Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003095.1 Hibiscus syriacus cultivar Beakdansim tig00006459_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: 59555
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1028 original size:107 final size:109
Alignment explanation
Indices: 783--1210 Score: 494
Period size: 113 Copynumber: 3.8 Consensus size: 109
773 TAGCAAAGAT
* * * *
783 TCAAATCCATCATTTGATGGATTAGCATTTTCCAATTCGAGTTCATAAT-GAAGAACTCATCATT
1 TCAAATCCATCACTTGATGGATCAGC-TTTTCCAGTTCGAGTTCATAATAGAAGAACT--TCATC
847 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTGTTTAACCTTTTTGC
63 T--AGAAGGAAGAAGAAATTCATAAT-AGAAGAATTGTTTAACC-TTTTGC
898 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAAT-GAAGAA-TTCATCT-G
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAGAAGAACTTCATCTAG
960 AAGGAAGAAGAAATTCATAAT-GAAGAATTTGTTTAAACCTTTTGC
66 AAGGAAGAAGAAATTCATAATAGAAGAA-TTGTTT-AACCTTTTGC
*
1005 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA-TTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAAT-AGAAGAACTTCATCT-
* **
1069 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAT
64 -AGAAGGAAGAAGAAATTCATAAT-AGAAGAA-TTGTTTAACCTTTTGC
* * * ****
1118 TCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTT-ATCT-
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAAT-AGAAGAACTTCATCTA
* *
1181 GAAGAGAAGAAGAAGTTCACAATGAGAAGA
65 GAAG-GAAGAAGAAATTCATAAT-AGAAGA
1211 GCCTGTTCAA
Statistics
Matches: 285, Mismatches: 17, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
106 6 0.02
107 59 0.21
108 26 0.09
109 13 0.05
110 4 0.01
111 29 0.10
112 21 0.07
113 62 0.22
114 41 0.14
115 24 0.08
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (109 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATAGAAGAACTTCATCTAG
AAGGAAGAAGAAATTCATAATAGAAGAATTGTTTAACCTTTTGC
Found at i:1097 original size:24 final size:23
Alignment explanation
Indices: 1054--1098 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1044 GTTCATAATG
*
1054 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
1077 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
1099 AACTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:1161 original size:113 final size:113
Alignment explanation
Indices: 842--1320 Score: 476
Period size: 113 Copynumber: 4.3 Consensus size: 113
832 GAAGAACTCA
* * *
842 TCATTTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA-TTGTTTAACCTTTT-TGCTCAAATC
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAT--TCAAATT
* ****
905 CATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAAT--GAAGAAT
64 CATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAT
* * **
953 TCATCT---GAAGGAAGAAGAAATTCATAAT--GAAGAATTTGTTTAAACCTTTTGCTCAAATTC
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT-AACCTTTTATTCAAATTC
* ****
1013 ATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAAT
65 ATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAT
1062 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTATTCAAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTATTCAAATTCA
* *
1127 TCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACT
66 TCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAA-T
* * * * * *
1176 T-ATCTGAAG-A-GAAGAAGAAGTTCACAATGAGAAGAGCCTGTTCAACCTTTTA--CATATT-T
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTATTCAAATTCA
* *
1235 TCACATAT-ATGTTAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAA-AAC
66 TCAC-T-TGATG---G-ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAT
*
1287 TCATCTGAA-AA--AAGAAGAAGTTAATAATGAGAAG
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG
1321 CTTATTCAAC
Statistics
Matches: 324, Mismatches: 25, Indels: 38
0.84 0.06 0.10
Matches are distributed among these distances:
106 6 0.02
107 53 0.16
