Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006258.1 Hibiscus syriacus cultivar Beakdansim tig00014933_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: 64303
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1270 original size:23 final size:24
Alignment explanation
Indices: 1234--1281 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1224 TCTTATACTC
*
1234 ATCCAACAAGAAAAA-AAAGAAAA
1 ATCCAACAAAAAAAAGAAAGAAAA
* *
1257 ATCCATCAAAAAAAAGAGAGAAAA
1 ATCCAACAAAAAAAAGAAAGAAAA
1281 A
1 A
1282 AAGAAAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.71, C:0.12, G:0.10, T:0.06
Consensus pattern (24 bp):
ATCCAACAAAAAAAAGAAAGAAAA
Found at i:3642 original size:113 final size:112
Alignment explanation
Indices: 3389--3721 Score: 517
Period size: 113 Copynumber: 3.0 Consensus size: 112
3379 GTGCCACGTT
**
3389 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTG-TCTTTGATTATCTGATCTGG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTAAG-TTATCTGATCTGG
3453 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
65 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
* *
3501 CTCATAGTAGAAATAAGGAGACCCAATAGCCTCTTCTGGAAGTGTTCTAAGTTATCTGATCTAGT
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTAAGTTATCTGATCTGGT
3566 TTGGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 TTGGTATGAACCCC-AAAACCAATCATTGGATTTGAAAGATGAATTTG
* * * *
3614 TTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGT-TCTTTGAGTTATATGATCTGG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGT-TCTAAGTTATCTGATCTGG
* * * *
3678 TTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
65 TTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAA
3722 CTGCATGATC
Statistics
Matches: 204, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
112 98 0.48
113 106 0.52
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (112 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTAAGTTATCTGATCTGGT
TTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
Found at i:5181 original size:73 final size:74
Alignment explanation
Indices: 5030--5188 Score: 187
Period size: 73 Copynumber: 2.2 Consensus size: 74
5020 AGCAATATTG
* * * *
5030 GGGCATACTGAAACCCTTTTTCAATCAAAATCAGGAATGTTGATGTATCCTGAATGTTTATATCA
1 GGGCATGCTGAAACCCTTTTTCAATCAAAATCAAGAATGTTGATGTATCCTGAACGTTCATATCA
5095 GCAAATGCT
66 GCAAATGCT
* * * ** *
5104 GGGCATGCTGAAAGCCTTTTTC-ATCAGAATGAAGAATGTTGATGTATTTTGAACGTTCGTATCA
1 GGGCATGCTGAAACCCTTTTTCAATCAAAATCAAGAATGTTGATGTATCCTGAACGTTCATATCA
* *
5168 G-AATTGTT
66 GCAAATGCT
5176 AGGGCATGCTGAA
1 -GGGCATGCTGAA
5189 GGCCCACATC
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
72 5 0.07
73 47 0.65
74 20 0.28
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (74 bp):
GGGCATGCTGAAACCCTTTTTCAATCAAAATCAAGAATGTTGATGTATCCTGAACGTTCATATCA
GCAAATGCT
Found at i:6173 original size:54 final size:53
Alignment explanation
Indices: 6047--6197 Score: 211
Period size: 54 Copynumber: 2.9 Consensus size: 53
6037 AGAAATCTTG
*
6047 GCAGAAGCCACAAAAAGGATGAATGTGTTGTCAAATGTTTT----ACATCTGA
1 GCAGAAGCCACAAAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGA
*
6096 GCAGAAGCCACAAAAAAGTATGAATGTATTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCCAC-AAAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGA
* * *
6150 GCAGAAGCCACAGGAAAGGATGAATGCACTGTCAAATGTTTTACGAAC
1 GCAGAAGCCACA-AAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
6198 CTGTTATTCT
Statistics
Matches: 90, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
49 11 0.12
50 28 0.31
53 1 0.01
54 50 0.56
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (53 bp):
GCAGAAGCCACAAAAAGGATGAATGTATTGTCAAATGTTTTACGAACATCTGA
Found at i:6590 original size:22 final size:22
Alignment explanation
Indices: 6559--6613 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
6549 ACATCTACTC
6559 TTCAAAGATGATAGACTCCT-TT
1 TTCAAAGATGATAGA-TCCTCTT
* *
6581 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATCCTCTT
6603 TTCAAAGATGA
1 TTCAAAGATGA
6614 AAGCTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATCCTCTT
Found at i:7548 original size:75 final size:76
Alignment explanation
Indices: 7277--8121 Score: 1417
Period size: 74 Copynumber: 11.4 Consensus size: 76
7267 CTATTTCCCA
7277 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC-GGAGCTTTTTGATG-TTTC-A
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
7339 AGCCTTC-GGT
66 AGCCTTCGGGT
*
7349 CATCTGT-AGTCCTGCAGTGCAAGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
7412 AGCCTTC-GGT
66 AGCCTTCGGGT
7422 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
7487 AACCTTCGGGT
66 AGCCTTCGGGT
7498 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
7561 AGCCTTC-GGT
66 AGCCTTCGGGT
7571 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTT-AA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
7634 AGCCTTAGGGA
66 AGCCTTCGGGT
7645 CATCTGTAAGTCCTGCAGTGCATGATGTTT-CAAAAAGCCTTCGGGAGC--TTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
7707 AGCCTTCGGGT
66 AGCCTTCGGGT
