Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003467.1 Hibiscus syriacus cultivar Beakdansim tig00007331_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: 93348
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:1043 original size:18 final size:21
Alignment explanation
Indices: 1020--1068 Score: 77
Period size: 18 Copynumber: 2.5 Consensus size: 21
1010 CAACAATTGG
1020 TAACAATTGGTAT-C-TTT-T
1 TAACAATTGGTATCCTTTTAT
1038 TAACAATTGGTATCCTTTTAT
1 TAACAATTGGTATCCTTTTAT
1059 TAACAATTGG
1 TAACAATTGG
1069 AATATTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.46
19 1 0.04
20 3 0.11
21 11 0.39
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (21 bp):
TAACAATTGGTATCCTTTTAT
Found at i:1081 original size:21 final size:21
Alignment explanation
Indices: 1020--1082 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1010 CAACAATTGG
*
1020 TAACAATTGGTATC--TTT-T
1 TAACAATTGGAATCATTTTAT
* *
1038 TAACAATTGGTATCCTTTTAT
1 TAACAATTGGAATCATTTTAT
1059 TAACAATTGGAAT-ATTTTCAT
1 TAACAATTGGAATCATTTT-AT
1080 TAA
1 TAA
1083 ACATTTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 14 0.36
20 7 0.18
21 18 0.46
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (21 bp):
TAACAATTGGAATCATTTTAT
Found at i:1414 original size:20 final size:20
Alignment explanation
Indices: 1370--1427 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1360 GAATACAGTT
* **
1370 AGTGTACCGATGCA-CCTAT
1 AGTGTACCGATACACCCTGC
1389 AGTGTACCGATACACCCTGC
1 AGTGTACCGATACACCCTGC
1409 AGTGTATCC-ATACACCCTG
1 AGTGTA-CCGATACACCCTG
1428 GCTGCAACGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.38
20 19 0.56
21 2 0.06
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (20 bp):
AGTGTACCGATACACCCTGC
Found at i:1814 original size:34 final size:34
Alignment explanation
Indices: 1775--1857 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
1765 CTTTTGTAAA
*
1775 GGGGAAAAGTTCTAGCTAAGCCCGTGTAAAAGCT
1 GGGGAAAAGTTCTAGCTAAGCCCGTGCAAAAGCT
* *
1809 GGGGAAATGTTCTAACTAAGCCCGTGCAAAAGCT
1 GGGGAAAAGTTCTAGCTAAGCCCGTGCAAAAGCT
* *
1843 AGGGAAAGGTTCTAG
1 GGGGAAAAGTTCTAG
1858 TTTATGTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (34 bp):
GGGGAAAAGTTCTAGCTAAGCCCGTGCAAAAGCT
Found at i:4414 original size:23 final size:24
Alignment explanation
Indices: 4387--4438 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
4377 GCTTCCCCCC
4387 AAAAATAGTTAGGAACATTTCT-G
1 AAAAATAGTTAGGAACATTTCTGG
*
4410 AAAAATAGTTAGGAACATTTTTGG
1 AAAAATAGTTAGGAACATTTCTGG
4434 AAAAA
1 AAAAA
4439 AGTAGAGACC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (24 bp):
AAAAATAGTTAGGAACATTTCTGG
Found at i:7636 original size:41 final size:42
Alignment explanation
Indices: 7517--7657 Score: 126
Period size: 41 Copynumber: 3.4 Consensus size: 42
7507 GCTTTCATAC
* * * *
7517 AAACACCGCTATAGAGTTGGATAGTAGTGGCATTTTTTTAGT
1 AAACACCGCTATAGAGTTGGACAATAGTGGCATTTTTGTAGA
* * * * * *
7559 AAACACCGCGATAGAGTAGCACTATAGAGGCGTTTTTGTA-A
1 AAACACCGCTATAGAGTTGGACAATAGTGGCATTTTTGTAGA
** *
7600 AAATGCCGCTATAGAGTTGGACAATAGTGGCATTTTT-TAGT
1 AAACACCGCTATAGAGTTGGACAATAGTGGCATTTTTGTAGA
*
7641 AAAGACCG-TGATAGAGT
1 AAACACCGCT-ATAGAGT
7658 AGCATTATAT
Statistics
Matches: 76, Mismatches: 21, Indels: 5
0.75 0.21 0.05
Matches are distributed among these distances:
40 3 0.04
41 42 0.55
42 31 0.41
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (42 bp):
AAACACCGCTATAGAGTTGGACAATAGTGGCATTTTTGTAGA
Found at i:7673 original size:82 final size:83
Alignment explanation
Indices: 7522--7675 Score: 247
Period size: 82 Copynumber: 1.9 Consensus size: 83
7512 CATACAAACA
* *
7522 CCGCTATAGAGTTGGATAGTAGTGGCATTTTTTTAGTAAACACCGCGATAGAGTAGCACTATAGA
1 CCGCTATAGAGTTGGACAATAGTGGCATTTTTTTAGTAAACACCGCGATAGAGTAGCACTATAGA
7587 GGCGTTTTTGTAAAAATG
66 GGCGTTTTTGTAAAAATG
* * * *
7605 CCGCTATAGAGTTGGACAATAGTGGCA-TTTTTTAGTAAAGACCGTGATAGAGTAGCATTATATA
1 CCGCTATAGAGTTGGACAATAGTGGCATTTTTTTAGTAAACACCGCGATAGAGTAGCACTATAGA
7669 GGCGTTT
66 GGCGTTT
