Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014713.1 Corchorus olitorius cultivar O-4 contig14746, 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: 31282
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:708 original size:21 final size:21
Alignment explanation
Indices: 684--723 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
674 CCTCCGCCGT
684 GAAACAAACTCTGAAATCCTC
1 GAAACAAACTCTGAAATCCTC
*
705 GAAACCAACTCTGAAATCC
1 GAAACAAACTCTGAAATCC
724 CTAATCCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.30, G:0.10, T:0.17
Consensus pattern (21 bp):
GAAACAAACTCTGAAATCCTC
Found at i:5567 original size:104 final size:103
Alignment explanation
Indices: 5322--5530 Score: 355
Period size: 104 Copynumber: 2.0 Consensus size: 103
5312 CAAATCTAGA
* *
5322 ACTACCTTGTTCACTATTTTAATGACAAACACAAAATCCTCTTGTTTTATTTCAAATTGTCGATA
1 ACTACCTTGTTCACTATATCAATGACAAACACAAAATCCTCTTGTTTTATTTCAAATTGTCGATA
5387 TTTTATGATTTTTCAGCAAAAACACAAACTATCTTTTG
66 TTTTATGATTTTTCAGCAAAAACACAAACTATCTTTTG
* *
5425 AACTACCTTGTTCACTATTTTAATGACAAACACAAAATCCTCTTGTTTTATTTCAAATTGTCGAT
1 -ACTACCTTGTTCACTATATCAATGACAAACACAAAATCCTCTTGTTTTATTTCAAATTGTCGAT
5490 ATTTTTATGATTTTTCAGCAAAAACACAAACTATCCTTTTG
65 A-TTTTATGATTTTTCAGCAAAAACACAAACTAT-CTTTTG
5531 CACTGTTCGA
Statistics
Matches: 103, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
104 65 0.63
105 32 0.31
106 6 0.06
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.41
Consensus pattern (103 bp):
ACTACCTTGTTCACTATATCAATGACAAACACAAAATCCTCTTGTTTTATTTCAAATTGTCGATA
TTTTATGATTTTTCAGCAAAAACACAAACTATCTTTTG
Found at i:6687 original size:21 final size:21
Alignment explanation
Indices: 6661--6702 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6651 AATCCTTCAA
6661 ACAGGAAATATACCAAATTCT
1 ACAGGAAATATACCAAATTCT
*
6682 ACAGGAAATGTACCAAATTCT
1 ACAGGAAATATACCAAATTCT
6703 TAGCATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (21 bp):
ACAGGAAATATACCAAATTCT
Found at i:12955 original size:46 final size:45
Alignment explanation
Indices: 12885--12977 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 45
12875 AAGTCATGTG
12885 TCTTTACTTTTACACATTTTGACAGAATAATAGAAGGAAGGAAAT
1 TCTTTACTTTTACACATTTTGACAGAATAATAGAAGGAAGGAAAT
* *
12930 TCTTTACTTTTACCACATTTTGACAGAATGATAGATGGAAGGAAAT
1 TCTTTACTTTTA-CACATTTTGACAGAATAATAGAAGGAAGGAAAT
12976 TC
1 TC
12978 AAAAGACTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 12 0.27
46 33 0.73
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (45 bp):
TCTTTACTTTTACACATTTTGACAGAATAATAGAAGGAAGGAAAT
Found at i:25545 original size:15 final size:16
Alignment explanation
Indices: 25522--25554 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
25512 TATGGGTATA
25522 TTTCTATTTTCGTTAT
1 TTTCTATTTTCGTTAT
*
25538 TTTC-ATTTTCTTTAT
1 TTTCTATTTTCGTTAT
25553 TT
1 TT
25555 GAATCAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTCTATTTTCGTTAT
Found at i:27038 original size:44 final size:44
Alignment explanation
Indices: 26892--27195 Score: 309
Period size: 44 Copynumber: 7.0 Consensus size: 44
26882 TAACAAACAT
* * * * *