7718 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
7782 AGCCTTCGGGT
66 AGCCTTCGGGT
** *
7793 CATCTGTAAGTCCTATAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
7857 AGCCTTAGGGT
66 AGCCTTCGGGT
*
7868 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
7933 AGCCTTAGGGT
66 AGCCTTCGGGT
*
7944 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGA--TTTTAAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
8007 AACCTTAGGGT
66 AGCCTTCGGGT
8018 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
8082 A-CCTTAGGGT
66 AGCCTTCGGGT
8092 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
8122 TTAAGACCTC
Statistics
Matches: 742, Mismatches: 17, Indels: 26
0.95 0.02 0.03
Matches are distributed among these distances:
71 34 0.05
72 32 0.04
73 140 0.19
74 247 0.33
75 155 0.21
76 134 0.18
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:8285 original size:3 final size:3
Alignment explanation
Indices: 8277--8341 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
8267 ATTTTTGTTT
* ** *
8277 TTA TTA TTA TTA TCA AAA TTA TTA TTA TTA TTA TTAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
*
8323 TTA -TA TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
8342 TACAAACAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.92
4 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:8303 original size:21 final size:22
Alignment explanation
Indices: 8277--8341 Score: 91
Period size: 21 Copynumber: 3.1 Consensus size: 22
8267 ATTTTTGTTT
8277 TTATTATTATTATCAAA-ATTA
1 TTATTATTATTATCAAATATTA
*
8298 TTATTATTATTATTAAATATTA
1 TTATTATTATTATCAAATATTA
*
8320 TTATTA-TATTAT-AATTATTA
1 TTATTATTATTATCAAATATTA
8340 TT
1 TT
8342 TACAAACAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
20 9 0.22
21 22 0.54
22 10 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATTATTATTATCAAATATTA
Found at i:8380 original size:26 final size:26
Alignment explanation
Indices: 8351--8402 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
8341 TTACAAACAA
* *
8351 TTACAAACAAAACTGGACCGGCCCAG
1 TTACAAACAAAACAGAACCGGCCCAG
8377 TTACAAACAAAACAGAACCGGCCCAG
1 TTACAAACAAAACAGAACCGGCCCAG
8403 ACCAACCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.31, G:0.17, T:0.10
Consensus pattern (26 bp):
TTACAAACAAAACAGAACCGGCCCAG
Found at i:8545 original size:17 final size:17
Alignment explanation
Indices: 8525--8559 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
8515 CCTCCACGTT
8525 GACGCCGTCAGTGCCAC
1 GACGCCGTCAGTGCCAC
8542 GACGCCGTCAGTGCCAC
1 GACGCCGTCAGTGCCAC
8559 G
1 G
8560 CCACCCCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.40, G:0.31, T:0.11
Consensus pattern (17 bp):
GACGCCGTCAGTGCCAC
Found at i:8750 original size:22 final size:22
Alignment explanation
Indices: 8725--8770 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
8715 AAAGACGGAG
8725 GACAGAAAAG-AAAAAAAAAAGA
1 GACAG-AAAGCAAAAAAAAAAGA
* *
8747 GACAGAGAGCAAAAAAAAGAGA
1 GACAGAAAGCAAAAAAAAAAGA
8769 GA
1 GA
8771 GCACGGACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.70, C:0.07, G:0.24, T:0.00
Consensus pattern (22 bp):
GACAGAAAGCAAAAAAAAAAGA
Found at i:15058 original size:39 final size:38
Alignment explanation
Indices: 15015--15089 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
15005 AAATTTAATT
* * *
15015 ATTATTATATTAATAAATTTGCTTTCTATATTAATTAAG
1 ATTATTAAATTAATAAA-TTGATTTCTATAATAATTAAG
*
15054 ATTATTAAATTAATAAATTGATTTTTATAATAATTA
1 ATTATTAAATTAATAAATTGATTTCTATAATAATTA
15090 TGAGCATTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 16 0.50
39 16 0.50
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.51
Consensus pattern (38 bp):
ATTATTAAATTAATAAATTGATTTCTATAATAATTAAG
Found at i:21425 original size:62 final size:60
Alignment explanation
Indices: 21349--21492 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 60
21339 ATACGAGATC
* * *
21349 AAAGGTTTTTATTTTAAAATTTCATTAAATA-TTTAAAATTCATGGAGGGAAGAGAAAAGAGG
1 AAAGGTTTTCATTTTAAAATTTCACTAAA-ACTTTAAAACT-AT-GAGGGAAGAGAAAAGAGG
* * * * *
21411 GAAGGTTTTCATTTT-GAATATTCACTAAAACTTTAAAACTATGAGTGAATAGAGAAGAGG
1 AAAGGTTTTCATTTTAAAAT-TTCACTAAAACTTTAAAACTATGAGGGAAGAGAAAAGAGG
*
21471 AAATGTTTTCATTTTAAAATTT
1 AAAGGTTTTCATTTTAAAATTT
21493 TACTGAAATT
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
60 30 0.44
61 9 0.13
62 29 0.43
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (60 bp):
AAAGGTTTTCATTTTAAAATTTCACTAAAACTTTAAAACTATGAGGGAAGAGAAAAGAGG
Found at i:21688 original size:4 final size:4
Alignment explanation
Indices: 21681--21707 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
21671 TATTCATAGA
21681 ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG
21708 AATTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:21738 original size:33 final size:32
Alignment explanation
Indices: 21696--21768 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
21686 TGTATGTATG
*
21696 TATGTATGTATGAATTTA-TAATTTAATACATGA
1 TATGTATGTAT-AATTTATTAATGTAATACAT-A
*
21729 TATGTATGTATAATTTATTCATGTAATACATA
1 TATGTATGTATAATTTATTAATGTAATACATA
