAATAAT
* * *
1568303 TTCCCAACTTCAGAGCCAATTTCAACTTCACAACGAAGGTTATTGGACTCAAGACAGCACAAGTT
1 TTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCT
* **
1568368 CAACTTCACGGCAAAGGGGCGGGTGACTGTCAACAAATAAT
66 CAACTTCACGGCGAAGGGGCGACTGACTGTCAACAAATAAT
* *
1568409 TTCCCAACTTCAGAGCCAATTTCAACTTCACGGTGAAGGATATTGGACTCAAGACAGCACAAGCT
1 TTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCT
* * *
1568474 CAACTTCACAGCGAAGAGGCGGCTGACTGTCAACAAATAAT
66 CAACTTCACGGCGAAGGGGCGACTGACTGTCAACAAATAAT
* *
1568515 TTCCCAACTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCT
1 TTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCT
*
1568580 CAACTTCACGGCGAAGGAGCGACTGACTGTCAACAAATAAT
66 CAACTTCACGGCGAAGGGGCGACTGACTGTCAACAAATAAT
* * *
1568621 TTCCCAACTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAACT
1 TTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCT
* * *
1568686 CAACTTCACGACGAAGGGGCGACTGACTGTCAACTAACAA-
66 CAACTTCACGGCGAAGGGGCGACTGACTGTCAACAAATAAT
* * * * * *
1568726 TTCCCTAATTTCATATCCAATTTCAACTTCACAGTGAAGGATATTGGACCCAAGAAAGCACAAGC
1 TTCCC-AACTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGC
*
1568791 TCAACTTCACGGCGAAGGGGCGACTGACTGTCAACAAACAAT
65 TCAACTTCACGGCGAAGGGGCGACTGACTGTCAACAAATAAT
* * * * * * *
1568833 TTTCC-AGTTCCAAAACAAATTTCAACTTTAC-GACGAAGGATATCGGACTC
1 TTCCCAACTT-CAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
1568883 GGAGCAATAC
Statistics
Matches: 525, Mismatches: 50, Indels: 10
0.90 0.09 0.02
Matches are distributed among these distances:
105 10 0.02
106 511 0.97
107 4 0.01
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
TTCCCAACTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCT
CAACTTCACGGCGAAGGGGCGACTGACTGTCAACAAATAAT
Found at i:1573058 original size:78 final size:78
Alignment explanation
Indices: 1572929--1573085 Score: 287
Period size: 78 Copynumber: 2.0 Consensus size: 78
1572919 TGCACTAGAC
*
1572929 AAATAGTCATGACTTGTCAAAATTGCATGATTATGATGGGGGCATGTATCTACAATAGGAATTAT
1 AAATAGTCATGACTTATCAAAATTGCATGATTATGATGGGGGCATGTATCTACAATAGGAATTAT
1572994 AATATTGTTTATA
66 AATATTGTTTATA
* *
1573007 AAATAGTCATGACTTATCAAAATTGCATGATTATGATGGGGGCATGTATCTACAATAGGATTTGT
1 AAATAGTCATGACTTATCAAAATTGCATGATTATGATGGGGGCATGTATCTACAATAGGAATTAT
1573072 AATATTGTTTATA
66 AATATTGTTTATA
1573085 A
1 A
1573086 TTTAATATAT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (78 bp):
AAATAGTCATGACTTATCAAAATTGCATGATTATGATGGGGGCATGTATCTACAATAGGAATTAT
AATATTGTTTATA
Found at i:1576233 original size:19 final size:21
Alignment explanation
Indices: 1576207--1576256 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 21
1576197 AGTAATTAAA
*
1576207 ATAAAAAAGTGTAGCACTAA-
1 ATAAAAAAGTGTAACACTAAC
1576227 A-AAAAAAGTGTAACACTAAC
1 ATAAAAAAGTGTAACACTAAC
1576247 ATAAAAAAGT
1 ATAAAAAAGT
1576257 TTAGAGATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.63
20 2 0.07
21 8 0.30
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.18
Consensus pattern (21 bp):
ATAAAAAAGTGTAACACTAAC
Found at i:1576395 original size:59 final size:59
Alignment explanation
Indices: 1576266--1576407 Score: 173
Period size: 59 Copynumber: 2.4 Consensus size: 59
1576256 TTTAGAGATC
* *
1576266 AATTTAGAATGAGATTCATAGTTTGGGGATGAAATTTGAATGTTCAAAACTTTAAGGTCT
1 AATTTAAAATGAGAGTCATAG-TTGGGGATGAAATTTGAATGTTCAAAACTTTAAGGTCT
* * *
1576326 AATTTAAAATGGGAGTCATAGTTGGAGGATGAAA-TTGAAATGTT-TAAAGTTTAAGGAT-T
1 AATTTAAAATGAGAGTCATAGTTGG-GGATGAAATTTG-AATGTTCAAAACTTTAAGG-TCT
*
1576385 AATTTGAAATGAGAGTCATAGTT
1 AATTTAAAATGAGAGTCATAGTT
1576408 TGGAAACATA
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
59 39 0.54
60 33 0.46
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.35
Consensus pattern (59 bp):
AATTTAAAATGAGAGTCATAGTTGGGGATGAAATTTGAATGTTCAAAACTTTAAGGTCT
Found at i:1576411 original size:60 final size:60
Alignment explanation
Indices: 1576251--1576411 Score: 181
Period size: 60 Copynumber: 2.7 Consensus size: 60
1576241 ACTAACATAA
* *
1576251 AAAAGTTT-AGAGATCAATTTAGAATGAGATTCATAGTTTGG-GGATGAAATTTGAATGTTC
1 AAAAGTTTAAG-GATTAATTTA-AATGAGAGTCATAGTTTGGAGGATGAAATTTGAATGTTC
* *
1576311 AAAACTTTAAGG-TCTAATTTAAAATGGGAGTCATAG-TTGGAGGATGAAA-TTGAAATGTT-
1 AAAAGTTTAAGGAT-TAATTT-AAATGAGAGTCATAGTTTGGAGGATGAAATTTG-AATGTTC
*
1576370 TAAAGTTTAAGGATTAATTTGAAATGAGAGTCATAGTTTGGA
1 AAAAGTTTAAGGATTAATTT-AAATGAGAGTCATAGTTTGGA
1576412 AACATATGAT
Statistics
Matches: 86, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
59 38 0.44
60 45 0.52
61 3 0.03
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (60 bp):
AAAAGTTTAAGGATTAATTTAAATGAGAGTCATAGTTTGGAGGATGAAATTTGAATGTTC
Found at i:1579591 original size:18 final size:17
Alignment explanation
Indices: 1579568--1579601 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1579558 AACCCATCAA
1579568 ATTAATGCTACAAAAAAG
1 ATTAAT-CTACAAAAAAG
*
1579586 ATTAATTTACAAAAAA
1 ATTAATCTACAAAAAA
1579602 AAAATCAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (17 bp):
ATTAATCTACAAAAAAG
Found at i:1580128 original size:26 final size:26
Alignment explanation
Indices: 1580081--1580131 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1580071 AGTTAATTCC
* ** *
1580081 ATTAGTTGATTTAATCATTTGATTTG
1 ATTAATTGATTTAAAAAGTTGATTTG
1580107 ATTAATTGATTTAAAAAGTTGATTT
1 ATTAATTGATTTAAAAAGTTGATTT
1580132 AAGAAATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (26 bp):
ATTAATTGATTTAAAAAGTTGATTTG
Found at i:1583335 original size:3 final size:3
Alignment explanation
Indices: 1583327--1583365 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
1583317 CGGTTTGTAG
1583327 TTA TTA TTA TTA -TA TTA TTA TTA TTTA TTTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TT
1583366 TTTTAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 25 0.74
4 7 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1583344 original size:11 final size:11
Alignment explanation
Indices: 1583328--1583361 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1583318 GGTTTGTAGT
1583328 TATTATTATTA
1 TATTATTATTA
1583339 TATTATTATTA
1 TATTATTATTA
1583350 T-TTATTTATTA
1 TATTA-TTATTA
1583361 T
1 T
1583362 TATTTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 3 0.14
11 19 0.86
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTATTATTA
Found at i:1583346 original size:14 final size:14
Alignment explanation
Indices: 1583327--1583370 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
1583317 CGGTTTGTAG
1583327 TTATTATTA-TTAT
1 TTATTATTATTTAT
1583340 ATTATTATTATTTAT
1 -TTATTATTATTTAT
1583355 TTATTATTATTT-T
1 TTATTATTATTTAT
1583368 TTA
1 TTA
1583371 ATAATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.14
14 21 0.72
15 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTATTATTTAT
Found at i:1583375 original size:3 final size:3
Alignment explanation
Indices: 1583369--1583434 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
1583359 TATTATTTTT
*
1583369 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
*
1583414 TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1583435 ACAAATAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.07
3 45 0.82
4 6 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1584554 original size:220 final size:223
Alignment explanation
Indices: 1583716--1584986 Score: 2204
Period size: 223 Copynumber: 5.7 Consensus size: 223
1583706 GTTCTTCTCA
* *
1583716 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTATGAACTTTTTCTGG-AAAGGCT
1 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAA-GCT
* * * *
1583780 GATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAA---TTCTCATTATGAACTTCTTCTT
65 AATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
*
1583842 CCTTCTTCAGATGAGTTATTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGG
