Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003020.1 Hibiscus syriacus cultivar Beakdansim tig00006274_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: 103470
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:15437 original size:35 final size:35
Alignment explanation
Indices: 15328--15430 Score: 179
Period size: 35 Copynumber: 2.9 Consensus size: 35
15318 TTCATGTTCA
* *
15328 AAATTCCAAAACACTTCAATTACATTCTAAACCCC
1 AAATTCCAAAATACTTCAATTATATTCTAAACCCC
15363 AAATTCCAAAATACTTCAATTATATTCTAAACCCC
1 AAATTCCAAAATACTTCAATTATATTCTAAACCCC
*
15398 AAATTCCAAAATACTTTAATTATATTCTAAACC
1 AAATTCCAAAATACTTCAATTATATTCTAAACC
15431 TTAAATTAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (35 bp):
AAATTCCAAAATACTTCAATTATATTCTAAACCCC
Found at i:17626 original size:23 final size:23
Alignment explanation
Indices: 17600--17644 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
17590 TATAGAAAAC
*
17600 CATTAGAGCTATTCTAACCCTAA
1 CATTAGAGCTACTCTAACCCTAA
*
17623 CATTAGATCTACTCTAACCCTA
1 CATTAGAGCTACTCTAACCCTA
17645 GCACCTCGTT
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:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (23 bp):
CATTAGAGCTACTCTAACCCTAA
Found at i:22917 original size:6 final size:6
Alignment explanation
Indices: 22906--22970 Score: 82
Period size: 6 Copynumber: 11.3 Consensus size: 6
22896 ATTTATCATT
* *
22906 TATTAA TATT-A -A-TAA TATTAA TATTAA TAATAA TATTAA TAATAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
*
22951 TATTAA TATTAA TAATAA TA
1 TATTAA TATTAA TATTAA TA
22971 ATAAAAGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 2 0.04
6 46 0.90
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TATTAA
Found at i:22926 original size:15 final size:15
Alignment explanation
Indices: 22906--22973 Score: 100
Period size: 15 Copynumber: 4.5 Consensus size: 15
22896 ATTTATCATT
22906 TATTAATATTAATAA
1 TATTAATATTAATAA
22921 TATTAATATTAATAA
1 TATTAATATTAATAA
* * *
22936 TAATATTAATAATAA
1 TATTAATATTAATAA
22951 TATTAATATTAATAA
1 TATTAATATTAATAA
*
22966 TAATAATA
1 TATTAATA
22974 AAAGAATAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTAATATTAATAA
Found at i:22938 original size:18 final size:18
Alignment explanation
Indices: 22909--22974 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
22899 TATCATTTAT
*
22909 TAATATTAATAATATTAA
1 TAATAATAATAATATTAA
*
22927 TATTAATAATAATATTAA
1 TAATAATAATAATATTAA
*
22945 TAATAATATTAATATTAA
1 TAATAATAATAATATTAA
22963 TAATAATAATAA
1 TAATAATAATAA
22975 AAGAATAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATAATATTAA
Found at i:23315 original size:119 final size:119
Alignment explanation
Indices: 23104--23408 Score: 398
Period size: 119 Copynumber: 2.6 Consensus size: 119
23094 AGACGGAAAT
* * * * *
23104 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGACGAGTTTTTATTATTATGAA
1 GTTGAACAAGCTCTTCTTATTATGAACTTTTTCTTCCTCTTCAGACGAGTTCTTATTATTATGAA
