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 1 of 9
Found at i:22 original size:3 final size:3
Alignment explanation
Indices: 1--2353 Score: 2819
Period size: 3 Copynumber: 797.3 Consensus size: 3
1 CTT C-T CTT C-T CTCT CTT CTT CTT CTT CTT CTT CTT CTT C-T CTT
1 CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* *
44 C-T CTT -TT CTCT CTT CTT CTT C-T CTT CTT CTT CCT CTT CTT CCT
1 CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * *
87 CTT CTT CCT CTT CCT CTT CTCT CTT CTT C-T CTT CTT CCT CTT CCT
1 CTT CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT
132 CTT CTT CTTT CTT CTTT CTT CTT CTT CTCT CTCT CTT CCTT CTT CTT
1 CTT CTT C-TT CTT C-TT CTT CTT CTT CT-T CT-T CTT -CTT CTT CTT
*
179 CTT C-T CTT CTT -TCT CTT C-T CTT CTT CTT CTT CCT CTT CTT C-T
1 CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * *
221 CTT CCT CTT C-T CCT CTT C-T CTT C-T CTT CCT CTT CTT CCTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT
*
264 CTTT CTT CTTT CCT CTT CTT CTCT CTT CTT CTT CTT CTT CTT C-T CTT
1 C-TT CTT C-TT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT
* * *
311 CTTT CTT -TT C-T CTCT CTT -AT CTT CTT CCT CTT CTT CTT CTT CCT
1 C-TT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
355 CTT CTT CTT C-T CTT CTCT CTT CTT CTT C-T CTT CTT CTT CTT CCT
1 CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * *
399 C-T CTT CCT C-T CTT CCT CTT CTT CTT CCT CTT CCT CTT CCTT CTTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT C-TT
* * * * *
444 CTT C-T CTT CTT CCTT CCT CTT CCT CTT C-T CCT CTT CTT CCT ATT
1 CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* *
488 CTT CCT CTT CCTT C-T CTT CTT CTT CTT ATT CTT CTT CTT -TT CTT
1 CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * *
532 CTT CTT CTT C-T CTT CTT C-T CTT C-T CCT CTT CCT CTT CTT CCT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * *
577 CTT CCT CTT CTT CCT -TT CCT C-G CTT CTT CTT TTT CTT CTT CTTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT
* * *
621 CTT CTT CTT CCT C-T CTTT CTT CTT CCT CTT CTT C-T CTT CCT CTT
1 CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * * *
665 CTT CCT CTT C-T CTTT CCT CCT CTT C-T CCT CTT CCT C-T CTT CCT
1 CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * *
708 CTT CCT CTT CTT CCT CTT CTT CTT CTT C-T CTT CTT TTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
755 CTT C-T CTT C-T CTT CTT CTT CTT CTT CCT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
801 CTT -TT CTT CTT CTT CTT CTT CTT CTT CCTT CTCT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CT-T CTT CTT CTT CTT
* *
847 CTT CCT C-T CTT CTT CTT C-T CTT CCT CTT CTTT CTT CTTT CTT C-T
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT C-TT CTT CTT
* * * * * *
891 CTT CCT CTT CCT CTT CTT CCT CTT CCT CTT CTT CCT -TT CCT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * *
938 CTCT CTTT CTT CTT CTT CCT CTT CTT CCT CTT CTT CTT CCT CTT CTC
1 CT-T C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* *
985 CTT CCT CTT CTT CTT CCT CTT CCTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT
1031 CTTT CTT CTT CTT C-T CTT CTT CTT CTT C-T CTT CTT C-T CTT CTT
1 C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
1074 TTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -TT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1121 CTT CTT CTT -TT CTT -TT CTT CTT C-T CTTT CTT CTT CTT -TCT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CT-T CTT
1164 CTT -TT CTT CTTT CTT -TT -TT CTT CTT CTT CTT CTT C-T CTT CTT
1 CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
1206 CTT CTTT CTT CTT CTT CTCT CTT CTT CTT C-T ATT CTT C-T CTT CTT
1 CTT C-TT CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT
1251 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTCT CTT C-T CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT CTT
1296 CTT CTT CTT CTT CTT CTT CTTT CTT CTTT CTT -TT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT C-TT CTT C-TT CTT CTT CTT CTT CTT CTT
1342 C-T CTT CTT CTT CTT CTTT CTT CTT C-T CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
1386 CTT CTTT CTT CTT CTT CTT C-T CTT CTT CTTT CTT CTT CTT -TT ATT
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT
*
1431 CTT CTT CTT CTT CTT CTT CTT ATT CTT CTT CTT CTT -TT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1478 CTT -TT CTT CTT CTT CTT C-T CTT CTT C-T CTT CTT C-T CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1522 CTT CTT CTT CTT CTT CTT C-T CTT C-T CTT CTT CTT -TT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * *
1567 CTTT CTT CTT CTT C-T CCT CTT CTT C-T CTT CTT CTT CTT CCT CCT
1 C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* *
1611 C-T CTT CTT C-T CTT CTT CTT CTTT CTT CCT CTT CTT CCT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT
*
1655 CTT CTT CTCT CTT C-T CTT CTT CTT CTT CTTT CTT CTT CCT CTTT CTT
1 CTT CTT CT-T CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT C-TT CTT
* *
1702 CTT CTT -TT C-T CTT CTT CCT CTT -TT TTT CTT C-T CTT CTT C-T CTTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT
*
1746 CTT CTT CCT CTT CTT CTT CTT CTT CTT C-T CTT CCTT CTT C-T CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT CTT
* *
1790 CTT CTT CTT CTT CTT CCT CTT CCT CTT CTT CTT CTT -TT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
1837 CTT CTT CTT C-T CTT C-T CCT CTT CTT CTT -TT CTT CTTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT
1880 CTT CTT C-T CTT CTT CTT CTT CTT CTT CTTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT
*
1925 CTT CTTT CTT CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1971 CTT CTT CTT CTT CTT C-T CTT CTT CTT CTT CTT C-T CTT CTTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT
2015 CTT CTT CTT CTT CTT CTT CTTT CTT CTT CTT CTT CTT CTT -TT -TT
1 CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT
2059 CTT CTT CTT CTT CTT CTT CTT C-T CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2106 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2154 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT
2200 CTT CTT CTT CTT CTT C-T CTT CTT CTT CTT CTT CTT CTT CTT CTTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT
2245 CTT CTT CTT CTT CTT -TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2292 CTT CTT CTT CTT CTT CTTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2338 CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT C
2354 ATAGAAAGAG
Statistics
Matches: 2063, Mismatches: 137, Indels: 300
0.83 0.05 0.12
Matches are distributed among these distances:
2 185 0.09
3 1716 0.83
4 161 0.08
5 1 0.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:4225 original size:42 final size:42
Alignment explanation
Indices: 4166--4285 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
4156 TTTCCCCGAA
*
4166 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
*
4208 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
4250 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
4286 TGTAATTCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
Found at i:4521 original size:22 final size:23
Alignment explanation
Indices: 4474--4534 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
4464 TAATTATTAA
* *
4474 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
4495 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
4518 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
4535 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:4615 original size:25 final size:25
Alignment explanation
Indices: 4587--4648 Score: 63
Period size: 28 Copynumber: 2.4 Consensus size: 25
4577 TTTATTTTAA
* *
4587 TAATAAATAATATTTTTTTTATATT
1 TAATAAATAATATTATTTATATATT
4612 TAATAATGAATAATATTATTTATATATT
1 TAAT-A--AATAATATTATTTATATATT
4640 TCAA-AAATA
1 T-AATAAATA
4649 TTTTAGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
25 8 0.26
26 1 0.03
27 1 0.03
28 19 0.61
29 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
TAATAAATAATATTATTTATATATT
Found at i:4615 original size:28 final size:28
Alignment explanation
Indices: 4547--4640 Score: 102
Period size: 28 Copynumber: 3.3 Consensus size: 28
4537 AAATAATCAA
*
4547 TTATATTATAATAATATAA-GATATTATATTT
