Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009016.1 Hibiscus syriacus cultivar Beakdansim tig00112406_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: 139424
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:3629 original size:20 final size:20
Alignment explanation
Indices: 3604--3641 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3594 CCCCCTTTGA
*
3604 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
3624 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
3642 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:6369 original size:74 final size:74
Alignment explanation
Indices: 6199--6404 Score: 245
Period size: 74 Copynumber: 2.8 Consensus size: 74
6189 CAAAGCCAAA
* * * **
6199 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTC-GAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
6264 TTTGGCTCCGAG
63 TTTGGCTCCGAG
* *
6276 ATTTCCAGAATGCTCGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACATTTT
1 AATTCCAGAATGCTCGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTT
* *
6341 TG-TTCGAG
66 GGCTCCGAG
* * * *
6349 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCC-CAGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTC-GAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCT
6405 GTTCAACGGT
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
73 37 0.32
74 52 0.46
76 13 0.11
77 12 0.11
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (74 bp):
AATTCCAGAATGCTCGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:10022 original size:12 final size:13
Alignment explanation
Indices: 10005--10043 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 13
9995 TTCAGAAAAC
10005 ATAATATATA-AT
1 ATAATATATATAT
10017 ATAATATATATAT
1 ATAATATATATAT
10030 AT-ATATATATAT
1 ATAATATATATAT
10042 AT
1 AT
10044 CAAGAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:10025 original size:2 final size:2
Alignment explanation
Indices: 10008--10043 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
9998 AGAAAACATA
10008 AT AT AT A- AT AT A- 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
10044 CAAGAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12667 original size:2 final size:2
Alignment explanation
Indices: 12660--12699 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12650 TTCAGAAAAC
12660 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
12700 CAAGAATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16330 original size:18 final size:17
Alignment explanation
Indices: 16274--16331 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
16264 TATTATATTC
16274 TTTAATATTATAATGAT
1 TTTAATATTATAATGAT
* * *
16291 ATATAATATTATACTTTTAT
1 -TTTAATATTATA--ATGAT
16311 TTTAATATATATAATGAT
1 TTTAATAT-TATAATGAT
16329 TTT
1 TTT
16332 TCAATAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
18 17 0.55
19 7 0.23
20 7 0.23
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAATATTATAATGAT
Found at i:19494 original size:23 final size:21
Alignment explanation
Indices: 19468--19521 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
19458 CATAATTCTA
19468 ATAATATGATATTATA-TTATATT
1 ATAATAT-ATA-TATACTT-TATT
19491 ATAATATATATATACTTTATT
1 ATAATATATATATACTTTATT
*
19512 TTAATA-ATAT
1 ATAATATATAT
19522 TTAATGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.14
21 13 0.45
22 5 0.17
23 7 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
ATAATATATATATACTTTATT
Found at i:20835 original size:2 final size:2
Alignment explanation
Indices: 20828--20852 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20818 TATTTCTTGG
20828 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 A
20853 AGATATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22228 original size:37 final size:37
Alignment explanation
Indices: 22152--22228 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
22142 AAATTAATTA
**
22152 TATAATATTAAAATAAAAGTATAATATTATATATCAT
1 TATAATATTAAAATAAAAGTATAATATTATATAGAAT
* *
22189 TATAATATTAAAGAATATAA-TATCATATTAT-TAGAAT
1 TATAATATT-AA-AATAAAAGTATAATATTATATAGAAT
22226 TAT
1 TAT
22229 GAGTAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 16 0.47
38 12 0.35
39 6 0.18
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.42
Consensus pattern (37 bp):
TATAATATTAAAATAAAAGTATAATATTATATAGAAT
Found at i:23727 original size:23 final size:23
Alignment explanation