* * * * * *
23169 CTCTTCTATTGGGAATGATGATCCATCTCATTCTGTGATGGAATTTAGCAAAAG
66 CTCGTCCACTGGGAATGACGATCCATCTCAGTCTGTGATGGAATCTAGCAAAAG
* * * * *
23223 GTTGAGCAAGCTCTTATTATTATGAACTTTTTCTTTCTCTTCTAGATGAGTTCTTCTTATTATGA
1 GTTGAACAAGCTCTTCTTATTATGAACTTTTTCTTCCTCTTC-AGACGAGTTCTTATTATTATGA
* * *
23288 ACTCGTCCACT-GGAATGACGATTCATCTCCGTCTGTGATGGAATCTATCAAAAG
65 ACTCGTCCACTGGGAATGACGATCCATCTCAGTCTGTGATGGAATCTAGCAAAAG
*
23342 GTTGAACAAACTCTTCTTATTATGAA-TTTCTTCTTCCTCTTCAGACGAGTTCTTATTATTATGA
1 GTTGAACAAGCTCTTCTTATTATGAACTTT-TTCTTCCTCTTCAGACGAGTTCTTATTATTATGA
23406 ACT
65 ACT
23409 TTTTCTGGAA
Statistics
Matches: 159, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
118 26 0.16
119 107 0.67
120 26 0.16
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (119 bp):
GTTGAACAAGCTCTTCTTATTATGAACTTTTTCTTCCTCTTCAGACGAGTTCTTATTATTATGAA
CTCGTCCACTGGGAATGACGATCCATCTCAGTCTGTGATGGAATCTAGCAAAAG
Found at i:23893 original size:35 final size:35
Alignment explanation
Indices: 23844--23913 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
23834 AAAGACTTAT
* * * *
23844 CATCTTGCTTGAAAGGCTTA-TAGATGACCCGAAGG
1 CATCATGCTCGAAAGACTTACTA-ATGACCCAAAGG
23879 CATCATGCTCGAAAGACTTACTAATGACCCAAAGG
1 CATCATGCTCGAAAGACTTACTAATGACCCAAAGG
23914 ATTTACAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 28 0.93
36 2 0.07
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (35 bp):
CATCATGCTCGAAAGACTTACTAATGACCCAAAGG
Found at i:24171 original size:42 final size:42
Alignment explanation
Indices: 24103--24184 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
24093 AAGATCTTAT
* *
24103 CATCTTGCTCGAAAGGCTTACAGATGACCTGAAGGATTTAAG
1 CATCATGCTCGAAAGACTTACAGATGACCTGAAGGATTTAAG
**
24145 CATCATGCTCGAAAGACTTATTGATGACCTGAAGGATTTA
1 CATCATGCTCGAAAGACTTACAGATGACCTGAAGGATTTA
24185 CTTTAATCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTACAGATGACCTGAAGGATTTAAG
Found at i:24391 original size:42 final size:42
Alignment explanation
Indices: 24336--24448 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
24326 TATCATCTTG
* * *
24336 CTCGAAAGGCTTACATATGACCCGGAGGATTTAAGCATCATA
1 CTCGAAAGACTTACATATGACCCGAAGGATTTAAACATCATA
* * *
24378 CTCGAAAGACTTAC-TGATGACCCAAAGAATTTAAACATCATG
1 CTCGAAAGACTTACAT-ATGACCCGAAGGATTTAAACATCATA
* *
24420 CTCGAAAGACTTACAGATGGCCCGAAGGA
1 CTCGAAAGACTTACATATGACCCGAAGGA
24449 CTTACAAATC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.02
42 58 0.98
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (42 bp):
CTCGAAAGACTTACATATGACCCGAAGGATTTAAACATCATA
Found at i:34806 original size:103 final size:103
Alignment explanation
Indices: 34627--34813 Score: 320
Period size: 103 Copynumber: 1.8 Consensus size: 103
34617 ACGGGATGAC
* *
34627 TCTACCTGACTAGCTTGGGGGTAGAAGGTATGCTCCCTTTCACCTAGAGTATGGGATGGTAGGTG
1 TCTACCCGACTAGCTTGGGGATAGAAGGTATGCTCCCTTTCACCTAGAGTATGGGATGGTAGGTG
34692 TGATGGGCTGACTCCCTTCATAGCAGAATAAAAAAAAA
66 TGATGGGCTGACTCCCTTCATAGCAGAATAAAAAAAAA
