Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014053.1 Corchorus capsularis cultivar CVL-1 contig14074, 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: 105916
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:144 original size:22 final size:22
Alignment explanation
Indices: 119--1184 Score: 201
Period size: 22 Copynumber: 48.7 Consensus size: 22
109 ATGATCCCAT
119 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** **
141 TATGAAATTTTAATAACGATAT
1 TATGAAATTTTGATAACCTTCC
* * * * **
163 TATGGAATTTCGAAAATCTTTT
1 TATGAAATTTTGATAACCTTCC
** * *
185 TAT-AAATTTTTTTTAACGTTCT
1 TATGAAA-TTTTGATAACCTTCC
* * *
207 TATTAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
229 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
* *
251 TATGAAATTTTAATAACTTTCC
1 TATGAAATTTTGATAACCTTCC
* * **
273 AATGAAATTTTAATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
296 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
317 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * * *
340 TATGAAAATTT-AAAAACTTACA
1 TATGAAATTTTGATAACCTT-CC
* *
362 TATG-AATTGTT-AGTAATC-ACAC
1 TATGAAATT-TTGA-TAACCTTC-C
* * * *
384 TCTGAAATATTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
* * *
406 TATGAAATTGTAATAACC-TCGT
1 TATGAAATTTTGATAACCTTC-C
* *
428 TATGAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* *
451 TATAAAATTTTGATAAACCTTTC
1 TATGAAATTTTGAT-AACCTTCC
* * *
474 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
496 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* * *
513 TGT-AAATTTTGATAAGCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
534 TAT-AATTTTTTGATAACC-TCAT
1 TATGAA-ATTTTGATAACCTTC-C
* * *
556 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
578 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
600 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
622 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
644 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
666 TATGAAATTTTGAT-ATCTTCC
1 TATGAAATTTTGATAACCTTCC
* *
687 -CTGAAATTTTGATTA--TTCC
1 TATGAAATTTTGATAACCTTCC
* * *
706 ATTATAAAAGTTTAATAACCTTCC
1 --TATGAAATTTTGATAACCTTCC
* *
730 --T--AA-TTTGATAACCATAC
1 TATGAAATTTTGATAACCTTCC
*
747 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *** * *
769 CA-GAACTCCCCAGA-AATAC-TAC
1 TATGAAAT--TTTGATAA-CCTTCC
791 TATGAAATTTTTG-TAATCACATT--
1 TATGAAA-TTTTGATAA-C-C-TTCC
* *
814 T-TGAAAATTTGATAACC-TCTT
1 TATGAAATTTTGATAACCTTC-C
* * * *
835 TATAAAATTTTGTTGACC-CCTC
1 TATGAAATTTTGATAACCTTC-C
* *
857 TATGAAATTCTGATAATCACAT--
1 TATGAAATTTTGATAA-C-CTTCC
*
879 TATGTAATTTTGATAACC-TCAC
1 TATGAAATTTTGATAACCTTC-C
* ***
901 TTTGAAATTTTGATAA-GAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
923 TATGAAATTTTGATAATCTTCA
1 TATGAAATTTTGATAACCTTCC
*
945 TAT-AAATTTTGATAATCCAATCTC
1 TATGAAATTTTGATAA-CC-TTC-C
* *
969 TATAAAATTTCGATAATCAC-T-C
1 TATGAAATTTTGATAA-C-CTTCC
*
991 TATGAGA-TTTGATAACCTT-C
1 TATGAAATTTTGATAACCTTCC
* *
1011 TATCAAATTTTGGT-A-C-TCC
1 TATGAAATTTTGATAACCTTCC
* *
1030 TTATGAAATTGAGACTTTTATAACCTTCA
1 -TATGAAA-T-----TTTGATAACCTTCC
*
1059 TATGAAATTTTGATAACC-ACAC
1 TATGAAATTTTGATAACCTTC-C
** *
1081 TACAAAATTTTGATAACCTACC
1 TATGAAATTTTGATAACCTTCC
* *
1103 CATGAAATATT-AGTAACC-TCC
1 TATGAAATTTTGA-TAACCTTCC
* *
1124 TACTGAAATTTTGTTAACC-ACAC
1 TA-TGAAATTTTGATAACCTTC-C
* *
1147 TATGAAATTCTT-ATTACCTTGC
1 TATGAAATT-TTGATAACCTTCC
*
1169 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
1185 TCTCTTTGAT
Statistics
Matches: 752, Mismatches: 201, Indels: 182
0.66 0.18 0.16
Matches are distributed among these distances:
16 11 0.01
17 13 0.02
18 4 0.01
19 9 0.01
20 30 0.04
21 74 0.10
22 477 0.63
23 92 0.12
24 11 0.01
25 14 0.02
26 5 0.01
27 2 0.00
28 8 0.01
29 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:1020 original size:20 final size:20
Alignment explanation
Indices: 931--1020 Score: 60
Period size: 21 Copynumber: 4.2 Consensus size: 20
921 ACTATGAAAT
931 TTTGATAAT-CTTCATATAAA
1 TTTGATAATCCTTC-TATAAA
951 TTTTGATAATCCAATCTCTATAAAA
1 -TTTGATAATCC--T-TCTAT-AAA
*
976 TTTCGATAATCAC-TCTATGAGA