1 TTATATT-TAATAATA-AATAATATT-T-TTT
4578 TTAT-TTTAATAATAAATAATATTTTTT
1 TTATATTTAATAATAAATAATATTTTTT
* *
4605 TTATATTTAATAATGAATAATATTATTT
1 TTATATTTAATAATAAATAATATTTTTT
*
4633 ATATATTT
1 TTATATTT
4641 CAAAAATATT
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.12
28 31 0.54
29 13 0.23
30 2 0.04
31 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
TTATATTTAATAATAAATAATATTTTTT
Found at i:4894 original size:20 final size:20
Alignment explanation
Indices: 4816--4885 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
4806 TTTCCAGATG
4816 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
4836 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
4856 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
4876 TTTTCCAGAA
1 TTTTCCAGAA
4886 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:4894 original size:40 final size:40
Alignment explanation
Indices: 4816--4894 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
4806 TTTCCAGATG
* **
4816 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
4856 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
4895 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:4904 original size:15 final size:15
Alignment explanation
Indices: 4868--4934 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
4858 TTACAGAAAT
**
4868 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
4883 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
** *
4897 GTAATTCATTTTTCA
1 GTAATTCAAATTCCA
4912 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
4927 GTAATTCA
1 GTAATTCA
4935 TTTTCTGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 12 0.28
15 31 0.72
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.40
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:4918 original size:30 final size:29
Alignment explanation
Indices: 4868--4939 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 29
4858 TTACAGAAAT
4868 GTAATTCATTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
*
4897 GTAATTCATTTTTCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAG-AATTCAAATTCCA
4927 GTAATTCATTTTC
1 GTAATTCATTTTC
4940 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:4952 original size:29 final size:30
Alignment explanation
Indices: 4868--4952 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 30
4858 TTACAGAAAT
* **
4868 GTAATTCATTTTCCA-GAATTCAAATTCCA
1 GTAATTCATTTTTCAGGAAAACAAATTCCA
* **
4897 GTAATTCATTTTTCAGTAATTCAAATTCCA
1 GTAATTCATTTTTCAGGAAAACAAATTCCA
* *
4927 GTAATTCA-TTTTCTGGAAAACCAATT
1 GTAATTCATTTTTCAGGAAAACAAATT
4953 ACAGCTAAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 27 0.56
30 21 0.44
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (30 bp):
GTAATTCATTTTTCAGGAAAACAAATTCCA
Found at i:5340 original size:4 final size:4
Alignment explanation
Indices: 5331--5389 Score: 61
Period size: 4 Copynumber: 15.2 Consensus size: 4
5321 TCAAAGGGAA
* *
5331 AAAT AAAT -AAT AAAT -TAT AAAT AAAT ATAAT AAAT AAAT AAAT -AAC
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT
*
5377 AAAT AAAA AAAT A
1 AAAT AAAT AAAT A
5390 TTGAAACTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
3 7 0.16
4 34 0.76
5 4 0.09
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:5367 original size:17 final size:16
Alignment explanation
Indices: 5331--5389 Score: 61
Period size: 15 Copynumber: 3.8 Consensus size: 16
5321 TCAAAGGGAA
5331 AAATAAAT-AATAAAT
1 AAATAAATAAATAAAT
*
5346 -TATAAATAAATATAAT
1 AAATAAATAAATA-AAT
*
5362 AAATAAATAAAT-AAC
1 AAATAAATAAATAAAT
*
5377 AAATAAAAAAATA
1 AAATAAATAAATA
5390 TTGAAACTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 6 0.17
15 17 0.47
16 3 0.08
17 10 0.28
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AAATAAATAAATAAAT
Found at i:5383 original size:32 final size:31
Alignment explanation
Indices: 5331--5390 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
5321 TCAAAGGGAA
* *
5331 AAATAAATAATAAATTATAAATAAATATAAT
1 AAATAAATAATAAATAATAAAAAAATATAAT
5362 AAATAAATAAATAACA-AATAAAAAAATAT
1 AAATAAAT-AATAA-ATAATAAAAAAATAT
5391 TGAAACTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 8 0.32
32 16 0.64
33 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (31 bp):
AAATAAATAATAAATAATAAAAAAATATAAT
Found at i:6539 original size:2 final size:2
Alignment explanation
Indices: 6528--6556 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6518 TTTTTAACTA
6528 AT AT -T 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
6557 TTACATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:6779 original size:27 final size:26
Alignment explanation
Indices: 6749--6823 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
6739 TTACCTAATA
6749 ATTATATATTAGTATTTT-TTCATATTT
1 ATTATATATTAGTATTTTATT-AT-TTT
* *
6776 ATTATTTATTACTATTTTATTATTTT
1 ATTATATATTAGTATTTTATTATTTT
*
6802 ACTTA-ATATTTGTATTTGTATT
1 A-TTATATATTAGTATTT-TATT
6824 TTCATTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 13 0.32
27 25 0.62
28 2 0.05
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (26 bp):
ATTATATATTAGTATTTTATTATTTT
Found at i:6809 original size:61 final size:57
Alignment explanation
Indices: 6703--6825 Score: 142
Period size: 59 Copynumber: 2.1 Consensus size: 57
6693 ATTGTTTTCA
*
6703 ATTTTTTTACTATTTATTATTATTATCATTATTATTTTACCTAATAATTATATATTAGT
1 ATTTTTTCACTATTTATTATTATTATCATTATTATTTTACCTAAT-ATT-TATATTAGT
* * *
6762 ATTTTTTCA-TATTTATTATTTATTA-CTATTTTATTATTTTACTTAATATTTGTATTTGT
1 ATTTTTTCACTATTTATTA-TTATTATC-A--TTATTATTTTACCTAATATTTATATTAGT
6821 ATTTT
1 ATTTT
6826 CATTTTTTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
58 10 0.18
59 27 0.48
60 3 0.05
61 16 0.29
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.63
Consensus pattern (57 bp):
ATTTTTTCACTATTTATTATTATTATCATTATTATTTTACCTAATATTTATATTAGT
Found at i:6882 original size:19 final size:20
Alignment explanation
Indices: 6855--6917 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 20
6845 GGTTTTTCTA
*
6855 ATTTATTTATTTCTT-GTTT
1 ATTTGTTTATTTCTTAGTTT
*
6874 ATTTGTTTATTT-TTATTTT
1 ATTTGTTTATTTCTTAGTTT
*
6893 ATTTGTTTATTATCTTATTTT
1 ATTTGTTTATT-TCTTAGTTT
6914 ATTT
1 ATTT
6918 TTCATTGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.05
19 25 0.64
20 1 0.03
21 11 0.28
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (20 bp):
ATTTGTTTATTTCTTAGTTT
Found at i:11367 original size:20 final size:21
Alignment explanation
Indices: 11342--11393 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
11332 TTTTCCCAGT
*
11342 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
11362 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
11383 TCGCAATGCGA
1 TCGCAATGCGA
11394 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:11406 original size:41 final size:41
Alignment explanation
Indices: 11379--11456 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
11369 GCGAATTGGG
*
11379 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
11420 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATA
11457 CTGACTTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:11407 original size:20 final size:20
Alignment explanation
Indices: 11382--11476 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
11372 AATTGGGAAA
*
11382 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
11402 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
11423 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
11443 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
11463 TTCGCAACGAGATA
1 ATCGCAACGCGATA
11477 ATACATAATC
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 2 0.03
20 46 0.71
21 15 0.23
22 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:11490 original size:21 final size:20
Alignment explanation
Indices: 11382--11496 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
11372 AATTGGGAAA
* *
11382 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAATGACT
*
11402 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATAATGAC--T
*
11423 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* *
11443 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* *
11463 TTCGCAACGAGATAAT-ACAT
1 ATCGCAACGCGATAATGAC-T
*
11483 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
