Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007850.1 Hibiscus syriacus cultivar Beakdansim tig00110209_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: 1775394
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:5501 original size:31 final size:31
Alignment explanation
Indices: 5463--5525 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
5453 CCCGAAGGAC
*
5463 CAGTCCATA-GATCCTGAAGAACCTAGGTAAA
1 CAGTCCATATGATCC-GAAGAACATAGGTAAA
*
5494 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGATCCGAAGAACATAGGTAAA
5525 C
1 C
5526 CCTCGACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGATCCGAAGAACATAGGTAAA
Found at i:11085 original size:18 final size:18
Alignment explanation
Indices: 11062--11098 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
11052 GGACATATGG
*
11062 ATAGTGGTCTTTCGGGAC
1 ATAGTGGTCATTCGGGAC
11080 ATAGTGGTCATTCGGGAC
1 ATAGTGGTCATTCGGGAC
11098 A
1 A
11099 AATATTCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (18 bp):
ATAGTGGTCATTCGGGAC
Found at i:12049 original size:2 final size:2
Alignment explanation
Indices: 12042--12073 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12032 TAATTTATGC
12042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12074 ATGAAAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12828 original size:21 final size:21
Alignment explanation
Indices: 12804--12877 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
12794 GAGTTAAGTT
12804 CTTTCGATGAAAGGACTTATC
1 CTTTCGATGAAAGGACTTATC
* * *
12825 CTTTTGATGAAAGGGCTTAAC
1 CTTTCGATGAAAGGACTTATC
*
12846 CTTTTCG-TGAAAGGATTTAATC
1 C-TTTCGATGAAAGGACTT-ATC
*
12868 TTTTC-ATGAA
1 CTTTCGATGAA
12878 GAGAATTGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
21 36 0.86
22 6 0.14
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (21 bp):
CTTTCGATGAAAGGACTTATC
Found at i:17113 original size:23 final size:22
Alignment explanation
Indices: 17087--17155 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
17077 CACCACAGCT
* *
17087 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACC-AAGTGCCA
*
17110 CGTAGAAATGCACCATAGTGCCA
1 CGTAGAATTGCACCA-AGTGCCA
* *
17133 CGTAGGATTACACCAAAGTGCCA
1 CGTAGAATTGCACC-AAGTGCCA
17156 TATAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (22 bp):
CGTAGAATTGCACCAAGTGCCA
Found at i:17438 original size:30 final size:29
Alignment explanation
Indices: 17385--17443 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
17375 TGTAAATATA
* *
17385 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
17415 TCACATATACATTTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
17444 GTAAATTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:18616 original size:20 final size:22
Alignment explanation
Indices: 18591--18648 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
18581 TTCCCCTTGA
18591 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
18611 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
18634 ACGTGCATCGATGCA
1 A-GTGCATCGATGCA
18649 CTAACCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:20974 original size:21 final size:22
Alignment explanation
Indices: 20943--20993 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 22
20933 GTGTTAAAAA
20943 TTTATTTATATAAAAT-TAA-AT
1 TTTA-TTATATAAAATATAACAT
20964 TGTTATTATATAAAATATAACAT
1 T-TTATTATATAAAATATAACAT
20987 TTTATTA
1 TTTATTA
20994 ATGAGATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 12 0.44
22 12 0.44
23 3 0.11
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTATTATATAAAATATAACAT
Found at i:21751 original size:31 final size:33
Alignment explanation
Indices: 21716--21787 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
21706 TACAATATTG
21716 TATATATACCCTT-AA-TTGTTTGTTAGCACTT-
1 TATATATACCCTTCAATTTGTTTGTTAGCA-TTA
* * *
21747 TATATATATCGTTCAATTTTTTTGTTAGCATTA
1 TATATATACCCTTCAATTTGTTTGTTAGCATTA
21780 TATATATA
1 TATATATA
21788 TATAACATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 11 0.31
32 4 0.11
33 20 0.57
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.51
Consensus pattern (33 bp):
TATATATACCCTTCAATTTGTTTGTTAGCATTA
Found at i:22524 original size:20 final size:21
Alignment explanation
Indices: 22499--22591 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
22489 TTTTCCCAAT
*
22499 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
22519 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
22540 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
22560 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
22581 TCGCAATGCGA
1 TCGCAATGCGA
22592 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:22544 original size:41 final size:41
Alignment explanation
Indices: 22499--22591 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
22489 TTTTCCCAAT
22499 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
22540 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
22581 TCGCAATGCGA
1 TCGCAATGCGA
22592 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:22604 original size:41 final size:41
Alignment explanation
Indices: 22518--22652 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
22508 GAATAAGTAA
* *
22518 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
22559 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
22600 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
22641 TTCGCAACGCGA
1 ATCGCAACGCGA
22653 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:22605 original size:20 final size:19
Alignment explanation
Indices: 22580--22714 Score: 99
Period size: 20 Copynumber: 6.7 Consensus size: 19
22570 AATTGGGAAA
*
22580 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* * *
22600 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTAC--T
*
22621 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAC-TACT
*
22641 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* *
22661 TTCGCAACGCGATTCTAACT
1 ATCGCAACGCGATACT-ACT
* *
22681 TTCGCAACGCGATAATACAT
1 ATCGCAACGCGATACTAC-T
*
22701 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
22715 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
19 5 0.05
20 64 0.67
21 23 0.24
22 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (19 bp):
ATCGCAACGCGATACTACT
Found at i:22910 original size:22 final size:22
Alignment explanation
Indices: 22882--22925 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
22872 CACTCTCTCA
22882 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
**
22904 CCCATCTCCGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
22926 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:23215 original size:20 final size:20
Alignment explanation
Indices: 23190--23227 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23180 CGATTCTCTC
23190 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
23210 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
23228 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:24567 original size:18 final size:18
Alignment explanation
Indices: 24546--24593 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
24536 TCCACTTCGG
*
24546 GAGCCATCATCTCGCCCA
1 GAGCCATCATCTCACCCA
* *
24564 GAGCTATCACCTCACCCA
1 GAGCCATCATCTCACCCA
24582 GAGCCATCATCT
1 GAGCCATCATCT
24594 GATCGACCCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.25, C:0.42, G:0.15, T:0.19
Consensus pattern (18 bp):
GAGCCATCATCTCACCCA
Found at i:25126 original size:19 final size:20
Alignment explanation
Indices: 25072--25117 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
25062 TAGTTTACTT
*
25072 TCGCAACACGAAAATGACTA
1 TCGCAACACGGAAATGACTA
*
25092 TCGCAACACGGAAATGGCTA
1 TCGCAACACGGAAATGACTA
25112 TCGCAA
1 TCGCAA
25118 TGCGAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGGAAATGACTA
Found at i:25134 original size:39 final size:36
Alignment explanation