7676 GGTTTACAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
82 40 0.62
83 25 0.38
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (83 bp):
CCGCTATAGAGTTGGACAATAGTGGCATTTTTTTAGTAAACACCGCGATAGAGTAGCACTATAGA
GGCGTTTTTGTAAAAATG
Found at i:11180 original size:28 final size:28
Alignment explanation
Indices: 11148--11204 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
11138 AATGCGCTAT
*
11148 ATACTAGATCTTTTACGGCGTTTTTATC
1 ATACTAGATCTTTTACAGCGTTTTTATC
11176 ATACTAGATCTTTTACAGCGTTTTTATC
1 ATACTAGATCTTTTACAGCGTTTTTATC
11204 A
1 A
11205 AAAAACACCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (28 bp):
ATACTAGATCTTTTACAGCGTTTTTATC
Found at i:13105 original size:2 final size:2
Alignment explanation
Indices: 13098--13127 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13088 TGTTGATTAA
13098 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
13128 CAAGATTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18710 original size:2 final size:2
Alignment explanation
Indices: 18703--18736 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18693 TTTCATGATC
18703 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
18737 TAAATCCCTT
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:18866 original size:2 final size:2
Alignment explanation
Indices: 18861--18898 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
18851 TCAACACACC
18861 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18899 AATTCTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32887 original size:36 final size:36
Alignment explanation
Indices: 32840--32908 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
32830 AGAATCGGCT
*
32840 GGTAGCAAGTTCGACTTCATGTGAACAAACTTAGCG
1 GGTAGCAAGTTCGACTTCATGTAAACAAACTTAGCG
32876 GGTAGCAAGTTCGACTTCATGTAAACAAACTTA
1 GGTAGCAAGTTCGACTTCATGTAAACAAACTTA
32909 CCGGTGGTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (36 bp):
GGTAGCAAGTTCGACTTCATGTAAACAAACTTAGCG
Found at i:33271 original size:18 final size:18
Alignment explanation
Indices: 33250--33328 Score: 92
Period size: 18 Copynumber: 4.5 Consensus size: 18
33240 TAATTAATTA
33250 TTTATTTTATTCTTATCT
1 TTTATTTTATTCTTATCT
* * *
33268 TTTATTTAATTGTT-T-A
1 TTTATTTTATTCTTATCT
33284 TTTATTTTA-TCTTTATCT
1 TTTATTTTATTC-TTATCT
*
33302 TTTATTTTATTCTAATCT
1 TTTATTTTATTCTTATCT
33320 TTTATTTTA
1 TTTATTTTA
33329 AAAACAAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
15 1 0.02
16 10 0.20
17 2 0.04
18 35 0.70
19 2 0.04
ACGTcount: A:0.20, C:0.08, G:0.01, T:0.71
Consensus pattern (18 bp):
TTTATTTTATTCTTATCT
Found at i:33277 original size:30 final size:28
Alignment explanation
Indices: 33238--33297 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 28
33228 TTACTTTAAA
33238 TTTAATTAATTATTTATTTTATTCTTATCT
1 TTTAATTAATTATTTA-TTTATT-TTATCT
* *
33268 TTTATTTAATTGTTTATTTATTTTATCT
1 TTTAATTAATTATTTATTTATTTTATCT
33296 TT
1 TT
33298 ATCTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 8 0.29
29 6 0.21
30 14 0.50
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (28 bp):
TTTAATTAATTATTTATTTATTTTATCT
Found at i:33278 original size:34 final size:34
Alignment explanation
Indices: 33237--33308 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
33227 ATTACTTTAA
33237 ATTTAATTAATTATTTATTTTAT-TCTTATCTTTT
1 ATTTAATTAATTATTTATTTTATCT-TTATCTTTT
**
33271 ATTTAATTGTTTATTTATTTTATCTTTATCTTTT
1 ATTTAATTAATTATTTATTTTATCTTTATCTTTT
33305 ATTT
1 ATTT
33309 TATTCTAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 34 0.97
35 1 0.03
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.69
Consensus pattern (34 bp):
ATTTAATTAATTATTTATTTTATCTTTATCTTTT
Found at i:34262 original size:29 final size:30
Alignment explanation
Indices: 34192--34251 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
34182 CAATTTAATG
*
34192 CAAAATGGTTTTTGGGCTTGAATTGATTTTA
1 CAAAAT-GTTTTTGGACTTGAATTGATTTTA
*
34223 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGATTTTA
34252 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 11 0.41
31 6 0.22
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGATTTTA
Found at i:34359 original size:21 final size:21
Alignment explanation
Indices: 34333--34373 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34323 GGTGTCAAAA
34333 TGCATCCATGCA-CCTCTGCAG
1 TGCATCCATGCATCC-CTGCAG
34354 TGCATCCATGCATCCCTGCA
1 TGCATCCATGCATCCCTGCA
34374 CCTACACTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.20, C:0.39, G:0.17, T:0.24
Consensus pattern (21 bp):
TGCATCCATGCATCCCTGCAG
Found at i:34365 original size:29 final size:30
Alignment explanation
Indices: 34332--34402 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
34322 GGGTGTCAAA
*
34332 ATGCATCCATGCACCT-CTGC-AGTGCATCC
1 ATGCATCCATGCACCTAC-ACTAGTGCATCC
* *
34361 ATGCATCCCTGCACCTACACTAGTGCATCG
1 ATGCATCCATGCACCTACACTAGTGCATCC
34391 ATGCAT-CATGCA
1 ATGCATCCATGCA
34403 ATGCATTCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (30 bp):
ATGCATCCATGCACCTACACTAGTGCATCC
Found at i:35810 original size:19 final size:20
Alignment explanation
Indices: 35786--35833 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
35776 AATGATTTTC
*
35786 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
35805 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
35825 TTTTGAAAA
1 TTTTGAAAA
35834 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:37134 original size:34 final size:30
Alignment explanation
Indices: 37096--37164 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
37086 TTGATATAAC
*
37096 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACAT-AATTG
37130 AATTT-ACAAAATGTTTTTGGACATAATTG
1 AATTTAACAAAATGTTTTTGGACATAATTG
37159 AATTTA
1 AATTTA
37165 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACATAATTG
Found at i:37175 original size:29 final size:30
Alignment explanation
Indices: 37105--37164 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
37095 CAATTTAAGG
*
37105 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACATGAATTGAATTTA
37136 CAAAATGTTTTTGGACAT-AATTGAATTTA
1 CAAAATGTTTTTGGACATGAATTGAATTTA
37165 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACATGAATTGAATTTA
Found at i:37407 original size:20 final size:20
Alignment explanation
Indices: 37342--37416 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
37332 AATGAAATTA
*
37342 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
* * ** *
37362 GTGTATCGGTGCATCAAGGTT
1 GTGCATCGATGCATC-CTGCT
37383 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
37403 GTGCAACGATGCAT
1 GTGCATCGATGCAT
37417 GAAGGCTGCA
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 28 0.67
21 14 0.33
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:37416 original size:41 final size:41
Alignment explanation
Indices: 37342--37421 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
37332 AATGAAATTA
* * * *
37342 GTGCATCGATGCATCCTTCTGTGTATCGGTGCATCAAGGTT
1 GTGCATCGATGCATCCTGCTGTGCAACGATGCATCAAGGTT
*
37383 GTGCATCGATGCATCCTGCTGTGCAACGATGCATGAAGG
1 GTGCATCGATGCATCCTGCTGTGCAACGATGCATCAAGG
37422 CTGCAACTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCAACGATGCATCAAGGTT
Found at i:37547 original size:21 final size:21
Alignment explanation
Indices: 37518--37557 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
37508 TTTGAGTAGA
37518 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAA-GGCTCC
*
37540 AAAA-CATCTCCAAAGGCT
1 AAAATCATCCCCAAAGGCT
37558 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.40, C:0.35, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAAAGGCTCC
Found at i:47468 original size:18 final size:17
Alignment explanation
Indices: 47425--47458 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
47415 CAACTGTGAC
47425 ACAACCGCATCTGCGAT
1 ACAACCGCATCTGCGAT
47442 ACAACCGCATCTGCGAT
1 ACAACCGCATCTGCGAT
47459 GGACACCGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (17 bp):
ACAACCGCATCTGCGAT