* * *
34730 TCTACCCGACTAGCTTGGGGATGGAAGGTATGCTCCCTTTCATCTAGAGTGTGGGATGGTAGGTG
1 TCTACCCGACTAGCTTGGGGATAGAAGGTATGCTCCCTTTCACCTAGAGTATGGGATGGTAGGTG
*
34795 TGATGGTCTGACTCCCTTC
66 TGATGGGCTGACTCCCTTC
34814 GTAAAAAAAC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 78 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (103 bp):
TCTACCCGACTAGCTTGGGGATAGAAGGTATGCTCCCTTTCACCTAGAGTATGGGATGGTAGGTG
TGATGGGCTGACTCCCTTCATAGCAGAATAAAAAAAAA
Found at i:37182 original size:90 final size:90
Alignment explanation
Indices: 37029--37198 Score: 236
Period size: 90 Copynumber: 1.9 Consensus size: 90
37019 CACCTTTATC
* * * * *
37029 AGGCTAGTTGAAACTTATTCATAAACTCGAGGCTATTAACCAATTGCTCTAGAGGAACAACTCAA
1 AGGCTAGCTGAAACTTATCCATAAACTCGAGGCCATTAACAAATTGCTCTACAGGAACAACTCAA
*
37094 TCTTTATTGCATATAATAGTATAAT
66 GCTTTATTGCATATAATAGTATAAT
* *
37119 AGGCTAGCTGAATA-TTATCCATAAAGTC-AGGTCCATTAACAAATTGCTCTACAGGGACAACTC
1 AGGCTAGCTGAA-ACTTATCCATAAACTCGAGG-CCATTAACAAATTGCTCTACAGGAACAACTC
37182 AAGCTTTATTGCATATA
64 AAGCTTTATTGCATATA
37199 TAATAATATA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
89 3 0.04
90 66 0.94
91 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (90 bp):
AGGCTAGCTGAAACTTATCCATAAACTCGAGGCCATTAACAAATTGCTCTACAGGAACAACTCAA
GCTTTATTGCATATAATAGTATAAT
Found at i:42155 original size:11 final size:11
Alignment explanation
Indices: 42139--42168 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
42129 TCATATGATT
42139 AAAATAAAATA
1 AAAATAAAATA
42150 AAAATAAAATA
1 AAAATAAAATA
42161 AAGAATAA
1 AA-AATAA
42169 TAATTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:43634 original size:3 final size:3
Alignment explanation
Indices: 43626--43664 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
43616 ATTTATCAAT
* *
43626 TAA TAA TAA AAA TAA TAA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43665 AAGAATAGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:43760 original size:14 final size:14
Alignment explanation
Indices: 43741--43814 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 14
43731 TGAGAACAAT
43741 ATATAAGCTATGTG
1 ATATAAGCTATGTG
*
43755 ATATAATCTATGTG
1 ATATAAGCTATGTG
43769 AT-TACATGAAC-ATGTG
1 ATATA-A-G--CTATGTG
*
43785 ATATAAGCCATGTG
1 ATATAAGCTATGTG
* *
43799 ACATAACCTATGTG
1 ATATAAGCTATGTG
43813 AT
1 AT
43815 TACTTGTCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
13 3 0.06
14 33 0.69
15 1 0.02
16 8 0.17
17 3 0.06
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (14 bp):
ATATAAGCTATGTG
Found at i:43768 original size:44 final size:44
Alignment explanation
Indices: 43711--43813 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 44
43701 TTTATGTGTT
* * *
43711 ATATGATCTATGTGAATATATGAGAACA-AT-ATATAAGCTATGTG
1 ATATAATCTATGTGAATACAT--GAACATATGATATAAGCCATGTG
* *
43755 ATATAATCTATGTGATTACATGAACATGTGATATAAGCCATGTG
1 ATATAATCTATGTGAATACATGAACATATGATATAAGCCATGTG
* *
43799 ACATAACCTATGTGA
