Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005594.1 Hibiscus syriacus cultivar Beakdansim tig00013014_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: 98198
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1133 original size:15 final size:15
Alignment explanation
Indices: 1113--1142 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1103 CATGATCACA
1113 ATAATTCCCTTAAGC
1 ATAATTCCCTTAAGC
1128 ATAATTCCCTTAAGC
1 ATAATTCCCTTAAGC
1143 TATCTTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (15 bp):
ATAATTCCCTTAAGC
Found at i:1164 original size:10 final size:10
Alignment explanation
Indices: 1136--1165 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1126 GCATAATTCC
*
1136 CTTAAGCTAT
1 CTTAAGCTTT
1146 CTTAAGCTTT
1 CTTAAGCTTT
1156 CTTAAGCTTT
1 CTTAAGCTTT
1166 TTTATCATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (10 bp):
CTTAAGCTTT
Found at i:3758 original size:52 final size:53
Alignment explanation
Indices: 3696--3798 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 53
3686 ATTTAGAATG
* *
3696 CTTAGACATTTGAGCAGAAGCTAAAC-AAGACTGTTTAAGGTACAAAGAAATA
1 CTTAGACATTTGAGCAGAAGCTAAACAAAAACTGTATAAGGTACAAAGAAATA
*
3748 CTTAGACATTTGAGCAGAAGCTAAACAAAAATTGTATAAGGTACAAAGAAA
1 CTTAGACATTTGAGCAGAAGCTAAACAAAAACTGTATAAGGTACAAAGAAA
3799 GAGGACGAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 26 0.55
53 21 0.45
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (53 bp):
CTTAGACATTTGAGCAGAAGCTAAACAAAAACTGTATAAGGTACAAAGAAATA
Found at i:9681 original size:16 final size:16
Alignment explanation
Indices: 9657--9697 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
9647 ATGGACGAAA
*
9657 CTCCACCCGACCTCCG
1 CTCCCCCCGACCTCCG
*
9673 CTCCCCCCGACCTCTG
1 CTCCCCCCGACCTCCG
9689 CTCCCCCCG
1 CTCCCCCCG
9698 GTGACCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.07, C:0.66, G:0.12, T:0.15
Consensus pattern (16 bp):
CTCCCCCCGACCTCCG
Found at i:12995 original size:3 final size:3
Alignment explanation
Indices: 12987--13077 Score: 139
Period size: 3 Copynumber: 30.0 Consensus size: 3
12977 CAGTTTGCTT
*
12987 TTA TTA TTA TTA TTA TTA TTA TTA TTA TACA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
*
13033 TACA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13078 AATTAAAAAA
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.02
3 75 0.93
4 4 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:14399 original size:21 final size:22
Alignment explanation
Indices: 14353--14397 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
14343 TCATTGTTTA
14353 TTTATAT-TTTAATTTTATATG
1 TTTATATATTTAATTTTATATG
14374 TTTATATATTTAATTATTAT-TG
1 TTTATATATTTAATT-TTATATG
14396 TT
1 TT
14398 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTATATATTTAATTTTATATG
Found at i:14814 original size:129 final size:129
Alignment explanation
Indices: 14566--14819 Score: 463
Period size: 129 Copynumber: 2.0 Consensus size: 129
14556 AGAAATAAAC
* *
14566 TGTCTTAAAGCACCTAGAAGTCGTTTTCTGATATTCTTAAATAAATAAATATCCTATTTTTATAA
1 TGTCTTAAAGCACCTAAAAGTCCTTTTCTGATATTCTTAAATAAATAAATATCCTATTTTTATAA
14631 ATTATATATTAATTTATTTTAATTATTTTTAGAGAAATGTTTTATTAATATTTATTTATTGGGT
66 ATTATATATTAATTTATTTTAATTATTTTTAGAGAAATGTTTTATTAATATTTATTTATTGGGT
* * *
14695 TGTCTTAAAGCACCTAAAAGTCCTTTTCTGATATTCTTAGATAAATAAATATCTTGTTTTTATAA
1 TGTCTTAAAGCACCTAAAAGTCCTTTTCTGATATTCTTAAATAAATAAATATCCTATTTTTATAA
14760 ATTATATATTAATTTATTTTAATTATTTTTAGAGAAATGTTTTATTAATATTTATTTATT
66 ATTATATATTAATTTATTTTAATTATTTTTAGAGAAATGTTTTATTAATATTTATTTATT
14820 TATTAATATT
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 120 1.00
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.50
Consensus pattern (129 bp):
TGTCTTAAAGCACCTAAAAGTCCTTTTCTGATATTCTTAAATAAATAAATATCCTATTTTTATAA
ATTATATATTAATTTATTTTAATTATTTTTAGAGAAATGTTTTATTAATATTTATTTATTGGGT
Found at i:14899 original size:23 final size:23
Alignment explanation
Indices: 14873--14926 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
14863 ATTTTCTGAC
* *