Indices: 23701--23745 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
23691 AATGAATTAT
* *
23701 TTTGTAATTATAAATAAAATAAA
1 TTTGCAATTAAAAATAAAATAAA
* *
23724 TTTGCATTTAAAAATGAAATAA
1 TTTGCAATTAAAAATAAAATAA
23746 TTAAACTATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
TTTGCAATTAAAAATAAAATAAA
Found at i:24814 original size:406 final size:405
Alignment explanation
Indices: 24063--24877 Score: 1310
Period size: 406 Copynumber: 2.0 Consensus size: 405
24053 TGCAAGTCCA
* *
24063 TCTTGTTCTGATGTTCACAATCGTAAAAGTCTTGAGCCATTACAGCTCCACTTGCAAAAATAACA
1 TCTTGTTATGATGTTCACAATCGTAAAAGTCTTGAGCCATTACAACTCCACTTGCAAAAATAACA
*
24128 AGAATCGCTATAGTAGCAAAAACGTTTAGATTAGCCATTGAAGCTTTTAGGGGCAAAAGGATTTT
66 AGAATCGCTATAGTAGCAAAAACGTTTAGAGTAGCCATTGAAGCTTTTAGGGGCAAAAGGATTTT
* * * * *
24193 ATGACTTTAGTCGGCATAAGACTTTACTGCTGTTGCAACAGTTTTTTACAACAAATATGGTCATT
131 ATGACTTTAGTCAGCAGAAGACCTTACTGCTGTTGCAACAATTTTTGACAACAAATATGGTCATT
*
24258 TATAGAGTATCTTAATGGTTGTGGAATGAATCTAAGGTTTTAAGAAAAATTAATAACATTTTCAC
196 TATAGAGTATCTTAATGGTTGTGGAATGAATATAAGGTTTTAAGAAAAATTAATAACATTTTCAC
* *
24323 TTTAATTATCAGTTTCACATCAATAAAACATTCAAGTAATGTTTTTAATTACCATTTAATTCAAT
261 TATAATTATCAGTTTCACATCAATAAAACATTCAAGGAATGTTTTTAATTACCATTTAATTCAAT
* * ** *
24388 ATACTGTAACAAATTTCATATAGTTTGAATAAGCTTCAATAGATTATTTAATGATAGTAATGATA
326 ATACAGTAACAAAATTCATATAGTTTGAATAAAATTCAATAGAGTATTTAATGATAGTAATGATA
*
24453 TTTCTTTGTTTGTTG
391 TTTCTTTGTTTCTTG
* *
24468 TCTTGTTATGGTGTTCACAATCGTAAAAGTCTTGAGCCATTACAACTCCACTTGCTAAAATAACA
1 TCTTGTTATGATGTTCACAATCGTAAAAGTCTTGAGCCATTACAACTCCACTTGCAAAAATAACA
* *
24533 AGAATCAG-TATAGTAGCATAAAGGTTTAGAGTAGCCATTGAAGCTTTTAGGGGCAAAAGGATTT
66 AGAATC-GCTATAGTAGCAAAAACGTTTAGAGTAGCCATTGAAGCTTTTAGGGGCAAAAGGATTT
* * * * * **
24597 TATGATTTTGGTCAGCAGAAGACCTTACTGTTGTTGCAACAATTCTTTGATAGCATTTATGGTCA
130 TATGACTTTAGTCAGCAGAAGACCTTACTGCTGTTGCAACAATT-TTTGACAACAAATATGGTCA
*
24662 TTTATAGAGTATCTTAATGGTTGT-GACATGAATATAAGGTTTTAAGAGAAATTAATAACATTTT
194 TTTATAGAGTATCTTAATGGTTGTGGA-ATGAATATAAGGTTTTAAGAAAAATTAATAACATTTT
* *
24726 CACTATAATTATCAGTTTCACATCAATAAAACTTTCATGGAATGTTTTTAATTACCATTTAATTC
258 CACTATAATTATCAGTTTCACATCAATAAAACATTCAAGGAATGTTTTTAATTACCATTTAATTC
24791 AATATACAGTAACAAAATTCATATAGTTTGAATAAAATTCAATAGAGTATTTAATGATAGTAATG
323 AATATACAGTAACAAAATTCATATAGTTTGAATAAAATTCAATAGAGTATTTAATGATAGTAATG
24856 ATATTTCTTTGTTTCTTG
388 ATATTTCTTTGTTTCTTG
24874 TCTT
1 TCTT
24878 TAGTTTAATA
Statistics
Matches: 376, Mismatches: 31, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
405 159 0.42
406 217 0.58
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (405 bp):
TCTTGTTATGATGTTCACAATCGTAAAAGTCTTGAGCCATTACAACTCCACTTGCAAAAATAACA
AGAATCGCTATAGTAGCAAAAACGTTTAGAGTAGCCATTGAAGCTTTTAGGGGCAAAAGGATTTT
ATGACTTTAGTCAGCAGAAGACCTTACTGCTGTTGCAACAATTTTTGACAACAAATATGGTCATT
TATAGAGTATCTTAATGGTTGTGGAATGAATATAAGGTTTTAAGAAAAATTAATAACATTTTCAC
TATAATTATCAGTTTCACATCAATAAAACATTCAAGGAATGTTTTTAATTACCATTTAATTCAAT
ATACAGTAACAAAATTCATATAGTTTGAATAAAATTCAATAGAGTATTTAATGATAGTAATGATA
TTTCTTTGTTTCTTG
Found at i:25930 original size:17 final size:18
Alignment explanation
Indices: 25892--25933 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
25882 TCATATCTTC
*
25892 TATATTTTAAATTTTATT
1 TATATTTTAAATTTTATA
*
25910 TATATTTTAATTTTTGATA
1 TATATTTTAAATTTT-ATA
25929 TATAT
1 TATAT
25934 ATATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TATATTTTAAATTTTATA
Found at i:25961 original size:18 final size:19
Alignment explanation
Indices: 25940--25980 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
25930 ATATATATAT
*
25940 ATATATATTTTTATGAA-A
1 ATATATATTTTTATAAATA
25958 ATAT-TATTTTTATAAATA
1 ATATATATTTTTATAAATA
25976 ATATA
1 ATATA
25981 AAATTACTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATATATATTTTTATAAATA
Found at i:27993 original size:166 final size:166
Alignment explanation
Indices: 27719--28065 Score: 543
Period size: 166 Copynumber: 2.1 Consensus size: 166
27709 ATGGTCATTT
* *
27719 ATAGAGTATTTTAATGGTTTTGACATGAATCTAAGGTTTTAATATAAATTAATAAAAGTTTCACT
1 ATAGAGTA-TTTAATGGTTCTGACATGAATCTAAGGTTTTAATAGAAATTAATAAAAGTTTCACT
* *
27784 TTAATTTTCAGTTTCACATCAATAAAACATTCATCGAATGTTTTAAATTACCATTTAATTCAATA
65 TAAATTATCAGTTTCACATCAATAAAACATTCATCGAATGTTTTAAATTACCATTTAATTCAATA
* **
27849 TACGGTAA-AAATTTCATATAGTTTGAATTAACTTCA
130 TACGGTAACAAAATTCATATAGTTTGAAAAAACTTCA
* * *
