Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001473.1 Hibiscus syriacus cultivar Beakdansim tig00002856_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: 78299
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:143 original size:13 final size:13
Alignment explanation
Indices: 125--151 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
115 CGTGAGTTCT
125 GCCGCCGGCCACC
1 GCCGCCGGCCACC
138 GCCGCCGGCCACC
1 GCCGCCGGCCACC
151 G
1 G
152 TTTCCGGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.59, G:0.33, T:0.00
Consensus pattern (13 bp):
GCCGCCGGCCACC
Found at i:852 original size:3 final size:3
Alignment explanation
Indices: 838--992 Score: 187
Period size: 3 Copynumber: 53.0 Consensus size: 3
828 AATTATTTAT
*
838 TAA TAA -AA TAA TAA TAA TAA TAA -AA TAA TAA T-A TAC T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
882 TAA TATA TAA TAA TAA TAA TAA TAA TGC TAA TAA TAA TAA TAC TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
928 TAA TAA TAA TAA TAA T-A TAA TAA T-A TTA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
974 TAT TAA TAA TAAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA
993 AATGGATAAA
Statistics
Matches: 131, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
2 11 0.08
3 114 0.87
4 6 0.05
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2168 original size:2 final size:2
Alignment explanation
Indices: 2161--2192 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2151 TTAATAATGC
2161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2193 TCTAAAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6781 original size:6 final size:6
Alignment explanation
Indices: 6770--6802 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
6760 ACTCGAGTTC
6770 ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA ACC
1 ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA ACC
6803 GTCTGTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCAAA
Found at i:11998 original size:20 final size:20
Alignment explanation
Indices: 11969--12011 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
11959 AACAACACAG
11969 TCTTTCGTTTTCCATAATAA
1 TCTTTCGTTTTCCATAATAA
*
11989 TCTTTTGTTTTCCATAATAA
1 TCTTTCGTTTTCCATAATAA
12009 TCT
1 TCT
12012 AACTCAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (20 bp):
TCTTTCGTTTTCCATAATAA
Found at i:18192 original size:81 final size:81
Alignment explanation
Indices: 18056--18355 Score: 281
Period size: 81 Copynumber: 3.7 Consensus size: 81
18046 AAAGTAACGA
* *
18056 CGTTTGTTGAAAAAACGCCACTA-TAGATGAACCCTATTACGGCATTTTTATACAAACACTGCT-
1 CGTTTGTTGAAAAAA-GCCACTATTAG-TGAA-CCTATTGCGGCGTTTTTATACAAACACTGCTA
* *
18119 AAGTATTACTCTTTTGTGG
63 AAGTAATACTCTTTTGCGG
*
18138 CGTTTGTTGAAAAAAGCCACT-TTAGTCGAAACCTATTGCGGCGTTTTTATACAAACA-TCGTTA
1 CGTTTGTTGAAAAAAGCCACTATTAGT-G-AACCTATTGCGGCGTTTTTATACAAACACT-GCTA
** **
18201 AAGTAATACT-TTGTCACAT
63 AAGTAATACTCTT-TTGCGG
* * * * * * * *
18220 CGTTTGTTGAGAAACGCCACTATGAATGAACCTATTGTGGCGTTTGTATAAAAACGCTGCTAAAG
1 CGTTTGTTGAAAAAAGCCACTATTAGTGAACCTATTGCGGCGTTTTTATACAAACACTGCTAAAG
*
18285 TACA-ACTCTGTTGCGG
66 TA-ATACTCTTTTGCGG
* * *
18301 TGTTTGTTGAAAAAAACCACTATATA-TGACCCTATTGCGGCGTTTTTATACAAAC
1 CGTTTGTTGAAAAAAGCCACTAT-TAGTGAACCTATTGCGGCGTTTTTATACAAAC
18356 GCCACTAAAC
Statistics
Matches: 175, Mismatches: 32, Indels: 23
0.76 0.14 0.10
