Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000186.1 Hibiscus syriacus cultivar Beakdansim tig00000329_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: 3152351
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 9 of 17
Found at i:1587133 original size:21 final size:21
Alignment explanation
Indices: 1587019--1587133 Score: 51
Period size: 21 Copynumber: 5.6 Consensus size: 21
1587009 CGCGAAATAA
**
1587019 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** *
1587039 AATCGCAAATC-A-TTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
1587058 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
** ** *
1587079 AATCGCAATACGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
1587099 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
1587121 AATCGCAACGCGA
1 AATCGCAACGCGA
1587134 ATATGAAAAT
Statistics
Matches: 68, Mismatches: 21, Indels: 11
0.68 0.21 0.11
Matches are distributed among these distances:
19 14 0.21
20 13 0.19
21 37 0.54
22 4 0.06
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:1587206 original size:57 final size:57
Alignment explanation
Indices: 1587140--1587306 Score: 180
Period size: 57 Copynumber: 2.9 Consensus size: 57
1587130 GCGAATATGA
*
1587140 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAATCGCAACGGATCCAT
1 AAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTAATCGCAACGGATCCAT
* * * * *
1587197 AAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATACGTATATCGCAATGCGTATCCGT
1 AAATCGCAACGCG-AACACGTAAATCGCAACGCGTATCCGTA-ATCGCAA--CGGATCCAT
*
1587257 AAATCGC--CGAC-AATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACG
1 AAATCGCAACG-CGAACACGT-AAATCGCAACGCGTATCCGT-AATCGCAACG
1587307 CGATTTTAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
57 37 0.40
58 14 0.15
59 26 0.28
60 15 0.16
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.19
Consensus pattern (57 bp):
AAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTAATCGCAACGGATCCAT
Found at i:1587219 original size:20 final size:20
Alignment explanation
Indices: 1587121--1587308 Score: 183
Period size: 20 Copynumber: 9.6 Consensus size: 20
1587111 GATTTTCCAG
* ** *
1587121 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1587141 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1587161 AATCGCAACGCGTATCCGT-
1 AATCGCAACGCGTATCCGTA
*
1587180 AATCGCAACG-G-ATCCATA
1 AATCGCAACGCGTATCCGTA
1587198 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1587218 AATCGCAATGCGTATACGTA
1 AATCGCAACGCGTATCCGTA
* *
1587238 TATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1587258 AATCGC--CGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
1587277 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1587297 AATCGCAACGCG
1 AATCGCAACGCG
1587309 ATTTTAAAGC
Statistics
Matches: 139, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.04
18 17 0.12
19 20 0.14
20 88 0.63
21 9 0.06
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1587221 original size:77 final size:79
Alignment explanation
Indices: 1587121--1587309 Score: 222
Period size: 77 Copynumber: 2.4 Consensus size: 79
1587111 GATTTTCCAG
* ** *
1587121 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT-AATCG
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCG
* *
1587185 -CAACGGATCCAT-A
66 CCAAC-AATACATAA
* * * * * *
1587198 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATACGTATATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCG
* *
1587263 CCGACAATACGTAA
66 CCAACAATACATAA
1587277 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1587310 TTTTAAAGCG
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
77 49 0.53
78 9 0.10
79 35 0.38
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (79 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCG
CCAACAATACATAA
Found at i:1587720 original size:32 final size:33
Alignment explanation
Indices: 1587682--1587751 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 33
1587672 TTCACTTAGA
1587682 TTTCATTTCGCGTTACGATTCTCTC-TTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1587714 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1587747 TTTCA
1 TTTCA
1587752 GTTAGTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 23 0.66
33 12 0.34
ACGTcount: A:0.11, C:0.24, G:0.16, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1587856 original size:21 final size:20
Alignment explanation
Indices: 1587830--1587901 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
1587820 TGCAGAAGAG
1587830 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
1587851 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
1587871 TCTGCAACGA-AAAATGAAAA
1 TC-GCAACGAGAAAATGAAAA
1587891 TCGCAACGAGA
1 TCGCAACGAGA
1587902 GAATCGCAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 7 0.16
20 20 0.47
21 16 0.37
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1587933 original size:18 final size:18
Alignment explanation
Indices: 1587903--1587946 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1587893 GCAACGAGAG
**
1587903 AATCGCAACGCGAAATGAA
1 AATCGC-ACGCGAAACCAA
1587922 AATCGCACGCGAAACCAA
1 AATCGCACGCGAAACCAA
1587940 AATCGCA
1 AATCGCA
1587947 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.09
Consensus pattern (18 bp):
AATCGCACGCGAAACCAA
Found at i:1588008 original size:34 final size:32
Alignment explanation
Indices: 1587947--1588019 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 32
1587937 CAAAATCGCA
1587947 TTGCGA-TTTTCATTCGCGTGCGATTCTCTCG
1 TTGCGATTTTTCATTCGCGTGCGATTCTCTCG
1587978 TTGCGATTTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTTCA-TTCGCG-TGCGATTCTCTCG
1588012 TTGCGATT
1 TTGCGATT
1588020 CATTTCTCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
31 6 0.15
32 6 0.15
33 6 0.15
34 21 0.54
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (32 bp):
TTGCGATTTTTCATTCGCGTGCGATTCTCTCG
Found at i:1588048 original size:20 final size:19
Alignment explanation
Indices: 1588003--1588056 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1587993 TCGCGTTGCG
*
1588003 ATTCTCTCGTTGCG-ATTC
1 ATTCTCTCGTTGCGAAGTC
1588021 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGA-AGTC
1588042 ATTCTCTCGTTGCGA
1 ATTCTCTCGTTGCGA
1588057 TTTTCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 1 0.03
19 13 0.41
20 14 0.44
21 4 0.12
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.41
Consensus pattern (19 bp):
ATTCTCTCGTTGCGAAGTC
Found at i:1588064 original size:20 final size:18
Alignment explanation
Indices: 1588003--1588058 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 18
1587993 TCGCGTTGCG
1588003 ATTCTCTCGTTGCGATTC
1 ATTCTCTCGTTGCGATTC
*
1588021 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCG--ATTC
1588042 ATTCTCTCGTTGCGATT
1 ATTCTCTCGTTGCGATT
1588059 TTCATTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.09
19 13 0.39
20 13 0.39
21 4 0.12
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.43
Consensus pattern (18 bp):
ATTCTCTCGTTGCGATTC
Found at i:1589875 original size:87 final size:91
Alignment explanation
Indices: 1589716--1590057 Score: 514
Period size: 87 Copynumber: 3.9 Consensus size: 91
1589706 TAGATTGCTT
*
1589716 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAA-TCTGCTAAACTGTG-ATTCTTTAACACTGTGAAATAGTA
1589781 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
64 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1589809 AGTAAATTTGTTC-GTTGCTGCCAATCTGCTAAACTGTG-TTCTTTAAC-CTGTG-AATAGTATT
1 AGTAAATTTGTTCGGTTGCTGCCAATCTGCTAAACTGTGATTCTTTAACACTGTGAAATAGTATT
1589870 TGTCTTTGTTTTGTCTTTTGGTTG-A
66 TGTCTTTGTTTTGTCTTTTGGTTGAA
1589895 AGTAAATTTGTTCGGTTGCTGCCAATCTGCTAAACTGTGTATTCTTT-A-ACTGTGAAATAG--T
1 AGTAAATTTGTTCGGTTGCTGCCAATCTGCTAAACTGTG-ATTCTTTAACACTGTGAAATAGTAT
* *
1589956 TTGTCTTTG-TTTATC-TTTGTTTGAA
65 TTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1589981 AGT-AATTTGTTC-GTTGCTGCCAATTTGCT-AACTGTGTATTCTTTAACACTGTGAAATAGTAT
1 AGTAAATTTGTTCGGTTGCTGCCAATCTGCTAAACTGTG-ATTCTTTAACACTGTGAAATAGTAT
1590043 TTGTCTTTGTTTTGT
65 TTGTCTTTGTTTTGT
1590058 GCTGCCAATT
Statistics
Matches: 233, Mismatches: 5, Indels: 27
0.88 0.02 0.10
Matches are distributed among these distances:
83 15 0.06
84 17 0.07
85 28 0.12
86 23 0.10
87 78 0.33
88 15 0.06
89 20 0.09
91 14 0.06
92 11 0.05
93 12 0.05
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (91 bp):
AGTAAATTTGTTCGGTTGCTGCCAATCTGCTAAACTGTGATTCTTTAACACTGTGAAATAGTATT
TGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1590240 original size:31 final size:32
Alignment explanation
Indices: 1590188--1590248 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
1590178 ACGAAACTTA
1590188 AAATCGCAACGAGAGAATCGCAACGCGAAATG
1 AAATCGCAACGAGAGAATCGCAACGCGAAATG
*
1590220 AAATCGCAACGA-CGAATCGCAACGCGAAA
1 AAATCGCAACGAGAGAATCGCAACGCGAAA
1590249 CCAAAATCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGAGAGAATCGCAACGCGAAATG
Found at i:1590256 original size:32 final size:33
Alignment explanation
Indices: 1590171--1590259 Score: 119
Period size: 32 Copynumber: 2.7 Consensus size: 33
1590161 ATAGTTTACT
*
1590171 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-TAAAATCGCAACGAGAGAA
* *
1590205 TCGCAACGCGAAA-TGAAATCGCAACGA-CGAA
1 TCGCAACGCGAAACTAAAATCGCAACGAGAGAA
*
1590236 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACTAAAATCGCA
1590260 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 16 0.33
32 21 0.43
34 12 0.24
ACGTcount: A:0.44, C:0.27, G:0.19, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAACTAAAATCGCAACGAGAGAA
Found at i:1590328 original size:26 final size:27
Alignment explanation