Indices: 25111--25208 Score: 114
Period size: 33 Copynumber: 2.7 Consensus size: 36
25101 GGAAATGGCT
25111 ATCGCAATGCGAAATGAAAATCGCAACGACAAA---
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAATGC
25144 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATCGC
1 ATCGCAATGCGAAATGAAAATCGCAACGAC-AAAT-GC
* *
25181 AACGCGAAACGCGAAATGAAAATCGCAA
1 ATCGC--AATGCGAAATGAAAATCGCAA
25209 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
32 13 0.24
33 19 0.35
37 4 0.07
39 10 0.18
40 9 0.16
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.11
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAATGC
Found at i:25146 original size:14 final size:14
Alignment explanation
Indices: 25127--25184 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
25117 ATGCGAAATG
25127 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
25141 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
25157 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
25173 AAAATCGCAACG
1 AAAATCGCAACG
25185 CGAAACGCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:25169 original size:32 final size:33
Alignment explanation
Indices: 25111--25189 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
25101 GGAAATGGCT
25111 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
25144 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
25176 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
25190 CGCGAAATGA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:25244 original size:14 final size:14
Alignment explanation
Indices: 25225--25282 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
25215 TTGTGTTTCG
25225 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
25239 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
25255 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
25271 CGTTGCGATTTT
1 CGTTGCGATTTT
25283 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:25259 original size:32 final size:33
Alignment explanation
Indices: 25220--25298 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
25210 GCGATTTGTG
25220 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
25252 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
25285 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
25299 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:25317 original size:20 final size:19
Alignment explanation
Indices: 25283--25338 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
25273 TTGCGATTTT
*
25283 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
25302 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
25322 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
25339 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:27227 original size:14 final size:14
Alignment explanation
Indices: 27208--27243 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
27198 ATTGTTTAAT
27208 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
27222 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
27236 TGATTTGT
1 TGATTTGT
27244 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:27382 original size:19 final size:19
Alignment explanation
Indices: 27360--27396 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
27350 ATCGCAACGA
*
27360 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGAGAAAT
27379 GAAAATCGCAATGAGAAA
1 GAAAATCGCAATGAGAAA
27397 ATCGCAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGAGAAAT
Found at i:27404 original size:14 final size:14
Alignment explanation
Indices: 27350--27405 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
27340 CGAAATGGCT
*
27350 ATCGCAACGAGAAA
1 ATCGCAATGAGAAA
27364 ATCGCAATGCGAAATGAAA
1 ATCGCAAT--G--A-GAAA
27383 ATCGCAATGAGAAA
1 ATCGCAATGAGAAA
27397 ATCGCAATG
1 ATCGCAATG
27406 CGATTTTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 12 0.33
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (14 bp):
ATCGCAATGAGAAA
Found at i:27421 original size:33 final size:33
Alignment explanation
Indices: 27331--27408 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
27321 AAAACAGACT
* ***
27331 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
27364 ATCGCAATGCGAAATGAAAATCGCAATGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
27397 ATCGCAATGCGA
1 ATCGCAATGCGA
27409 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:27452 original size:20 final size:20
Alignment explanation
Indices: 27427--27484 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
27417 TCGCATTGCG
*
27427 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
27447 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
27467 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
27485 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:28568 original size:24 final size:24
Alignment explanation
Indices: 28541--28594 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
28531 GTATTCAAAA
* *
28541 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
28565 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
28589 TTTGAT
1 TTTGAT
28595 GAAGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:31161 original size:19 final size:19
Alignment explanation
Indices: 31137--31199 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 19
31127 AACGCTAATT
31137 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
**
31156 TCGCAA--CG--A-GGGAA
1 TCGCAATGCGAAATGAAAA
31170 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
* *
31189 TTGCAACGCGA
1 TCGCAATGCGA
31200 TTTTAATTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
14 9 0.27
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.55
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.14
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:31218 original size:19 final size:20
Alignment explanation
Indices: 31196--31240 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
31186 AAATTGCAAC
*
31196 GCGATTTT-AATTTCGTGTT
1 GCGATTTTCAATTTCGCGTT
*
31215 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAATTTCGCGTT
31235 GCGATT
1 GCGATT
31241 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
GCGATTTTCAATTTCGCGTT
Found at i:31271 original size:19 final size:19
Alignment explanation
Indices: 31196--31272 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 19
31186 AAATTGCAAC
* *
31196 GCGATTTTAATTTCGTGTT
1 GCGATTTTCATTTCGCGTT
31215 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
*
31235 GCGA--TTC---TCTCGTT
1 GCGATTTTCATTTCGCGTT
*
31249 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCGTT
31268 GCGAT
1 GCGAT
31273 AGTACTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
14 10 0.21
16 3 0.06
18 3 0.06
19 19 0.40
20 12 0.26
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:31398 original size:14 final size:14
Alignment explanation
Indices: 31379--31415 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
31369 CATCAATTAA
31379 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
31393 ACAAATCACCTTTT
1 ACAAATCAACTTTT
31407 ACAAATCAA
1 ACAAATCAA
31416 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:32795 original size:21 final size:20
Alignment explanation
Indices: 32729--32795 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
32719 GTGAATCGGG
*
32729 CTCTTGAATGGTGGGAGGGA
1 CTCTTGAACGGTGGGAGGGA
* * ** *
32749 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAG-GGA
32771 CTCTTGAACGGTGGGAGAGGA
1 CTCTTGAACGGTGGGAG-GGA
32792 CTCT
1 CTCT
32796 CGAGGAATGA
Statistics
Matches: 33, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGA
Found at i:32814 original size:42 final size:40
Alignment explanation
Indices: 32729--32851 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 40
32719 GTGAATCGGG
* * * *
32729 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTC-TCGAGGATGACAGGGGC
*
32771 CTCTTGAACGGTGGGAGAGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAG-GGACTCTCGAGG-ATGACAGGGGC
* * * *
32813 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAG-GGACTCTCGA-GGATGACAGG
32852 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.87
43 5 0.07
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.22
Consensus pattern (40 bp):
CTCTTGAACGGTGGGAGGGACTCTCGAGGATGACAGGGGC
Found at i:35140 original size:21 final size:21
Alignment explanation
Indices: 35114--35158 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35104 GATTTCTGGG
* *
35114 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
35135 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
35156 CAA
1 CAA
35159 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:35212 original size:22 final size:22
Alignment explanation
Indices: 35185--35246 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
35175 AGTATGTCAT
35185 GGGGGAACCGATACCCCCATAG
1 GGGGGAACCGATACCCCCATAG
35207 GGGGGAACCGATACCCCCATAG
1 GGGGGAACCGATACCCCCATAG
*
35229 GGGGGAACCGATTCCCCC
1 GGGGGAACCGATACCCCC
35247 TAAAGGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.10
Consensus pattern (22 bp):
GGGGGAACCGATACCCCCATAG
Found at i:36206 original size:2 final size:2
Alignment explanation
Indices: 36199--36232 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
36189 GAACATGTGA
36199 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
36233 GTTTAAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36905 original size:13 final size:13
Alignment explanation
Indices: 36887--36949 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
36877 TTATATGGCA
36887 CTACGGTGCAATT
1 CTACGGTGCAATT
36900 CTACGG-GC-A--
1 CTACGGTGCAATT
*
36909 CTTCGGTGCAATT
1 CTACGGTGCAATT
36922 CTACGG-GC-A--
1 CTACGGTGCAATT
*
36931 CTTCGGTGCAATT
1 CTACGGTGCAATT
36944 CTACGG
1 CTACGG
36950 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:36915 original size:22 final size:22
Alignment explanation
Indices: 36883--36963 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
36873 ATCATTATAT
*
36883 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
36905 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
36927 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
36950 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
36964 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:40164 original size:21 final size:21
Alignment explanation
Indices: 40138--40182 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40128 GATTTCTGGG
* *
40138 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
40159 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
40180 CAA
1 CAA
40183 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:40236 original size:22 final size:22
Alignment explanation
Indices: 40209--40270 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
40199 AGTATGTCAT
40209 GGGGGAACCGATACCCCCATAG
1 GGGGGAACCGATACCCCCATAG
40231 GGGGGAACCGATACCCCCATAG
1 GGGGGAACCGATACCCCCATAG
*
40253 GGGGGAACCGATTCCCCC
1 GGGGGAACCGATACCCCC
40271 TAAAGGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.10
Consensus pattern (22 bp):
GGGGGAACCGATACCCCCATAG
Found at i:41228 original size:2 final size:2
Alignment explanation
Indices: 41221--41270 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
41211 GAACATGTGA
41221 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
41263 AT AT AT AT
1 AT AT AT AT
41271 GTTTAAGAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41943 original size:13 final size:13
Alignment explanation
Indices: 41925--41987 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
41915 TTATATGGCA
41925 CTACGGTGCAATT
1 CTACGGTGCAATT
41938 CTACGG-GC-A--
1 CTACGGTGCAATT
*
41947 CTTCGGTGCAATT
1 CTACGGTGCAATT
41960 CTACGG-GC-A--
1 CTACGGTGCAATT
*
41969 CTTCGGTGCAATT
1 CTACGGTGCAATT
41982 CTACGG
1 CTACGG
41988 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:41953 original size:22 final size:22
Alignment explanation
Indices: 41921--42001 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
41911 ATCATTATAT
*
41921 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
41943 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
41965 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
41988 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
42002 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:43193 original size:33 final size:33
Alignment explanation
Indices: 43136--43234 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
43126 ACGAGATAAT
*
43136 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
43170 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
43203 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
43235 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:43228 original size:19 final size:19
Alignment explanation
Indices: 43111--43295 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
43101 TCTTTTGGTT
*
43111 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
43130 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
43150 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
43168 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
43184 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
43202 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
43217 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
* *
43237 GAAATAAAAATCGCAACGG
1 GAAATGAAAATCGCAACGC
43256 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
43275 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
43294 GA
1 GA
43296 TTTTTGTTTC
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 60 0.44
20 45 0.33
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:43249 original size:39 final size:38
Alignment explanation
Indices: 43206--43295 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
43196 GCGACCAGAC
43206 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
* *
43245 AATCGCAACGGGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
43283 AATCGCAATGCGA
1 AATCGCAACGCGA
43296 TTTTTGTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 21 0.45
39 26 0.55
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:43327 original size:19 final size:19
Alignment explanation
Indices: 43291--43335 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
43281 AAAATCGCAA
*
43291 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
43310 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
43329 TGCGATT
1 TGCGATT
43336 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:43954 original size:20 final size:20
Alignment explanation
Indices: 43929--43982 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
43919 GATTTTGTAT
43929 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
43949 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
*
43969 TATTGCATTGCGAT
1 TATCGCATTGCGAT
43983 TTTCCCAATT
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:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:44093 original size:21 final size:21
Alignment explanation
Indices: 44053--44093 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
44043 ACTGTATACC
**
44053 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
44074 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
44094 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:46812 original size:2 final size:2
Alignment explanation
Indices: 46805--46836 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46795 TATTTAAAAT
46805 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
46837 GAGAGAGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53206 original size:18 final size:18
Alignment explanation
Indices: 53185--53308 Score: 58
Period size: 18 Copynumber: 6.6 Consensus size: 18
53175 TACTTAAATT
*
53185 AATTATATTTTTAATAAA
1 AATTATAATTTTAATAAA
