Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001395.1 Hibiscus syriacus cultivar Beakdansim tig00002725_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: 72781
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:255 original size:139 final size:134
Alignment explanation
Indices: 3--455 Score: 430
Period size: 139 Copynumber: 3.3 Consensus size: 134
1 GA
* * * *
3 AGAATTTTTAATTTGGTTC-TCGCTTTTGCTCGAGGTTCCAAATTAATTATTTGATTCAATAAAT
1 AGAATTTTTAATTTGG-TCATCGCTTTTGTTCGAGGTTTCAAATTAATTATTTAATTCAATAATT
** * * *
67 GATTAAAATTAATTAGGATTAATATTAGAGTATTCACTTTAGGTCTAATTTTAAATTTAATCCTT
65 GA-TAAAATTAA-TA-GATTAATATTAGAGCCTTCATTTTAGGT-TAA-TTTAAAATTAGTCCTT
132 TTAATTTAGG
125 TTAATTTAGG
* *
142 AGAATTTTTAATTTGGTCATCGCTTTTGTTCAAGGTTTCAAGTTAATTATTTAATTCAATAATTG
1 AGAATTTTTAATTTGGTCATCGCTTTTGTTCGAGGTTTCAAATTAATTATTTAATTCAATAATTG
* *
207 ATGCAAATTAATAAGAATTAATATTAGAGCCTCCATTTTAGGCTTAATTTAAAACTTAGTCCTTT
66 AT-AAAATTAAT-AG-ATTAATATTAGAGCCTTCATTTTAGG-TTAATTTAAAA-TTAGTCCTTT
272 TAATTTAGG
126 TAATTTAGG
* * * * * ** *
281 AAAATTTTTAATTTAGTCCTCACTTTTGTTCTA-GTTTCCATTTTAATTA-TTAGAATCAATAAT
1 AGAATTTTTAATTTGGTCATCGCTTTTGTTCGAGGTTT-CAAATTAATTATTTA-ATTCAATAAT
* * * * * *
344 TGATTATAATTGAATAGGTTAATACTTAGAGCCTTCATTTCAAGTTTAATTTCATAACTAGTCC-
64 TGA-TAAAATT-AATAGATTAATA-TTAGAGCCTTCATTT-TAGGTTAATTT-AAAATTAGTCCT
408 TTTAATTTAGG
124 TTTAATTTAGG
* * *
419 AGAATTTTTTATTTGAT-ATTCGCTTATGTTCGAGGTT
1 AGAATTTTTAATTTGGTCA-TCGCTTTTGTTCGAGGTT
456 CCACTTTGAC
Statistics
Matches: 262, Mismatches: 37, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
138 59 0.23
139 193 0.74
140 10 0.04
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (134 bp):
AGAATTTTTAATTTGGTCATCGCTTTTGTTCGAGGTTTCAAATTAATTATTTAATTCAATAATTG
ATAAAATTAATAGATTAATATTAGAGCCTTCATTTTAGGTTAATTTAAAATTAGTCCTTTTAATT
TAGG
Found at i:4933 original size:9 final size:9
Alignment explanation
Indices: 4921--4946 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
4911 ATTTTTAATG
4921 ATATTAAAA
1 ATATTAAAA
4930 ATATTAAAA
1 ATATTAAAA
4939 ATATTAAA
1 ATATTAAA
4947 TTTAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATATTAAAA
Found at i:6125 original size:27 final size:27
Alignment explanation
Indices: 6063--6126 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
6053 TTAATCACAT
6063 AAAAATTTTATATTAAAATAGCAAATA
1 AAAAATTTTATATTAAAATAGCAAATA
***
6090 AATTTTTTTATATTAAAATAGCAAATA
1 AAAAATTTTATATTAAAATAGCAAATA
6117 AAAAATTTTA
1 AAAAATTTTA
6127 GTGGGACCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (27 bp):
AAAAATTTTATATTAAAATAGCAAATA
Found at i:6555 original size:103 final size:100
Alignment explanation
Indices: 6379--6580 Score: 341
Period size: 103 Copynumber: 2.0 Consensus size: 100
6369 CTTAAATGAC
*
6379 TGTTGAAAAGTAGTAGTAAATCAAAGAAGAAATCAAACTAAGATTCTGCAACTGAATGAGAAGAA
1 TGTTGAAAAGTAGTAGTAAATCAAAGAAGAAATCAAACTAAGATTCTGCAACTGAATCAGAAGAA
*
6444 GAAATACCCAGTTCATCATCACTTGTTCTTCTGAA
66 GAAATACCCAGTTCATCATCACTTGTTCCTCTGAA
* *
6479 TGTTGAAAAGTAGTAGTAAATCAAAGAAGAAGAAATCAAACTAAGATTGTGCAATTGAATCAGAA
1 TGTTGAAAAGTAGTAGTAAATC--A-AAGAAGAAATCAAACTAAGATTCTGCAACTGAATCAGAA
6544 GAAGAAATACCCAGTTCATCATCACTTGTTCCTCTGA