Indices: 1590261--1590345 Score: 91
Period size: 33 Copynumber: 3.0 Consensus size: 27
1590251 AAAATCGCAT
*
1590261 TGCGATTTTCATTTCGCGTTGCGATTCTCTC
1 TGCGATTTTCATTTCGCATTGCGA---T-TC
1590292 GTTGCGATTTTCATTTCGCATTGCGATTC
1 --TGCGATTTTCATTTCGCATTGCGATTC
*
1590321 TGCG-TTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
1590346 TTGGTTCACG
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
26 20 0.40
27 4 0.08
29 2 0.04
30 1 0.02
33 23 0.46
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (27 bp):
TGCGATTTTCATTTCGCATTGCGATTC
Found at i:1590347 original size:19 final size:19
Alignment explanation
Indices: 1590255--1590400 Score: 83
Period size: 19 Copynumber: 7.7 Consensus size: 19
1590245 GAAACCAAAA
*
1590255 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1590274 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1590288 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1590307 TCGCATTGCGATTCTGCGTTTTCATT
1 TCGCGTTGCGA-------TTTTCATT
**
1590333 TCGCGTTGCGATTTT-GGT
1 TCGCGTTGCGATTTTCATT
* **
1590351 TCACG-TGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1590369 T-TCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
1590387 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1590401 AAGTTTCGTG
Statistics
Matches: 97, Mismatches: 15, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
14 10 0.10
16 3 0.03
17 14 0.14
18 19 0.20
19 33 0.34
26 18 0.19
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1590379 original size:18 final size:18
Alignment explanation
Indices: 1590336--1590380 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
1590326 TTTCATTTCG
1590336 CGTTGCGATTTTGGTTCA
1 CGTTGCGATTTTGGTTCA
**
1590354 CG-TGCGATTTTGGTTTT
1 CGTTGCGATTTTGGTTCA
1590371 CGTTGCGATT
1 CGTTGCGATT
1590381 CTCATTTCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (18 bp):
CGTTGCGATTTTGGTTCA
Found at i:1590407 original size:19 final size:18
Alignment explanation
Indices: 1590331--1590416 Score: 61
Period size: 18 Copynumber: 4.7 Consensus size: 18
1590321 TGCGTTTTCA
*
1590331 TTTCGCGTTGCGATTTTG
1 TTTCGCGTTGCGATTTAG
* * *
1590349 GTTCACG-TGCGATTTTGG
1 TTTCGCGTTGCGA-TTTAG
*
1590367 TTT-TCGTTGCGATTCTCA-
1 TTTCGCGTTGCGATT-T-AG
1590385 TTTCGCGTTGCGATTTAAG
1 TTTCGCGTTGCGATTT-AG
*
1590404 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
1590417 AAGTAAACTA
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
17 9 0.17
18 22 0.42
19 22 0.42
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.45
Consensus pattern (18 bp):
TTTCGCGTTGCGATTTAG
Found at i:1592325 original size:14 final size:14
Alignment explanation
Indices: 1592306--1592339 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1592296 ATTGTTTAAT
1592306 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1592320 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1592334 TGATTT
1 TGATTT
1592340 TTGTAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1592456 original size:19 final size:19
Alignment explanation
Indices: 1592432--1592518 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
1592422 GCATTATGTT
1592432 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1592451 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
1592468 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1592484 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1592503 GGAAATG-AAATCGCAA
1 -GAAATGAAAATCGCAA
1592519 CGAGAGATCG
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 38 0.63
20 6 0.10
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:1592514 original size:52 final size:51
Alignment explanation
Indices: 1592432--1592536 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 51
1592422 GCATTATGTT
1592432 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG-ATCGCAATGC
1592484 GAAATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGATCGCAATGC
1 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGATCGCAATGC
1592535 GA
1 GA
1592537 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
51 12 0.23
52 34 0.65
53 6 0.12
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (51 bp):
GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGATCGCAATGC
Found at i:1592554 original size:19 final size:19
Alignment explanation
Indices: 1592526--1592767 Score: 272
Period size: 19 Copynumber: 13.7 Consensus size: 19
1592516 CAACGAGAGA
*
1592526 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1592545 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1592564 CCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1592580 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1592597 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1592616 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1592632 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1592649 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1592668 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
1592685 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1592702 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1592721 TCCGCATTGCGATTTTC--T
1 T-CGCATTGCGATTTTCATT
*
1592739 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1592755 TCGCATTGCGATT
1 TCGCATTGCGATT
1592768 CTCTCGTTGC
Statistics
Matches: 190, Mismatches: 11, Indels: 44
0.78 0.04 0.18
Matches are distributed among these distances:
14 28 0.15
16 21 0.11
17 21 0.11
18 5 0.03
19 90 0.47
20 25 0.13
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1592697 original size:53 final size:53
Alignment explanation
Indices: 1592532--1592767 Score: 431
Period size: 53 Copynumber: 4.5 Consensus size: 53
1592522 GAGATCGCAA
1592532 TGCGATTTTCATTTCGCATTGCGATTTTCA-TTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1592584 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1592636 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
* *
1592689 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
1592742 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
1592768 CTCTCGTTGC
Statistics
Matches: 179, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
52 82 0.46
53 97 0.54
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:1592713 original size:86 final size:84
Alignment explanation
Indices: 1592602--1592781 Score: 242
Period size: 86 Copynumber: 2.1 Consensus size: 84
1592592 TCATTTCGCA
1592602 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCGATTTTCATTTCGCATTGCGATTT
1 TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTC--TT-G--TTGCGATTT
1592663 TCATTTCCGCATTGCGATTCTCTCG
61 TCATTT-CGCATTGCGATTCTCTCG
* *
1592688 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGTTGGGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-ATTGCGATTTTCTTGTTGCGATTTTCA
1592753 TTTCGCATTGCGATTCTCTCG
64 TTTCGCATTGCGATTCTCTCG
1592774 TTGCGATT
1 TTGCGATT
1592782 GTAATTTCCG
Statistics
Matches: 86, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
86 51 0.59
87 14 0.16
88 3 0.03
89 3 0.03
90 4 0.05
92 11 0.13
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (84 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCTTGTTGCGATTTTCATT
TCGCATTGCGATTCTCTCG
Found at i:1592765 original size:33 final size:33
Alignment explanation
Indices: 1592532--1592781 Score: 181
Period size: 33 Copynumber: 7.2 Consensus size: 33
1592522 GAGATCGCAA
1592532 TGCGATTTTCATTTCGCATTGCGATTTTCATTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTC-TT--G--T
*
1592570 TGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTC--TT-G--T
* *
1592603 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
*
1592636 TGCGATTTTCATTTCGCATTGCGATTTTCAT-T
1 TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
* * * *
1592668 TCCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCG-ATTTTC-ATT-TCGCATTGCGATTTTC--TT-G--T
1592708 TGCGATTTTCATTTCCGCATTGCGATTTTCTTGT
1 TGCGATTTTCATTT-CGCATTGCGATTTTCTTGT
* * *
1592742 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
1592775 TGCGATT
1 TGCGATT
1592782 GTAATTTCCG
Statistics
Matches: 174, Mismatches: 21, Indels: 39
0.74 0.09 0.17
Matches are distributed among these distances:
32 7 0.04
33 77 0.44
34 30 0.17
35 8 0.05
36 10 0.06
37 2 0.01
38 16 0.09
39 17 0.10
40 7 0.04
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCTTGT
Found at i:1593441 original size:20 final size:20
Alignment explanation
Indices: 1593413--1593641 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
1593403 AAATTTCAGT
* * *
1593413 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1593433 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1593453 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1593473 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1593493 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1593513 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1593533 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
1593553 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
1593573 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1593593 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1593613 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1593633 GTTGCGATT
1 GTTGCGATT
1593642 CTTGAAAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1593694 original size:21 final size:21
Alignment explanation
Indices: 1593670--1593727 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1593660 AATTTGTACT
* *
1593670 ATCGCATTGCAATTTTCAAGA
1 ATCGCGTTGCGATTTTCAAGA
1593691 ATCGCGTTGCGATTTTCAAGA
1 ATCGCGTTGCGATTTTCAAGA
1593712 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
