Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004592.1 Hibiscus syriacus cultivar Beakdansim tig00010255_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: 46290
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:37 original size:21 final size:21
Alignment explanation
Indices: 11--77 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
1 TTTTTTTAGT
11 GAGCTTAACA-AGCAACGAGTC
1 GAGCTTAA-AGAGCAACGAGTC
32 GAGCTTAAAGAGCAACGAGTC
1 GAGCTTAAAGAGCAACGAGTC
*
53 GAGCCTAAAGAGCAACGAGTC
1 GAGCTTAAAGAGCAACGAGTC
74 GAGC
1 GAGC
78 CGAGTTGAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 1 0.02
21 43 0.98
ACGTcount: A:0.37, C:0.22, G:0.28, T:0.12
Consensus pattern (21 bp):
GAGCTTAAAGAGCAACGAGTC
Found at i:1079 original size:37 final size:38
Alignment explanation
Indices: 1005--1091 Score: 117
Period size: 37 Copynumber: 2.3 Consensus size: 38
995 TTTCACCCAA
* *
1005 ATCCTACCCGAATATCACACTTTAAAAAATTCAACCCG
1 ATCCGACCCGAATATCACACTTTAAAAAATCCAACCCG
1043 A-CTCGACCCGAATATCACAC-TTAAAAAA-CCAGACCCG
1 ATC-CGACCCGAATATCACACTTTAAAAAATCCA-ACCCG
1080 ATCCGACCCGAA
1 ATCCGACCCGAA
1092 ATAATAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
36 2 0.05
37 24 0.55
38 18 0.41
ACGTcount: A:0.39, C:0.34, G:0.09, T:0.17
Consensus pattern (38 bp):
ATCCGACCCGAATATCACACTTTAAAAAATCCAACCCG
Found at i:3925 original size:14 final size:15
Alignment explanation
Indices: 3896--3927 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3886 AAATAATTAA
3896 AATAATATATTTTAT
1 AATAATATATTTTAT
3911 AATAATATA-TTTAT
1 AATAATATATTTTAT
3925 AAT
1 AAT
3928 TATTTAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:3988 original size:41 final size:41
Alignment explanation
Indices: 3911--4010 Score: 107
Period size: 41 Copynumber: 2.4 Consensus size: 41
3901 TATATTTTAT
* *
3911 AATAATAT-ATTTATAATTATTTAGTATATTCAAATAATTA
1 AATAATATAATTTATAATGATTTAGTATATTCAAATAAATA
* *
3951 GATTAATATAATTTATAATGATTTTA-TATTTTC-AATAAATA
1 -AATAATATAATTTATAATGA-TTTAGTATATTCAAATAAATA
*
3992 AATAATATATTTTAATAAT
1 AATAATATAATTT-ATAAT
4011 ATAAAAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
40 11 0.22
41 19 0.38
42 16 0.32
43 4 0.08
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (41 bp):
AATAATATAATTTATAATGATTTAGTATATTCAAATAAATA
Found at i:4003 original size:22 final size:21
Alignment explanation
Indices: 3975--4019 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
3965 ATAATGATTT
3975 TATATTTTCAATAA-ATAAATAA
1 TATATTTT-AATAATATAAA-AA
3997 TATATTTTAATAATATAAAAA
1 TATATTTTAATAATATAAAAA
4018 TA
1 TA
4020 AAGGTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TATATTTTAATAATATAAAAA
Found at i:13166 original size:23 final size:23
Alignment explanation
Indices: 13140--13206 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
13130 CCACAGCTCA
13140 TATAATTGCACCGAAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
* *
13163 TATAATTGCACCGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCACG
* *
13186 TAGAATTGCACCGTAGTGCCA
1 TATAATTGCACCGAAGTGCCA
13207 TATAATAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACG
Found at i:13393 original size:103 final size:103
Alignment explanation
Indices: 13222--13439 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
13212 TAATGTCCAT
* *
13222 AAGGACCACATATTATTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGAGATCAAGTATGTGTCTCACCA
13287 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
13325 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAG-GATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-ACAAGAGATCAAGTATGTGTCTCACC
13389 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
13428 AAGGACCACATA
1 AAGGACCACATA
13440 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 108 0.97