1 TTT-GATAATC-CTTCTAT-AAA
998 TTTGATAA-CCTTCTATCAAA
1 TTTGATAATCCTTCTAT-AAA
1018 TTT
1 TTT
1021 TGGTACTCCT
Statistics
Matches: 57, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
19 1 0.02
20 11 0.19
21 14 0.25
22 11 0.19
24 7 0.12
25 12 0.21
26 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.42
Consensus pattern (20 bp):
TTTGATAATCCTTCTATAAA
Found at i:1133 original size:114 final size:115
Alignment explanation
Indices: 930--1136 Score: 246
Period size: 112 Copynumber: 1.8 Consensus size: 115
920 CACTATGAAA
* * * * *
930 TTTTGATAATCTTCATATAAATTTTGATAATCCAATCTCTATAAAATTTCGATAATCACTCTATG
1 TTTTGATAACCTTCATATAAATTTTGATAATCCAATCACTACAAAATTTCGATAACCACTCCATG
* *
995 AGATTTGATAACCTTCTATCAAATTTTGGTACTCCTTATGAAATTGAGAC
66 AAATTTGATAACCTCCTATCAAATTTTGGTACTCCTTATGAAATTGAGAC
*
1045 TTTT-ATAACCTTCATATGAAATTTTGATAA-CC-A-CACTACAAAATTTTGATAACCTAC-CCA
1 TTTTGATAACCTTCATAT-AAATTTTGATAATCCAATCACTACAAAATTTCGATAACC-ACTCCA
*
1105 TGAAATATT-AGTAACCTCCTACTGAAATTTTG
64 TGAAAT-TTGA-TAACCTCCTA-TCAAATTTTG
1137 TTAACCACAC
Statistics
Matches: 78, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
112 25 0.32
113 14 0.18
114 23 0.29
115 16 0.21
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (115 bp):
TTTTGATAACCTTCATATAAATTTTGATAATCCAATCACTACAAAATTTCGATAACCACTCCATG
AAATTTGATAACCTCCTATCAAATTTTGGTACTCCTTATGAAATTGAGAC
Found at i:1284 original size:46 final size:46
Alignment explanation
Indices: 1227--1315 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
1217 AATTAACCAC
*
1227 CCTATTAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTCAATAACCACA-CTAAGAAATTTTAATAACCTGAT
*** * *
1273 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCT
1 CCTATGAAATTTCAATAACCACACTAAGAAATTTTAATAACCT
1316 CCTCATGAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
46 35 0.97
47 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (46 bp):
CCTATGAAATTTCAATAACCACACTAAGAAATTTTAATAACCTGAT
Found at i:1323 original size:22 final size:22
Alignment explanation
Indices: 1220--1360 Score: 106
Period size: 22 Copynumber: 6.3 Consensus size: 22
1210 TTGTGATAAT
* * **
1220 TAACCACCCTATTAAATTTCAA
1 TAACCATCCTATGAAATTTTGA
* * *
1242 TAACCAACCTAAGAAATTTTAA
1 TAACCATCCTATGAAATTTTGA
*
1264 TAACCTGATCCTATGAAATTTTGG
1 TAACC--ATCCTATGAAATTTTGA
1288 TAACCA-CACTATGAAATTTTGA
1 TAACCATC-CTATGAAATTTTGA
* * *
1310 TAACC-TCCTCATGAGATTATAA
1 TAACCATCCT-ATGAAATTTTGA
* *
1332 TAACCATCTTTATGAAATTCTGA
1 TAACCATC-CTATGAAATTTTGA
1355 TAACCA
1 TAACCA
1361 CACATAGAGA
Statistics
Matches: 96, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.03
22 57 0.59
23 17 0.18
24 19 0.20
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.33
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTGA
Found at i:5958 original size:30 final size:29
Alignment explanation
Indices: 5909--5999 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 29
5899 TGACACGTGG
*
5909 CACATGGCATTTTTG-ACACGTGGCATGC
1 CACATGACATTTTTGTACACGTGGCATGC
** * * *
5937 CATGTGTCCTTATTTGTACACGTGGCATGT
1 CACATGACATT-TTTGTACACGTGGCATGC
5967 CACATGACATTTTTGGTACACGTGGCATGC
1 CACATGACATTTTT-GTACACGTGGCATGC
5997 CAC
1 CAC
6000 GTCGGATGCT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
28 7 0.14
29 7 0.14
30 36 0.72
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (29 bp):
CACATGACATTTTTGTACACGTGGCATGC
Found at i:10934 original size:21 final size:21
Alignment explanation
Indices: 10909--10948 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
10899 AGTTTTTGAC
10909 TTTTTGTTCCATTACATATTT
1 TTTTTGTTCCATTACATATTT
10930 TTTTTGTTCCATTACATAT
1 TTTTTGTTCCATTACATAT
10949 ATACAGCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTTTGTTCCATTACATATTT
Found at i:14259 original size:3 final size:3
Alignment explanation
Indices: 14251--14289 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
14241 TATGATAAGA
14251 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14290 ATATAAGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:14441 original size:5 final size:5
Alignment explanation
Indices: 14433--14483 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