1593728 GGAAACTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTCAAGA
Found at i:1596512 original size:32 final size:32
Alignment explanation
Indices: 1596431--1596513 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
1596421 AAAATTTTAT
1596431 TCGACTCG-TGCTCGTTAAGAAAACTTATTGC
1 TCGACTCGTTGCTCGTTAAGAAAACTTATTGC
* * * *
1596462 TCGATTCATTACTCGTTAAGAAAACTTGTTGC
1 TCGACTCGTTGCTCGTTAAGAAAACTTATTGC
*
1596494 TCGACTCGTTGCTAGTTAAG
1 TCGACTCGTTGCTCGTTAAG
1596514 CTCGTTGAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 6 0.14
32 37 0.86
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Consensus pattern (32 bp):
TCGACTCGTTGCTCGTTAAGAAAACTTATTGC
Found at i:1601675 original size:20 final size:21
Alignment explanation
Indices: 1601650--1601743 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
1601640 TTTTCCCAAT
*
1601650 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1601670 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
1601691 TCGCAATTTCGAA-TAAGTAAA
1 TCGCAA-TGCGAATTAAGAAAA
* **
1601712 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1601733 TCGCAATGCGA
1 TCGCAATGCGA
1601744 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 5
0.74 0.20 0.07
Matches are distributed among these distances:
20 15 0.27
21 37 0.66
22 4 0.07
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1601708 original size:42 final size:42
Alignment explanation
Indices: 1601650--1601743 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
1601640 TTTTCCCAAT
1601650 TCGCAA-TGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATTGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
1601691 TCGCAATTTCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATTGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1601733 TCGCAA-TGCGA
1 TCGCAATTGCGA
1601744 TACTGACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
41 10 0.20
42 40 0.80
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.19
Consensus pattern (42 bp):
TCGCAATTGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1601757 original size:20 final size:20
Alignment explanation
Indices: 1601732--1601846 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
1601722 AATTGGGAAA
*
1601732 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1601752 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
1601773 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1601793 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1601813 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
1601833 TTTGCAACGCGATA
1 ATCGCAACGCGATA
1601847 ATACATAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1601774 original size:41 final size:41
Alignment explanation
Indices: 1601729--1601866 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
1601719 GCGAATTGGG
* * *
1601729 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
1601770 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** * *
1601812 --TTTCGCAACGCGATTCTGACTTTTGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
1601851 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1601867 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 2 0.03
40 30 0.38
41 44 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:1602062 original size:22 final size:22
Alignment explanation
Indices: 1602034--1602077 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1602024 CACTTTCTCA
1602034 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1602056 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1602078 TATCTCCATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1602395 original size:20 final size:20
Alignment explanation
Indices: 1602341--1602399 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1602331 GCGATTCTCT
**
1602341 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1602361 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1602381 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1602400 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1603733 original size:18 final size:18
Alignment explanation
Indices: 1603712--1603756 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1603702 TCCACTTCGG
*
1603712 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1603730 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1603748 GAGCCATCA
1 GAGCCATCA
1603757 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1604263 original size:20 final size:20
Alignment explanation
Indices: 1604238--1604283 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1604228 TAGTTTACTT
*
1604238 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1604258 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1604278 TCGCAA
1 TCGCAA
1604284 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1604292 original size:19 final size:20
Alignment explanation
Indices: 1604249--1604304 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1604239 CGCAACATGA
1604249 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
1604269 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
1604288 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
1604305 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:1604353 original size:19 final size:19
Alignment explanation
Indices: 1604277--1604358 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
1604267 GGAAATGGCT
1604277 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1604296 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
1604310 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
* *
1604328 ATTGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1604347 ATCGCAATGCGA
1 ATCGCAATGCGA
1604359 TTTGTGTTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 17 0.33
19 19 0.37
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1606338 original size:14 final size:14
Alignment explanation
Indices: 1606319--1606354 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1606309 ATTGTTTAAT
1606319 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1606333 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1606347 TGATTTGT
1 TGATTTGT
1606355 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1606461 original size:14 final size:14
Alignment explanation
Indices: 1606442--1606494 Score: 61
Period size: 14 Copynumber: 3.4 Consensus size: 14
1606432 AAAACAGACT
1606442 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1606456 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1606475 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1606489 ATCGCA
1 ATCGCA
1606495 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 17 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1606488 original size:19 final size:19
Alignment explanation
Indices: 1606452--1606488 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1606442 ATCGCAACGA
* *
1606452 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
1606471 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
1606489 ATCGCATTGC
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:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:1606544 original size:20 final size:20
Alignment explanation
Indices: 1606519--1606556 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1606509 TCGCATTGCG
*
1606519 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1606539 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1606557 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1607664 original size:24 final size:24
Alignment explanation
Indices: 1607613--1607666 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1607603 GTATTCAAAA
* *
1607613 TTTGATCTTGGTCAATACCCGAAC
1 TTTGATATTGGTCAATACACGAAC
* *
1607637 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGAAC
1607661 TTTGAT
1 TTTGAT
1607667 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGAAC
Found at i:1610187 original size:33 final size:33
Alignment explanation
Indices: 1610145--1610271 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
1610135 GGAAATTACT
1610145 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
*
1610178 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
* * **
1610210 TTTCGCAATGCGAAATGAAAATCGTAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGATAGA
*
1610244 ATCGCAATGTGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1610272 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGATAGA
Found at i:1610252 original size:66 final size:66
Alignment explanation
Indices: 1610146--1610278 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
1610136 GAAATTACTA
* *
1610146 TCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1610211 T
66 T
* * *
1610212 TCGCAATGCGAAATGAAAATCGTAACGAGGGAATCGCAATGTGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1610277 T
66 T
1610278 T
1 T
1610279 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1610322 original size:33 final size:33
Alignment explanation
Indices: 1610271--1610360 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
1610261 AAATCGCAAC
* * *
1610271 GCGAATTTAATTTCGCGTTGCGTTTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1610304 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
1610337 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
1610361 AGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:1610324 original size:19 final size:19
Alignment explanation
Indices: 1610300--1610360 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1610290 GCGTTTCTCT
1610300 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1610319 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
