Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003205.1 Hibiscus syriacus cultivar Beakdansim tig00006744_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: 57367
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:8334 original size:22 final size:22
Alignment explanation
Indices: 8309--8351 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
8299 TAATATTATG
8309 TAATAT-AGTCCCTAAGAATCAA
1 TAATATCA-TCCCTAAGAATCAA
*
8331 TAATATCATCCTTAAGAATCA
1 TAATATCATCCCTAAGAATCA
8352 TCTTGGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (22 bp):
TAATATCATCCCTAAGAATCAA
Found at i:12810 original size:18 final size:18
Alignment explanation
Indices: 12787--12832 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
12777 AGGCATTTGA
12787 TCCTCTGGCT-GTGCTTGT
1 TCCTCT-GCTCGTGCTTGT
12805 TCCTCTGCTCGTGCTTGT
1 TCCTCTGCTCGTGCTTGT
12823 TCCTCGTGCT
1 TCCTC-TGCT
12833 GTTCTGGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.00, C:0.33, G:0.24, T:0.43
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:12842 original size:18 final size:19
Alignment explanation
Indices: 12797--12847 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
12787 TCCTCTGGCT
*
12797 GTGCTTGTTCCTC-TGCTC
1 GTGCTGGTTCCTCGTGCTC
*
12815 GTGCTTGTTCCTCGTGCT-
1 GTGCTGGTTCCTCGTGCTC
* *
12833 GTTCTGGTTCATCGT
1 GTGCTGGTTCCTCGT
12848 CGGAGTCGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.02, C:0.27, G:0.25, T:0.45
Consensus pattern (19 bp):
GTGCTGGTTCCTCGTGCTC
Found at i:14109 original size:22 final size:22
Alignment explanation
Indices: 14028--14108 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
14018 AGAACCCCAG
* *
14028 GGGGGTATCGATTCCCCTAC-A
1 GGGGGAATCGATTCCCCTTCAA
14049 -GGGGAATCGATTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
* *
14070 AGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
14092 GGGGGGTATCGATTCCC
1 -GGGGGAATCGATTCCC
14109 TCTGCACTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
20 17 0.33
21 1 0.02
22 20 0.39
23 13 0.25
ACGTcount: A:0.20, C:0.27, G:0.30, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:17956 original size:22 final size:21
Alignment explanation
Indices: 17914--17953 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17904 GAGTTTTTTT
*
17914 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
17935 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
17954 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:21905 original size:23 final size:23
Alignment explanation
Indices: 21879--21923 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21869 CACCACAGCT
* *
21879 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTACACCGAAGTGCCG
*
21902 CGTAGAATTACACCGTAGTGCC
1 CGTAGAATTACACCGAAGTGCC
21924 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCG
Found at i:22161 original size:149 final size:149
Alignment explanation
Indices: 21891--22205 Score: 519
Period size: 149 Copynumber: 2.1 Consensus size: 149
21881 TATAATTGCA
21891 CCGAAGTG-CCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
21955 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTATCCAAACTTCACACATGTT
* *
22020 CTAAAGAATATACATATGTC
130 CCAAAGAATATACATATATC
*
22040 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
* *
22105 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCAT-CAGACTTCACACATGT
66 TCCTTAAGAATCATATACATATACTAGGGATCA-AGTATGTGTCT-ATCCAAACTTCACACATGT
*
22168 TCCAAAGAATATATATATATC
129 TCCAAAGAATATACATATATC
22189 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
22206 CCATCGACTC
Statistics
Matches: 156, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
148 1 0.01
149 153 0.98
150 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTATCCAAACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:23119 original size:18 final size:18
Alignment explanation
Indices: 23098--23132 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
23088 TCCCATCTAG
23098 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
23116 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
23133 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:23748 original size:21 final size:21
Alignment explanation
Indices: 23718--23762 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
23708 TCTTGTTCGT
*
23718 TTGAAGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
23739 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
23760 TTG
1 TTG
23763 CTCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:26923 original size:23 final size:23
Alignment explanation
