Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005210.1 Hibiscus syriacus cultivar Beakdansim tig00011788_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: 76572
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:68 original size:2 final size:2
Alignment explanation
Indices: 61--89 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
51 TACACGTTTA
61 AT AT 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 AT AT A
90 AGAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1876 original size:7 final size:7
Alignment explanation
Indices: 1844--1895 Score: 50
Period size: 7 Copynumber: 6.9 Consensus size: 7
1834 AGATCTAACT
1844 GTTGACC
1 GTTGACC
*
1851 ATTGACC
1 GTTGACC
*
1858 AGTCTGATC
1 -GT-TGACC
1867 GTTGACC
1 GTTGACC
1874 GTTGACC
1 GTTGACC
1881 GGTATGACC
1 -GT-TGACC
1890 GTTGAC
1 GTTGAC
1896 TTTGACCCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 21 0.57
8 7 0.19
9 9 0.24
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (7 bp):
GTTGACC
Found at i:1878 original size:23 final size:23
Alignment explanation
Indices: 1844--1895 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1834 AGATCTAACT
* *
1844 GTTGACCATTGACCAGTCTGATC
1 GTTGACCATTGACCAGTATGACC
* *
1867 GTTGACCGTTGACCGGTATGACC
1 GTTGACCATTGACCAGTATGACC
1890 GTTGAC
1 GTTGAC
1896 TTTGACCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (23 bp):
GTTGACCATTGACCAGTATGACC
Found at i:2456 original size:27 final size:27
Alignment explanation
Indices: 2426--2484 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
2416 TGTTGATTAC
*
2426 AAAATTA-CAAAATTAACCC-TGAAGTGT
1 AAAATTACCAAAA-T-ACCCTTGAAGAGT
2453 AAAATTACCAAAATACCCTTGAAGAGT
1 AAAATTACCAAAATACCCTTGAAGAGT
2480 AAAAT
1 AAAAT
2485 GACTATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 4 0.14
27 20 0.69
28 5 0.17
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGAAGAGT
Found at i:8529 original size:228 final size:228
Alignment explanation
Indices: 8132--8592 Score: 877
Period size: 228 Copynumber: 2.0 Consensus size: 228
8122 ACTCATGAAG
*
8132 GAACCAATGAAGTGAGGGAAACCAAGATTAGTCTTCTCAACCATAGTTATGAAAATTTCAAGATG
1 GAACCAATGAAGTGAGGGAAACCAAGATTAGTCTTCTCAACCATAGCTATGAAAATTTCAAGATG
*
8197 AAATCAGATGAAGACATCAAAGCTATGAAAGATAGATTTCCATGATTGTCAATGGTCTCAAGGGA
66 AAATCAGATGAAGACATCAAAGCTATGAAAGATAGATTTCCATGATTATCAATGGTCTCAAGGGA
*
8262 TTTGGAGAAGTAATCCCTAATAAGAAGCTTATGAGAAAGATGATATACTCTCTTCCAAAGTCTTG
131 TTTGGAGAAATAATCCCTAATAAGAAGCTTATGAGAAAGATGATATACTCTCTTCCAAAGTCTTG
8327 GCAATCAAAGAATATGACGATTATAAAAGCTAA
196 GCAATCAAAGAATATGACGATTATAAAAGCTAA
8360 GAACCAATGAAGTGAGGGAAACCAAGATTAGTCTTCTCAACCATAGCTATGAAAATTTCAAGATG
1 GAACCAATGAAGTGAGGGAAACCAAGATTAGTCTTCTCAACCATAGCTATGAAAATTTCAAGATG
*
8425 AAATCAGATGAAGACATCAAAGCTATGAACGATAGATTTCCATGATTATCAATGGTCTCAAGGGA
66 AAATCAGATGAAGACATCAAAGCTATGAAAGATAGATTTCCATGATTATCAATGGTCTCAAGGGA
*
8490 TTTGGAGAAATAATCCCTAATAAGAAGCTTATGAGAAAGATGATATACTCTCTTCTAAAGTCTTG
131 TTTGGAGAAATAATCCCTAATAAGAAGCTTATGAGAAAGATGATATACTCTCTTCCAAAGTCTTG
8555 GCAATCAAAGAATATGACGATTATAAAAGCTAA
196 GCAATCAAAGAATATGACGATTATAAAAGCTAA
8588 GAACC
1 GAACC
8593 TTAAGTCACT
Statistics
Matches: 228, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
228 228 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (228 bp):
GAACCAATGAAGTGAGGGAAACCAAGATTAGTCTTCTCAACCATAGCTATGAAAATTTCAAGATG
AAATCAGATGAAGACATCAAAGCTATGAAAGATAGATTTCCATGATTATCAATGGTCTCAAGGGA
TTTGGAGAAATAATCCCTAATAAGAAGCTTATGAGAAAGATGATATACTCTCTTCCAAAGTCTTG