14423 GATTAGAATT
* *
14433 ATATA ATATA ATATT A-AT- ATATA ATAATA ATATG ATATA ATATA AT-TA
1 ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA ATATA
14481 ATA
1 ATA
14484 ATATATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
3 1 0.03
4 8 0.21
5 25 0.64
6 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:14456 original size:13 final size:13
Alignment explanation
Indices: 14438--14506 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 13
14428 GAATTATATA
*
14438 ATATAATATTAAT
1 ATATAATAATAAT
14451 ATATAATAATAAT
1 ATATAATAATAAT
14464 ATGAT-ATAAT-AT
1 AT-ATAATAATAAT
14476 A-ATTAATAATATATT
1 ATA-TAATAATA-A-T
*
14491 ATATGTATAATAAT
1 ATAT-AATAATAAT
14505 AT
1 AT
14507 TAGATGTGGT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
10 1 0.02
11 1 0.02
12 8 0.17
13 19 0.41
14 6 0.13
15 4 0.09
16 7 0.15
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:14464 original size:19 final size:19
Alignment explanation
Indices: 14432--14508 Score: 77
Period size: 19 Copynumber: 3.9 Consensus size: 19
14422 AGATTAGAAT
14432 TATATAAT-ATAATATTAA
1 TATATAATAATAATATTAA
*
14450 TATATAATAATAATATGATA
1 TATATAATAATAATATTA-A
*
14470 TAATATAATTAATAATA-TAT
1 T-ATATAA-TAATAATATTAA
*
14490 TATATGTATAATAATATTA
1 TATAT-AATAATAATATTA
14509 GATGTGGTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
18 8 0.16
19 20 0.41
20 6 0.12
21 7 0.14
22 8 0.16
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
TATATAATAATAATATTAA
Found at i:17741 original size:17 final size:17
Alignment explanation
Indices: 17719--17751 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
17709 AACTCCAAAT
17719 TTTCTCTATTCTTGTAA
1 TTTCTCTATTCTTGTAA
17736 TTTCTCTATTCTTGTA
1 TTTCTCTATTCTTGTA
17752 TCTTTTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTCTCTATTCTTGTAA
Found at i:18754 original size:69 final size:69
Alignment explanation
Indices: 18676--18882 Score: 335
Period size: 70 Copynumber: 3.0 Consensus size: 69
18666 AAATATAAGG
*
18676 ACCCTCAAGTATTCAAATTGACAAGTTGTGAAAAAATAAATTATTACAAGAATAAGTATATATTT
1 ACCCTCAAGTATTCAAATTGACAAGTTGTGAAAAAATAAATTAATACAAGAATAAGTATATATTT
18741 TAGA
66 TAGA
** *
18745 ACCCTCAAGTAGCCAAATTGACAAGTCGTGAAAAAAAATAAATTAATACAAGAATAA-TATATAT
1 ACCCTCAAGTATTCAAATTGACAAGTTGTG--AAAAAATAAATTAATACAAGAATAAGTATATAT
18809 TTTAGA
64 TTTAGA
*
18815 ACCCTCAAGTATTCAAATTGACAAGTTGTGAAAAAGATAGATTAATACAAGAATAAGTATATATT
1 ACCCTCAAGTATTCAAATTGACAAGTTGTGAAAAA-ATAAATTAATACAAGAATAAGTATATATT
18880 TTA
65 TTA
18883 CATAGACTGG
Statistics
Matches: 126, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
68 5 0.04
69 46 0.37
70 51 0.40
71 24 0.19
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.29
Consensus pattern (69 bp):
ACCCTCAAGTATTCAAATTGACAAGTTGTGAAAAAATAAATTAATACAAGAATAAGTATATATTT
TAGA
Found at i:18819 original size:70 final size:70
Alignment explanation
Indices: 18676--18882 Score: 337
Period size: 69 Copynumber: 3.0 Consensus size: 70
18666 AAATATAAGG
*
18676 ACCCTCAAGTATTCAAATTGACAAGTTGTG-AAAAAATAAATTATTACAAGAATAAGTATATATT
1 ACCCTCAAGTATTCAAATTGACAAGTTGTGAAAAAAATAAATTAATACAAGAATAAGTATATATT
18740 TTAGA
66 TTAGA
** *
18745 ACCCTCAAGTAGCCAAATTGACAAGTCGTGAAAAAAAATAAATTAATACAAGAATAA-TATATAT
1 ACCCTCAAGTATTCAAATTGACAAGTTGTG-AAAAAAATAAATTAATACAAGAATAAGTATATAT
18809 TTTAGA
65 TTTAGA
* *
18815 ACCCTCAAGTATTCAAATTGACAAGTTGTGAAAAAGATAGATTAATACAAGAATAAGTATATATT
1 ACCCTCAAGTATTCAAATTGACAAGTTGTGAAAAAAATAAATTAATACAAGAATAAGTATATATT
18880 TTA
66 TTA
18883 CATAGACTGG
Statistics
Matches: 126, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
69 51 0.40
70 51 0.40
71 24 0.19
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.29
Consensus pattern (70 bp):
ACCCTCAAGTATTCAAATTGACAAGTTGTGAAAAAAATAAATTAATACAAGAATAAGTATATATT
TTAGA
Found at i:20694 original size:12 final size:12
Alignment explanation
Indices: 20677--20701 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20667 ATAAGGAGAA
20677 ACTTGATAAAAC
1 ACTTGATAAAAC
20689 ACTTGATAAAAC
1 ACTTGATAAAAC
20701 A
1 A
20702 GAGAAGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (12 bp):
ACTTGATAAAAC