14873 ATTTCTAAGTAAATAAATATATT
1 ATTTATAAATAAATAAATATATT
* *
14896 ATTTATAAATATATATATATATAT
1 ATTTATAAATAAATAAATATAT-T
*
14920 ATATATA
1 ATTTATA
14927 TTAATATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTTATAAATAAATAAATATATT
Found at i:14909 original size:2 final size:2
Alignment explanation
Indices: 14889--14935 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
14879 AAGTAAATAA
* *
14889 AT AT AT -T AT TT AT AA AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14929 A- AT AT AT
1 AT AT AT AT
14936 TTTCTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:23727 original size:54 final size:53
Alignment explanation
Indices: 23644--23805 Score: 198
Period size: 54 Copynumber: 3.0 Consensus size: 53
23634 TGATTGAGAA
* *
23644 ATCTGGGCAGAATCCACAGGAAAGGATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGGGCAGAAACCACAAGAAA-GATGAATGTATTGTCAAATGTTTTACGAAC
* * *
23698 ATCTGGGCAGAAGCCACAAGAAAGAATGAATGTATTGTCAAATGTTTTACTAGC
1 ATCTGGGCAGAAACCACAAGAAAG-ATGAATGTATTGTCAAATGTTTTACGAAC
* * * * * *
23752 ATCTGAGCAGAAACCACATGAGATGATGAATATGTTGTCAAATGTTTTATGAAC
1 ATCTGGGCAGAAACCACAAGA-AAGATGAATGTATTGTCAAATGTTTTACGAAC
23806 TAGTTATTCT
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
53 1 0.01
54 90 0.97
55 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (53 bp):
ATCTGGGCAGAAACCACAAGAAAGATGAATGTATTGTCAAATGTTTTACGAAC
Found at i:24208 original size:22 final size:22
Alignment explanation
Indices: 24176--24255 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
24166 TACATTCTTT
*
24176 AAAGATGATAGATTCTATATTC
1 AAAGATGATAGATTCTCTATTC
* *
24198 AAATATGATAGATTCTCTCTTC
1 AAAGATGATAGATTCTCTATTC
*
24220 AAAGATGATAGATTCTCTTTTC
1 AAAGATGATAGATTCTCTATTC
*
24242 AAAGATGAAAGATT
1 AAAGATGATAGATT
24256 TATTGGATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTATTC
Found at i:25195 original size:45 final size:45
Alignment explanation
Indices: 25131--25227 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 45
25121 CTTTTTGATA
* * ** *
25131 TTTAAAGCTTCCAGGTCATCTGTAAGACCTACAGTGCATGATGTT
1 TTTAAAACCTCCAGGTCATCCATAAGACCTACAGTGCAGGATGTT
25176 TTTAAAACCTCCAGGTCATCCATAAGACCTACAGTGCAGGATGTT
1 TTTAAAACCTCCAGGTCATCCATAAGACCTACAGTGCAGGATGTT
*
25221 TTCAAAA
1 TTTAAAA
25228 AGCCTTCAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (45 bp):
TTTAAAACCTCCAGGTCATCCATAAGACCTACAGTGCAGGATGTT
Found at i:25245 original size:119 final size:119
Alignment explanation
Indices: 24912--25292 Score: 608
Period size: 119 Copynumber: 3.2 Consensus size: 119
24902 CTATTTCCCA
* *
24912 CATCTGTAAGACCTACAGTGCATGATGTTTTTAAAACCTCCGGGTCATCCATAAGACCTACAGTG
1 CATCTGTAAGACCTACAGTGCAAGATGTTTTTAAAACCTCCAGGTCATCCATAAGACCTACAGTG
*
24977 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTTAAAGCCTCCGGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTTAAAGCCTCCAGGT
* * * *
25031 CATCTGTAAGACCTACAGTGCAAGATG---ATAAGACCT-CAGGGCCATCCATAAAACCTACAGT
1 CATCTGTAAGACCTACAGTGCAAGATGTTTTTAAAACCTCCA-GGTCATCCATAAGACCTACAGT
* * *
25092 GCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAGCTTCCAGGT
65 GCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTTAAAGCCTCCAGGT
*
25147 CATCTGTAAGACCTACAGTGCATGATGTTTTTAAAACCTCCAGGTCATCCATAAGACCTACAGTG
1 CATCTGTAAGACCTACAGTGCAAGATGTTTTTAAAACCTCCAGGTCATCCATAAGACCTACAGTG
* *
25212 CAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATTTTTAAAGCCTCTAGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTTAAAGCCTCCAGGT
25266 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCAAGATG
25293 ATAAGACCTA
Statistics
Matches: 236, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
115 1 0.00
116 104 0.44
119 129 0.55
120 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (119 bp):
CATCTGTAAGACCTACAGTGCAAGATGTTTTTAAAACCTCCAGGTCATCCATAAGACCTACAGTG
CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTTAAAGCCTCCAGGT
Found at i:25314 original size:22 final size:22
Alignment explanation
Indices: 25272--25314 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