*
21761 CATGTATG
1 TATGTATG
21769 ATATTAATGC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 14 0.39
33 22 0.61
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.45
Consensus pattern (32 bp):
TATGTATGTATAATTTATTAATGTAATACATA
Found at i:21916 original size:23 final size:24
Alignment explanation
Indices: 21873--21919 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
21863 AATCATACAC
*
21873 ACATGTAATACATGCATTATGCAT
1 ACATGTAATACATGCAATATGCAT
21897 ACATGT-ATACAT-CACATATGCAT
1 ACATGTAATACATGCA-ATATGCAT
21920 GTATGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 13 0.62
24 6 0.29
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (24 bp):
ACATGTAATACATGCAATATGCAT
Found at i:24281 original size:46 final size:46
Alignment explanation
Indices: 24178--24274 Score: 194
Period size: 46 Copynumber: 2.1 Consensus size: 46
24168 TAGATCCCAA
24178 ATTTTAGGGTTTATGAACATGTTATGGTTTCATGAATTGATGATGG
1 ATTTTAGGGTTTATGAACATGTTATGGTTTCATGAATTGATGATGG
24224 ATTTTAGGGTTTATGAACATGTTATGGTTTCATGAATTGATGATGG
1 ATTTTAGGGTTTATGAACATGTTATGGTTTCATGAATTGATGATGG
24270 ATTTT
1 ATTTT
24275 GAGGTTTTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.26, C:0.04, G:0.25, T:0.45
Consensus pattern (46 bp):
ATTTTAGGGTTTATGAACATGTTATGGTTTCATGAATTGATGATGG
Found at i:24743 original size:19 final size:19
Alignment explanation
Indices: 24697--24745 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
24687 ATGGAATATG
*
24697 ATGT-AAATTAATGCTAGA
1 ATGTGAAATTGATGCTAGA
* *
24715 GTGTTGAAATTGATGTTAGA
1 ATG-TGAAATTGATGCTAGA
24735 ATGTGAAATTG
1 ATGTGAAATTG
24746 GATTTGGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 2 0.08
19 9 0.36
20 14 0.56
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (19 bp):
ATGTGAAATTGATGCTAGA
Found at i:25581 original size:2 final size:2
Alignment explanation
Indices: 25574--25635 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
25564 GGCATAAATA
25574 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
25616 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
25636 TTCTTTAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25952 original size:22 final size:22
Alignment explanation
Indices: 25924--25967 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
25914 ACTGGTTATA
25924 ATATATGAAGTTTATTATGAAT
1 ATATATGAAGTTTATTATGAAT
* *
25946 ATATATGATGTTTATTGTGAAT
1 ATATATGAAGTTTATTATGAAT
25968 GTTATTTTGG
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (22 bp):
ATATATGAAGTTTATTATGAAT
Found at i:26219 original size:39 final size:39
Alignment explanation
Indices: 26134--26220 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
26124 AAGGATACCT
* * *
26134 AGAGCATATGGTGGTCACAACCTTATGTGTTAGCACTTG
1 AGAGCATATGGTGGGCACAACCTTATGTGTAAGCACTTC
* * *
26173 GGAGCATATGGTGGGCACGACCTTATGTGTAAGCGCTTC
1 AGAGCATATGGTGGGCACAACCTTATGTGTAAGCACTTC
*
26212 AGTGCATAT
1 AGAGCATAT
26221 TTGAATCGAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (39 bp):
AGAGCATATGGTGGGCACAACCTTATGTGTAAGCACTTC
Found at i:26470 original size:41 final size:41
Alignment explanation
Indices: 26420--26519 Score: 123
Period size: 43 Copynumber: 2.4 Consensus size: 41
26410 ATGCATTGAT
*
26420 TATTGTTACTCATTT-TTGTAATGTGGT-CATAATACCTTAAA
1 TATTATTACTCATTTATT-T-ATGTGGTGCATAATACCTTAAA
* *
26461 TATTATTACTCATTTACATTTATGTGTTGCATAATGCCTTAAA
1 TATTATTACTCATTT--ATTTATGTGGTGCATAATACCTTAAA
26504 TATTATTACTCATTTA
1 TATTATTACTCATTTA
26520 CATATATGTG
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
41 15 0.29
42 6 0.12
43 29 0.56
44 2 0.04
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (41 bp):
TATTATTACTCATTTATTTATGTGGTGCATAATACCTTAAA
Found at i:26501 original size:43 final size:43
Alignment explanation
Indices: 26447--26535 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
26437 GTAATGTGGT
*
26447 CATAATACCTTAAATATTATTACTCATTTACATTTATGTGTTG
1 CATAATACCTTAAATATTATTACTCATTTACATATATGTGTTG
*
26490 CATAATGCCTTAAATATTATTACTCATTTACATATATGTGTTG
1 CATAATACCTTAAATATTATTACTCATTTACATATATGTGTTG
26533 CAT
1 CAT
26536 TACATTGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.45
Consensus pattern (43 bp):
CATAATACCTTAAATATTATTACTCATTTACATATATGTGTTG
Found at i:28482 original size:20 final size:20
Alignment explanation
Indices: 28435--28684 Score: 182
Period size: 20 Copynumber: 12.2 Consensus size: 20
28425 AATGACCAAC
* *
28435 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
28454 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
28474 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
* * **
28494 AAGATCGCAACACGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* * *
28515 AAGAATCGCAATGCGATTCAT
1 AA-AATCGCAACGCGATTTAG
**
28536 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* *
28557 AAGAATCGCAACGCGATTCAT
1 AA-AATCGCAACGCGATTTAG
*
28578 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* *
28598 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTTAG
*
28618 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