1610333 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1610352 CATTGCGAT
1 CGTTGCGAT
1610361 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1610340 original size:14 final size:14
Alignment explanation
Indices: 1610286--1610342 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1610276 TTTAATTTCG
*
1610286 CGTTGCGTTTCTCT
1 CGTTGCGATTCTCT
*
1610300 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1610319 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1610333 CGTTGCGATT
1 CGTTGCGATT
1610343 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.07, C:0.25, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1610485 original size:14 final size:14
Alignment explanation
Indices: 1610466--1610502 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1610456 CATCAATTAA
1610466 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1610480 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1610494 ACAAATCAA
1 ACAAATCAA
1610503 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1611883 original size:21 final size:20
Alignment explanation
Indices: 1611859--1611918 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
1611849 TGAATCGGGT
*
1611859 TCTTGAATGGTGAGAGGGACC
1 TCTTGAACGGTGAGAGGG-CC
* * *
1611880 TCTTCAACGATGACAGTGGCC
1 TCTTGAACGGTGAGAG-GGCC
*
1611901 TCTTGAACGGTGGGAGGG
1 TCTTGAACGGTGAGAGGG
1611919 GACTCTCGAG
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (20 bp):
TCTTGAACGGTGAGAGGGCC
Found at i:1611943 original size:42 final size:42
Alignment explanation
Indices: 1611897--1611976 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
1611887 CGATGACAGT
* * *
1611897 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1611939 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
1611977 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1612374 original size:91 final size:90
Alignment explanation
Indices: 1612196--1612382 Score: 295
Period size: 91 Copynumber: 2.0 Consensus size: 90
1612186 ATATTTCAAA
*
1612196 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
*
1612261 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGAAGCAACCGAATAAATTT
1612289 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
1612353 CAGTATTGGAAGCAACCGAATAAATTT
64 CAGAATTGGAAGCAACCGAATAAATTT
1612380 ACT
1 ACT
1612383 AAGCAATCTA
Statistics
Matches: 89, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.46
93 21 0.24
95 27 0.30
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGAAGCAACCGAATAAATTT
Found at i:1612621 original size:63 final size:63
Alignment explanation
Indices: 1612549--1612679 Score: 235
Period size: 63 Copynumber: 2.1 Consensus size: 63
1612539 TAAAGTAGAC
1612549 ACCTCCACACACCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACACCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
* * *
1612612 ACCTCCACACGCCATGCACCATTGTTATCGCGTAGAGTACCGATCTCCTCACGCAATGCATTG
1 ACCTCCACACACCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1612675 ACCTC
1 ACCTC
1612680 ATCACGTAAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.22
Consensus pattern (63 bp):
ACCTCCACACACCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:1614182 original size:19 final size:19
Alignment explanation
Indices: 1614132--1614210 Score: 104
Period size: 19 Copynumber: 4.1 Consensus size: 19
1614122 TCTTTTGGTT
* *
1614132 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGC
*
1614151 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
*
1614171 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
1614190 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1614209 GA
1 GA
1614211 TTTTGGTTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
19 36 0.69
20 16 0.31
ACGTcount: A:0.48, C:0.16, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1614204 original size:38 final size:39
Alignment explanation
Indices: 1614132--1614210 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
1614122 TCTTTTGGTT
* * *
1614132 GAAATGAAAATCGCAATGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCACAACGAGATAATGAAAATCGCAACGC
* *
1614171 GAAATGAAAATCACAACGCGA-AATGAAAATCGCAATGC
1 GAAATGAAAATCACAACGAGATAATGAAAATCGCAACGC
1614209 GA
1 GA
1614211 TTTTGGTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
38 17 0.49
39 18 0.51
ACGTcount: A:0.48, C:0.16, G:0.22, T:0.14
Consensus pattern (39 bp):
GAAATGAAAATCACAACGAGATAATGAAAATCGCAACGC
Found at i:1614830 original size:20 final size:20
Alignment explanation
Indices: 1614805--1614857 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1614795 GCACTATGTA
1614805 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1614825 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1614845 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1614858 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1614891 original size:20 final size:20
Alignment explanation
Indices: 1614866--1614919 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1614856 GATTTTGTAT
1614866 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1614886 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
*
1614906 TATCGCATTACGAT
1 TATCGCATTGCGAT
1614920 TTTTCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1614920 original size:61 final size:61
Alignment explanation
Indices: 1614806--1614922 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
1614796 CACTATGTAA
* * * * * *
1614806 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTTTGTATT
* * *
1614867 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTACGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTTT
1614923 TCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTTTGTATT
Found at i:1614938 original size:61 final size:61
Alignment explanation
Indices: 1614801--1614940 Score: 151
Period size: 61 Copynumber: 2.3 Consensus size: 61
1614791 AATGGCACTA
* * * * * *
1614801 TGTAA-ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTT
* * * *
1614861 TGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTACGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTT
1614922 T-TCCAAT-TCGCGTTGCGAT
1 TGT--AATATCGCGTTGCGAT
1614941 TTACTTATTC
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
60 5 0.08
61 58 0.89
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTACGATTT
Found at i:1615030 original size:21 final size:21
Alignment explanation
Indices: 1614990--1615030 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1614980 ACTGTAGACC
**
1614990 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1615011 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1615031 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1622707 original size:19 final size:18
Alignment explanation
Indices: 1622683--1622720 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1622673 TATATGTATA
1622683 TATTTAATTATATT-TAATT
1 TATTT-ATT-TATTATAATT
1622702 TATTTATTTATTATAATT
1 TATTTATTTATTATAATT
1622720 T
1 T
1622721 TTTTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATTTATTATAATT
Found at i:1622720 original size:10 final size:9
Alignment explanation
Indices: 1622683--1622720 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
1622673 TATATGTATA
1622683 TATTTAATT
1 TATTTAATT
1622692 ATATTTAATT
1 -TATTTAATT
1622702 TATTT-ATT
1 TATTTAATT
1622710 TATTATAATT
1 TATT-TAATT
1622720 T
1 T
1622721 TTTTCATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 7 0.27
9 6 0.23
10 13 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTTAATT
Found at i:1622754 original size:25 final size:25
Alignment explanation
Indices: 1622726--1622774 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1622716 AATTTTTTTC
1622726 ATTTTTCT-TTACGTTATAT-TATATT
1 ATTTTTCTATTA--TTATATATATATT
1622751 ATTTTTCTATTATTATATATATAT
1 ATTTTTCTATTATTATATATATAT
1622775 ATTATATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.27
25 13 0.59
26 3 0.14
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (25 bp):
ATTTTTCTATTATTATATATATATT
Found at i:1622825 original size:12 final size:12
Alignment explanation
Indices: 1622808--1622832 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1622798 TGTTTACTTA
1622808 TTTACTATATTT
1 TTTACTATATTT
1622820 TTTACTATATTT
1 TTTACTATATTT
1622832 T
1 T
1622833 CCTAACGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTACTATATTT
Found at i:1622848 original size:2 final size:2
Alignment explanation
Indices: 1622841--1622873 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1622831 TTCCTAACGT
1622841 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 T
1622874 TCTTACTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1622974 original size:32 final size:32
Alignment explanation
Indices: 1622904--1622992 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 32
1622894 TATTTCTATG
* *
1622904 ATTACTATTTTTTAGTTAATATTA-TATGTAT
1 ATTACTATTTTTTATTTATTATTATTATGTAT
1622935 ATT--TATTTTTTATTTATTATTATTAT-TATT
1 ATTACTATTTTTTATTTATTATTATTATGTA-T
**
1622965 ATTACTATTTAGTATTTTATTA-TATTAT
1 ATTACTATTTTTTA-TTTATTATTATTAT
1622993 ACATACATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
29 19 0.39
30 7 0.14
31 3 0.06
32 13 0.27
33 7 0.14
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.64
Consensus pattern (32 bp):
ATTACTATTTTTTATTTATTATTATTATGTAT
Found at i:1623013 original size:21 final size:22
Alignment explanation
Indices: 1622978--1623053 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 22
1622968 ACTATTTAGT
*
1622978 ATTTTATTA-TATTATACATAC
1 ATTTTATTATTTTTATACATAC
* *
1622999 ATTTTA-TATTTTTATATATAT
1 ATTTTATTATTTTTATACATAC
* **