130 CCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGG
1583907 ATTCAGGCAAAAGGTTGAACAAATTCTTCTC
195 ATTCAGGCAAAAGGTTGAACAAATTC-T-TC
* *
1583938 ATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTATGAACTTTCTCTGGCAAAGCT
1 -TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCT
* *
1584003 AATCTATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT
65 AATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
*
1584068 CCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGG
130 CCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGG
1584133 ATTCAGGCAAAAGGTTGAACAAATTCTTC
195 ATTCAGGCAAAAGGTTGAACAAATTCTTC
1584162 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTA
1 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTA
*
1584227 ATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTC
66 ATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
* *
1584292 CTTCTTCAGAGGAGTTCTTCTTATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGA
131 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGA
1584357 TTCAGGCAAAAGGTTGAACAAATTCTTC
196 TTCAGGCAAAAGGTTGAACAAATTCTTC
1584385 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTA
1 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTA
1584450 ATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATT-TT-TC-TTATGAACTTCTTCTTC
66 ATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
*
1584512 CTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGA
131 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGA
1584577 TTCAGGCAAAAGGTTGAACAAATTCTTC
196 TTCAGGCAAAAGGTTGAACAAATTCTTC
*
1584605 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGCAAAGCTA
1 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTA
1584670 ATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTC-T-TC-TTATGAACTTCTTCTTC
66 ATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1584732 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGA
131 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGA
*
1584797 TTCAGGAAAAAGGTTGAACAAATTCTTC
196 TTCAGGCAAAAGGTTGAACAAATTCTTC
1584825 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTA
1 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTA
* * * * * *
1584890 ATCCATCAAGTGATAGATT-TGAACAAAAGGTTGGACAAATTCTTCTCATTATGAATTTTTTCTT
66 ATCCATCAAGTGATGGATTCAG-GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT
1584954 CCTTCTTCAGATGAGTTCTTCTCATTATGAACT
130 CCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1584987 CGAACTGGTA
Statistics
Matches: 1013, Mismatches: 26, Indels: 18
0.96 0.02 0.02
Matches are distributed among these distances:
219 1 0.00
220 424 0.42
221 3 0.00
222 4 0.00
223 465 0.46
224 5 0.00
225 1 0.00
226 110 0.11
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (223 bp):
TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTA
ATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGA
TTCAGGCAAAAGGTTGAACAAATTCTTC
Found at i:1585022 original size:113 final size:111
Alignment explanation
Indices: 1583707--1584986 Score: 2157
Period size: 110 Copynumber: 11.5 Consensus size: 111
1583697 TCTTGATGAG
* *
1583707 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTATGAACTTTTTCTG
1 TTCTT-TC-TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
1583772 G-AAAGGCTGATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAA
64 GCAAA-GCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
*
1583820 TTC--TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTTCTCTGG
1 TTCTTTC-TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1583883 CAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
65 CAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
* *
1583930 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTATGAACTTTCTCTG
1 TTCTT-TC-TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
1583995 GCAAAGCTAATCTATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
64 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
* *
1584043 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTG
1 TTCTT-TC-TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1584108 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
64 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
1584156 TTC-TTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
1 TTCTTTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
1584220 AAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
66 AAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
* * *
1584266 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAGGAGTTCTTCTTATTATGAACTTTCTCTG
1 TTCTT-TC-TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1584331 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
64 GCAAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
1584379 TTC-TTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
1 TTCTTTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
1584443 AAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
66 AAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
*
1584489 TT-TTTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGC
1 TTCTTTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
1584553 AAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
66 AAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
*
1584599 TTC-TTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGC
1 TTCTTTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
1584663 AAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
66 AAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
1584709 TTC-TTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
1 TTCTTTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
*
1584773 AAAGCTAATCCATCAAGTGATGGATTCAGGAAAAAGGTTGAACAAA
66 AAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
1584819 TTC-TTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
1 TTCTTTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
* * * *
1584883 AAAGCTAATCCATCAAGTGATAGATT-TGAACAAAAGGTTGGACAAA
66 AAAGCTAATCCATCAAGTGATGGATTCAG-GCAAAAGGTTGAACAAA
* *
1584929 TTCTTCTCATTATGAATTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTT-TC-TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1584987 CGAACTGGTA
Statistics
Matches: 1122, Mismatches: 32, Indels: 26
0.95 0.03 0.02
Matches are distributed among these distances:
109 1 0.00
110 736 0.66
111 9 0.01
112 6 0.01
113 370 0.33
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (111 bp):
TTCTTTCTTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
AAAGCTAATCCATCAAGTGATGGATTCAGGCAAAAGGTTGAACAAA
Found at i:1585503 original size:22 final size:22
Alignment explanation
Indices: 1585425--1585498 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
1585415 GATAAAGCTT
* *
1585425 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
*
1585447 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
*
1585469 TCATCTTTAAAGAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
1585491 TCATCTTT
1 TCATCTTT
1585499 GAAGAATGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:1588419 original size:165 final size:164
Alignment explanation
Indices: 1588164--1588541 Score: 625
Period size: 165 Copynumber: 2.3 Consensus size: 164
1588154 CATACCGAAT
* * *
1588164 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCCTCTAAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTAAAATTCAATG
*
1588229 ATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATT
66 ATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATT
* *
1588294 CCTC-T-CAAATTCAATGATTGGTTTTTATCAAAC
131 ACTCTTCCAAATTCAATGATTGG-TTTTACCAAAC
* *
1588327 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTC-T-AAAATTCAA
*
1588392 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