Matches are distributed among these distances:
80 2 0.01
81 119 0.68
82 51 0.29
83 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (81 bp):
CGTTTGTTGAAAAAAGCCACTATTAGTGAACCTATTGCGGCGTTTTTATACAAACACTGCTAAAG
TAATACTCTTTTGCGG
Found at i:18251 original size:163 final size:163
Alignment explanation
Indices: 18056--18355 Score: 394
Period size: 163 Copynumber: 1.8 Consensus size: 163
18046 AAAGTAACGA
* *
18056 CGTTTGTTGAAAAAACGCCACTATAGATGAACCCTATTACGGCATTTTTATACAAACACTGCT-A
1 CGTTTGTTGAAAAAACGCCACTATAGATGAA-CCTATTACGGCATTTGTATAAAAACACTGCTAA
** * * *
18120 AGTATTACTCTTTTGTGGCGTTTGTTGAAAAAAGCCACT-T-TAGTCGAAACCTATTGCGGCGTT
65 AGTACAACTCTGTTGCGGCGTTTGTTGAAAAAAACCACTATATA-T-G-AACCTATTGCGGCGTT
18183 TTTATACAAACATCGTTAAAGTAATACTTTGTCACAT
127 TTTATACAAACATCGTTAAAGTAATACTTTGTCACAT
* ** * *
18220 CGTTTGTTG-AGAAACGCCACTAT-GAATGAACCTATTGTGGCGTTTGTATAAAAACGCTGCTAA
1 CGTTTGTTGAAAAAACGCCACTATAG-ATGAACCTATTACGGCATTTGTATAAAAACACTGCTAA
* *
18283 AGTACAACTCTGTTGCGGTGTTTGTTGAAAAAAACCACTATATATGACCCTATTGCGGCGTTTTT
65 AGTACAACTCTGTTGCGGCGTTTGTTGAAAAAAACCACTATATATGAACCTATTGCGGCGTTTTT
18348 ATACAAAC
130 ATACAAAC
18356 GCCACTAAAC
Statistics
Matches: 118, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
162 52 0.44
163 53 0.45
164 11 0.09
165 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (163 bp):
CGTTTGTTGAAAAAACGCCACTATAGATGAACCTATTACGGCATTTGTATAAAAACACTGCTAAA
GTACAACTCTGTTGCGGCGTTTGTTGAAAAAAACCACTATATATGAACCTATTGCGGCGTTTTTA
TACAAACATCGTTAAAGTAATACTTTGTCACAT
Found at i:18396 original size:81 final size:81
Alignment explanation
Indices: 18136--18386 Score: 202
Period size: 81 Copynumber: 3.1 Consensus size: 81
18126 ACTCTTTTGT
* * * * * ** **
18136 GGCGTTTGTTGAAAAAAGCCACT-TTAGTCGAAACCTATTGCGGCGTTTTTATACAAACATCGTT
1 GGCGTTTGTTGAAAAAAACCACTATGAAT-G-AACCTATTGCGGCGTTTGTATAAAAACGCCACT
* *
18200 AAAGTA-ATACTTTGTCAC
64 AAACTACA-ACTCTGTCAC
** * ** * **
18218 ATCGTTTGTTGAGAAACGCCACTATGAATGAACCTATTGTGGCGTTTGTATAAAAACGCTGCTAA
1 GGCGTTTGTTGAAAAAAACCACTATGAATGAACCTATTGCGGCGTTTGTATAAAAACGCCACTAA
* **
18283 AGTACAACTCTGTTGC
66 ACTACAACTCTGTCAC
* * * *
18299 GGTGTTTGTTGAAAAAAACCACTAT-ATATGACCCTATTGCGGCGTTTTTATACAAACGCCACTA
1 GGCGTTTGTTGAAAAAAACCACTATGA-ATGAACCTATTGCGGCGTTTGTATAAAAACGCCACTA
*
18363 AACTACTACTCTGTCAC
65 AACTACAACTCTGTCAC
18380 GGCGTTT
1 GGCGTTT
18387 TGAATAAAAA
Statistics
Matches: 133, Mismatches: 33, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
80 1 0.01
81 108 0.81
82 21 0.16
83 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (81 bp):
GGCGTTTGTTGAAAAAAACCACTATGAATGAACCTATTGCGGCGTTTGTATAAAAACGCCACTAA
ACTACAACTCTGTCAC
Found at i:28071 original size:139 final size:139
Alignment explanation
Indices: 27919--28193 Score: 532
Period size: 139 Copynumber: 2.0 Consensus size: 139
27909 AACAATATAT
27919 ATATATATATATAAGGGTTGTAAGACATTAAATATATACATACATATAATAATTTATTGTAACCA
1 ATATATATATATAAGGGTTGTAAGACATTAAATATATACATACATATAATAATTTATTGTAACCA
27984 TAATATCTACTGTGTATGAAAACAACTATGTAAGATACAAAGCATTCGTACACAAACAAATAAAT
66 TAATATCTACTGTGTATGAAAACAACTATGTAAGATACAAAGCATTCGTACACAAACAAATAAAT
28049 AAATAATAC
131 AAATAATAC
*
28058 ATATATATATATAAGGGTTGTAAGACATTAAATATATACATACATATAATAATTTATTGTAACCT
1 ATATATATATATAAGGGTTGTAAGACATTAAATATATACATACATATAATAATTTATTGTAACCA
*
28123 TAATATCTACTGTGTATGAAAACAACTATGTAAGATACAAAGCATTCGTACACAAATAAATAAAT