27885 ATAGAGTATCTTAATGGTTCTGACATGACTCTAAGGTTTTAATAGAAATTAATAACATTTTCACT
1 ATAGAGTAT-TTAATGGTTCTGACATGAATCTAAGGTTTTAATAGAAATTAATAAAAGTTTCACT
* *
27950 TAAATTATCAGTTTCACATCAATAAAACATTCATGGAATGTTTTTAATTACCATTTAATTCAATA
65 TAAATTATCAGTTTCACATCAATAAAACATTCATCGAATGTTTTAAATTACCATTTAATTCAATA
*
28015 TACGGTAACAAAATTCTTATAGTTTGAAAAAACTTCA
130 TACGGTAACAAAATTCATATAGTTTGAAAAAACTTCA
*
28052 TTAGAGTATTTAAT
1 ATAGAGTATTTAAT
28066 TATAGTAACG
Statistics
Matches: 165, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
165 1 0.01
166 132 0.80
167 32 0.19
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40
Consensus pattern (166 bp):
ATAGAGTATTTAATGGTTCTGACATGAATCTAAGGTTTTAATAGAAATTAATAAAAGTTTCACTT
AAATTATCAGTTTCACATCAATAAAACATTCATCGAATGTTTTAAATTACCATTTAATTCAATAT
ACGGTAACAAAATTCATATAGTTTGAAAAAACTTCA
Found at i:30059 original size:38 final size:39
Alignment explanation
Indices: 30009--30083 Score: 125
Period size: 38 Copynumber: 1.9 Consensus size: 39
29999 GGGCCGAGTA
30009 TTTATATTTAAATTAAATATATAAATATTATATATATTT
1 TTTATATTTAAATTAAATATATAAATATTATATATATTT
* *
30048 TTTA-ATTTAAATTAAATTTATTAATATTATATATAT
1 TTTATATTTAAATTAAATATATAAATATTATATATAT
30084 ATAATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 30 0.88
39 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (39 bp):
TTTATATTTAAATTAAATATATAAATATTATATATATTT
Found at i:30092 original size:38 final size:38
Alignment explanation
Indices: 30014--30092 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
30004 GAGTATTTAT
* **
30014 ATTTAAATTAAATATATAAATATTATATATATTTTTTA
1 ATTTAAATTAAATATATAAATATTATATATATATAATA
* *
30052 ATTTAAATTAAATTTATTAATATTATATATATATAATA
1 ATTTAAATTAAATATATAAATATTATATATATATAATA
30090 ATT
1 ATT
30093 ATTTTTAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
ATTTAAATTAAATATATAAATATTATATATATATAATA
Found at i:31945 original size:12 final size:12
Alignment explanation
Indices: 31928--31998 Score: 72
Period size: 12 Copynumber: 5.9 Consensus size: 12
31918 CAGAAACCAA
31928 AACAGAATTCAG
1 AACAGAATTCAG
*
31940 ATCAG-ATATCAG
1 AACAGAAT-TCAG
*
31952 AACAGAATCCAG
1 AACAGAATTCAG
* *
31964 ATCAGAAATCAG
1 AACAGAATTCAG
* *
31976 AACAGAAATCAT
1 AACAGAATTCAG
31988 AACAGAATTCA
1 AACAGAATTCA
31999 AATAGGAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.17
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:31955 original size:24 final size:24
Alignment explanation
Indices: 31917--31982 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
31907 AACAGAGATG
* * *
31917 TCAGAAACCAAAACAGAATTCAGA
1 TCAGAAATCAGAACAGAATCCAGA
*
31941 TCAGATATCAGAACAGAATCCAGA
1 TCAGAAATCAGAACAGAATCCAGA
31965 TCAGAAATCAGAACAGAA
1 TCAGAAATCAGAACAGAA
31983 ATCATAACAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.52, C:0.20, G:0.15, T:0.14
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATCCAGA
Found at i:31993 original size:24 final size:24
Alignment explanation
Indices: 31917--32013 Score: 90
Period size: 24 Copynumber: 4.0 Consensus size: 24
31907 AACAGAGATG
* * *
31917 TCAGAAACCAAAACAGAATTCAGA
1 TCAGAAATCAGAACAGAAATCAGA
*
31941 TCAGATATCAGAACAG-AATCCAGA
1 TCAGAAATCAGAACAGAAAT-CAGA
*
31965 TCAGAAATCAGAACAGAAATCATA
1 TCAGAAATCAGAACAGAAATCAGA
* * *
31989 ACAGAATTCA-AATAGGAAATCAGA
1 TCAGAAATCAGAACA-GAAATCAGA
32013 T
1 T
32014 AAAACATTCA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
23 5 0.08
24 51 0.86
25 3 0.05
ACGTcount: A:0.52, C:0.18, G:0.14, T:0.16
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAAATCAGA
Found at i:36125 original size:18 final size:18
Alignment explanation
Indices: 36082--36118 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
36072 TTGTGTTATA
*
36082 AATATTAAATTATTTAAT
1 AATATTAAATTATGTAAT
36100 AATATTAAATTTATGTAAT
1 AATATTAAA-TTATGTAAT
36119 TTATTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AATATTAAATTATGTAAT
Found at i:38030 original size:2 final size:2
Alignment explanation
Indices: 38025--38051 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38015 AAAATATCTT
38025 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 T
38052 TCCAATAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44071 original size:3 final size:3
Alignment explanation
Indices: 44063--44089 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44053 ATATTAATTT
44063 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