GCAATCAAAGAATATGACGATTATAAAAGCTAA
Found at i:14830 original size:50 final size:50
Alignment explanation
Indices: 14705--14830 Score: 157
Period size: 50 Copynumber: 2.5 Consensus size: 50
14695 GTAGCAGTAA
* * *
14705 AGCGCGCCCCCTGAAT-TGCGCTATACGCTGATTTGGCGTCACGTGGGCAT
1 AGCGCGCCCCCTG-ATCCGCACTATACGCTGATTTGGCGCCACGTGGGCAT
** * *
14755 AGCGCGCCCCCTGCCCCGCGA-TATACGGTGATTTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGATCCGC-ACTATACGCTGATTTGGCGCCACGTGGGCAT
14805 AGCGCGCCCCCTGATCCGCACTATAC
1 AGCGCGCCCCCTGATCCGCACTATAC
14831 TTAGGTATCT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
49 1 0.02
50 63 0.98
ACGTcount: A:0.16, C:0.35, G:0.29, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCCTGATCCGCACTATACGCTGATTTGGCGCCACGTGGGCAT
Found at i:15072 original size:17 final size:18
Alignment explanation
Indices: 15035--15075 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
15025 CTATTATGTA
*
15035 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
15053 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
15070 TTTACT
1 TTTACT
15076 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:15331 original size:111 final size:111
Alignment explanation
Indices: 15137--15358 Score: 374
Period size: 111 Copynumber: 2.0 Consensus size: 111
15127 TGGAAATCAT
*
15137 ATATCTCTACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
15202 TATTTAGTTGATTTATTTAATGCATGATTATTATATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
15248 ATATCTCGATACTTTGGTGATAC-AGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
1 ATATCTCGACACTTTGCTGATACGA-TAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
*
15312 CTAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
65 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
15359 TTTTTGTAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
110 1 0.01
111 103 0.99
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:16751 original size:93 final size:93
Alignment explanation
Indices: 16592--16785 Score: 379
Period size: 93 Copynumber: 2.1 Consensus size: 93
16582 GTGAGGCATC
*
16592 ATGAGTGGGTCGTGTTGTGGGAGGATCGACATCGGCGCCTTCCACGTAGAGAGCCCATTTTTATT
1 ATGAGTGGGTCGTGTTGTGGGAGGATCGACATCGACGCCTTCCACGTAGAGAGCCCATTTTTATT
16657 GACTTCTTGATTTATGCTGAGGATTATT
66 GACTTCTTGATTTATGCTGAGGATTATT
16685 ATGAGTGGGTCGTGTTGTGGGAGGATCGACATCGACGCCTTCCACGTAGAGAGCCCATTTTTATT
1 ATGAGTGGGTCGTGTTGTGGGAGGATCGACATCGACGCCTTCCACGTAGAGAGCCCATTTTTATT
16750 GACTTCTTGATTTATGCTGAGGATTATT
66 GACTTCTTGATTTATGCTGAGGATTATT
16778 ATGAGTGG
1 ATGAGTGG
16786 TTCAACAGTA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 100 1.00
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.34
Consensus pattern (93 bp):
ATGAGTGGGTCGTGTTGTGGGAGGATCGACATCGACGCCTTCCACGTAGAGAGCCCATTTTTATT
GACTTCTTGATTTATGCTGAGGATTATT
Found at i:17328 original size:3 final size:3
Alignment explanation
Indices: 17320--17372 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
17310 ACCTGCTCAG
* * * **
17320 GAC GAC GAC GAC GAC GAT GAC GAT GAC GAT GGT GAC GAC GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
17368 GAC GA
1 GAC GA
17373 TGATGATAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.25, G:0.36, T:0.08
Consensus pattern (3 bp):
GAC
Found at i:32723 original size:12 final size:12
Alignment explanation
Indices: 32706--32742 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
32696 ATTTATAAAA
32706 GAGGAGAGATGC