108 34 0.10
109 22 0.07
110 1 0.00
111 65 0.20
112 33 0.10
113 96 0.30
114 14 0.04
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.30
Consensus pattern (113 bp):
TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTATTCAAATTCA
TCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAT
Found at i:1570 original size:3 final size:3
Alignment explanation
Indices: 1564--1609 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
1554 TACTCATTTA
* *
1564 TAT TAT TAT TAT TAT TAT TAT TAT T-T AAT TAT AAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1610 AAAAATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 1 0.03
3 37 0.97
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1594 original size:20 final size:20
Alignment explanation
Indices: 1571--1608 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1561 TTATATTATT
*
1571 ATTATTATTATTATTATTTA
1 ATTATAATTATTATTATTTA
1591 ATTATAATTATTATTATT
1 ATTATAATTATTATTATT
1609 AAAAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTATAATTATTATTATTTA
Found at i:1617 original size:20 final size:20
Alignment explanation
Indices: 1577--1620 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1567 TATTATTATT
* **
1577 ATTATTATTATTTAATTATA
1 ATTATTATTATTAAAAAATA
1597 ATTATTATTATTAAAAAATA
1 ATTATTATTATTAAAAAATA
1617 ATTA
1 ATTA
1621 CAAAACAGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTATTATTATTAAAAAATA
Found at i:1618 original size:26 final size:26
Alignment explanation
Indices: 1565--1620 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
1555 ACTCATTTAT
* ** **
1565 ATTATTATTATTATTATTATTATTTA
1 ATTATAATTATTATTATTAAAAAATA
1591 ATTATAATTATTATTATTAAAAAATA
1 ATTATAATTATTATTATTAAAAAATA
1617 ATTA
1 ATTA
1621 CAAAACAGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTATAATTATTATTATTAAAAAATA
Found at i:3087 original size:22 final size:22
Alignment explanation
Indices: 3045--3087 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3035 ATATTATAAA
* *
3045 AAATTATTATTTAATTTTATTC
1 AAATTAATATTTAATTATATTC
3067 AAATTAATATTT-ATTAATATT
1 AAATTAATATTTAATT-ATATT
3088 AAAGAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AAATTAATATTTAATTATATTC
Found at i:4648 original size:51 final size:50
Alignment explanation
Indices: 4585--4708 Score: 151
Period size: 51 Copynumber: 2.4 Consensus size: 50
4575 GTAAAACGCA
* * *
4585 CCCCCTGTACCACGCTATATGCTGATTTGGCGTT-ACGTTAAGTATAGCGCG
1 CCCCCTGTACCACGCTATACGCTGA-CTGG-GTTAACGTGAAGTATAGCGCG
* *
4636 CCTCCTGTACCACGCTATACGCTGACTGGGTTACACGTGAGGTATAGCGCG
1 CCCCCTGTACCACGCTATACGCTGACTGGGTTA-ACGTGAAGTATAGCGCG
* *
4687 CCCCCTGTTCCGCGCTATACGC
1 CCCCCTGTACCACGCTATACGC
4709 CACGTAGGGG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
49 3 0.05
50 3 0.05
51 57 0.90
ACGTcount: A:0.18, C:0.32, G:0.24, T:0.26
Consensus pattern (50 bp):
CCCCCTGTACCACGCTATACGCTGACTGGGTTAACGTGAAGTATAGCGCG
Found at i:8550 original size:9 final size:9
Alignment explanation
Indices: 8536--8564 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
8526 GAGGATTTCT
8536 TCGTCATCG
1 TCGTCATCG
8545 TCGTCATCG
1 TCGTCATCG
8554 TCGTCATCG
1 TCGTCATCG
8563 TC
1 TC
8565 ATCCTGAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.34, G:0.21, T:0.34
Consensus pattern (9 bp):
TCGTCATCG
Found at i:8929 original size:18 final size:18
Alignment explanation
Indices: 8906--8945 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
8896 AAAGGCGATG
8906 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
8924 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
8942 GCGG
1 GCGG
8946 TGGCTGCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.25
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:10477 original size:111 final size:111
Alignment explanation
Indices: 10335--10555 Score: 388