Found at i:48412 original size:108 final size:108
Alignment explanation
Indices: 48258--48673 Score: 460
Period size: 108 Copynumber: 3.8 Consensus size: 108
48248 CTAGCGCCTT
* * * * *
48258 TTTAAGCTAATAGAGCCATAGAAATCCAACGATAACAAAATAGGTTAATTACTTAATTTGTTATC
1 TTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAACAGGTTAATTACTTAATTTGTTATC
*
48323 AATATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAG
66 AATATTATCAACATATTAGGTAACGCTTAAAATGTTACCAAAG
* * * * *
48366 TTTAAGCTGATGGAGCCTTATAAATTCGACGATAACATAACCGGTTAATTACTTGATTTGTTATC
1 TTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAACAGGTTAATTACTTAATTTGTTATC
* * * * * **
48431 AACCATAAT-AACATATTAGGTAGCGCTTATGTAAT-ATAATAAGTAGTG
66 AA-TATTATCAACATATTAGGTAACGCTTA--AAATGTTACCAA--A--G
* *
48479 TCTTTTTAAAGCTGGT-GAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTG
1 ----TTT-AAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAACAGGTTAATTACTTAATTTG
*
48543 TTATCAGTATTATCAACATATTAGGTAACGCTTAAAATGTTACCAAAG
61 TTATCAATATTATCAACATATTAGGTAACGCTTAAAATGTTACCAAAG
* * * * *
48591 TTTAAGCTGATGGAGCCTTAGAAATTCGACGATAACATAACCGATTAATTACTTGATTTGTTATC
1 TTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAACAGGTTAATTACTTAATTTGTTATC
*
48656 AGTATTATCAACATATTA
66 AATATTATCAACATATTA
48674 TCTTGTACAT
Statistics
Matches: 253, Mismatches: 40, Indels: 30
0.78 0.12 0.09
Matches are distributed among these distances:
107 7 0.03
108 143 0.57
109 8 0.03
110 3 0.01
111 1 0.00
112 1 0.00
113 1 0.00
114 1 0.00
115 3 0.01
116 8 0.03
117 70 0.28
118 7 0.03
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (108 bp):
TTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACAAAACAGGTTAATTACTTAATTTGTTATC
AATATTATCAACATATTAGGTAACGCTTAAAATGTTACCAAAG
Found at i:48673 original size:225 final size:225
Alignment explanation
Indices: 48205--48656 Score: 764
Period size: 225 Copynumber: 2.0 Consensus size: 225
48195 GAAACATTAC
*
48205 CAACCATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGCTAGCGCCTTTTTAAGCTAATA
1 CAACCATAATAACATATTAGGTAGCGCTTATGTAACATAATAGCTAGCGCCTTTTTAAGCTAATA
48270 GAGCCATAGAAATCCAACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAATATTATCAAC
66 GAGCCATAGAAATCCAACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAATATTATCAAC
*
48335 ATATTAGGTAACGCCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTATAAATTCGACGATA
131 ATATTAGGTAACGCCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATTCGACGATA
*
48400 ACATAACCGGTTAATTACTTGATTTGTTAT
196 ACATAACCGATTAATTACTTGATTTGTTAT
* * * **
48430 CAACCATAATAACATATTAGGTAGCGCTTATGTAATATAATAAG-TAGTGTCTTTTTAAAGCTGG
1 CAACCATAATAACATATTAGGTAGCGCTTATGTAACATAAT-AGCTAGCGCCTTTTT-AAGCTAA
* * *
48494 T-GAGCCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCA
64 TAGAGCCATAGAAATCCAACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAATATTATCA
*
48558 ACATATTAGGTAACGCTTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATTCGACGA
129 ACATATTAGGTAACGCCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATTCGACGA
48623 TAACATAACCGATTAATTACTTGATTTGTTAT
194 TAACATAACCGATTAATTACTTGATTTGTTAT
48655 CA
1 CA
48657 GTATTATCAA
Statistics
Matches: 213, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
225 205 0.96
226 8 0.04
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (225 bp):
CAACCATAATAACATATTAGGTAGCGCTTATGTAACATAATAGCTAGCGCCTTTTTAAGCTAATA
GAGCCATAGAAATCCAACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAATATTATCAAC
ATATTAGGTAACGCCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATTCGACGATA
ACATAACCGATTAATTACTTGATTTGTTAT
Found at i:49452 original size:15 final size:15
Alignment explanation
Indices: 49432--49483 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
49422 AAGGTCCAAA
49432 TGGTAAGTTAGGAAT
1 TGGTAAGTTAGGAAT
49447 TGGTAAGTTAGGAAT
1 TGGTAAGTTAGGAAT
* *
49462 TTGTAAGCTAGGAAT
1 TGGTAAGTTAGGAAT
*
49477 TAGTAAG
1 TGGTAAG
49484 ATAAGCTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.35, C:0.02, G:0.31, T:0.33