1 GAGGAGAGATGC
*
32718 GA-G-GAGATGT
1 GAGGAGAGATGC
32728 GAGGAGAGATGC
1 GAGGAGAGATGC
32740 GAG
1 GAG
32743 AAGCGGAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.32, C:0.05, G:0.51, T:0.11
Consensus pattern (12 bp):
GAGGAGAGATGC
Found at i:38640 original size:27 final size:27
Alignment explanation
Indices: 38602--38655 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
38592 AAATTTAAAT
38602 CAGTTGATGGAGTAAAAGGATTGTGAC
1 CAGTTGATGGAGTAAAAGGATTGTGAC
38629 CAGTTGATGGAGTAAAAGGATTGTGAC
1 CAGTTGATGGAGTAAAAGGATTGTGAC
38656 GGTTGTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.26
Consensus pattern (27 bp):
CAGTTGATGGAGTAAAAGGATTGTGAC
Found at i:45794 original size:18 final size:21
Alignment explanation
Indices: 45766--45806 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
45756 TCATTAGAAA
45766 TATATTAAAT-A-TTTTTCAT
1 TATATTAAATAATTTTTTCAT
45785 TATA-TAAATAATTTTTTCAT
1 TATATTAAATAATTTTTTCAT
45805 TA
1 TA
45807 ATTTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 5 0.25
20 10 0.50
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATTAAATAATTTTTTCAT
Found at i:45813 original size:21 final size:18
Alignment explanation
Indices: 45770--45813 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
45760 TAGAAATATA
45770 TTAAATATTTTTCATTAT
1 TTAAATATTTTTCATTAT
*
45788 ATAAATAATTTTTTCATTAAT
1 TTAAAT-A-TTTTTCATT-AT
45809 TTAAA
1 TTAAA
45814 ATAAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 5 0.24
19 1 0.05
20 9 0.43
21 6 0.29
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAATATTTTTCATTAT
Found at i:45928 original size:25 final size:25
Alignment explanation
Indices: 45881--45928 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
45871 TTTATTCATA
* * * *
45881 AATAATGTATTTTTAATATATATTT
1 AATAATATAATTTTAAAAAATATTT
45906 AATAATATAATTTTAAAAAATAT
1 AATAATATAATTTTAAAAAATAT
45929 AAAATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
AATAATATAATTTTAAAAAATATTT
Found at i:49318 original size:22 final size:22
Alignment explanation
Indices: 49293--49337 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
49283 CATCGAAGTT
49293 AGAAGAGTCCTCTTCTCTTGGG
1 AGAAGAGTCCTCTTCTCTTGGG
49315 AGAAGAGTCCTCTTCTCTTGGG
1 AGAAGAGTCCTCTTCTCTTGGG
49337 A
1 A
49338 ACTAGACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (22 bp):
AGAAGAGTCCTCTTCTCTTGGG
Found at i:54028 original size:22 final size:24
Alignment explanation
Indices: 53986--54038 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
53976 TTCATTTTAT
* *
53986 AAAACATTTAATTCACTTAAA-AG
1 AAAACATATAATTAACTTAAATAG
54009 AAAACATAT-ATTAACTTAAATAG
1 AAAACATATAATTAACTTAAATAG
54032 ACAAACA
1 A-AAACA
54039 AAAAGAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 11 0.42
24 5 0.19
ACGTcount: A:0.57, C:0.13, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAACATATAATTAACTTAAATAG
Found at i:54517 original size:59 final size:59
Alignment explanation
Indices: 54421--54758 Score: 451
Period size: 59 Copynumber: 5.9 Consensus size: 59
54411 AAAGTCCATA
* * *
54421 GGAAATTCATACAATTAGTATGATTTCCTTATAATTTTAGCACACTTAGTGCTCTATCT
1 GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
* * * * ** * *
54480 GGAAATTCATACACATAGTATAATTTCCCTATCATTTTAGCACACGAAGTGCCCTATAT
1 GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
* * **
54539 GG-AA---AT-C-C--A-TATGATTTCCCTCTCATTTTAGCACACGAAGTGCTCTATCT
1 GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