63 GAAGAAATACCCAGTTCATCATCACTTGTTCCTCTGA
6581 CCTCTGCATT
Statistics
Matches: 95, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
100 22 0.23
102 1 0.01
103 72 0.76
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (100 bp):
TGTTGAAAAGTAGTAGTAAATCAAAGAAGAAATCAAACTAAGATTCTGCAACTGAATCAGAAGAA
GAAATACCCAGTTCATCATCACTTGTTCCTCTGAA
Found at i:7303 original size:2 final size:2
Alignment explanation
Indices: 7296--7326 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7286 GCTTAATGCT
7296 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 T
7327 TTGTTTACGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8565 original size:13 final size:13
Alignment explanation
Indices: 8547--8593 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
8537 TGCGTCATAA
*
8547 ATTTATGACACGC
1 ATTTATGACGCGC
*
8560 ATTTATGACGCAC
1 ATTTATGACGCGC
8573 ATTTATGACGCGC
1 ATTTATGACGCGC
8586 ATTTATGA
1 ATTTATGA
8594 AGTTCATTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:8678 original size:85 final size:85
Alignment explanation
Indices: 8573--8738 Score: 201
Period size: 85 Copynumber: 2.0 Consensus size: 85
8563 TATGACGCAC
* * * * * * *
8573 ATTTATGACGCGCATTTATGAAGTT-CATTGAGCGTCATTGAATCCCCCGTCA-TAAATTAAAAT
1 ATTTATGACACGCATGTATG-ACTTACATTGAGCGTCATTGAAGCACACGTCATTAAAAT-AAAT
*
8636 GACACACATTTGTGTGTCATAA
64 GACACACATTCGTGTGTCATAA
* * *
8658 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACGTCATTAAAATAGATGA
1 ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACGTCATTAAAATAAATGA
8723 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
8739 GTGATTGTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
84 3 0.04
85 60 0.88
86 5 0.07
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACGTCATTAAAATAAATGA
CACACATTCGTGTGTCATAA
Found at i:15567 original size:15 final size:15
Alignment explanation
Indices: 15543--15573 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15533 AAGGAAGAAG
*
15543 AAGATTAAGAAAAGA
1 AAGATAAAGAAAAGA
15558 AAGATAAAGAAAAGA
1 AAGATAAAGAAAAGA
15573 A
1 A
15574 GGAAATGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (15 bp):
AAGATAAAGAAAAGA
Found at i:27867 original size:21 final size:21
Alignment explanation
Indices: 27817--27868 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
27807 AGATGAACTA
*
27817 TGGCTTTGCAAAAGTGTTGTT
1 TGGCTTTGTAAAAGTGTTGTT
*
27838 TGGCTTTGTAAAATTGTTGTT
1 TGGCTTTGTAAAAGTGTTGTT
27859 TGGCTTTGTA
1 TGGCTTTGTA
27869 GCAAATTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.08, G:0.27, T:0.48
Consensus pattern (21 bp):
TGGCTTTGTAAAAGTGTTGTT
Found at i:27957 original size:20 final size:21
Alignment explanation
Indices: 27919--27957 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27909 CATCAAGGTC
*
27919 TTTGTTGAGGTCATGAAATCT
1 TTTGTTGAGGCCATGAAATCT
27940 TTTGTTGAGGCCAT-AAAT
1 TTTGTTGAGGCCATGAAAT
27958 TCCTGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (21 bp):
TTTGTTGAGGCCATGAAATCT
Found at i:31801 original size:20 final size:20
Alignment explanation
Indices: 31776--31827 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
31766 CTACTAGAAC