64 TGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACA
*
1588457 TTATTCTTCCAAATTCAATGATTGGTTTTACCAAAC
129 TTACTCTTCCAAATTCAATGATTGGTTTTACCAAAC
1588493 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1588542 GCATTTATTC
Statistics
Matches: 201, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
163 49 0.24
164 1 0.00
165 75 0.37
166 60 0.30
167 16 0.08
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (164 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTAAAATTCAATG
ATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATT
ACTCTTCCAAATTCAATGATTGGTTTTACCAAAC
Found at i:1588444 original size:83 final size:81
Alignment explanation
Indices: 1588164--1588541 Score: 621
Period size: 83 Copynumber: 4.6 Consensus size: 81
1588154 CATACCGAAT
* * * *
1588164 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCCTCTAAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTCAAATTCAATG
1588229 ATTGGTTTTACCAAAC
66 ATTGGTTTTACCAAAC
* * *
1588245 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCCTCTCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTCAAATTCAATG
*
1588310 ATTGGTTTTTATCAAAC
66 ATTGG-TTTTACCAAAC
*
1588327 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTC-T-CAAATTCAA
1588392 TGATTGGTTTTACCAAAC
64 TGATTGGTTTTACCAAAC
*
1588410 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTC-T-CAAATTCAA
1588475 TGATTGGTTTTACCAAAC
64 TGATTGGTTTTACCAAAC
1588493 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1588542 GCATTTATTC
Statistics
Matches: 287, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
81 69 0.24
82 59 0.21
83 143 0.50
84 16 0.06
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (81 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTCAAATTCAATG
ATTGGTTTTACCAAAC
Found at i:1590734 original size:23 final size:23
Alignment explanation
Indices: 1590685--1590735 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1590675 CTTGATTTAA
* * *
1590685 TTTTTTTCTTTTTCTTTTTTGTT
1 TTTTTTTCTATTTCTTTCTTGTC
1590708 TTTTTTTCTATTTCTTTCCTT-TC
1 TTTTTTTCTATTTCTTT-CTTGTC
1590731 TTTTT
1 TTTTT
1590736 CTTTTTCCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (23 bp):
TTTTTTTCTATTTCTTTCTTGTC
Found at i:1590757 original size:6 final size:6
Alignment explanation
Indices: 1590687--1590742 Score: 53
Period size: 6 Copynumber: 9.0 Consensus size: 6
1590677 TGATTTAATT
*
1590687 TTTTTC TTTTTC TTTTT- TGTTTT- TTTTTC TATTTC TTTCCTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC -TT--TTTC TTTTTC
1590737 TTTTTC
1 TTTTTC
1590743 CTCTTTTTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
5 5 0.12
6 31 0.72
7 1 0.02
8 2 0.05
9 4 0.09
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:1590763 original size:15 final size:14
Alignment explanation
Indices: 1590686--1590759 Score: 62
Period size: 16 Copynumber: 5.0 Consensus size: 14
1590676 TTGATTTAAT
1590686 TTTTTTC-TTTTTC
1 TTTTTTCTTTTTTC
* *
1590699 TTTTTTGTTTTTTT
1 TTTTTTCTTTTTTC
1590713 TTCTATTTCTTTCCTTTC
1 TT-T-TTTCTTT--TTTC
1590731 -TTTTTCTTTTTCCTC
1 TTTTTTCTTTTT--TC
1590746 TTTTTTCTTTTTTC
1 TTTTTTCTTTTTTC
1590760 CTTTCTTTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
13 8 0.16
14 9 0.18
15 10 0.20
16 18 0.37
17 1 0.02
18 3 0.06
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.80
Consensus pattern (14 bp):
TTTTTTCTTTTTTC
Found at i:1590778 original size:43 final size:44
Alignment explanation
Indices: 1590687--1590787 Score: 98
Period size: 44 Copynumber: 2.3 Consensus size: 44
1590677 TGATTTAATT
* * ***
1590687 TTTTTCTTTTTCTTTTTTGTTTTTTTTTCTATTTCTTTCCTTTC
1 TTTTTCTTTTTCTCTTTTGTTCTTTTTTCTATTTCTTTCCTGGA
* *
1590731 TTTTTCTTTTTCCTCTTTT-TTCTTTTTTC-CTTTCTTTGCTGGA
1 TTTTTCTTTTT-CTCTTTTGTTCTTTTTTCTATTTCTTTCCTGGA
*
1590774 TTTTTTTTCTTTCT
1 TTTTTCTT-TTTCT
1590788 TTGCTGGATG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
43 18 0.38
44 23 0.49
45 6 0.13
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (44 bp):
TTTTTCTTTTTCTCTTTTGTTCTTTTTTCTATTTCTTTCCTGGA
Found at i:1590786 original size:22 final size:22
Alignment explanation
Indices: 1590753--1590796 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1590743 CTCTTTTTTC
1590753 TTTTTTCCTTTCTTTGCTGGAT
1 TTTTTTCCTTTCTTTGCTGGAT
*
1590775 TTTTTTTCTTTCTTTGCTGGAT
1 TTTTTTCCTTTCTTTGCTGGAT
1590797 GAGTATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.14, T:0.66
Consensus pattern (22 bp):
TTTTTTCCTTTCTTTGCTGGAT
Found at i:1597583 original size:3 final size:3
Alignment explanation
Indices: 1597575--1597613 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
1597565 CGGTTTGTAG
1597575 TTA TTA TTA TTA -TA TTA TTA TTA TTTA TTTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TT
1597614 TTTTAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 25 0.74
4 7 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1597592 original size:11 final size:11
Alignment explanation
Indices: 1597576--1597609 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1597566 GGTTTGTAGT
1597576 TATTATTATTA
1 TATTATTATTA
1597587 TATTATTATTA
1 TATTATTATTA
1597598 T-TTATTTATTA
1 TATTA-TTATTA
1597609 T
1 T
1597610 TATTTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 3 0.14
11 19 0.86
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTATTATTA
Found at i:1597594 original size:14 final size:14
Alignment explanation
Indices: 1597575--1597618 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
1597565 CGGTTTGTAG
1597575 TTATTATTA-TTAT
1 TTATTATTATTTAT
1597588 ATTATTATTATTTAT
1 -TTATTATTATTTAT
1597603 TTATTATTATTT-T
1 TTATTATTATTTAT
1597616 TTA
1 TTA
1597619 ATAATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.14
14 21 0.72
15 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTATTATTTAT
Found at i:1597623 original size:3 final size:3
Alignment explanation
Indices: 1597617--1597694 Score: 90
Period size: 3 Copynumber: 26.0 Consensus size: 3
1597607 TATTATTTTT
1597617 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA T-A TATA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TA-A
* *
1597662 TAA TAA TTA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1597695 ACAAATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
2 6 0.09
3 50 0.77
4 9 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1606336 original size:21 final size:21
Alignment explanation
Indices: 1606310--1606350 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1606300 GGGAGATTGT
1606310 TAAAAGTCAGGAAAGCCATGC
1 TAAAAGTCAGGAAAGCCATGC
*
1606331 TAAAAGTCAGGAAAGTCATG
1 TAAAAGTCAGGAAAGCCATG
1606351 TTGTTTTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.17
Consensus pattern (21 bp):
TAAAAGTCAGGAAAGCCATGC
Found at i:1609817 original size:31 final size:31
Alignment explanation
Indices: 1609782--1609841 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1609772 AATAAAAGAG
*
1609782 GGAAACCATATAGGGCCTTAAATATGATGAT
1 GGAAACCAGATAGGGCCTTAAATATGATGAT
1609813 GGAAACCAGATAGGGCCTTAAATATGATG
1 GGAAACCAGATAGGGCCTTAAATATGATG
1609842 TTTATAGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.23
Consensus pattern (31 bp):
GGAAACCAGATAGGGCCTTAAATATGATGAT
Found at i:1614107 original size:81 final size:81
Alignment explanation
Indices: 1613978--1614130 Score: 297
Period size: 81 Copynumber: 1.9 Consensus size: 81
1613968 CTGCCCACTT
*
1613978 TCTTTATCTTCTTCAGGCGTACAAGTAGCTTTAGGAGTTTTCTTTGAAGATGCATAGGAACAAAA
1 TCTTTATCTTCTTCAGGCGTACAAGTAACTTTAGGAGTTTTCTTTGAAGATGCATAGGAACAAAA
1614043 GGCCTTATTATCTTTA
66 GGCCTTATTATCTTTA
1614059 TCTTTATCTTCTTCAGGCGTACAAGTAACTTTAGGAGTTTTCTTTGAAGATGCATAGGAACAAAA
1 TCTTTATCTTCTTCAGGCGTACAAGTAACTTTAGGAGTTTTCTTTGAAGATGCATAGGAACAAAA
1614124 GGCCTTA
66 GGCCTTA
1614131 CCATTTGCCC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (81 bp):