Found at i:22443 original size:45 final size:45
Alignment explanation
Indices: 22392--22522 Score: 244
Period size: 45 Copynumber: 2.9 Consensus size: 45
22382 TAATAGAGTA
22392 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGGTAG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGGTAG
*
22437 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGGTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGGTAG
*
22482 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAG
22523 CTGGAGAAGT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 84 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGGTAG
Found at i:22988 original size:13 final size:14
Alignment explanation
Indices: 22963--22992 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
22953 ATATAAAAAT
22963 TATTATACATAATA
1 TATTATACATAATA
22977 TATTAT-CATAATA
1 TATTATACATAATA
22990 TAT
1 TAT
22993 GGTCAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTATACATAATA
Found at i:28054 original size:8 final size:8
Alignment explanation
Indices: 28041--28067 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
28031 TTTCATGTGA
28041 TGCTTTAT
1 TGCTTTAT
28049 TGCTTTAT
1 TGCTTTAT
28057 TGCTTTAT
1 TGCTTTAT
28065 TGC
1 TGC
28068 CATCGGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.59
Consensus pattern (8 bp):
TGCTTTAT
Found at i:32885 original size:2 final size:2
Alignment explanation
Indices: 32878--32904 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32868 TTTTAAATTG
32878 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
32905 ACCGCAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35304 original size:36 final size:36
Alignment explanation
Indices: 35229--35305 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
35219 GGTGATGCCA
* ***
35229 CTGCAAATACCGCTGTAATTGCCGCTGTAGATGCTG
1 CTGCAAATACCGCTGGAATTGCCGCTGTAGATAAAG
35265 CTGCAAATACCGCTGGAGA-TGCCGCTAG-AGATAAAG
1 CTGCAAATACCGCTGGA-ATTGCCGCT-GTAGATAAAG
35301 CTGCA
1 CTGCA
35306 GATGCCCTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
36 33 0.94
37 2 0.06
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (36 bp):
CTGCAAATACCGCTGGAATTGCCGCTGTAGATAAAG
Found at i:36314 original size:3 final size:3
Alignment explanation
Indices: 36306--36348 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
36296 TAAACTCATA
36306 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
36349 TAGGGATGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:56140 original size:15 final size:15
Alignment explanation
Indices: 56120--56237 Score: 64
Period size: 16 Copynumber: 7.9 Consensus size: 15
56110 GGCGGGTTTC
56120 GGGTTCGGGTCATTT
1 GGGTTCGGGTCATTT
**
56135 GGGTTCGGGTCAAAT
1 GGGTTCGGGTCATTT
**
56150 GGG-TCATG-CAGTTT
1 GGGTTCGGGTCA-TTT
* *
56164 --TTTCGGGTCATTC
1 GGGTTCGGGTCATTT
*
56177 GGGTTACGGGTCATCT
1 GGGTT-CGGGTCATTT
* * *
56193 AGGTTCGGGTTATTC
1 GGGTTCGGGTCATTT
* *
56208 AGGTCTCGGGTCATTC
1 GGGT-TCGGGTCATTT
56224 GGGTCTCGGGTCAT
1 GGGT-TCGGGTCAT
56238 ACGGGTTTTG
Statistics
Matches: 77, Mismatches: 19, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
13 7 0.09
14 6 0.08
15 29 0.38
16 35 0.45
ACGTcount: A:0.12, C:0.18, G:0.36, T:0.35
Consensus pattern (15 bp):
GGGTTCGGGTCATTT
Found at i:56188 original size:16 final size:15
Alignment explanation
Indices: 56165--56244 Score: 81
Period size: 16 Copynumber: 5.1 Consensus size: 15
56155 ATGCAGTTTT
56165 TTCGGGTCATTCGGG
1 TTCGGGTCATTCGGG
*
56180 TTACGGGTCA-TCTAGG
1 TT-CGGGTCATTC-GGG
* *
56196 TTCGGGTTATTCAGG
1 TTCGGGTCATTCGGG
56211 TCTCGGGTCATTCGGG
1 T-TCGGGTCATTCGGG
*
56227 TCTCGGGTCATACGGG
1 T-TCGGGTCATTCGGG
56243 TT
1 TT
56245 TTGGGTCTCG
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
15 15 0.27
16 41 0.73
ACGTcount: A:0.11, C:0.20, G:0.35, T:0.34
Consensus pattern (15 bp):
TTCGGGTCATTCGGG
Found at i:56202 original size:31 final size:30
Alignment explanation
Indices: 56165--56244 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
56155 ATGCAGTTTT
56165 TTCGGGTCATTCGGGTTACGGGTCA-TCTAGG
1 TTCGGGTCATTCGGGTT-CGGGTCATTC-AGG
* * *
56196 TTCGGGTTATTCAGGTCTCGGGTCATTCGGG