11497 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.05
20 48 0.61
21 25 0.32
22 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATAATGACT
Found at i:12009 original size:20 final size:20
Alignment explanation
Indices: 11972--12028 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 20
11962 GATTCTCTCG
* **
11972 TTGCAATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
**
11992 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCA
**
12012 TTGCGATTTTCATTTTC
1 TTGCGATAGTCATTTTC
12029 AGAAACTATT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:12219 original size:25 final size:24
Alignment explanation
Indices: 12165--12219 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
12155 TGTTTATTAT
* *
12165 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
12189 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
12215 TGTTT
1 TGTTT
12220 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:13369 original size:18 final size:18
Alignment explanation
Indices: 13348--13392 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
13338 TCCACTTTGG
*
13348 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
13366 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
13384 GAGCCATCA
1 GAGCCATCA
13393 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:13928 original size:19 final size:20
Alignment explanation
Indices: 13885--13929 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
13875 AGCAACACGA
13885 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
13905 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
13924 AAATGA
1 AAATGA
13930 AATCGCAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:14006 original size:14 final size:14
Alignment explanation
Indices: 13987--14077 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 14
13977 TTGTGTTTCG
*
13987 CGTTGCGATTTTGT
1 CGTTGCGATTTTTT
14001 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TTT
*
14017 CGCATTACGATTTTTT
1 CG--TTGCGATTTTTT
14033 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TTT
* *
14050 CGCATTGTGATTTTGT
1 CG--TTGCGATTTTTT
14066 CGTTGCGATTTT
1 CGTTGCGATTTT
14078 CATTTCGCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 25 0.40
15 3 0.05
16 13 0.21
17 5 0.08
18 11 0.18
19 5 0.08
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:14051 original size:33 final size:33
Alignment explanation
Indices: 13982--14093 Score: 181
Period size: 33 Copynumber: 3.4 Consensus size: 33
13972 GCGATTTGTG
*
13982 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* *
14014 TTTCGCATTACGATTTTTTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
14047 TTTCGCATTGTGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
14080 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
14094 AGCCATTCCC
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 24 0.33
33 48 0.67
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:14092 original size:19 final size:18
Alignment explanation
Indices: 14003--14093 Score: 81
Period size: 18 Copynumber: 5.4 Consensus size: 18
13993 GATTTTGTCG
14003 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
*
14021 TTACGATTT--TTTCG--
1 TTGCGATTTCATTTCGCA
14035 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
* *
14054 TTGTGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
14068 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
14087 TTGCGAT
1 TTGCGAT
14094 AGCCATTCCC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 10 0.18
15 6 0.11
16 9 0.16
17 9 0.16
18 12 0.21
19 11 0.19
ACGTcount: A:0.14, C:0.18, G:0.19, T:0.49
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:14593 original size:41 final size:42
Alignment explanation
Indices: 14497--14584 Score: 124
Period size: 41 Copynumber: 2.1 Consensus size: 42
14487 GAATCACCTG
* *
14497 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* * *
14539 TCCTCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
14580 TCATC
1 TCATC
14585 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 22 0.55
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:16016 original size:14 final size:14
Alignment explanation
Indices: 15997--16032 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
15987 ATTGTTTAAT
15997 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
16011 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
16025 TGATTTGT
1 TGATTTGT
16033 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:16234 original size:20 final size:20
Alignment explanation
Indices: 16211--16298 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
16201 CGATTTTCTA
*
16211 GTTGCGATAGCCATTTTTGC
1 GTTGCGATAGCCATTTTCGC
*** **
16231 GTTGCGATTTTTCA-TTTCAA
1 GTTGCGA-TAGCCATTTTCGC
*
16251 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
16271 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
16291 GTTGCGAT
1 GTTGCGAT
16299 TTCCCCGTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
19 3 0.06
20 47 0.89
21 3 0.06
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:16537 original size:20 final size:20
Alignment explanation
Indices: 16512--16603 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
16502 TTGAAGATGA
16512 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
16532 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
16552 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
16573 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
16593 TTGCGATTTTC
1 TTGCGATTTTC
16604 CAAATTCACA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:16635 original size:20 final size:21
Alignment explanation
Indices: 16588--16639 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
16578 ATAGTCAGTA
*
16588 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
16609 TCACATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
16629 TCGCATTGCGA
1 TCGCATTGCGA
16640 ATTAGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:16855 original size:12 final size:12
Alignment explanation
Indices: 16836--16869 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
16826 CTCTCCGGCG
16836 ACATCCGTTCCT
1 ACATCCGTTCCT
*
16848 ATATCCGTTCCT
1 ACATCCGTTCCT
16860 ACATCC-TTCC
1 ACATCCGTTCC
16870 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:17475 original size:24 final size:24
Alignment explanation
Indices: 17424--17477 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
17414 GTATTCGAAA
* *
17424 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* *
17448 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
17472 TTTGAT
1 TTTGAT
17478 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:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:17669 original size:12 final size:12
Alignment explanation
Indices: 17652--17688 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
17642 ATATAATTCT
17652 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
17664 GAAGAAGAAAAG
1 GAAGAAGAAAAA
17676 GAAGAAGAAAAA
1 GAAGAAGAAAAA
17688 G
1 G
17689 TCCCCGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:20002 original size:19 final size:19
Alignment explanation
Indices: 19980--20038 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
19970 GGAAATTACT
19980 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
19999 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
20013 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
20032 ATCGCAA
1 ATCGCAA
20039 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:20022 original size:33 final size:33
Alignment explanation
Indices: 19980--20106 Score: 166
Period size: 33 Copynumber: 3.8 Consensus size: 33
19970 GGAAATTACT
19980 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
20013 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
20045 TTTCGTAATGCGAAATAAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
20079 ACCGCAATGCGAAATGAAAATTGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
20107 CGAATTTAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
32 1 0.01
33 77 0.97
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:20091 original size:66 final size:66
Alignment explanation
Indices: 19985--20113 Score: 213
Period size: 66 Copynumber: 2.0 Consensus size: 66
19975 TTACTATCGC
* * *
