Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000981.1 Hibiscus syriacus cultivar Beakdansim tig00001964_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: 54060
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1427 original size:83 final size:84
Alignment explanation
Indices: 1275--1524 Score: 316
Period size: 83 Copynumber: 3.0 Consensus size: 84
1265 AAACTCAAGT
* * * * *
1275 TTTAGGATAATATTTTAAA-CAT-TATA-TTTATCTTTATTTTAGATA-TTTAGTTTAAATAGAT
1 TTTAGGATATTATTTTAAATAATATTTATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGAT
* *
1336 GTTGGTATTTCAATTAGTA
66 GTTAGTATTTCAATTAGGA
* *
1355 TTTAGGATATTA-TTTAAATAGTATTTATTTTATCTTTGTTTTAGGTATTTTCGTTTAAATAGAT
1 TTTAGGATATTATTTTAAATAATATTTATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGAT
1419 GTTAGTATTTCAATTAGGA
66 GTTAGTATTTCAATTAGGA
* *
1438 TTTAGGATGTTATTTTAAATAATATTTA-TTTATCTTTGTTTTAGGTATTTTAGTTTAAGTAG-T
1 TTTAGGATATTATTTTAAATAATATTTATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGAT
* * *
1501 CTTAAGTGTTTTAATTAGGA
66 GTT-AGTATTTCAATTAGGA
1521 TTTA
1 TTTA
1525 TTATATTTTA
Statistics
Matches: 148, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
79 6 0.04
80 12 0.08
81 3 0.02
82 20 0.14
83 93 0.63
84 14 0.09
ACGTcount: A:0.30, C:0.03, G:0.14, T:0.53
Consensus pattern (84 bp):
TTTAGGATATTATTTTAAATAATATTTATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGAT
GTTAGTATTTCAATTAGGA
Found at i:2140 original size:10 final size:10
Alignment explanation
Indices: 2119--2152 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2109 TTTATCCCAA
2119 TTTATTTA-T
1 TTTATTTATT
2128 TTTATTTATT
1 TTTATTTATT
*
2138 TTTATTAATT
1 TTTATTTATT
2148 TTTAT
1 TTTAT
2153 CTCATTATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTATTTATT
Found at i:3712 original size:16 final size:14
Alignment explanation
Indices: 3682--3708 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3672 TAAATATTTA
3682 TATATTCTAATATC
1 TATATTCTAATATC
3696 TATATTCTAATAT
1 TATATTCTAATAT
3709 ATCTTCTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATTCTAATATC
Found at i:7968 original size:21 final size:21
Alignment explanation
Indices: 7944--7983 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7934 CAATGGGATT
*
7944 AGGATTAGGAATTGGATTTTG
1 AGGATTAGGAAGTGGATTTTG
*
7965 AGGATTTGGAAGTGGATTT
1 AGGATTAGGAAGTGGATTT
7984 AGTTGACGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.38
Consensus pattern (21 bp):
AGGATTAGGAAGTGGATTTTG
Found at i:8701 original size:20 final size:20
Alignment explanation
Indices: 8672--8709 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8662 CAGAACCCCA
*
8672 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
8692 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
8710 TCAAAGGGAG
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:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:15188 original size:29 final size:29
Alignment explanation
Indices: 15132--15281 Score: 139
Period size: 29 Copynumber: 5.3 Consensus size: 29
15122 TTTACACATT
15132 TATCACCCTTTT-AAAAAAATTA-TAAAAA
1 TATCACCCTTTTCAAAAAAATTACT-AAAA
*
15160 TATCACCCTTTTCAAAATAATTACTAAAA
1 TATCACCCTTTTCAAAAAAATTACTAAAA
*** * *
15189 TATCATTTTTTTAAAAAAAATTA-TGAAAT
1 TATCACCCTTTTCAAAAAAATTACT-AAAA
* * *
15218 TATCA--CTTTTTAAAAAAAATACGAAAA
1 TATCACCCTTTTCAAAAAAATTACTAAAA
* * *
15245 TAGCACCATTTTCAAAATAATTACTAAAA
1 TATCACCCTTTTCAAAAAAATTACTAAAA
15274 TATCACCC
1 TATCACCC
15282 GGTCAACGGT
Statistics
Matches: 96, Mismatches: 20, Indels: 11
0.76 0.16 0.09
Matches are distributed among these distances:
27 20 0.21
28 13 0.14
29 62 0.65
30 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (29 bp):
TATCACCCTTTTCAAAAAAATTACTAAAA
Found at i:15312 original size:18 final size:18
Alignment explanation