*
53203 AATTATAATTTTATTAAA
1 AATTATAATTTTAATAAA
*
53221 AGTATAATTAAATTTTAAT--A
1 A--ATTA-T-AATTTTAATAAA
* *
53241 AATGATTAATTTTAA-ATA
1 AATTA-TAATTTTAATAAA
* *
53259 AATTCTTATTTTGTAAATATTAA
1 AATT-ATAATTT-T-AATA--AA
*
53282 AATTATAATTTTAAT-AG
1 AATTATAATTTTAATAAA
53299 AATTATAATT
1 AATTATAATT
53309 AAATTATAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
17 19 0.23
18 31 0.38
19 1 0.01
20 10 0.12
21 3 0.04
22 13 0.16
23 5 0.06
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (18 bp):
AATTATAATTTTAATAAA
Found at i:53422 original size:17 final size:18
Alignment explanation
Indices: 53400--53433 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
53390 TAAAATTATA
53400 ATTAATTTT-AATAAATG
1 ATTAATTTTAAATAAATG
53417 ATTAATTTTAAATAAAT
1 ATTAATTTTAAATAAAT
53434 CTTTATACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTAATTTTAAATAAATG
Found at i:55387 original size:23 final size:21
Alignment explanation
Indices: 55328--55389 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
55318 AATGTAGACG
*
55328 AACAACGTGTCACAAGAATAGA
1 AACAA-GTGCCACAAGAATAGA
*
55350 AACAAGTGCTACAAGAATAGA
1 AACAAGTGCCACAAGAATAGA
* *
55371 GTAACACGTGCCGCAAGAA
1 --AACAAGTGCCACAAGAA
55390 CATAGTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 14 0.42
22 5 0.15
23 14 0.42
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (21 bp):
AACAAGTGCCACAAGAATAGA
Found at i:55967 original size:18 final size:18
Alignment explanation
Indices: 55930--55972 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
55920 TATTAATTTT
*
55930 TTTTTGTAATTTTTTGTA
1 TTTTTGTAATTTTTTATA
55948 TTTTTGT-A-TTTTTATA
1 TTTTTGTAATTTTTTATA
*
55964 TATTTGTAA
1 TTTTTGTAA
55973 AATTAATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 13 0.59
17 2 0.09
18 7 0.32
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (18 bp):
TTTTTGTAATTTTTTATA
Found at i:57684 original size:2 final size:2
Alignment explanation
Indices: 57677--57705 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57667 TCAAATACTA
57677 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
57706 ATAATGATTC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:63240 original size:22 final size:23
Alignment explanation
Indices: 63189--63241 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
63179 TTTTTCTCGG
*
63189 TTTTGTCTC-TTGTTTCTCTGTA
1 TTTTGTCTCTTTGTTCCTCTGTA
* *
63211 TCTT-TCTCTTTGTTCCTCT-TT
1 TTTTGTCTCTTTGTTCCTCTGTA
63232 TTTTGTCTCT
1 TTTTGTCTCT
63242 GTCCCTGGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.02, C:0.23, G:0.09, T:0.66
Consensus pattern (23 bp):
TTTTGTCTCTTTGTTCCTCTGTA
Found at i:63682 original size:3 final size:3
Alignment explanation
Indices: 63674--63713 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
63664 TTAATATATT
*
63674 TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
63714 TAATTAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:64179 original size:112 final size:111
Alignment explanation
Indices: 64049--64683 Score: 1049
Period size: 112 Copynumber: 5.7 Consensus size: 111
64039 CAAAAAGTTG
* *
64049 TCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCT-GAAAATGTTGATCCATCAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAA-GATGATCCATCAA
* * * **
64113 TTGATGAATTCATGTAAAAGGTTAAACAAGCTCTTCTCATTATGAACT
65 ATGATGGATTCA-GTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
64161 T-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
1 TCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAGATGATCCATCA
* * *
64225 AGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
64 AATGATGGATTCAG-TAAAAGGTTGAACAAATTCTTCTCATTATGAACT
*
64274 TCTTCTTCCTTCTTCTGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
64339 TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
66 TGATGGATTCA-GTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
*
64386 TCTTCTTCCTTATTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
64451 TGATGGATTCAGATAAAAGGTTGAACAAATTCTTCTCATTATGAACT
66 TGATGGATTCAG-TAAAAGGTTGAACAAATTCTTCTCATTATGAACT
* *
64498 TCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCCAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
64563 TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
66 TGATGGATTCA-GTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
64610 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
*
64675 TGATAGATT
66 TGATGGATT
64684 TGAATCTTTG
Statistics
Matches: 496, Mismatches: 19, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
111 2 0.00
112 391 0.79
113 97 0.20
114 6 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (111 bp):
TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
TGATGGATTCAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
Found at i:64390 original size:17 final size:17
Alignment explanation
Indices: 64368--64428 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 17
64358 GTTGAACAAA
64368 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* *
64385 TTCTTCTTCCTTATTCAGATGAG
1 TTCTTC-TCATTA-T--GA--AC
64408 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
64425 TTCT
1 TTCT
64429 CTGGAAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
17 11 0.32
18 5 0.15
19 3 0.09
21 3 0.09
22 5 0.15
23 7 0.21
ACGTcount: A:0.20, C:0.23, G:0.08, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:65491 original size:92 final size:84
Alignment explanation
Indices: 65405--65724 Score: 509
Period size: 83 Copynumber: 3.7 Consensus size: 84
65395 GTAGTTCTTA
*
65405 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCAAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCAAA
65470 ATTCAATGATTGGTTCTGTAGTTCTT
66 ATTCAATGATTGGTTC--T-G----T
*
65496 ACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCAA
65561 AATTCAATGATTGGTTCTGT
65 AATTCAATGATTGGTTCTGT
* *
65581 CC-AACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCAAA
65645 ATTCAATGATTGGTTCTG-
66 ATTCAATGATTGGTTCTGT
*
65663 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTC
65725 CAATTAATGT
Statistics
Matches: 221, Mismatches: 6, Indels: 11
0.93 0.03 0.05
Matches are distributed among these distances:
82 2 0.01
83 135 0.61
84 2 0.01
85 1 0.00
89 1 0.00
90 1 0.00
92 79 0.36
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (84 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCAAA
ATTCAATGATTGGTTCTGT
Found at i:66517 original size:16 final size:18
Alignment explanation
Indices: 66479--66523 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
66469 TTCATAGAAG
*
66479 AATAAATTGAATTTCCAA
1 AATAAATTGAATCTCCAA
66497 AATAAATTGAATCT-C-A
1 AATAAATTGAATCTCCAA
66513 AATAAATTGAA
1 AATAAATTGAA
66524 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 13 0.50
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (18 bp):
AATAAATTGAATCTCCAA
Found at i:66868 original size:11 final size:10
Alignment explanation
Indices: 66854--66893 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
66844 CCCCTTTCTT
66854 TTTTCTTTTTC
1 TTTT-TTTTTC
66865 TTTTTTTCTTC
1 TTTTTTT-TTC
66876 -TTTTTTTTC
1 TTTTTTTTTC
66885 TTTTTTTTT
1 TTTTTTTTT
66894 TTCAAGCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 3 0.11
10 17 0.63
11 7 0.26
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:66876 original size:24 final size:24
Alignment explanation
Indices: 66849--66896 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
66839 TGACCCCCCT
66849 TTCTTTTTTCTT-TTTCTTTTTTTC
1 TTCTTTTTT-TTCTTTCTTTTTTTC
*
66873 TTCTTTTTTTTCTTTTTTTTTTTC
1 TTCTTTTTTTTCTTTCTTTTTTTC
66897 AAGCATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (24 bp):
TTCTTTTTTTTCTTTCTTTTTTTC
Found at i:66880 original size:12 final size:12
Alignment explanation
Indices: 66849--66896 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
66839 TGACCCCCCT
*
66849 TTCTTTTTTCTTT
1 TTCTTTTTT-TTC