Period size: 111 Copynumber: 2.0 Consensus size: 111
10325 ATTACAAAAA
* *
10335 TTAATTCTTAATCTAGTAATCATGCATTAAATAAATCAACTAATTACTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATACTACTAATAATTTAAATTA
*
10400 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
10446 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATACTACTAATAATTTAAATTA
* *
10511 AATTAAAACGTTAAAATGTTACCGTATTAGTAAAGTGTAGAGATA
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATA
10556 CATGATTTCC
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATACTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:11262 original size:18 final size:18
Alignment explanation
Indices: 11235--11278 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
11225 GATGATCAAA
*
11235 TTGATTATTGACCATAGT
1 TTGATGATTGACCATAGT
11253 TTGATGATTGACCATAGT
1 TTGATGATTGACCATAGT
*
11271 TTAATGAT
1 TTGATGAT
11279 CTCCCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (18 bp):
TTGATGATTGACCATAGT
Found at i:19031 original size:20 final size:19
Alignment explanation
Indices: 19008--19046 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
18998 TACTAAACAT
19008 TTGGTATCGATACCCACCTG
1 TTGGTATCGATACCC-CCTG
*
19028 TTGGTATTGATACCCCCTG
1 TTGGTATCGATACCCCCTG
19047 GCGGTTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (19 bp):
TTGGTATCGATACCCCCTG
Found at i:21030 original size:21 final size:21
Alignment explanation
Indices: 20942--21072 Score: 95
Period size: 21 Copynumber: 6.1 Consensus size: 21
20932 AGAGTTCTAC
*
20942 GTGGTCCTTTGGGACATATAT
1 GTGGTCCTTTGGAACATATAT
**
20963 GTAATCCTTTGGAACATATAT
1 GTGGTCCTTTGGAACATATAT
* * *
20984 GCGATTCTTTGAGACACATAT-T
1 GTGGTCCTTTG-GA-ACATATAT
*
21006 -TGGTCCTTTGGAATATATAT
1 GTGGTCCTTTGGAACATATAT
* ** *
21026 GTGGTCCTTAAGGAGATTTCTAT
1 GTGGTCCTT-TGGA-ACATATAT
* *
21049 GTGGTCATTTGGGACATATAT
1 GTGGTCCTTTGGAACATATAT
21070 GTG
1 GTG
21073 ATCCATCGGG
Statistics
Matches: 85, Mismatches: 19, Indels: 12
0.73 0.16 0.10
Matches are distributed among these distances:
19 5 0.06
20 3 0.04
21 49 0.58
22 8 0.09
23 20 0.24
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (21 bp):
GTGGTCCTTTGGAACATATAT
Found at i:21105 original size:44 final size:44
Alignment explanation
Indices: 21006--21105 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 44
20996 GACACATATT
* * * * * *
21006 TGGTCCTTTGGAATATATATGTGGTCCTTAAGGAGATTTCTATG
1 TGGTCCTTTGGGACATATATGTGATCCATAAGGACATTTCTACG
* **
21050 TGGTCATTTGGGACATATATGTGATCCATCGGGACATTTCTACG
1 TGGTCCTTTGGGACATATATGTGATCCATAAGGACATTTCTACG
21094 TGGTCCTTTGGG
1 TGGTCCTTTGGG
21106 GAAATTTTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.38
Consensus pattern (44 bp):
TGGTCCTTTGGGACATATATGTGATCCATAAGGACATTTCTACG
Found at i:21791 original size:65 final size:66
Alignment explanation
Indices: 21715--21870 Score: 192
Period size: 65 Copynumber: 2.4 Consensus size: 66
21705 ACACCCTATT
*
21715 TCGAATGCATTTAGTGTACCGATGCATAAG-CCATGCATCGATACACCC-TTGAATATTTTGAAA
1 TCGAATGCATTTAGTGTACCGATGCATAAGACCATGCATCGATACACCCATAG-ATATTTTGAAA
21778 CA
65 CA
* * * * * *
21780 TCGAATGCATTTAGTGTACTGATGC-TCAGACCATGCATCGATGCACTCATAGTTATTTTGAAAT
1 TCGAATGCATTTAGTGTACCGATGCATAAGACCATGCATCGATACACCCATAGATATTTTGAAAC
21844 A
66 A
* * *
21845 TCAAATGTAATTAGTGTACCGATGCA
1 TCGAATGCATTTAGTGTACCGATGCA
21871 CCCCTAGTGT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 3 0.04
65 72 0.94
66 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (66 bp):
TCGAATGCATTTAGTGTACCGATGCATAAGACCATGCATCGATACACCCATAGATATTTTGAAAC
A
Found at i:23709 original size:12 final size:12
Alignment explanation
Indices: 23692--23716 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23682 TAGCTTGCTC
23692 AAGAAGAAGATA
1 AAGAAGAAGATA
23704 AAGAAGAAGATA
1 AAGAAGAAGATA
23716 A
1 A
23717 TAGCTTGGGA