**
28638 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
28659 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
28680 AAAAT
1 AAAAT
28685 GAGTAAATTC
Statistics
Matches: 182, Mismatches: 38, Indels: 21
0.76 0.16 0.09
Matches are distributed among these distances:
19 19 0.10
20 103 0.57
21 21 0.12
22 39 0.21
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:28543 original size:42 final size:42
Alignment explanation
Indices: 28497--28675 Score: 226
Period size: 42 Copynumber: 4.3 Consensus size: 42
28487 TGAAAAGAAG
* *
28497 ATCGCAACACGATCTTCCAAGAATCGCAATGCGATTCATAAA
1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCATAAA
28539 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCATAAA
1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCATAAA
* *
28581 ATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAGAAA
1 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCATAAA
* *
28621 ATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATCTTCCA-AGA
1 ATCGCAACGCGATCTTCCA-AGAATCGCAACGCGA--TT-CATAAA
28663 ATCGCAACGCGAT
1 ATCGCAACGCGAT
28676 TAAGAAAATG
Statistics
Matches: 125, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
39 2 0.02
40 54 0.43
42 68 0.54
43 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (42 bp):
ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCATAAA
Found at i:28824 original size:5 final size:5
Alignment explanation
Indices: 28784--28851 Score: 91
Period size: 5 Copynumber: 12.6 Consensus size: 5
28774 CGTATTACCA
28784 CGACC ACGACC ACGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC
1 CGACC -CGACC -CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC
28834 CGACC CGACC CGACC CGA
1 CGACC CGACC CGACC CGA
28852 GACGGCGGCG
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 33 0.53
6 29 0.47
ACGTcount: A:0.26, C:0.54, G:0.19, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:29383 original size:6 final size:5
Alignment explanation
Indices: 29334--29406 Score: 101
Period size: 5 Copynumber: 13.6 Consensus size: 5
29324 CCGTCTCGTC
29334 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGCGG TCGCGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG
29386 TCGCGG TCGCGG TCGCGG TCG
1 TCG-GG TCG-GG TCG-GG TCG
29407 TGGTAATACG
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 38 0.57
6 29 0.43
ACGTcount: A:0.00, C:0.26, G:0.55, T:0.19
Consensus pattern (5 bp):
TCGGG
Found at i:29543 original size:22 final size:22
Alignment explanation
Indices: 29515--29633 Score: 156
Period size: 22 Copynumber: 5.6 Consensus size: 22
29505 CATTTTCTTA
29515 ATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAAG
***
29537 ATCGCGTTGCGATT-TTCTTA-
1 ATCGCGTTGCGATTCTTGGAAG
29557 ATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAAG
***
29579 ATCGCGTTGCGATT-TTCTTA-
1 ATCGCGTTGCGATTCTTGGAAG
29599 ATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAAG
29621 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
29634 CTTCTTTTCA
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
20 28 0.35
21 12 0.15
22 41 0.51
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (22 bp):
ATCGCGTTGCGATTCTTGGAAG
Found at i:29562 original size:20 final size:20
Alignment explanation
Indices: 29506--29695 Score: 150
Period size: 20 Copynumber: 9.2 Consensus size: 20
29496 GAATTTACTC
29506 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
29526 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
29548 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
29568 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
29590 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
***
29610 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCG
* * *
29632 ATCTTCTT-TTCAACGTTGCG
1 ATTTTCTTAATC-GCGTTGCG
* *
29652 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
* **
29672 GTTTTGAT-ATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCG
29691 ATTTT
1 ATTTT
29696 GTTGGTCATT
Statistics
Matches: 131, Mismatches: 31, Indels: 17
0.73 0.17 0.09
Matches are distributed among these distances:
19 17 0.13
20 54 0.41
21 19 0.15
22 41 0.31
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTTCTTAATCGCGTTGCG
Found at i:29649 original size:84 final size:82
Alignment explanation
Indices: 29506--29693 Score: 254
Period size: 84 Copynumber: 2.3 Consensus size: 82
29496 GAATTTACTC
* *
29506 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGATT
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATCTTCTTAATCACGTTGCGATT
*
29571 CTTGGAAGATCGCGTTGCG
66 -TTCGAA-ATCGCGTTGCG
* *
29590 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATCTTCTT-TTCAACGTTGCGCT
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATCTTCTTAATC-ACGTTGCGAT
*
29654 TTTCTAAATCGCGTTGCG
65 TTTCGAAATCGCGTTGCG
* **
29672 GTTTTGAT-ATCGCGTTGCGATT
1 ATTTTCTTAATCGCGTTGCGATT
29694 TTGTTGGTCA
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
81 14 0.15
82 16 0.17
83 6 0.06
84 58 0.62
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (82 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATCTTCTTAATCACGTTGCGATT
TTCGAAATCGCGTTGCG
Found at i:29651 original size:42 final size:42
Alignment explanation
Indices: 29506--29639 Score: 259
Period size: 42 Copynumber: 3.2 Consensus size: 42
29496 GAATTTACTC
29506 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
29548 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
29590 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
*
29632 ATCTTCTT
1 ATTTTCTT
29640 TTCAACGTTG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (42 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
Found at i:31990 original size:130 final size:131
Alignment explanation
Indices: 31757--32237 Score: 698
Period size: 130 Copynumber: 3.7 Consensus size: 131
31747 TATCAACATA
* * *
31757 TTACCATGTACATTGTTAATTTACCTATTACTTTAAAGTAATTGGTTTCGAAATTAGAAGTATCG
1 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
* * *
31822 ATAC-TTATATGA-CAGTATCGATGCTTGTACATTTACGCCTATTTTCATTATACCGGTAGAAAC
66 ATACTTTATAT-ATGAGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAGAAAC
31885 GT
130 GT
* *
31887 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAATAATAGGTTTTGAAATTATAAGTATC-
1 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
* * * * *
31951 ATACTTTATACATGAGTATCTATACTAGGGCATTTACGCCTATTTTCATTATACCGATAGAAACG
66 ATACTTTATATATGAGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAGAAACG
32016 T
131 T
* *
32017 TTATCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCG
1 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
* * * * *
32082 ATACTTTGTATATAAGAATCGATACTTGGACATTTACGCCTATTTTCATTATACTGGTAGAAATG
66 ATACTTTATATATGAGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAGAAACG
32147 T
131 T
* * * * *
32148 TTACCCTGTACATTGTTAATTTACATATTACTTTAAAGTAATAGGCTTCCAAATTATAAATATCG
1 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
*
32213 ATACTTTATATATGTGTATCGATAC
66 ATACTTTATATATGAGTATCGATAC
32238 ATTTTGCGTG
Statistics
Matches: 311, Mismatches: 37, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
129 5 0.02
130 170 0.55
131 136 0.44
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (131 bp):
TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
ATACTTTATATATGAGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAGAAACG
T
Found at i:35711 original size:200 final size:199
Alignment explanation
Indices: 35363--36145 Score: 941
Period size: 200 Copynumber: 4.0 Consensus size: 199
35353 AGATCGAAAG
* * ** * *
35363 TATCGATACCTATATAAAAGTATCGATACTTAGTATTTATTCCTATTATCAATATACTGGTAGAC
1 TATCCATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGAC
* * *
35428 TTTTATCGTTTACATTGTTAATTTACCCATTACTTTAAAGTAATAGGTTTCGAAATTCCATGTAT
66 TTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTAT
* * *
35493 CGATATTTTATATATGTGTATCGATA-ATTTTTACGGTGCAAATTGTTTGAGAATCATATTAGAA
131 CGATACTTTATATATGTGTATCGATACA-TTTTAC-GTGCAAATTGTTTGAGAAGCATACTAGAA
35557 TAAAAA
194 TAAAAA
* * * *
35563 TATCCATACCTATATAAAAGCATCGATACTTGGTATTTACACCAATTATCATTATACCAGTAGAC
1 TATCCATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGAC
* * * *
35628 TTTTACCGTTTACATTGTCAAGTTACCTATTACTTTAAAGTAATAGGTTTTGAAATTTCAAGTAT
66 TTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTAT
* * *
35693 AGATATTTTATATATGTGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAGCATACTAG----
131 CGATACTTTATATATGTGTATCGATACATTTTACGTGCAAATTGTTTGAGAAGCATACTAGAATA
35754 ----
196 AAAA
* * * *
35754 -----------A-ATAAAAGTATCGATCCTTGGTATTTAGGCCTATTATCATTATACCTGTATAC
1 TATCCATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGAC
** * *
35807 TTTTACATTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTCCAAGCAT
66 TTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTAT
* * *
35872 CGATACTTTATACA--TGTATTGATACATTTTGCGTGCAAATTGTTTGAGAAGCATACTAGAATA
131 CGATACTTTATATATGTGTATCGATACATTTTACGTGCAAATTGTTTGAGAAGCATACTAGAATA
*
35935 AAAG
196 AAAA
* * * * *
35939 TATCCATGCCCATATAAAGAGTATTGATACTTGGTATTTACGTCTATTATCA-TATACCGGTAGT
1 TATCCATACCTATATAAA-AGTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGA
* * *
36003 CTTTTACCATTTACAGTGTTAATTTACCTAATTACTTTAAAGGAATAGGTTT-GAAATTCCAAGT
65 CTTTTACCGTTTACATTGTTAATTTACCT-ATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGT
* *
36067 ATTGATACTTTATATATGTGTATCGATACATTTTACGTGCAAATTGTTTGAGAATCATACTAGAA
129 ATCGATACTTTATATATGTGTATCGATACATTTTACGTGCAAATTGTTTGAGAAGCATACTAGAA
*
36132 TAAAAG
194 TAAAAA
36138 TATCCATA
1 TATCCATA
36146 TCGACATAAG
Statistics
Matches: 500, Mismatches: 58, Indels: 51
0.82 0.10 0.08
Matches are distributed among these distances:
177 44 0.09
179 113 0.23
180 1 0.00
196 1 0.00
197 64 0.13
198 50 0.10
199 82 0.16
200 144 0.29
201 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (199 bp):
TATCCATACCTATATAAAAGTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGAC
TTTTACCGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTAT
CGATACTTTATATATGTGTATCGATACATTTTACGTGCAAATTGTTTGAGAAGCATACTAGAATA
AAAA
Found at i:36096 original size:376 final size:378
Alignment explanation