TCTTTATCTTCTTCAGGCGTACAAGTAACTTTAGGAGTTTTCTTTGAAGATGCATAGGAACAAAA
GGCCTTATTATCTTTA
Found at i:1625154 original size:15 final size:15
Alignment explanation
Indices: 1625134--1625169 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
1625124 TCATATGAAA
1625134 ATGTGATAAAGAACT
1 ATGTGATAAAGAACT
1625149 ATGTG--AAAGAACT
1 ATGTGATAAAGAACT
1625162 ATGTGATA
1 ATGTGATA
1625170 TGAATGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.68
15 6 0.32
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (15 bp):
ATGTGATAAAGAACT
Found at i:1626322 original size:12 final size:12
Alignment explanation
Indices: 1626299--1626337 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1626289 ATATATTTTA
1626299 TAATCTCATGTAT
1 TAATC-CATGTAT
1626312 TAATCCATGTAT
1 TAATCCATGTAT
1626324 TAA-CCAATGTAT
1 TAATCC-ATGTAT
1626336 TA
1 TA
1626338 GCCCATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 2 0.08
12 18 0.72
13 5 0.20
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (12 bp):
TAATCCATGTAT
Found at i:1626445 original size:17 final size:17
Alignment explanation
Indices: 1626423--1626487 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
1626413 CGTATAAATG
1626423 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
** *
1626440 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGACCT-ATC---A
*
1626461 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTATCA
1626478 TCCCGAAGGA
1 TCCCGAAGGA
1626488 TGTAATCTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 21 0.57
18 3 0.08
20 2 0.05
21 11 0.30
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (17 bp):
TCCCGAAGGACCTATCA
Found at i:1626466 original size:21 final size:21
Alignment explanation
Indices: 1626440--1626508 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
1626430 GGACCTATCA
1626440 TCCCGAAGGATGTCATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
1626461 TCCCGAAGGA---C--CTGTCA
1 TCCCGAAGGATGTCATCTGT-G
*
1626478 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTCATCTGTG
*
1626499 TCCCGTAGGA
1 TCCCGAAGGA
1626509 CCTATCATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.25
Consensus pattern (21 bp):
TCCCGAAGGATGTCATCTGTG
Found at i:1626472 original size:38 final size:38
Alignment explanation
Indices: 1626421--1626516 Score: 165
Period size: 38 Copynumber: 2.5 Consensus size: 38
1626411 CTCGTATAAA
*
1626421 TGTCCCGAAGGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
1626459 TGTCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
*
1626497 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
1626517 ATGTCTTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:1629264 original size:30 final size:29
Alignment explanation
Indices: 1629199--1629264 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
1629189 CTTTGGTCCT
* *
1629199 TAAACTTTTCAAAGTTTATACTTTAGTCAC
1 TAAAC-TTTCAAAATTTATAATTTAGTCAC
*
1629229 CAAACTTTCAAAATCTTATAATTT-GATCAC
1 TAAACTTTCAAAAT-TTATAATTTAG-TCAC
1629259 TAAACT
1 TAAACT
1629265 AAATCCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (29 bp):
TAAACTTTCAAAATTTATAATTTAGTCAC
Found at i:1633087 original size:69 final size:71
Alignment explanation
Indices: 1633008--1633200 Score: 216
Period size: 76 Copynumber: 2.7 Consensus size: 71
1632998 TATTTTAAAC
* *
1633008 ATTATATTTTATCTTTGTTTT-AGATATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTT
1 ATTATATTTTATCTTTGTTTTAAG-TATTTTAGTTTAAATAGGTTTTAATATTTTAATTAAGATT
1633072 TAGGATATT
65 TA-GA-ATT
* * *
1633081 ATTTTTATATTTTATCTTTGTTTTAATTATTTTAGTTTAAATAGGATTTAATATTTTAATTAGGA
1 A---TTATATTTTATCTTTGTTTTAAGTATTTTAGTTTAAATAGGTTTTAATATTTTAATTAAGA
1633146 TTTAG-ATT
63 TTTAGAATT
* * *
1633154 ATCAT-TTTAAATATTT-TTTTAAGTATTTTAGTTTAAATA-GTTTTAAT
1 ATTATATTT-TATCTTTGTTTTAAGTATTTTAGTTTAAATAGGTTTTAAT
1633201 TAGGATTTAA
Statistics
Matches: 105, Mismatches: 10, Indels: 15
0.81 0.08 0.12
Matches are distributed among these distances:
68 7 0.07
69 25 0.24
70 8 0.08
73 5 0.05
75 1 0.01
76 58 0.55
77 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (71 bp):
ATTATATTTTATCTTTGTTTTAAGTATTTTAGTTTAAATAGGTTTTAATATTTTAATTAAGATTT
AGAATT
Found at i:1633150 original size:76 final size:76
Alignment explanation
Indices: 1633009--1633150 Score: 232
Period size: 76 Copynumber: 1.9 Consensus size: 76
1632999 ATTTTAAACA
* * *
1633009 TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGATTTAATATTTTAATTAAGATTTA
1633074 GGATATTATTT
66 GGATATTATTT
*
1633085 TTATATTTTATCTTTGTTTTA-ATTATTTTAGTTTAAATAGGATTTAATATTTTAATTAGGATTT
1 TTATATTTTATCTTTGTTTTAGA-TATTTTAGTTTAAATAGGATTTAATATTTTAATTAAGATTT
1633149 AG
65 AG
1633151 ATTATCATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 1 0.02
76 60 0.98
ACGTcount: A:0.29, C:0.01, G:0.11, T:0.58
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGATTTAATATTTTAATTAAGATTTA
GGATATTATTT
Found at i:1633161 original size:76 final size:76
Alignment explanation
Indices: 1633009--1633170 Score: 229
Period size: 76 Copynumber: 2.1 Consensus size: 76
1632999 ATTTTAAACA
* * *
1633009 TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGATTTAATATTTTAATTAAGATTTA
*
1633074 GGATATTATTT
66 GGATATCATTT
*
1633085 TTATATTTTATCTTTGTTTTA-ATTATTTTAGTTTAAATAGGATTTAATATTTTAATTAGGATTT
1 TTATATTTTATCTTTGTTTTAGA-TATTTTAGTTTAAATAGGATTTAATATTTTAATTAAGATTT
1633149 A-GATTATCATTT
65 AGGA-TATCATTT
*
1633161 TAAATATTTT
1 T-TATATTTT
1633171 TTTAAGTATT
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
75 3 0.04
76 67 0.87
77 7 0.09
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.59
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGATTTAATATTTTAATTAAGATTTA
GGATATCATTT
Found at i:1634264 original size:21 final size:22
Alignment explanation
Indices: 1634235--1634280 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1634225 GATATATATA
1634235 TATATATATAGA-AAGTTTGTTT
1 TATATATATAGATAAG-TTGTTT
*
1634257 TATA-ATATATATAAGTTGTTT
1 TATATATATAGATAAGTTGTTT
1634278 TAT
1 TAT
1634281 GTTGGTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (22 bp):
TATATATATAGATAAGTTGTTT
Found at i:1637377 original size:2 final size:2
Alignment explanation
Indices: 1637366--1637411 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1637356 AGGAATCAAT
1637366 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1637407 TA TA T
1 TA TA T
1637412 TAGTTAATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1640363 original size:78 final size:78
Alignment explanation
Indices: 1640234--1640389 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
1640224 TCGAGCTTTT
1640234 AGCTAGAAATCTTCAGCACTGGTCCACTAACTTCTCGTCTTATGTTTCCAGTACTGTTTTCAGCT
1 AGCTAGAAATCTTCAGCACTGGTCCACTAACTTCTCGTCTTATGTTTCCAGTACTGTTTTCAGCT
1640299 CAAGAGAAGTGGG
66 CAAGAGAAGTGGG
1640312 AGCTAGAAATCTTCAGCACTGGTCCACTAACTTCTCGTCTTATGTTTCCAGTACTGTTTTCAGCT
1 AGCTAGAAATCTTCAGCACTGGTCCACTAACTTCTCGTCTTATGTTTCCAGTACTGTTTTCAGCT
1640377 CAAGAGAAGTGGG
66 CAAGAGAAGTGGG
1640390 CTTTGAATAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (78 bp):
AGCTAGAAATCTTCAGCACTGGTCCACTAACTTCTCGTCTTATGTTTCCAGTACTGTTTTCAGCT
CAAGAGAAGTGGG
Found at i:1649335 original size:147 final size:147
Alignment explanation
Indices: 1649064--1649356 Score: 541
Period size: 147 Copynumber: 2.0 Consensus size: 147
1649054 CCTTTTAGTT
*
1649064 CTTTAAAATCAAAGAACCATTCTCTATTAGGGGTCATATAGTGGCTACAAGCTGAATCTAACAAC
1 CTTTAAAATCAAAGAACCATTCTCTATTAGGGGTCATATAGTGGCTACAAGCTAAATCTAACAAC
* *
1649129 CATGAACTGGAACAGCTGGTTGATGGCGTAGCAGCGAATGCGAAATCTGAATCTGTATCATCATA
66 CATGAACTGGAACAACTGGTTGATGGCGTAGCAGCGAATGCGAAATCTGAATCTATATCATCATA
1649194 CTCGACCACATTTGGTC
131 CTCGACCACATTTGGTC
* *
1649211 CTTTAAAATCAAAGAACCATTCTCTATTGGGGGTCATATAGTGGCTACAAGCTAAATCTAATAAC
1 CTTTAAAATCAAAGAACCATTCTCTATTAGGGGTCATATAGTGGCTACAAGCTAAATCTAACAAC