44090 TATTCTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44381 original size:12 final size:12
Alignment explanation
Indices: 44364--44396 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
44354 TATAATTTAA
*
44364 TAATTAAAATTT
1 TAATTAAAATGT
44376 TAATTAAAATGT
1 TAATTAAAATGT
44388 TAA-TAAAAT
1 TAATTAAAAT
44397 AGTATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATTAAAATGT
Found at i:48547 original size:24 final size:24
Alignment explanation
Indices: 48520--48591 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
48510 GTAAACGGAG
*
48520 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
48544 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
48568 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
48591 A
1 A
48592 GATAACGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 15 0.36
24 27 0.64
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:48551 original size:12 final size:12
Alignment explanation
Indices: 48524--48593 Score: 63
Period size: 12 Copynumber: 5.9 Consensus size: 12
48514 ACGGAGATAT
* *
48524 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
48536 CAGAATTCATAT
1 CAGAATTCAGAA
48548 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
48560 CAGAATCCAGAT
1 CAGAATTCAGAA
48572 CAGAA-TCAGAA
1 CAGAATTCAGAA
48583 CAGAATTCAGA
1 CAGAATTCAGA
48594 TAACGTATAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 11 0.24
12 33 0.72
13 2 0.04
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:48607 original size:47 final size:48
Alignment explanation
Indices: 48522--48612 Score: 123
Period size: 47 Copynumber: 1.9 Consensus size: 48
48512 AAACGGAGAT
* * *
48522 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATAAGAACAGAATCCAG
*
48570 ATCAG-AATCAGAACAGAATTCAGATAACG-TATAAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCAGATAA-GATATAAGAACAGAAT
48613 TCAATTTGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
47 32 0.84
48 6 0.16
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATAAGATATAAGAACAGAATCCAG
Found at i:48611 original size:24 final size:23
Alignment explanation
Indices: 48529--48615 Score: 102
Period size: 24 Copynumber: 3.7 Consensus size: 23
48519 GATATCAGAA
* *
48529 ATCAAAACAGAATTCATATCAGAT
1 ATCAGAACAGAATTCAGATCAG-T
* *
48553 ATCAGAACAGAATCCAGATCAGA
1 ATCAGAACAGAATTCAGATCAGT
*
48576 ATCAGAACAGAATTCAGATAACGT
1 ATCAGAACAGAATTCAGATCA-GT
*
48600 ATAAGAACAGAATTCA
1 ATCAGAACAGAATTCA
48616 ATTTGGAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 19 0.35
24 35 0.65
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (23 bp):
ATCAGAACAGAATTCAGATCAGT
Found at i:51091 original size:13 final size:13
Alignment explanation
Indices: 51069--51099 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
51059 CAACGGTCAA
*
51069 CGGGTCAACGGGT
1 CGGGTAAACGGGT
51082 CGGGTAAACGGGT
1 CGGGTAAACGGGT
51095 CGGGT
1 CGGGT
51100 CGGGTTATGA
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:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTAAACGGGT
Found at i:54057 original size:12 final size:12
Alignment explanation
Indices: 54040--54072 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54030 TATAATTTAA
*
54040 TAATTAAAATTT
1 TAATTAAAATGT
54052 TAATTAAAATGT
1 TAATTAAAATGT
54064 TAA-TAAAAT
1 TAATTAAAAT
54073 AGTATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATTAAAATGT
Found at i:54342 original size:15 final size:15
Alignment explanation
Indices: 54322--54357 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
54312 TTCATAATTG
54322 ATAAATTATAATTTC
1 ATAAATTATAATTTC
*
54337 ATAAATTATATTTTC
1 ATAAATTATAATTTC
54352 -TAAATT
1 ATAAATT
54358 TTATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAAATTATAATTTC
Found at i:54349 original size:14 final size:14
Alignment explanation
Indices: 54322--54363 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
54312 TTCATAATTG
54322 ATAAATTATAATTTC
1 ATAAATTAT-ATTTC
54337 ATAAATTATATTTTC
1 ATAAATTATA-TTTC
*
54352 -TAAATTTTATTT
1 ATAAATTATATTT
54364 ATATTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 3 0.12
14 9 0.36
15 13 0.52
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (14 bp):
ATAAATTATATTTC
Found at i:54423 original size:18 final size:19
Alignment explanation
Indices: 54389--54429 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
54379 ATATATATAT
*
54389 ATATTATTTTTTCTAAAAA
1 ATATTATTTTTTATAAAAA