1623020 TTTTTATTA-TTTTATTTATAC
1 ATTTTATTATTTTTATACATAC
1623041 -TATTTATTATTTT
1 AT-TTTATTATTTT
1623054 CATTATATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.07
21 37 0.82
22 5 0.11
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTTATTATTTTTATACATAC
Found at i:1623020 original size:12 final size:12
Alignment explanation
Indices: 1623003--1623066 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 12
1622993 ACATACATTT
1623003 TATATTTTTATA
1 TATATTTTTATA
1623015 TATATTTTT-TA
1 TATATTTTTATA
*
1623026 T-TA-TTTTATT
1 TATATTTTTATA
* *
1623036 TATACTATT-TA
1 TATATTTTTATA
*
1623047 T-TATTTTCAT-
1 TATATTTTTATA
1623057 TATATTTTTA
1 TATATTTTTA
1623067 GTTTCTTTGC
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
9 4 0.10
10 9 0.22
11 15 0.38
12 12 0.30
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (12 bp):
TATATTTTTATA
Found at i:1623026 original size:42 final size:42
Alignment explanation
Indices: 1622979--1623065 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
1622969 CTATTTAGTA
*
1622979 TTTTATTATATTATACATAC-ATTT-TATATTTTTATATATATT
1 TTTTATTATATTATACATACTATTTAT-TATTTTCAT-TATATT
* **
1623021 TTTTATTATTTTATTTATACTATTTATTATTTTCATTATATT
1 TTTTATTATATTATACATACTATTTATTATTTTCATTATATT
1623063 TTT
1 TTT
1623066 AGTTTCTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 26 0.67
43 12 0.31
44 1 0.03
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (42 bp):
TTTTATTATATTATACATACTATTTATTATTTTCATTATATT
Found at i:1623178 original size:20 final size:19
Alignment explanation
Indices: 1623151--1623206 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1623141 TTTTATCTTC
1623151 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
1623170 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
1623190 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
1623207 ATTATTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:1624078 original size:27 final size:27
Alignment explanation
Indices: 1624040--1624095 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1624030 AGAGAGGGGC
1624040 TACTTTATTCATAATATTTAACTATTA
1 TACTTTATTCATAATATTTAACTATTA
1624067 TACTTTATTCATAATATTTAACTATTA
1 TACTTTATTCATAATATTTAACTATTA
1624094 TA
1 TA
1624096 ATATTGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.52
Consensus pattern (27 bp):
TACTTTATTCATAATATTTAACTATTA
Found at i:1624098 original size:16 final size:16
Alignment explanation
Indices: 1624045--1624100 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
1624035 GGGGCTACTT
1624045 TATTCATAATATTTAAC
1 TATT-ATAATATTTAAC
*
1624062 TATTAT-A-CTTT-A-
1 TATTATAATATTTAAC
*
1624074 T-TCATAATATTTAAC
1 TATTATAATATTTAAC
1624089 TATTATAATATT
1 TATTATAATATT
1624101 GATTTTACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 11
0.67 0.09 0.24
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 4 0.13
14 4 0.13
15 2 0.07
16 11 0.37
17 4 0.13
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTATAATATTTAAC
Found at i:1624320 original size:16 final size:19
Alignment explanation
Indices: 1624294--1624332 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
1624284 ATTCGTTCCA
1624294 AAAATTAACAAAA-AAAG-
1 AAAATTAACAAAAGAAAGT
1624311 AAAA-TAACAAAAGAAAGT
1 AAAATTAACAAAAGAAAGT
1624329 AAAA
1 AAAA
1624333 ATAAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 8 0.40
18 4 0.20
ACGTcount: A:0.77, C:0.05, G:0.08, T:0.10
Consensus pattern (19 bp):
AAAATTAACAAAAGAAAGT
Found at i:1624335 original size:19 final size:17
Alignment explanation
Indices: 1624293--1624358 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
1624283 TATTCGTTCC
1624293 AAAAATTAACAAAAAAAG
1 AAAAA-TAACAAAAAAAG
1624311 -AAAATAACAAAAGAAAG
1 AAAAATAACAAAA-AAAG
* *
1624328 TAAAAATAA-AATAAAAT
1 -AAAAATAACAAAAAAAG
1624345 AAAAA-AACCAAAAA
1 AAAAATAA-CAAAAA
1624359 TCAGACTCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
15 2 0.05
16 13 0.32
17 15 0.38
18 3 0.08
19 7 0.17
ACGTcount: A:0.79, C:0.06, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAAATAACAAAAAAAG
Found at i:1628518 original size:49 final size:50
Alignment explanation
Indices: 1628440--1628576 Score: 136
Period size: 52 Copynumber: 2.7 Consensus size: 50
1628430 GTTAGATATA
* * * * *
1628440 GGGTTACAGAAGATGAATAGAAATGGAAGAAGAAGATGATGAATA-TTATCGGTT
1 GGGTTAGAGAAGATGAACAG-AA--GAAGAAGATGATGATGAACAGTCA--GGTT
*
1628494 AGGGTTAGAGAAGATGTACAGAAGAAGAAGATGATGATGAACAGTCAAGGTT
1 -GGGTTAGAGAAGATGAACAGAAGAAGAAGATGATGATGAACAGTC-AGGTT
1628546 GGGTTAGAGAAGATGAACAG-AG-AGAAGATGA
1 GGGTTAGAGAAGATGAACAGAAGAAGAAGATGA
1628577 AGAGGCTCGG
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
49 9 0.12
50 2 0.03
51 19 0.26
52 22 0.30
53 1 0.01
54 3 0.04
55 17 0.23
ACGTcount: A:0.43, C:0.04, G:0.33, T:0.20
Consensus pattern (50 bp):
GGGTTAGAGAAGATGAACAGAAGAAGAAGATGATGATGAACAGTCAGGTT
Found at i:1628524 original size:55 final size:55
Alignment explanation
Indices: 1628438--1628579 Score: 134
Period size: 55 Copynumber: 2.6 Consensus size: 55
1628428 TGGTTAGATA
* * * * * *
1628438 TAGGGTTACAGAAGATGAATAGAA-ATGGAAGAAGAAGATGATGAATA-TTATCGGT
1 TAGGGTTAGAGAAGATGAACAGAAGA-AGAAGAAGAAGATGATGAACAGTCA-AGGT
* *
1628493 TAGGGTTAGAGAAGATGTAC---AGAAGAAGAAGATGATGATGAACAGTCAAGGT
1 TAGGGTTAGAGAAGATGAACAGAAGAAGAAGAAGAAGATGATGAACAGTCAAGGT
*
1628545 T-GGGTTAGAGAAGATGAACAGAGAGAAGATGAAGA
1 TAGGGTTAGAGAAGATGAACAGA-AGAAGAAGAAGA
1628580 GGCTCGGTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
51 17 0.24
52 23 0.32
53 3 0.04
55 28 0.39
ACGTcount: A:0.44, C:0.04, G:0.32, T:0.20
Consensus pattern (55 bp):
TAGGGTTAGAGAAGATGAACAGAAGAAGAAGAAGAAGATGATGAACAGTCAAGGT
Found at i:1628698 original size:53 final size:51
Alignment explanation
Indices: 1628544--1628704 Score: 184
Period size: 51 Copynumber: 3.1 Consensus size: 51
1628534 ACAGTCAAGG
* *
1628544 TTGGGTTAGAGAAGATGAACAGAG-AG-AAGATGAAGAGGCTCGGTTTGGGT
1 TTGGGTTAGAGAAGATGAACAGAGAAGAAAG-TGAAGAGGCTAGGTTAGGGT
* *
1628594 TTGAGGTTAGAGAAGATGAACAAAGAA-AAAATGAAGAGGCTAGGTTAGGGT
1 TTG-GGTTAGAGAAGATGAACAGAGAAGAAAGTGAAGAGGCTAGGTTAGGGT
* * * *
1628645 TTGGGATTAGAGAAGATAAATAGAGATAGAAAGTGAAGAGACTTGGTTAGGGT
1 TTGGG-TTAGAGAAGATGAACAGAGA-AGAAAGTGAAGAGGCTAGGTTAGGGT
*
1628698 TTAGGTT
1 TTGGGTT
1628705 TGGCCCACGT
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
50 5 0.05
51 58 0.62
52 6 0.06
53 25 0.27
ACGTcount: A:0.37, C:0.04, G:0.35, T:0.24
Consensus pattern (51 bp):
TTGGGTTAGAGAAGATGAACAGAGAAGAAAGTGAAGAGGCTAGGTTAGGGT
Found at i:1628988 original size:33 final size:32
Alignment explanation
Indices: 1628951--1629056 Score: 78
Period size: 33 Copynumber: 3.2 Consensus size: 32
1628941 TCAATTAATA
1628951 TATATATTTATATTAATAAATTAATATATAGTT
1 TATATA-TTATATTAATAAATTAATATATAGTT
* *
1628984 TATATA-TACTAATGAACTATA-TAATATATA-TT
1 TATATATTA-T-ATTAA-TAAATTAATATATAGTT
*
1629016 T-TATA-TATACTAATGAACATTATAATATATAGTT
1 TATATATTATATTAAT-AA-A-T-TAATATATAGTT
1629050 TATATAT
1 TATATAT
1629057 ACCAATAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 19
0.70 0.06 0.23
Matches are distributed among these distances:
28 1 0.02
29 4 0.07
30 2 0.04
31 8 0.14
32 4 0.07
33 28 0.49
34 6 0.11
35 4 0.07
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (32 bp):
TATATATTATATTAATAAATTAATATATAGTT
Found at i:1629004 original size:26 final size:24
Alignment explanation
Indices: 1628950--1629015 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 24
1628940 TTCAATTAAT
*
1628950 ATATATATTTATATTAATAAATTA
1 ATATATATTTATATTAATAAATGA
*
1628974 ATATATAGTTTATATATACT-AATGA
1 ATATATA-TTTATAT-TAATAAATGA
*
1628999 ACTATATAATATATATT
1 A-TATAT-ATTTATATT
1629016 TTATATATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
24 7 0.20
25 13 0.37
26 14 0.40
27 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (24 bp):
ATATATATTTATATTAATAAATGA
Found at i:1629057 original size:33 final size:34
Alignment explanation
Indices: 1628972--1629105 Score: 197
Period size: 33 Copynumber: 4.1 Consensus size: 34
1628962 ATTAATAAAT
1628972 TAATATATAGTTTATATATACTAATGAAC-TATA
1 TAATATATAGTTTATATATACTAATGAACATATA
*
1629005 TAATATATATTTTATATATACTAATGAACAT-TA
1 TAATATATAGTTTATATATACTAATGAACATATA
*
1629038 TAATATATAGTTTATATATACCAAT-AA-ATTATA
1 TAATATATAGTTTATATATACTAATGAACA-TATA
*
1629071 TAATATATAGTTTATTTATACTAATGAAC-TATA
1 TAATATATAGTTTATATATACTAATGAACATATA
1629104 TA
1 TA
1629106 GTTTATTAAT
Statistics
Matches: 91, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
31 1 0.01
32 3 0.03
33 84 0.92
34 3 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (34 bp):
TAATATATAGTTTATATATACTAATGAACATATA
Found at i:1629193 original size:2 final size:2
Alignment explanation
Indices: 1629183--1629223 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1629173 ATACAAAAAC
1629183 TA TA T- 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
1629224 AACCATATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1629284 original size:37 final size:35
Alignment explanation
Indices: 1629235--1629308 Score: 85
Period size: 37 Copynumber: 2.1 Consensus size: 35
1629225 ACCATATAAA
* * * * *
1629235 ATGTAGTTTATATATAGTTTTTGTATTAATAAACT
1 ATGTAGTTTATATAAACTATATATATTAATAAACT
1629270 ATGTAGTGTATATATAAACTATATATATTAATAAACT
1 ATGTAGT-T-TATATAAACTATATATATTAATAAACT
1629307 AT
1 AT
1629309 AAACTATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 7 0.22
36 1 0.03
37 24 0.75
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (35 bp):
ATGTAGTTTATATAAACTATATATATTAATAAACT
Found at i:1629352 original size:11 final size:11
Alignment explanation
Indices: 1629336--1629385 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
1629326 TTAATAAACC