104 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGAGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:14372 original size:64 final size:63
Alignment explanation
Indices: 14220--14381 Score: 155
Period size: 64 Copynumber: 2.5 Consensus size: 63
14210 TTCCCTATCG
* * ** * ** ** *
14220 GTGCATCGATGCACTACCTGTGCATCGGTGCATAAAATACATTCGATGTTTGTTTATTACTGG
1 GTGCATCGATGCACTACTTGTGCATCGATGCACCAAATACATTCGATGTTTCTAGATTAAAGA
* * * *
14283 GATGCATCGATGCA-TGCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTAGATTAAAAG
1 G-TGCATCGATGCACT-ACTTGTGCATCGATGCACCAAATACATTCGATGTTTCTAGATT-AAAG
14347 A
63 A
*
14348 GTGCATCGATGCACTACTTGTGCATCGATACACC
1 GTGCATCGATGCACTACTTGTGCATCGATGCACC
14382 TTCAAACAAT
Statistics
Matches: 78, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
63 2 0.03
64 72 0.92
65 4 0.05
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTACTTGTGCATCGATGCACCAAATACATTCGATGTTTCTAGATTAAAGA
Found at i:14522 original size:17 final size:17
Alignment explanation
Indices: 14500--14541 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
14490 GATTAAATCC
14500 TTCATATTTCAACCCCT
1 TTCATATTTCAACCCCT
14517 TTCATATTTCAACCCCT
1 TTCATATTTCAACCCCT
14534 TTCATATT
1 TTCATATT
14542 CCTAACTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (17 bp):
TTCATATTTCAACCCCT
Found at i:15535 original size:22 final size:22
Alignment explanation
Indices: 15494--15561 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
15484 CTCGTATAAA
15494 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
15517 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
15539 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
15561 T
1 T
15562 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:15888 original size:29 final size:29
Alignment explanation
Indices: 15855--15926 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
15845 TTTTCTGCAT
**
15855 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
15884 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
15913 ATTCATGTCATGTA
1 ATTCATGTCATGTA
15927 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:16376 original size:66 final size:67
Alignment explanation
Indices: 16229--16401 Score: 215
Period size: 67 Copynumber: 2.6 Consensus size: 67
16219 TTTTTCTCAT
* * *
16229 GGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTT--CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
16294 TGAG
64 TGAG
* * * *
16298 GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTTG
1 GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
16362 AG
66 AG
* *
16364 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
16402 AACCCAGAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
65 6 0.06
66 19 0.20
67 57 0.61
69 11 0.12
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
AG
Found at i:22452 original size:22 final size:22
Alignment explanation
Indices: 22435--22501 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
22425 CTCGTATAAA
22435 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
22457 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
22479 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
22501 T
1 T
22502 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:22828 original size:29 final size:29
Alignment explanation
Indices: 22795--22866 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
22785 TTTTCTGCAT
**
22795 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
22824 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
22853 ATTCATGTCATGTA
1 ATTCATGTCATGTA
22867 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:23315 original size:66 final size:67
Alignment explanation
Indices: 23169--23340 Score: 222
Period size: 67 Copynumber: 2.6 Consensus size: 67
23159 TTTTTCTCAT
* * *