26892 TAAAAAAAGGTGATCGATGAGAGCTCTCTCTCTAAAC-ATTTAAC
1 TAAAAAAA-GTGACCGATGAGAGCTATCTCTCCAAACAATTAAAA
* * * *
26936 T-AAAAGAGTGACCGATGAGAGCTGTCTCTCCAAAC-GTT-GAA
1 TAAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAATTAAAA
* * * *
26977 T-TAAAAAGTGACCGATGAGAGTTACCTCTCGAAACAATTAAAA
1 TAAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAATTAAAA
* * ** * *
27020 TAAAAAAAGTAACTGATGAGAGCCGTCTCTCCAAAC-ATTTAAT
1 TAAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAATTAAAA
*
27063 TAAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAACATT-GAA
1 TAAAAAAAGTGACCGATGAGAGCTATCTCTCCAAAC-A-ATTAAAA
* *
27108 TTAAAAAAGTGACCGATGAGAGCTATCTCTCGAAACAATTAAAA
1 TAAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAATTAAAA
*
27152 T-AAAAAAGTAGACCGATGAGAGCTGTCTCTCCAAACAATTAAAA
1 TAAAAAAAGT-GACCGATGAGAGCTATCTCTCCAAACAATTAAAA
27196 AGGTGACAAA
Statistics
Matches: 216, Mismatches: 36, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
41 30 0.14
42 29 0.13
43 56 0.26
44 63 0.29
45 35 0.16
46 3 0.01
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (44 bp):
TAAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAATTAAAA
Found at i:27153 original size:132 final size:127
Alignment explanation
Indices: 26906--27193 Score: 409
Period size: 132 Copynumber: 2.2 Consensus size: 127
26896 AAAAGGTGAT
* * *
26906 CGATGAGAGCTC-TCTCTCTAAACATTTAACTAAAAGAGTGACCGATGAGAGCTGTCTCTCCAAA
1 CGATGAGAGC-CGTCTCTCCAAACATTTAACTAAAAAAGTGACCGATGAGAGCTATCTCTCCAAA
* *
26970 CGTTGAATTAAAAAGTGACCGATGAGAGTTACCTCTCGAAACAATTAAAATAAAAAAAGTA-AC
65 CATTGAATTAAAAAGTGACCGATGAGAGCTACCTCTCGAAACAATTAAAAT-AAAAAAGTAGAC
* *
27033 TGATGAGAGCCGTCTCTCCAAACATTTAATTAAAAAAAGTGACCGATGAGAGCTATCTCTCCAAA
1 CGATGAGAGCCGTCTCTCCAAACATTTAACT-AAAAAAGTGACCGATGAGAGCTATCTCTCC--A
*
27098 CAACATTGAATTAAAAAAGTGACCGATGAGAGCTATCTCTCGAAACAATTAAAATAAAAAAGTAG
63 -AACATTGAATT-AAAAAGTGACCGATGAGAGCTACCTCTCGAAACAATTAAAATAAAAAAGTAG
27163 AC
126 AC
* *
27165 CGATGAGAGCTGTCTCTCCAAACAATTAA
1 CGATGAGAGCCGTCTCTCCAAACATTTAA
27194 AAAGGTGACA
Statistics
Matches: 143, Mismatches: 11, Indels: 9
0.88 0.07 0.06
Matches are distributed among these distances:
126 1 0.01
127 26 0.18
128 28 0.20
130 1 0.01
131 19 0.13
132 68 0.48
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (127 bp):
CGATGAGAGCCGTCTCTCCAAACATTTAACTAAAAAAGTGACCGATGAGAGCTATCTCTCCAAAC
ATTGAATTAAAAAGTGACCGATGAGAGCTACCTCTCGAAACAATTAAAATAAAAAAGTAGAC
Found at i:27336 original size:98 final size:97
Alignment explanation
Indices: 27113--27381 Score: 367
Period size: 98 Copynumber: 2.7 Consensus size: 97
27103 TTGAATTAAA
* * *
27113 AAAGTGACCGATGAGAGCTATCTCTCGAAACAATTAAAATAAAAAAGTAGACCGATGAGAGCTGT
1 AAAGAGACCGATGAGAGCTATCTCTCGAAACAA-CAAATTAAAAAAGT-GACCGATGAGAGCTGT
* *
27178 CTCTCCAAACAATTAAAAAGGTGACAAATATTTAAG
64 CTCTCC--ACAATTAAAAAAGTGACAAATATTGAAG
* * *
27214 AAAGTGACCGGTGAGAGCTATCTCTCGAAACAACAAATTAAAAAAGTGACCGATGAGAGATGTCT
1 AAAGAGACCGATGAGAGCTATCTCTCGAAACAACAAATTAAAAAAGTGACCGATGAGAGCTGTCT
27279 CTCCACAATTAAAAAAAGTGACAAATATTGAAG
66 CTCCACAATT-AAAAAAGTGACAAATATTGAAG
* * * * * *
27312 AAAGAGATCGATGAGAGTTCTCTCTCAAAACAACAAATTGAAAAAGTGACCAATGAGAGCTGTCT