Indices: 35376--36141 Score: 1096
Period size: 376 Copynumber: 2.0 Consensus size: 378
35366 CGATACCTAT
**
35376 ATAAAAGTATCGATACTTAGTATTTATTCCTATTATCAATATACTGGTAGACTTTTATCGTTTAC
1 ATAAAAGTATCGATACTTAGTATTTAGGCCTATTATCAATATACTGGTAGACTTTTATCGTTTAC
* * * * *
35441 ATTGTTAATTTACCCATTACTTTAAAGTAATAGGTTTCGAAATTCCATGTATCGATATTTTATAT
66 ATTGTTAATTTACCCATTACTTTAAAGTAATAGGTTTCAAAATTCCAAGCATCGATACTTTATAC
* *
35506 ATGTGTATCGATAATTTTTACGGTGCAAATTGTTTGAGAATCATATTAGAATAAAAATATCCATA
131 A-GTGTATCGATAATTTTTACGGTGCAAATTGTTTGAGAAGCATACTAGAATAAAAATATCCATA
* *
35571 CCTATATAAAAGCATCGATACTTGGTATTTACACCAATTATCATTATACCAGTAGACTTTTACCG
195 CCCATATAAAAGCATCGATACTTGGTATTTACACCAATTATCATTATACCAGTAGACTTTTACCA
* * * *
35636 TTTACATTGTCAAGTTACCTATTACTTTAAAGTAATAGGTTTTGAAATTTCAAGTATAGATATTT
260 TTTACAGTGTCAAGTTACCTATTACTTTAAAGGAATAGGTTTTGAAATTCCAAGTATAGATACTT
*
35701 TATATATGTGTATCGATACATTTTGCGTGCAAATTGTTTGAGAAGCATACTAGA
325 TATATATGTGTATCGATACATTTTACGTGCAAATTGTTTGAGAAGCATACTAGA
* * * * *
35755 ATAAAAGTATCGATCCTTGGTATTTAGGCCTATTATCATTATACCT-GTATACTTTTA-CATTTT
1 ATAAAAGTATCGATACTTAGTATTTAGGCCTATTATCAATATA-CTGGTAGACTTTTATC-GTTT
*
35818 ACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTCCAAGCATCGATACTTTAT
64 ACATTGTTAATTTACCCATTACTTTAAAGTAATAGGTTTCAAAATTCCAAGCATCGATACTTTAT
* * *
35883 ACA-TGTATTGATACA-TTTTGC-GTGCAAATTGTTTGAGAAGCATACTAGAATAAAAGTATCCA
129 ACAGTGTATCGATA-ATTTTTACGGTGCAAATTGTTTGAGAAGCATACTAGAATAAAAATATCCA
* * * ** * * *
35945 TGCCCATATAAAGAGTATTGATACTTGGTATTTACGTCTATTATCA-TATACCGGTAGTCTTTTA
193 TACCCATATAAA-AGCATCGATACTTGGTATTTACACCAATTATCATTATACCAGTAGACTTTTA
* * *
36009 CCATTTACAGTGTTAATTTACCTAATTACTTTAAAGGAATAGG-TTTGAAATTCCAAGTATTGAT
257 CCATTTACAGTGTCAAGTTACCT-ATTACTTTAAAGGAATAGGTTTTGAAATTCCAAGTATAGAT
*
36073 ACTTTATATATGTGTATCGATACATTTTACGTGCAAATTGTTTGAGAATCATACTAGA
321 ACTTTATATATGTGTATCGATACATTTTACGTGCAAATTGTTTGAGAAGCATACTAGA
36131 ATAAAAGTATC
1 ATAAAAGTATC
36142 CATATCGACA
Statistics
Matches: 345, Mismatches: 37, Indels: 13
0.87 0.09 0.03
Matches are distributed among these distances:
376 168 0.49
377 60 0.17
378 2 0.01
379 113 0.33
380 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (378 bp):
ATAAAAGTATCGATACTTAGTATTTAGGCCTATTATCAATATACTGGTAGACTTTTATCGTTTAC
ATTGTTAATTTACCCATTACTTTAAAGTAATAGGTTTCAAAATTCCAAGCATCGATACTTTATAC
AGTGTATCGATAATTTTTACGGTGCAAATTGTTTGAGAAGCATACTAGAATAAAAATATCCATAC
CCATATAAAAGCATCGATACTTGGTATTTACACCAATTATCATTATACCAGTAGACTTTTACCAT
TTACAGTGTCAAGTTACCTATTACTTTAAAGGAATAGGTTTTGAAATTCCAAGTATAGATACTTT
ATATATGTGTATCGATACATTTTACGTGCAAATTGTTTGAGAAGCATACTAGA
Found at i:36161 original size:21 final size:21
Alignment explanation
Indices: 36131--36204 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
36121 TCATACTAGA
* *
36131 ATAA-AAGTATCCATATCGAC
1 ATAAGAAGTATCCATAACGTC
36151 ATAAGAAGTATCCATAACGTC
1 ATAAGAAGTATCCATAACGTC
36172 ATAAGAAGTATCCATAACGTC
1 ATAAGAAGTATCCATAACGTC
36193 ATAAGAAGTATC
1 ATAAGAAGTATC
36205 AATACTTCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 4 0.08
21 47 0.92
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.24
Consensus pattern (21 bp):
ATAAGAAGTATCCATAACGTC
Found at i:37101 original size:49 final size:49
Alignment explanation
Indices: 37042--37135 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 49
37032 CAATATTTGC
*
37042 TAACTTTGGTAATCACATGCATAATTTCATTCACATACAAAATTTGTTG
1 TAACTTTGGTAATCACATACATAATTTCATTCACATACAAAATTTGTTG
37091 TAACTTTGGTAATCACATACATAATTTCATTCACATACAAAATTT
1 TAACTTTGGTAATCACATACATAATTTCATTCACATACAAAATTT
37136 ACAAACTAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.38
Consensus pattern (49 bp):
TAACTTTGGTAATCACATACATAATTTCATTCACATACAAAATTTGTTG
Found at i:39011 original size:12 final size:12
Alignment explanation
Indices: 38994--39026 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
38984 CTCCCTACTA
38994 CCTTCTCTTCCT
1 CCTTCTCTTCCT
*
39006 CCTTCTCTTCTT
1 CCTTCTCTTCCT
39018 CCTTCTCTT
1 CCTTCTCTT
39027 GATCTTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (12 bp):
CCTTCTCTTCCT
Found at i:39050 original size:18 final size:16
Alignment explanation
Indices: 38999--39050 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
38989 TACTACCTTC
38999 TCTTCCTC-CTTCTCT
1 TCTTCCTCTCTTCTCT
*
39014 TCTTCCTTCTCTTGATCT
1 TCTTCC-TCTCTT-CTCT
39032 TCTTCCTCATCTTCCTCT
1 TCTTCCTC-TCTT-CTCT
39050 T
1 T
39051 TGCCAATAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 6 0.20
16 2 0.07
17 5 0.17
18 17 0.57
ACGTcount: A:0.04, C:0.40, G:0.02, T:0.54
Consensus pattern (16 bp):
TCTTCCTCTCTTCTCT
Found at i:41686 original size:197 final size:198
Alignment explanation
Indices: 41199--41754 Score: 680
Period size: 197 Copynumber: 2.8 Consensus size: 198
41189 GTAGCGTTTT
* * * *
41199 ACCGGTTTTGTCAAATTTGGAACCTGTTATATTGTCATGTATCAATACACGTGTCTAAGGTATCG
1 ACCGGTTTTGTCAAATTT-AAACATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCG
* * * * *
41264 ATACTTTATAAGCACTA-TATTGAAATTCTTTGAAATTCCTAAAGTACTGATACTTTGGTACATA
65 AAACTTTATAACCACTATTATTGCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATA
* *
41328 TACTTATAAAA-GTATC-ATTACAAATTTCAACCATTCCGGTAGCTCCTTACCGGTTTCGTCAAA
130 TACTTATAAAACGTATCGA-TACAAATTTCAACAATTCCGGTAGCTCCTTACAGGTTTCGTCAAA
41391 TTGAA
194 TTGAA
** * * * * * * *
41396 ACCTATTTTCTAAAATTTAAACTTGTTGTATTATCATGTATCGATACATGTTTCTAAGGTATTG-
1 ACCGGTTTTGTCAAATTTAAACATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGA
* * * *
41460 AATTTTATAGCCACTATTATTGCAATTCTTTTAAATTCCTAAAGTACGGACACTTTGGTACATAT
66 AACTTTATAACCACTATTATTGCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATAT
* * * * **
41525 ACTTATAAAACATATCGATACAAATTTCAACAATTTCGGTAGCTCTTTACAGTTTTTTTCAAATT
131 ACTTATAAAACGTATCGATACAAATTTCAACAATTCCGGTAGCTCCTTACAGGTTTCGTCAAATT
41590 GAA
196 GAA
* * * *
41593 ACCGGTTTTGTCAAATTTCAACATG-TATATTGTCACGTATCGACACATGTGTGTAAGGTATCGA
1 ACCGGTTTTGTCAAATTTAAACATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGA
* ** *
41657 AACTTTATAACCACTATTATTGCAATTCTTTTAAATTCATGCAGTACCGATATTTTGGTAC--AT
66 AACTTTATAACCACTATTATTGCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATAT
41720 ACTTAT--AACTGTATCGATACAAATTTCAACAATTC
131 ACTTATAAAAC-GTATCGATACAAATTTCAACAATTC
41755 TAATAGCTCT
Statistics
Matches: 303, Mismatches: 51, Indels: 13
0.83 0.14 0.04
Matches are distributed among these distances:
193 3 0.01
194 23 0.08
195 20 0.07
196 123 0.41
197 133 0.44
198 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (198 bp):
ACCGGTTTTGTCAAATTTAAACATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGA
AACTTTATAACCACTATTATTGCAATTCTTTTAAATTCCTAAAGTACCGATACTTTGGTACATAT
ACTTATAAAACGTATCGATACAAATTTCAACAATTCCGGTAGCTCCTTACAGGTTTCGTCAAATT
GAA
Found at i:42354 original size:53 final size:52
Alignment explanation
Indices: 42250--42352 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
42240 TTTTTTCCCA
42250 AACTTTAATTCGAATTCCAATTTATGTTAAAAAATTATTTGAATTTATTTTG
1 AACTTTAATTCGAATTCCAATTTATGTTAAAAAATTATTTGAATTTATTTTG
* * *
42302 AACTTTAATTCGAATTTCCAATTTATGTT-CAAAATTATTTTAATTTGTTTT
1 AACTTTAATTCGAA-TTCCAATTTATGTTAAAAAATTATTTGAATTTATTTT
42353 TGCTTGGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 33 0.70
53 14 0.30
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (52 bp):
AACTTTAATTCGAATTCCAATTTATGTTAAAAAATTATTTGAATTTATTTTG
Found at i:46956 original size:17 final size:17
Alignment explanation
Indices: 46927--46964 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
46917 AATTTTTCAC
*
46927 AAGATGAAAACTCAACA
1 AAGATGAAAACTCAAAA
46944 AAGAT-AAAGACTCAAAA
1 AAGATGAAA-ACTCAAAA
46961 AAGA
1 AAGA
46965 GAATAAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.63, C:0.13, G:0.13, T:0.11
Consensus pattern (17 bp):
AAGATGAAAACTCAAAA
Found at i:47391 original size:20 final size:20
Alignment explanation
Indices: 47328--47391 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 20
47318 CAAAGGAAGA
*
47328 GTTCATAATGAGAAGAACTC
1 GTTCATAATGAGAAGAACTT
* *
47348 GTCTGATGATAGAGAAGAA--T
1 GT-TCATAAT-GAGAAGAACTT
47368 -TTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
47387 GTTCA
1 GTTCA
47392 ACCTTGGTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 2 0.06
20 6 0.18
21 5 0.15
22 8 0.24
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:47523 original size:116 final size:116
Alignment explanation
Indices: 47306--47546 Score: 324
Period size: 116 Copynumber: 2.1 Consensus size: 116
47296 AGAGAAGACA
* * *
47306 GATCTACATTTCCAAAGGAAGAGTTCATAATGAGAAGAACTCGTCTGATGATAGAGAAGAATTTC
1 GATCAACATTTCCAAAGGAAGAGTTCATAATGAGAAGAACTCGACTGATGATAGAGAAGAAGTTC
*** *
47371 ATAATGAGAAGAACTTGTTCAACCTTGGTTCATCCATTACAAAAGGAAG-TG
66 ATAATGAGAAGAACTTGTTCAACCTTAACTCATCCATCACAAAAGG-AGTTG
* * * *
47422 GATCAACATTTTCAATGGAAGAGTTCATAATGAGAAGAACTCGACTGATGA-GGCTGAAGAAGTT
1 GATCAACATTTCCAAAGGAAGAGTTCATAATGAGAAGAACTCGACTGATGATAG-AGAAGAAGTT
* * *
47486 CCTAATGAGAAGAACTTGTTCAACCTTAACTCGTCCATCACATAAGGAGTTG
65 CATAATGAGAAGAACTTGTTCAACCTTAACTCATCCATCACAAAAGGAGTTG
47538 GATCAACAT
1 GATCAACAT
47547 CACCTTTCTA
Statistics
Matches: 109, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
115 3 0.03
116 106 0.97
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (116 bp):
GATCAACATTTCCAAAGGAAGAGTTCATAATGAGAAGAACTCGACTGATGATAGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTAACTCATCCATCACAAAAGGAGTTG
Found at i:47601 original size:40 final size:43
Alignment explanation
Indices: 47519--47601 Score: 109
Period size: 46 Copynumber: 1.9 Consensus size: 43
47509 CCTTAACTCG
*
47519 TCCATCACATAAGGAGTTGGATCAACATCACCTTTCTATGCTCGAT
1 TCCATCACATAAAGAGTTGGATCAACATCA-C--TCTATGCTCGAT
47565 TCCATCACATAAAGAGTTGGATC-ACATCA-TCT-TGCTC
1 TCCATCACATAAAGAGTTGGATCAACATCACTCTATGCTC
47602 AAGATAGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
40 5 0.14
41 3 0.08
45 6 0.17
46 22 0.61
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (43 bp):
TCCATCACATAAAGAGTTGGATCAACATCACTCTATGCTCGAT
Found at i:47741 original size:37 final size:35
Alignment explanation
Indices: 47649--47766 Score: 105
Period size: 37 Copynumber: 3.2 Consensus size: 35
47639 TTTACTCAAG
* * * *