25262 AGGTCATCTG
*
25272 TAAGACCTACAGTGCAAGATGA
1 TAAGACCTACAGTACAAGATGA
*
25294 TAAGACCTACAGTACATGATG
1 TAAGACCTACAGTACAAGATG
25315 TTTTCAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (22 bp):
TAAGACCTACAGTACAAGATGA
Found at i:25396 original size:98 final size:96
Alignment explanation
Indices: 25197--25399 Score: 336
Period size: 96 Copynumber: 2.1 Consensus size: 96
25187 CAGGTCATCC
* *
25197 ATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATTTTTAAAGCCTCT
1 ATAAGACCTACAGTACAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATTTTTAAAGCCTCG
25262 AGGTCATCTGTAAGACCTACAGTGCAAGATG
66 AGGTCATCTGTAAGACCTACAGTGCAAGATG
* *
25293 ATAAGACCTACAGTACATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCT
1 ATAAGACCTACAGTACAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGAT-TTTT-AAAGCC-
25358 TCGA-GTCATCTGTAAGACCTACAGTGCAAGATG
63 TCGAGGTCATCTGTAAGACCTACAGTGCAAGATG
25391 ATAAGACCT
1 ATAAGACCT
25400 CAGGGCCATC
Statistics
Matches: 100, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
96 49 0.49
97 4 0.04
98 44 0.44
99 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (96 bp):
ATAAGACCTACAGTACAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATTTTTAAAGCCTCG
AGGTCATCTGTAAGACCTACAGTGCAAGATG
Found at i:25501 original size:118 final size:118
Alignment explanation
Indices: 25293--25537 Score: 436
Period size: 118 Copynumber: 2.1 Consensus size: 118
25283 GTGCAAGATG
*
25293 ATAAGACCTACAGTACATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCT
1 ATAAGACCTACAGTACAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCT
*
25358 TCGAGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCC
66 CCGAGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCC
*
25411 ATAAGACCTATAGTACAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCT
1 ATAAGACCTACAGTACAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCT
* * *
25476 CCGGGTCATTTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATTC
66 CCGAGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCC
25529 ATAAGACCT
1 ATAAGACCT
25538 CTGGGCAGAA
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 121 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (118 bp):
ATAAGACCTACAGTACAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCT
CCGAGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCC
Found at i:25689 original size:3 final size:3
Alignment explanation
Indices: 25681--25755 Score: 73
Period size: 3 Copynumber: 25.0 Consensus size: 3
25671 CAAATTGCTT
* ** * *
25681 TTA TTA TTA TTA TT- TT- TTA TTA TTA TTA TTA ATA AGA ATA TACA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
25725 TTA TTA TTA TTA TTA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
25756 AATAAAAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.06
3 54 0.86
4 5 0.08
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:25700 original size:13 final size:14
Alignment explanation
Indices: 25679--25754 Score: 55
Period size: 16 Copynumber: 5.1 Consensus size: 14
25669 TTCAAATTGC
25679 TTTTATTATTATTA
1 TTTTATTATTATTA
25693 TTTT-TTATTATTA
1 TTTTATTATTATTA
* **
25706 TTATTAATAAGAATATA
1 TT-TT-ATTATTAT-TA
**
25723 CATTATTATTATTA
1 TTTTATTATTATTA
25737 TTATTATATATTATTA
1 TT-TTAT-TATTATTA
25753 TT
1 TT
25755 AAATAAAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
13 11 0.24
14 8 0.17
15 9 0.20
16 16 0.35
17 2 0.04
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:25700 original size:16 final size:16
Alignment explanation
Indices: 25679--25710 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25669 TTCAAATTGC
25679 TTTTATTATTATTATT
1 TTTTATTATTATTATT
25695 TTTTATTATTATTATT
1 TTTTATTATTATTATT
25711 AATAAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTATTATTATTATT
Found at i:25727 original size:22 final size:22
Alignment explanation
Indices: 25702--25756 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
25692 ATTTTTTATT
25702 ATTATTATTAATAAGAATATAC
1 ATTATTATTAATAAGAATATAC
* ** * *