1629336 ATATAGTTTAT
1 ATATAGTTTAT
*
1629347 ATATAGTATAT
1 ATATAGTTTAT
1629358 AATATAGTTTAT
1 -ATATAGTTTAT
*
1629370 ATATAGTTCAT
1 ATATAGTTTAT
1629381 ATATA
1 ATATA
1629386 CACTACATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (11 bp):
ATATAGTTTAT
Found at i:1629366 original size:23 final size:23
Alignment explanation
Indices: 1629308--1629376 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
1629298 TAATAAACTA
* *
1629308 TAAACTATATAGTTTATAT-TAA
1 TAAACAATATAGTTTATATATAG
*
1629330 TAAACCATATAGTTTATATATAG
1 TAAACAATATAGTTTATATATAG
* *
1629353 TATATAATATAGTTTATATATAG
1 TAAACAATATAGTTTATATATAG
1629376 T
1 T
1629377 TCATATATAC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 18 0.44
23 23 0.56
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (23 bp):
TAAACAATATAGTTTATATATAG
Found at i:1629444 original size:2 final size:2
Alignment explanation
Indices: 1629439--1629483 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
1629429 CTATATAGTT
*
1629439 TA TA TA TA T- TA TA T- TA -A TA TA TA CTT 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
1629479 TA TA T
1 TA TA T
1629484 TAATAAACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.89
3 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1629461 original size:17 final size:17
Alignment explanation
Indices: 1629439--1629488 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
1629429 CTATATAGTT
1629439 TATATATATTATATTAA
1 TATATATATTATATTAA
1629456 TATATACT-TTATA-T-A
1 TATATA-TATTATATTAA
1629471 TATATATA-TATATTAA
1 TATATATATTATATTAA
1629487 TA
1 TA
1629489 AACCATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
14 5 0.17
15 8 0.28
16 4 0.14
17 11 0.38
18 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATTATATTAA
Found at i:1629497 original size:265 final size:267
Alignment explanation
Indices: 1629183--1629755 Score: 1082
Period size: 265 Copynumber: 2.2 Consensus size: 267
1629173 ATACAAAAAC
*
1629183 TATATT-ATATATA-TATATATATATATATATATATATATATAAACCATATAAAATGTAGTTTAT
1 TATATTAATATATACTTTATATATATATATATATATATATATAAACCATATAAAATGTAGTTTAT
1629246 ATATAGTTTTTGTATTAATAAACTATGTAGTGTATATATAAACTATATATATTAATAAACTATAA
66 ATATAGTTTTTGTATTAATAAACTATGTAGTGTATATATAAACTATATATATTAATAAACTATAA
*
1629311 ACTATATAGTTTATATTAATAAACCATATAGTTTATATATAGTATATAATATAGTTTATATATAG
131 AATATATAGTTTATATTAATAAACCATATAGTTTATATATAGTATATAATATAGTTTATATATAG
*
1629376 TTCATATATACACTACATAGTTTATATACAATGTATAAAATTATAAATATAAACTATATAGTTTA
196 TTCATATATACACTACATAGTTTATATACAATATATAAAATTATAAATATAAACTATATAGTTTA
*
1629441 TATATAT
261 TACATAT
1629448 TATATTAATATATACTTTATATATATATATATATAT-TA-ATAAACCATATAAAATGTAGTTTAT
1 TATATTAATATATACTTTATATATATATATATATATATATATAAACCATATAAAATGTAGTTTAT
1629511 ATATAGTTTTTGTATTAATAAACTATGTAGTGTATATATAAACTATATATATTAATAAACTATAA
66 ATATAGTTTTTGTATTAATAAACTATGTAGTGTATATATAAACTATATATATTAATAAACTATAA
1629576 AATATATAGTTTATATTAATAAACCATATAGTTTATATATAGTATATAATATAGTTTATATATAG
131 AATATATAGTTTATATTAATAAACCATATAGTTTATATATAGTATATAATATAGTTTATATATAG
1629641 TTCATATATACACTACATAGTTTATATACAATATATAAAATTATAAATATAAACTATATAGTTTA
196 TTCATATATACACTACATAGTTTATATACAATATATAAAATTATAAATATAAACTATATAGTTTA
1629706 TACATAT
261 TACATAT
1629713 TATATTAATATATACTTTATATATATATATATATATATATATA
1 TATATTAATATATACTTTATATATATATATATATATATATATA
1629756 TATATATAAT
Statistics
Matches: 300, Mismatches: 4, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
265 266 0.89
266 11 0.04
267 23 0.08
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (267 bp):
TATATTAATATATACTTTATATATATATATATATATATATATAAACCATATAAAATGTAGTTTAT
ATATAGTTTTTGTATTAATAAACTATGTAGTGTATATATAAACTATATATATTAATAAACTATAA
AATATATAGTTTATATTAATAAACCATATAGTTTATATATAGTATATAATATAGTTTATATATAG
TTCATATATACACTACATAGTTTATATACAATATATAAAATTATAAATATAAACTATATAGTTTA
TACATAT
Found at i:1629549 original size:37 final size:35
Alignment explanation
Indices: 1629500--1629573 Score: 85
Period size: 37 Copynumber: 2.1 Consensus size: 35
1629490 ACCATATAAA
* * * * *
1629500 ATGTAGTTTATATATAGTTTTTGTATTAATAAACT
1 ATGTAGTTTATATAAACTATATATATTAATAAACT
1629535 ATGTAGTGTATATATAAACTATATATATTAATAAACT
1 ATGTAGT-T-TATATAAACTATATATATTAATAAACT
1629572 AT
1 AT
1629574 AAAATATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 7 0.22
36 1 0.03
37 24 0.75
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (35 bp):
ATGTAGTTTATATAAACTATATATATTAATAAACT
Found at i:1629616 original size:2 final size:2
Alignment explanation
Indices: 1629609--1629763 Score: 74
Period size: 2 Copynumber: 77.0 Consensus size: 2
1629599 CCATATAGTT
*
1629609 TA TA TA TA GTA TA TA -A TA TA GTT TA TA TA TA GT- TCA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA -TA T-A TA TA TA
* * * * * *
1629651 CA CTA CA TA GTT TA TA TA CA -A TA TA TA -A AA T- TA TA AA TA TA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1629692 AA CTA TA TA GTT TA TA CA TA T- TA TA T- TA -A TA TA TA CTT TA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
1629732 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
1629764 ATTGTTTTAA
Statistics
Matches: 116, Mismatches: 20, Indels: 34
0.68 0.12 0.20
Matches are distributed among these distances:
1 8 0.07
2 98 0.84
3 10 0.09
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1629617 original size:11 final size:11
Alignment explanation
Indices: 1629601--1629650 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
1629591 TTAATAAACC
1629601 ATATAGTTTAT
1 ATATAGTTTAT
*
1629612 ATATAGTATAT
1 ATATAGTTTAT
1629623 AATATAGTTTAT
1 -ATATAGTTTAT
*
1629635 ATATAGTTCAT
1 ATATAGTTTAT
1629646 ATATA
1 ATATA
1629651 CACTACATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (11 bp):
ATATAGTTTAT
Found at i:1629631 original size:23 final size:23
Alignment explanation
Indices: 1629579--1629641 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1629569 ACTATAAAAT
* *
1629579 ATATAGTTTATAT-TAATAAACC
1 ATATAGTTTATATATAGTAAACA
* *
1629601 ATATAGTTTATATATAGTATATA
1 ATATAGTTTATATATAGTAAACA
1629624 ATATAGTTTATATATAGT
1 ATATAGTTTATATATAGT
1629642 TCATATATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 13 0.36
23 23 0.64
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (23 bp):
ATATAGTTTATATATAGTAAACA
Found at i:1629691 original size:54 final size:56
Alignment explanation
Indices: 1629575--1629691 Score: 123
Period size: 54 Copynumber: 2.1 Consensus size: 56
1629565 ATAAACTATA
* * * * *
1629575 AAATATATAGTTTATATTAATAAACCATATAGTTTATATATAGTATATAATATAGT
1 AAATATATAGTTCATATTAATAAACCACATAGTTTATATACAATATATAAAATAGT
** * *
1629631 TTATATATAGTTCATA-T-ATACACTACATAGTTTATATACAATATATAAAATTA-T
1 AAATATATAGTTCATATTAATAAACCACATAGTTTATATACAATATATAAAA-TAGT
1629685 AAATATA
1 AAATATA
1629692 AACTATATAG
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
54 33 0.67
55 3 0.06
56 13 0.27
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (56 bp):
AAATATATAGTTCATATTAATAAACCACATAGTTTATATACAATATATAAAATAGT
Found at i:1633737 original size:18 final size:18
Alignment explanation
Indices: 1633716--1633800 Score: 57
Period size: 18 Copynumber: 4.6 Consensus size: 18
1633706 AAATTTAAAT
1633716 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATTA
* **
1633734 TTAAAATTAAAATTATTA
1 TTAAATTTATTATTATTA
*
1633752 TTAATAGTGTTATTAATATTA
1 TTAA-A-T-TTATTATTATTA
* *
1633773 AT-AATATA-TATTATTTA
1 TTAAATTTATTATTA-TTA
1633790 TTAAATATTAT
1 TTAAAT-TTAT
1633801 AAGCCCAAGA
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
16 4 0.08
17 6 0.12
18 23 0.48
19 4 0.08
20 1 0.02
21 10 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TTAAATTTATTATTATTA
Found at i:1635213 original size:28 final size:27
Alignment explanation
Indices: 1635174--1635264 Score: 67
Period size: 28 Copynumber: 3.1 Consensus size: 27
1635164 ACTTTTTTAA
*
1635174 ATTTATTGTTATAATTTTAATTATTTT
1 ATTTATTATTATAATTTTAATTATTTT
**
1635201 ATTTGATTATTATCTAATTACAAATTTATTTT
1 ATTT-ATTATTA--TAATT-TTAA-TTATTTT
* *
1635233 ATTTCTATTATTAT-ACTTTAATTATTAT
1 A-TT-TATTATTATAATTTTAATTATTTT
1635261 ATTT
1 ATTT
1635265 CATTTCATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
26 1 0.02
27 6 0.12
28 13 0.26
29 2 0.04
30 7 0.14
31 3 0.06
32 8 0.16
33 9 0.18
34 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (27 bp):
ATTTATTATTATAATTTTAATTATTTT
Found at i:1640107 original size:14 final size:14
Alignment explanation
Indices: 1640069--1640101 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1640059 TCAAAATGAT
1640069 ATAATAATA-ATAA
1 ATAATAATATATAA
1640082 ATAATAATATATAA
1 ATAATAATATATAA
1640096 ATAATA
1 ATAATA
1640102 GAATATTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAATATATAA
Found at i:1649670 original size:60 final size:61
Alignment explanation
Indices: 1649560--1649675 Score: 198
Period size: 60 Copynumber: 1.9 Consensus size: 61
1649550 TAGAAATGTA
1649560 TTACTTTGAATCCTAAACTACTGGAAACACTAAACAAAGATCAAATAGATGAGTTACTAAC
1 TTACTTTGAATCCTAAACTACTGGAAACACTAAACAAAGATCAAATAGATGAGTTACTAAC
* * *
1649621 TTACTTTGAATCCTAAGCTACT-GAAACACTAGACAATGATCAAATAGATGAGTTA
1 TTACTTTGAATCCTAAACTACTGGAAACACTAAACAAAGATCAAATAGATGAGTTA
1649676 TTGACTTGCT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 31 0.60
61 21 0.40
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (61 bp):
TTACTTTGAATCCTAAACTACTGGAAACACTAAACAAAGATCAAATAGATGAGTTACTAAC
Found at i:1651581 original size:20 final size:20
Alignment explanation
Indices: 1651556--1651609 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
1651546 AGTTTGAAGG
1651556 TAAGTAAACACAATTACACA
1 TAAGTAAACACAATTACACA
1651576 TAAGTAAACACAATTACACA
1 TAAGTAAACACAATTACACA
1651596 TAAGTAAACACAAT
1 TAAGTAAACACAAT