1 TTCGGGTCATTCGGGT-TCGGGTCATTCAGG
*
56227 TCTCGGGTCATACGGGTT
1 T-TCGGGTCATTCGGGTT
56245 TTGGGTCTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
31 25 0.62
32 15 0.38
ACGTcount: A:0.11, C:0.20, G:0.35, T:0.34
Consensus pattern (30 bp):
TTCGGGTCATTCGGGTTCGGGTCATTCAGG
Found at i:56250 original size:16 final size:16
Alignment explanation
Indices: 56166--56289 Score: 67
Period size: 16 Copynumber: 7.4 Consensus size: 16
56156 TGCAGTTTTT
*
56166 TCGGGTCATTCGGGT-
1 TCGGGTCATACGGGTC
*
56181 TACGGGTCAT-CTAGGT-
1 T-CGGGTCATAC-GGGTC
* * *
56197 TCGGGTTATTCAGGTC
1 TCGGGTCATACGGGTC
*
56213 TCGGGTCATTCGGGTC
1 TCGGGTCATACGGGTC
56229 TCGGGTCATACGGGTTTTGGGTC
1 TCGGGTCATAC-------GGGTC
*
56252 TCGGGTCATTCGGGTC
1 TCGGGTCATACGGGTC
56268 TCGGGTC-TACCGGGTC
1 TCGGGTCATA-CGGGTC
56284 TCGGGT
1 TCGGGT
56290 TGGGCGGGTT
Statistics
Matches: 90, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
15 14 0.16
16 61 0.68
23 15 0.17
ACGTcount: A:0.09, C:0.22, G:0.37, T:0.32
Consensus pattern (16 bp):
TCGGGTCATACGGGTC
Found at i:56250 original size:23 final size:23
Alignment explanation
Indices: 56222--56275 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
56212 CTCGGGTCAT
*
56222 TCGGGTCTCGGGTCATACGGGTT
1 TCGGGTCTCGGGTCATACGGGTC
* *
56245 TTGGGTCTCGGGTCATTCGGGTC
1 TCGGGTCTCGGGTCATACGGGTC
56268 TCGGGTCT
1 TCGGGTCT
56276 ACCGGGTCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.06, C:0.22, G:0.39, T:0.33
Consensus pattern (23 bp):
TCGGGTCTCGGGTCATACGGGTC
Found at i:56761 original size:21 final size:21
Alignment explanation
Indices: 56736--56783 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
56726 TAGCCAATTT
56736 ATAATAGGTAAAATAATAACA
1 ATAATAGGTAAAATAATAACA
* *
56757 ATAATTGGTAAAATTATAACA
1 ATAATAGGTAAAATAATAACA
56778 ATAATA
1 ATAATA
56784 TAAACGAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.29
Consensus pattern (21 bp):
ATAATAGGTAAAATAATAACA
Found at i:57071 original size:20 final size:20
Alignment explanation
Indices: 57046--57084 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
57036 ATGATAAGAA
57046 TGATGGTTCTCATCAAATAG
1 TGATGGTTCTCATCAAATAG
57066 TGATGGTTCTCATCAAATA
1 TGATGGTTCTCATCAAATA
57085 TGGTATGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (20 bp):
TGATGGTTCTCATCAAATAG
Found at i:57709 original size:22 final size:22
Alignment explanation
Indices: 57683--57729 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
57673 ATTTATTCAT
57683 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
57705 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
57727 TAT
1 TAT
57730 AGTATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:57725 original size:11 final size:11
Alignment explanation
Indices: 57683--57725 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
57673 ATTTATTCAT
*
57683 TATTAATTAAC
1 TATTAATTAGC
*
57694 TATTAATTAGA
1 TATTAATTAGC
57705 TATTAATTAGC
1 TATTAATTAGC
57716 TATTAATTAG
1 TATTAATTAG
57726 ATATAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:58016 original size:16 final size:16
Alignment explanation
Indices: 57978--58130 Score: 120
Period size: 16 Copynumber: 9.6 Consensus size: 16
57968 TCGGGTTAAT
*
57978 GTCTCGGGTTATTCGG
1 GTCTCGGGTCATTCGG
* * * *
57994 ATTTCGGGTCATACGA
1 GTCTCGGGTCATTCGG
58010 GTCTCGGGTCATTCGG
1 GTCTCGGGTCATTCGG
* *
58026 GTTTCAGGTCA-TCTGG
1 GTCTCGGGTCATTC-GG
58042 GT-TACGGGTCATTCGG
1 GTCT-CGGGTCATTCGG
58058 GTCTCGGGTCA-TCTGG
1 GTCTCGGGTCATTC-GG
58074 GT-TGCGGGTCATTCGG
1 GTCT-CGGGTCATTCGG
* *
58090 GTCACGGGT-TTGTCGG
1 GTCTCGGGTCAT-TCGG
**
58106 GTCTCGGGTCAGGCGG
1 GTCTCGGGTCATTCGG
58122 GT-TCGGGTC
1 GTCTCGGGTC
58131 GTTTACTTTT
Statistics
Matches: 109, Mismatches: 18, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
15 14 0.13
16 90 0.83
17 5 0.05
ACGTcount: A:0.09, C:0.21, G:0.39, T:0.31
Consensus pattern (16 bp):
GTCTCGGGTCATTCGG
Found at i:58076 original size:48 final size:48
Alignment explanation
Indices: 57998--58116 Score: 136
Period size: 48 Copynumber: 2.5 Consensus size: 48
57988 ATTCGGATTT
* * * *
57998 CGGGTCATACGAGTCTCGGGTCATTCGGGTTTCAGGTCA-TCTGGGTTA