1649276 CATGAACTGGAACAACTGGTTGATGGCGTAGCAGCGAATGCGAAATCTGAATCTATATCATCATA
66 CATGAACTGGAACAACTGGTTGATGGCGTAGCAGCGAATGCGAAATCTGAATCTATATCATCATA
1649341 CTCGACCACATTTGGT
131 CTCGACCACATTTGGT
1649357 TCTGAGACAA
Statistics
Matches: 141, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 141 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (147 bp):
CTTTAAAATCAAAGAACCATTCTCTATTAGGGGTCATATAGTGGCTACAAGCTAAATCTAACAAC
CATGAACTGGAACAACTGGTTGATGGCGTAGCAGCGAATGCGAAATCTGAATCTATATCATCATA
CTCGACCACATTTGGTC
Found at i:1656577 original size:17 final size:17
Alignment explanation
Indices: 1656555--1656589 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1656545 ATGAGCTGAA
1656555 ATGTTTAAAAAAGAGAT
1 ATGTTTAAAAAAGAGAT
1656572 ATGTTTAAAAAAGAGAT
1 ATGTTTAAAAAAGAGAT
1656589 A
1 A
1656590 GAGAACAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (17 bp):
ATGTTTAAAAAAGAGAT
Found at i:1658199 original size:83 final size:83
Alignment explanation
Indices: 1658083--1658321 Score: 238
Period size: 83 Copynumber: 2.9 Consensus size: 83
1658073 AAACGCCGTG
* * * **
1658083 AAAGAGTAGTACTTTAGTGGTGTTTGTATAAAAACGCTGCAATAGGTTCATCAATAGTGGCATTT
1 AAAGAGTAGTACTTTAGCGGCGTTT-TATAAAAACGCTGCAATAGGGTCATGTATAGTGGCATTT
*
1658148 TTTCAAAACAAATGCCGCA
65 TTTCAAAACAAATACCGCA
**
1658167 AAAGAGTTA-TACTTTAGCGGCGTTTTATAAAAACG-TCGCAATAGGGTCATGTATAGTGGTGTT
1 AAAGAG-TAGTACTTTAGCGGCGTTTTATAAAAACGCT-GCAATAGGGTCATGTATAGTGGCATT
* *
1658230 TTTT---GACAAATACCGCT
64 TTTTCAAAACAAATACCGCA
* * * *
1658247 AAAGAGTATTA-TTGTAGCGGCGTTTTTTTATAAAAACGCCGTAATAGGGTCATGTATAGTGGCT
1 AAAGAGTAGTACTT-TAGCGGCG---TTTTATAAAAACGCTGCAATAGGGTCATGTATAGTGGCA
1658311 TTTTTTACAAA
62 TTTTTT-CAAA
1658322 CGCCGCTATA
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
79 4 0.03
80 26 0.20
82 1 0.01
83 75 0.59
84 20 0.16
85 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (83 bp):
AAAGAGTAGTACTTTAGCGGCGTTTTATAAAAACGCTGCAATAGGGTCATGTATAGTGGCATTTT
TTCAAAACAAATACCGCA
Found at i:1658314 original size:41 final size:41
Alignment explanation
Indices: 1658189--1658317 Score: 99
Period size: 41 Copynumber: 3.1 Consensus size: 41
1658179 TTTAGCGGCG
* *
1658189 TTTTATAAAAACGTCGCAATAGGGTCATGTATAGTGG-TGTT
1 TTTTATAAAAACGCCGTAATAGGGTCATGTATAGTGGCT-TT
* * * *
1658230 TTTTGACAAATA--CCGCTAA-AGAGT-AT-TATTGTAGCGGCGTTT
1 TTTT-ATAAAAACGCCG-TAATAGGGTCATGTA---TAGTGGC-TTT
1658272 TTTTATAAAAACGCCGTAATAGGGTCATGTATAGTGGCTTT
1 TTTTATAAAAACGCCGTAATAGGGTCATGTATAGTGGCTTT
1658313 TTTTA
1 TTTTA
1658318 CAAACGCCGC
Statistics
Matches: 66, Mismatches: 10, Indels: 24
0.66 0.10 0.24
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 6 0.09
41 24 0.36
42 20 0.30
43 8 0.12
44 2 0.03
45 2 0.03
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.38
Consensus pattern (41 bp):
TTTTATAAAAACGCCGTAATAGGGTCATGTATAGTGGCTTT
Found at i:1658315 original size:42 final size:42
Alignment explanation
Indices: 1658189--1658316 Score: 97
Period size: 42 Copynumber: 3.1 Consensus size: 42
1658179 TTTAGCGGCG
* *
1658189 TTTTATAAAAACGTCGCAATAGGGTCATGTATAGTGG-TGTTT
1 TTTTATAAAAACGCCGTAATAGGGTCATGTATAGTGGCT-TTT
* * * * * *
1658231 TTTGACAAATA--CCGCTAA-AGAGT-AT-TATTGTAGCGGCGTTT
1 TTTTATAAAAACGCCG-TAATAGGGTCATGTA---TAGTGGCTTTT
1658272 TTTTATAAAAACGCCGTAATAGGGTCATGTATAGTGGCTTTT
1 TTTTATAAAAACGCCGTAATAGGGTCATGTATAGTGGCTTTT
1658314 TTT
1 TTT
1658317 ACAAACGCCG
Statistics
Matches: 62, Mismatches: 14, Indels: 20
0.65 0.15 0.21
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 6 0.10
41 18 0.29
42 23 0.37
43 7 0.11
44 2 0.03
45 2 0.03
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (42 bp):
TTTTATAAAAACGCCGTAATAGGGTCATGTATAGTGGCTTTT
Found at i:1658366 original size:40 final size:41
Alignment explanation
Indices: 1658303--1658436 Score: 184
Period size: 41 Copynumber: 3.3 Consensus size: 41
1658293 GGGTCATGTA
*
1658303 TAGTGGC-TTTTTTTACAAACGCCGCTATAGA-TTAGTATTG
1 TAGTGGCATTTTTATACAAACGCCGCTATAGACTT-GTATTG
* * *
1658343 TAGCGGCATTTTTATAC-AACGCCGCTATAAACTTGTATTT
1 TAGTGGCATTTTTATACAAACGCCGCTATAGACTTGTATTG
*
1658383 TAGTGGCATTTTTATACAAACGCCGCTATAGACTTGTACTG
1 TAGTGGCATTTTTATACAAACGCCGCTATAGACTTGTATTG
*
1658424 TAGTGGCGTTTTT
1 TAGTGGCATTTTT
1658437 GCTTACAAAC
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
40 40 0.49
41 42 0.51
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (41 bp):
TAGTGGCATTTTTATACAAACGCCGCTATAGACTTGTATTG
Found at i:1659528 original size:2 final size:2
Alignment explanation
Indices: 1659521--1659550 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1659511 AAAGTATCAC
*
1659521 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1659551 TTAGGGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1659762 original size:154 final size:157
Alignment explanation
Indices: 1659573--1659962 Score: 423
Period size: 154 Copynumber: 2.5 Consensus size: 157
1659563 TAAAGAAGAC
* * *
1659573 ATTTATTTA-TTTAAAAATATCAGAAA-AGGAA-ATCTAGTTGTTTTAAGACTGTATTTTCTTTA
1 ATTTATTTATTTTTAAAATATCA-AAATA-GAACATCTAGTTGCTTTAAGACTGTCTTTTCTTTA
*
1659635 AT-TTTAATAAATAAATATTAATAAGAATATAATAATTTTCCTAAAAAA-AA-TGAAGTAAATA-
64 ATATTTAATAAATAAATATTAATAA-AA-ATAATAATTTTCCTAAAAAATAATTGAAATAAA-AC
*
1659696 AATATATA-TATAT-ATTTTTATAAGCATGAT
126 AATATATATTATATGATTTTTATAAGCAGGAT
*
1659726 ATTTATTTATTTTTAAAATATCAAAATAAAACATCTAGTTGCTTTAAGACTGTCTTTTC-TTAAT
1 ATTTATTTATTTTTAAAATATCAAAATAGAACATCTAGTTGCTTTAAGACTGTCTTTTCTTTAAT
* * *
1659790 ATTTGAA-AAATAAATAAATATTAAAAATAATAATTTTCCTAAAAAATAATTTAAATAAAACAAT
66 ATTT-AATAAATAAAT-ATTAATAAAAATAATAATTTTCCTAAAAAATAATTGAAATAAAACAAT
* * * * *
1659854 ATGTATTTTCTGGTTTTTATAAGTAGGAT
129 ATATATTATATGATTTTTATAAGCAGGAT
* * * *
1659883 ATTT-TTT-TTTTT-AAATATCAGAATAGTACATCTGGTTGCTTTAAGACTGCCCTTTTCTTT-A
1 ATTTATTTATTTTTAAAATATCAAAATAGAACATCTAGTTGCTTTAAGACTG-TCTTTTCTTTAA
**
1659944 TATAAAATAAATAAATATT
65 TATTTAATAAATAAATATT
1659963 TATTTATTAT
Statistics
Matches: 201, Mismatches: 22, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
153 39 0.19
154 91 0.45
155 45 0.22
156 8 0.04
157 18 0.09
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (157 bp):
ATTTATTTATTTTTAAAATATCAAAATAGAACATCTAGTTGCTTTAAGACTGTCTTTTCTTTAAT
ATTTAATAAATAAATATTAATAAAAATAATAATTTTCCTAAAAAATAATTGAAATAAAACAATAT
ATATTATATGATTTTTATAAGCAGGAT
Found at i:1659984 original size:2 final size:2
Alignment explanation
Indices: 1659977--1660018 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1659967 TATTATTTAA
1659977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1660019 GACTAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1660033 original size:8 final size:9
Alignment explanation
Indices: 1659976--1660034 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 9
1659966 TTATTATTTA
1659976 AATATATAT
1 AATATATAT
1659985 -ATATATAT
1 AATATATAT
1659993 -ATATATAT
1 AATATATAT
1660001 ATATATATAT
1 A-ATATATAT
1660011 ATATATATGACT
1 A-ATATAT-A-T
1660023 AATATA-AT
1 AATATATAT
1660031 AATA
1 AATA
1660035 AAATAATAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
8 21 0.46
9 1 0.02
10 16 0.35
11 6 0.13
12 2 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (9 bp):
AATATATAT
Found at i:1660335 original size:3 final size:3
Alignment explanation
Indices: 1660327--1660396 Score: 59
Period size: 3 Copynumber: 22.3 Consensus size: 3
1660317 TATTTTTAAA
* ** * **
1660327 ATT ATT ATT ATT ATT ATT AAAT ATT AAC AAT ATT ATT ATT AAA ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
1660373 ATT ATT ATAT ATT AATT ATT ATT A
1 ATT ATT AT-T ATT -ATT ATT ATT A
1660397 AATAAATAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 46 0.85
4 8 0.15
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (3 bp):
ATT
Found at i:1661594 original size:12 final size:11
Alignment explanation