1651610 ATATAAATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.20
Consensus pattern (20 bp):
TAAGTAAACACAATTACACA
Found at i:1656084 original size:29 final size:29
Alignment explanation
Indices: 1655990--1656088 Score: 78
Period size: 29 Copynumber: 3.3 Consensus size: 29
1655980 ATATATATTT
1655990 AGTTTG-GGATAAAATTGAAATGTTCAAAA
1 AGTTTGAGGATAAAATTGAAATGTTC-AAA
* ** * *
1656019 AGTTTGGGGA-CCAATTGAGAATAAAGGTC-AT
1 AGTTTGAGGATAAAATTGA-AAT---GTTCAAA
*
1656050 AGTTTGAGGATGAAATTGAAATGTTCAAA
1 AGTTTGAGGATAAAATTGAAATGTTCAAA
1656079 AGTTTGAGGA
1 AGTTTGAGGA
1656089 CTAATTTAGA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
28 3 0.06
29 23 0.43
30 6 0.11
31 13 0.24
32 6 0.11
33 3 0.06
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.29
Consensus pattern (29 bp):
AGTTTGAGGATAAAATTGAAATGTTCAAA
Found at i:1656113 original size:60 final size:60
Alignment explanation
Indices: 1655989--1656156 Score: 205
Period size: 60 Copynumber: 2.8 Consensus size: 60
1655979 TATATATATT
* * *
1655989 TAGTTTG-GGATAAAATTGAAATGTTCAAAAAGTTTGGGGACCAATTGAGAATAAAGGTCA
1 TAGTTTGAGGATGAAATTGAAATGTTC-AAAAGTTTGGGGACTAATTTAGAATAAAGGTCA
* * * *
1656049 TAGTTTGAGGATGAAATTGAAATGTTCAAAAGTTTGAGGACTAATTTAGATTGATA-GTCG
1 TAGTTTGAGGATGAAATTGAAATGTTCAAAAGTTTGGGGACTAATTTAGAAT-AAAGGTCA
* ** *
1656109 TAGTTTAAGGATGAAATTGAAACATTTAAAAGTTTGGGGACTAATTTA
1 TAGTTTGAGGATGAAATTGAAATGTTCAAAAGTTTGGGGACTAATTTA
1656157 AAATGGGGTC
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
60 74 0.79
61 20 0.21
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (60 bp):
TAGTTTGAGGATGAAATTGAAATGTTCAAAAGTTTGGGGACTAATTTAGAATAAAGGTCA
Found at i:1658873 original size:17 final size:18
Alignment explanation
Indices: 1658853--1658891 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1658843 GATACAAAGC
1658853 AAAC-GAATTTACATT-AG
1 AAACTGAATTTA-ATTGAG
1658870 AAACTGAATTTAATTGAG
1 AAACTGAATTTAATTGAG
1658888 AAAC
1 AAAC
1658892 CAACTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (18 bp):
AAACTGAATTTAATTGAG
Found at i:1664772 original size:38 final size:39
Alignment explanation
Indices: 1664730--1664842 Score: 169
Period size: 38 Copynumber: 3.0 Consensus size: 39
1664720 CTTCTAAAAG
*
1664730 AGTC-ATTAAACAAGTTTGTTCATGAACATAAACGAACA
1 AGTCAATTAAACGAGTTTGTTCATGAACATAAACGAACA
*
1664768 AGTCAATT-AACGAGCTTGTTCATGAACATAAACGAACA
1 AGTCAATTAAACGAGTTTGTTCATGAACATAAACGAACA
* *
1664806 AGTCGA-TAAACGAGTTTGTTCGTGAACATAAACGAAC
1 AGTCAATTAAACGAGTTTGTTCATGAACATAAACGAAC
1664843 CAAACACTCC
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
37 1 0.01
38 64 0.94
39 3 0.04
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (39 bp):
AGTCAATTAAACGAGTTTGTTCATGAACATAAACGAACA
Found at i:1668626 original size:29 final size:29
Alignment explanation
Indices: 1668594--1668652 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1668584 CCTAAATTAA
1668594 TTTGATCTCATTGCTCACATCAATTTAGT
1 TTTGATCTCATTGCTCACATCAATTTAGT
* *
1668623 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATCTCATTGCTCACATCAATTTAGT
1668652 T
1 T
1668653 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (29 bp):
TTTGATCTCATTGCTCACATCAATTTAGT
Found at i:1673285 original size:29 final size:29
Alignment explanation
Indices: 1673251--1673309 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1673241 CCTAAATTAA
1673251 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1673280 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1673309 T
1 T
1673310 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1673783 original size:29 final size:29
Alignment explanation
Indices: 1673710--1673769 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1673700 ATTTTCACCT
*
1673710 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
1673739 AACTAAATTAATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
1673768 AA
1 AA
1673770 TAATTTAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.23
Consensus pattern (29 bp):
AACTAAATTAATGTAAGCAATGACATCAA
Found at i:1680520 original size:24 final size:20
Alignment explanation
Indices: 1680470--1680507 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1680460 TTCCCATTAA
*
1680470 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1680490 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
1680508 TTAACAGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1684644 original size:20 final size:20
Alignment explanation
Indices: 1684619--1684676 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
1684609 TTCCCATTGA
*
1684619 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
1684639 AGTGCATTGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1684662 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
1684677 CTACCATGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1687974 original size:195 final size:194
Alignment explanation
Indices: 1687618--1688075 Score: 524
Period size: 195 Copynumber: 2.4 Consensus size: 194
1687608 GCTTATATTA
* * * * * *
1687618 ACCTATTTTCTCATAAAACC-GTAAATTTAAACC-GTTACATTATAAATTGACCTATTACATTAT
1 ACCTATTCTCTCAT-GAACCGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTAT
* * *
1687681 GTATATCGGTTTCGATGTTTTCAGTATCGATACAATTTTAAATGTATCGACACTTATGCGTGCAA
65 AT-TATCGATTTCGATGTTTTCAGTATCGATACAATTTTAAATGTATCGACACTTATGCGTACAA
* * * * *
1687746 CTCGTTTGTGCTTTATTTTGGAAAAAAGTATCGACACATATTTAAAGAGTGTCGATACATAATGT
129 CTCGTTTGTGCTTCATTTTGGAAAAAAGTATCGACACAAATTAAAAAAGTATCGATAC-TAATGT
1687811 AG
193 AG
* * *
1687813 ACCTATT-TGCT-ATTAACCGGTATATTTTAACCGGTTACATTGTAAATTTACCTGTTACATAAT
1 ACCTATTCT-CTCATGAACCGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTAT
*
1687876 AATTATCGATTTCGATG-TTTCGAG-ATCGATAC-TTTTTACAAATGTATCGACACTTTATGCGT
65 -ATTATCGATTTCGATGTTTTC-AGTATCGATACAATTTT--AAATGTATCGACAC-TTATGCGT
* * * *
1687938 ACACCTCGTTT-TTCATTCATTTT-GAAAAATGTATCGACACAAATTAAAAAAGTATCGATACTT
125 ACAACTCGTTTGTGC-TTCATTTTGGAAAAAAGTATCGACACAAATTAAAAAAGTATCGATACTA
*
1688001 ATGTTG
189 ATGTAG
1688007 ACCTATTCTCTCATGAACCCGGTATATTTCT-ACCGGTTACATTG-AAATTTACCTATTACATTA
1 ACCTATTCTCTCATGAA-CCGGTATATTT-TAACCGGTTACATTGTAAATTTACCTATTACATTA
1688070 TATTAT
64 TATTAT
1688076 GGGTCTCTTT
Statistics
Matches: 226, Mismatches: 24, Indels: 27
0.82 0.09 0.10
Matches are distributed among these distances:
193 8 0.04
194 46 0.20
195 122 0.54
196 49 0.22
197 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.39
Consensus pattern (194 bp):
ACCTATTCTCTCATGAACCGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATA
TTATCGATTTCGATGTTTTCAGTATCGATACAATTTTAAATGTATCGACACTTATGCGTACAACT
CGTTTGTGCTTCATTTTGGAAAAAAGTATCGACACAAATTAAAAAAGTATCGATACTAATGTAG
Found at i:1693089 original size:15 final size:15
Alignment explanation
Indices: 1693069--1693121 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
1693059 TAATTTCCTC
*
1693069 AGAAGAGCTAGGTTG
1 AGAAGAGCTGGGTTG
*
1693084 AGAAGAGGTGGGTTG
1 AGAAGAGCTGGGTTG
* *
1693099 AGAATAGATGGGTTG
1 AGAAGAGCTGGGTTG
1693114 AGAAGAGC
1 AGAAGAGC
1693122 CCCGATTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.34, C:0.04, G:0.43, T:0.19
Consensus pattern (15 bp):
AGAAGAGCTGGGTTG
Found at i:1693840 original size:195 final size:196
Alignment explanation
Indices: 1693598--1694202 Score: 918
Period size: 198 Copynumber: 3.1 Consensus size: 196
1693588 CCATTTACAT
* * *
1693598 TGGACAAAAAGTATCGATACAAATTCAAAAAGTGTCGATATTTCATGTACACCTGTTTTCTCATA
1 TGGACACAAAGTATCGACACAAATTCAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATA
*
1693663 AACCGGTGTATTTAGACTGGTTAGATTGATAATTTACCTATT-ATTATAATTATGGGTCTCGATG
66 AACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATTAATTATAATTATGGGTCTCGATG
* *
1693727 TTTTTGGATCGATACTTTTTATAAATGTATCGAAACCTTATGGTGACCTTGGTAAGGAAATCATT
131 TTTTTGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
1693792 C
196 C
*
1693793 TGGACACAAAGTATCGACACAAATTCAAAGAGTGTCGATACTTCATGTACACCTGTTTTCTCATA
1 TGGACACAAAGTATCGACACAAATTCAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATA
*
1693858 AACCGGTGTAATTAGACCGGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTCGAT
66 AACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATTA-ATTATAATTATGGGTCTCGAT
*
1693923 GTTTTTTGGATCGATACTTTTTATAGATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCA
130 G-TTTTTGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCA
*
1693988 TTG
194 TTC
* *
1693991 TGGACACAAAGTATGGGATCGACACAATT-AAAAAGTGTCGATACTTTATGTACACCTGTTTTCT
1 TGGACACAAAGTAT-CGA-C-ACA-AATTCAAAAAGTGTCGATACTTCATGTACACCTGTTTTCT
1694055 CATAAACC-G-GTATTTAGACCGGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTCT
62 CATAAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATTA-ATTATAATTATGGGTCT
* ** *
1694118 TGATGTTTTTGGGATCGATAC-TTTTATAAATGTATCGACACATT-TCCATG-CACTTGGGAAGG
126 CGATGTTTTT-GGATCGATACTTTTTATAAATGTATCGACACATTAT-GGTGAC-CTTGGTAAGG
*
1694180 ACATCATTC
188 AAATCATTC
1694189 TGGACACAAAGTAT
1 TGGACACAAAGTAT
1694203 ACTTGGACAA
Statistics
Matches: 379, Mismatches: 21, Indels: 17
0.91 0.05 0.04
Matches are distributed among these distances:
195 101 0.27
197 24 0.06
198 135 0.36
199 69 0.18
200 2 0.01
201 44 0.12
202 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (196 bp):
TGGACACAAAGTATCGACACAAATTCAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATA
AACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATTAATTATAATTATGGGTCTCGATG
TTTTTGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
C
Found at i:1694512 original size:19 final size:19
Alignment explanation
Indices: 1694474--1694521 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1694464 TTACATTCAC
1694474 ATACAAAATT--AAATCGT