1 CGGGTCATTCGGGTCTCGGGTCATTCGGGTTGCAGGTCATTC-GGGTCA
*
58046 CGGGTCATTCGGGTCTCGGGTCA-TCTGGGTTGCGGGTCATTCGGGTCA
1 CGGGTCATTCGGGTCTCGGGTCATTC-GGGTTGCAGGTCATTCGGGTCA
*
58094 CGGGT-TTGTCGGGTCTCGGGTCA
1 CGGGTCAT-TCGGGTCTCGGGTCA
58117 GGCGGGTTCG
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
47 3 0.05
48 57 0.92
49 2 0.03
ACGTcount: A:0.10, C:0.22, G:0.38, T:0.30
Consensus pattern (48 bp):
CGGGTCATTCGGGTCTCGGGTCATTCGGGTTGCAGGTCATTCGGGTCA
Found at i:58098 original size:32 final size:32
Alignment explanation
Indices: 58014--58098 Score: 134
Period size: 32 Copynumber: 2.7 Consensus size: 32
58004 ATACGAGTCT
* *
58014 CGGGTCATTCGGGTTTCAGGTCATCTGGGTTA
1 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTA
*
58046 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTG
1 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTA
*
58078 CGGGTCATTCGGGTCACGGGT
1 CGGGTCATTCGGGTCTCGGGT
58099 TTGTCGGGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.09, C:0.21, G:0.39, T:0.31
Consensus pattern (32 bp):
CGGGTCATTCGGGTCTCGGGTCATCTGGGTTA
Found at i:58124 original size:48 final size:46
Alignment explanation
Indices: 57998--58130 Score: 135
Period size: 48 Copynumber: 2.8 Consensus size: 46
57988 ATTCGGATTT
* * * *
57998 CGGGTCATACGAGTCTCGGGTCATTCGGGTTTCAGGTCATCTGGGTTA
1 CGGGTCATTCGGGTCTCGGGTCA-TCGGG-TTCGGGTCATCTGGGTCA
58046 CGGGTCATTCGGGTCTCGGGTCATCTGGGTTGCGGGTCAT-TCGGGTCA
1 CGGGTCATTCGGGTCTCGGGTCATC-GGGTT-CGGGTCATCT-GGGTCA
* *
58094 CGGGT-TTGTCGGGTCTCGGGTCAGGCGGGTTCGGGTC
1 CGGGTCAT-TCGGGTCTCGGGTCA-TCGGGTTCGGGTC
58131 GTTTACTTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
47 12 0.16
48 61 0.82
49 1 0.01
ACGTcount: A:0.09, C:0.22, G:0.40, T:0.29
Consensus pattern (46 bp):
CGGGTCATTCGGGTCTCGGGTCATCGGGTTCGGGTCATCTGGGTCA
Found at i:61517 original size:24 final size:24
Alignment explanation
Indices: 61485--61571 Score: 79
Period size: 24 Copynumber: 3.6 Consensus size: 24
61475 CCACTCGATA
61485 TGCAGATACCGCTGTAGATGCTGC
1 TGCAGATACCGCTGTAGATGCTGC
**
61509 TGCAGATACCGCTAG-AGATGCCAC
1 TGCAGATACCGCT-GTAGATGCTGC
* ** *
61533 TG-AGGATGCCATTGTAGATGATGC
1 TGCA-GATACCGCTGTAGATGCTGC
*
61557 TGTAGATACCGCTGT
1 TGCAGATACCGCTGT
61572 TGCAAACACC
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
23 2 0.04
24 44 0.92
25 2 0.04
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (24 bp):
TGCAGATACCGCTGTAGATGCTGC
Found at i:65922 original size:12 final size:13
Alignment explanation
Indices: 65905--65935 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
65895 TGAAATGAAA
*
65905 TTTTTTCTTGTTT
1 TTTTTTCTTCTTT
65918 TTTTTTCTTCTTT
1 TTTTTTCTTCTTT
65931 TTTTT
1 TTTTT
65936 GGGTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (13 bp):
TTTTTTCTTCTTT
Found at i:67420 original size:336 final size:325
Alignment explanation
Indices: 66802--68366 Score: 1253
Period size: 336 Copynumber: 4.7 Consensus size: 325
66792 CACATTGGAT
* * *
66802 TGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAATAATAGGAAAAACGATATTAGAAGC
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAA-AATATGAAAAACGATATTAAAAGC
* * * * * *
66867 ATGAAAA-ACCTTTCAATTTTTTTCGTGTTGAATTATATA-ATTTTTATGAGTA-TAGTAGCTAA
64 GTGAAAAGTCC--TCAATCTTTTTGGCGTTGAATTATATATA-TTTTATGAGTATTA-TGGCTAA
* * * * * *
66929 AAATTAAGGAAATAA-CTCTCGGGTAAAATTTTTGCAAAATTTTAACCGAAATCGTGTAATACTC
125 AAATTGAGGAAAAAATTTC-CAGAT-CAATTTTTGCAAAATTTTAACCGAAATCGTGT-ATAC-C
* * * * *
66993 ATCACGGTTTTCGGCTAAAAACGTGTTCTGGGACCCCGGCTAAGTTTTGCAA-GATTTTTGGCAC
186 ATCACGGTTTTTGGCTAAAAACGCGTTTTGGG--CCCGGCTAAGTTTTGCAATGATTTTTTGC-G
** * * * * *
67057 CAAGACTCCTTGAGTTATCCATATTCATCTAATCAAATCTCAGCTACATTAGTTTTAAGAATTTA
248 CAAGACTCCTTGAAATATCTATATTCATCTAATCAAATATCAGCCACATT-GTTTTAAGGATTTG
67122 TTTTTACGAGCATC
312 TTTTTACGAGCATC
* * *
67136 TGAATCTTGTTTCGAATTAATTAGAAATTAATACAGAAAAATATGAAAACCGATATTAAAAGCGT
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGT
* * * * *
67201 GAAAAGTGCTCAAACATTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAG-TCAAAAAT
66 GAAAAGTCCTCAATC-TTTTTGGCGTTGAATTATATATATTTTATGAGTATTATGGCT-AAAAAT
* * * * *