66862 TTC-TTTTTTTC
1 TTCTTTTTTTTC
66873 TTCTTTTTTTTC
1 TTCTTTTTTTTC
*
66885 TTTTTTTTTTTC
1 TTCTTTTTTTTC
66897 AAGCATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
11 5 0.16
12 24 0.75
13 3 0.09
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTCTTTTTTTTC
Found at i:66884 original size:20 final size:21
Alignment explanation
Indices: 66848--66891 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
66838 TTGACCCCCC
*
66848 TTTCTTTTTTCTTTTTCTTTT
1 TTTCTTCTTTCTTTTTCTTTT
66869 TTTCTTCTTT-TTTTTCTTTT
1 TTTCTTCTTTCTTTTTCTTTT
66889 TTT
1 TTT
66892 TTTTCAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTCTTCTTTCTTTTTCTTTT
Found at i:66890 original size:9 final size:9
Alignment explanation
Indices: 66852--66892 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
66842 CCCCCCTTTC
66852 TTTTTTCTT
1 TTTTTTCTT
*
66861 TTTCTT-TT
1 TTTTTTCTT
*
66869 TTTCTTCTT
1 TTTTTTCTT
66878 TTTTTTCTT
1 TTTTTTCTT
66887 TTTTTT
1 TTTTTT
66893 TTTCAAGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 8 0.28
9 21 0.72
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:79683 original size:11 final size:11
Alignment explanation
Indices: 79662--79691 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
79652 TGTAATTAAT
79662 TATTT-ATATA
1 TATTTAATATA
79672 TATTTAATATA
1 TATTTAATATA
79683 TATTTAATA
1 TATTTAATA
79692 ATAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTTAATATA
Found at i:79695 original size:3 final size:3
Alignment explanation
Indices: 79687--79760 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
79677 AATATATATT
*
79687 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
79735 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
79761 TGGATAAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:83769 original size:6 final size:6
Alignment explanation
Indices: 83758--83800 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
83748 GACACGTATT
83758 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
83801 GACGGGACGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:84690 original size:41 final size:42
Alignment explanation
Indices: 84575--84857 Score: 437
Period size: 42 Copynumber: 6.8 Consensus size: 42
84565 ATTTGGACTA
84575 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
1 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
*
84617 TCGCAATGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
1 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
* * *
84659 TCGCAACGAA-TTGGGATGAATTGCAATGCGAACTTCGCCTG
1 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
* *
84700 TCGCAAC-AAATTGGAATGAATCGCAATGCGAACTTCGCCTG
1 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
* *
84741 TCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGACTA
1 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
* * *
84782 TTGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGACTA
1 TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
*
84824 TTGCAACGAATTTGGAATGAATCGCAACGCGAAC
1 TCGCAACGAATTTGGAATGAATCGCAACGCGAAC
84858 CTCGACTATC
Statistics
Matches: 227, Mismatches: 11, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
40 2 0.01
41 108 0.48
42 117 0.52
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.22
Consensus pattern (42 bp):
TCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTG
Found at i:88219 original size:21 final size:21
Alignment explanation
Indices: 88193--88233 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
88183 GATTTTTTGT
88193 TTTTGTTATTTTTTTACTTTC
1 TTTTGTTATTTTTTTACTTTC
* *
88214 TTTTGTTTTTTTTTTTCTTT
1 TTTTGTTATTTTTTTACTTT
88234 TCCTTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.83
Consensus pattern (21 bp):
TTTTGTTATTTTTTTACTTTC
Found at i:88234 original size:27 final size:28
Alignment explanation
Indices: 88187--88244 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
88177 TTTTCTGATT
88187 TTTTGTTTTTGTTATTTTTTTAC-TTTC
1 TTTTGTTTTTGTTATTTTTTTACTTTTC
* *
88214 TTTTGTTTTT-TTTTTTCTTTTCCTTTTC
1 TTTTGTTTTTGTTATTT-TTTTACTTTTC
88242 TTT
1 TTT
88245 GTTACATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 5 0.19
27 15 0.56
28 7 0.26
ACGTcount: A:0.03, C:0.10, G:0.05, T:0.81
Consensus pattern (28 bp):
TTTTGTTTTTGTTATTTTTTTACTTTTC
Found at i:88235 original size:22 final size:22
Alignment explanation
Indices: 88193--88240 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
88183 GATTTTTTGT
88193 TTTTGTTATTTTTTTACTTT-C
1 TTTTGTTATTTTTTTACTTTCC
* *
88214 TTTTGTTTTTTTTTTTCTTTTCC
1 TTTTGTTATTTTTTTAC-TTTCC
88237 TTTT
1 TTTT
88241 CTTTGTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
22 3 0.13
23 5 0.22
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.81
Consensus pattern (22 bp):
TTTTGTTATTTTTTTACTTTCC
Found at i:88247 original size:27 final size:27
Alignment explanation
Indices: 88167--88223 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
88157 AATATATACT
*
88167 TTTTTGTTATTTTTCTGA--TT-TTTTG
1 TTTTTGTTATTTTT-TTACTTTCTTTTG
88192 TTTTTGTTATTTTTTTACTTTCTTTTG
1 TTTTTGTTATTTTTTTACTTTCTTTTG
88219 TTTTT
1 TTTTT
88224 TTTTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 2 0.07
25 14 0.50
26 2 0.07
27 10 0.36
ACGTcount: A:0.07, C:0.05, G:0.09, T:0.79
Consensus pattern (27 bp):
TTTTTGTTATTTTTTTACTTTCTTTTG
Found at i:89286 original size:20 final size:20
Alignment explanation
Indices: 89261--89298 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
89251 TGTTGGGAAA
*
89261 TTAATTGAGTTCCCTAATCT
1 TTAATTGAGTGCCCTAATCT
89281 TTAATTGAGTGCCCTAAT
1 TTAATTGAGTGCCCTAAT
89299 AGCAATTCTT
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:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (20 bp):
TTAATTGAGTGCCCTAATCT
Found at i:90036 original size:18 final size:19
Alignment explanation
Indices: 90001--90041 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
89991 TTGTTGTTGT
*
90001 TTTTGTTTTTTTACTTT-C
1 TTTTGTTATTTTACTTTCC
90019 TTTTGTTATTTT-CTTTTCC
1 TTTTGTTATTTTAC-TTTCC
90038 TTTT
1 TTTT
90042 CCTTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.70
19 5 0.25
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTGTTATTTTACTTTCC
Found at i:92762 original size:2 final size:2
Alignment explanation
Indices: 92755--92820 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
92745 GGTTAATAGA
92755 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
92797 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
92821 TGAAACAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96218 original size:315 final size:315
Alignment explanation
Indices: 95646--96594 Score: 1817
Period size: 315 Copynumber: 3.0 Consensus size: 315
95636 ACATTTACTA
95646 GGAAACATATTTTGCCCAAGTGGAAGATTGTAGGATTAAAATCCATAATTATGGGCATATGTTTA
1 GGAAACATATTTTGCCCAAGTGGAAGATTGTAGGATTAAAATCCATAATTATGGGCATATGTTTA
95711 TAATGCATATTGTTATCATAAAATATAGCATAAATTAAGTGATCGATTATGTTATAAAGTCATAA
66 TAATGCATATTGTTATCATAAAATATAGCATAAATTAAGTGATCGATTATGTTATAAAGTCATAA
*
95776 GGTATTAGAAGTGTCATGGAAATAAAAGTGTAGATACTATTAAAATTGTATTTATATTTCGATGA
131 GGTATTAGAAGTGTCATGGAAATAAAAGTGTAGATACTATTAAAATTGTATTTATAATTCGATGA
95841 AGACAATAACTTATTCTTAAATCAACTATATAAAGGGGTTGTGGTCCCCAAGAAATAGACAATCT
196 AGACAATAACTTATTCTTAAATCAACTATATAAAGGGGTTGTGGTCCCCAAGAAATAGACAATCT
*
95906 TGTATTTACTCTTATCCTCGTCATAGAGTTTATACTTAAGGGACTCTATCTTCTT
261 CGTATTTACTCTTATCCTCGTCATAGAGTTTATACTTAAGGGACTCTATCTTCTT
95961 GGAAACATATTTTGCCCAAGTGGAAGATTGTAGGATTAAAATCCATAATTATGGGCATATGTTTA
1 GGAAACATATTTTGCCCAAGTGGAAGATTGTAGGATTAAAATCCATAATTATGGGCATATGTTTA
*
96026 TAATGCATATTGTTATCATAAAATATAGCATAAATTAAGTGATCAATTATGTTATAAAGTCATAA
66 TAATGCATATTGTTATCATAAAATATAGCATAAATTAAGTGATCGATTATGTTATAAAGTCATAA
96091 GGTATTAGAAGTGTCATGGAAATAAAAGTGTAGATACTATTAAAATTGTATTTATAATTCGATGA
131 GGTATTAGAAGTGTCATGGAAATAAAAGTGTAGATACTATTAAAATTGTATTTATAATTCGATGA