1 ATACAAAATTAAAAATCGT
*
1694491 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCGT
1694510 ATACAAAATTAA
1 ATACAAAATTAA
1694522 CCCTACATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 10 0.36
19 18 0.64
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.29
Consensus pattern (19 bp):
ATACAAAATTAAAAATCGT
Found at i:1695993 original size:18 final size:17
Alignment explanation
Indices: 1695970--1696007 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
1695960 TTCTCTTCAT
1695970 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTC-TC
1695988 TTCCTCCATCTTTTCTC
1 TTCCTCCATCTTTTCTC
1696005 TTC
1 TTC
1696008 AAATTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.55
Consensus pattern (17 bp):
TTCCTCCATCTTTTCTC
Found at i:1696379 original size:15 final size:15
Alignment explanation
Indices: 1696359--1696388 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1696349 CCTCTGTTTT
1696359 CCCTGACCGTAATCC
1 CCCTGACCGTAATCC
*
1696374 CCCTGACCGTCATCC
1 CCCTGACCGTAATCC
1696389 ACATCCAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.50, G:0.13, T:0.20
Consensus pattern (15 bp):
CCCTGACCGTAATCC
Found at i:1696465 original size:16 final size:17
Alignment explanation
Indices: 1696434--1696469 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1696424 CTCTCTTCAT
1696434 TTCCTCCATCTTTCTTC
1 TTCCTCCATCTTTCTTC
1696451 TTCCTCCAT-TTTCTTC
1 TTCCTCCATCTTTCTTC
1696467 TTC
1 TTC
1696470 AAATTTTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.56
Consensus pattern (17 bp):
TTCCTCCATCTTTCTTC
Found at i:1696736 original size:457 final size:459
Alignment explanation
Indices: 1695961--1696870 Score: 1479
Period size: 457 Copynumber: 2.0 Consensus size: 459
1695951 TGACATCCTT
1695961 TCTCTTCATTTCCTCCATCTTTTCTTCTTCCTCCATCTTTTCTCTTCAAATTTTCTCAGTTCATC
1 TCTCTTCATTTCCTCCATCTTTTCTTCTTCCTCCATCTTTTCTCTTCAAATTTTCTCAGTTCATC
* *
1696026 GATTTTTTCTCTACATATCTCTTCATCTCTTTTATTACCCTTCAATTTCTCCCTTCATCCAAGCT
66 GATTTTTTCTCTACATAGCTCTTCATCTCTTTTATTACCCTTCAATTTCCCCCTTCATCCAAGC-
*
1696091 TTTTCTGAACCACCTTCTTCACCCCCAAAAGTTCACATCCTTATTTCCATAACCTCCTTGACAAC
130 TTTTCTGAACCACC-TCTTCACCCCCAAAAGTTCACATCCTTATTTCCACAACCTCCTTGACAAC
1696156 TCCATCAATTTTTCCACCCGTCACAATATTAACTTCACCACTCAACACCTCAACTTTTTTCACCA
194 TCCATCAATTTTTCCACCCGTCACAATATTAACTTCACCACTCAACACCTCAACTTTTTTCACCA
*
1696221 ATACATCTATCTTTCCTTCCACTTCCATCTTATGCCTGTTCATGTGTCTCTTGACTCTTGATTGT
259 ATACATCTATCTTTCCTTCCACTTCCATCTTATGCCTGTTCATGTGTCTCTTGACTCTTGAATGT
*
1696286 CTTTAATGAATATCAAAAACGATTTTTTTA-ATCAGCCAATTCA-ACATCAAAATATCGAATTTA
324 CTTTAATGAATATCAAAAACGATTTTTTAATATCAGCCAATTCAGACATCAAAATATCGAATTTA
1696349 CCTCTGTTTTCCCTGACCGTAATCCCCCTGACCGTCATCCACATCCAACCATCTC-TCTTCCCTC
389 ---CTGTTTT-CC-GACCGTAATCCCCCTGACCGTCATCCACATCCAACCATCTCTTCTT-CCTC
1696413 TCCTGTACATCC
448 TCCTGTACATCC
1696425 TCTCTTCATTTCCTCCATC-TTTCTTCTTCCTCCA--TTTTCTTCTTCAAATTTTCTCAGTTCAT
1 TCTCTTCATTTCCTCCATCTTTTCTTCTTCCTCCATCTTTTC-TCTTCAAATTTTCTCAGTTCAT
1696487 CGTATTTTTTCTCTACATAGCTCTTCATCTCTTTT-TTCACCCTTCAATTTCCCCCTTTCATCCA
65 CG-ATTTTTTCTCTACATAGCTCTTCATCTCTTTTATT-ACCCTTCAATTTCCCCC-TTCATCCA
*
1696551 AG-TTTT-TGAACCACC-CTTCACCCCCGAAAGTTCAC-TCCTTATTTCCACAACCTCCTTG-CA
127 AGCTTTTCTGAACCACCTCTTCACCCCCAAAAGTTCACATCCTTATTTCCACAACCTCCTTGACA
1696611 ACTCCATCAATTTTTCCACCCGTCA-ACATATTAACTTCACCACTCAACACCTCAACTTTTTTCA
192 ACTCCATCAATTTTTCCACCCGTCACA-ATATTAACTTCACCACTCAACACCTCAACTTTTTTCA
*
1696675 CCAATACATCTATCTTTCCTTCCACTTCCATCTTATGCCT-TTTATGTGTCTCTTCGACTCTTGA
256 CCAATACATCTATCTTTCCTTCCACTTCCATCTTATGCCTGTTCATGTGTCTCTT-GACTCTTGA
* * *
1696739 ATGTCTTTGATGAATATCCAAAACGATTTTTTAATATCAGCCAATTCAGACATCAAAATGTCGAA
320 ATGTCTTTAATGAATATCAAAAACGATTTTTTAATATCAGCCAATTCAGACATCAAAATATCGAA
* * *
1696804 TTTACTGTTTTCCGACCGTAATCCCCCTTACCGTCATCCCCCTCCAACCATCTCTTCTTCCTCTC
385 TTTACTGTTTTCCGACCGTAATCCCCCTGACCGTCATCCACATCCAACCATCTCTTCTTCCTCTC
1696869 CT
450 CT
1696871 CTGCCTCCTC
Statistics
Matches: 424, Mismatches: 13, Indels: 28
0.91 0.03 0.06
Matches are distributed among these distances:
454 46 0.11
455 6 0.01
456 21 0.05
457 143 0.34
458 35 0.08
459 38 0.09
461 14 0.03
462 30 0.07
463 62 0.15
464 29 0.07
ACGTcount: A:0.22, C:0.33, G:0.05, T:0.39
Consensus pattern (459 bp):
TCTCTTCATTTCCTCCATCTTTTCTTCTTCCTCCATCTTTTCTCTTCAAATTTTCTCAGTTCATC
GATTTTTTCTCTACATAGCTCTTCATCTCTTTTATTACCCTTCAATTTCCCCCTTCATCCAAGCT
TTTCTGAACCACCTCTTCACCCCCAAAAGTTCACATCCTTATTTCCACAACCTCCTTGACAACTC
CATCAATTTTTCCACCCGTCACAATATTAACTTCACCACTCAACACCTCAACTTTTTTCACCAAT
ACATCTATCTTTCCTTCCACTTCCATCTTATGCCTGTTCATGTGTCTCTTGACTCTTGAATGTCT
TTAATGAATATCAAAAACGATTTTTTAATATCAGCCAATTCAGACATCAAAATATCGAATTTACT
GTTTTCCGACCGTAATCCCCCTGACCGTCATCCACATCCAACCATCTCTTCTTCCTCTCCTGTAC
ATCC
Found at i:1697128 original size:22 final size:24
Alignment explanation
Indices: 1697100--1697157 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1697090 AACCTGCATT
1697100 TATAATAAAAT-TA-ATCATTTTA
1 TATAATAAAATATACATCATTTTA
*
1697122 TATAAT-AACTATACCATCATTTTA
1 TATAATAAAATATA-CATCATTTTA
*
1697146 TATAAAAAAATA
1 TATAATAAAATA
1697158 AAAAACATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 3 0.10
22 8 0.28
24 14 0.48
25 4 0.14
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.40
Consensus pattern (24 bp):
TATAATAAAATATACATCATTTTA
Found at i:1699595 original size:182 final size:181
Alignment explanation
Indices: 1698939--1699580 Score: 816
Period size: 182 Copynumber: 3.6 Consensus size: 181
1698929 TATTAAGTAC
* * * ** * * *
1698939 CGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATA-C-GATTTTGTCAT
1 CGACACTTTCAATAT-ATCGGTAACTTTTTACCGATTTTATCATTTCGAAACCTG-TTTTGTCAT
* * * * *
1699002 ATT-TTACCT-AT-TATTGTTATGGATCGATACGTTTTCATAAAGTATCGACACTTTTTAGACGC
64 ATTATTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTTTAGGCGC
* *
1699064 --TAATTTATTCTC-TTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
129 TATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
* * *
1699114 CGACACTTTCAGTATATACGGTATCTTTTTACCGATTTTATCATTTCGAGACCTGTTTTGTCATA
1 CGACACTTTCAATATAT-CGGTAACTTTTTACCGATTTTATCATTTCGAAACCTGTTTTGTCATA
* * *
1699179 TTATTACATGTTATATTGCTATGGATCGATACATTTATATAAAGTATCGACACTTTTTAGGCGTT
65 TTATTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTTTAGGCGCT
* * *
1699244 ATTACTTCTTCTCTTTTAAATTACGAAAGTGTCTATACTTATATTAATGTAT
130 ATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
* * *
1699296 CGACACTTTCAATATATCCGGTAGCTTTTTATCGATTTTATCATTTCGAAACATGTTTTGTCATA
1 CGACACTTTCAATATAT-CGGTAACTTTTTACCGATTTTATCATTTCGAAACCTGTTTTGTCATA
* *
1699361 TTATTACTTGTTATATTGCTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCT
65 TTATTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTTTAGGCGCT
*
1699426 ATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTAT
130 ATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
* ** * * * * *
1699478 CGACACTTTCAATATATCTGATAACGGTTTACCGGTTTTATCATAAT-GACACCGGTTTTATCAT
1 CGACACTTTCAATATATC-GGTAACTTTTTACCGATTTTATCAT-TTCGAAACCTGTTTTGTCAT
*
1699542 ATTTTTACCTGTTATATTGCTATGGATCGATACATTTTT
64 ATTATTACCTGTTATATTGCTATGGATCGATACATTTTT
1699581 CATTTGTATC
Statistics
Matches: 407, Mismatches: 49, Indels: 15
0.86 0.10 0.03
Matches are distributed among these distances:
174 1 0.00
175 40 0.10
176 13 0.03
177 6 0.01
178 1 0.00
179 45 0.11
181 10 0.02
182 290 0.71
183 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (181 bp):
CGACACTTTCAATATATCGGTAACTTTTTACCGATTTTATCATTTCGAAACCTGTTTTGTCATAT
TATTACCTGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACACTTTTTAGGCGCTA
TAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTATATTAATTTAT
Found at i:1700012 original size:3 final size:3
Alignment explanation
Indices: 1700004--1700028 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1699994 ATCATTTTAT
1700004 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1700029 AACAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1706458 original size:34 final size:34
Alignment explanation
Indices: 1706361--1706458 Score: 160
Period size: 34 Copynumber: 2.9 Consensus size: 34
1706351 ACATAAAAAA
*
1706361 TTTATACATAGAATGAATATAAATAAAATAAAAT
1 TTTATACATAGAATGAATATAAATAAAATTAAAT
*
1706395 TTTATACATAGAACGAATATAAATAAAATTAAAT
1 TTTATACATAGAATGAATATAAATAAAATTAAAT
* *
1706429 TTTATACATATAATGAATATAAATTAAATT
1 TTTATACATAGAATGAATATAAATAAAATT
1706459 TAGATTCTAG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (34 bp):
TTTATACATAGAATGAATATAAATAAAATTAAAT
Found at i:1709240 original size:33 final size:33
Alignment explanation
Indices: 1709203--1709268 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1709193 CATCTTAATA
*
1709203 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1709236 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1709269 CTATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1709326 original size:21 final size:21
Alignment explanation
Indices: 1709301--1709365 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1709291 CCCCTTATGC
* *
1709301 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
1709322 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
1709343 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1709364 CT
1 CT
1709366 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1711617 original size:17 final size:18
Alignment explanation
Indices: 1711595--1711637 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1711585 ATATATCCGG
1711595 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1711612 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1711632 TATCAT
1 TATCAT
1711638 ATTTTTACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Done.