Indices: 15289--15327 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
15279 CCCGGTCAAC
15289 GGTCAACGGGTAGGGTCG
1 GGTCAACGGGTAGGGTCG
*
15307 GGTCAACGGGTTGGGTCG
1 GGTCAACGGGTAGGGTCG
15325 GGT
1 GGT
15328 TGGAACCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.15, G:0.51, T:0.21
Consensus pattern (18 bp):
GGTCAACGGGTAGGGTCG
Found at i:22444 original size:29 final size:28
Alignment explanation
Indices: 22404--22565 Score: 139
Period size: 29 Copynumber: 5.8 Consensus size: 28
22394 CCTTTTTAAA
*
22404 AAAAT-TTACAAAAATATCACCCTTTTC
1 AAAATATTACAAAAATATCACCATTTTC
* *** *
22431 AAAATATTACCAAAATATCATGTTTTTT
1 AAAATATTACAAAAATATCACCATTTTC
** * ** *
22459 AAAAT-TTACGGAATTATCACTTTTTTA
1 AAAATATTACAAAAATATCACCATTTTC
* *
22486 AAAAAATTACAAAAATAACACCATTTTC
1 AAAATATTACAAAAATATCACCATTTTC
*
22514 AAAATAATTACTAAAATATCACCATTTTC
1 AAAAT-ATTACAAAAATATCACCATTTTC
* *
22543 AAAATAATAACTAAAATATCACC
1 AAAAT-ATTACAAAAATATCACC
22566 GATCAACGGT
Statistics
Matches: 109, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
27 25 0.23
28 41 0.38
29 43 0.39
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAATATTACAAAAATATCACCATTTTC
Found at i:30472 original size:22 final size:23
Alignment explanation
Indices: 30447--30489 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
30437 TTAACCAAAA
30447 TAATCAATTA-CAAATTTAAATG
1 TAATCAATTATCAAATTTAAATG
* *
30469 TAATTAATTATTAAATTTAAA
1 TAATCAATTATCAAATTTAAA
30490 AACAACAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATCAATTATCAAATTTAAATG
Found at i:35486 original size:92 final size:92
Alignment explanation
Indices: 35383--35573 Score: 319
Period size: 92 Copynumber: 2.1 Consensus size: 92
35373 GTATGAAACA
* * * * *
35383 TTATTGAATTGTCATGTTGATGCTTGAAAGTGGACTTGATTTTGATGTTGACATAATATATTTTG
1 TTATTGTATTGTCATCTTGATGCCTGAAAATGGACTTGATTTGGATGTTGACATAATATATTTTG
35448 ATTTTACACGATTAAGTAGTTTTGATT
66 ATTTTACACGATTAAGTAGTTTTGATT
* *
35475 TTATTGTATTGTCATCTTGCTGCCTGAAAATGGAGTTGATTTGGATGTTGACATAATATATTTTG
1 TTATTGTATTGTCATCTTGATGCCTGAAAATGGACTTGATTTGGATGTTGACATAATATATTTTG
35540 ATTTTACACGATTAAGTAGTTTTGATT
66 ATTTTACACGATTAAGTAGTTTTGATT
35567 TTATTGT
1 TTATTGT
35574 TAAATTTGAT
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.47
Consensus pattern (92 bp):
TTATTGTATTGTCATCTTGATGCCTGAAAATGGACTTGATTTGGATGTTGACATAATATATTTTG
ATTTTACACGATTAAGTAGTTTTGATT
Found at i:42666 original size:2 final size:2
Alignment explanation
Indices: 42659--42687 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
42649 ACCCAACAAA
42659 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42688 GTGTATACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45415 original size:36 final size:37
Alignment explanation
Indices: 45329--45461 Score: 187
Period size: 37 Copynumber: 3.6 Consensus size: 37
45319 AGAAAAGTCA
* * *
45329 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGTAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
45366 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA-CC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* *
45402 ATCTTAAGTCTTCACCAAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
* * *
45439 ATTTTAAGCCTTCTCAGAAGAGT
1 ATCTTAAGCCTTCACCGAAGAGT
45462 GTTGGAACAA
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
36 33 0.39
37 52 0.61
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
Found at i:45448 original size:73 final size:73
Alignment explanation
Indices: 45329--45477 Score: 194
Period size: 73 Copynumber: 2.0 Consensus size: 73
45319 AGAAAAGTCA
** * *
45329 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGTAAATCAATCTTAAGCCTTCACCGAAGAGTAG-T-
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACAGAAGAGT-GTTG
45392 GAAGCAAACC
65 GAA-CAAACC
* * * *
45402 ATCTTAAGTCTTCACCAAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCTCAGAAGAGTGTTGG
1 ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACAGAAGAGTGTTGG
45467 AACAAACC
66 AACAAACC
45475 ATC
1 ATC
45478 AGACCATCAG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
72 1 0.02
73 62 0.94
74 3 0.05
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (73 bp):
ATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACAGAAGAGTGTTGG
AACAAACC
Found at i:45918 original size:54 final size:54
Alignment explanation
Indices: 45859--46371 Score: 580
Period size: 54 Copynumber: 9.4 Consensus size: 54
45849 TGAAGCAAAT
* *
45859 GAAGATTTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAA
1 GAAGATTTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAA
* * *
45913 GAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTCGCA
1 GAAGATT-TTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAA
* * * * * **
45968 GAAGATTTTCGAGTTCTATACTCCTTGAAGAAAGAGGGAGTGAACTCGTAAGAA
1 GAAGATTTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAA
* * * *
46022 GAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGCA
1 GAAGATTTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAA
* * * * **
46076 GCAGATTGTTTGAGTTCCATACTCCCTGAAGAAAGAGGGAGGGAACCCGTAGGAA
1 GAAGATT-TTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAA
* * * * * **
46131 GAAGATGTCCGAGTTCCATAGTCTCTAGAGAAAGAGGGAGCGAACCCGTTTGTT
1 GAAGATTTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAA
* * * **
46185 GAAGATTGTTCGAGTTCCATACTTCCTAAAGAAAGAGGGACCGAACCTGTAAGAA
1 GAAGATT-TTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAA
* * *
46240 GAAGATGTCCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCTTTTGAA
1 GAAGATTTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAA
* ** * *
46294 GAAGATGTTCGAGTTTTATACTCCCTGAAA-AAAGAAGGAGCGAACCCGTTTGCA
1 GAAGATTTTCGAGTTCCATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTGAA
46348 GAAGATTATTCGAG-TCTCATACTC
1 GAAGATT-TTCGAGTTC-CATACTC
46372 TTTGAAGAAA
Statistics
Matches: 380, Mismatches: 73, Indels: 11
0.82 0.16 0.02
Matches are distributed among these distances:
54 228 0.60
55 152 0.40
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (54 bp):
GAAGATTTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAA
Found at i:46091 original size:109 final size:109
Alignment explanation
Indices: 45859--46342 Score: 650
Period size: 109 Copynumber: 4.5 Consensus size: 109
45849 TGAAGCAAAT
* * ** * *
45859 GAAGATT-TTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGAAGATTATT
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGA-TGTC
* *
45923 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTCGCA
65 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGCA
* * *
45968 GAAGATT-TTCGAGTTCTATACTCCTTGAAGAAAGAGGGAGTGAACTCGTAAGAAGAAGATGTCC
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTCC
*
46032 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGCA
66 GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGCA
* * * * *
46076 GCAGATTGTTTGAGTTCCATACTCCCTGAAGAAAGAGGGAGGGAACCCGTAGGAAGAAGATGTCC
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTCC
* * * **
46141 GAGTTCCATAGTCTCTAGAGAAAGAGGGAGCGAACCCGTTTGTT
66 GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGCA
* * * * *
46185 GAAGATTGTTCGAGTTCCATACTTCCTAAAGAAAGAGGGACCGAACCTGTAAGAAGAAGATGTCC
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTCC
* *
46250 GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCTTTTGAA
66 GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGCA
* * *
46294 GAAGA-TGTTCGAGTTTTATACTCCCTGAAAAAAGAAGGAGCGAACCCGT
1 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGT
46343 TTGCAGAAGA
Statistics
Matches: 329, Mismatches: 45, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
108 86 0.26
109 243 0.74
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (109 bp):
GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTCC
GAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGCA
Found at i:46343 original size:163 final size:164
Alignment explanation
Indices: 45859--46371 Score: 622
Period size: 163 Copynumber: 3.1 Consensus size: 164
45849 TGAAGCAAAT
* * *
45859 GAAGATT-TTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGAAGATTATT
1 GAAGATTGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTT
* * *
45923 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTCGCAGAAGATTTTCGAGTTCTATA
66 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTCGAAGAAGATGTTCGAGTTCTATA
* * * **
45988 CTCCTTGAAGAAAGAGGGAGTGAACTCGTAAGAA
131 CTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAA
* * * *
46022 GAAGA-TGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGCAGCAGATTGTT
1 GAAGATTGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTT
* * * ** * *
46086 TGAGTTCCATACTCCCTGAAGAAAGAGGGAGGGAACCCGTAGGAAGAAGATGTCCGAGTTCCATA
66 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTCGAAGAAGATGTTCGAGTTCTATA
* * **
46151 GTCTCT-AGAGAAAGAGGGAGCGAACCCGTTTGTT
131 CTCCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAA
* * * ** *
46185 GAAGATTGTTCGAGTTCCATACTTCCTAAAGAAAGAGGGACCGAACCTGTAAGAAGAAGA-TGTC
1 GAAGATTGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTT
* * *
46249 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCTTTTGAAGAAGATGTTCGAGTTTTATA
66 CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTCGAAGAAGATGTTCGAGTTCTATA
* * *
46314 CTCCCTGAAAAAAGAAGGAGCGAACCCGTTTGCA
131 CTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAA
*
46348 GAAGATTATTCGAG-TCTCATACTC
1 GAAGATTGTTCGAGTTC-CATACTC
46372 TTTGAAGAAA
Statistics
Matches: 292, Mismatches: 53, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
162 4 0.01
163 242 0.83
164 46 0.16
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (164 bp):
GAAGATTGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATTGTT
CGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTCGAAGAAGATGTTCGAGTTCTATA
CTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAA
Found at i:46389 original size:55 final size:55
Alignment explanation
Indices: 45859--46853 Score: 627
Period size: 55 Copynumber: 18.3 Consensus size: 55
45849 TGAAGCAAAT
* * * * *
45859 GAAGATT-TTCGAGT-TCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAA
1 GAAGATTGTTCGAGTCTC-ATACTCTCTGAAGAAAGAGGGAGCGAACACGTTTGTA
* * * * * *
45913 GAAGATTATTCGAGT-TCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTCGCA
1 GAAGATTGTTCGAGTCTC-ATACTCTCTGAAGAAAGAGGGAGCGAACACGTTTGTA
* * ** *
45968 GAAGATT-TTCGAGT-TCTATACTC-CTTGAAGAAAGAGGGAGTGAACTCGTAAGAA
1 GAAGATTGTTCGAGTCTC-ATACTCTC-TGAAGAAAGAGGGAGCGAACACGTTTGTA
* * * *
46022 GAAGA-TGTCCGAGT-TCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGCA
1 GAAGATTGTTCGAGTCT-CATACTCTCTGA-AGAAAGAGGGAGCGAACACGTTTGTA
* * * * * ** *
46076 GCAGATTGTTTGAGT-TCCATACTCCCTGAAGAAAGAGGGAGGGAACCCGTAGGAA
1 GAAGATTGTTCGAGTCT-CATACTCTCTGAAGAAAGAGGGAGCGAACACGTTTGTA
* * * *
46131 GAAGA-TGTCCGAGT-TCCATAGTCTCT-AGAGAAAGAGGGAGCGAACCCGTTTGTT
1 GAAGATTGTTCGAGTCT-CATACTCTCTGA-AGAAAGAGGGAGCGAACACGTTTGTA
* * ** *
46185 GAAGATTGTTCGAGT-TCCATACT-TCCTAAAGAAAGAGGGACCGAAC-CTGTAAGAA
1 GAAGATTGTTCGAGTCT-CATACTCT-CTGAAGAAAGAGGGAGCGAACAC-GTTTGTA
* * * * * *
46240 GAAGA-TGTCCGAGT-TCCATACTCCCTAAAGAAAGAGGGAGCGAACCCTTTTGAA
1 GAAGATTGTTCGAGTCT-CATACTCTCTGAAGAAAGAGGGAGCGAACACGTTTGTA
* * * * * * *
46294 GAAGA-TGTTCGAGTTTTATACTCCCTGAAAAAAGAAGGAGCGAACCCGTTTGCA
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAGAGGGAGCGAACACGTTTGTA
* * ** * *
46348 GAAGATTATTCGAGTCTCATACTCTTTGAAGAAATTGGGAGC-ATACACG-ATGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAGAGGGAGCGA-ACACGTTTGTA
* * * * * *