*
54408 ATATTA-TTTTTATAAATA
1 ATATTATTTTTTATAAAAA
54426 ATAT
1 ATAT
54430 AAAATTACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
ATATTATTTTTTATAAAAA
Found at i:55774 original size:2 final size:2
Alignment explanation
Indices: 55769--55801 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55759 AAAAATATCT
55769 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 T
55802 TTCCAAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56916 original size:3 final size:3
Alignment explanation
Indices: 56908--56934 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
56898 GTATTAATTT
56908 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
56935 TATTTTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:57226 original size:12 final size:12
Alignment explanation
Indices: 57209--57241 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
57199 TATAATTTAG
*
57209 TAATTAAAATTT
1 TAATTAAAATGT
57221 TAATTAAAATGT
1 TAATTAAAATGT
57233 TAA-TAAAAT
1 TAATTAAAAT
57242 AGTATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATTAAAATGT
Found at i:58205 original size:24 final size:24
Alignment explanation
Indices: 58178--58253 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
58168 TATAACAAAA
* *
58178 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAAGTCAAGT
* *
58202 ATCATATCAGAAATCAAGTCAAGT
1 ATCAAAACAGAAATCAAGTCAAGT
* * *
58226 AACATATCAG-AATCCAAGTCAAGT
1 ATCAAAACAGAAAT-CAAGTCAAGT
58250 ATCA
1 ATCA
58254 GATCAGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAAATCAAGTCAAGT
Found at i:58258 original size:24 final size:24
Alignment explanation
Indices: 58195--58304 Score: 125
Period size: 24 Copynumber: 4.6 Consensus size: 24
58185 CATAAATCAG
*
58195 GTCAAGTATCATATCAGAAAT-CAA
1 GTCAAGTATCAGATCAG-AATCCAA
* *
58219 GTCAAGTAACATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
58243 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
58267 GTC-AGATATCAGATCAGAATCCAA
1 GTCAAG-TATCAGATCAGAATCCAA
* * *
58291 ATCGAGAATCAGAT
1 GTCAAGTATCAGAT
58305 AAAATATTCA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
23 5 0.07
24 69 0.91
25 2 0.03
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:62588 original size:24 final size:24
Alignment explanation
Indices: 62561--62612 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
62551 AACGGATATA
*
62561 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
62585 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
62609 TCAA
1 TCAA
62613 GTAACATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:62613 original size:24 final size:25
Alignment explanation
Indices: 62577--62678 Score: 117
Period size: 24 Copynumber: 4.3 Consensus size: 25
62567 ATCAAAACAT
62577 AAAT-CAGGTCAAGTATCATATCAG
1 AAATCCAGGTCAAGTATCATATCAG
*
62601 AAAT-CAGGTCAAGTAACATATCAG
1 AAATCCAGGTCAAGTATCATATCAG
* *
62625 -AATCCAAGTCAAGTATCAGATCAG
1 AAATCCAGGTCAAGTATCATATCAG
*
62649 -AATCCATGTC-AGATATCATATCAG
1 AAATCCAGGTCAAG-TATCATATCAG
62673 -AATCCA
1 AAATCCA
62679 AATCGAAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
23 5 0.07
24 65 0.93
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (25 bp):
AAATCCAGGTCAAGTATCATATCAG
Found at i:62650 original size:48 final size:48
Alignment explanation
Indices: 62584--62679 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
62574 CATAAATCAG
*
62584 GTCAAGTATCATATCAGAAAT-CAGGTCA-AGTAACATATCAGAATCCAA
1 GTCAAGTATCAGATCAG-AATCCAGGTCAGA-TAACATATCAGAATCCAA
* *
62632 GTCAAGTATCAGATCAGAATCCATGTCAGATATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAGGTCAGATAACATATCAGAATCCAA
62680 ATCGAAAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
47 3 0.07
48 39 0.91
49 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGATAACATATCAGAATCCAA
Found at i:65222 original size:13 final size:13
Alignment explanation
Indices: 65204--65233 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
65194 GCCGGTCAAC
65204 GGTCAACAGGTCG
1 GGTCAACAGGTCG
*
65217 GGTCAACGGGTCG
1 GGTCAACAGGTCG
65230 GGTC
1 GGTC
65234 GGGACCGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:66092 original size:2 final size:2
Alignment explanation
Indices: 66087--66112 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
66077 TTAATTCTTG
66087 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
66113 TTTTTTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68714 original size:27 final size:29