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:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (12 bp):
AAGAAGAAGATA
Found at i:24181 original size:42 final size:41
Alignment explanation
Indices: 24135--24253 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 41
24125 TTTGTTGTAA
*
24135 AAACGCTACAATAGAGTTGACATATAGCGGCGTTTTTACAAC
1 AAACGC-ACAATAGAGTTGAAATATAGCGGCGTTTTTACAAC
* * * *
24177 AAACGCCACAATAGAGTGGTAAAT-TAGCGGCGTTTATACCAT
1 AAACG-CACAATAGAGTTG-AAATATAGCGGCGTTTTTACAAC
*
24219 AAACGCAGCAATAGA-TT-AATATATAGTGGCGTTTT
1 AAACGCA-CAATAGAGTTGAA-ATATAGCGGCGTTTT
24254 AGCCAAAACG
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 13 0.20
42 43 0.67
43 4 0.06
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (41 bp):
AAACGCACAATAGAGTTGAAATATAGCGGCGTTTTTACAAC
Found at i:24280 original size:82 final size:83
Alignment explanation
Indices: 24154--24331 Score: 227
Period size: 82 Copynumber: 2.1 Consensus size: 83
24144 AATAGAGTTG
* * *
24154 ACATATAGCGGCGTTTTTA-CAACAAACGCCACAATAGAGTGGTAAATTAGCGGCGTTTATACCA
1 ACATATAGTGGCG-TTTTAGCCA-AAACGCCACAATAGAGTGGTAAATTAGCGGCATTTATACCA
*
24218 TAAACGCAGCAATAGATTA-
64 CAAACGCAGCAATAGATTAC
* **
24237 ATATATAGTGGCGTTTTAGCCAAAACGCCGTAATAGA-TCGGTAAATTAGCGGCATTTATACCAC
1 ACATATAGTGGCGTTTTAGCCAAAACGCCACAATAGAGT-GGTAAATTAGCGGCATTTATACCAC
* *
24301 AAACGCCGTAATAGATTAC
65 AAACGCAGCAATAGATTAC
24320 ACATATAGTGGC
1 ACATATAGTGGC
24332 ATTTATTCTT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
81 1 0.01
82 57 0.70
83 24 0.29
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (83 bp):
ACATATAGTGGCGTTTTAGCCAAAACGCCACAATAGAGTGGTAAATTAGCGGCATTTATACCACA
AACGCAGCAATAGATTAC
Found at i:24307 original size:42 final size:41
Alignment explanation
Indices: 24159--24316 Score: 162
Period size: 42 Copynumber: 3.8 Consensus size: 41
24149 AGTTGACATA
* * *
24159 TAGCGGCGTTTTTACAACAAACGCCACAATAGAGTGGTAAAT
1 TAGCGGCGTTTATACCACAAACGCCGCAATAGA-TGGTAAAT
* *
24201 TAGCGGCGTTTATACCATAAACGCAGCAATAGAT--TAATAT
1 TAGCGGCGTTTATACCACAAACGCCGCAATAGATGGTAA-AT
* *
24241 ATAGTGGCGTTT-TAGCCA-AAACGCCGTAATAGATCGGTAAAT
1 -TAGCGGCGTTTATA-CCACAAACGCCGCAATAGAT-GGTAAAT
* *
24283 TAGCGGCATTTATACCACAAACGCCGTAATAGAT
1 TAGCGGCGTTTATACCACAAACGCCGCAATAGAT
24317 TACACATATA
Statistics
Matches: 98, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
39 3 0.03
40 18 0.18
41 26 0.27
42 48 0.49
43 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (41 bp):
TAGCGGCGTTTATACCACAAACGCCGCAATAGATGGTAAAT
Found at i:24333 original size:42 final size:41
Alignment explanation
Indices: 24209--24438 Score: 152
Period size: 41 Copynumber: 5.6 Consensus size: 41
24199 ATTAGCGGCG
* * *
24209 TTTATACCATAAACGCAGCAATAGAT-TAATATATAGTGGCG
1 TTTATACCA-AAACGCCGTAATAGATCTAATATATAGTGGCA
*
24250 TTT-TAGCCAAAACGCCGTAATAGATCGGTAA-AT-TAGCGGCA
1 TTTATA-CCAAAACGCCGTAATAGATC--TAATATATAGTGGCA
*
24291 TTTATACCACAAACGCCGTAATAGAT-TACACATATAGTGGCA
1 TTTATACCA-AAACGCCGTAATAGATCTA-ATATATAGTGGCA
* * * * * *
24333 TTTATTCTTAAAATGCCGTAATAGTTCTAATAAATAGTGGCG
1 TTTATAC-CAAAACGCCGTAATAGATCTAATATATAGTGGCA
* * * *
24375 TTTTTA-GACAAACGCCGTAATAG-TGTTAATCA-ATAGTGGCG
1 TTTATACCA-AAACGCCGTAATAGAT-CTAAT-ATATAGTGGCA
* * *
24416 TTTTTACAAAAACGCCGCAATAG
1 TTTATACCAAAACGCCGTAATAG
24439 TTTTAATCAA
Statistics
Matches: 155, Mismatches: 19, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
39 2 0.01
40 19 0.12
41 65 0.42
42 63 0.41
43 6 0.04
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (41 bp):
TTTATACCAAAACGCCGTAATAGATCTAATATATAGTGGCA
Found at i:24386 original size:83 final size:82
Alignment explanation
Indices: 24299--24502 Score: 204
Period size: 82 Copynumber: 2.5 Consensus size: 82
24289 CATTTATACC
* * *
24299 ACAAACGCCGTAATAG-ATTACA-CATATAGTGGCATTTATT-CTTAAAATGCCGTAATAGTTCT
1 ACAAACGCCGTAATAGTATTA-ATCA-ATAGTGGCATTT-TTAC-AAAAACGCCGCAATAGTTCT