96156 AGACAATAACTTATTCTTAAATCAACTATATAAAGGGGTTGTGGTCCCCAAGAAATAGACAATCT
196 AGACAATAACTTATTCTTAAATCAACTATATAAAGGGGTTGTGGTCCCCAAGAAATAGACAATCT
*
96221 CGTATTTACTCTTATCCCCGTCATAGAGTTTATACTTAAGGGACTCTATCTTCTT
261 CGTATTTACTCTTATCCTCGTCATAGAGTTTATACTTAAGGGACTCTATCTTCTT
* * *
96276 GGAAACATATTTTTCCCAAATGGAAGATTGTAGGATTAAAATCCATAATTATAGGCATATGTTTA
1 GGAAACATATTTTGCCCAAGTGGAAGATTGTAGGATTAAAATCCATAATTATGGGCATATGTTTA
96341 TAATGCATATTGTTATCATAAAATATAGCATAAATTAAGTGATCGATTATGTTATAAAGTCATAA
66 TAATGCATATTGTTATCATAAAATATAGCATAAATTAAGTGATCGATTATGTTATAAAGTCATAA
96406 GGTATTAGAAGTGTCATGGAAATAAAAGTGTAGATACTATTAAAATTGTATTTATAATTCGATGA
131 GGTATTAGAAGTGTCATGGAAATAAAAGTGTAGATACTATTAAAATTGTATTTATAATTCGATGA
* *
96471 AGACAATAACTTATTATTAAATCAACTATATAAAGGGGTTGTGGTCCCTAAGAAATAGACAATCT
196 AGACAATAACTTATTCTTAAATCAACTATATAAAGGGGTTGTGGTCCCCAAGAAATAGACAATCT
96536 CGTATTTACTCTTATCCTCGTCATAGAGTTTATACTTAAGGGACTCTATCTTCTT
261 CGTATTTACTCTTATCCTCGTCATAGAGTTTATACTTAAGGGACTCTATCTTCTT
96591 GGAA
1 GGAA
96595 GATCACAACG
Statistics
Matches: 623, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
315 623 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (315 bp):
GGAAACATATTTTGCCCAAGTGGAAGATTGTAGGATTAAAATCCATAATTATGGGCATATGTTTA
TAATGCATATTGTTATCATAAAATATAGCATAAATTAAGTGATCGATTATGTTATAAAGTCATAA
GGTATTAGAAGTGTCATGGAAATAAAAGTGTAGATACTATTAAAATTGTATTTATAATTCGATGA
AGACAATAACTTATTCTTAAATCAACTATATAAAGGGGTTGTGGTCCCCAAGAAATAGACAATCT
CGTATTTACTCTTATCCTCGTCATAGAGTTTATACTTAAGGGACTCTATCTTCTT
Found at i:97156 original size:32 final size:32
Alignment explanation
Indices: 97118--97215 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 32
97108 TTGATCAATA
97118 TCGGGTCGGGTCAATACCAGATCGGTTGATTT
1 TCGGGTCGGGTCAATACCAGATCGGTTGATTT
* ** * *
97150 TTGGGTCTAGTTAATACCTGATCGGTTAGA-TT
1 TCGGGTCGGGTCAATACCAGATCGGTT-GATTT
* *
97182 TCGGGTAGGGTCAATATCAGATCGGTTGATTT
1 TCGGGTCGGGTCAATACCAGATCGGTTGATTT
97214 TC
1 TC
97216 AATTTAGGTC
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
31 2 0.04
32 48 0.92
33 2 0.04
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.36
Consensus pattern (32 bp):
TCGGGTCGGGTCAATACCAGATCGGTTGATTT
Found at i:98055 original size:22 final size:22
Alignment explanation
Indices: 98004--98084 Score: 68
Period size: 22 Copynumber: 4.0 Consensus size: 22
97994 GTTCGGGTTA
*
98004 ATTTCGATTC-GGTTAATTTCG
1 ATTTCGGTTCGGGTTAATTTCG
*
98025 GTTTCGGTTCGGGTTAATTTCG
1 ATTTCGGTTCGGGTTAATTTCG
*
98047 A-TTC---T--GGTTGATTTCG
1 ATTTCGGTTCGGGTTAATTTCG
**
98063 ATTTCGGTTCGAATTAATTTCG
1 ATTTCGGTTCGGGTTAATTTCG
98085 GTTCTGATTG
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
16 11 0.24
17 3 0.07
18 1 0.02
20 1 0.02
21 11 0.24
22 19 0.41
ACGTcount: A:0.16, C:0.14, G:0.23, T:0.47
Consensus pattern (22 bp):
ATTTCGGTTCGGGTTAATTTCG
Found at i:98070 original size:38 final size:38
Alignment explanation
Indices: 97993--98106 Score: 167
Period size: 38 Copynumber: 3.0 Consensus size: 38
97983 AGTTTCTTTT
*
97993 GGTTCGGGTTAATTTCGATTC-GGTTAATTTCGGTTTC
1 GGTTCGGGTTAATTTCGATTCTGGTTGATTTCGGTTTC
*
98030 GGTTCGGGTTAATTTCGATTCTGGTTGATTTCGATTTC
1 GGTTCGGGTTAATTTCGATTCTGGTTGATTTCGGTTTC
** * *
98068 GGTTCGAATTAATTTCGGTTCTGATTGATTTCGGTTTC
1 GGTTCGGGTTAATTTCGATTCTGGTTGATTTCGGTTTC
98106 G
1 G
98107 CTAAATTTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
37 21 0.30
38 48 0.70
ACGTcount: A:0.14, C:0.13, G:0.26, T:0.46
Consensus pattern (38 bp):
GGTTCGGGTTAATTTCGATTCTGGTTGATTTCGGTTTC
Found at i:98071 original size:16 final size:16
Alignment explanation
Indices: 97999--98065 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 16
97989 TTTTGGTTCG
97999 GGTTAATTTCGATTC-
1 GGTTAATTTCGATTCT
*
98014 GGTTAATTTCGGTTTCGGTT
1 GGTTAATTTC-GATTC---T
98034 CGGGTTAATTTCGATTCT
1 --GGTTAATTTCGATTCT
*
98052 GGTTGATTTCGATT
1 GGTTAATTTCGATT
98066 TCGGTTCGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
15 10 0.24
16 17 0.40
18 1 0.02
21 4 0.10
22 10 0.24
ACGTcount: A:0.15, C:0.12, G:0.25, T:0.48
Consensus pattern (16 bp):
GGTTAATTTCGATTCT
Found at i:98082 original size:16 final size:16
Alignment explanation
Indices: 98063--98103 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
98053 GTTGATTTCG
98063 ATTTCGGTTC-GAATTA
1 ATTTCGGTTCTG-ATTA
*
98079 ATTTCGGTTCTGATTG
1 ATTTCGGTTCTGATTA
98095 ATTTCGGTT
1 ATTTCGGTT
98104 TCGCTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 22 0.96
17 1 0.04
ACGTcount: A:0.17, C:0.12, G:0.22, T:0.49
Consensus pattern (16 bp):
ATTTCGGTTCTGATTA
Found at i:98687 original size:30 final size:30
Alignment explanation
Indices: 98651--98709 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
98641 TGTTGCTTTT
*
98651 TAACACTGACTCAACAATATAATGTCTCAC
1 TAACACTAACTCAACAATATAATGTCTCAC
98681 TAACACTAACTCAACAATATAATGTCTCA
1 TAACACTAACTCAACAATATAATGTCTCA
98710 TGCCTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.25, G:0.05, T:0.27
Consensus pattern (30 bp):
TAACACTAACTCAACAATATAATGTCTCAC
Found at i:99620 original size:2 final size:2
Alignment explanation
Indices: 99613--99651 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
99603 TTCAAATAAT
99613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
99652 TACACACTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:104392 original size:2 final size:2
Alignment explanation
Indices: 104378--104436 Score: 70
Period size: 2 Copynumber: 30.0 Consensus size: 2
104368 AAATATAGTA
*
104378 AT AT AT A- AA AT AT AT A- AT AGT GAT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT
104419 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
104437 TAAAATGACG
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
1 3 0.06
2 45 0.88
3 2 0.04
4 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:104520 original size:16 final size:15
Alignment explanation
Indices: 104485--104546 Score: 63
Period size: 16 Copynumber: 4.0 Consensus size: 15
104475 TAAACAAATA
*
104485 ATAATAAAAATAATAG
1 ATAATAAAAAT-ATAT
104501 ATAATACAAAATATAT
1 ATAATA-AAAATATAT
*
104517 ATAAT-TAAATATAT
1 ATAATAAAAATATAT
*
104531 AAAATAATAAATATAT
1 ATAATAA-AAATATAT
104547 TGTTTAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 12 0.31
16 22 0.56
17 5 0.13
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
ATAATAAAAATATAT
Found at i:107749 original size:8 final size:7
Alignment explanation
Indices: 107733--107779 Score: 60
Period size: 8 Copynumber: 6.4 Consensus size: 7
107723 ACCAACCTTA
107733 TTTTTCT
1 TTTTTCT
107740 TTTGTTCT
1 TTT-TTCT
107748 TTTTCTCT
1 TTTT-TCT
107756 TTTTTCT
1 TTTTTCT
107763 CTTTTTCT
1 -TTTTTCT
107771 TTTTT-T
1 TTTTTCT
107777 TTT
1 TTT
107780 CAATTTAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 4 0.11
7 12 0.32
8 21 0.57
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:107845 original size:8 final size:8
Alignment explanation
Indices: 107834--107900 Score: 70
Period size: 8 Copynumber: 8.8 Consensus size: 8
107824 CTTTTTTTGG
107834 TTTTTCCT
1 TTTTTCCT
107842 TTTTT-CT
1 TTTTTCCT
*
107849 TTTTCCCT
1 TTTTTCCT
*
107857 TTTTCCCT
1 TTTTTCCT
107865 TTTTT-CT
1 TTTTTCCT
*
107872 TTTTCCCT
1 TTTTTCCT
107880 TTTTT-C-
1 TTTTTCCT
107886 TTTTTCTCT
1 TTTTTC-CT
107895 TTTTTC
1 TTTTTC
107901 AACTTAGGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
6 5 0.10
7 13 0.26
8 26 0.52
9 6 0.12
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTCCT
Found at i:107860 original size:23 final size:23
Alignment explanation
Indices: 107834--107898 Score: 105
Period size: 23 Copynumber: 2.8 Consensus size: 23
107824 CTTTTTTTGG
107834 TTTTTCCTTTTTTCTTTTTCCCT
1 TTTTTCCTTTTTTCTTTTTCCCT
*
107857 TTTTCCCTTTTTTCTTTTTCCCT
1 TTTTTCCTTTTTTCTTTTTCCCT
107880 TTTTT-CTTTTTCTCTTTTT
1 TTTTTCCTTTTT-TCTTTTT
107899 TCAACTTAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.15
23 33 0.85
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTTTCCTTTTTTCTTTTTCCCT