25724 ATTATTATTATTATTATTATAT
1 ATTATTATTAATAAGAATATAC
25746 ATTATTATTAA
1 ATTATTATTAA
25757 ATAAAAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTATTATTAATAAGAATATAC
Found at i:25768 original size:44 final size:44
Alignment explanation
Indices: 25681--25768 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
25671 CAAATTGCTT
* *
25681 TTATTATTATTATTTTTTATTATTATTATTAATAAGAATATACA
1 TTATTATTATTATTTTATATTATTATTATTAATAAGAAAATACA
25725 TTATTATTATTATTATTATA-TATTATTATTAAATAA-AAAATACA
1 TTATTATTATTATT-TTATATTATTATTATT-AATAAGAAAATACA
25769 AACCCTGAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 31 0.77
45 9 0.22
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (44 bp):
TTATTATTATTATTTTATATTATTATTATTAATAAGAAAATACA
Found at i:27249 original size:23 final size:23
Alignment explanation
Indices: 27231--27291 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
27221 CTCATATAAA
27231 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
*
27254 TGCACC-ATAGTGCCGCATAGAAT
1 TGCACCGA-AGTGCCACATAGAAT
*
27277 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
27292 TATAATAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:27425 original size:18 final size:18
Alignment explanation
Indices: 27402--27437 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
27392 GAATACATAT
27402 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
27420 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
27438 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:27512 original size:121 final size:121
Alignment explanation
Indices: 27298--27540 Score: 432
Period size: 121 Copynumber: 2.0 Consensus size: 121
27288 GCCATATAAT
* * *
27298 AATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
1 AATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGC
27363 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
* * *
27419 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 AATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGC
27484 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
27540 A
1 A
27541 TATCATTCCT
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 116 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.24
Consensus pattern (121 bp):
AATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGC
GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
Found at i:27515 original size:62 final size:63
Alignment explanation
Indices: 27328--27523 Score: 155
Period size: 62 Copynumber: 3.2 Consensus size: 63
27318 ATCATTCCTT
* * *
27328 AAGAAT-CATATACATATACTAGGGATCAAGTATGCGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
* * * * * *
27390 AAGAATACATAT--ATGTCCCGAAGGACCACA--A--TGTC-C-CGAAGGAC--CACATATCATT
1 AAGAATACATATACATATACC-AAGGATCA-AGTATGTGTCTCAC-CA-GACTTCACACAT-GTT
*
27445 CCTT
61 CC-A
*
27449 AAGAAT-CATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
27511 AAGAATACATATA
1 AAGAATACATATA
27524 TGTCCCGAAG
Statistics
Matches: 99, Mismatches: 17, Indels: 35
0.66 0.11 0.23
Matches are distributed among these distances:
57 7 0.07
58 12 0.12
59 19 0.19
60 6 0.06
61 5 0.05
62 25 0.25
63 18 0.18
64 7 0.07
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.24
Consensus pattern (63 bp):
AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
Found at i:27599 original size:103 final size:103
Alignment explanation
Indices: 27420--27645 Score: 416
Period size: 103 Copynumber: 2.2 Consensus size: 103
27410 AAGGACCACA
*
27420 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
27485 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
* * *
27523 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATATATATACTAGGGATCAAGTATGTG
1 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
27588 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
27626 ATGTCCCGAAGGACCACATA
1 ATGTCCCGAAGGACCACATA
27646 GACCCTCGAC
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 119 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:28951 original size:21 final size:21