Consensus pattern (15 bp):
TGGTAAGTTAGGAAT
Found at i:52056 original size:66 final size:66
Alignment explanation
Indices: 51972--52297 Score: 501
Period size: 66 Copynumber: 4.9 Consensus size: 66
51962 TGAATGAATA
* * * * *
51972 AAAATTATTGATCAATTTTGATTATTGCATAATGGTACATTATCAGCATAAAAGGTGCCACTAAT
1 AAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCAGCATAAAAGGTGCCACTAAT
52037 G
66 G
*
52038 AAAATTATCGATCGATTTTGATTAATGCATAACGATGCATTATCAGCATAAAAGGTGCCACTAAT
1 AAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCAGCATAAAAGGTGCCACTAAT
52103 G
66 G
* * *
52104 AAAATTATTGATCGATTTTGATTAATGAATAACGATGCATTATC-GACATAAAAGGTGCCACTAA
1 AAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCAG-CATAAAAGGTGCCACTAA
52168 TG
65 TG
* *
52170 AAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCGGTATAAAAGGTGCCACTAAT
1 AAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCAGCATAAAAGGTGCCACTAAT
52235 G
66 G
* * * *
52236 AAAATTATCGATCGATTTTGAATAATGCATAATGGTGCATTATCGGCATAAAATGTGCCACT
1 AAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCAGCATAAAAGGTGCCACT
52298 CATGGTATTC
Statistics
Matches: 242, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
65 1 0.00
66 240 0.99
67 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (66 bp):
AAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCAGCATAAAAGGTGCCACTAAT
G
Found at i:60261 original size:66 final size:66
Alignment explanation
Indices: 60148--60406 Score: 394
Period size: 66 Copynumber: 3.9 Consensus size: 66
60138 TGAATGGGTT
* * * *
60148 AAAATTAT-GATCGATTTTGATTAATTCATAACGGTTCATTATAGGCATAAAAGGTGCCACTAAT
1 AAAATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAAT
60212 G
66 G
* * * * * *
60213 AAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATAATTGGCATAAAATGTGACATTAAT
1 AAAATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAAT
60278 G
66 G
60279 AAAATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAAT
1 AAAATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAAT
60344 G
66 G
* * *
60345 AAAATTATTGATCGATTTTGATTAATGAATAACAATGCATTATCGGCATAAAAGGTGCCACT
1 AAAATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACT
60407 CATGGTATTC
Statistics
Matches: 177, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
65 8 0.05
66 169 0.95
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (66 bp):
AAAATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTGCCACTAAT
G
Found at i:60961 original size:13 final size:13
Alignment explanation
Indices: 60943--60994 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
60933 GTCATAAATC
60943 TATGACACGCATT
1 TATGACACGCATT
**
60956 TATGACAAACATT
1 TATGACACGCATT
*
60969 TATGACACGTATT
1 TATGACACGCATT
*
60982 TATGACGCGCATT
1 TATGACACGCATT
60995 GCGCGTCATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:61079 original size:13 final size:13
Alignment explanation
Indices: 61063--61105 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
61053 TTATGACACG
61063 CATTTATGACTTA
1 CATTTATGACTTA
61076 CATTTATGACTTA
1 CATTTATGACTTA
*
61089 CATTTACGACTTA
1 CATTTATGACTTA
61102 CATT
1 CATT
61106 GTCTGTCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (13 bp):
CATTTATGACTTA
Found at i:61156 original size:111 final size:110
Alignment explanation
Indices: 60882--61157 Score: 274
Period size: 111 Copynumber: 2.5 Consensus size: 110
60872 GACACACAAA
* ** * *
60882 TGCGCGTCATTGAGGTCAC-CGTCATAAATCTCAGATGACACGCAATTGTGTGTCATAAATCTAT
1 TGCGCGTCATTGAAG-CACACGTCATAAAT-AAAGATGACACACATTTGTGTGTCATAAATCTAT
* *
60946 GACACGCATTTATGACAAACATTTATGACACGTATTTATGACGCGCAT
64 GACACGCATTTATGACAAACATTTATGACACG-ATTTACGACGCACAT
* * * * * * *
60994 TGCGCGTCATTGAAGCTCCCTTCATAAATGAAGATGACATAGATTTGTGTGTCATAAATTTATGA
1 TGCGCGTCATTGAAGCACACGTCATAAATAAAGATGACACACATTTGTGTGTCATAAATCTATGA
** **
61059 CACGCATTTATGACTTACATTTATGACTTAC-ATTTACGACTTACAT
66 CACGCATTTATGACAAACATTTATGAC--ACGATTTACGACGCACAT
*
61105 TGTC-TGTCATTGAAGCACACGTCATTAAA-AAAGATGACACACATTCT-TGTGTC