1 ATATAATCTATGTGA
43814 TTACTTGTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 5 0.10
43 1 0.02
44 44 0.88
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (44 bp):
ATATAATCTATGTGAATACATGAACATATGATATAAGCCATGTG
Found at i:43835 original size:44 final size:44
Alignment explanation
Indices: 43743--43835 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
43733 AGAACAATAT
* * * *
43743 ATAAGCTATGTGATATAATCTATGTGATTACATGAACATGTGAT
1 ATAAGCCATGTGACATAACCTATGTGATTACATGAACATGTGAA
* *
43787 ATAAGCCATGTGACATAACCTATGTGATTACTTG-TCTATGTGAA
1 ATAAGCCATGTGACATAACCTATGTGATTACATGAAC-ATGTGAA
43831 ATAAG
1 ATAAG
43836 ATATAATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (44 bp):
ATAAGCCATGTGACATAACCTATGTGATTACATGAACATGTGAA
Found at i:43949 original size:23 final size:23
Alignment explanation
Indices: 43919--44019 Score: 114
Period size: 23 Copynumber: 4.4 Consensus size: 23
43909 GAGTCGAGGG
43919 TTCTACGTGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* * *
43942 TTCTACGTGGTCTTTCGAGACAT
1 TTCTACGTGGTCCTTCGGGACAA
* *
43965 TTCTACGCGGTCCTTCGGGATAA
1 TTCTACGTGGTCCTTCGGGACAA
* * *
43988 TACTATGTGGTCCTCCGGGAC-A
1 TTCTACGTGGTCCTTCGGGACAA
*
44010 TTCTATGTGG
1 TTCTACGTGG
44020 CATTTCGGTG
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
22 10 0.16
23 54 0.84
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.34
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:44214 original size:31 final size:31
Alignment explanation
Indices: 44179--44239 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
44169 CATAATGGGA
*
44179 TATGTTATTATTGGTTAAATACATGATGATG
1 TATGTTATTATTGATTAAATACATGATGATG
* * *
44210 TATGTTCTTATTGATTAGATATATGATGAT
1 TATGTTATTATTGATTAAATACATGATGAT
44240 TCATGTACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.31, C:0.03, G:0.18, T:0.48
Consensus pattern (31 bp):
TATGTTATTATTGATTAAATACATGATGATG
Found at i:46150 original size:19 final size:20
Alignment explanation
Indices: 46126--46168 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
46116 CTTTTAATAT
*
46126 TTTAATTTGA-AAATAAAAA
1 TTTAATTTCATAAATAAAAA
*
46145 TTTAATTTCATAGATAAAAA
1 TTTAATTTCATAAATAAAAA
46165 TTTA
1 TTTA
46169 TTAAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTAATTTCATAAATAAAAA
Found at i:52403 original size:60 final size:60
Alignment explanation
Indices: 52330--52450 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
52320 ACAATTAAAA
52330 ATATTTTAATGATAACTTTTAGATTGCAATCATCATACTTATACAATTTATATAATTTTT
1 ATATTTTAATGATAACTTTTAGATTGCAATCATCATACTTATACAATTTATATAATTTTT
52390 ATATTTTAATGATAACTTTTAGATTGCAATCATCATACTTATACAATTTATATAATTTTT
1 ATATTTTAATGATAACTTTTAGATTGCAATCATCATACTTATACAATTTATATAATTTTT
52450 A
1 A
52451 ATGAAAAACA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (60 bp):
ATATTTTAATGATAACTTTTAGATTGCAATCATCATACTTATACAATTTATATAATTTTT
Found at i:82087 original size:22 final size:22
Alignment explanation