23169 GGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
23234 GAG
65 GAG
* * * *
23237 GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTTG
1 GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
23301 AG
66 AG
* *
23303 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
23341 AACCCAGAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
65 6 0.06
66 19 0.20
67 57 0.61
68 11 0.12
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
AG
Found at i:26635 original size:33 final size:33
Alignment explanation
Indices: 26598--26711 Score: 131
Period size: 33 Copynumber: 3.5 Consensus size: 33
26588 GGTGTCTAAA
* *
26598 CCTCCGCCAGTTCCAGTATATGAA-AAACCACTT
1 CCTCCGCCAGTTCCAATATAT-AAGAAACCACAT
* * * *
26631 CCTCCACCAGTTCCAAAATACAAGAAGCCACAT
1 CCTCCGCCAGTTCCAATATATAAGAAACCACAT
*
26664 CCTCCGCCAGTTCCAATCTATAAGAAACCACAT
1 CCTCCGCCAGTTCCAATATATAAGAAACCACAT
* *
26697 CCACCTCCAGTTCCA
1 CCTCCGCCAGTTCCA
26712 GCTTACAAGC
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
32 2 0.03
33 65 0.97
ACGTcount: A:0.32, C:0.38, G:0.10, T:0.20
Consensus pattern (33 bp):
CCTCCGCCAGTTCCAATATATAAGAAACCACAT
Found at i:28786 original size:31 final size:31
Alignment explanation
Indices: 28745--28819 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
28735 AAAAAAACAT
28745 AAGATGTGGTCACTTTCACTTTCATTTAATG
1 AAGATGTGGTCACTTTCACTTTCATTTAATG
* * *** * *
28776 AAGATATGGTCATTTTTGTTTTTATTTAATT
1 AAGATGTGGTCACTTTCACTTTCATTTAATG
28807 AAGATGTGGTCAC
1 AAGATGTGGTCAC
28820 CCCGAGTTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (31 bp):
AAGATGTGGTCACTTTCACTTTCATTTAATG
Found at i:30293 original size:17 final size:17
Alignment explanation
Indices: 30267--30299 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
30257 TTTTGTTTTT
30267 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
30285 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
30300 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:30301 original size:17 final size:19
Alignment explanation
Indices: 30262--30301 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
30252 TAATATTTTG
*
30262 TTTTTAATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
30281 -TTTAAATTT-TTTAA-TA
1 TTTTAAATTTATTTAAGTA
30297 TTTTA
1 TTTTA
30302 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 9 0.47
18 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:31633 original size:35 final size:32
Alignment explanation
Indices: 31598--31678 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 32
31588 TTTGGTTAAT
31598 TTTGTT-TATTACCATTTAATATCAGTTATTGTAA
1 TTTGTTATATTACCATTTAATA-C--TTATTGTAA
31632 TTTGTTTATCATTTACCATTTAATACTTATTGTAA
1 TTTG-TTAT-A-TTACCATTTAATACTTATTGTAA
*
31667 GTTTGTTGTATT
1 -TTTGTTATATT
31679 TAAATTATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
33 2 0.05
34 5 0.12
35 14 0.34
36 5 0.12
37 2 0.05
38 13 0.32
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.56
Consensus pattern (32 bp):
TTTGTTATATTACCATTTAATACTTATTGTAA
Found at i:35600 original size:20 final size:20
Alignment explanation
Indices: 35575--35623 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
35565 TATCTCCAAC
35575 TATATAACCTTACCTTCAGT
1 TATATAACCTTACCTTCAGT
35595 TATATAACCTTACCTTCAGT
1 TATATAACCTTACCTTCAGT
35615 TATATAACC
1 TATATAACC
35624 AACCTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (20 bp):
TATATAACCTTACCTTCAGT
Found at i:36432 original size:21 final size:19
Alignment explanation
Indices: 36390--36433 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
36380 GCCTTATTTG
*
36390 TTTATTAAATTATGTGATA
1 TTTATTAAATCATGTGATA
*
36409 TTTATTATAATCATGCTTATA
1 TTTATTA-AATCATG-TGATA
36430 TTTA
1 TTTA
36434 GGAAGGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 6 0.29
21 8 0.38
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55