47649 ATTTTATCTCACTTGAGAGTGTTTATATTAAAAACAA
1 ATTTCATCTCACTTAAGA-TGTTTTTCTT-AAAACAA
*
47686 ATCTT-ATCTCA-TCGAAGATCGTTTTTCTTAAGAACAA
1 AT-TTCATCTCACT-TAAGAT-GTTTTTCTTAA-AACAA
*
47723 ATTTCATCTCACTTAAGATTTTTTTCTTTAAAACAA
1 ATTTCATCTCACTTAAGATGTTTTTC-TTAAAACAA
47759 ATTTCATC
1 ATTTCATC
47767 CCGCCTAAGA
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
36 25 0.37
37 40 0.59
38 3 0.04
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (35 bp):
ATTTCATCTCACTTAAGATGTTTTTCTTAAAACAA
Found at i:47776 original size:36 final size:36
Alignment explanation
Indices: 47707--47777 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
47697 TCGAAGATCG
* *
47707 TTTTTCTTAAGAACAAATTTCATCTCACTTAAGATT
1 TTTTTCTTAAGAACAAATTTCATCCCACCTAAGATT
*
47743 TTTTTCTTTAA-AACAAATTTCATCCCGCCTAAGAT
1 TTTTTC-TTAAGAACAAATTTCATCCCACCTAAGAT
47778 AGTTTCTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (36 bp):
TTTTTCTTAAGAACAAATTTCATCCCACCTAAGATT
Found at i:50354 original size:23 final size:24
Alignment explanation
Indices: 50328--50391 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
50318 AAAAATGCTT
* *
50328 AAAGATAATTCC-TAGTAAA-TGCA
1 AAAGATAATTCCTTA-AAAATTACA
50351 AAAGATAATTCCTTAAAAATTACA
1 AAAGATAATTCCTTAAAAATTACA
50375 AAAGATAATTCCCTTAA
1 AAAGATAATT-CCTTAA
50392 TTGTTTGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 15 0.42
24 15 0.42
25 6 0.17
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (24 bp):
AAAGATAATTCCTTAAAAATTACA
Found at i:50987 original size:23 final size:24
Alignment explanation
Indices: 50958--51013 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
50948 ATGCTTAAAT
* * *
50958 ATAATTCCTAATAAA-TGCAAAAG
1 ATAATTCCCAAAAAATTACAAAAG
50981 ATAATTCCCAAAAAATTACAAAAG
1 ATAATTCCCAAAAAATTACAAAAG
51005 ATAATTCCC
1 ATAATTCCC
51014 TTAATTGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 13 0.45
24 16 0.55
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (24 bp):
ATAATTCCCAAAAAATTACAAAAG
Found at i:53189 original size:18 final size:18
Alignment explanation
Indices: 53166--53205 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
53156 AGAATTCGAG
*
53166 GAAATTAATCATGAATTA
1 GAAATTAAACATGAATTA
*
53184 GAAATTAAACGTGAATTA
1 GAAATTAAACATGAATTA
53202 GAAA
1 GAAA
53206 AAAAAAGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.28
Consensus pattern (18 bp):
GAAATTAAACATGAATTA
Found at i:63937 original size:54 final size:54
Alignment explanation
Indices: 63869--64046 Score: 240
Period size: 54 Copynumber: 3.4 Consensus size: 54
63859 TATGAATTAC
* * *
63869 TTGCAAACACAGTGCCAATATGGAAATTCATAAACTCATTATTAATTTCTTAAA
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTATTAATTTCTTAAG
* * ** *
63923 TTGCACATATAGTGCCAATACAAAAATTCATAAACTCATTA-TGA-TT-TTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTATTAATTTCTTAAG
*
63974 TTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTATTAATTTCTTAAG
64028 TTG--CACACAGTGCCAATAC
1 TTGCACACACAGTGCCAATAC
64047 AGTAAAATAC
Statistics
Matches: 107, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
51 41 0.38
52 19 0.18
53 4 0.04
54 43 0.40
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (54 bp):
TTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTATTAATTTCTTAAG
Found at i:64001 original size:51 final size:53
Alignment explanation
Indices: 63869--64046 Score: 238
Period size: 51 Copynumber: 3.4 Consensus size: 53
63859 TATGAATTAC
* * * *
63869 TTGCAAACACAGTGCCAATATGGAAATTCATAAACTCATTATTAATTTCTTAAA
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTA-TGATTTCTTAAG
* * **
63923 TTGCACATATAGTGCCAATACAAAAATTCATAAACTCATTATGA-TT-TTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTATGATTTCTTAAG
63974 TTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTATG-ATTTCTTAAG
64028 TTG--CACACAGTGCCAATAC
1 TTGCACACACAGTGCCAATAC
64047 AGTAAAATAC
Statistics
Matches: 109, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
51 43 0.39
52 19 0.17
53 4 0.04
54 43 0.39
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (53 bp):
TTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTATGATTTCTTAAG
Found at i:64054 original size:105 final size:102
Alignment explanation
Indices: 63852--64047 Score: 295
Period size: 105 Copynumber: 1.9 Consensus size: 102
63842 CGGTAATTCC
* *
63852 AACTCATTATGAATTACTTGCAAACACAGTGCCAATATGGAAATTCATAAACTCATTATTAATTT
1 AACTCATTATGAATTACTTGCAAACACAGTGCCAATACGGAAATTCATAAACTCATTATGAATTT
*
63917 CTTAAATTGCACATATAGTGCCAATACAAAAATTCATA
66 CTTAAATTGCACA-ACAGTGCCAATACAAAAATTCATA
* * *
63955 AACTCATTATGATTTTAAGTTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTATGAAT
1 AACTCATTATGA-ATT-ACTTGCAAACACAGTGCCAATACGGAAATTCATAAACTCATTATGAAT
*
64020 TTCTTAAGTTGCAC-ACAGTGCCAATACA
64 TTCTTAAATTGCACAACAGTGCCAATACA
64048 GTAAAATACA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
103 25 0.30
104 2 0.02
105 57 0.68
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (102 bp):
AACTCATTATGAATTACTTGCAAACACAGTGCCAATACGGAAATTCATAAACTCATTATGAATTT
CTTAAATTGCACAACAGTGCCAATACAAAAATTCATA
Done.