Alignment explanation
Indices: 68670--68738 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 29
68660 ATTAAATAAT
* * *
68670 TTAATAATAATACATTTA-TG-TAATTTA
1 TTAATAATATTACATTTATTGAAAATTCA
**
68697 TTAATAATATTATTTTTATTGAAAATTCA
1 TTAATAATATTACATTTATTGAAAATTCA
68726 TTATATAATATTA
1 TTA-ATAATATTA
68739 AAATAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 15 0.44
28 2 0.06
29 8 0.24
30 9 0.26
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (29 bp):
TTAATAATATTACATTTATTGAAAATTCA
Found at i:68840 original size:12 final size:12
Alignment explanation
Indices: 68823--68855 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
68813 TATAATTTAA
*
68823 TAATTAAAATTT
1 TAATTAAAATGT
68835 TAATTAAAATGT
1 TAATTAAAATGT
68847 TAA-TAAAAT
1 TAATTAAAAT
68856 AGTATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATTAAAATGT
Found at i:76201 original size:24 final size:24
Alignment explanation
Indices: 76173--76252 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
76163 CACTTAACAA
76173 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
* *
76197 TGCATCGATTCAT-CATGTTG-A--
1 TGCATCGATGCATCCCT-TTGAATG
*
76218 TGCACCGATGCA-CGCC-TTGAATG
1 TGCATCGATGCATC-CCTTTGAATG
76241 TGCATCGATGCA
1 TGCATCGATGCA
76253 CAGGGTCATG
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
20 3 0.07
21 11 0.25
22 1 0.02
23 14 0.32
24 15 0.34
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:78057 original size:14 final size:15
Alignment explanation
Indices: 78035--78065 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
78025 TAAATTGTCA
78035 TTTCATAAATTCTAT
1 TTTCATAAATTCTAT
78050 TTTC-TAAATTCTAT
1 TTTCATAAATTCTAT
78064 TT
1 TT
78066 ATATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTCATAAATTCTAT
Found at i:79495 original size:2 final size:2
Alignment explanation
Indices: 79488--79522 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
79478 AAAAATATCT
79488 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 T
79523 TTCCAAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:80823 original size:27 final size:29
Alignment explanation
Indices: 80779--80847 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 29
80769 ATTAAATAAT
* * *
80779 TTAATAATAATACATTTA-TG-TAATTTA
1 TTAATAATATTACATTTATTGAAAATTCA
**
80806 TTAATAATATTATTTTTATTGAAAATTCA
1 TTAATAATATTACATTTATTGAAAATTCA
80835 TTATATAATATTA
1 TTA-ATAATATTA
80848 AAATAAAAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 15 0.44
28 2 0.06
29 8 0.24
30 9 0.26
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (29 bp):
TTAATAATATTACATTTATTGAAAATTCA
Found at i:81901 original size:19 final size:19
Alignment explanation
Indices: 81877--81932 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
81867 GAACGTTGAA
81877 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
81896 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
81917 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
81933 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:81912 original size:11 final size:11
Alignment explanation
Indices: 81877--81925 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
81867 GAACGTTGAA
81877 AACCGGTTTTG
1 AACCGGTTTTG
81888 -ACCGG-TTT-
1 AACCGGTTTTG
81896 AACCGGTTTTG
1 AACCGGTTTTG
81907 AACCGGTTTTG
1 AACCGGTTTTG
81918 -ACCGGTTT
1 AACCGGTTT
81926 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:81928 original size:9 final size:10
Alignment explanation
Indices: 81878--81932 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
81868 AACGTTGAAA
81878 ACCGGTTTTG
1 ACCGGTTTTG
*
81888 ACCGG-TTTA
1 ACCGGTTTTG
81897 ACCGGTTTTG
1 ACCGGTTTTG
81907 AACCGGTTTTG
1 -ACCGGTTTTG
81918 ACCGG-TTTG
1 ACCGGTTTTG
81927 ACCGGT
1 ACCGGT
81933 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:82056 original size:29 final size:29
Alignment explanation
Indices: 81994--82069 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
81984 ACCGTTGACC
*** *
81994 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
*
82023 TGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
82052 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
82070 TTTTTAAAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.43
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:88047 original size:37 final size:37
Alignment explanation