19985 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTCG
1 AATGCGAAATAAAAATCGCAACGAGAGAACCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
20050 T
66 T
* *
20051 AATGCGAAATAAAAATCGCAACGAGGGAACCGCAATGCGAAATGAAAATTGCAACGCGAATTT
1 AATGCGAAATAAAAATCGCAACGAGAGAACCGCAATGCGAAATGAAAATCGCAACGCGAATTT
20114 AATTTCGCGT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (66 bp):
AATGCGAAATAAAAATCGCAACGAGAGAACCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
T
Found at i:20138 original size:14 final size:14
Alignment explanation
Indices: 20121--20177 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
20111 TTTAATTTCG
20121 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
20135 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
20154 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
20168 CGTTGCGATT
1 CGTTGCGATT
20178 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:20157 original size:33 final size:33
Alignment explanation
Indices: 20106--20195 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
20096 AAATTGCAAC
* *
20106 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
20139 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
20172 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
20196 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:20159 original size:19 final size:19
Alignment explanation
Indices: 20135--20195 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
20125 GCGATTCTCT
20135 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
20154 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
20168 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
20187 CATTGCGAT
1 CGTTGCGAT
20196 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:20321 original size:14 final size:14
Alignment explanation
Indices: 20302--20338 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
20292 CATCAATTAA
20302 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
20316 ACAAATCACCTTTT
1 ACAAATCAACTTTT
20330 ACAAATCAA
1 ACAAATCAA
20339 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:21760 original size:21 final size:21
Alignment explanation
Indices: 21736--21844 Score: 53
Period size: 21 Copynumber: 5.2 Consensus size: 21
21726 ATGCAGTGGC
21736 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** *
21757 CTCTCG-A-GGAATGATAGGGGC
1 CTCTTGAACGG--TGGGAGGGGA
* * * *
21778 CTCTTCAACGATAGGAGTGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** * *
21799 CTCTTG-AGGGATGACAGTGGC
1 CTCTTGAACGG-TGGGAGGGGA
21820 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
21841 CTCT
1 CTCT
21845 CGAGGAATGA
Statistics
Matches: 58, Mismatches: 24, Indels: 12
0.62 0.26 0.13
Matches are distributed among these distances:
19 2 0.03
20 3 0.05
21 48 0.83
22 4 0.07
23 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:21780 original size:42 final size:42
Alignment explanation
Indices: 21733--21896 Score: 202
Period size: 42 Copynumber: 3.9 Consensus size: 42
21723 ACGATGCAGT
* * *
21733 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * * * *
21775 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGT
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
21817 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
21859 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
21897 CAGGCGAGTC
Statistics
Matches: 100, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 100 1.00
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:21835 original size:84 final size:84
Alignment explanation
Indices: 21725--21899 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
21715 CCTCTTCAAC
21725 GATG-CAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
21789 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
21808 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
21873 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
21892 GATGACAG
1 GATGACAG
21900 GCGAGTCGGG
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 4 0.04
84 87 0.96
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:22228 original size:93 final size:91
Alignment explanation
Indices: 22118--22302 Score: 293
Period size: 91 Copynumber: 2.0 Consensus size: 91
22108 ATTTCAAACT
*
22118 TTCAACAAAAAGAC-AAA-AAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 TTCAACAAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTA
22181 GCAGAATTGGCAGCAACCGAATAAATTTAC
62 GCAGAATTGGCAGCAACCGAATAAATTTAC
*
22211 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
1 TTCAACAAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
*
22276 TATTGGCAGCAACCGAATAAATTTAC
66 AATTGGCAGCAACCGAATAAATTTAC
22302 T
1 T
22303 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 13 0.15
94 3 0.03
95 29 0.33
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (91 bp):
TTCAACAAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
AATTGGCAGCAACCGAATAAATTTAC
Found at i:24055 original size:14 final size:14
Alignment explanation
Indices: 24036--24090 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
24026 GGAAATGACT
*
24036 ATCGCAACGAGAGA
1 ATCGCAACGAAAGA
24050 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAAA-GA
24067 CTATCGCAACGAAAGA
1 --ATCGCAACGAAAGA
24083 ATCGCAAC
1 ATCGCAAC
24091 ACGAAATGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 15 0.43
16 6 0.17
17 7 0.20
19 7 0.20
ACGTcount: A:0.42, C:0.25, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAAAGA
Found at i:24069 original size:33 final size:33
Alignment explanation
Indices: 24012--24110 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
24002 ACGAGATAAT
24012 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
24046 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* * **
24079 AAGAATCGCAACACGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
24111 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:24074 original size:19 final size:18
Alignment explanation
Indices: 23987--24132 Score: 110
Period size: 19 Copynumber: 8.1 Consensus size: 18
23977 TCTTTTGGTT
*
23987 GAAATGAAAATCGCAACGA
1 GAAATG-AAATCGCAACGC
24006 GATAATGAGAATCGCAACGC
1 GA-AATGA-AATCGCAACGC
*
24026 GGAAATGACTATCGCAA--C
1 -GAAATGA-AATCGCAACGC
*
24044 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
*
24060 GAAATGACTATCGCAA--C
1 GAAATGA-AATCGCAACGC
*
24077 GAAA-G-AATCGCAACAC
1 GAAATGAAATCGCAACGC
24093 GAAATGAAAATCGCAACGC
1 GAAATG-AAATCGCAACGC
*
24112 GAAATGAAAATCGCAATGC
1 GAAATG-AAATCGCAACGC
24131 GA
1 GA
24133 TTTTGGTTTC
Statistics
Matches: 104, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
14 14 0.13
16 11 0.11
17 10 0.10
18 1 0.01
19 40 0.38
20 26 0.25
21 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.12
Consensus pattern (18 bp):
GAAATGAAATCGCAACGC
Found at i:24704 original size:20 final size:20
Alignment explanation
Indices: 24679--24751 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
24669 GCGCTATGTA
24679 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
24699 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
24719 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
24739 TATCTCGTTGCGA
1 AATCGCGTTGCGA
24752 TTTTGTATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:24785 original size:20 final size:20
Alignment explanation
Indices: 24760--24813 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
24750 GATTTTGTAT
24760 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
24780 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
24800 TATCGCATTGCGAT
1 TATCGCATTGCGAT
24814 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:24785 original size:61 final size:61
Alignment explanation
Indices: 24700--24816 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
24690 GAAAGTCAGA
* * * * *
24700 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
24761 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
24817 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:24813 original size:40 final size:40
Alignment explanation
Indices: 24680--24812 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 40
24670 CGCTATGTAA
* * * *
24680 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGAAAGTCAGTATCGCGTTGCGATAGTCAGT
* * * *