31776 AGTATCGATACTGTTCAAGA
1 AGTATCGATACTGTTCAAGA
* *
31796 ATTATCGATATTGTTCAAGA
1 AGTATCGATACTGTTCAAGA
31816 AGTATCGATACT
1 AGTATCGATACT
31828 AAAACCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (20 bp):
AGTATCGATACTGTTCAAGA
Found at i:37180 original size:21 final size:22
Alignment explanation
Indices: 37137--37253 Score: 130
Period size: 23 Copynumber: 5.2 Consensus size: 22
37127 ATAAAATGAA
37137 CCGAAGTG-CCACATAGAATGTC
1 CCGAAG-GACCACATAGAATGTC
*
37159 CTGAAGGACCACATAG-ATGTC
1 CCGAAGGACCACATAGAATGTC
* *
37180 CTGAAGGACCACGTAGAAATGTC
1 CCGAAGGACCACATAG-AATGTC
*
37203 CCGAAAGACCACATAGAATTGTC
1 CCGAAGGACCACATAGAA-TGTC
**
37226 CCGAAGGACCATGTAGAATTGTC
1 CCGAAGGACCACATAGAA-TGTC
37249 CCGAA
1 CCGAA
37254 CGATCGCGTA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
21 21 0.25
22 15 0.18
23 47 0.57
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (22 bp):
CCGAAGGACCACATAGAATGTC
Found at i:37412 original size:44 final size:44
Alignment explanation
Indices: 37353--37467 Score: 212
Period size: 44 Copynumber: 2.6 Consensus size: 44
37343 TATATTCACA
* *
37353 TAGATTATGTTACATAGCTTATATCTTATGTTCATGTAATCTCG
1 TAGATCATGTCACATAGCTTATATCTTATGTTCATGTAATCTCG
37397 TAGATCATGTCACATAGCTTATATCTTATGTTCATGTAATCTCG
1 TAGATCATGTCACATAGCTTATATCTTATGTTCATGTAATCTCG
37441 TAGATCATGTCACATAGCTTATATCTT
1 TAGATCATGTCACATAGCTTATATCTT
37468 GTTCTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 69 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (44 bp):
TAGATCATGTCACATAGCTTATATCTTATGTTCATGTAATCTCG
Found at i:43585 original size:24 final size:24
Alignment explanation
Indices: 43481--43605 Score: 157
Period size: 23 Copynumber: 5.3 Consensus size: 24
43471 GAGTCGATGG
*
43481 TTCTACGCGGTCCTTCGGGAC-AA
1 TTCTACGTGGTCCTTCGGGACAAA
* * *
43504 TTCTATGTGGTACTTCAGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
* *
43528 -TCTATGTGGTCCTTAGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
43551 -TCTACGTGGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
* *
43574 TTCTACGCGGTCCTTCGGGAAAAA
1 TTCTACGTGGTCCTTCGGGACAAA
43598 TTCTACGT
1 TTCTACGT
43606 AGCACTTCGG
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
23 58 0.66
24 30 0.34
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:43615 original size:24 final size:24
Alignment explanation
Indices: 43536--43604 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
43526 AATCTATGTG
* * **
43536 GTCCTTAGGGACAAA-TCTACGTG
1 GTCCTTCGGGAAAAATTCTACGCA
* *
43559 GTCCTTCGGGACAAATTCTACGCG
1 GTCCTTCGGGAAAAATTCTACGCA
43583 GTCCTTCGGGAAAAATTCTACG
1 GTCCTTCGGGAAAAATTCTACG
43605 TAGCACTTCG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 14 0.33
24 28 0.67
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (24 bp):
GTCCTTCGGGAAAAATTCTACGCA
Found at i:45027 original size:17 final size:18
Alignment explanation
Indices: 44992--45029 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
44982 GAGTTGAAGT
* *
44992 TTCAAAAGTTATTTTGAA
1 TTCAAAAGTCATTTGGAA
45010 TTCAAAA-TCATTTGGAA
1 TTCAAAAGTCATTTGGAA
45027 TTC
1 TTC
45030 TTTGATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (18 bp):
TTCAAAAGTCATTTGGAA