24361 AATAAATAGTGGCGTTTTTAG
62 AATAAATAGTGGCGTTTTTAG
* * * *
24382 ACAAACGCCGTAATAGTGTTAATCAATAGTGGCGTTTTTACAAAAACGCCGCAATAGTTTTAATC
1 ACAAACGCCGTAATAGTATTAATCAATAGTGGCATTTTTACAAAAACGCCGCAATAGTTCTAATA
*
24447 AATAGTGTCGTTTTTTTA-
66 AATAGTGGCG--TTTTTAG
** *
24465 ACAAACGCCACAATA--ATGTAATCAATAGTGGCGTTTTT
1 ACAAACGCCGTAATAGTAT-TAATCAATAGTGGCATTTTT
24503 TTGTATAAAC
Statistics
Matches: 104, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
81 1 0.01
82 50 0.48
83 42 0.40
84 11 0.11
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (82 bp):
ACAAACGCCGTAATAGTATTAATCAATAGTGGCATTTTTACAAAAACGCCGCAATAGTTCTAATA
AATAGTGGCGTTTTTAG
Found at i:24398 original size:41 final size:39
Alignment explanation
Indices: 24347--24502 Score: 177
Period size: 41 Copynumber: 3.8 Consensus size: 39
24337 TTCTTAAAAT
* *
24347 GCCGTAATAGTTCTAATAAATAGTGGCGTTTTTAGACAAAC
1 GCCGCAATAGTT-TAATCAATAGTGGCGTTTTTA-ACAAAC
* *
24388 GCCGTAATAGTGTTAATCAATAGTGGCGTTTTTACAAAAAC
1 GCCGCAATAGT-TTAATCAATAGTGGCGTTTTTA-ACAAAC
*
24429 GCCGCAATAGTTTTAATCAATAGTGTCGTTTTTTTAACAAAC
1 GCCGCAATAG-TTTAATCAATAGTGGCG--TTTTTAACAAAC
* * *
24471 GCCACAATAATGTAATCAATAGTGGCGTTTTT
1 GCCGCAATAGTTTAATCAATAGTGGCGTTTTT
24503 TTGTATAAAC
Statistics
Matches: 101, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
39 5 0.05
41 75 0.74
42 15 0.15
43 6 0.06
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (39 bp):
GCCGCAATAGTTTAATCAATAGTGGCGTTTTTAACAAAC
Found at i:24487 original size:82 final size:82
Alignment explanation
Indices: 24342--24502 Score: 218
Period size: 82 Copynumber: 2.0 Consensus size: 82
24332 ATTTATTCTT
* * ** *
24342 AAAATGCCGTAATAGTTCTAATAAATAGTGGCGTTTTTAGACAAACGCCGTAATAGTGTTAATCA
1 AAAACGCCGCAATAGTTCTAATAAATAGTGGCGTTTTTAGACAAACGCCACAATAATGTTAATCA
24407 ATAGTGGCGTTTTTACA
66 ATAGTGGCGTTTTTACA
* * *
24424 AAAACGCCGCAATAGTTTTAATCAATAGTGTCGTTTTTTTA-ACAAACGCCACAATAATG-TAAT
1 AAAACGCCGCAATAGTTCTAATAAATAGTGGCG--TTTTTAGACAAACGCCACAATAATGTTAAT
24487 CAATAGTGGCGTTTTT
64 CAATAGTGGCGTTTTT
24503 TTGTATAAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
82 48 0.70
83 15 0.22
84 6 0.09
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (82 bp):
AAAACGCCGCAATAGTTCTAATAAATAGTGGCGTTTTTAGACAAACGCCACAATAATGTTAATCA
ATAGTGGCGTTTTTACA
Found at i:25079 original size:43 final size:42
Alignment explanation
Indices: 25008--25270 Score: 168
Period size: 41 Copynumber: 6.3 Consensus size: 42
24998 TAAAAGGTAA
* * * *
25008 TTAGCGGCGTTTGTATCTAGAAACGCCGCTATAGA-TCTGACAT
1 TTAGTGGCGTTTGTATCCAAAAACGCCGCTATAAACTCT-AC-T
* *
25051 TTTGTGGCGTTTGTATCCAAAAATGCCGCTATAAACTCTACT
1 TTAGTGGCGTTTGTATCCAAAAACGCCGCTATAAACTCTACT
* * *
25093 TTAGTGGCGTTTTGAATGC--AAACGCCTCTA-AAGACTCGTACT
1 TTAGTGGCG-TTTGTATCCAAAAACGCCGCTATAA-ACTC-TACT
** * * * * *
25135 TTAGTAACGTTTTTAT--ATAAACGCTGCTATAGACTAGTACT
1 TTAGTGGCGTTTGTATCCAAAAACGCCGCTATAAACT-CTACT
* * *
25176 TTAGTGGCGTTTTTAT--ACAAACGCCGCTATAGACTCGTACT
1 TTAGTGGCGTTTGTATCCAAAAACGCCGCTATAAACTC-TACT
* * * *
25217 GTAGTGGCGTTTTGAATGC--AAACGCCGCTATAGACTCGTACT
1 TTAGTGGCG-TTTGTATCCAAAAACGCCGCTATAAACTC-TACT
25259 TTAGTGGCGTTT
1 TTAGTGGCGTTT
25271 TGAATACAAA
Statistics
Matches: 180, Mismatches: 28, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
40 2 0.01
41 80 0.44
42 57 0.32
43 38 0.21
44 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (42 bp):
TTAGTGGCGTTTGTATCCAAAAACGCCGCTATAAACTCTACT
Found at i:25169 original size:41 final size:41
Alignment explanation
Indices: 25028--25327 Score: 293
Period size: 42 Copynumber: 7.2 Consensus size: 41
25018 TTGTATCTAG
* * *
25028 AAACGCCGCTATAGA-TC-TGACATTTTGTGGCGTTTGTATCCAA
1 AAACGCCGCTATAGACTCGT-AC-TTTAGTGGCGTTTTTAT--AC
* * * *
25071 AAATGCCGCTATAAACTC-TACTTTAGTGGCGTTTTGAATGC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTT-TATAC