Indices: 87971--88047 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
87961 AAATTCATTA
**
87971 TATAATATTAAAATAAAAGTATAATATTATATATCAT
1 TATAATATTAAAATAAAAGTATAATATTATATAGAAT
* *
88008 TATAATATTAAAGAATATAA-TATCATATTAT-TAGAAT
1 TATAATATT-AA-AATAAAAGTATAATATTATATAGAAT
88045 TAT
1 TAT
88048 GAGTAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 16 0.47
38 12 0.35
39 6 0.18
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.42
Consensus pattern (37 bp):
TATAATATTAAAATAAAAGTATAATATTATATAGAAT
Found at i:91454 original size:19 final size:19
Alignment explanation
Indices: 91430--91481 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
91420 TTCTAGGTAA
91430 GGTGCATCGATGCATAAGT
1 GGTGCATCGATGCATAAGT
91449 GGTGCATCGATGCATAAGT
1 GGTGCATCGATGCATAAGT
* *
91468 AGTGCGTCGATGCA
1 GGTGCATCGATGCA
91482 CACCTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (19 bp):
GGTGCATCGATGCATAAGT
Found at i:92047 original size:58 final size:57
Alignment explanation
Indices: 91951--92227 Score: 222
Period size: 58 Copynumber: 4.7 Consensus size: 57
91941 ATGGCACTTT
* * *
91951 GTGTGCTATAATGATATGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGA
1 GTGTGCTA-AATGATAAGGAAATCATACTGAATGTATGGATTTCCAGATGGAGCACT-A
* ** *
92010 GTGTGCTAAATGATAAGGAAATCATATTGAAAT-TATGGATTTCCAGATAGGGAATATTA
1 GTGTGCTAAATGATAAGGAAATCATACTG-AATGTATGGATTTCCAGAT--GGAGCACTA
* * * * **
92069 -TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATAAAGCACTA
1 GTGTGCT-AAATGATAAGGAAATCATACTGAATGTATGGATTTCCAGATGGAGCACTA
* * * **
92126 GGGGTGCTAAATGATAAGGAAATCATATTTAAAATATGGATTTCCAGATAGG-GCACATTA
1 -GTGTGCTAAATGATAAGGAAATCATACTGAATGTATGGATTTCCAGAT-GGAGCAC--TA
* **
92186 -TGTGCTAAAATGGTAACAAAATCATACT-AATGGTATGGATTT
1 GTGTGCT-AAATGATAAGGAAATCATACTGAAT-GTATGGATTT
92228 TTGAATAGGG
Statistics
Matches: 171, Mismatches: 35, Indels: 24
0.74 0.15 0.10
Matches are distributed among these distances:
57 4 0.02
58 85 0.50
59 75 0.44
60 7 0.04
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (57 bp):
GTGTGCTAAATGATAAGGAAATCATACTGAATGTATGGATTTCCAGATGGAGCACTA
Found at i:92164 original size:117 final size:117
Alignment explanation
Indices: 91952--92227 Score: 376
Period size: 117 Copynumber: 2.4 Consensus size: 117
91942 TGGCACTTTG
* * * * ** *
91952 TGTGCTATAATGATATGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTGAGGGTGCT
* *
92017 AAATGATAAGGAAATCATATTGAAATTATGGATTTCCAGATAGGGAATATTA
66 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGAACATTA
* *
92069 TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATGGGTTTCCAGATAAAGCACT-AGGGGTGC
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTGA-GGGTGC
* *
92133 TAAATGATAAGGAAATCATATTTAAAATATGGATTTCCAGATAGGGCACATTA
65 TAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGAACATTA
** *
92186 TGTGCTAAAATGGTAACAAAATCATACT-AATGGTATGGATTT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGT-GTATGGATTT
92228 TTGAATAGGG
Statistics
Matches: 139, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
116 3 0.02
117 136 0.98
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTGAGGGTGCT
AAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAGGGAACATTA
Found at i:98990 original size:24 final size:24
Alignment explanation
Indices: 98922--99030 Score: 91
Period size: 24 Copynumber: 4.5 Consensus size: 24
98912 AAATATTTTA
*
98922 TCTGATTTCTGA-CTTGAATTTTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* *
98946 TATGA-TACATGA-CTTGAATTCTGT
1 TCTGATTTC-TGATC-TGAATTCTGT
*
98970 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
98994 TCTGATATT-TGTTCTGAATTCTAT
1 TCTGAT-TTCTGATCTGAATTCTGT
*
99018 TTTGATTTCTGAT
1 TCTGATTTCTGAT
99031 ATCTCCGTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
23 4 0.06
24 60 0.87
25 5 0.07
ACGTcount: A:0.19, C:0.13, G:0.17, T:0.51
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:99855 original size:2 final size:2
Alignment explanation
Indices: 99848--99873 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
99838 TTAATTCTTG
99848 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
99874 TTTTTCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102671 original size:37 final size:37
Alignment explanation
Indices: 102595--102671 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
102585 AAATTCGTTA
**
102595 TATAATATTAAAATAAAAGTATAATATTATATATCAT
1 TATAATATTAAAATAAAAGTATAATATTATATAGAAT