Indices: 26897--26941 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
26887 CACCACAGCT
*
26897 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
26920 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
26942 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:27179 original size:149 final size:149
Alignment explanation
Indices: 26909--27223 Score: 546
Period size: 149 Copynumber: 2.1 Consensus size: 149
26899 TATAATTGCA
26909 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
26973 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTATCCAGACTTCACACATGTT
*
27038 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATATC
27058 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
*
27123 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCAT-CAGACTTCACACATGT
66 TCCTTAAGAATCATATACATATACTAGGGATCA-AGTATGTGTCT-ATCCAGACTTCACACATGT
*
27186 TCCAAAGAATATATATATATC
129 TCCAAAGAATATACATATATC
27207 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
27224 CCCTCGACTC
Statistics
Matches: 159, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
148 1 0.01
149 156 0.98
150 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTATCCAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:27979 original size:2 final size:2
Alignment explanation
Indices: 27972--27997 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27962 CTATTATTTC
27972 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
27998 ATCTAATCTG
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):
TA
Found at i:28146 original size:17 final size:18
Alignment explanation
Indices: 28124--28157 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28114 TCCCATCTAG
28124 CTTATC-TATATGTTCAT
1 CTTATCATATATGTTCAT
*
28141 CTTATCATTTATGTTCA
1 CTTATCATATATGTTCA
28158 AATCTCCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (18 bp):
CTTATCATATATGTTCAT
Found at i:28759 original size:21 final size:21
Alignment explanation
Indices: 28735--28779 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28725 TCTTGTTCGT
* *
28735 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
28756 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
28777 TTG
1 TTG
28780 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:34923 original size:31 final size:31
Alignment explanation
Indices: 34850--35015 Score: 162
Period size: 32 Copynumber: 5.3 Consensus size: 31
34840 AGAGTTGAGG
34850 GTATACCTATGT-TCTACG-GAACATATGGACA
1 GTATACCTATGTCT-TACGAG-ACATATGGACA
* *
34881 GAATTACCTATGTCTTTCGAGACATATGGACA
1 GTA-TACCTATGTCTTACGAGACATATGGACA
34913 GTATACCTATGT-TCTACG-GAACATATGGACA
1 GTATACCTATGTCT-TACGAG-ACATATGGACA
* * *
34944 GAATTACCTATGTCTTTCGAGACATATAGACA
1 GTA-TACCTATGTCTTACGAGACATATGGACA
* *
34976 GTATACCTATGTTCTAAGGA-ACATATGGACA
1 GTATACCTATG-TCTTACGAGACATATGGACA
*
35007 GTTTACCTA
1 GTATACCTA
35016 GGTTCTTCGG
Statistics
Matches: 113, Mismatches: 13, Indels: 18
0.78 0.09 0.12
Matches are distributed among these distances:
30 2 0.02
31 53 0.47
32 54 0.48
33 4 0.04
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTCTTACGAGACATATGGACA
Found at i:34949 original size:63 final size:63
Alignment explanation
Indices: 34850--35015 Score: 298
Period size: 63 Copynumber: 2.7 Consensus size: 63
34840 AGAGTTGAGG
*
34850 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
34913 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
* *
34976 GTATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
35016 GGTTCTTCGG
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 7 0.07
63 93 0.93
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATAGACA
Found at i:35021 original size:31 final size:31
Alignment explanation
Indices: 34853--35040 Score: 195
Period size: 31 Copynumber: 6.0 Consensus size: 31
34843 GTTGAGGGTA
*
34853 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* *
34885 TACCTATG-TCTTTC-GAGACATATGGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
34916 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* * *
34948 TACCTATG-TCTTTC-GAGACATATAGACAGTA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
34979 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * *
35010 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
35041 GCCGAGGATC
Statistics
Matches: 129, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
31 78 0.60
32 51 0.40
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:35089 original size:30 final size:30
Alignment explanation
Indices: 35027--35098 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
35017 GTTCTTCGGA
* * * *