66 TAATATCTACTGTGTATGAAAACAACTATGTAAGATACAAAGCATTCGTACACAAACAAATAAAT
28188 AAATAA
131 AAATAA
28194 ATAATACACA
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 134 1.00
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (139 bp):
ATATATATATATAAGGGTTGTAAGACATTAAATATATACATACATATAATAATTTATTGTAACCA
TAATATCTACTGTGTATGAAAACAACTATGTAAGATACAAAGCATTCGTACACAAACAAATAAAT
AAATAATAC
Found at i:29606 original size:24 final size:26
Alignment explanation
Indices: 29579--29664 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 26
29569 ATGTAACCTG
* *
29579 TAAAATAA-AATAAAAAT-GTTATTA
1 TAAAATAATAATAAAAATAGTGATAA
*
29603 T-AAATAATAATAATAATAGTGATAA
1 TAAAATAATAATAAAAATAGTGATAA
* * *
29628 TAATAATAATAATAATAATAATAATAA
1 TAA-AATAATAATAAAAATAGTGATAA
29655 TAATAATAAT
1 TAA-AATAAT
29665 CCGGACAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.11
24 9 0.17
25 6 0.11
26 1 0.02
27 31 0.58
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (26 bp):
TAAAATAATAATAAAAATAGTGATAA
Found at i:29611 original size:3 final size:3
Alignment explanation
Indices: 29605--29664 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
29595 TGTTATTATA
* *
29605 AAT AAT AAT AAT AAT AGT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29653 AAT AAT AAT AAT
1 AAT AAT AAT AAT
29665 CCGGACAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:30767 original size:58 final size:59
Alignment explanation
Indices: 30671--30785 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 59
30661 ATCATGTGAT
* *
30671 ATGATACATTTTGTAACTTTTAATAGCCGAGAGACTTAATAAAACAACATTCTATAGAC
1 ATGATACATTTTGTAACTTTTAATAGCCAAGAGACTTAATAAAACAACATCCTATAGAC
* * * *
30730 ATGAT-CATTTTGTAACTTTTAATAGTCAAGGGACTTAATAAAGCAATATCCTATAG
1 ATGATACATTTTGTAACTTTTAATAGCCAAGAGACTTAATAAAACAACATCCTATAG
30786 TCGGGGAACC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 45 0.90
59 5 0.10
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (59 bp):
ATGATACATTTTGTAACTTTTAATAGCCAAGAGACTTAATAAAACAACATCCTATAGAC
Found at i:31863 original size:2 final size:2
Alignment explanation
Indices: 31856--31880 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31846 AAATTTATTA
31856 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 A
31881 AAATAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31974 original size:36 final size:35
Alignment explanation
Indices: 31934--32014 Score: 90
Period size: 36 Copynumber: 2.3 Consensus size: 35
31924 ACTAAACCCA
* *
31934 TCCCCGTCCCGGTCCCCGTTTAACATAAACGATTTT
1 TCCCCGTCCC-GTCCCCATATAACATAAACGATTTT
* * *
31970 TCCCCATCTCCGTCCCCATATAGCATAAATGATTTT
1 TCCCCGTC-CCGTCCCCATATAACATAAACGATTTT
*
32006 TTCCCGTCC
1 TCCCCGTCC
32015 TCGTTTAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
35 1 0.03
36 34 0.92
37 2 0.05
ACGTcount: A:0.20, C:0.37, G:0.11, T:0.32
Consensus pattern (35 bp):
TCCCCGTCCCGTCCCCATATAACATAAACGATTTT
Found at i:40636 original size:16 final size:17
Alignment explanation
Indices: 40586--40636 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
40576 AAAAAAATTA
40586 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
40603 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
40618 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
40634 AAT
1 AAT
40637 CAAGTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 3 0.11
15 8 0.29
16 10 0.36
17 4 0.14