1 TG-CGCGTCATTGAAGCACACGTCA-TAAATAAAGATGACACACATT-TGTGTGTC
61158 GTGATTGTAT
Statistics
Matches: 135, Mismatches: 23, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
111 104 0.77
112 29 0.21
113 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (110 bp):
TGCGCGTCATTGAAGCACACGTCATAAATAAAGATGACACACATTTGTGTGTCATAAATCTATGA
CACGCATTTATGACAAACATTTATGACACGATTTACGACGCACAT
Found at i:61184 original size:2 final size:2
Alignment explanation
Indices: 61177--61215 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
61167 TGTCGTAAAT
61177 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
61216 TGTAGATTGA
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:68398 original size:40 final size:40
Alignment explanation
Indices: 68344--68424 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
68334 GTTATTTATA
*
68344 TTTAATCGATTTTGTCAAATTT-TAACCGGTTTTGTCAAAT
1 TTTAACCGATTTTGTC-AATTTCTAACCGGTTTTGTCAAAT
* * *
68384 TTTAACCGTTTTTGTCAATTTCTAATCGGTTTTTTCAAAT
1 TTTAACCGATTTTGTCAATTTCTAACCGGTTTTGTCAAAT
68424 T
1 T
68425 CCTTACCTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
39 5 0.14
40 31 0.86
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.51
Consensus pattern (40 bp):
TTTAACCGATTTTGTCAATTTCTAACCGGTTTTGTCAAAT
Found at i:68403 original size:19 final size:20
Alignment explanation
Indices: 68353--68424 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
68343 ATTTAATCGA
68353 TTTTGTCAAATTTTAACCGG
1 TTTTGTCAAATTTTAACCGG
*
68373 TTTTGTCAAATTTTAACCGT
1 TTTTGTCAAATTTTAACCGG
*
68393 TTTTGTC-AATTTCTAATCGG
1 TTTTGTCAAATTT-TAACCGG
*
68413 TTTTTTCAAATT
1 TTTTGTCAAATT
68425 CCTTACCTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 5 0.11
20 37 0.80
21 4 0.09
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (20 bp):
TTTTGTCAAATTTTAACCGG
Found at i:68648 original size:20 final size:20
Alignment explanation
Indices: 68625--68668 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
68615 GTTGATAAGC
*
68625 ATACCAAACTAAAA-GTATCG
1 ATACCAAAC-AAAACGTATCA
*
68645 ATACCATACAAAACGTATCA
1 ATACCAAACAAAACGTATCA
68665 ATAC
1 ATAC
68669 TTTCTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.50, C:0.23, G:0.07, T:0.20
Consensus pattern (20 bp):
ATACCAAACAAAACGTATCA
Found at i:68829 original size:20 final size:21
Alignment explanation
Indices: 68804--68849 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
68794 TTTGAGATGC
* *
68804 ATACTGGAGTAA-AAGTTTCG
1 ATACTGGAATAATAAGTATCG
68824 ATACTGGAATAATAAGTATCG
1 ATACTGGAATAATAAGTATCG
68845 ATACT
1 ATACT
68850 TTATGTTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (21 bp):
ATACTGGAATAATAAGTATCG
Found at i:70319 original size:229 final size:228
Alignment explanation
Indices: 69915--70370 Score: 727
Period size: 229 Copynumber: 2.0 Consensus size: 228
69905 AACAGATTCC
69915 TTCAAAGGAATGGGAATACTCTCTACTACAAGTATCGGTACCTTTATACAACCTACAATATCATT
1 TTCAAAGGAATGGGAATACTCTCTACTACAAGTATCGGTACCTTTATACAACCTACAATATCATT
*
69980 TTCTACATATAATATTATATAAAAGTATCGATATTTATTTTCTACCTAGAATATCACTTTCTAAC
66 TTCTACATATAATATTATATAAAAGTATCGATATTTATTTTATACCTAGAATATCACTTTCTAAC
* * * *
70045 TGTAATCGGTCCCAAATCCTTCTTTGCTTCGAAAAAGCCAAACCCATAAACCTAATCCCTAATTT
131 TATAATCGGTCCCAAATCCTTCTTTACTTCGAAAAACCCAAACCCATAAACCTAACCCCT-ATTT
*
70110 -AAAATATTGTAATACTAAAAAAACTAGGGTTTCT
195 CAAAATACTGTAATACT-AAAAAACTAGGGTTTCT
*
70144 TTCAAAGGAATGGGAATACTCTCTATTACAAGTATCGGTACCTTTATACAACCTACAATATCATT
1 TTCAAAGGAATGGGAATACTCTCTACTACAAGTATCGGTACCTTTATACAACCTACAATATCATT
* * * *
70209 TTCTACCTATAATATTATATAAAAGTGTCGATATTTATTTTATACCTAGAATATCACTTTTTACC
66 TTCTACATATAATATTATATAAAAGTATCGATATTTATTTTATACCTAGAATATCACTTTCTAAC
* **
70274 TATAATCGGTCTCAAATGTTTCTTTACTTC-AAAAACCCTAAACCCATAAACCTAACCCCTATTT
131 TATAATCGGTCCCAAATCCTTCTTTACTTCGAAAAACCC-AAACCCATAAACCTAACCCCTATTT
* *
70338 CCAATTACTGTAATACTAAAAAACTAGGGTTTC
195 CAAAATACTGTAATACTAAAAAACTAGGGTTTC
70371 GACAACGTGC
Statistics