Found at i:107867 original size:15 final size:15
Alignment explanation
Indices: 107834--107898 Score: 78
Period size: 15 Copynumber: 4.3 Consensus size: 15
107824 CTTTTTTTGG
*
107834 TTTTTCCTTTTT-TC
1 TTTTTCCTTTTTCCC
107848 TTTTTCCCTTTTTCCC
1 TTTTT-CCTTTTTCCC
*
107864 TTTTTTCTTTTTCCC
1 TTTTTCCTTTTTCCC
* *
107879 TTTTTTCTTTTTCTC
1 TTTTTCCTTTTTCCC
107894 TTTTT
1 TTTTT
107899 TCAACTTAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
14 5 0.11
15 35 0.76
16 6 0.13
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTCCTTTTTCCC
Found at i:107899 original size:15 final size:15
Alignment explanation
Indices: 107855--107900 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
107845 TTCTTTTTCC
107855 CTTTTTCCCTTTTTT
1 CTTTTTCCCTTTTTT
107870 CTTTTTCCCTTTTTT
1 CTTTTTCCCTTTTTT
*
107885 CTTTTTCTCTTTTTT
1 CTTTTTCCCTTTTTT
107900 C
1 C
107901 AACTTAGGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTTTCCCTTTTTT
Found at i:117579 original size:194 final size:195
Alignment explanation
Indices: 117250--117638 Score: 771
Period size: 194 Copynumber: 2.0 Consensus size: 195
117240 CTAAAAAACA
117250 AACACATGCAAAAATTTAGTACAATAAAAATAAATAAATATAAAATGTCGAAATGGAAAACACAT
1 AACACATGCAAAAATTTAGTACAATAAAAATAAATAAATATAAAATGTCGAAATGGAAAACACAT
117315 AAAAAAGAAACATGGTTAGGGTAAAAATATCATAGGTTTTGGATGTGGTTTCGGGGTAGGCTCTA
66 AAAAAAGAAACATGGTTAGGGTAAAAATATCATAGGTTTTGGATGTGGTTTCGGGGTAGGCTCTA
117380 ATTCTTTATAGTCTCCCGGTTTAGGTTCTAAAAAACGGTACCCGAGTT-TCCTTGCCAGCGCCCC
131 ATTCTTTATAGTCTCCCGGTTTAGGTTCTAAAAAACGGTACCCGAGTTCTCCTTGCCAGCGCCCC
117444 AACACATGCAAAAATTTAGTACAATAAAAATAAATAAATATAAAATGTCGAAATGGAAAACACAT
1 AACACATGCAAAAATTTAGTACAATAAAAATAAATAAATATAAAATGTCGAAATGGAAAACACAT
117509 AAAAAAGAAACATGGTTAGGGTAAAAATATCATAGGTTTTGGATGTGGTTTCGGGGTAGGCTCTA
66 AAAAAAGAAACATGGTTAGGGTAAAAATATCATAGGTTTTGGATGTGGTTTCGGGGTAGGCTCTA
117574 ATTCTTTATAGTCTCCCGGTTTAGGTTCTAAAAAACGGTACCCGAGTTCTCCTTGCCAGCGCCCC
131 ATTCTTTATAGTCTCCCGGTTTAGGTTCTAAAAAACGGTACCCGAGTTCTCCTTGCCAGCGCCCC
117639 CTTGGGCTTA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
194 178 0.92
195 16 0.08
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (195 bp):
AACACATGCAAAAATTTAGTACAATAAAAATAAATAAATATAAAATGTCGAAATGGAAAACACAT
AAAAAAGAAACATGGTTAGGGTAAAAATATCATAGGTTTTGGATGTGGTTTCGGGGTAGGCTCTA
ATTCTTTATAGTCTCCCGGTTTAGGTTCTAAAAAACGGTACCCGAGTTCTCCTTGCCAGCGCCCC
Found at i:118730 original size:2 final size:2
Alignment explanation
Indices: 118716--118770 Score: 62
Period size: 2 Copynumber: 28.0 Consensus size: 2
118706 AAATATAGTA
*
118716 AT AT AT A- AA AT AT AT A- AT AGT GAT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT
118757 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
118771 TAAAATGACG
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
1 3 0.06
2 41 0.87
3 2 0.04
4 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:118770 original size:16 final size:15
Alignment explanation
Indices: 118707--118769 Score: 67
Period size: 14 Copynumber: 4.1 Consensus size: 15
118697 ATAGTGATAA
118707 AATATAGTA-ATATAT
1 AATATA-TATATATAT
*
118722 AAAATATATAATAGTGAT
1 AATATATAT-ATA-T-AT
118740 AATATATATATATAT
1 AATATATATATATAT
118755 -ATATATATATATAT
1 AATATATATATATAT
118769 A
1 A
118770 TTAAAATGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 16 0.39
15 7 0.17
16 4 0.10
17 4 0.10
18 10 0.24
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:118840 original size:16 final size:15
Alignment explanation
Indices: 118815--118874 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 15
118805 AACGCAAACA
*
118815 AATAAAAATAAAAAT
1 AATAATAATAAAAAT
118830 AATAGATAATACAAAA-
1 AATA-ATAATA-AAAAT
*
118846 AATATATAATTAAATAT
1 AATA-ATAA-TAAAAAT
118863 ATATAATAATAA
1 A-ATAATAATAA
118875 CTATACTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.11
16 19 0.51
17 11 0.30
18 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
AATAATAATAAAAAT
Found at i:120872 original size:22 final size:22
Alignment explanation
Indices: 120844--120889 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
120834 TGCCAATTTA
120844 CTCATTAAATTTTTGAATTACT
1 CTCATTAAATTTTTGAATTACT
120866 CTCATTAAATTTTTGAATTACT
1 CTCATTAAATTTTTGAATTACT
120888 CT
1 CT
120890 TATTTTGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.50
Consensus pattern (22 bp):
CTCATTAAATTTTTGAATTACT
Found at i:123064 original size:21 final size:20
Alignment explanation
Indices: 123025--123065 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
123015 AAGTCGAGCT
*
123025 ATAAAATACAACTCAAATAA
1 ATAAAATACAACCCAAATAA
*
123045 ATAAAATAGTAACCCAAATAA
1 ATAAAATA-CAACCCAAATAA
123066 CTAGAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.63, C:0.15, G:0.02, T:0.20
Consensus pattern (20 bp):
ATAAAATACAACCCAAATAA
Found at i:123547 original size:15 final size:15
Alignment explanation
Indices: 123527--123555 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
123517 ATATGTATTG
123527 TGCCTTTGAACTTTA
1 TGCCTTTGAACTTTA
123542 TGCCTTTGAACTTT
1 TGCCTTTGAACTTT
123556 CTTTTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48
Consensus pattern (15 bp):
TGCCTTTGAACTTTA
Found at i:123927 original size:10 final size:10
Alignment explanation
Indices: 123909--123944 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
123899 TTCATCACAC
123909 CAAATCCTCT
1 CAAATCCTCT
*
123919 CAAAACCTCT
1 CAAATCCTCT
*
123929 TAAATCCTCT
1 CAAATCCTCT
123939 CAAATC
1 CAAATC
123945 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:124012 original size:19 final size:20
Alignment explanation
Indices: 123990--124034 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
123980 GAAGGTAATA
123990 TATTATATTA-TATTTTATT
1 TATTATATTAGTATTTTATT
*
124009 TATT-TTTTAGTATTTTATT
1 TATTATATTAGTATTTTATT
124028 TAATTAT
1 T-ATTAT
124035 TTAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.18
19 14 0.64
20 3 0.14
21 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TATTATATTAGTATTTTATT
Found at i:124049 original size:28 final size:27
Alignment explanation
Indices: 124004--124057 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
123994 ATATTATATT
*
124004 TTATTTATTTTTTAGTATTTTATTTAA
1 TTATTTATTATTTAGTATTTTATTTAA
124031 TTATTTAATTATTTAGTATTTTATTTA
1 TTATTT-ATTATTTAGTATTTTATTTA
124058 TTTTTTTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.69
Consensus pattern (27 bp):
TTATTTATTATTTAGTATTTTATTTAA
Found at i:124059 original size:16 final size:16
Alignment explanation
Indices: 124007--124060 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 16
123997 TTATATTTTA
124007 TTTATTT-TTTAGTAT
1 TTTATTTATTTAGTAT
*
124022 TTTATTTA---ATTA-
1 TTTATTTATTTAGTAT
*
124034 TTTAATTATTTAGTAT
1 TTTATTTATTTAGTAT
124050 TTTATTTATTT
1 TTTATTTATTT
124061 TTTTGCAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
15 10 0.33
16 10 0.33
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (16 bp):
TTTATTTATTTAGTAT
Found at i:127890 original size:16 final size:16
Alignment explanation
Indices: 127864--127904 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
127854 CCATTTTTTC
127864 AAATAATTATATATAAA
1 AAAT-ATTATATATAAA
*
127881 AAATATTATATATTAA
1 AAATATTATATATAAA
127897 AAAT-TTAT
1 AAATATTAT
127905 CTTACAACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.17
16 15 0.65
17 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATATTATATATAAA
Found at i:127992 original size:30 final size:30
Alignment explanation
Indices: 127947--128037 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
127937 CAAAGATAAG
* * *
127947 AGGATTGTCGGGTGATATTTACGGGTTGAA
1 AGGATTGTTGTGTGATGTTTACGGGTTGAA
* * *
127977 AGGATTGTTGTGTGATGTTTTCAGGTTGAC
1 AGGATTGTTGTGTGATGTTTACGGGTTGAA
**
128007 ATAATTGTTGTGTGAATGTTTACCGGGTTGA
1 AGGATTGTTGTGTG-ATGTTTA-CGGGTTGA
128038 GAGCATTTCA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