18 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:41327 original size:2 final size:2
Alignment explanation
Indices: 41320--41357 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
41310 AGATTCATTC
41320 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41358 GATTGTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42017 original size:87 final size:87
Alignment explanation
Indices: 41860--42021 Score: 252
Period size: 87 Copynumber: 1.9 Consensus size: 87
41850 ATATTATATC
* * *
41860 ATTTAACTGAAAATATTATCAAGCACAATAACATATTAGGTATCGCTTATATAATGCAATAAGTA
1 ATTTAACCGAAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGCAATAAGTA
*
41925 GCGCTTATATAATAAAATATGT
66 ACGCTTATATAATAAAATATGT
* * * *
41947 ATTTAACCGGAAATATTATCAAGTACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCGAAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGCAATAAGTA
42012 ACGCTTATAT
66 ACGCTTATAT
42022 TGACCTATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.33
Consensus pattern (87 bp):
ATTTAACCGAAAATATTATCAAGCACAATAACAAATTAGGTAGCGCTTATATAATGCAATAAGTA
ACGCTTATATAATAAAATATGT
Found at i:42584 original size:182 final size:181
Alignment explanation
Indices: 42271--42847 Score: 826
Period size: 182 Copynumber: 3.2 Consensus size: 181
42261 ATTTATATAA
* * *
42271 TTTACTTGTTATATTGA-TATGGACCGATACATTTGTATAAAGTATCGACACGTTTTAGGCGCTA
1 TTTACCTGTTATATT-ACTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTA
*
42335 TAACTTCTTCTCTTTTAAA-TATCAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAAT
65 TAACTT-TACTCTTTTAAATTA-CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAAT
** ** * * *
42399 ATATCCAATAGCTTTTTACCGGTTTTATCAT-TTCGAAACCTGTTTTGTCATATT
128 ATATCCGGTAGCGGTTTACCGGTTTTATCATAAT-GACACCTGTTTTATCATATT
* * *
42453 ATTACCTGTTATATTACTATGGATCGATACATTTGTATAAAGTATCGACATTTTTTAGGGGCTAT
1 TTTACCTGTTATATTACTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTAT
42518 AACTTATACTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATAT
66 AACTT-TACTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATAT
*
42583 ATCCGGTAACGGTTTACCGGTTTTATCATAATGACA-CTGGTTTTATCATATT
130 ATCCGGTAGCGGTTTACCGGTTTTATCATAATGACACCT-GTTTTATCATATT
* ** * *
42635 TTTACCTGTTATATTTCTATTTATCGATATATTTGTATAAAGTATCGACACTTTATAGGCGCTAT
1 TTTACCTGTTATATTACTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTAT
*
42700 AAC-TTA-TCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATTGACACTTTCAATATA
66 AACTTTACTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATA
*
42763 TCCGGTAGCGGTTTACCGGTTTTATCATAATGACACCGGTTTTATCATATT
131 TCCGGTAGCGGTTTACCGGTTTTATCATAATGACACCTGTTTTATCATATT
* *
42814 TTTACCTGTTATA-TAGTTATGAATCGATACATTT
1 TTTACCTGTTATATTA-CTATGGATCGATACATTT
42848 TTCATTTGTA
Statistics
Matches: 357, Mismatches: 32, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
178 1 0.00
179 130 0.36
180 3 0.01
181 4 0.01
182 216 0.61
183 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (181 bp):
TTTACCTGTTATATTACTATGGATCGATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTAT
AACTTTACTCTTTTAAATTACAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATA
TCCGGTAGCGGTTTACCGGTTTTATCATAATGACACCTGTTTTATCATATT
Found at i:43935 original size:16 final size:17
Alignment explanation
Indices: 43893--43935 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
43883 AATTTTTTCA