Alignment explanation
Indices: 28925--28968 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
28915 ATTTTATTCG
* *
28925 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
28946 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
28967 CT
1 CT
28969 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:32742 original size:23 final size:23
Alignment explanation
Indices: 32716--32776 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
32706 CTCATATAAA
*
32716 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
32739 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
32762 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
32777 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:33031 original size:18 final size:18
Alignment explanation
Indices: 33008--33043 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
32998 TAATACATAT
33008 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
33026 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
33044 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:33143 original size:121 final size:121
Alignment explanation
Indices: 32783--33146 Score: 647
Period size: 121 Copynumber: 3.0 Consensus size: 121
32773 GCCATATAAT
** *
32783 AATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGT
*
32848 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACAAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
* * *
32904 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGT
*
32969 GTCTCACCAGACTTCACACATGTTCCAAATAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
*
33025 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATATATATACTAAGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGT
33090 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
33146 A
1 A
33147 TAGACCCTCG
Statistics
Matches: 230, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 230 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (121 bp):
AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGT
GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
Found at i:34454 original size:21 final size:21
Alignment explanation
Indices: 34428--34471 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
34418 ATTTTATTCG
* *
34428 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
34449 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
34470 CT
1 CT
34472 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:35825 original size:21 final size:22
Alignment explanation
Indices: 35779--35823 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
35769 TCATTGTTTA
35779 TTTATAT-TTTAATTTTATATG
1 TTTATATATTTAATTTTATATG
35800 TTTATATATTTAATTATTAT-TG
1 TTTATATATTTAATT-TTATATG
35822 TT
1 TT
35824 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTATATATTTAATTTTATATG
Found at i:36189 original size:122 final size:125
Alignment explanation
Indices: 35990--36239 Score: 425
Period size: 122 Copynumber: 2.0 Consensus size: 125
35980 TATTAAGAAA
*
35990 TGGGTTGTCTTAAAGCTCCTAGAAGTCATTTTATGATATTCTTAAATAAATAAATATCATATTTT
1 TGGGTTGTCTTAAAGCACCTAGAAGTCATTTTATGATATTCTTAAATAAATAAATATCATATTTT
36055 TATAAATTATATATTAATTTATTTAATTA-TAGAGAAATG-TTT-TTAATATTTATTTAT
66 TATAAATTATATATTAATTTATTTAATTATTAGAGAAATGTTTTATTAATATTTATTTAT
* * *
36112 TGGGTTGTCTTAAAGCACCTAGAAGTCCTTTTCTGATATTCTTAAATAAATAAATATCATGTTTT
1 TGGGTTGTCTTAAAGCACCTAGAAGTCATTTTATGATATTCTTAAATAAATAAATATCATATTTT
36177 TATAAATTATATATTAATTTATTTAATTATTTTAGAGAAATGTTTTATTAATATTTATTTAT
66 TATAAATTATATATTAATTTATTTAATTA--TTAGAGAAATGTTTTATTAATATTTATTTAT
36239 T
1 T
36240 TTTTAATATT
Statistics
Matches: 119, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
122 90 0.76
125 10 0.08
126 3 0.03
127 16 0.13
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (125 bp):
TGGGTTGTCTTAAAGCACCTAGAAGTCATTTTATGATATTCTTAAATAAATAAATATCATATTTT
TATAAATTATATATTAATTTATTTAATTATTAGAGAAATGTTTTATTAATATTTATTTAT
Found at i:41350 original size:3 final size:3
Alignment explanation