30 36 0.73
31 6 0.12
32 7 0.14
ACGTcount: A:0.21, C:0.07, G:0.33, T:0.40
Consensus pattern (30 bp):
AGGATTGTTGTGTGATGTTTACGGGTTGAA
Found at i:130274 original size:25 final size:25
Alignment explanation
Indices: 130217--130267 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
130207 ATCTTATAAG
130217 TTACAAAAAAAATTTAGATTAACTA
1 TTACAAAAAAAATTTAGATTAACTA
130242 TTACAAAAAAAATTTAGATTAACTA
1 TTACAAAAAAAATTTAGATTAACTA
130267 T
1 T
130268 CTGAAAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (25 bp):
TTACAAAAAAAATTTAGATTAACTA
Found at i:132573 original size:2 final size:2
Alignment explanation
Indices: 132566--132621 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
132556 GTTTGATGAG
132566 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
132608 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
132622 GAAGGTGGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133165 original size:43 final size:41
Alignment explanation
Indices: 133081--133188 Score: 117
Period size: 41 Copynumber: 2.6 Consensus size: 41
133071 GCCGCAAAGG
* *
133081 GTCAAATCTATAGCGGCATTTTTTGGAACAAACACAACAAAAA
1 GTCAGATCTATAGCGGC-GTTTTTGGAACAAACACAAC-AAAA
* * * **
133124 TGTTAGATCTATAGCGGCGTTTTTGGAACGAACGCCGCAAAA
1 -GTCAGATCTATAGCGGCGTTTTTGGAACAAACACAACAAAA
*
133166 GTCAGATCTATAGCGGTGTTTTT
1 GTCAGATCTATAGCGGCGTTTTT
133189 TTAAACAAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
41 21 0.38
42 4 0.07
43 15 0.27
44 15 0.27
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (41 bp):
GTCAGATCTATAGCGGCGTTTTTGGAACAAACACAACAAAA
Found at i:133187 original size:41 final size:41
Alignment explanation
Indices: 133069--133203 Score: 119
Period size: 42 Copynumber: 3.2 Consensus size: 41
133059 TAGCGGCGTT
* *
133069 ACGCCGCAAAGGGTCAAATCTATAGCGGCAT-TTTTTGGAACAA
1 ACGCCGCAAA-AGTCAGATCTATAGCGG--TGTTTTTGGAACAA
* ** * * *
133112 ACACAACAAAAATGTTAGATCTATAGCGGCGTTTTTGGAACGA
1 ACGCCGC-AAAA-GTCAGATCTATAGCGGTGTTTTTGGAACAA
**
133155 ACGCCGCAAAAGTCAGATCTATAGCGGTGTTTTTTTAAACAA
1 ACGCCGCAAAAGTCAGATCTATAGCGGTG-TTTTTGGAACAA
133197 ACGCCGC
1 ACGCCGC
133204 TAATTACCTT
Statistics
Matches: 72, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
41 16 0.22
42 20 0.28
43 19 0.26
44 17 0.24
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (41 bp):
ACGCCGCAAAAGTCAGATCTATAGCGGTGTTTTTGGAACAA
Found at i:134582 original size:12 final size:12
Alignment explanation
Indices: 134565--134600 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
134555 TATCATGTTC
134565 TCATATCACATG
1 TCATATCACATG
*
134577 TCATATCACATA
1 TCATATCACATG
134589 TCATATCACATG
1 TCATATCACATG
134601 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:135018 original size:64 final size:63
Alignment explanation
Indices: 134910--135130 Score: 246
Period size: 64 Copynumber: 3.5 Consensus size: 63
134900 TAATGAAGGT
* * ** * **
134910 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTATTATTAATGGG
* **
134974 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTT-ATTATTAATGGG
* ** *
135038 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTT-TTATTTTAAAAGA
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTA--TTAATGGG
* **
135102 ATGCATCGATGCCCTACCAATGCATCGAT
1 ATGCATCGATGCACTACTTATGCATCGAT
135131 ACACCTTCAA
Statistics
Matches: 135, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
62 3 0.02
63 2 0.01
64 130 0.96
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATTAATGGG
Found at i:142700 original size:13 final size:13
Alignment explanation
Indices: 142682--142747 Score: 59
Period size: 13 Copynumber: 5.2 Consensus size: 13
142672 ATATGATTTC
142682 ATAAGAATATGAA
1 ATAAGAATATGAA
142695 ATAAGAAGTATGAA
1 ATAAGAA-TATGAA
* *
142709 A-AGGACATA--AG
1 ATAAGA-ATATGAA
142720 A-AAGAATATGAA
1 ATAAGAATATGAA
142732 ATAAGAAGTATGAA
1 ATAAGAA-TATGAA
142746 AT
1 AT
142748 GGACATAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 5 0.12
12 2 0.05
13 17 0.40
14 16 0.37
ACGTcount: A:0.59, C:0.02, G:0.20, T:0.20
Consensus pattern (13 bp):
ATAAGAATATGAA
Found at i:142720 original size:20 final size:20
Alignment explanation
Indices: 142695--142758 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
142685 AGAATATGAA
142695 ATAAGAAGTATGAAAAGGAC
1 ATAAGAAGTATGAAAAGGAC
* * *
142715 ATAAGAA--A-GAATATGAA
1 ATAAGAAGTATGAAAAGGAC
*
142732 ATAAGAAGTATGAAATGGAC
1 ATAAGAAGTATGAAAAGGAC
142752 ATAAGAA
1 ATAAGAA
142759 AGAATATGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 13 0.38
18 1 0.03
19 1 0.03
20 19 0.56
ACGTcount: A:0.58, C:0.03, G:0.22, T:0.17
Consensus pattern (20 bp):
ATAAGAAGTATGAAAAGGAC
Found at i:142728 original size:37 final size:37
Alignment explanation
Indices: 142684--142771 Score: 167
Period size: 37 Copynumber: 2.4 Consensus size: 37
142674 ATGATTTCAT
142684 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
1 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
*
142721 AAGAATATGAAATAAGAAGTATGAAATGGACATAAGA
1 AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
142758 AAGAATATGAAATA
1 AAGAATATGAAATA
142772 TACAGAATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.59, C:0.02, G:0.20, T:0.18
Consensus pattern (37 bp):
AAGAATATGAAATAAGAAGTATGAAAAGGACATAAGA
Found at i:143301 original size:30 final size:30
Alignment explanation
Indices: 143060--143298 Score: 469
Period size: 30 Copynumber: 8.0 Consensus size: 30
143050 ACATAGGGAT
143060 AGTTACCGAGGATCTTTATGACCTCTGGAC
1 AGTTACCGAGGATCTTTATGACCTCTGGAC
143090 AGTTACCGAGGATCTTTATGACCTCTGGAC
1 AGTTACCGAGGATCTTTATGACCTCTGGAC
143120 AGTTACCGAGGATCTTTATGACCTCTGGAC
1 AGTTACCGAGGATCTTTATGACCTCTGGAC
143150 AGTTACCGAGGATCTTTATGACCTCTGGAC
1 AGTTACCGAGGATCTTTATGACCTCTGGAC
143180 AGTTACCGAGGATCTTTATGACCTCTGGAC
1 AGTTACCGAGGATCTTTATGACCTCTGGAC
143210 AGTTACCGAGGATCTTTATGACCTCTGGAC
1 AGTTACCGAGGATCTTTATGACCTCTGGAC
*
143240 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAC
143270 AGTTACCGAGGATCTTTATGACCTCTGGA
1 AGTTACCGAGGATCTTTATGACCTCTGGA
143299 TAGGTCCTTC
Statistics
Matches: 208, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 208 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTGGAC
Found at i:144158 original size:12 final size:12
Alignment explanation
Indices: 144141--144176 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
144131 TATCATGTTC
144141 TCATATCACATG
1 TCATATCACATG
*
144153 TCATATCACATA
1 TCATATCACATG
*
144165 TTATATCACATG
1 TCATATCACATG
144177 AACATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (12 bp):
TCATATCACATG
Found at i:144563 original size:64 final size:64
Alignment explanation
Indices: 144486--144706 Score: 212
Period size: 64 Copynumber: 3.5 Consensus size: 64
144476 TAATGAAGGT
* * * **
144486 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGTATTCGATGT-TTCATTATTAATGGG
* * ** *
144550 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGTATTTGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGTATTCGATGTTTCATTATTAATGGG
* ** ** * * ** *
144614 ATGCATCGATGCACTACTTATGCATCTATGCATGAATTGCATTCGATGTTTTTATT-TTAAAAGA
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGTATTCGATG-TTTCATTATTAATGGG
**
144678 ATGCATCGATGCACTACCAATGCATCGAT
1 ATGCATCGATGCACTACTTATGCATCGAT
144707 ACACCTTCAA
Statistics
Matches: 132, Mismatches: 23, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
63 2 0.02
64 124 0.94
65 6 0.05
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAAGGTATTCGATGTTTCATTATTAATGGG
Found at i:144767 original size:21 final size:21
Alignment explanation
Indices: 144741--144796 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
144731 TTAACCTTGA
144741 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
144762 TGCATCGATGCACTATGAATG
1 TGCATCGATGCACTATGAATG
144783 TGCATCGATGCACT
1 TGCATCGATGCACT
144797 CTGCCCAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACTATGAATG
Done.