Indices: 82034--82087 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
82024 CTCAGATGTT
* * *
82034 ATAACTCCCGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* *
82056 GTAACCCCTGAAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
82078 ATAACTCCTG
1 ATAACTCCTG
82088 TAACTCCTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:82386 original size:12 final size:12
Alignment explanation
Indices: 82369--82393 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
82359 TATTATTACG
82369 ACCACGACCACA
1 ACCACGACCACA
82381 ACCACGACCACA
1 ACCACGACCACA
82393 A
1 A
82394 GCTGAGCCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.48, G:0.08, T:0.00
Consensus pattern (12 bp):
ACCACGACCACA
Found at i:83353 original size:21 final size:21
Alignment explanation
Indices: 83323--83366 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
83313 CAAAACCCTA
*
83323 ATGACGCCGAGAGATCCAAGC
1 ATGACACCGAGAGATCCAAGC
83344 ATGACACCGAGAGATCCAAGC
1 ATGACACCGAGAGATCCAAGC
83365 AT
1 AT
83367 TTGCATGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.27, G:0.25, T:0.11
Consensus pattern (21 bp):
ATGACACCGAGAGATCCAAGC
Found at i:83540 original size:2 final size:2
Alignment explanation
Indices: 83533--83593 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
83523 AATTCACAAT
83533 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
83575 TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA
83594 GAGTAAAGAG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:85662 original size:35 final size:36
Alignment explanation
Indices: 85611--85681 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
85601 ACCGACTCTT
*
85611 ATATATATAATTATTATTATTGTACTTATTTAATAA
1 ATATATATAATAATTATTATTGTACTTATTTAATAA
*
85647 ATATATAT-ATAATTATTATTGTGCTTATTTAATAA
1 ATATATATAATAATTATTATTGTACTTATTTAATAA
85682 TGATGTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 25 0.76
36 8 0.24
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (36 bp):
ATATATATAATAATTATTATTGTACTTATTTAATAA
Found at i:87059 original size:29 final size:29
Alignment explanation
Indices: 86997--87061 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
86987 TGAGTTCCTT
*
86997 AACTATTAAAATCTACAAAACTGTCTCTC
1 AACTATTAAAATCTACAAAACTGTCACTC
*
87026 GACTATTAAAAAT-TACAAAA-TAGTCACTC
1 AACTATT-AAAATCTACAAAACT-GTCACTC
87055 AACTATT
1 AACTATT
87062 CATATATTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 1 0.03
29 25 0.81
30 5 0.16
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.31
Consensus pattern (29 bp):
AACTATTAAAATCTACAAAACTGTCACTC
Found at i:89053 original size:23 final size:23
Alignment explanation
Indices: 89027--89070 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
89017 TAATTTTTTT
*
89027 TAAA-TTATTATTTTTAAAAAAAA
1 TAAACTTA-TATTATTAAAAAAAA
89050 TAAACTTATATTATTAAAAAA
1 TAAACTTATATTATTAAAAAA
89071 GTATTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAACTTATATTATTAAAAAAAA
Found at i:91103 original size:48 final size:48
Alignment explanation
Indices: 91032--91300 Score: 385
Period size: 48 Copynumber: 5.6 Consensus size: 48
91022 TTTTATGTTG
* * *
91032 AAATGCACCGTTATGTATTTAATTTTCATTAGTGGCACTTTTCTACCA
1 AAATGCACCGTTATGCATTTAATTTTCATTAGTGGCACATTTCTGCCA
*** *
91080 AAATGCACCGTTATGCATTTAATTTTCATTAGTAATACTTTTCTGCCA
1 AAATGCACCGTTATGCATTTAATTTTCATTAGTGGCACATTTCTGCCA
* * * *
91128 AAATGCACCGTTATGCATTTAATTTCCATTAGTGACACCTTTATGCCA
1 AAATGCACCGTTATGCATTTAATTTTCATTAGTGGCACATTTCTGCCA
*
91176 AAATGCACCGTTATGCATTTAATTTTCATTAGTGGCACATTTATGCCCA
1 AAATGCACCGTTATGCATTTAATTTTCATTAGTGGCACATTTCTG-CCA
* * *
91225 AAATGTACCGTTATCCATTTAATTTTCATTAGTGGCACATTTCTTCCA
1 AAATGCACCGTTATGCATTTAATTTTCATTAGTGGCACATTTCTGCCA
*
91273 AAATGCACCGTTATGCATTTAGTTTTCA
1 AAATGCACCGTTATGCATTTAATTTTCA
91301 CTATAGAGTA
Statistics
Matches: 200, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
48 156 0.78
49 44 0.22
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.39
Consensus pattern (48 bp):
AAATGCACCGTTATGCATTTAATTTTCATTAGTGGCACATTTCTGCCA
Found at i:96942 original size:10 final size:10
Alignment explanation
Indices: 96927--97000 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
96917 CATTTAATAA
96927 ATAAACGAAC
1 ATAAACGAAC
96937 ATAAACGAAC
1 ATAAACGAAC
**
96947 ACGAAC-ATA-
1 ATAAACGA-AC
96956 ATGAACACGAAC
1 AT-AA-ACGAAC
*
96968 ATAAATGAAC
1 ATAAACGAAC
96978 ----ACGAAC
1 ATAAACGAAC
96984 ATAAACGAAC
1 ATAAACGAAC
96994 ATAAACG
1 ATAAACG
97001 TTGACCCTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
6 5 0.10
9 2 0.04
10 34 0.69
11 5 0.10
12 3 0.06
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:96952 original size:16 final size:16
Alignment explanation
Indices: 96931--96994 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
96921 TAATAAATAA
96931 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
96947 ACGAACAT-AATGAAC
1 ACGAACATAAACGAAC
*
96962 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
96978 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
96994 A
1 A
96995 TAAACGTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.31
16 31 0.69
ACGTcount: A:0.56, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:98088 original size:10 final size:10
Alignment explanation
Indices: 98073--98143 Score: 54
Period size: 10 Copynumber: 6.4 Consensus size: 10
98063 ATAAATGAAT
98073 GAACATAAAC
1 GAACATAAAC
98083 GAACATAACCGAAC
1 GAACAT-A---AAC
98097 GAACAT-AAC
1 GAACATAAAC
98106 GAACATAACCGAAC
1 GAACAT-A---AAC
98120 GAACATAAAC
1 GAACATAAAC
*
98130 GAACATAACC
1 GAACATAAAC
98140 GAAC
1 GAAC
98144 GAACATAAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 18
0.73 0.01 0.26
Matches are distributed among these distances:
9 9 0.18
10 22 0.43
11 1 0.02
13 1 0.02
14 18 0.35
ACGTcount: A:0.54, C:0.25, G:0.13, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:98097 original size:14 final size:14
Alignment explanation