* * ** *
25112 AAACGCCTCTAAAGACTCGTACTTTAGTAACGTTTTTATAT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
25153 AAACGCTGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
25194 AAACGCCGCTATAGACTCGTACTGTAGTGGCGTTTTGAATGC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTT-TATAC
*
25236 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTT-TATAC
** *
25278 AAACGCTACTA-ATGACTCGTACTTTAGTGGCGTTTGTATTTAC
1 AAACGCCGCTATA-GACTCGTACTTTAGTGGCGTTT-T-TATAC
25321 AAACGCC
1 AAACGCC
25328 ATAATTTTAC
Statistics
Matches: 215, Mismatches: 36, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
41 84 0.39
42 101 0.47
43 27 0.13
44 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (41 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
Found at i:25240 original size:124 final size:126
Alignment explanation
Indices: 25054--25327 Score: 367
Period size: 124 Copynumber: 2.2 Consensus size: 126
25044 CTGACATTTT
** * * *
25054 GTGGCGTTTGTATCCAAAAATGCCGCTATAAACTCTACTTTAGTGGCGTTTTGAATGCAAACGCC
1 GTGGCGTTTGTATATACAAACGCCGCTATAAACTCTACTGTAGTGGCGTTTTGAATGCAAACGCC
* * * *
25119 TCTAAAGACTCGTACTTTAGTAACGTTTT-TATATAAACGCTGCT-ATAGACTAGTACTTTA
66 GCTAAAGACTCGTACTTTAGTAACGTTTTGAATACAAACGCTACTAAT-GACTAGTACTTTA
*
25179 GTGGCGTTT-T-TATACAAACGCCGCTATAGACTCGTACTGTAGTGGCGTTTTGAATGCAAACGC
1 GTGGCGTTTGTATATACAAACGCCGCTATAAACTC-TACTGTAGTGGCGTTTTGAATGCAAACGC
* ** *
25242 CGCTATAGACTCGTACTTTAGTGGCGTTTTGAATACAAACGCTACTAATGACTCGTACTTTA
65 CGCTAAAGACTCGTACTTTAGTAACGTTTTGAATACAAACGCTACTAATGACTAGTACTTTA
*
25304 GTGGCGTTTGTATTTACAAACGCC
1 GTGGCGTTTGTATATACAAACGCC
25328 ATAATTTTAC
Statistics
Matches: 129, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
123 18 0.14
124 55 0.43
125 42 0.33
126 3 0.02
127 11 0.09
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (126 bp):
GTGGCGTTTGTATATACAAACGCCGCTATAAACTCTACTGTAGTGGCGTTTTGAATGCAAACGCC
GCTAAAGACTCGTACTTTAGTAACGTTTTGAATACAAACGCTACTAATGACTAGTACTTTA
Found at i:27858 original size:21 final size:21
Alignment explanation
Indices: 27827--27944 Score: 173
Period size: 21 Copynumber: 5.6 Consensus size: 21
27817 AGGGAAACAG
* * *
27827 AGAGAGCAGCAGCGGAAGCAG
1 AGAGAGAAGCAGCGGCAGCAC
* *
27848 AGAAAGAAGCAGCGGTAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
27869 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
*
27890 AGAGAGAAGCAACGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
*
27911 AGAGAGAAGCAACGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
27932 AGAGAGAAGCAGC
1 AGAGAGAAGCAGC
27945 ATATCAGAAG
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 89 1.00
ACGTcount: A:0.42, C:0.21, G:0.36, T:0.01
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:28647 original size:43 final size:43
Alignment explanation
Indices: 28409--28647 Score: 266
Period size: 43 Copynumber: 5.6 Consensus size: 43
28399 GTCGCAAGAC
* * * * * *
28409 ATCAACACCTACTGTGGCGTTTTAGC-GAAAAATGCCACTAAAC
1 ATCAACACCTATTGCGGCGTTTT-TCTGAAAAACGCCGCTAAAT
* *
28452 ATCATA-ACCTATTGCGGCGTTTGTCTGAAAAACGCTGCTAAAT
1 ATCA-ACACCTATTGCGGCGTTTTTCTGAAAAACGCCGCTAAAT
* * *
28495 ATTAACACCTATTGCGACGTTTTTATGAAAAACGCCGCTAAAT
1 ATCAACACCTATTGCGGCGTTTTTCTGAAAAACGCCGCTAAAT
* * * *
28538 ATCAACACCTATTACAGCGTTTGTCTGAAAAACGCTGCTAAAT
1 ATCAACACCTATTGCGGCGTTTTTCTGAAAAACGCCGCTAAAT
* *
28581 ATCAACACCTATTGCGGCGTTTTTGTGACAAACGCCGCTAAAT
1 ATCAACACCTATTGCGGCGTTTTTCTGAAAAACGCCGCTAAAT
* * *
28624 ATCAATACCTATTGTGGCATTTTT
1 ATCAACACCTATTGCGGCGTTTTT
28648 TTGTGAAAAA
Statistics
Matches: 164, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
42 2 0.01
43 161 0.98
44 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (43 bp):
ATCAACACCTATTGCGGCGTTTTTCTGAAAAACGCCGCTAAAT
Found at i:31599 original size:23 final size:23
Alignment explanation
Indices: 31570--31696 Score: 200