Indices: 1661579--1661613 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1661569 ATTTTATATG
1661579 TTTAATTATTA
1 TTTAATTATTA
1661590 CTTTAATTATTA
1 -TTTAATTATTA
*
1661602 TTTTATTATTA
1 TTTAATTATTA
1661613 T
1 T
1661614 ATTAGTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTAATTATTA
Found at i:1661634 original size:2 final size:2
Alignment explanation
Indices: 1661621--1661658 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1661611 TATATTAGTC
*
1661621 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1661659 TTTAAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1662087 original size:2 final size:2
Alignment explanation
Indices: 1662080--1662110 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1662070 ACAATAACCC
*
1662080 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1662111 GATACTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1662699 original size:76 final size:76
Alignment explanation
Indices: 1662552--1662827 Score: 430
Period size: 76 Copynumber: 3.7 Consensus size: 76
1662542 GAGGTCTTAT
* * * *
1662552 CATCTTGCACTGTAGGTCTTACAGATAACCCTGAGGCTTT--AAATATCAAAAAGCTCCCGAAGG
1 CATCCTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAAAACATCAAAAAGCTCCCGAAGG
1662615 CTTTTTGAAAA
66 CTTTTTGAAAA
** * * *
1662626 CATTATGCTCTGTAGGTCTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGAATG
1 CATCCTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAAAACATCAAAAAGCTCCCGAAGG
1662691 CTTTTTGAAAA
66 CTTTTTGAAAA
* *
1662702 CATCCTGCACTGTAGGTCTTACGGATGACCCGGAGGCTTTAAAAACATCAAAAAGCTCTCGAAGG
1 CATCCTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAAAACATCAAAAAGCTCCCGAAGG
1662767 CTTTTTGAAAA
66 CTTTTTGAAAA
*
1662778 CATCCTGCACTGTAGGTCTTACGGATGACCCGGAGGCTTTAAAAACATCA
1 CATCCTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAAAACATCA
1662828 TGCACTATAG
Statistics
Matches: 185, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
74 34 0.18
76 151 0.82
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (76 bp):
CATCCTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAAAACATCAAAAAGCTCCCGAAGG
CTTTTTGAAAA
Found at i:1663539 original size:22 final size:22
Alignment explanation
Indices: 1663514--1663573 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
1663504 AATAAAGCTT
*
1663514 TCATCTTTGAAAAGTGAATCTA
1 TCATCTTTGAAAAGTGAATATA
*
1663536 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGTGAATATA
*
1663558 TCATCTTTGAAGAGTG
1 TCATCTTTGAAAAGTG
1663574 TAGATGTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGTGAATATA
Found at i:1664078 original size:54 final size:53
Alignment explanation
Indices: 1663951--1664095 Score: 204
Period size: 54 Copynumber: 2.7 Consensus size: 53
1663941 AAAACATTTA
* *
1663951 ACAACACATTCATTCTTTACTGTTGCTCCTGCCCAGATGTTCGTAAAGCTTTTG
1 ACAACACATTCATTCTTT-CTGTGGCTTCTGCCCAGATGTTCGTAAAGCTTTTG
1664005 ACAACACATTCATTCTTTCTTGTGGCTTCTGCCCAGATGTTCGTAAAGCTTTTG
1 ACAACACATTCATTCTTTC-TGTGGCTTCTGCCCAGATGTTCGTAAAGCTTTTG
**
1664059 ACAA-ACATTCA-TCATTTTCTGTGTTTTCTGCCCAGAT
1 ACAACACATTCATTC--TTTCTGTGGCTTCTGCCCAGAT
1664096 TTCTGGTCAG
Statistics
Matches: 84, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
52 2 0.02
53 24 0.29
54 58 0.69
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (53 bp):
ACAACACATTCATTCTTTCTGTGGCTTCTGCCCAGATGTTCGTAAAGCTTTTG
Found at i:1665117 original size:75 final size:74
Alignment explanation
Indices: 1665002--1665202 Score: 269
Period size: 75 Copynumber: 2.7 Consensus size: 74
1664992 TACTGATATG
* *
1665002 AACGTTCAAAATACATCAACATTGCTGATTCTGATTGAAATGGTCTTTCAGCACGCCCCAACATT
1 AACGTTCAAAATACATCAACATTCCTGATTCTGATTGAAATGG-CTTTCAGCACGCCACAACATT
*
1665067 TGCTGATACA
65 TGATGATACA
* * *
1665077 AACGTTTAAAATACATCAACATTCCTGATTCTGATTGAAATAGGCTTTCAGCATGCCACAATATT
1 AACGTTCAAAATACATCAACATTCCTGATTCTGATTGAAAT-GGCTTTCAGCACGCCACAACATT
1665142 TGATGATACA
65 TGATGATACA
* * * *
1665152 AACATTCAAAATACATTAATATTCC-AATTTCTGATTGAAATGGGCTTTCAG
1 AACGTTCAAAATACATCAACATTCCTGA-TTCTGATTGAAAT-GGCTTTCAG
1665203 TATGTCCCAG
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
74 1 0.01
75 109 0.97
76 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (74 bp):
AACGTTCAAAATACATCAACATTCCTGATTCTGATTGAAATGGCTTTCAGCACGCCACAACATTT
GATGATACA
Found at i:1668603 original size:7 final size:7
Alignment explanation
Indices: 1668591--1668629 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
1668581 TTGATTCAAT
1668591 TTTTTCC
1 TTTTTCC
1668598 TTTTTCC
1 TTTTTCC
1668605 TTTTTCC
1 TTTTTCC
1668612 TTTTTCC
1 TTTTTCC
1668619 TTTTTCC
1 TTTTTCC
1668626 TTTT
1 TTTT
1668630 CTCTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCC
Found at i:1668617 original size:21 final size:22
Alignment explanation
Indices: 1668591--1668638 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
1668581 TTGATTCAAT
1668591 TTTTTCCTTTTTCCTTTT-TCC
1 TTTTTCCTTTTTCCTTTTCTCC
*
1668612 TTTTTCCTTTTTCCTTTTCTCT
1 TTTTTCCTTTTTCCTTTTCTCC
1668634 TTTTT
1 TTTTT
1668639 TATGAATGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTCCTTTTTCCTTTTCTCC
Found at i:1673885 original size:2 final size:2
Alignment explanation
Indices: 1673878--1673928 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1673868 GAAAAATTAT
1673878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1673920 TA TA TA TA T
1 TA TA TA TA T
1673929 TTAGGGTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1674230 original size:145 final size:148
Alignment explanation
Indices: 1673951--1674332 Score: 349
Period size: 145 Copynumber: 2.5 Consensus size: 148
1673941 TGAAGAAGAC
*
1673951 ATTTATTTATTTAAAAGTATCAGAAAATGACATCTAGTTGCTTTAAGACTGCATTTTCTTTAATT
1 ATTTATTTATTTAAAAGTATCAGAAAATAACATCTAGTTGCTTTAAGACTGCATTTTCTTTAATT
* * * *
1674016 TTAATAAATAAATATTAATAAGAATATAATAATTTTCCTAAACAATAATGAAGTAAATATATATA
66 TTAATAAATAAATAATAATAAGAATATAATAATTTTCCTAAAAAATAATGAAATAAATAAATATA
1674081 TATTTTTATAAGCAGGAT
131 TATTTTTATAAGCAGGAT
*
1674099 ATTTA-TT-TTTAAAA-TATCAGAATAA-AATATCTAGTTGCTTTAAGACTGTC-TTTTC-TTAA
1 ATTTATTTATTTAAAAGTATCAGAA-AATAACATCTAGTTGCTTTAAGACTG-CATTTTCTTTAA
* *
1674158 TATTTGAA-AAATAAATAAATATTAA-AA-ATAATAATTTTCCTAAAAAATAATTTAAATAAA-A
64 T-TTT-AATAAATAAAT-AATAATAAGAATATAATAATTTTCCTAAAAAATAA-TGAAATAAATA
* * *
1674219 CAATATGTATTTTCTGGTTTTTAAAAGTAGGAT
125 -AATA--TA-----T-ATTTTTATAAGCAGGAT
* * *
1674252 ATTTATTTATTTTTAAAA-TATCAGAATAGT-ACATCTAGTTACTTTAAGACTGCCCTTTTCTTT
1 ATTTATTTA--TTTAAAAGTATCAGAA-AATAACATCTAGTTGCTTTAAGACTG-CATTTTCTTT
* * *
1674315 -ATATAAAAAAATAAATAA
62 AATTTTAATAAATAAATAA
1674333 ATATTTATTA
Statistics
Matches: 194, Mismatches: 17, Indels: 38
0.78 0.07 0.15
Matches are distributed among these distances:
144 28 0.14
145 57 0.29
146 18 0.09
147 4 0.02
148 5 0.03
152 1 0.01
153 19 0.10
154 2 0.01
156 4 0.02
157 47 0.24
158 7 0.04
159 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (148 bp):
ATTTATTTATTTAAAAGTATCAGAAAATAACATCTAGTTGCTTTAAGACTGCATTTTCTTTAATT
TTAATAAATAAATAATAATAAGAATATAATAATTTTCCTAAAAAATAATGAAATAAATAAATATA
TATTTTTATAAGCAGGAT
Found at i:1674367 original size:2 final size:2
Alignment explanation
Indices: 1674360--1674397 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1674350 AAATACATAC
1674360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1674398 GACTAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1675857 original size:16 final size:16
Alignment explanation
Indices: 1675833--1675873 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1675823 TTGGTTTTAG
*
1675833 GGTTTGGCTAGATACA
1 GGTTGGGCTAGATACA
*
1675849 GGTTGGGCTAGATCCA
1 GGTTGGGCTAGATACA
1675865 GGTTGGGCT
1 GGTTGGGCT
1675874 TATATCTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.39, T:0.29
Consensus pattern (16 bp):
GGTTGGGCTAGATACA
Found at i:1675952 original size:3 final size:3
Alignment explanation