1 AAAGAGACCGATGAGAGCTATCTCTCGAAACAACAAATTAAAAAAGTGACCGATGAGAGCTGTCT
27377 CTCCA
66 CTCCA
27382 AACATTTAAT
Statistics
Matches: 152, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
97 6 0.04
98 81 0.53
99 21 0.14
100 12 0.08
101 32 0.21
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (97 bp):
AAAGAGACCGATGAGAGCTATCTCTCGAAACAACAAATTAAAAAAGTGACCGATGAGAGCTGTCT
CTCCACAATTAAAAAAGTGACAAATATTGAAG
Found at i:27432 original size:152 final size:152
Alignment explanation
Indices: 27252--27543 Score: 345
Period size: 152 Copynumber: 1.9 Consensus size: 152
27242 AACAACAAAT
* * * *
27252 TAAAAAAGTGACCGATGAGAGATGTCTCTCC-ACAATTAAAAAAAGTGACAAATATTGAAGAAAG
1 TAAAAAAGTGACCGATGAGAGATATCTCTCCAACAATT--AAAAAGTAAAAAATATTGAAAAAAG
* * * * *
27316 AGATCGATGAGAGTTCTCTCTCAAAACAACAAATT-GAAAAAGTGACCAATGAGAGCTGTCTCTC
64 AGACCGATGAGAGCTCTCTCCCAAAACAACAAATTAAAAAAAGTGACCAATGAGAGCTATCTCTC
*
27380 CAAACATTTAATTAAACATTTAAC
129 CAAACAATTAATTAAACATTTAAC
* * * * **
27404 TAAAAACGTGACCGATGCGAGTTATCTCTCCTAACAATTAAAAAGTAAAAAATATTTAAAAAATT
1 TAAAAAAGTGACCGATGAGAGATATCTCTCC-AACAATTAAAAAGTAAAAAATATTGAAAAAAGA
* * ** * *
27469 GACCGATGAGAGCTGTCTCCCCAAACAGTAAATTAAAAAAAGTGACCGATGAGAGCTATCTCTCG
65 GACCGATGAGAGCTCTCTCCCAAAACAACAAATTAAAAAAAGTGACCAATGAGAGCTATCTCTCC
27534 AAACAATTAA
130 AAACAATTAA
27544 AAAAAAAAGT
Statistics
Matches: 115, Mismatches: 22, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
152 74 0.64
153 35 0.30
154 6 0.05
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (152 bp):
TAAAAAAGTGACCGATGAGAGATATCTCTCCAACAATTAAAAAGTAAAAAATATTGAAAAAAGAG
ACCGATGAGAGCTCTCTCCCAAAACAACAAATTAAAAAAAGTGACCAATGAGAGCTATCTCTCCA
AACAATTAATTAAACATTTAAC
Found at i:27549 original size:42 final size:41
Alignment explanation
Indices: 27461--27625 Score: 176
Period size: 42 Copynumber: 4.0 Consensus size: 41
27451 AAAAATATTT
* * * *
27461 AAAAAATTGACCGATGAGAGCTGTCTCCCCAAACAGTAAATTA
1 AAAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTAAA--A
*
27504 AAAAAAGTGACCGATGAGAGCTATCTCTCGAAACAATTAAAA
1 AAAAAAGTGACCGATGAGAGCTATCTCTCCAAAC-ATTAAAA
* * *
27546 AAAAAAGTGATCGATGAGAGCTGTCTCTCCAAAC-TT---T
1 AAAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTAAAA
* *
27583 AAAATAGTGACCGATAAGAGCTATCTCTCCAAACAATTAAAA
1 AAAAAAGTGACCGATGAGAGCTATCTCTCCAAAC-ATTAAAA
27625 A
1 A
27626 GGTGACAAAT
Statistics
Matches: 102, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
37 30 0.29
39 2 0.02
40 2 0.02
42 33 0.32
43 30 0.29
44 5 0.05
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTAAAA
Found at i:27730 original size:36 final size:39
Alignment explanation
Indices: 27683--27764 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 39
27673 AATTAAAAGA
27683 AAAAACTGACCGA-G-CAG-TCTCTCCAAACATTTAATT
1 AAAAACTGACCGATGACAGATCTCTCCAAACATTTAATT
* *
27719 AAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTTAATT
1 AAAAACTGACCGATGACAG--ATCTCTCCAAACATTTAATT
27760 AAAAA
1 AAAAA
27765 AAATGACCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
36 12 0.31
37 1 0.03
38 2 0.05
41 24 0.62
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (39 bp):