46402 GAAGATTGTTCGAGTCTTATACTCTCT-AAAAAATAGGGAAC-AGACACGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAGAGGGAGCGA-ACACGTTTGTA
* * * * * * * * *
46456 GAAGATTGTTTGAGTCTTATACTCTCTGAAAAAATAGGGTGC-ATTCACGATTATT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAGAGGGAGCGA-ACACGTTTGTA
* * * *
46511 GAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGAGC-AGACACGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAGAGGGAGCGA-ACACGTTTGTA
* * * *
46566 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAGAGGGAGCGAACACGTTTGTA
* * * * *
46621 GAAGATTGATCGAGTCTCATACTCTTTGAAGAAATAAGGAGC-AGACACG-ATGTTA
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAGAGGGAGCGA-ACACGTTTG-TA
* * * * *
46676 -AAGATTGTTCGAGTCTTATA--CTCTAAAAAAATAGGGAG-TAGACACGATTAT-TA
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAGAGGGAGCGA-ACACG-TT-TGTA
* * *
46729 -AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGC-AGACACGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAGAGGGAGCGA-ACACGTTTGTA
** * * * * ** * *
46783 GAAGATTACTCGAGTCTTATACTCTCTGAAGAAATAGGGAACAAATGCGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAGAGGGAGCGAACACGTTTGTA
46838 GAAGATTGTTCGAGTC
1 GAAGATTGTTCGAGTC
46854 ATGCCCTAAA
Statistics
Matches: 795, Mismatches: 113, Indels: 65
0.82 0.12 0.07
Matches are distributed among these distances:
52 21 0.03
53 43 0.05
54 305 0.38
55 422 0.53
56 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAGAGGGAGCGAACACGTTTGTA
Found at i:46758 original size:217 final size:218
Alignment explanation
Indices: 46348--46853 Score: 757
Period size: 217 Copynumber: 2.3 Consensus size: 218
46338 CCCGTTTGCA
* * *
46348 GAAGATTATTCGAGTCTCATACTCTTTGAAGAAATTGGGAGCATACACGA-TGTTGAAGATTGTT
1 GAAGATTATTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTTGAAGATTGTT
* * * *
46412 CGAGTCTTATACTCTCTAAAAAATAGGGAACAGACACGATTGTTGAAGATTGTTTGAGTCTTATA
66 CGAGTCTCATACTCTCTAAAAAATAAGGAACAGACACGATTGTTAAAGATTGTTCGAGTCTTATA
* * ** *
46477 CTCTCTGAAAAAATAGGGTGCATTCACGATTATTGAAGATTGTTCAAGTCTCATACTCTCTGAAG
131 C-CTCTAAAAAAATAGGGAGCAGACACGATTATTAAAGATTGTTCAAGTCTCATACTCTCTGAAG
46542 AAATAGGGAGCAGACACGATTGTT
195 AAATAGGGAGCAGACACGATTGTT
* *
46566 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTTGAAGATTGAT
1 GAAGATTATTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTTGAAGATTGTT
* * *
46631 CGAGTCTCATACTCTTTGAAGAAATAAGGAGCAGACACGA-TGTTAAAGATTGTTCGAGTCTTAT
66 CGAGTCTCATACTCTCT-AAAAAATAAGGAACAGACACGATTGTTAAAGATTGTTCGAGTCTTAT
* *
46695 A-CTCTAAAAAAATAGGGAGTAGACACGATTATTAAAGATTGTTCGAGTCTCATACTCTCTGAAG
130 ACCTCTAAAAAAATAGGGAGCAGACACGATTATTAAAGATTGTTCAAGTCTCATACTCTCTGAAG
46759 AAATAGGGAGCAGACACGATTGTT
195 AAATAGGGAGCAGACACGATTGTT
* * * **
46783 GAAGATTACTCGAGTCTTATACTCTCTGAAGAAATAGGGAACAAATGCGATTGTTGAAGATTGTT
1 GAAGATTATTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTTGAAGATTGTT
46848 CGAGTC
66 CGAGTC
46854 ATGCCCTAAA
Statistics
Matches: 260, Mismatches: 26, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
217 144 0.55
218 46 0.18
219 51 0.20
220 19 0.07
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (218 bp):
GAAGATTATTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTTGAAGATTGTT
CGAGTCTCATACTCTCTAAAAAATAAGGAACAGACACGATTGTTAAAGATTGTTCGAGTCTTATA
CCTCTAAAAAAATAGGGAGCAGACACGATTATTAAAGATTGTTCAAGTCTCATACTCTCTGAAGA
AATAGGGAGCAGACACGATTGTT
Found at i:50949 original size:38 final size:38
Alignment explanation
Indices: 50898--50977 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
50888 TGTTTGATCG
* * *
50898 TATATGTCGTTTCATAGTTGAAATTAATTATCAAACAA
1 TATATGGCGTTTCAAAGTTGAAATTAATTAACAAACAA
50936 TATATGGCGTTTCAAAGTTGAAATTAATTAACAAACAA
1 TATATGGCGTTTCAAAGTTGAAATTAATTAACAAACAA
50974 TATA
1 TATA
50978 CTGTGACAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.36
Consensus pattern (38 bp):
TATATGGCGTTTCAAAGTTGAAATTAATTAACAAACAA
Done.