Indices: 98080--98151 Score: 81
Period size: 14 Copynumber: 5.8 Consensus size: 14
98070 AATGAACATA
98080 AACGAACATAACCG
1 AACGAACATAACCG
98094 AACGAACAT-----
1 AACGAACATAACCG
98103 AACGAACATAACCG
1 AACGAACATAACCG
98117 AACGAACAT-A---
1 AACGAACATAACCG
98127 AACGAACATAACCG
1 AACGAACATAACCG
98141 AACGAACATAA
1 AACGAACATAA
98152 ACATAACCGA
Statistics
Matches: 49, Mismatches: 0, Indels: 18
0.73 0.00 0.27
Matches are distributed among these distances:
9 9 0.18
10 9 0.18
11 1 0.02
13 1 0.02
14 29 0.59
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:98100 original size:24 final size:24
Alignment explanation
Indices: 98073--98153 Score: 155
Period size: 24 Copynumber: 3.4 Consensus size: 24
98063 ATAAATGAAT
98073 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
98097 GAACAT-AACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
98120 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
98144 GAACATAAAC
1 GAACATAAAC
98154 ATAACCGAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
23 23 0.41
24 33 0.59
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:98129 original size:47 final size:44
Alignment explanation
Indices: 98058--98164 Score: 160
Period size: 47 Copynumber: 2.4 Consensus size: 44
98048 AAGATTGAGT
** *
98058 TAAACATAAATGAATGAACATAAACGAACATAACCGAACGAACA
1 TAAACATAACCGAACGAACATAAACGAACATAACCGAACGAACA
98102 TAACGAACATAACCGAACGAACATAAACGAACATAACCGAACGAACA
1 T-A--AACATAACCGAACGAACATAAACGAACATAACCGAACGAACA
98149 TAAACATAACCGAACG
1 TAAACATAACCGAACG
98165 TTCACGAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
44 15 0.26
45 1 0.02
46 1 0.02
47 40 0.70
ACGTcount: A:0.54, C:0.22, G:0.12, T:0.11
Consensus pattern (44 bp):
TAAACATAACCGAACGAACATAAACGAACATAACCGAACGAACA
Found at i:98174 original size:20 final size:20
Alignment explanation
Indices: 98081--98186 Score: 97
Period size: 20 Copynumber: 5.0 Consensus size: 20
98071 ATGAACATAA
98081 ACGAACATAACCGAACGAAC
1 ACGAACATAACCGAACGAAC
98101 ATAACGAACATAACCGAACGAAC
1 ---ACGAACATAACCGAACGAAC
98124 ATAAACGAACATAACCGAACGAAC
1 ----ACGAACATAACCGAACGAAC
** **
98148 ATAAACATAACCGAACGTTC
1 ACGAACATAACCGAACGAAC
*
98168 ACGAACATAA-TGAACGAAC
1 ACGAACATAACCGAACGAAC
98187 GAGACCTATG
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 6 0.08
20 24 0.34
23 20 0.28
24 21 0.30
ACGTcount: A:0.51, C:0.25, G:0.13, T:0.10
Consensus pattern (20 bp):
ACGAACATAACCGAACGAAC
Found at i:99567 original size:45 final size:47
Alignment explanation
Indices: 99393--99673 Score: 297
Period size: 48 Copynumber: 6.0 Consensus size: 47
99383 TTAAACCATG
* * * * * *
99393 AGTGGCATCTTTTATGCCGAAATGCACC-GTATTCATTTAACTGTCATT
1 AGTGGCATC--TTCTGCCAAAATGCACCATTATGCATTTAATTTTCATT
* * *
99441 AGT-GCATTTTTCTGCCAAAATACACCGTTATGCATTTAATTTTCATT
1 AGTGGCA-TCTTCTGCCAAAATGCACCATTATGCATTTAATTTTCATT
* * ** *
99488 AGTGACATATTTCTGCCAAAATGCACTGTTATGCATTTAATTTTTATT
1 AGTGGCAT-CTTCTGCCAAAATGCACCATTATGCATTTAATTTTCATT