Indices: 1675944--1676018 Score: 96
Period size: 3 Copynumber: 24.3 Consensus size: 3
1675934 TTTATTTAGT
* *
1675944 TAA TAA TAA TAA TAA TATA TTA TAA TAA TAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1675990 TAA TATT TAA TAA TAA TAA TGA TAA TAA T
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA T
1676019 TTTAAAAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 58 0.94
4 4 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1675959 original size:28 final size:26
Alignment explanation
Indices: 1675936--1676016 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 26
1675926 TGTAATTATT
*
1675936 TATTTAGTTAATAATAATAATAAT-A
1 TATTTATTTAATAATAATAATAATAA
*
1675961 TA-TTATAATAATAATAATAATAATAA
1 TATTTAT-TTAATAATAATAATAATAA
*
1675987 TATTAATATTTAATAATAATAATGATAA
1 TATT--TATTTAATAATAATAATAATAA
1676015 TA
1 TA
1676017 ATTTTAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
24 3 0.06
25 18 0.38
26 3 0.06
27 1 0.02
28 19 0.40
29 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TATTTATTTAATAATAATAATAATAA
Found at i:1678127 original size:43 final size:43
Alignment explanation
Indices: 1678066--1678345 Score: 205
Period size: 43 Copynumber: 6.5 Consensus size: 43
1678056 GGTGTTTGCA
* * * *
1678066 TCCAAAAATGCCGTTATATATCTCGACCTTCTGCATCGTTTGT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCATCGTTTGT
*
1678109 TCCAAAAACGCCGCTATATATCT-GACCTTTTGCGA-CGTTT-T
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGC-ATCGTTTGT
** *
1678150 CTCCAAAAAAAACCGCTATAGATCTCGACCTTTTGCAGT-ATTTGT
1 -TCC-AAAAACGCCGCTATAGATCTCGACCTTTTGCA-TCGTTTGT
* * * *
1678195 TCCAAAAACACCGCTATAGATC-CTACCTTTTG--TTGTGTTTT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCATCGT-TTGT
* * * * ** *
1678236 CTCCAAAAATGTCGCTATAGATCTCGACATATTGCGGCGTTTAT
1 -TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCATCGTTTGT
* * * * * * ** *
1678280 TCCAAAAATGTCGCTATAAAGCTTGACCTATTGCGGCATTTGT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCATCGTTTGT
1678323 TCCAAAAACGCCGCTATAGATCT
1 TCCAAAAACGCCGCTATAGATCT
1678346 AGACATAATG
Statistics
Matches: 194, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 4 0.02
42 45 0.23
43 121 0.62
44 19 0.10
45 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (43 bp):
TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCATCGTTTGT
Found at i:1680406 original size:58 final size:58
Alignment explanation
Indices: 1680297--1680710 Score: 378
Period size: 58 Copynumber: 7.1 Consensus size: 58
1680287 AAATCACTAG
* * * * *
1680297 ATTTATTTCATTGTTAGAATCTTGCATTGATTCTAACTTTGTAA-TAGAAATAAATTATTGA
1 ATTTATTTCCTTG--AGAATCTT-AAATGATTCTAACTTTGTAAGGA-AAATAAATTGTTGA
* * * * * * *
1680358 ATCTATTTCCTTAATAATCTTAAATGATTTTAATTTTGTAAGGAAAATAAATCGCTGA
1 ATTTATTTCCTTGAGAATCTTAAATGATTCTAACTTTGTAAGGAAAATAAATTGTTGA
* *
1680416 ATTTATTTCCTTGAGAATC-TAGAATGATTCTAACCTTGTAA-GAGAAATATATTGTTGA
1 ATTTATTTCCTTGAGAATCTTA-AATGATTCTAACTTTGTAAGGA-AAATAAATTGTTGA
* *
1680474 ATTTATTTCTTTGAGAATCTTAAATGATTCTAACTTTGTAAGGAAAATAGATTGTTGA
1 ATTTATTTCCTTGAGAATCTTAAATGATTCTAACTTTGTAAGGAAAATAAATTGTTGA
* * * * *
1680532 ATTTATCTCCTT---AATCTTGAATGATTTTAACTTTGTAAGAAAAATAAATTGTCGA
1 ATTTATTTCCTTGAGAATCTTAAATGATTCTAACTTTGTAAGGAAAATAAATTGTTGA
* * ** * * ** *
1680587 ATTTATTTTCTTGAGAATCGTGGATGATTCTATCCTT-TAAACAGAAATAAATTGTTAA
1 ATTTATTTCCTTGAGAATCTTAAATGATTCTAACTTTGTAAGGA-AAATAAATTGTTGA
* * * *
1680645 AATTATTTTCTTGAGAATCTTAAATGATTCT-ATTTTGTTAAAGG-AAATAAATTGTTAA
1 ATTTATTTCCTTGAGAATCTTAAATGATTCTAACTTTG-T-AAGGAAAATAAATTGTTGA
1680703 ATTTATTT
1 ATTTATTT
1680711 TCTCGGGAAT
Statistics
Matches: 289, Mismatches: 52, Indels: 27
0.79 0.14 0.07
Matches are distributed among these distances:
55 48 0.17
57 10 0.03
58 206 0.71
59 13 0.04
60 2 0.01
61 10 0.03
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (58 bp):
ATTTATTTCCTTGAGAATCTTAAATGATTCTAACTTTGTAAGGAAAATAAATTGTTGA
Found at i:1680616 original size:171 final size:173
Alignment explanation
Indices: 1680297--1680708 Score: 473
Period size: 171 Copynumber: 2.4 Consensus size: 173
1680287 AAATCACTAG
* * * * * *
1680297 ATTTATTTCATTGTTAGAATCTTGCATTGATTCTAACTTTGTAA-TAGAAATAAATTATTGAATC
1 ATTTATTTC-TT-TGAGAATCTT-AAATGATTCTAACTTTGTAAGGA-AAATAAATTGTTGAATT
* * *
1680361 TATTTCCTTAATAATCTTAAATGATTTTAATTTTGTAAGGAAAATAAATCGCTGAATTTATTTCC
62 TATCTCCTT-ATAATCTTAAATGATTTTAACTTTGTAAGAAAAATAAATCGCTGAATTTATTTCC
* * *
1680426 TTGAGAATCTAGAATGATTCTAACCTTGT-AAGAGAAATATATTGTTGA
126 TTGAGAATCTAGAATGATTCTAACCTT-TAAACAGAAATAAATTGTTAA
*
1680474 ATTTATTTCTTTGAGAATCTTAAATGATTCTAACTTTGTAAGGAAAATAGATTGTTGAATTTATC
1 ATTTATTTCTTTGAGAATCTTAAATGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATC
* * *
1680539 TCC-T-TAATCTTGAATGATTTTAACTTTGTAAGAAAAATAAATTG-TCGAATTTATTTTCTTGA
66 TCCTTATAATCTTAAATGATTTTAACTTTGTAAGAAAAATAAATCGCT-GAATTTATTTCCTTGA
* *
1680601 GAATCGT-GGATGATTCTATCCTTTAAACAGAAATAAATTGTTAA
130 GAATC-TAGAATGATTCTAACCTTTAAACAGAAATAAATTGTTAA
* * *
1680645 AATTATTT-TCTTGAGAATCTTAAATGATTCT-ATTTTGTTAAAGG-AAATAAATTGTTAAATTT
1 ATTTATTTCT-TTGAGAATCTTAAATGATTCTAACTTTG-T-AAGGAAAATAAATTGTTGAATTT
1680707 AT
63 AT
1680709 TTTCTCGGGA
Statistics
Matches: 206, Mismatches: 22, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
170 8 0.04
171 133 0.65
172 5 0.02
173 1 0.00
174 38 0.18
175 10 0.05
176 2 0.01
177 9 0.04
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (173 bp):
ATTTATTTCTTTGAGAATCTTAAATGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATC
TCCTTATAATCTTAAATGATTTTAACTTTGTAAGAAAAATAAATCGCTGAATTTATTTCCTTGAG
AATCTAGAATGATTCTAACCTTTAAACAGAAATAAATTGTTAA
Found at i:1680826 original size:39 final size:39
Alignment explanation
Indices: 1680783--1681050 Score: 179
Period size: 39 Copynumber: 6.8 Consensus size: 39
1680773 TCTATCTTTT
* *
1680783 TAAAAGGAAATAAATAGCCAAATTTATTTTCCTAGTTTA
1 TAAAAGGAAATAAATAGTCGAATTTATTTTCCTAGTTTA
* *
1680822 TAAAAGGAAATAAATCA-TC-AGATTTATTTTCTTATTTTGA
1 TAAAAGGAAATAAAT-AGTCGA-ATTTATTTTCCTAGTTT-A
* * * * *
1680862 -AAAAGGAAACAACTTGTTGAATTTACTTTCCT-GTTTTGTA
1 TAAAAGGAAATAAATAGTCGAATTTATTTTCCTAG--TT-TA
* * * * *
1680902 TAAAA-AAAATAAATATTTGGATTTATTTTCCTATTTTA
1 TAAAAGGAAATAAATAGTCGAATTTATTTTCCTAGTTTA
* * * * * *
1680940 TGAAAGAAAATAAATCGTTGATTTTATTTTCCTATTTTA
1 TAAAAGGAAATAAATAGTCGAATTTATTTTCCTAGTTTA
* * * *
1680979 TGAAAGGAAATAAATCGGTCG-ATTTATTTTCCTTGTTTG
1 TAAAAGGAAATAAAT-AGTCGAATTTATTTTCCTAGTTTA
* * * *
1681018 TAGAAGGAAATATATCGTTGAATTTATTTTCCT
1 TAAAAGGAAATAAATAGTCGAATTTATTTTCCT
1681051 GTAAATCTTA
Statistics
Matches: 181, Mismatches: 35, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
38 10 0.06
39 137 0.76
40 29 0.16
41 5 0.03
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (39 bp):
TAAAAGGAAATAAATAGTCGAATTTATTTTCCTAGTTTA
Found at i:1680885 original size:78 final size:76
Alignment explanation
Indices: 1680803--1681050 Score: 218
Period size: 78 Copynumber: 3.2 Consensus size: 76
1680793 TAAATAGCCA
1680803 AATTTATTTTCCTAGTTTATAAAAGGAAATAAATCATCAGATTTATTTTCTTATTTTGAAAAAGG
1 AATTTATTTTCCTAGTTTATAAAAGGAAATAAATCATC-GATTTATTTTCTTATTTTGAAAAAGG
* *
1680868 AAACAACTTGTTG
65 AAATAA-TCGTTG
* * * * *
1680881 AATTTACTTTCCT-GTTTTGTATAAAA-AAAATAAAT-ATTTGGATTTATTTTCCTATTTT-ATG
1 AATTTATTTTCCTAG--TT-TATAAAAGGAAATAAATCA--TCGATTTATTTTCTTATTTTGA-A
*
1680942 AAAGAAAATAAATCGTTG
60 AAAGGAAAT-AATCGTTG
* * * * * * *
1680960 ATTTTATTTTCCTATTTTATGAAAGGAAATAAATCGGTCGATTTATTTTCCTT-GTTTGTAGAAG
1 AATTTATTTTCCTAGTTTATAAAAGGAAATAAATC-ATCGATTTATTTT-CTTATTTTGAAAAAG
1681024 GAAATATATCGTTG
64 GAAATA-ATCGTTG
1681038 AATTTATTTTCCT
1 AATTTATTTTCCT
1681051 GTAAATCTTA
Statistics
Matches: 134, Mismatches: 22, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
77 8 0.06
78 64 0.48
79 52 0.39
80 10 0.07
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (76 bp):