Period size: 23 Copynumber: 5.5 Consensus size: 23
31560 GCACCGAATT
* *
31570 ACCACATAGATTTGTCCCGAAGG
1 ACCACATAGAATTGTCCTGAAGG
** *
31593 AAAACATAGAATTATCCTGAAGG
1 ACCACATAGAATTGTCCTGAAGG
31616 ACCACATAGAATTGTCCTGAAGG
1 ACCACATAGAATTGTCCTGAAGG
*
31639 ACCACATAGAATTGTCTTGAAGG
1 ACCACATAGAATTGTCCTGAAGG
31662 ACCACATAGAATTGTCCTGAAGG
1 ACCACATAGAATTGTCCTGAAGG
31685 ACCACATAGAAT
1 ACCACATAGAAT
31697 CCTTCAACTC
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 94 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (23 bp):
ACCACATAGAATTGTCCTGAAGG
Found at i:36375 original size:45 final size:45
Alignment explanation
Indices: 36326--36619 Score: 428
Period size: 45 Copynumber: 6.5 Consensus size: 45
36316 TTTAAATCTA
* *
36326 ATTATCGACATAAAAGGTGCCATTAATGAAAATGCATAACTGTGC
1 ATTATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGGTGC
* * *
36371 ATTATCGAAATAAAATGTGCCACTAATGAAAATACATAACGGTGC
1 ATTATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGGTGC
* ** *
36416 ATTATCGGCATAAAAGGTGCCACTAATGAAGCTGCATAACGGTGT
1 ATTATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGGTGC
* * * *
36461 ATTATCAACATAAAAGGTGTCATTAATGAAAATGCATAACTGTGC
1 ATTATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGGTGC
* *
36506 ATTATCAACATAAAAGGTGCCACTAATGAAAATGCATAACTGTGC
1 ATTATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGGTGC
*
36551 ATTATCGGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGC
1 ATTATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGGTGC
36596 ATTATC-AGCATAAAAGGTGCCACT
1 ATTATCGA-CATAAAAGGTGCCACT
36620 CGTGGTATTC
Statistics
Matches: 222, Mismatches: 26, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 222 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (45 bp):
ATTATCGACATAAAAGGTGCCACTAATGAAAATGCATAACGGTGC
Found at i:36501 original size:135 final size:135
Alignment explanation
Indices: 36326--36617 Score: 487
Period size: 135 Copynumber: 2.2 Consensus size: 135
36316 TTTAAATCTA
* *
36326 ATTATCGACATAAAAGGTGCCATTAATGAAAATGCATAACTGTGCATTATCGAA-ATAAAATGTG
1 ATTATCAACATAAAAGGTGCCATTAATGAAAATGCATAACTGTGCATTATC-AACATAAAAGGTG
**
36390 CCACTAATGAAAATACATAACGGTGCATTATCGGCATAAAAGGTGCCACTAATGAAGCTGCATAA
65 CCACTAATGAAAATACATAACGGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATGCATAA
*
36455 CGGTGT
130 CGGTGC
*
36461 ATTATCAACATAAAAGGTGTCATTAATGAAAATGCATAACTGTGCATTATCAACATAAAAGGTGC
1 ATTATCAACATAAAAGGTGCCATTAATGAAAATGCATAACTGTGCATTATCAACATAAAAGGTGC
* *
36526 CACTAATGAAAATGCATAACTGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATGCATAAC
66 CACTAATGAAAATACATAACGGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATGCATAAC
36591 GGTGC
131 GGTGC
*
36596 ATTATCAGCATAAAAGGTGCCA
1 ATTATCAACATAAAAGGTGCCA
36618 CTCGTGGTAT
Statistics
Matches: 146, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
134 2 0.01
135 144 0.99
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (135 bp):
ATTATCAACATAAAAGGTGCCATTAATGAAAATGCATAACTGTGCATTATCAACATAAAAGGTGC
CACTAATGAAAATACATAACGGTGCATTATCGGCATAAAAGGTGCCACTAATGAAAATGCATAAC
GGTGC
Found at i:42730 original size:20 final size:21
Alignment explanation
Indices: 42701--42741 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
42691 ATATGTAATT
42701 AATATACATAT-ATATGTTTTA
1 AATATACATATGATA-GTTTTA
42722 AATAT-CATATGATAGTTTTA
1 AATATACATATGATAGTTTTA
42742 CTTGAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (21 bp):
AATATACATATGATAGTTTTA
Found at i:43212 original size:24 final size:24
Alignment explanation
Indices: 43163--43230 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
43153 TGATTAGGAC
* *
43163 ATAATAAGCCAAGATATA--CAAA
1 ATAATAGGCCAAAATATATCCAAA
* * *
43185 ATAAT-GATCCAACATATATCCAAC
1 ATAATAG-GCCAAAATATATCCAAA
43209 ATAATAGGCCAAAATATATCCA
1 ATAATAGGCCAAAATATATCCA