* *
102632 TATAATATTAAAGAATATAA-TATCATATTAT-TAGAAT
1 TATAATATT-AA-AATAAAAGTATAATATTATATAGAAT
102669 TAT
1 TAT
102672 GAGTAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 16 0.47
38 12 0.35
39 6 0.18
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.42
Consensus pattern (37 bp):
TATAATATTAAAATAAAAGTATAATATTATATAGAAT
Found at i:107294 original size:2 final size:2
Alignment explanation
Indices: 107287--107312 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
107277 CATTATAAAA
107287 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
107313 TTCCAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120329 original size:38 final size:37
Alignment explanation
Indices: 120259--120331 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 37
120249 TAAAGGAAAA
*
120259 ATCATTATATATTATTAAAATAAAAATAATATTATAT
1 ATCATTATATATTATAAAAATAAAAATAATATTATAT
* *
120296 ATCATTATAATATTA-AAAAATATAATATCATATTAT
1 ATCATTAT-ATATTATAAAAATA-AAAATAATATTAT
120332 TAGAATTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 14 0.45
38 17 0.55
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (37 bp):
ATCATTATATATTATAAAAATAAAAATAATATTATAT
Found at i:120793 original size:18 final size:18
Alignment explanation
Indices: 120755--120794 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
120745 ATATATATAT
*
120755 ATATTATTTTTTATGAAA
1 ATATTATTTTTTATAAAA
120773 ATATTA-TTTTTATAAATA
1 ATATTATTTTTTATAAA-A
120791 ATAT
1 ATAT
120795 AAAATTCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
ATATTATTTTTTATAAAA
Found at i:123924 original size:2 final size:2
Alignment explanation
Indices: 123917--123942 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
123907 TTAATTCTTG
123917 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
123943 TATTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:126675 original size:29 final size:31
Alignment explanation
Indices: 126614--126699 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
126604 AATAATTTAA
*
126614 TAATAATAAAGGAA-A-AATAATTATATATTAT
1 TAATAATAAA-GAATATAAT-ATTATATATCAT
*
126645 TAA-AATAAA-AGTATAATATTATATATCAT
1 TAATAATAAAGAATATAATATTATATATCAT
* *
126674 TAATATTAAAGAATATAATATCATAT
1 TAATAATAAAGAATATAATATTATAT
126700 TATTAGAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.02
29 15 0.33
30 14 0.30
31 16 0.35
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (31 bp):
TAATAATAAAGAATATAATATTATATATCAT
Found at i:126691 original size:31 final size:29
Alignment explanation
Indices: 126633--126699 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
126623 AGGAAAAATA
* *
126633 ATTATATATTATTAAAATAAAAGTATAAT
1 ATTATATATCATTAAAATAAAAATATAAT
*
126662 ATTATATATCATTAATATTAAAGAATATAAT
1 ATTATATATCATTAA-AATAAA-AATATAAT
*
126693 ATCATAT
1 ATTATAT
126700 TATTAGAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.44
30 5 0.16
31 13 0.41
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (29 bp):
ATTATATATCATTAAAATAAAAATATAAT
Found at i:126710 original size:29 final size:26
Alignment explanation
Indices: 126626--126710 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 26
126616 ATAATAAAGG
* *
126626 AAAAATA-ATTATATATTATTAAAAT
1 AAAAATATAATATATATTATTAAATT
*
126651 AAAAGTATAATATTATATATCATTAATATT
1 AAAAATATAATA-TATAT-T-ATTAA-ATT
126681 AAAGAATATAATATCATATTATTAGAATT
1 AAA-AATATAATAT-ATATTATTA-AATT
126710 A
1 A
126711 TGAGTAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
25 6 0.12
26 3 0.06
27 5 0.10
28 1 0.02
29 13 0.27
30 8 0.17
31 12 0.25
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (26 bp):
AAAAATATAATATATATTATTAAATT
Found at i:127158 original size:18 final size:19
Alignment explanation
Indices: 127128--127168 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
127118 ATATATATAT
127128 ATATTATTTTTTATGAAA-A
1 ATATTATTTTTTAT-AAATA
127147 ATATTA-TTTTTATAAATA
1 ATATTATTTTTTATAAATA
127165 ATAT
1 ATAT
127169 AAAAGTCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 12 0.57
19 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATATTATTTTTTATAAATA
Found at i:130290 original size:2 final size:2
Alignment explanation
Indices: 130283--130312 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
130273 TTTATTCTTG
130283 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
130313 TATTTGTTTC
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
Done.