Found at i:48597 original size:17 final size:17
Alignment explanation
Indices: 48575--48607 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
48565 GAATTAAGGT
*
48575 GTGAATATATGTTATAA
1 GTGAATATATGCTATAA
48592 GTGAATATATGCTATA
1 GTGAATATATGCTATA
48608 TGAAAGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.39
Consensus pattern (17 bp):
GTGAATATATGCTATAA
Found at i:48938 original size:24 final size:24
Alignment explanation
Indices: 48849--48973 Score: 114
Period size: 24 Copynumber: 5.3 Consensus size: 24
48839 GATTCGAGGG
* **
48849 TTCTACGTGGTCCTTCAAGAC-AA
1 TTCTATGTGGTCCTTCGGGACAAA
*
48872 TTCTATGTGGTCCTTCGGGA-TAA
1 TTCTATGTGGTCCTTCGGGACAAA
** * *
48895 TTCTACATGGTCTTTTGGGACAAA
1 TTCTATGTGGTCCTTCGGGACAAA
48919 TTCTATGCT-GTCCTTCGGGACAAA
1 TTCTATG-TGGTCCTTCGGGACAAA
*
48943 TTCTATGTGG-CACTTCGGTACAAA
1 TTCTATGTGGTC-CTTCGGGACAAA
*
48967 TTATATG
1 TTCTATG
48974 AATAGTGGTG
Statistics
Matches: 83, Mismatches: 14, Indels: 9
0.78 0.13 0.08
Matches are distributed among these distances:
23 37 0.45
24 45 0.54
25 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (24 bp):
TTCTATGTGGTCCTTCGGGACAAA
Found at i:58891 original size:8 final size:8
Alignment explanation
Indices: 58880--58907 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
58870 TTTTTTTTTT
58880 TTTTCTTC
1 TTTTCTTC
58888 TTTTCTTC
1 TTTTCTTC
58896 TTTTCTTC
1 TTTTCTTC
58904 TTTT
1 TTTT
58908 TCCTTTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTCTTC
Found at i:58915 original size:7 final size:7
Alignment explanation
Indices: 58903--58944 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
58893 TTCTTTTCTT
58903 CTTTTTC
1 CTTTTTC
58910 CTTTTTC
1 CTTTTTC
58917 CTTTTTC
1 CTTTTTC
58924 CTTTTTC
1 CTTTTTC
58931 CTTTTTC
1 CTTTTTC
58938 CTTTTTC
1 CTTTTTC
58945 TTATTTCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (7 bp):
CTTTTTC
Found at i:58915 original size:8 final size:8
Alignment explanation
Indices: 58877--58943 Score: 54
Period size: 7 Copynumber: 8.6 Consensus size: 8
58867 TTTTTTTTTT
*
58877 TTTTTTTC
1 TTTTTTCC
58885 TTCTTTT-C
1 TT-TTTTCC
*
58893 TTCTTTTCT
1 TT-TTTTCC
58902 TCTTTTTCC
1 T-TTTTTCC
58911 -TTTTTCC
1 TTTTTTCC
58918 -TTTTTCC
1 TTTTTTCC
58925 -TTTTTCC
1 TTTTTTCC
58932 -TTTTTCC
1 TTTTTTCC
58939 TTTTT
1 TTTTT
58944 CTTATTTCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
7 28 0.53
8 14 0.26
9 10 0.19
10 1 0.02
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCC
Found at i:58951 original size:21 final size:20
Alignment explanation
Indices: 58901--58951 Score: 84
Period size: 21 Copynumber: 2.5 Consensus size: 20
58891 TCTTCTTTTC
58901 TTCTTTTTCCTTTTTCCTTT
1 TTCTTTTTCCTTTTTCCTTT
58921 TTCCTTTTTCCTTTTTCCTTT
1 TT-CTTTTTCCTTTTTCCTTT
58942 TTCTTATTTC
1 TTCTT-TTTC
58952 TTTGTGAGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.17
21 24 0.83
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (20 bp):
TTCTTTTTCCTTTTTCCTTT
Found at i:65514 original size:22 final size:22
Alignment explanation
Indices: 65477--65536 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 22
65467 ATATAGTGAA
65477 CCTATAACCAGAACCTAGGTAGAG