* * *
99536 AGTGGTA-CAT-TACCAAAATGCACCATTATGCATTTAATTTTCATT
1 AGTGGCATCTTCTGCCAAAATGCACCATTATGCATTTAATTTTCATT
* *
99581 AGTTGGCATTTTCTGCCAAAATGCACC-GT-TGCATTTAATTTTCATT
1 AG-TGGCATCTTCTGCCAAAATGCACCATTATGCATTTAATTTTCATT
99627 AGTGGCATCTTCTGCCAAAATGCA-CATTATGCATTTAATTTTCATT
1 AGTGGCATCTTCTGCCAAAATGCACCATTATGCATTTAATTTTCATT
99673 A
1 A
99674 TAGAGTAGTC
Statistics
Matches: 197, Mismatches: 27, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
44 1 0.01
45 55 0.28
46 56 0.28
47 25 0.13
48 60 0.30
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (47 bp):
AGTGGCATCTTCTGCCAAAATGCACCATTATGCATTTAATTTTCATT
Found at i:99572 original size:93 final size:93
Alignment explanation
Indices: 99402--99673 Score: 320
Period size: 93 Copynumber: 2.9 Consensus size: 93
99392 GAGTGGCATC
* * * * * ** * *
99402 TTTTATGCCGAAATGCACCGTATTCATTTAACTGTCATTAGT-GCATTTTTCTGCCAAAATACAC
1 TTTTCTGCCAAAATGCACCGT-TGCATTTAATTTTCATTAGTGGCA-TCATCTACCAAAATGCAC
*
99466 CGTTATGCATTTAATTTTCATTAG-TGACA
64 CATTATGCATTTAATTTTCATTAGTTGACA
* * *
99495 TATTTCTGCCAAAATGCACTGTTATGCATTTAATTTTTATTAGTGGTA-CAT-TACCAAAATGCA
1 T-TTTCTGCCAAAATGCACCG-T-TGCATTTAATTTTCATTAGTGGCATCATCTACCAAAATGCA
*
99558 CCATTATGCATTTAATTTTCATTAGTTGGCA
63 CCATTATGCATTTAATTTTCATTAGTTGACA
* *
99589 TTTTCTGCCAAAATGCACCGTTGCATTTAATTTTCATTAGTGGCATCTTCTGCCAAAATGCA-CA
1 TTTTCTGCCAAAATGCACCGTTGCATTTAATTTTCATTAGTGGCATCATCTACCAAAATGCACCA
99653 TTATGCATTTAATTTTCATTA
66 TTATGCATTTAATTTTCATTA
99674 TAGAGTAGTC
Statistics
Matches: 154, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
91 22 0.14
92 26 0.17
93 64 0.42
94 22 0.14
95 18 0.12
96 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (93 bp):
TTTTCTGCCAAAATGCACCGTTGCATTTAATTTTCATTAGTGGCATCATCTACCAAAATGCACCA
TTATGCATTTAATTTTCATTAGTTGACA
Found at i:99621 original size:46 final size:46
Alignment explanation
Indices: 99393--99673 Score: 309
Period size: 46 Copynumber: 6.0 Consensus size: 46
99383 TTAAACCATG
* * * * *
99393 AGTGGCATCTTTTATGCCGAAATGCACCGTATTCATTTAACTGTCATT
1 AGTGGCA--TTTTCTGCCAAAATGCACCGTATGCATTTAATTTTCATT
*
99441 AGT-GCATTTTTCTGCCAAAATACACCGTTATGCATTTAATTTTCATT
1 AGTGGCA-TTTTCTGCCAAAATGCACCG-TATGCATTTAATTTTCATT
* * *
99488 AGTGACATATTTCTGCCAAAATGCACTGTTATGCATTTAATTTTTATT
1 AGTGGCAT-TTTCTGCCAAAATGCACCG-TATGCATTTAATTTTCATT
* ** * *
99536 AGTGGTA-CAT-TACCAAAATGCACCATTATGCATTTAATTTTCATT
1 AGTGGCATTTTCTGCCAAAATGCACC-GTATGCATTTAATTTTCATT
99581 AGTTGGCATTTTCTGCCAAAATGCACCGT-TGCATTTAATTTTCATT
1 AG-TGGCATTTTCTGCCAAAATGCACCGTATGCATTTAATTTTCATT
* **
99627 AGTGGCATCTTCTGCCAAAATGCACATTATGCATTTAATTTTCATT
1 AGTGGCATTTTCTGCCAAAATGCACCGTATGCATTTAATTTTCATT
99673 A
1 A
99674 TAGAGTAGTC
Statistics
Matches: 198, Mismatches: 27, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
45 55 0.28
46 59 0.30
47 25 0.13
48 59 0.30
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (46 bp):
AGTGGCATTTTCTGCCAAAATGCACCGTATGCATTTAATTTTCATT
Done.