67265 TGAGGAAAAAATTTTCAGATCATTTTTTTTTTGCCAAATTTTAGCTGAAATCGTGTACTAACCAT
129 TGAGGAAAAAATTTCCAGATCA----ATTTTTGCAAAATTTTAACCGAAATCGTGTA-T-ACCAT
* *
67330 CACGGGTTTTTGGCTAAAAACGCGTTTATGGGCCCTGCCTTAGTTTTG-AATGATTTTTTGCGCT
188 CAC-GGTTTTTGGCTAAAAACGCGTTT-TGGGCCC-GGCTAAGTTTTGCAATGATTTTTTGCGC-
* * * **
67394 GAGACTCCTTGAAATATCTATATTCATCTAATCAAATTTCAGCCATATTGAAATTAAGGATTTGT
249 AAGACTCCTTGAAATATCTATATTCATCTAATCAAATATCAGCCACATTG-TTTTAAGGATTTGT
67459 TTTTACGAGCATC
313 TTTTACGAGCATC
*
67472 TGAATTTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGT
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGT
* * *
67537 GAAAAGTCCTCCAATTTTCTTTTTTGCGTTGAATTATATATATATTATGAGTATTATGGCTAACA
66 GAAAAGTCCT-CAA---TCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTATGGCTAAAA
* * *
67602 ATTGATG-AAAAATATTCCGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTG--TACCATCAC
127 ATTGAGGAAAAAAT-TTCCAGATCAATTTTTGCAAAATTTTAACCGAAATCGTGTATACCATCAC
* * * * * * * * *
67664 AGTTTTTTGGCTAAAAACGCGTTTCGGAACCCGGGTCAGTTTTGCATTAATTTTGGTG-GCAAAA
191 -GGTTTTTGGCTAAAAACGCGTTTTGG-GCCCGGCTAAGTTTTGCAATGATTTT-TTGCGCAAGA
* * *
67728 CTCCTTGAAATTTCTATATTCATCTAACCAAATATTAGCCACATTGTATTTAAGGATTTGTTTTT
253 CTCCTTGAAATATCTATATTCATCTAATCAAATATCAGCCACATTGT-TTTAAGGATTTGTTTTT
*
67793 ACGAGCATT
317 ACGAGCATC
* * * * * * *
67802 TGAATCATGTTTCGATTTAATTAGAAATTAATTTGAAAAAAAAAGGAAAAACGATAATAGAAGCG
1 TGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCAGAAAAATATGAAAAACGATATTAAAAGCG
* * *
67867 TGAGAAA-CCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAA
65 TGA-AAAGTCC-TCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTATGGCTAAAAA
** * *
67931 TTG-GGAAAAATATTTCGTG-TCAATTTTTGCAAAATTTTAGCCGAAATCATGTATCAGAAACCA
128 TTGAGGAAAAA-ATTTCCAGATCAATTTTTGCAAAATTTTAACCGAAATCGTGTAT-----ACCA
* * * * * * ** * *
67994 -GAAGTTTTTTTTTTTTTGCTGAAGACGCGTTTTGAAACCTCGGGTCAGTTTTGC-ATGATTTTT
187 TCACG------GTTTTTGGCTAAAAACGCGTTTTG-GGCC-CGGCTAAGTTTTGCAATGATTTTT
* * * * * * *
68057 GGAACGGAA-ACTGCTTAAAATATATCTATATTCATCTAACCAAATCTCAGTCACATTGTATTTA
244 TG--CGCAAGACTCCTT-GAA-ATATCTATATTCATCTAATCAAATATCAGCCACATTGT-TTTA
* *
68121 AGGATTTGTTTTTACGAGTATA
304 AGGATTTGTTTTTACGAGCATC
* * * *
68143 TAAATCTTGTTTCGATTTAATCAGAAATTAATT-TGAAAATATAATAGGAAAAACGATATTAGAA
1 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAA-AT-AT--GAAAAACGATATTAAAA
* * * ** * * *
68207 GCGTGAAAAAGGAT-TTCATTTTTTTTGGCGTTGTGTTATATATTTTTTATGAGTATTTTAGCTA
62 GCGTG-AAAA-G-TCCTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTATGGCTA
* * * * * ** *
68271 GAAATTGTGG-AAAAATCTTTCGGGTCAATTTTTATAAAATTTTAGCCGAAATCGTGTACTAACC
124 AAAATTGAGGAAAAAAT-TTCCAGATCAATTTTTGCAAAATTTTAACCGAAATCGTGTA-T-ACC
* * * * *
68335 ATCACGGTTCTCGACTAAAAATGCGTTCTGGG
186 ATCACGGTTTTTGGCTAAAAACGCGTTTTGGG
68367 GCTCGACTGA
Statistics
Matches: 1006, Mismatches: 159, Indels: 130
0.78 0.12 0.10
Matches are distributed among these distances:
327 31 0.03
328 55 0.05
329 3 0.00
330 107 0.11
331 83 0.08
332 85 0.08
333 8 0.01
334 38 0.04
335 65 0.06
336 176 0.17
337 23 0.02
338 35 0.03
339 75 0.07
340 10 0.01
341 88 0.09
342 5 0.00
343 28 0.03
344 57 0.06
345 33 0.03
346 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (325 bp):
TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGT
GAAAAGTCCTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTATGGCTAAAAATTG
AGGAAAAAATTTCCAGATCAATTTTTGCAAAATTTTAACCGAAATCGTGTATACCATCACGGTTT
TTGGCTAAAAACGCGTTTTGGGCCCGGCTAAGTTTTGCAATGATTTTTTGCGCAAGACTCCTTGA
AATATCTATATTCATCTAATCAAATATCAGCCACATTGTTTTAAGGATTTGTTTTTACGAGCATC
Found at i:72190 original size:43 final size:43
Alignment explanation
Indices: 72129--72236 Score: 216
Period size: 43 Copynumber: 2.5 Consensus size: 43
72119 CTAAACCGAC
72129 ATATAATTACATCAAGAACTATCAAGCAACTTTCGATATTATT
1 ATATAATTACATCAAGAACTATCAAGCAACTTTCGATATTATT
72172 ATATAATTACATCAAGAACTATCAAGCAACTTTCGATATTATT
1 ATATAATTACATCAAGAACTATCAAGCAACTTTCGATATTATT
72215 ATATAATTACATCAAGAACTAT
1 ATATAATTACATCAAGAACTAT
72237 ATATCCAGCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (43 bp):
ATATAATTACATCAAGAACTATCAAGCAACTTTCGATATTATT