*
43893 AAAATATATGAAATTTAT
1 AAAATAT-TTAAATTTAT
43911 AAAAT-TTTAAA-TTAT
1 AAAATATTTAAATTTAT
43926 AAAATATTTA
1 AAAATATTTA
43936 TTATTGTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
16 8 0.35
17 1 0.04
18 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAAATATTTAAATTTAT
Found at i:44443 original size:322 final size:323
Alignment explanation
Indices: 43737--44723 Score: 1391
Period size: 322 Copynumber: 3.0 Consensus size: 323
43727 TATTAAATTC
43737 TAATTTTATTAAAAATGAATAAACATTATTAACTTTTGTTAAAAATTAATAATTAATGAATAATA
1 TAATTTTATTAAAAATGAATAAACATTATTAA-TTTTGTTAAAAA-TAATAATTAATGAATAATA
43802 ATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATA-TTTTTTATATTTTTAAACAAT
64 ATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTATATTTTTAAAC---
* *
43866 TAATTTTAAAAGTCAATAATTTTTTCAAAAATATATGAAATTTATAAAATTTTAAATTATAAAAT
126 -AA---T--AAGTCAATAAATTTTTCAAAAATATATGAAATTTATAAATTTTTAAATTATAAAAT
*
43931 ATTTATTATTGTCATCATCATCATTTTGCAAAAGAAATACTGGTTATAAAACTTTTATAAAATTA
185 A-TTATTA---TCATCATCATCATTTTG-TAAA-AAATACTGGTTATAAAACTTTTATAAAATTA
* *
43996 TTCATATTTTAAAATACTCACCCTCAAAGTTTTTCTATACTAAATTATACATATTGTGTAATTTC
244 TTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAAATTATACATATTGTGTAATTTC
44061 ATGCAAAAATCAAAA
309 ATGCAAAAATCAAAA
* *
44076 TAATTTTATTAAAAAAGAATAAACATTATTAAAATTTGTTAAAAATAATAATTAATGAATAATAA
1 TAATTTTATTAAAAATGAATAAACATTATT-AATTTTGTTAAAAATAATAATTAATGAATAATAA
*
44141 TTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTATATTTTTAAACAATA
65 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTATATTTTTAAACAATA
*
44206 AGTCAATAAATTTTTCAAAAATATAT-AACATTTAT-AATTTTTAAATTGTAAAATA-T-TTATC
130 AGTCAATAAATTTTTCAAAAATATATGAA-ATTTATAAATTTTTAAATTATAAAATATTATTATC
*
44267 ATCATCATCATCTTGTAAACAAATACTGGTTATAAAACTTTTATAAAATTATTCATATTTTAAAA
194 ATCATCATCATTTTGTAAA-AAATACTGGTTATAAAACTTTTATAAAATTATTCATATTTTAAAA
* * *
44332 TACTTACCCTCAAAGTTTTCCTATACTATATTATACATATTGTATAATTTCAAGCAAAAATCAAA
258 TACTTACCCTCAAAGTTTTCCTATACTAAATTATACATATTGTGTAATTTCATGCAAAAATCAAA
44397 A
323 A
44398 TAATTTTATTAAAAATGAATAAACATTATTAATTGTTGTTAAAAATAATAATTAATGAATAATAA
1 TAATTTTATTAAAAATGAATAAACATTATTAATT-TTGTTAAAAATAATAATTAATGAATAATAA
** * *
44463 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTAAACAATTAATTT---TA
65 TTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTA-TATT--TTTAAACA
* *
44525 A-AAGTCAATAAA-TTTTAAAAAATATATGAAATTTTTAAATTTTTAAATTATAAAATATTTATT
127 ATAAGTCAATAAATTTTTCAAAAATATATGAAATTTATAAATTTTTAAATTATAAAATA-TTATT
* * * *
44588 ATCATCATCATCATTTTGTAAAAGAAGTAATAGTTATAAAATTTTTAAAAAATTATTCATATTTT
191 ATCATCATCATCATTTTGTAAAA-AA-TACTGGTTATAAAACTTTTATAAAATTATTCATATTTT
* * * * * *
44653 AAAATATTTAACCTCAAAGTTTTCATATACTAGATTTTACATATCGTGTAATTTCATGCAAAAAT
254 AAAATACTTACCCTCAAAGTTTTCCTATACTAAATTATACATATTGTGTAATTTCATGCAAAAAT
*
44718 TAAAA
319 CAAAA
44723 T
1 T
44724 TTATCGAGTT
Statistics
Matches: 596, Mismatches: 38, Indels: 42
0.88 0.06 0.06
Matches are distributed among these distances:
320 19 0.03
321 35 0.06
322 217 0.36
323 21 0.04
324 25 0.04
325 99 0.17
326 3 0.01
327 1 0.00
329 20 0.03
330 32 0.05
332 1 0.00
335 2 0.00
338 61 0.10
339 58 0.10
340 2 0.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (323 bp):
TAATTTTATTAAAAATGAATAAACATTATTAATTTTGTTAAAAATAATAATTAATGAATAATAAT
TCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTTATATTTTTAAACAATAA
GTCAATAAATTTTTCAAAAATATATGAAATTTATAAATTTTTAAATTATAAAATATTATTATCAT
CATCATCATTTTGTAAAAAATACTGGTTATAAAACTTTTATAAAATTATTCATATTTTAAAATAC
TTACCCTCAAAGTTTTCCTATACTAAATTATACATATTGTGTAATTTCATGCAAAAATCAAAA
Found at i:47931 original size:17 final size:16
Alignment explanation
Indices: 47887--47940 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
47877 AATAATAAAC
47887 AAAACAAAAATAAAGAA
1 AAAACAAAAAT-AAGAA
**
47904 AAATGATAAAATAAGTAA
1 AAAACA-AAAATAAG-AA
47922 AAAACAAAAATAA-AA
1 AAAACAAAAATAAGAA
47937 AAAA
1 AAAA
47941 TAATTAGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 6 0.19
17 14 0.45
18 11 0.35
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.11
Consensus pattern (16 bp):
AAAACAAAAATAAGAA
Found at i:48035 original size:17 final size:17
Alignment explanation
Indices: 48000--48037 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
47990 AAAAGAAAGA
*
48000 AAAAATAAAAGCAGAAT
1 AAAAATAAAAGCAAAAT
48017 AAAAATAAAA-CAAACAT
1 AAAAATAAAAGCAAA-AT
48034 AAAA
1 AAAA
48038 CAAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.76, C:0.08, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAAATAAAAGCAAAAT
Found at i:48202 original size:3 final size:3
Alignment explanation
Indices: 48180--48320 Score: 89
Period size: 3 Copynumber: 47.3 Consensus size: 3
48170 ATACATATAT
* * *
48180 ATA AT- ATA ATA TACA ATA ATA ATA ATA A-A ATA TATA ATG GTA A-A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
* * ** * *
48224 ACA A-A AAA ATA ATA ATA ATA ACG ATA ATA ATA ATA A-A AAA ATG A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
48269 ATA TATA TATA ATA TATA ATA ATA ATA ATA ATA A-A ATA TATA GTA ATA
1 ATA -ATA -ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
48317 ATA A
1 ATA A
48321 AAACGTAATA
Statistics
Matches: 110, Mismatches: 16, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
2 13 0.12
3 79 0.72
4 18 0.16
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:48230 original size:99 final size:94
Alignment explanation
Indices: 48105--48310 Score: 276
Period size: 102 Copynumber: 2.1 Consensus size: 94
48095 TGAAATACAA
*
48105 AATAAAATAT-T--TGGTAAAATAAAAAA-ATATAATAATAACCATAATAATAATAAAAAAGGAG
1 AATAAAATATATAATGGTAAAACAAAAAATA-ATAATAATAACCATAATAATAATAAAAAA--A-
48166 TGAAATACATATATATAATATAATATACAATAATAAT
62 TGAAAT--ATATATATAATAT-ATA-ACAATAATAAT
*
48203 AATAAAATATATAATGGTAAAACAAAAAAATAATAATAATAACGATAATAATAATAAAAAAATGA
1 AATAAAATATATAATGGTAAAAC-AAAAAATAATAATAATAACCATAATAATAATAAAAAAATGA
*
48268 AATATATATATAATATATAATAATAATAAT
65 AATATATATATAATATATAACAATAATAAT
48298 AATAAAATATATA
1 AATAAAATATATA
48311 GTAATAATAA
Statistics
Matches: 100, Mismatches: 3, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
95 23 0.23
96 3 0.03
97 13 0.13
98 10 0.10
99 7 0.07
100 1 0.01
101 8 0.08
102 34 0.34
103 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.29
Consensus pattern (94 bp):
AATAAAATATATAATGGTAAAACAAAAAATAATAATAATAACCATAATAATAATAAAAAAATGAA
ATATATATATAATATATAACAATAATAAT
Found at i:48261 original size:37 final size:35
Alignment explanation
Indices: 48194--48322 Score: 114
Period size: 37 Copynumber: 3.5 Consensus size: 35
48184 TATAATATAC
**
48194 AATAATAATAATAAAATATATAATGGTAAAACAAAAA
1 AATAATAATAATAAAATA-ATAATAATAAAA-AAAAA
* *
48231 AATAATAATAATAACGATAATAATAATAAAAAAATGA