35027 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCCTTATG
* *
35057 ACCTCTGGATAGTTACCGAGGTTCCTTGTG
1 ACCTCTGGATAGTTACCGAGGATCCTTATG
35087 ACCTCTGGATAG
1 ACCTCTGGATAG
35099 GTCCTTCGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCCTTATG
Found at i:37267 original size:23 final size:23
Alignment explanation
Indices: 37236--37296 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
37226 GTCGAGGGTT
*
37236 CTATGTGGTCCTTCAAGAAAAAA
1 CTATATGGTCCTTCAAGAAAAAA
* * *
37259 CTATATGGTCCTCCAGGACAAAA
1 CTATATGGTCCTTCAAGAAAAAA
*
37282 CTATATGGTCATTCA
1 CTATATGGTCCTTCA
37297 TGTGGTCCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (23 bp):
CTATATGGTCCTTCAAGAAAAAA
Found at i:37322 original size:21 final size:21
Alignment explanation
Indices: 37296--37335 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
37286 ATGGTCATTC
37296 ATGTGGTC-CTTCGGGGCAAAT
1 ATGTGG-CACTTCGGGGCAAAT
*
37317 ATGTGGCACTTCGGTGCAA
1 ATGTGGCACTTCGGGGCAA
37336 TTTATGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.28
Consensus pattern (21 bp):
ATGTGGCACTTCGGGGCAAAT
Found at i:42952 original size:20 final size:20
Alignment explanation
Indices: 42907--42960 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
42897 CCGATTGAAG
* *
42907 AAGTATCGATACTGAGGTAG
1 AAGTATCGATACTAAGGTAA
*
42927 AGGTATCGATACTAAGAG-AA
1 AAGTATCGATACTAAG-GTAA
42947 AAGTATCGATACTA
1 AAGTATCGATACTA
42961 TTTTTGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
AAGTATCGATACTAAGGTAA
Found at i:43635 original size:21 final size:23
Alignment explanation
Indices: 43585--43637 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
43575 GTCGAGGGTT
*
43585 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGCCCTTCGGGACAAAA
*
43608 CTATGTGGCCCTTCGGGTC-AAA
1 CTATGTGGCCCTTCGGGACAAAA
43630 -TATGTGGC
1 CTATGTGGC
43638 ACTTTGATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 8 0.29
22 3 0.11
23 17 0.61
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (23 bp):
CTATGTGGCCCTTCGGGACAAAA
Found at i:44391 original size:3 final size:3
Alignment explanation
Indices: 44385--44457 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
44375 TAATATTTTT
44385 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44433 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
44458 CATTTCAGAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:47602 original size:21 final size:21
Alignment explanation
Indices: 47577--47635 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
47567 ATCCTTTATG
*
47577 AAAAGGTTAAGCCTTTTGATC
1 AAAAGGTTAAGCCTTTTAATC
** *
47598 AAAAGGAGAAGTCTTTTAATC
1 AAAAGGTTAAGCCTTTTAATC
47619 AAAAGGTTAAGTCCTTT
1 AAAAGGTTAAG-CCTTT
47636 CATTGAAAGG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (21 bp):
AAAAGGTTAAGCCTTTTAATC
Found at i:48213 original size:15 final size:15
Alignment explanation
Indices: 48193--48231 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
48183 AATTTACAGA
48193 TTTTCCATGAAATAT
1 TTTTCCATGAAATAT
48208 TTTTCCATGAAATAT
1 TTTTCCATGAAATAT
48223 TTTT-CATGA
1 TTTTCCATGA
48232 CTCGCATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.49
Consensus pattern (15 bp):
TTTTCCATGAAATAT
Found at i:48433 original size:5 final size:5
Alignment explanation
Indices: 48243--48431 Score: 369
Period size: 5 Copynumber: 37.8 Consensus size: 5
48233 TCGCATCATA
48243 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
48293 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
48343 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
*
48393 AATAT AATAT AATAT AATAT AATAT AATAT AATAC AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATA
48432 CACATCAAAT
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 183 1.00
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:48744 original size:18 final size:19
Alignment explanation
Indices: 48717--48754 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
48707 GAAAATATAA
48717 ATAATATCGAAAATTTATG
1 ATAATATCGAAAATTTATG
*
48736 ATAAT-TCGAAACTTTATG
1 ATAATATCGAAAATTTATG
48754 A
1 A
48755 GGGATCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (19 bp):
ATAATATCGAAAATTTATG
Found at i:49620 original size:27 final size:27
Alignment explanation
Indices: 49582--49642 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
49572 ATGAAGATCT
*
49582 TGATGATGTGGACTTTCAAGTTCAAAG
1 TGATGATATGGACTTTCAAGTTCAAAG
49609 TGATGATATGGACTTTCAAGTTCAAAG
1 TGATGATATGGACTTTCAAGTTCAAAG
*
49636 TGGTGAT
1 TGATGAT
49643 GACGATGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (27 bp):
TGATGATATGGACTTTCAAGTTCAAAG
Done.