24720 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGAAAGTCAGTATCGCGTTGCGA--TAGTCAGT
* * *
24761 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGAAAGTCAGTATCGCGTTGCGATAGTCAGT
24801 ATCGCATTGCGA
1 ATCGCATTGCGA
24813 TTTTCCCAAT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 44 0.57
41 28 0.36
42 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (40 bp):
ATCGCATTGCGAAAGTCAGTATCGCGTTGCGATAGTCAGT
Found at i:24832 original size:61 final size:61
Alignment explanation
Indices: 24700--24834 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
24690 GAAAGTCAGA
* * * * * ** *
24700 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
24761 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
24823 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
24835 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:29870 original size:14 final size:14
Alignment explanation
Indices: 29853--29886 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29843 CGACCACTTT
*
29853 TAAATATGAATAAA
1 TAAAAATGAATAAA
29867 TAAAAATGAATAAA
1 TAAAAATGAATAAA
*
29881 CAAAAA
1 TAAAAA
29887 CAATATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (14 bp):
TAAAAATGAATAAA
Found at i:36567 original size:29 final size:28
Alignment explanation
Indices: 36534--36588 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
36524 ATATTTGTAT
*
36534 ATTAACTTATTAAATATATTTTTTATTAA
1 ATTAACTTA-AAAATATATTTTTTATTAA
* *
36563 ATTAATTTAAAAATATTTTTTTTATT
1 ATTAACTTAAAAATATATTTTTTATT
36589 TTCATTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTAACTTAAAAATATATTTTTTATTAA
Found at i:36779 original size:31 final size:31
Alignment explanation
Indices: 36739--36811 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
36729 ACCCATGATA
* *
36739 ACCACATCTTAATTAAATAAAAATGAAAGTG
1 ACCATATCTTAATTAAATAAAAACGAAAGTG
*
36770 ACCATATCTTGATTAAATAAAAACGAAAGTG
1 ACCATATCTTAATTAAATAAAAACGAAAGTG
*
36801 ACAATATCTTA
1 ACCATATCTTA
36812 TGTTTTTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (31 bp):
ACCATATCTTAATTAAATAAAAACGAAAGTG
Found at i:39648 original size:13 final size:13
Alignment explanation
Indices: 39630--39655 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39620 CTCACAGATG
39630 TATATAGCAATTC
1 TATATAGCAATTC
39643 TATATAGCAATTC
1 TATATAGCAATTC
39656 GAATAAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
TATATAGCAATTC
Found at i:46597 original size:22 final size:23
Alignment explanation
Indices: 46567--46621 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
46557 AGATTTTTTA
* *
46567 TGAATAGTGATGAACAGTA-CCG
1 TGAACAGTGATGAACAATACCCG
46589 TGAACAGTGATGAACAATACCCG
1 TGAACAGTGATGAACAATACCCG
46612 TGAACAGTGA
1 TGAACAGTGA
46622 CTGTACCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.20
Consensus pattern (23 bp):
TGAACAGTGATGAACAATACCCG
Found at i:47317 original size:40 final size:40
Alignment explanation
Indices: 47273--47394 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
47263 ACCGTAGTGC
47273 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
47313 TACACATAAGGTCGTGCCCACCATATACAACGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
47353 TACACATAAGGTCGTTCCCACCATATACACCGAAATGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
47393 TA
1 TA
47395 TAAACCTACA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:61488 original size:16 final size:15
Alignment explanation
Indices: 61447--61537 Score: 69
Period size: 15 Copynumber: 6.1 Consensus size: 15
61437 CGAATATATT
*
61447 TATATTTTTAAAATAA
1 TATA-TTTTATAATAA
61463 TATATTTTATAATAA
1 TATATTTTATAATAA
*
61478 TATATATTTATAATTA
1 TATAT-TTTATAATAA
* * **
61494 TTTATTATATTTTAA
1 TATATTTTATAATAA
* *
61509 -AT-TATTAAAATAA
1 TATATTTTATAATAA
*
61522 TATATTATATAATAA
1 TATATTTTATAATAA
61537 T
1 T
61538 TTTTATATTT
Statistics
Matches: 56, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
13 6 0.11
14 3 0.05
15 30 0.54
16 17 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTTTATAATAA
Found at i:61544 original size:42 final size:41
Alignment explanation
Indices: 61479--61576 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 41
61469 TTATAATAAT
* *
61479 ATATATTTATAATTATTTATTATATTTTAAATTATTAAAATA
1 ATATATTTATAATAATTTATTATATTTTAAATAATT-AAATA
* *
61521 ATATATTATATAATAATTT-TTATATTTTTAATAATTAAAGA
1 ATATATT-TATAATAATTTATTATATTTTAAATAATTAAATA
61562 ATATATTT-TAATAAT
1 ATATATTTATAATAAT
61577 ATCAAAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
39 7 0.14
40 1 0.02
41 11 0.22
42 22 0.43
43 10 0.20
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (41 bp):
ATATATTTATAATAATTTATTATATTTTAAATAATTAAATA
Found at i:61571 original size:64 final size:59
Alignment explanation
Indices: 61438--61586 Score: 147
Period size: 59 Copynumber: 2.4 Consensus size: 59
61428 AACCCGACTC
* * * **
61438 GAATATA-TTTATATTTTTAAAATAATATATTTTATAATAATATATATTTATAATTATT
1 GAATATATTTTAAATTATTAAAATAATATATTATATAATAATATATATTTATAATTAAA
* * *
61496 TATTATATTTTAAATTATTAAAATAATATATTATATAATAATTTTTATATTTTTAATAATTAAA
1 GAATATATTTTAAATTATTAAAATAATATATTATATAATAA----TATATATTT-ATAATTAAA
* *
61560 GAATATATTTTAATAATATCAAAATAA
1 GAATATATTTTAA-ATTATTAAAATAA
61587 AAATCCGTAA
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
58 5 0.07
59 30 0.42
63 8 0.11
64 18 0.25
65 11 0.15
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (59 bp):
GAATATATTTTAAATTATTAAAATAATATATTATATAATAATATATATTTATAATTAAA
Found at i:73364 original size:26 final size:28
Alignment explanation
Indices: 73317--73368 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
73307 AAATTAAAGT
73317 TTTTTATAAATATAATAATTTTTTAATG
1 TTTTTATAAATATAATAATTTTTTAATG
**
73345 TTTTTA-AAA-ATAATTTTTTTTTAA
1 TTTTTATAAATATAATAATTTTTTAA
73369 ATTACTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.59
27 3 0.14
28 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTTTATAAATATAATAATTTTTTAATG
Found at i:75499 original size:2 final size:2
Alignment explanation
Indices: 75488--75518 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
75478 TAGTATTCAT
75488 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75519 ACAATATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:76443 original size:43 final size:43
Alignment explanation
Indices: 76396--76532 Score: 109
Period size: 43 Copynumber: 3.2 Consensus size: 43
76386 TTACAACATA
* *
76396 TAGCGGCGATTGTTCA-ACAAACGCCGCAAAAAGTATTGATATT
1 TAGCGGCGATTG-GCATAAAAACGCCGCAAAAAGTATTGATATT
* * * *
76439 TAGCGGCGCTTGGCATAAAAACGCCGCAATAGGTGTTGATATT
1 TAGCGGCGATTGGCATAAAAACGCCGCAAAAAGTATTGATATT
* * * * * * *
76482 TAACGGC-ATTTGGCAGACAAACACCGC-AATAGTCGTTGATGTT
1 TAGCGGCGA-TTGGCATAAAAACGCCGCAAAAAGT-ATTGATATT
76525 TAGCGGCG
1 TAGCGGCG
76533 TTTTCTTCAC
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
42 5 0.07
43 69 0.93
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (43 bp):
TAGCGGCGATTGGCATAAAAACGCCGCAAAAAGTATTGATATT
Found at i:76545 original size:43 final size:41
Alignment explanation
Indices: 76457--76592 Score: 107
Period size: 43 Copynumber: 3.2 Consensus size: 41
76447 CTTGGCATAA
* * ** *
76457 AAACGCCGCAATAGGTGTTGATATTTAACGGCATTTGGCA-GAC
1 AAACGCCGCAATAGATGTTGAT-TTT-ACGGCGTTT-TTATCAC
*
76500 AAACACCGCAATAG-TCGTTGATGTTTAGCGGCGTTTTCT-TCAC
1 AAACGCCGCAATAGAT-GTTGAT-TTTA-CGGCGTTTT-TATCAC
* * *
76543 AAACGCCGTAGTAGATGTTTATTTTACGGCGTTTTTATCAC
1 AAACGCCGCAATAGATGTTGATTTTACGGCGTTTTTATCAC
76584 AAACGCCGC
1 AAACGCCGC
76593 TAAATGTATG
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
40 1 0.01
41 21 0.28
42 6 0.08
43 47 0.62
44 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (41 bp):
AAACGCCGCAATAGATGTTGATTTTACGGCGTTTTTATCAC
Found at i:76957 original size:21 final size:21
Alignment explanation
Indices: 76933--76994 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
76923 ATATATTACT
* *
76933 TCTCTCTGTTCTGTCGCTGCC
1 TCTCTCTGTGCTGCCGCTGCC
* *
76954 TCTCTGTGTGCTGCCGCTGCT
1 TCTCTCTGTGCTGCCGCTGCC
* *
76975 TCTCTCTTTGCTTCCGCTGC
1 TCTCTCTGTGCTGCCGCTGC
76995 TGCTCTAGCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.00, C:0.37, G:0.21, T:0.42
Consensus pattern (21 bp):
TCTCTCTGTGCTGCCGCTGCC
Found at i:76995 original size:21 final size:21
Alignment explanation
Indices: 76931--77023 Score: 64
Period size: 21 Copynumber: 4.4 Consensus size: 21