1 AATAATAATAATAA-AATAATAATAATAAAAAAA-AA
* *
48268 AATATATATATAATATATAATAATAATAATAATAAAATA
1 AATA-ATA-ATAATA-A-AATAATAATAATAAAAAAAAA
* *
48307 TATAGTAATAATAAAA
1 AATAATAATAATAAAA
48323 ACGTAATATA
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
35 2 0.03
36 4 0.05
37 35 0.45
38 8 0.10
39 10 0.13
40 18 0.23
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (35 bp):
AATAATAATAATAAAATAATAATAATAAAAAAAAA
Found at i:48330 original size:24 final size:24
Alignment explanation
Indices: 48277--48345 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
48267 AAATATATAT
* *
48277 ATAATATATAATAATAATAATAAT
1 ATAATATATAATAATAATAAAAAC
* *
48301 AAAATATATAGTAATAATAAAAAC
1 ATAATATATAATAATAATAAAAAC
* *
48325 GTAATATACTAAGAA-AATAAA
1 ATAATATA-TAATAATAATAAA
48346 TAAAAGAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
24 32 0.89
25 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (24 bp):
ATAATATATAATAATAATAAAAAC
Found at i:48851 original size:7 final size:7
Alignment explanation
Indices: 48839--48863 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
48829 AAAATAGTAA
48839 AATAAAT
1 AATAAAT
48846 AATAAAT
1 AATAAAT
48853 AATAAAT
1 AATAAAT
48860 AATA
1 AATA
48864 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:48868 original size:2 final size:2
Alignment explanation
Indices: 48861--48907 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
48851 ATAATAAATA
* * *
48861 AT AT AT AT AT AT AT AT AT AT AT GT TT AT -T AT A- AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48901 AT AT AT A
1 AT AT AT A
48908 CGAGTATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:49322 original size:18 final size:18
Alignment explanation
Indices: 49290--49337 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
49280 TTAAACCCCA
49290 TTTTA-TTTTTC-TTTTC
1 TTTTATTTTTTCTTTTTC
49306 TTTTATTTTTTCTTTTTC
1 TTTTATTTTTTCTTTTTC
*
49324 TTTTGTTTTTTCTT
1 TTTTATTTTTTCTT
49338 CTTCAAGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 5 0.17
17 6 0.21
18 18 0.62
ACGTcount: A:0.04, C:0.10, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTATTTTTTCTTTTTC
Found at i:52529 original size:2 final size:2
Alignment explanation
Indices: 52522--52558 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
52512 TATTTTACAT
52522 TA TA TA 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 TA TA TA T
52559 TGAAATCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53102 original size:16 final size:17
Alignment explanation
Indices: 53052--53102 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
53042 TAAAAATTTA
53052 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
53069 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
53084 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
53100 AAT
1 AAT
53103 CAAGTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 3 0.11
15 8 0.29
16 10 0.36
17 4 0.14
18 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:53160 original size:16 final size:16
Alignment explanation
Indices: 53139--53175 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
53129 CCAAAATAAA
53139 AGTGAGAAGATAGTTG
1 AGTGAGAAGATAGTTG
*
53155 AGTGAGAAGATAGTTT
1 AGTGAGAAGATAGTTG
53171 AGTGA
1 AGTGA
53176 CAAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.27
Consensus pattern (16 bp):
AGTGAGAAGATAGTTG
Found at i:54021 original size:20 final size:20