43231 TATGAAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
22 14 0.39
24 21 0.58
25 1 0.03
ACGTcount: A:0.51, C:0.19, G:0.07, T:0.22
Consensus pattern (24 bp):
ATAATAGGCCAAAATATATCCAAA
Found at i:43298 original size:18 final size:18
Alignment explanation
Indices: 43277--43316 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
43267 ATATGAAATC
43277 CAAAATAT-TCATCATAAT
1 CAAAATATCTCA-CATAAT
*
43295 CAAAATATCTGACATAAT
1 CAAAATATCTCACATAAT
43313 CAAA
1 CAAA
43317 TCATCCCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.28
Consensus pattern (18 bp):
CAAAATATCTCACATAAT
Found at i:43520 original size:21 final size:21
Alignment explanation
Indices: 43496--43537 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43486 GAAATGAGTC
*
43496 TCCAAGGTGCGAAGATGAGCA
1 TCCAAGGTGCCAAGATGAGCA
* *
43517 TCCATGGTGCCAATATGAGCA
1 TCCAAGGTGCCAAGATGAGCA
43538 GTCACATCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (21 bp):
TCCAAGGTGCCAAGATGAGCA
Found at i:46867 original size:58 final size:56
Alignment explanation
Indices: 46766--46929 Score: 161
Period size: 58 Copynumber: 2.9 Consensus size: 56
46756 GTCCACATTC
* * * *
46766 AAAAATTACAAAAATATCACTTTATTAAAAATAATTACAAAAATATCACCG-TTATA
1 AAAAATTCCCAAAATATCA-TTTTTTAAAAATAATTACCAAAATATCACCGTTTATA
* ** *
46822 CAAATAATTCCCAAAATATCATTGTTTTAAAAATAATTACCAAAATGTCAATGTTTTTA
1 -AAA-AATTCCCAAAATATCATT-TTTTAAAAATAATTACCAAAATATCACCGTTTATA
* * *
46881 AAAAATTCCCAAAATGTTACA-TTTTTCAAAATAATTCCCAAAATATCAC
1 AAAAATTCCCAAAAT-AT-CATTTTTTAAAAATAATTACCAAAATATCAC
46930 TGGGTCGGGT
Statistics
Matches: 89, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
57 40 0.45
58 43 0.48
59 6 0.07
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (56 bp):
AAAAATTCCCAAAATATCATTTTTTAAAAATAATTACCAAAATATCACCGTTTATA
Found at i:46876 original size:29 final size:29
Alignment explanation
Indices: 46776--46928 Score: 141
Period size: 29 Copynumber: 5.3 Consensus size: 29
46766 AAAAATTACA
* * *
46776 AAAATATCACT-TTATTAAAAATAATTACA
1 AAAATATCAATGTT-TTAAAAATAATTCCC
** * *
46805 AAAATATCACCGTTATACAAATAATTCCC
1 AAAATATCAATGTTTTAAAAATAATTCCC
* *
46834 AAAATATCATTGTTTTAAAAATAATTACC
1 AAAATATCAATGTTTTAAAAATAATTCCC
* *
46863 AAAATGTCAATGTTTTTAAAA-AATTCCC
1 AAAATATCAATGTTTTAAAAATAATTCCC
* * *
46891 AAAATGTTACAT-TTTTCAAAATAATTCCC
1 AAAATATCA-ATGTTTTAAAAATAATTCCC
46920 AAAATATCA
1 AAAATATCA
46929 CTGGGTCGGG
Statistics
Matches: 103, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
28 22 0.21
29 79 0.77
30 2 0.02
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATATCAATGTTTTAAAAATAATTCCC
Found at i:48424 original size:20 final size:20
Alignment explanation
Indices: 48395--48449 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
48385 TATCGGACCC
*
48395 AAAGTATCGAAACT-TTAAGG
1 AAAGTTTCGAAACTCTTAA-G
* *
48415 AAAGTTTCGAAGCTCTTGAG
1 AAAGTTTCGAAACTCTTAAG
*
48435 ATAGTTTCGAAACTC
1 AAAGTTTCGAAACTC
48450 AGGAAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (20 bp):
AAAGTTTCGAAACTCTTAAG
Found at i:54110 original size:6 final size:6
Alignment explanation
Indices: 54099--54124 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
54089 TTAAAGGTAA
54099 GTAAAT GTAAAT GTAAAT GTAAAT GT
1 GTAAAT GTAAAT GTAAAT GTAAAT GT
54125 TTTAAGGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (6 bp):
GTAAAT
Found at i:57579 original size:24 final size:24
Alignment explanation
Indices: 57547--57603 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
57537 TGATATTCGA
57547 TCTTCATCATCATCATGTTCAAGT
1 TCTTCATCATCATCATGTTCAAGT
57571 TCTTCATCATCATCATGTTCAAGT
1 TCTTCATCATCATCATGTTCAAGT
57595 TCTTCATCA
1 TCTTCATCA
57604 CGCCTAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.26, G:0.07, T:0.42
Consensus pattern (24 bp):
TCTTCATCATCATCATGTTCAAGT
Done.