Consensus pattern (19 bp):
TTTATTAAATCATGTGATA
Found at i:39409 original size:33 final size:33
Alignment explanation
Indices: 39371--39460 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
39361 CCCGATACAC
*
39371 AAGAAACCACTTCCTCCACCAATTCCATTATAT
1 AAGAAACCACTTCCTCCACCAATTCCAGTATAT
* *
39404 AAGAAACCACTTCCTCCACCAGTTCGAGTATAT
1 AAGAAACCACTTCCTCCACCAATTCCAGTATAT
* *
39437 AA-AAA-AACTTCCTCCACCTATTCC
1 AAGAAACCACTTCCTCCACCAATTCC
39461 TGCATACAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 15 0.30
32 3 0.06
33 32 0.64
ACGTcount: A:0.36, C:0.33, G:0.06, T:0.26
Consensus pattern (33 bp):
AAGAAACCACTTCCTCCACCAATTCCAGTATAT
Found at i:43648 original size:31 final size:33
Alignment explanation
Indices: 43611--43697 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
43601 CGATACACAG
*
43611 AAACCACTTCCTCCACCAATTCCA-T-TATATA
1 AAACCACTTCCTCCACCAATTCCAGTATATAAA
* * *
43642 GAACCACTTCCTCCACCAGTTCGAGTATATAAA
1 AAACCACTTCCTCCACCAATTCCAGTATATAAA
*
43675 AAACCACTTCCTCCACCTATTCC
1 AAACCACTTCCTCCACCAATTCC
43698 TGCATACAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 21 0.46
32 1 0.02
33 24 0.52
ACGTcount: A:0.32, C:0.37, G:0.05, T:0.26
Consensus pattern (33 bp):
AAACCACTTCCTCCACCAATTCCAGTATATAAA
Found at i:45032 original size:313 final size:306
Alignment explanation
Indices: 44466--45045 Score: 1013
Period size: 313 Copynumber: 1.9 Consensus size: 306
44456 AACTTGTATG
44466 TCTCCTCTCTCTCGATTTTGATGGAGAGTTTTTATAGTGATTTTAAGTGTTAATGTTAAGTGTAG
1 TCTCCTCTCTCTCGATTTTGATGGAGAGTTTTTATAGTGATTTTAAGTGTTAATGTTAAGTGTAG
44531 ATCTATGATCATTATGTAAGTTTAAACAAACAAATTTATTGACGTGATTAACTGTCAATTGATTT
66 ATCTATGATCATTATGTAAGTTTAAACAAACAAATTTATTGACGTGATTAACTGTCAATTGATTT
44596 TAATAAATTAGAGAATATTTAGAAGTTATATCAAAAGATTGTGATTTCTCTAAGGATATAAGGCT
131 TAATAAATTAGAGAATATTTAGAAGTTATATCAAAAGATTGTGATTTCTCTAAGGATATAAGGCT
44661 TCGAGTGTCTTATGTCTCGTGCTTAGAAATATTTTTTGGGGCACTCCTCTCTGAAGGAGGAGAGA
196 TCGAGTGTCTTATGTCTCGTGCTTAGAAATATTTTTTGGGGCACTCCTCTCTGAAGGAGGAGAGA
44726 CCATGATGTGTAGAGTGGAGGAGATTCGAAGAACTTGGATGTCTCC
261 CCATGATGTGTAGAGTGGAGGAGATTCGAAGAACTTGGATGTCTCC
*
44772 TCTCTCTCTCTCTCTATTTTGATGGAGAGTTTTTATAGTGATTTTAAGTGTTAATGTTAAGTGTA
1 TCTC-CTCTCTCTCGATTTTGATGGAGAGTTTTTATAGTGATTTTAAGTGTTAATGTTAAGTGTA
*
44837 GATCTATGATCATTATATGTAAGTTAACTAAACAAACAAATTTATTGGATGTGATTAACTGTCAA
65 GATCTATGATCA-T-TATGTAAGTT---TAAACAAACAAATTTATT-GACGTGATTAACTGTCAA
* *
44902 TTGATTTTGATAAATCATAGAGAATTTTTAGAAGTTATATCAAAAGATTGTGA-TT-TCTAAGGA
124 TTGATTTTAATAAAT--TAGAGAATATTTAGAAGTTATATCAAAAGATTGTGATTTCTCTAAGGA
44965 TATAAGGCTTCGAGTGTC-TATGTCTCGTGCTTAGAAATATTTTTTTGGGGCACTCCTCTCTGAA
187 TATAAGGCTTCGAGTGTCTTATGTCTCGTGCTTAGAAATA-TTTTTTGGGGCACTCCTCTCTGAA
45029 GGAGGAGAGACCATGAT
251 GGAGGAGAGACCATGAT
45046 AGGGATGGCA
Statistics
Matches: 260, Mismatches: 4, Indels: 13
0.94 0.01 0.05
Matches are distributed among these distances:
306 4 0.02
307 71 0.27
308 1 0.00
309 10 0.04
312 39 0.15
313 98 0.38
314 2 0.01
315 35 0.13
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.38
Consensus pattern (306 bp):
TCTCCTCTCTCTCGATTTTGATGGAGAGTTTTTATAGTGATTTTAAGTGTTAATGTTAAGTGTAG
ATCTATGATCATTATGTAAGTTTAAACAAACAAATTTATTGACGTGATTAACTGTCAATTGATTT
TAATAAATTAGAGAATATTTAGAAGTTATATCAAAAGATTGTGATTTCTCTAAGGATATAAGGCT
TCGAGTGTCTTATGTCTCGTGCTTAGAAATATTTTTTGGGGCACTCCTCTCTGAAGGAGGAGAGA
CCATGATGTGTAGAGTGGAGGAGATTCGAAGAACTTGGATGTCTCC
Found at i:46048 original size:17 final size:17
Alignment explanation
Indices: 46019--46063 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
46009 TATAGGATCC
46019 TATTTTTATTACATTTTT
1 TATTTTTA-TACATTTTT
46037 TATTTTTATACATTTTT
1 TATTTTTATACATTTTT
*
46054 TATCTTTATA
1 TATTTTTATA
46064 ATTAATCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTTATACATTTTT
Done.