Matches: 209, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
228 27 0.13
229 182 0.87
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (228 bp):
TTCAAAGGAATGGGAATACTCTCTACTACAAGTATCGGTACCTTTATACAACCTACAATATCATT
TTCTACATATAATATTATATAAAAGTATCGATATTTATTTTATACCTAGAATATCACTTTCTAAC
TATAATCGGTCCCAAATCCTTCTTTACTTCGAAAAACCCAAACCCATAAACCTAACCCCTATTTC
AAAATACTGTAATACTAAAAAACTAGGGTTTCT
Found at i:71147 original size:20 final size:19
Alignment explanation
Indices: 71102--71155 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
71092 GCTTTTTACT
*
71102 GGTTTTGTCAAATTTCAGCC
1 GGTTTTGTC-AATTTCAACC
* *
71122 GATTTTGTCAATTTCCAATC
1 GGTTTTGTCAATTT-CAACC
71142 GGTTTTGTCCAATT
1 GGTTTTGT-CAATT
71156 CATTACTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.18
20 18 0.64
21 5 0.18
ACGTcount: A:0.20, C:0.19, G:0.17, T:0.44
Consensus pattern (19 bp):
GGTTTTGTCAATTTCAACC
Found at i:78338 original size:21 final size:21
Alignment explanation
Indices: 78303--78386 Score: 80
Period size: 21 Copynumber: 3.8 Consensus size: 21
78293 AGAACCCGTG
*
78303 GGGGGTATCGATTCCCTT-AA
1 GGGGGAATCGATTCCCTTCAA
*
78323 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCC-TTC-AA
*
78347 GGGGGGAATCGGTTCCCCTTCAA
1 -GGGGGAATCGATT-CCCTTCAA
*
78370 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
78387 CTGCCCTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
20 2 0.04
21 16 0.30
22 13 0.24
23 2 0.04
24 16 0.30
25 5 0.09
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTTCAA
Found at i:78353 original size:24 final size:23
Alignment explanation
Indices: 78302--78374 Score: 87
Period size: 24 Copynumber: 3.2 Consensus size: 23
78292 TAGAACCCGT
* *
78302 GGGGGGTATCGATTCCC-TT-AA
1 GGGGGGAATCGGTTCCCATTCAA
*
78323 GGAGGGAATCGGTTCCCATTCAAA
1 GGGGGGAATCGGTTCCCATTC-AA
*
78347 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCATTCAA
78370 GGGGG
1 GGGGG
78375 TATCGATTCC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
21 14 0.32
22 2 0.05
23 7 0.16
24 21 0.48
ACGTcount: A:0.21, C:0.21, G:0.37, T:0.22
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCATTCAA
Found at i:83761 original size:19 final size:19
Alignment explanation
Indices: 83733--83770 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
83723 CGTTGAACAG
*
83733 TGGGGGGAATCGGTACCCT
1 TGGGGAGAATCGGTACCCT
*
83752 TGGGGAGAATCGGTTCCCT
1 TGGGGAGAATCGGTACCCT
83771 CCGAGCATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.39, T:0.24
Consensus pattern (19 bp):
TGGGGAGAATCGGTACCCT
Found at i:84781 original size:21 final size:21
Alignment explanation
Indices: 84748--84801 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
84738 TATCTTTTAA
* * *
84748 ATATGAATCATTCAATCGAAT
1 ATATTAATTATTCAATCAAAT
**
84769 ATATTAATTATTCTGTCAAAT
1 ATATTAATTATTCAATCAAAT
*
84790 ATATTATTTATT
1 ATATTAATTATT
84802 ATTTAAATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (21 bp):
ATATTAATTATTCAATCAAAT
Found at i:85515 original size:21 final size:21
Alignment explanation
Indices: 85491--85552 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
85481 AAAACCCTGC
85491 GGGCTAGGAATGTAACCTTGA
1 GGGCTAGGAATGTAACCTTGA
* * * * *
85512 GGGCTGGGTATGTACCCCTGT
1 GGGCTAGGAATGTAACCTTGA
* *
85533 GGACTATGAATGTAACCTTG
1 GGGCTAGGAATGTAACCTTG
85553 CGGTAGTGGC
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (21 bp):
GGGCTAGGAATGTAACCTTGA
Found at i:87165 original size:26 final size:27
Alignment explanation
Indices: 87135--87203 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 27
87125 TCATTTTCCT
87135 AATTAATAAATATTC-T-AAAAATTTAA
1 AATTAATAAATATTCATGAAAAATTT-A
*
87161 AATTAATATAA-ATTCATGAAAACTTTA
1 AATTAATA-AATATTCATGAAAAATTTA
87188 AATTAAATAAAATATT
1 AATT-AAT-AAATATT
87204 AAACATTTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
26 12 0.33
27 8 0.22
28 12 0.33
29 4 0.11
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (27 bp):
AATTAATAAATATTCATGAAAAATTTA
Found at i:87416 original size:17 final size:17
Alignment explanation