54589 GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
1 GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
* *
54648 GGAAATCCATACACTTAATATGATTTCCTTATCATTTTAGCACACTTAGTACTCTATCT
1 GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
*
54707 TGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGC
1 GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGC
54759 CCTTTTTGTA
Statistics
Matches: 248, Mismatches: 22, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
50 39 0.16
51 3 0.01
53 1 0.00
54 3 0.01
55 3 0.01
56 1 0.00
58 3 0.01
59 195 0.79
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.37
Consensus pattern (59 bp):
GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
Found at i:54577 original size:50 final size:50
Alignment explanation
Indices: 54502--54599 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 50
54492 ACATAGTATA
54502 ATTTCCCTATCATTTTAGCACACGAAGTGCCCTATATGGAAATCCATATG
1 ATTTCCCTATCATTTTAGCACACGAAGTGCCCTATATGGAAATCCATATG
* * *
54552 ATTTCCCTCTCATTTTAGCACACGAAGTGCTCTATCTGGAAATCCATA
1 ATTTCCCTATCATTTTAGCACACGAAGTGCCCTATATGGAAATCCATA
54600 CACTTAGTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (50 bp):
ATTTCCCTATCATTTTAGCACACGAAGTGCCCTATATGGAAATCCATATG
Found at i:54755 original size:31 final size:31
Alignment explanation
Indices: 54658--54756 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 31
54648 GGAAATCCAT
*
54658 ACACTTAATATGATTTCCTTATCATTTTAGC
1 ACACTTAGTATGATTTCCTTATCATTTTAGC
* * * ** *
54689 ACACTTAGTACT-CTAT-CTTGA--AATCCA-T
1 ACACTTAGTA-TGATTTCCTT-ATCATTTTAGC
54717 ACACTTAGTATGATTTCCTTATCATTTTAGC
1 ACACTTAGTATGATTTCCTTATCATTTTAGC
54748 ACACTTAGT
1 ACACTTAGT
54757 GCCCTTTTTG
Statistics
Matches: 48, Mismatches: 13, Indels: 14
0.64 0.17 0.19
Matches are distributed among these distances:
27 1 0.02
28 13 0.27
29 6 0.12
30 6 0.12
31 21 0.44
32 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (31 bp):
ACACTTAGTATGATTTCCTTATCATTTTAGC
Found at i:55122 original size:22 final size:20
Alignment explanation
Indices: 55084--55155 Score: 94
Period size: 22 Copynumber: 3.5 Consensus size: 20
55074 TGGCCATTCA
55084 GTATCGATACCCCTACTATG
1 GTATCGATACCCCTACTATG
55104 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACTATG
*
55126 GTATCGATACCCC--CTATCA
1 GTATCGATACCCCTACTAT-G
55145 GTATCGATACC
1 GTATCGATACC
55156 AAAATTAGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
18 4 0.08
19 11 0.23
20 13 0.27
22 20 0.42
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:55229 original size:95 final size:95
Alignment explanation
Indices: 55103--55306 Score: 239
Period size: 95 Copynumber: 2.1 Consensus size: 95
55093 CCCCTACTAT
* *
55103 GGTATCGATACTACCCTACTATGGTATCGATACCCCCTATCAG-TATCGATACCAAAATTAGCTT
1 GGTATCGATACTACCATACTATGGTAGCGATACCCCC-ATCAGATATCGATACCAAAATTAGCTT
*
55167 CGATGTGGCCTGGTATCGATACACTCACAAC
65 CGATGTGGCCTGGTATAGATACACTCACAAC
* ** * * * *
55198 GGTATCGATACTACTATGTTATGGTAGCGATACCCCCCTCCGATATCGATACCAACATTAGGTTC
1 GGTATCGATACTACCATACTATGGTAGCGATACCCCCATCAGATATCGATACCAAAATTAGCTTC
** * * * *
55263 GATGTTTCCTGGTATAGATACCCTTACCAT
66 GATGTGGCCTGGTATAGATACACTCACAAC
*
55293 GGTATCAATACTAC
1 GGTATCGATACTAC
55307 ATCGTTCGGT
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
94 3 0.03
95 88 0.97
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (95 bp):
GGTATCGATACTACCATACTATGGTAGCGATACCCCCATCAGATATCGATACCAAAATTAGCTTC
GATGTGGCCTGGTATAGATACACTCACAAC