AATTTATTTTCCTAGTTTATAAAAGGAAATAAATCATCGATTTATTTTCTTATTTTGAAAAAGGA
AATAATCGTTG
Found at i:1681155 original size:38 final size:39
Alignment explanation
Indices: 1681072--1681206 Score: 177
Period size: 38 Copynumber: 3.5 Consensus size: 39
1681062 ATGATTCTGA
*
1681072 TTTGTAAAAGGAAATAAATC-GTAGAATTTATTTTTCTTGT
1 TTTGTAAAAGAAAATAAATCAGT-GAATTTA-TTTTCTTGT
* *
1681112 TTTGTAAAAGGAAATAAATCAGTGAATTTA-TTTCTTAT
1 TTTGTAAAAGAAAATAAATCAGTGAATTTATTTTCTTGT
* * *
1681150 TTTGTAAAAGAAAATAAATCAATGACTTTATTTTATTGT
1 TTTGTAAAAGAAAATAAATCAGTGAATTTATTTTCTTGT
1681189 TTTG-AAAAGAAAATAAAT
1 TTTGTAAAAGAAAATAAAT
1681207 TATTGGATTG
Statistics
Matches: 87, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
38 48 0.55
39 10 0.11
40 27 0.31
41 2 0.02
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (39 bp):
TTTGTAAAAGAAAATAAATCAGTGAATTTATTTTCTTGT
Found at i:1686544 original size:2 final size:2
Alignment explanation
Indices: 1686537--1686607 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
1686527 CAAGAGTATG
1686537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1686579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1686608 CGAAGTCAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1690483 original size:23 final size:23
Alignment explanation
Indices: 1690441--1690523 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
1690431 CATTATTATA
*
1690441 TGGCACTA-GGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
*
1690463 TGGCACTACGGTACAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
**
1690486 TGGCACTTTGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1690509 TGGAACTTCGGTGCA
1 TGGCACTACGGTGCA
1690524 TTTATACGAG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 8 0.15
23 45 0.85
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1693617 original size:14 final size:15
Alignment explanation
Indices: 1693598--1693630 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1693588 GAAAATAAAC
*
1693598 AATAAAAATGAA-TA
1 AATAAAAATAAAGTA
1693612 AATAAAAATAAAGTA
1 AATAAAAATAAAGTA
1693627 AATA
1 AATA
1693631 GTAAAAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (15 bp):
AATAAAAATAAAGTA
Found at i:1698881 original size:35 final size:35
Alignment explanation
Indices: 1698828--1698907 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 35
1698818 AAATTCAAGA
*
1698828 TTTTA-GAATTATCTTTGGATTTAATTTAAAATAT
1 TTTTAGGATTTATCTTTGGATTTAATTTAAAATAT
*
1698862 TTTTAGGATTTATCTTTGGATTTAATTTAAACTAT
1 TTTTAGGATTTATCTTTGGATTTAATTTAAAATAT
1698897 TTTTAGGATTT
1 TTTTAGGATTT
1698908 TCAAAACCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
34 5 0.12
35 38 0.88
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (35 bp):
TTTTAGGATTTATCTTTGGATTTAATTTAAAATAT
Found at i:1704854 original size:26 final size:25
Alignment explanation
Indices: 1704824--1704891 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
1704814 TTTAAGTTGT
1704824 ACACA-TCATCTTCAATCTCTTACATA
1 ACACACTCAT-TTC-ATCTCTTACATA
* *
1704850 ACACACTCCTTTCATCTCTTACACA
1 ACACACTCATTTCATCTCTTACATA
* *
1704875 TCACACTCTTTTCATCT
1 ACACACTCATTTCATCT
1704892 TCAATCTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 26 0.70
26 8 0.22
27 3 0.08
ACGTcount: A:0.28, C:0.35, G:0.00, T:0.37
Consensus pattern (25 bp):
ACACACTCATTTCATCTCTTACATA
Found at i:1704865 original size:32 final size:32
Alignment explanation
Indices: 1704829--1704923 Score: 89
Period size: 32 Copynumber: 3.2 Consensus size: 32
1704819 GTTGTACACA
1704829 TCATCTTCAATCTCTTACATAACACACTCCTT
1 TCATCTTCAATCTCTTACATAACACACTCCTT
*
1704861 TCATC-TC--T-TAC--ACAT--CACACTCTTT
1 TCATCTTCAATCT-CTTACATAACACACTCCTT
* * *
1704886 TCATCTTCAATCTCTTACACAACAAACTACTT
1 TCATCTTCAATCTCTTACATAACACACTCCTT
1704918 TCATCT
1 TCATCT
1704924 AAAAAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
25 14 0.29
26 2 0.04
27 4 0.08
28 3 0.06
29 3 0.06
30 3 0.06
31 2 0.04
32 18 0.37
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (32 bp):
TCATCTTCAATCTCTTACATAACACACTCCTT
Found at i:1704871 original size:25 final size:25
Alignment explanation
Indices: 1704838--1704891 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
1704828 ATCATCTTCA
*
1704838 ATCTCTTACATAACACACTCCTTTC
1 ATCTCTTACACAACACACTCCTTTC
* *
1704863 ATCTCTTACACATCACACTCTTTTC
1 ATCTCTTACACAACACACTCCTTTC
1704888 ATCT
1 ATCT
1704892 TCAATCTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (25 bp):
ATCTCTTACACAACACACTCCTTTC
Found at i:1705683 original size:18 final size:17
Alignment explanation
Indices: 1705643--1705685 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1705633 TAACTACGAT
1705643 GTTATGTGAAATCCTGA
1 GTTATGTGAAATCCTGA
** *
1705660 AATATGTGATATGCCTGA
1 GTTATGTGAAAT-CCTGA
1705678 GTTATGTG
1 GTTATGTG
1705686 CTGCCCACTG
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (17 bp):
GTTATGTGAAATCCTGA
Found at i:1712026 original size:17 final size:19
Alignment explanation
Indices: 1712004--1712052 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
1711994 TTCCAAATAA
1712004 ATTAAAAAAATA-TTT-TT
1 ATTAAAAAAATATTTTATT
1712021 ATTAAAAATAATATTTTATT
1 ATTAAAAA-AATATTTTATT
1712041 ATTAAAAAAATA
1 ATTAAAAAAATA
1712053 AAAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.28
18 4 0.14
19 7 0.24
20 10 0.34
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTAAAAAAATATTTTATT
Found at i:1712677 original size:21 final size:21
Alignment explanation
Indices: 1712624--1712668 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1712614 AAATCAAGAA
*
1712624 AATATCAACGACTAACATTAT
1 AATATCGACGACTAACATTAT
1712645 AATATCGACGACTAACATTAT
1 AATATCGACGACTAACATTAT
1712666 AAT
1 AAT
1712669 TGGTGCGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.29
Consensus pattern (21 bp):
AATATCGACGACTAACATTAT
Found at i:1716005 original size:229 final size:229
Alignment explanation
Indices: 1715604--1716324 Score: 1320
Period size: 229 Copynumber: 3.1 Consensus size: 229
1715594 GTTATATTGT
* * *
1715604 AAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGT-AAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATT
*
1715668 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAA
* *
1715733 ATAATTTTGTGTGTAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTA
130 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTA
*
1715798 AAAAAAATTGAAATATAAATTACATAACTTTAAAA
195 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
*
1715833 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATT
1715898 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
1715963 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
*
1716028 AAAAAATTGAAACATAAATTACAAAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
1716062 AATA-TATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTAT
1 AA-AGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTAT
*
1716126 TATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAA
65 TATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAA
1716191 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTA
130 ATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTA
1716256 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
195 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
1716291 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
1 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
1716325 GTATAAAAGT
Statistics
Matches: 477, Mismatches: 12, Indels: 6
0.96 0.02 0.01
Matches are distributed among these distances:
228 1 0.00
229 405 0.85
230 71 0.15
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.39
Consensus pattern (229 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATT
ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
AAAAAATTGAAACATAAATTACATAACTTTAAAA
Done.