76921 TGATATATTA
76931 CTTCTCTCTGTT-CTGT-CGCTG
1 CTTCTCTCT-TTGCT-TCCGCTG
* * * *
76952 CCTCTCTGTGTGCTGCCGCTG
1 CTTCTCTCTTTGCTTCCGCTG
76973 CTTCTCTCTTTGCTTCCGCTG
1 CTTCTCTCTTTGCTTCCGCTG
* *** *
76994 CTGCTCTAGCTACTTCCGCTG
1 CTTCTCTCTTTGCTTCCGCTG
*
77015 CTGCTCTCT
1 CTTCTCTCT
77024 CTGTTTCCCT
Statistics
Matches: 55, Mismatches: 15, Indels: 4
0.74 0.20 0.05
Matches are distributed among these distances:
20 1 0.02
21 54 0.98
ACGTcount: A:0.02, C:0.38, G:0.19, T:0.41
Consensus pattern (21 bp):
CTTCTCTCTTTGCTTCCGCTG
Found at i:77031 original size:21 final size:21
Alignment explanation
Indices: 76962--77031 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
76952 CCTCTCTGTG
* * *
76962 TGCTGCCGCTGCTTCTCTCTT
1 TGCTTCCGCTGCTGCTCTCTC
**
76983 TGCTTCCGCTGCTGCTCTAGC
1 TGCTTCCGCTGCTGCTCTCTC
*
77004 TACTTCCGCTGCTGCTCTCTC
1 TGCTTCCGCTGCTGCTCTCTC
*
77025 TGTTTCC
1 TGCTTCC
77032 CTTGCTTCAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.03, C:0.39, G:0.19, T:0.40
Consensus pattern (21 bp):
TGCTTCCGCTGCTGCTCTCTC
Found at i:84619 original size:41 final size:41
Alignment explanation
Indices: 84509--84622 Score: 122
Period size: 41 Copynumber: 2.7 Consensus size: 41
84499 TTAAAGGACA
* * **
84509 ATTGCGGCGTTTATATTAAAAATGCCACCAAGGAACTATTCT
1 ATTGCGGCGTTTAT-TAAAAAATGCCACTAAGGAACTACACT
* * *
84551 ATTACGGCGTTTATTACGAAAATGCCACTAAGGGA-TACACT
1 ATTGCGGCGTTTATTA-AAAAATGCCACTAAGGAACTACACT
*
84592 ATTGCGGCGTTTATGTAAAAAACGCCACTAA
1 ATTGCGGCGTTTAT-TAAAAAATGCCACTAA
84623 AGTAAAACTT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
41 30 0.50
42 30 0.50
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (41 bp):
ATTGCGGCGTTTATTAAAAAATGCCACTAAGGAACTACACT
Found at i:84686 original size:41 final size:41
Alignment explanation
Indices: 84606--84687 Score: 94
Period size: 41 Copynumber: 2.0 Consensus size: 41
84596 CGGCGTTTAT
* *
84606 GTAAAAAACGCCACTAAAGTAAAACTTTTTAGGGGCGTTTG
1 GTAAAAAACGCCACTAAAGTAAAACTTTTTAGCGACGTTTG
* * * *
84647 GTAACAAACGCCACTAAATTCAAAGTATTTTA-CGACGTTTG
1 GTAAAAAACGCCACTAAAGTAAAACT-TTTTAGCGACGTTTG
84688 CTTAAAACAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 29 0.85
42 5 0.15
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (41 bp):
GTAAAAAACGCCACTAAAGTAAAACTTTTTAGCGACGTTTG
Found at i:85107 original size:38 final size:37
Alignment explanation
Indices: 85037--85108 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
85027 TATACAAAAA
* **
85037 AAACGCCACTATTGATTACACTATTGTGGCGTTTAAC
1 AAACGCCACTATTGATTAAACTATTACGGCGTTTAAC
85074 AAACGCCACTATTGATTAAAACTATTACGGCGTTT
1 AAACGCCACTATTGATT-AAACTATTACGGCGTTT
85109 GTGGTATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 17 0.55
38 14 0.45
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (37 bp):
AAACGCCACTATTGATTAAACTATTACGGCGTTTAAC
Found at i:91705 original size:2 final size:2
Alignment explanation
Indices: 91698--91741 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
91688 ACCAGTAGCA
91698 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
91740 AT
1 AT
91742 TATCACCCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92224 original size:20 final size:20
Alignment explanation
Indices: 92199--92239 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
92189 TATCAACCAA
92199 CTCCTCTTGTTAATAACTTT
1 CTCCTCTTGTTAATAACTTT
*
92219 CTCCTCTTGTTAGTAACTTT
1 CTCCTCTTGTTAATAACTTT
92239 C
1 C
92240 CATTAGGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.27, G:0.07, T:0.49
Consensus pattern (20 bp):
CTCCTCTTGTTAATAACTTT
Found at i:94203 original size:29 final size:29
Alignment explanation
Indices: 94160--94218 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
94150 TGATATTGTT
* **
94160 CTTGTAGTATCGATACTTTTATCAATACC
1 CTTGGAGTATCGATACTCGTATCAATACC
*
94189 CTTGGAGTATTGATACTCGTATCAATACC
1 CTTGGAGTATCGATACTCGTATCAATACC
94218 C
1 C
94219 GTATCAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (29 bp):
CTTGGAGTATCGATACTCGTATCAATACC
Found at i:94216 original size:12 final size:12
Alignment explanation
Indices: 94201--94287 Score: 79
Period size: 12 Copynumber: 7.2 Consensus size: 12
94191 TGGAGTATTG
94201 ATACTCGTATCA
1 ATACTCGTATCA
*
94213 ATACCCGTATCA
1 ATACTCGTATCA
94225 ATAC-CAGTATCA
1 ATACTC-GTATCA
*
94237 ATAC-CCTCATCA
1 ATACTCGT-ATCA
*
94249 ATACTAGTATCA
1 ATACTCGTATCA
* *
94261 ATACTTGCATCA
1 ATACTCGTATCA
* *
94273 ATACTAGTGTCA
1 ATACTCGTATCA
94285 ATA
1 ATA
94288 TTGTCCAATA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
11 2 0.03
12 60 0.95
13 1 0.02
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (12 bp):
ATACTCGTATCA
Found at i:94228 original size:24 final size:24
Alignment explanation
Indices: 94201--94287 Score: 104
Period size: 24 Copynumber: 3.6 Consensus size: 24
94191 TGGAGTATTG
*
94201 ATACTCGTATCAATACCCGTATCA
1 ATACTAGTATCAATACCCGTATCA
*
94225 ATACCAGTATCAATACCC-TCATCA
1 ATACTAGTATCAATACCCGT-ATCA
** *
94249 ATACTAGTATCAATACTTGCATCA
1 ATACTAGTATCAATACCCGTATCA
*
94273 ATACTAGTGTCAATA
1 ATACTAGTATCAATA
94288 TTGTCCAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.02
24 53 0.98
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30
Consensus pattern (24 bp):
ATACTAGTATCAATACCCGTATCA
Found at i:102769 original size:12 final size:12
Alignment explanation
Indices: 102754--102788 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
102744 TCAATCATCC
*
102754 ATTCATTCATTT
1 ATTCATCCATTT
102766 ATTCATCCATTT
1 ATTCATCCATTT
102778 ATTCATCCATT
1 ATTCATCCATT
102789 CTTTTGGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTCATCCATTT
Found at i:104181 original size:6 final size:6
Alignment explanation
Indices: 104172--104202 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
104162 CGCTCCTTTT
104172 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC T
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC T
104203 ACCACAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TCCTTC
Found at i:106379 original size:20 final size:20
Alignment explanation
Indices: 106340--106379 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
106330 TTTTCTATTG
**
106340 TTTTTATTATAAATTTGATA
1 TTTTTATTATAAATAAGATA
*
106360 TTTTTATTATAAGTAAGATA
1 TTTTTATTATAAATAAGATA
106380 AGTAAACTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTTTATTATAAATAAGATA
Found at i:106642 original size:22 final size:22
Alignment explanation
Indices: 106614--106661 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
106604 CGGATTAAAA
*
106614 TTCGGTTCAGGTTTCTTTCGGT
1 TTCGGTTCAGGTTACTTTCGGT
*
106636 TTCGGTTCGGGTTACTTTCGGT
1 TTCGGTTCAGGTTACTTTCGGT
106658 TTCG
1 TTCG
106662 TTAAATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.04, C:0.19, G:0.29, T:0.48
Consensus pattern (22 bp):
TTCGGTTCAGGTTACTTTCGGT
Found at i:111522 original size:20 final size:20
Alignment explanation
Indices: 111499--111536 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
111489 CAGCCCAGAG
111499 TATCAATACTCAC-TGAACAA
1 TATCAATAC-CACATGAACAA
111519 TATCAATACCACATGAAC
1 TATCAATACCACATGAAC
111537 GATTTCCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (20 bp):
TATCAATACCACATGAACAA
Found at i:113398 original size:21 final size:20
Alignment explanation
Indices: 113369--113437 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
113359 GGACCTATCA
*
113369 TCCCAAAGGATGTCATCTGTG
1 TCCCGAAGGATGT-ATCTGTG
** *
113390 TCCCGAAGGACCTATC-AT-
1 TCCCGAAGGATGTATCTGTG
113408 T-CCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGT-ATCTGTG
*
113428 TTCCGAAGGA
1 TCCCGAAGGA
113438 CCTATCATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 9 0.24
18 4 0.11
19 2 0.05
20 4 0.11
21 18 0.49
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (20 bp):
TCCCGAAGGATGTATCTGTG
Found at i:113401 original size:38 final size:38
Alignment explanation
Indices: 113350--113445 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
113340 GTATAAACTA
* *
113350 TGTCCCAAAGGACCTATCATCCCAAAGGATGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATCTG
* *
113388 TGTCCCGAAGGACCTATCATTCCGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATCTG
*
113426 TGTTCCGAAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
113446 ATGTCTCGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCAAAGGATGTAATCTG
Found at i:120112 original size:20 final size:20
Alignment explanation
Indices: 120075--120123 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
120065 CTCTAAATCA
***
120075 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCAAATTTTG
120095 TTTTTCAAAATCAAATTTTG
1 TTTTTCAAAATCAAATTTTG
*
120115 -CTTTCAAAA
1 TTTTTCAAAA
120124 GAAAATCGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTTCAAAATCAAATTTTG
Found at i:125293 original size:44 final size:43
Alignment explanation
Indices: 125221--125339 Score: 134
Period size: 44 Copynumber: 2.7 Consensus size: 43
125211 TTGATTGGGG
125221 CCTCGACAGGAAAAAAGAAATTAATTTTAACCTTGGTTGGGAC
1 CCTCGACAGGAAAAAAGAAATTAATTTTAACCTTGGTTGGGAC
* * *
125264 CCTCGATAGGAAACAGAA-AAATTAATTTTAACCTTTGTT-GGAGG
1 CCTCGACAGGAAA-A-AAGAAATTAATTTTAACCTTGGTTGGGA-C
*
125308 CCTCAACAGGAAAAATATGAAAATTAATTTTA
1 CCTCGACAGGAAAAA-A-G-AAATTAATTTTA
125340 CTTTGATAGG
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
42 1 0.02
43 17 0.27
44 32 0.50
45 2 0.03
46 12 0.19
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (43 bp):
CCTCGACAGGAAAAAAGAAATTAATTTTAACCTTGGTTGGGAC
Found at i:129117 original size:10 final size:10
Alignment explanation
Indices: 129102--129150 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
129092 TCACTTTTTT
129102 TAAAAATAAA
1 TAAAAATAAA
129112 TAAAAATACAA
1 TAAAAATA-AA
*
129123 TAAAAATGAA
1 TAAAAATAAA
* *
129133 TAAAATTCAA
1 TAAAAATAAA
129143 TAAAAATA
1 TAAAAATA
129151 TAATGTGAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:129137 original size:20 final size:21
Alignment explanation
Indices: 129102--129150 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
129092 TCACTTTTTT
129102 TAAAAATAAATAAAAATACAA
1 TAAAAATAAATAAAAATACAA
* *
129123 TAAAAATGAAT-AAAATTCAA
1 TAAAAATAAATAAAAATACAA
129143 TAAAAATA
1 TAAAAATA
129151 TAATGTGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAAAATAAATAAAAATACAA
Found at i:130063 original size:21 final size:21
Alignment explanation
Indices: 130026--130084 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
130016 TTTTACATTA
* *
130026 TATTTTTATTGAATTTTATT-
1 TATTTTTATTCATTTTTATTG
130046 TATTTTTAATTCATTTTTATTG
1 TATTTTT-ATTCATTTTTATTG
*
130068 TATTTTTATTTATTTTT
1 TATTTTTATTCATTTTT
130085 TAAAAAAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 20 0.59
22 7 0.21
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.73
Consensus pattern (21 bp):
TATTTTTATTCATTTTTATTG
Found at i:130086 original size:11 final size:10
Alignment explanation
Indices: 130026--130084 Score: 73
Period size: 10 Copynumber: 5.7 Consensus size: 10
130016 TTTTACATTA
130026 TATTTTTATT
1 TATTTTTATT
* *
130036 GAATTTTATT
1 TATTTTTATT
130046 TATTTTTAATT
1 TATTTTT-ATT
*
130057 CATTTTTATT
1 TATTTTTATT
130067 GTATTTTTATT
1 -TATTTTTATT
130078 TATTTTT
1 TATTTTT
130085 TAAAAAAGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 23 0.56
11 18 0.44
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.73
Consensus pattern (10 bp):
TATTTTTATT
Found at i:131138 original size:37 final size:36
Alignment explanation
Indices: 131095--131168 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
131085 GTTGAAAAAT
* *
131095 ATTTATATACTTCCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATAATTCCTTTAAAAAATTTAAAAT-ATAAA
** *
131132 ATTTATATAATTTTTTTACAAAATTTAAAATATAAA
1 ATTTATATAATTCCTTTAAAAAATTTAAAATATAAA
131168 A
1 A
131169 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
36 6 0.19
37 26 0.81
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.45
Consensus pattern (36 bp):
ATTTATATAATTCCTTTAAAAAATTTAAAATATAAA
Found at i:144184 original size:75 final size:77
Alignment explanation
Indices: 144015--144218 Score: 261
Period size: 76 Copynumber: 2.7 Consensus size: 77
144005 GTTGTAAAAG
* * * * * * *
144015 GGGGGGAATCGGTACCCCCT-TGGGGGGGATCAGTTCCCTCCAAGCATACTGGAATTCTCGGAGC
1 GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGC
** *
144079 AAAACTGTTTTA
66 AAAACTCATTCA
144091 GGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGC
1 GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGC
*
144155 CAAAC-CATTCA
66 AAAACTCATTCA
* *
144166 GGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 GGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTG
144219 TAATTTTTGG
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
75 25 0.22
76 59 0.53
77 28 0.25
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.24
Consensus pattern (77 bp):
GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGC
AAAACTCATTCA
Found at i:146857 original size:21 final size:21
Alignment explanation
Indices: 146831--146870 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
146821 CAGAACCCCA
*
146831 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
146852 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
146871 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:150747 original size:22 final size:21
Alignment explanation
Indices: 150705--150744 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
150695 GAGTTTGTTT
*
150705 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
150726 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
150745 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:152830 original size:74 final size:76
Alignment explanation
Indices: 152663--152863 Score: 264
Period size: 75 Copynumber: 2.7 Consensus size: 76
152653 TTGTAAAAGG
* * * * * *
152663 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCAAGCATACTGGAATTCTCGGAGCA
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCA
** *
152727 AAACTGTTTTA
66 AAACTCATTCA
*
152738 GGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCA
152802 AAAC-CATTCA
66 AAACTCATTCA
* *
152812 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTG
152864 TAATTTTTGG
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
74 24 0.22
75 59 0.53
76 28 0.25
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.24
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCA
AAACTCATTCA
Found at i:160649 original size:2 final size:2
Alignment explanation
Indices: 160642--160698 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
160632 TTAATTAGAA
160642 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
160684 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
160699 GACACGAACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:166214 original size:2 final size:2
Alignment explanation
Indices: 166207--166260 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
166197 CATGCATAAG
166207 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
166249 AT AT AT AT AT AT
1 AT AT AT AT AT AT
166261 GTTCATATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:166653 original size:27 final size:27
Alignment explanation
Indices: 166584--166653 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
166574 GGAGTGGTCC
*
166584 TTCGAGACAAATACAATACATAAGTCA
1 TTCGAGACAAATACAGTACATAAGTCA
*
166611 TTCGAGACAAATACAGTACATAGGTCA
1 TTCGAGACAAATACAGTACATAAGTCA
* *
166638 TTCGGGATAAATACAG
1 TTCGAGACAAATACAG
166654 AGGTCCTTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (27 bp):
TTCGAGACAAATACAGTACATAAGTCA
Found at i:166657 original size:22 final size:22
Alignment explanation
Indices: 166627--166671 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
166617 ACAAATACAG
* *
166627 TACATAGGTCATTCGGGATAAA
1 TACAGAGGTCATTCGGGACAAA
*
166649 TACAGAGGTCCTTCGGGACAAA
1 TACAGAGGTCATTCGGGACAAA
166671 T
1 T
166672 TTCATATACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (22 bp):
TACAGAGGTCATTCGGGACAAA
Found at i:167233 original size:21 final size:22
Alignment explanation
Indices: 167207--167254 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
167197 AAAATTACTA
*
167207 TAGCAGGGTATCGATA-CGCTG
1 TAGCAGGGTATCGATACCCCTG
167228 TAGCAGGGTATCGATACCCCTG
1 TAGCAGGGTATCGATACCCCTG
167250 TAGCA
1 TAGCA
167255 TTCTGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (22 bp):
TAGCAGGGTATCGATACCCCTG
Found at i:170196 original size:15 final size:17
Alignment explanation
Indices: 170176--170207 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
170166 TCTTGGTTAT
170176 GAAAG-AAT-AAAAGGA
1 GAAAGAAATGAAAAGGA