Found at i:61038 original size:22 final size:24
Alignment explanation
Indices: 60996--61048 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
60986 TTCATTTTAT
* *
60996 AAAACATTTAATTCACTTAAA-AG
1 AAAACATATAATTAACTTAAATAG
61019 AAAACATAT-ATTAACTTAAATAG
1 AAAACATATAATTAACTTAAATAG
61042 ATAAACA
1 A-AAACA
61049 AAAAGAGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.38
23 11 0.42
24 5 0.19
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.28
Consensus pattern (24 bp):
AAAACATATAATTAACTTAAATAG
Found at i:61562 original size:59 final size:59
Alignment explanation
Indices: 61425--61767 Score: 437
Period size: 59 Copynumber: 5.9 Consensus size: 59
61415 AAATTTCATA
* * *
61425 GGAAATTCATACAATTAGTATGATTTCCTTATCATTGTAGCACACTTAGTG----ATCT
1 GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
* ** * ** * *
61480 AGAAATTTATACACTTAGTATGATTTCCCTATCATTTTAGCACACGAAGTGCCCTATAT
1 GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
* * * **
61539 GGAAATCCATACACTTAGTATGATTT-TTCTCTCATTTTAGCCCACGAAGTGCTCTATCT
1 GGAAATCCATACACTTAGTATGATTTCCT-TATCATTTTAGCACACTTAGTGCTCTATCT
*
61598 GGAAATCCATACACTTAGTATG-TATTCCTTATCATTTTAGTACACTTAGTGCTCTATCT
1 GGAAATCCATACACTTAGTATGAT-TTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
* *
61657 AGAAATCCATACACTTAGTATGATTTCCTTATAATTTTAGCACACTTAGTGCTCTATCT
1 GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
* *
61716 TGAAATCCATACACTTAGTATGATTTCCTTATCATTTTGGCACACTTAGTGC
1 GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGC
61768 CCTTTTTGTA
Statistics
Matches: 251, Mismatches: 29, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
55 44 0.18
58 1 0.00
59 204 0.81
60 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (59 bp):
GGAAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCT
Found at i:61734 original size:28 final size:28
Alignment explanation
Indices: 61638--61734 Score: 74
Period size: 28 Copynumber: 3.4 Consensus size: 28
61628 ATCATTTTAG
*
61638 TACACTTAGTGCTCTATCTAGAAATCCA
1 TACACTTAGTGCTCTATCTTGAAATCCA
* **
61666 TACACTTAGTATGAT-T-TCCTT-ATAATTTTA
1 TACACTTAG--TGCTCTAT-CTTGA-AA-TCCA
*
61696 GCACACTTAGTGCTCTATCTTGAAATCCA
1 -TACACTTAGTGCTCTATCTTGAAATCCA
61725 TACACTTAGT
1 TACACTTAGT
61735 ATGATTTCCT
Statistics
Matches: 51, Mismatches: 9, Indels: 18
0.65 0.12 0.23
Matches are distributed among these distances:
28 20 0.39
29 10 0.20
30 11 0.22
31 10 0.20
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (28 bp):
TACACTTAGTGCTCTATCTTGAAATCCA
Found at i:62131 original size:22 final size:20
Alignment explanation
Indices: 62093--62163 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 20
62083 TTGTCGTTCA
*
62093 GTATCGATACCCCTACTGTG
1 GTATCGATACCCCTACTATG
62113 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACTATG
* *
62135 GTATCGATACCCATA-TA-A
1 GTATCGATACCCCTACTATG
62153 GTATCGATACC
1 GTATCGATACC
62164 AAAATTACCT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
18 11 0.24
19 2 0.04
20 14 0.30
22 19 0.41
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:72725 original size:19 final size:19
Alignment explanation
Indices: 72701--72741 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
72691 TTTTAACAAC
72701 CTTAACCAACTCCTAACAG
1 CTTAACCAACTCCTAACAG
72720 CTTAACCAACTCCTAACAG
1 CTTAACCAACTCCTAACAG
72739 CTT
1 CTT
72742 GCTAACAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.37, G:0.05, T:0.24
Consensus pattern (19 bp):
CTTAACCAACTCCTAACAG
Done.