Indices: 41344--41398 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
41334 ATAATTTTTT
*
41344 TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA -AA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41390 TAAA TAA TA
1 T-AA TAA TA
41399 TTCAAAAGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 41 0.87
4 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:51715 original size:122 final size:122
Alignment explanation
Indices: 51515--51758 Score: 461
Period size: 122 Copynumber: 2.0 Consensus size: 122
51505 TGGTTTCCTT
*
51515 GTGAGCCAAAAGAGTGCTCATTTATTGTCTGAGTCAACGGATTTGTCATTATAGCAGAGCTGCAG
1 GTGAGCCAAAAGAGTGCTCATTTATTGTCTGAGTCAACGGATTTGTCAGTATAGCAGAGCTGCAG
* *
51580 AATACAAGTTAAATAATTTAAATGATCTTTAAATGAATAAATGATATGAAATATATA
66 AATACAAGTTAAATAATTCAAATGATCTTTAAATGAAAAAATGATATGAAATATATA
51637 GTGAGCCAAAAGAGTGCTCATTTATTGTCTGAGTCAACGGATTTGTCAGTATAGCAGAGCTGCAG
1 GTGAGCCAAAAGAGTGCTCATTTATTGTCTGAGTCAACGGATTTGTCAGTATAGCAGAGCTGCAG
51702 AATACAAGTTAAATAATTCAAATGATCTTTAAATGAAAAAATGATATGAAATATATA
66 AATACAAGTTAAATAATTCAAATGATCTTTAAATGAAAAAATGATATGAAATATATA
51759 TTCTCATACT
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 119 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (122 bp):
GTGAGCCAAAAGAGTGCTCATTTATTGTCTGAGTCAACGGATTTGTCAGTATAGCAGAGCTGCAG
AATACAAGTTAAATAATTCAAATGATCTTTAAATGAAAAAATGATATGAAATATATA
Found at i:55583 original size:21 final size:21
Alignment explanation
Indices: 55572--55756 Score: 243
Period size: 21 Copynumber: 8.9 Consensus size: 21
55562 AATGTGATAG
55572 TCGACTATCGCAATGCGAACT
1 TCGACTATCGCAATGCGAACT
* *
55593 TGGACTATCGCAATGCGGACT
1 TCGACTATCGCAATGCGAACT
55614 TCGACTATCGCAATGCGAACT
1 TCGACTATCGCAATGCGAACT
*
55635 TGGACTATCGCAATGCGAACT
1 TCGACTATCGCAATGCGAACT
55656 TCGACTATCGCAATGCGAACT
1 TCGACTATCGCAATGCGAACT
*
55677 TGGACTATCGCAATGCGAA-T
1 TCGACTATCGCAATGCGAACT
* * *
55697 AT-GTA-AATCACAATGCGATA-G
1 -TCG-ACTATCGCAATGCGA-ACT
55718 TCGACTATCGCAATGCGAACT
1 TCGACTATCGCAATGCGAACT
*
55739 TGGACTATCGCAATGCGA
1 TCGACTATCGCAATGCGA
55757 TTTATTCCAA
Statistics
Matches: 144, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
20 16 0.11
21 128 0.89
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGACTATCGCAATGCGAACT
Found at i:56403 original size:6 final size:6
Alignment explanation
Indices: 56387--56425 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
56377 GTCCGTCTCG
56387 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
56426 ATACGTGTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.00, C:0.18, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:56569 original size:21 final size:21
Alignment explanation
Indices: 56543--56740 Score: 201
Period size: 21 Copynumber: 9.5 Consensus size: 21
56533 TTGGAATAAA
56543 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
56564 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
56585 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
56606 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
56626 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
* * *
56647 TCACATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
56667 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
*
56688 TCACATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
56709 TCGCATTGCGATAGTCAAAGT
1 TCGCATTGCGATAGTCCAAGT
*
56730 TCGCGTTGCGA
1 TCGCATTGCGA
56741 ATCTGGAAAC
Statistics
Matches: 149, Mismatches: 18, Indels: 20
0.80 0.10 0.11
Matches are distributed among these distances:
19 1 0.01
20 30 0.20
21 116 0.78
22 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:56589 original size:42 final size:42
Alignment explanation
Indices: 56542--56740 Score: 221
Period size: 41 Copynumber: 4.8 Consensus size: 42
56532 TTTGGAATAA
*
56542 ATCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAGT
1 ATCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCG-ACT
56585 -TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACT
1 ATCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACT
* * *
56626 ATCGCATTGCGAT-TTACATA-TTCACATTGCGATAGTCGACT
1 ATCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCGACT
* * * * *
56667 ATCGCATTGCGAT-TTACATA-TTCACATTGCGATAGTCCAAGT
1 ATCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGT-CGACT
* *
56709 -TCGCATTGCGATAGTCAAAGTTCGCGTTGCGA
1 ATCGCATTGCGATAGTCCAAGTTCGCATTGCGA
56741 ATCTGGAAAC
Statistics
Matches: 140, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
41 74 0.53
42 66 0.47
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (42 bp):
ATCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACT
Found at i:56655 original size:20 final size:20
Alignment explanation
Indices: 56630--56699 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
56620 TCGACTATCG
56630 CATTGCGATTTACATATTCA
1 CATTGCGATTTACATATTCA
* *
56650 CATTGCGATAGT-CGACTA-TCG
1 CATTGCGAT-TTAC-A-TATTCA
56671 CATTGCGATTTACATATTCA
1 CATTGCGATTTACATATTCA
56691 CATTGCGAT
1 CATTGCGAT
56700 AGTCCAAGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 2 0.05
20 23 0.56
21 14 0.34
22 2 0.05
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (20 bp):
CATTGCGATTTACATATTCA
Found at i:56716 original size:62 final size:62
Alignment explanation
Indices: 56543--56740 Score: 174
Period size: 62 Copynumber: 3.2 Consensus size: 62
56533 TTGGAATAAA
* * * * *
56543 TCGCATTGCGATAGTCCAAGT-TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGT-CGACTATCACATTGCGATAGTCCAAGTTCGCATTGCGATAGT-CAACT
* * * * *
56606 TCGCATTGCGATAGTCGACTATCGCATTGCGAT-TTACATA-TTCACATTGCGATAGTCGACT
1 TCGCATTGCGATAGTCGACTATCACATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCAACT
* *
56667 ATCGCATTGCGAT--T-TACATATTCACATTGCGATAGTCCAAGTTCGCATTGCGATAGTCAAAG
1 -TCGCATTGCGATAGTCGAC-TA-TCACATTGCGATAGTCCAAGTTCGCATTGCGATAGTC-AAC
56729 T
62 T
*
56730 TCGCGTTGCGA
1 TCGCATTGCGA
56741 ATCTGGAAAC
Statistics
Matches: 111, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
59 2 0.02
60 3 0.03
61 15 0.14
62 61 0.55
63 30 0.27
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (62 bp):
TCGCATTGCGATAGTCGACTATCACATTGCGATAGTCCAAGTTCGCATTGCGATAGTCAACT
Found at i:60282 original size:21 final size:20
Alignment explanation
Indices: 60257--60316 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
60247 CAGAACCCCA
60257 GGGGGGTATCGATTCCC-C-T
1 GGGGGG-ATCGATTCCCTCAT
*
60276 GTAGGGGGAATCGGTTCCCTCAT
1 G--GGGGG-ATCGATTCCCTCAT
60299 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
60317 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 1 0.03
20 11 0.32
21 19 0.56
22 1 0.03
23 2 0.06
ACGTcount: A:0.13, C:0.25, G:0.37, T:0.25
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAT
Found at i:60302 original size:20 final size:20
Alignment explanation
Indices: 60279--60316 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
60269 TTCCCCTGTA
*
60279 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
60299 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
60317 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:64126 original size:22 final size:21
Alignment explanation
Indices: 64084--64123 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
64074 GAGTTTGTTT
*
64084 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
64105 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
64124 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:66971 original size:60 final size:57
Alignment explanation
Indices: 66828--66971 Score: 157
Period size: 57 Copynumber: 2.5 Consensus size: 57
66818 AACACAATGA
* * *
66828 ATAGTCGAGTGACCATTTTGTAACTTTTAATAGTTAAAGGACTTAAAACAATGACTT
1 ATAGTCAAGGGACCATTTTGTAACTTTTAATAGTCAAAGGACTTAAAACAATGACTT
* * * * *
66885 ATAATCAAGGGACCATTTTATAACTTTTAATAGTCAGAGGACTCAATAAAATAAT-ATTCT
1 ATAGTCAAGGGACCATTTTGTAACTTTTAATAGTCAAAGGACT---TAAAACAATGACT-T
66945 ATAGTCAAGGGACCATTTGTGT-ACTTT
1 ATAGTCAAGGGACCATTT-TGTAACTTT
66972 ACCCTAAATT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
57 37 0.51
59 2 0.03
60 31 0.43
61 2 0.03