170191 GAAAGAAATGAAAAGGA
1 GAAAGAAATGAAAAGGA
170208 TTGAGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 3 0.20
17 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.06
Consensus pattern (17 bp):
GAAAGAAATGAAAAGGA
Found at i:174171 original size:3 final size:3
Alignment explanation
Indices: 174116--174159 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
174106 AGGTAATTGC
174116 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
174160 CATGTTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:175743 original size:30 final size:30
Alignment explanation
Indices: 175699--175915 Score: 222
Period size: 30 Copynumber: 7.2 Consensus size: 30
175689 GAGGAAGATA
* *
175699 TAATCTCATGCAGATGTCAGAACAAGGAAT
1 TAATCCCATGCAGATGTCAGAACAGGGAAT
* * *
175729 TAATTCCATACAGATGTCAGAACAGGGAAC
1 TAATCCCATGCAGATGTCAGAACAGGGAAT
* * * ** *
175759 TAATCCCATGGAGAGGTCAAAATGGGGAAC
1 TAATCCCATGCAGATGTCAGAACAGGGAAT
* *
175789 TAATCCCTTGCAGAAGTCAGAACAGGGAAT
1 TAATCCCATGCAGATGTCAGAACAGGGAAT
* * *
175819 TAATCTCATGC-GTATGTTAGAATAGGGAAT
1 TAATCCCATGCAG-ATGTCAGAACAGGGAAT
*
175849 TAATCCCATGCAGATGTCAGAACGGGGAAT
1 TAATCCCATGCAGATGTCAGAACAGGGAAT
* * *
175879 TAATCCTATGCAGATGTTAGAA-TGGGAAAT
1 TAATCCCATGCAGATGTCAGAACAGGG-AAT
175909 TAATCCC
1 TAATCCC
175916 TTGTAGAATC
Statistics
Matches: 152, Mismatches: 32, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
29 4 0.03
30 147 0.97
31 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (30 bp):
TAATCCCATGCAGATGTCAGAACAGGGAAT
Found at i:176775 original size:15 final size:15
Alignment explanation
Indices: 176755--176794 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
176745 GAAGAATAAG
176755 AGAAAAGAAAGAAAT
1 AGAAAAGAAAGAAAT
*
176770 AGAAAAGAATGAAAT
1 AGAAAAGAAAGAAAT
176785 -GAAAAAGAAA
1 AG-AAAAGAAA
176795 AAAGGTTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 1 0.05
15 21 0.95
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.07
Consensus pattern (15 bp):
AGAAAAGAAAGAAAT
Found at i:178432 original size:19 final size:20
Alignment explanation
Indices: 178408--178459 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 20
178398 ATGTCAAAAT
178408 GGTATCGGTACCA-AAAGGG
1 GGTATCGGTACCATAAAGGG
*
178427 GGTATCGATACCATAAAGGG
1 GGTATCGGTACCATAAAGGG
178447 GAAGTATCGGTAC
1 G--GTATCGGTAC
178460 TGTAGGGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
20 7 0.25
22 9 0.32
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.19
Consensus pattern (20 bp):
GGTATCGGTACCATAAAGGG
Found at i:178466 original size:20 final size:19
Alignment explanation
Indices: 178443--178481 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
178433 GATACCATAA
*
178443 AGGGGAAGTATCGGTACTGT
1 AGGGGAAGTA-CCGTACTGT
*
178463 AGGGGGAGTACCGTACTGT
1 AGGGGAAGTACCGTACTGT
178482 TGAACATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.23, C:0.13, G:0.41, T:0.23
Consensus pattern (19 bp):
AGGGGAAGTACCGTACTGT
Found at i:178923 original size:2 final size:2
Alignment explanation
Indices: 178916--178944 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
178906 AAGCCCAAGG
178916 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 T
178945 GAGGATTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:187078 original size:32 final size:32
Alignment explanation
Indices: 187037--187134 Score: 187
Period size: 32 Copynumber: 3.1 Consensus size: 32
187027 GAGCCTAAGA
187037 ATGTCAAATAAACATTAAATGATGAACATTGG
1 ATGTCAAATAAACATTAAATGATGAACATTGG
*
187069 ATGTCAAATAAACATTAAATGATAAACATTGG
1 ATGTCAAATAAACATTAAATGATGAACATTGG
187101 ATGTCAAATAAACATTAAATGATGAACATTGG
1 ATGTCAAATAAACATTAAATGATGAACATTGG
187133 AT
1 AT
187135 TATGGTTATG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (32 bp):
ATGTCAAATAAACATTAAATGATGAACATTGG
Found at i:187084 original size:18 final size:18
Alignment explanation
Indices: 187061--187116 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
187051 TTAAATGATG
187061 AACATTGGATGTCAAATA
1 AACATTGGATGTCAAATA
**
187079 AACATTAAATG----ATA
1 AACATTGGATGTCAAATA
187093 AACATTGGATGTCAAATA
1 AACATTGGATGTCAAATA
187111 AACATT
1 AACATT
187117 AAATGATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 12 0.40
18 18 0.60
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (18 bp):
AACATTGGATGTCAAATA
Found at i:205822 original size:23 final size:23
Alignment explanation
Indices: 205779--205829 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
205769 TCGTTTAAAT
*
205779 GTTCACGAACATATTCATTTAGC
1 GTTCACGAACATATTCATTTACC
*
205802 GTTCACGAACAT-TTTATTTTACC
1 GTTCACGAACATATTCA-TTTACC
205825 GTTCA
1 GTTCA
205830 TTTATATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (23 bp):
GTTCACGAACATATTCATTTACC
Found at i:206821 original size:15 final size:16
Alignment explanation
Indices: 206788--206822 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
206778 TTCGTTAGAA
206788 TTAAGAGTTAGAATATT
1 TTAAGAGTTAG-ATATT
206805 TTAAGAGTTAG-TATT
1 TTAAGAGTTAGATATT
206820 TTA
1 TTA
206823 TTTTCATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
17 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (16 bp):
TTAAGAGTTAGATATT
Found at i:214393 original size:23 final size:24
Alignment explanation
Indices: 214365--214411 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
214355 TAGTTTGCAT
* *
214365 ATAATTTTTATTTAGGAT-TTTTA
1 ATAATTATTAATTAGGATATTTTA
214388 ATAATTATTAATTAGGATATTTTA
1 ATAATTATTAATTAGGATATTTTA
214412 GTTCGTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (24 bp):
ATAATTATTAATTAGGATATTTTA
Found at i:215113 original size:14 final size:14
Alignment explanation
Indices: 215085--215117 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
215075 ATGCATAAAT
215085 ACTAATAAAACTAA
1 ACTAATAAAACTAA
215099 ACTAAGTAAAA-TAA
1 ACTAA-TAAAACTAA
215113 ACTAA
1 ACTAA
215118 AATAGGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.64, C:0.12, G:0.03, T:0.21
Consensus pattern (14 bp):
ACTAATAAAACTAA
Found at i:221751 original size:7 final size:7
Alignment explanation
Indices: 221731--221776 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
221721 AAATAGCAAT
*
221731 ATCAGAA
1 ATCAGAG
221738 ATCAGAG
1 ATCAGAG
221745 --CAGAG
1 ATCAGAG
*
221750 AGCAGAG
1 ATCAGAG
221757 ATCAGAG
1 ATCAGAG
221764 ATCAGAG
1 ATCAGAG
221771 ATCAGA
1 ATCAGA
221777 ACAGAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 5 0.14
7 30 0.86
ACGTcount: A:0.46, C:0.15, G:0.28, T:0.11
Consensus pattern (7 bp):
ATCAGAG
Found at i:226840 original size:32 final size:32
Alignment explanation
Indices: 226804--226872 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
226794 AATAATGTAT
226804 AATCATTCAAAATCAAAACTCATGCATGCATA
1 AATCATTCAAAATCAAAACTCATGCATGCATA
226836 AATCATTCAAAATCAAAACTCATGCATGCATA
1 AATCATTCAAAATCAAAACTCATGCATGCATA
226868 AATCA
1 AATCA
226873 AAATGAGCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.25
Consensus pattern (32 bp):
AATCATTCAAAATCAAAACTCATGCATGCATA
Found at i:238513 original size:15 final size:15
Alignment explanation
Indices: 238495--238550 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
238485 TAACCGGTTT
238495 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
238510 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
238527 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
238542 CGATTTTAA
1 CGGTTTTAA
238551 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:238523 original size:17 final size:17
Alignment explanation
Indices: 238498--238548 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
238488 CCGGTTTCGG
238498 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
238515 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
238530 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
238547 TT
1 TT
238549 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:238967 original size:13 final size:13
Alignment explanation
Indices: 238946--239000 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
238936 AAGTTCGATA
*
238946 AATTCAAATACTT
1 AATTGAAATACTT
238959 AATTGAAATACTT
1 AATTGAAATACTT
* *
238972 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
238986 AATTGAAATACTT
1 AATTGAAATACTT
238999 AA
1 AA
239001 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Done.