1 CCTA-AACCA-AACCTAGGTAGAG
65501 CCTAAACCAAACCTAGGTAGAG
1 CCTAAACCAAACCTAGGTAGAG
*
65523 CCTAACCCAAACCT
1 CCTAAACCAAACCT
65537 TAATAGTCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 26 0.74
23 5 0.14
24 4 0.11
ACGTcount: A:0.38, C:0.32, G:0.15, T:0.15
Consensus pattern (22 bp):
CCTAAACCAAACCTAGGTAGAG
Found at i:72456 original size:42 final size:42
Alignment explanation
Indices: 72392--72488 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
72382 AATTGGTAAG
* *
72392 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGCAAGTCTTTCGAGCAAGATGATTAAA
* * * *
72434 TCCTTCGGGTCATCTGCCAGTCTTTCGAGCAAGATGA-TAAG
1 TCCTTCGGGCCATCAGCAAGTCTTTCGAGCAAGATGATTAAA
72475 TCC-TCTGGGCCATC
1 TCCTTC-GGGCCATC
72489 CGTAAGACCT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
40 2 0.04
41 13 0.28
42 32 0.68
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.30
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGCAAGTCTTTCGAGCAAGATGATTAAA
Found at i:72691 original size:256 final size:257
Alignment explanation
Indices: 72130--72781 Score: 963
Period size: 256 Copynumber: 2.5 Consensus size: 257
72120 TTCTTACATA
* **
72130 GTAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGATTAAATTTTTCGGGTCATCTGTC
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
* * * *
72195 AGTCTTTCAAGCAAGATGATAAGTCTTTTGGGCCATCTGTAAGACCATCGGGTAGGATGTTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCAGTAAGACCTTCGGGTAGGATGTTTTCA
* *
72260 CATGAATTTGAAAAAAGGGAAAGCGATTTTCAAAGTTTCTCATTTAATATATTCAGAAAATAAAA
131 CATGAATTTTAAAAAAGGGAAAGCAATTTTCAAAGTTTCTCATTTAATATATTCAGAAAATAAAA
** ** * * * *
72325 TTTTTGAAAATTATTAAAGTGATTTTCAAAGTTTCTTACCTATTAAACTATTTCCAAAATTG
196 TTTTTGAAAAGAAAGAAAATGATTTCCAAAGTTTATTACCTAGTAAACTATTTCCAAAATTG
*
72387 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGCC
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
* *
72452 AGTCTTTCGAGCAAGATGATAAGTCCTCTGGGCCATCCGTAAGACCTTCGGGTAGGATGTTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCAGTAAGACCTTCGGGTAGGATGTTTTCA
* *
72517 CATGAATTTTAAAAAATGGGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTCA-AAAA-AAA
131 CATGAATTTTAAAAAA-GGGAAAGCAATTTTCAAAGTTTCTCATTTAATATATTCAGAAAATAAA
72580 ATTTTTGAAAAGAAAGAAAATGATTTCCAAAGTTTATTACCTAGTAAACTATTTCCAAAATTG
195 ATTTTTGAAAAGAAAGAAAATGATTTCCAAAGTTTATTACCTAGTAAACTATTTCCAAAATTG
* * * * * *
72643 GTAAGTCATTCAGGCCATCAATAAGTCTTTCGAGTATGGTGATTAAATCCTTCGGGTCATCTATC
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
* *
72708 AGTCTTTCGAGCAAGATGATAAGT-CTTTCGGGCCATCAATAAGA-CTTACGGGTAAGATGTTTT
66 AGTCTTTCGAGCAAGATGATAAGTCCTTT-GGGCCATCAGTAAGACCTT-CGGGTAGGATGTTTT
*
72771 CACGTG-ATTTT
129 CACATGAATTTT
Statistics
Matches: 359, Mismatches: 33, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
255 11 0.03
256 172 0.48
257 140 0.39
258 36 0.10
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (257 bp):
GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTC
AGTCTTTCGAGCAAGATGATAAGTCCTTTGGGCCATCAGTAAGACCTTCGGGTAGGATGTTTTCA
CATGAATTTTAAAAAAGGGAAAGCAATTTTCAAAGTTTCTCATTTAATATATTCAGAAAATAAAA
TTTTTGAAAAGAAAGAAAATGATTTCCAAAGTTTATTACCTAGTAAACTATTTCCAAAATTG
Done.