Alignment explanation
Indices: 53996--54035 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
53986 AATGTTAACT
53996 TGTGATTGTATGCATGAGAG
1 TGTGATTGTATGCATGAGAG
*
54016 TGTGATTGTATGCGTGAGAG
1 TGTGATTGTATGCATGAGAG
54036 AGTAAGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.05, G:0.38, T:0.35
Consensus pattern (20 bp):
TGTGATTGTATGCATGAGAG
Found at i:61325 original size:21 final size:20
Alignment explanation
Indices: 61267--61326 Score: 50
Period size: 24 Copynumber: 2.8 Consensus size: 20
61257 ATCTCCAGTT
*
61267 TCATCATC-TCATCCTTCAAA
1 TCATCATCTTCA-CCATCAAA
61287 TCTATCATCTTTTACACCATCAACA
1 TC-ATCATC--TT-CACCATCAA-A
61312 TCATCATCTTCACCA
1 TCATCATCTTCACCA
61327 CATTATTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
20 2 0.06
21 11 0.33
22 2 0.06
24 13 0.39
25 5 0.15
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (20 bp):
TCATCATCTTCACCATCAAA
Found at i:66375 original size:46 final size:47
Alignment explanation
Indices: 66308--66398 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 47
66298 AAATGAATAC
* * **
66308 TAAACGAACATGTTCACGAACAAGTTTGCGAACAT-TAAACGAACGT
1 TAAACAAACATGATCACGAACAAGTTCACGAACATATAAACGAACGT
* * *
66354 TAAACAAACATGATCATGAACACGTTCATGAACATATAAACGAAC
1 TAAACAAACATGATCACGAACAAGTTCACGAACATATAAACGAAC
66399 ATGTTCACGA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 28 0.76
47 9 0.24
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (47 bp):
TAAACAAACATGATCACGAACAAGTTCACGAACATATAAACGAACGT
Found at i:66439 original size:23 final size:23
Alignment explanation
Indices: 66369--66440 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
66359 AAACATGATC
*
66369 ATGAACACGTTCATGAACATATAA
1 ATGAACATGTTCATGAACA-ATAA
* * * *
66393 ACGAACATGTTCACGAATATTAA
1 ATGAACATGTTCATGAACAATAA
* *
66416 ATGAAGATGTTCGTGAACAATAA
1 ATGAACATGTTCATGAACAATAA
66439 AT
1 AT
66441 AAACGAATAA
Statistics
Matches: 37, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 22 0.59
24 15 0.41
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.26
Consensus pattern (23 bp):
ATGAACATGTTCATGAACAATAA
Found at i:74961 original size:2 final size:2
Alignment explanation
Indices: 74954--74982 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
74944 TCAATCTACA
74954 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
74983 ATTACGAAAT
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:75185 original size:13 final size:13
Alignment explanation
Indices: 75145--75189 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
75135 CTCAATTCAC
*
75145 GTCATAAATGAGC
1 GTCATAAATGAGT
*
75158 GTCATAAATGTGT
1 GTCATAAATGAGT
*
75171 GTCATAAATGCGT
1 GTCATAAATGAGT
75184 GTCATA
1 GTCATA
75190 GATTTGTGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (13 bp):
GTCATAAATGAGT
Found at i:75197 original size:26 final size:26
Alignment explanation
Indices: 75145--75216 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
75135 CTCAATTCAC
* *
75145 GTCATAAATGAGCGTCATAAATGTGT
1 GTCATAAATGCGTGTCATAAATGTGT
* *
75171 GTCATAAATGCGTGTCATAGATTTGT
1 GTCATAAATGCGTGTCATAAATGTGT
* *
75197 GACAAACAATTGCGTGTCAT
1 GTCATA-AA-TGCGTGTCAT
75217 CTAGATTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 26 0.68
27 2 0.05
28 10 0.26
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (26 bp):
GTCATAAATGCGTGTCATAAATGTGT
Done.