Found at i:76928 original size:125 final size:126
Alignment explanation
Indices: 76760--77002 Score: 418
Period size: 125 Copynumber: 1.9 Consensus size: 126
76750 CTTTGAGTGT
* *
76760 TTGGCTAGCAGTGTTCATTGTAACTTTGGTCTATATTTTTATATATAGATTTTTATTGCGTTTC-
1 TTGGCTAGCAGTGTTCATTGTAACTCTGGTCTATATTTTTATATATAGATTTTAATTGCGTTTCA
76824 AAAAAAAAATCTTAGATATTTTCAAGCTCTTTGGGAGATTTGAGCAATTAAATGTCATTGC
66 AAAAAAAAATCTTAGATATTTTCAAGCTCTTTGGGAGATTTGAGCAATTAAATGTCATTGC
* *
76885 TTGGCTAGCATTGTTCATTGTAACTCTGG-CTTGTATTTTTATATATAGATTTTAATTGCGTTTC
1 TTGGCTAGCAGTGTTCATTGTAACTCTGGTC-TATATTTTTATATATAGATTTTAATTGCGTTTC
*
76949 AAAAAAAAAATCTTATATATTTTCAAGCTCTTTGGGAGATTTGAGCAATTAAAT
65 AAAAAAAAAATCTTAGATATTTTCAAGCTCTTTGGGAGATTTGAGCAATTAAAT
77003 ATCAGTGTTC
Statistics
Matches: 111, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
124 1 0.01
125 58 0.52
126 52 0.47
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (126 bp):
TTGGCTAGCAGTGTTCATTGTAACTCTGGTCTATATTTTTATATATAGATTTTAATTGCGTTTCA
AAAAAAAAATCTTAGATATTTTCAAGCTCTTTGGGAGATTTGAGCAATTAAATGTCATTGC
Found at i:81704 original size:21 final size:20
Alignment explanation
Indices: 81655--81705 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
81645 TAGCGCTGGA
* *
81655 CGCCCATGTGGTATGCTTGG
1 CGCCCATGTGGTATGCCTCG
*
81675 CGCCTCATGTGGTTTGCCTCG
1 CGCC-CATGTGGTATGCCTCG
81696 CGACCCATGT
1 CG-CCCATGT
81706 ACTCCAGTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 20 0.77
22 2 0.08
ACGTcount: A:0.10, C:0.31, G:0.29, T:0.29
Consensus pattern (20 bp):
CGCCCATGTGGTATGCCTCG
Found at i:93355 original size:15 final size:16
Alignment explanation
Indices: 93306--93359 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
93296 TTGGAACCAT
93306 ATGACCCAAAACCGAAAA
1 ATGACCC-AAACC-AAAA
*
93324 A-CACCCAAACCAAAA
1 ATGACCCAAACCAAAA
*
93339 ATGACCCAAACC-CAA
1 ATGACCCAAACCAAAA
93354 ATGACC
1 ATGACC
93360 AGACATTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 13 0.41
16 14 0.44
17 4 0.12
18 1 0.03
ACGTcount: A:0.52, C:0.35, G:0.07, T:0.06
Consensus pattern (16 bp):
ATGACCCAAACCAAAA
Found at i:95576 original size:6 final size:6
Alignment explanation
Indices: 95560--95617 Score: 82
Period size: 6 Copynumber: 9.5 Consensus size: 6
95550 GTACTTTTAT
*
95560 ATATA- ATATAG ATATAG ATAGATAG ATATAG ATATAG ATATAG ATATAA
1 ATATAG ATATAG ATATAG AT--ATAG ATATAG ATATAG ATATAG ATATAG
95609 ATATAG ATA
1 ATATAG ATA
95618 GATATGTACT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
5 5 0.10
6 37 0.77
8 6 0.12
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:97409 original size:14 final size:13
Alignment explanation
Indices: 97384--97408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
97374 TTGGTTTGGA
97384 AAAAGTGCTTTTG
1 AAAAGTGCTTTTG
97397 AAAAGTGCTTTT
1 AAAAGTGCTTTT
97409 TTAAATTGCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
AAAAGTGCTTTTG
Found at i:97844 original size:22 final size:22
Alignment explanation
Indices: 97816--97863 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
97806 AAATTGGGTC
*
97816 AAAGCTTGGGTTGTATATCTTT
1 AAAGCTTGGGTTCTATATCTTT
*
97838 AAAGCTTGGTTTCTATATCTTT
1 AAAGCTTGGGTTCTATATCTTT
97860 AAAG
1 AAAG
97864 AACAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (22 bp):
AAAGCTTGGGTTCTATATCTTT
Found at i:102952 original size:18 final size:19
Alignment explanation
Indices: 102926--102963 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
102916 TTGGAGAAAT
*
102926 AGAAAGAAATAGAT-TGAA
1 AGAAAGAAAGAGATATGAA
*
102944 AGAATGAAAGAGATATGAA
1 AGAAAGAAAGAGATATGAA
102963 A
1 A
102964 TCAAGAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.16
Consensus pattern (19 bp):
AGAAAGAAAGAGATATGAA
Found at i:105153 original size:15 final size:15
Alignment explanation
Indices: 105133--105161 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
105123 TAATATATGT
105133 TGTTATAGATATAGA
1 TGTTATAGATATAGA
105148 TGTTATAGATATAG
1 TGTTATAGATATAG
105162 TAACAGAGGA
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:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (15 bp):
TGTTATAGATATAGA
Done.