Indices: 87386--87439 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
87376 TATTTAATAA
*
87386 AAAAGAATATACTAATTT
1 AAAA-AATAAACTAATTT
87404 AAAAAATAAACTAATTT
1 AAAAAATAAACTAATTT
*
87421 AAAAAGATATAACAAATTT
1 AAAAA-ATA-AACTAATTT
87440 TTAAAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 17 0.53
18 7 0.22
19 8 0.25
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.30
Consensus pattern (17 bp):
AAAAAATAAACTAATTT
Found at i:87830 original size:13 final size:14
Alignment explanation
Indices: 87804--87833 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
87794 CTCGCGAATG
87804 CGCTCCCCCGAAAA
1 CGCTCCCCCGAAAA
*
87818 CGCTCCCCCAAAAA
1 CGCTCCCCCGAAAA
87832 CG
1 CG
87834 TGCCTTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.50, G:0.13, T:0.07
Consensus pattern (14 bp):
CGCTCCCCCGAAAA
Found at i:88147 original size:2 final size:2
Alignment explanation
Indices: 88140--88196 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
88130 TAAATACCCA
88140 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
88181 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
88197 TCGATAATTA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:89421 original size:16 final size:16
Alignment explanation
Indices: 89400--89431 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
89390 ACCCTCACTC
89400 TAAATTAGTCTCTAAA
1 TAAATTAGTCTCTAAA
89416 TAAATTAGTCTCTAAA
1 TAAATTAGTCTCTAAA
89432 CTTTTTAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
TAAATTAGTCTCTAAA
Found at i:90024 original size:55 final size:55
Alignment explanation
Indices: 89921--90026 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
89911 TGACCCTGTT
* * * * **
89921 TAAATTAGTTCTTAAACTTTTGAATATTCCAATTTCATCCCCGGACTATGAGTTC
1 TAAATTAATCCTTAAACTTTTGAACATCCCAATTTCATCCCCAAACTATGAGTTC
* **
89976 TAAATTAATCCTTCAACTTTTGAACATCCCAATTTCATCCTTAAACTATGA
1 TAAATTAATCCTTAAACTTTTGAACATCCCAATTTCATCCCCAAACTATGA
90027 CCCTTATATA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 42 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.39
Consensus pattern (55 bp):
TAAATTAATCCTTAAACTTTTGAACATCCCAATTTCATCCCCAAACTATGAGTTC
Found at i:90333 original size:60 final size:60
Alignment explanation
Indices: 90216--90333 Score: 130
Period size: 59 Copynumber: 2.0 Consensus size: 60
90206 TTGGGATGAA
* * ** * * * * **
90216 ATTGAAGTATTCAAAAAGTTTGGGGACTATTTTAGAATGAAAGCCATTGTTGGGGATGGC
1 ATTGAAATATTCAAAAAGTTAGAAGACTAATTTAAAATCAAAGCCATAGTTAAGGATGGC
90276 ATTGAAATATTC-AAAAGTTAGAAGACTAATTTAAAATCAAAGCCATAGTTTAAGGATG
1 ATTGAAATATTCAAAAAGTTAGAAGACTAATTTAAAATCAAAGCCATAG-TTAAGGATG
90334 AAATTGGAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
59 29 0.62
60 18 0.38
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (60 bp):
ATTGAAATATTCAAAAAGTTAGAAGACTAATTTAAAATCAAAGCCATAGTTAAGGATGGC
Found at i:90345 original size:60 final size:60
Alignment explanation
Indices: 90209--90346 Score: 136
Period size: 60 Copynumber: 2.3 Consensus size: 60
90199 ATATAATTTG
* ** * * * * **
90209 GGATGAAATT-GAAGTATTCAAAAAGTTTGGGGACTATTTTAGAATGAAAGCCATTGTTGG
1 GGATGAAATTGGAA-TATTCAAAAAGTTAGAAGACTAATTTAAAATCAAAGCCATAGTTAA
** *
90269 GGATGGCATTGAAATATTC-AAAAGTTAGAAGACTAATTTAAAATCAAAGCCATAGTTTAA
1 GGATGAAATTGGAATATTCAAAAAGTTAGAAGACTAATTTAAAATCAAAGCCATAG-TTAA
90329 GGATGAAATTGGAATATT
1 GGATGAAATTGGAATATT
90347 TGGAAGTTTA
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
59 29 0.48
60 30 0.49
61 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.30
Consensus pattern (60 bp):
GGATGAAATTGGAATATTCAAAAAGTTAGAAGACTAATTTAAAATCAAAGCCATAGTTAA
Found at i:92482 original size:14 final size:15
Alignment explanation
Indices: 92455--92486 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
92445 ATCGATACTC
92455 TACTTGGAGTATCGA
1 TACTTGGAGTATCGA
92470 TACTTGG-GTATCGA
1 TACTTGGAGTATCGA
92484 TAC
1 TAC
92487 CACCCTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (15 bp):
TACTTGGAGTATCGA
Done.