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (57 bp):
ATAGTCAAGGGACCATTTTGTAACTTTTAATAGTCAAAGGACTTAAAACAATGACTT
Found at i:67174 original size:25 final size:25
Alignment explanation
Indices: 67140--67192 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
67130 ATATCGTAAT
* * *
67140 GCACTACTAAAGCGGCGGCCGAAAC
1 GCACCACTAAAGCAGCGACCGAAAC
*
67165 GCACCACTAAAGCAGCGACTGAAAC
1 GCACCACTAAAGCAGCGACCGAAAC
67190 GCA
1 GCA
67193 TCACAAGCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.32, G:0.25, T:0.08
Consensus pattern (25 bp):
GCACCACTAAAGCAGCGACCGAAAC
Found at i:79296 original size:2 final size:2
Alignment explanation
Indices: 79291--79315 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
79281 AAAATATAAA
79291 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
79316 ATTAATATAA
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:79315 original size:45 final size:44
Alignment explanation
Indices: 79263--79349 Score: 165
Period size: 45 Copynumber: 2.0 Consensus size: 44
79253 GAAAATATTT
79263 TATATATAATTAATATAAAAAATATAAAATATATATATATATATA
1 TATATATAATTAATATAAAAAATATAAAATAT-TATATATATATA
79308 TATATATAATTAATATAAAAAATATAAAATATTATATATATA
1 TATATATAATTAATATAAAAAATATAAAATATTATATATATA
79350 GTCGGGACGG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 10 0.24
45 32 0.76
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (44 bp):
TATATATAATTAATATAAAAAATATAAAATATTATATATATATA
Found at i:79323 original size:36 final size:36
Alignment explanation
Indices: 79254--79349 Score: 103
Period size: 36 Copynumber: 2.8 Consensus size: 36
79244 CTCGAACCCG
*
79254 AAAATAT-TTTATATATA-AT-TAATATAAAAAATAT
1 AAAATATATATATATATATATAT-ATATAAAAAATAT
**
79288 AAAATATATATATATATATATATATATAATTAATAT
1 AAAATATATATATATATATATATATATAAAAAATAT
* *
79324 AAAAAATATA-AAATAT-TATATATATA
1 AAAATATATATATATATATATATATATA
79350 GTCGGGACGG
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
34 17 0.31
35 14 0.26
36 22 0.41
37 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (36 bp):
AAAATATATATATATATATATATATATAAAAAATAT
Found at i:83453 original size:13 final size:13
Alignment explanation
Indices: 83435--83460 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
83425 TGAAACCGAG
83435 AAAATATAATAAT
1 AAAATATAATAAT
83448 AAAATATAATAAT
1 AAAATATAATAAT
83461 TTAGATTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATATAATAAT
Found at i:88462 original size:12 final size:13
Alignment explanation
Indices: 88430--88473 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
88420 AATTCAAATT
*
88430 ATATAATCTAAAA
1 ATATAATATAAAA
*
88443 ATAAAATATAAAA
1 ATATAATATAAAA
88456 A-ATAATATAAAA
1 ATATAATATAAAA
*
88468 TTATAA
1 ATATAA
88474 CTAAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (13 bp):
ATATAATATAAAA
Found at i:89031 original size:19 final size:19
Alignment explanation
Indices: 89007--89058 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
88997 TATTTTTACT
89007 TTTTTTAATAATAAAAAT-A
1 TTTTTTAATAA-AAAAATAA
89026 TTTTTT-ATAAAAAAATAA
1 TTTTTTAATAAAAAAATAA
89044 TTTATTTAA-AAAAAA
1 TTT-TTTAATAAAAAA
89059 CTCCAAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.20
18 8 0.27
19 15 0.50
20 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTTTTAATAAAAAAATAA
Found at i:90961 original size:20 final size:20
Alignment explanation
Indices: 90920--90963 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
90910 CAAGCAGGGG
*
90920 GTATCGATACCAAGTGTCTA
1 GTATCGATACCAAGGGTCTA
*
90940 GTATCGATACTGAAGGGT-TA
1 GTATCGATAC-CAAGGGTCTA
90960 GTAT
1 GTAT
90964 TGGTACCCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (20 bp):
GTATCGATACCAAGGGTCTA
Found at i:94456 original size:17 final size:18
Alignment explanation
Indices: 94431--94477 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
94421 TATGGAATTG
* *
94431 GATTCCAATTCC-TGACA
1 GATTTCAATTCCTTCACA
94448 GATTTCAATTCCTTCACA
1 GATTTCAATTCCTTCACA
94466 GATTTCAATTCC
1 GATTTCAATTCC
94478 CTCAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Done.