AAAAACTGACCGATGACAGATCTCTCCAAACATTTAATT
Found at i:27748 original size:41 final size:40
Alignment explanation
Indices: 27638--27799 Score: 136
Period size: 42 Copynumber: 4.0 Consensus size: 40
27628 TGACAAATAT
*
27638 TTAAGAAAGTGACCGATGAGAGCTATCTCT-CAAACAATTAAAA
1 TTAA-AAAGTGACCGATGAGAGCT-TCTCTCCAAAC-ATT-TAA
** * *
27681 GAAAAAACTGACCGA-G-CAG--TCTCTCCAAACATTTAA
1 TTAAAAAGTGACCGATGAGAGCTTCTCTCCAAACATTTAA
27717 TTAAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTTAA
1 TTAAAAAGTGACCGATGAGAGCT-TCTCTCCAAACATTTAA
* * * * *
27758 TTAAAAAAAATGACCAATGAGAGCTGCTTTCCAAACAATTAA
1 TT--AAAAAGTGACCGATGAGAGCTTCTCTCCAAACATTTAA
27800 AAAGGTGACA
Statistics
Matches: 97, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
36 14 0.14
37 9 0.09
38 7 0.07
40 2 0.02
41 20 0.21
42 24 0.25
43 21 0.22
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.23
Consensus pattern (40 bp):
TTAAAAAGTGACCGATGAGAGCTTCTCTCCAAACATTTAA
Found at i:27750 original size:135 final size:133
Alignment explanation
Indices: 27507--27757 Score: 355
Period size: 135 Copynumber: 1.8 Consensus size: 133
27497 TAAATTAAAA
* *
27507 AAAGTGACCGATGAGAGCTATCTCTCGAAACAATTAAAAAAAAAAGTGATCGATGAGAGCTGTCT
1 AAAGTGACCGATGAGAGCTATCTCTCGAAACAATTAAAAAAAAAACTGATC---GAGAGCAGTCT
*
27572 CTCCAAACTTTAAAATAGTGACCGATAAGAGCTATCTCTCCAAACAATTAAAAAGGTGACAAATA
63 CTCCAAACTTTAAAAAAGTGACCGATAAGAGCTATCTCTCCAAACAATTAAAAAGGTGACAAATA
27637 TTTAAG
128 TTTAAG
*
27643 AAAGTGACCGATGAGAGCTATCTCTC-AAACAATTAAAAGAAAAAACTGA-C-CGAGCAGTCTCT
1 AAAGTGACCGATGAGAGCTATCTCTCGAAACAATTAAAA-AAAAAACTGATCGAGAGCAGTCTCT
* *
27705 CCAAACATTTAATTAAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTTAA
65 CCAAAC-TTT-A--AAAAAGTGACCGATAAGAGCTATCTCTCCAAACAATTAA
27758 TTAAAAAAAA
Statistics
Matches: 104, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
131 16 0.15
132 3 0.03
133 1 0.01
135 49 0.47
136 35 0.34
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (133 bp):
AAAGTGACCGATGAGAGCTATCTCTCGAAACAATTAAAAAAAAAACTGATCGAGAGCAGTCTCTC
CAAACTTTAAAAAAGTGACCGATAAGAGCTATCTCTCCAAACAATTAAAAAGGTGACAAATATTT
AAG
Found at i:27780 original size:43 final size:40
Alignment explanation
Indices: 27700--27799 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 40
27690 GACCGAGCAG
* *
27700 TCTCTCCAAACATTTAATTAAAAAGTGACCGATGAGAGCT
1 TCTCTCCAAACATTTAATTAAAAAATGACCAATGAGAGCT
27740 ATCTCTCCAAACATTTAATTAAAAAAAATGACCAATGAGAGCT
1 -TCTCTCCAAACATTTAATT--AAAAAATGACCAATGAGAGCT
* * *
27783 GCTTTCCAAACAATTAA
1 TCTCTCCAAACATTTAA
27800 AAAGGTGACA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
41 19 0.37
42 14 0.27
43 19 0.37
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (40 bp):
TCTCTCCAAACATTTAATTAAAAAATGACCAATGAGAGCT
Found at i:27792 original size:42 final size:41
Alignment explanation
Indices: 27701--27799 Score: 128
Period size: 43 Copynumber: 2.4 Consensus size: 41
27691 ACCGAGCAGT
* * *
27701 CTCTCCAAACATTTAATTAAAAAGTGACCGATGAGAGCTAT
1 CTCTCCAAACATTTAATTAAAAAATGACCAATGAGAGCTAG
27742 CTCTCCAAACATTTAATTAAAAAAAATGACCAATGAGAGCT-G
1 CTCTCCAAACATTTAATT--AAAAAATGACCAATGAGAGCTAG
* *
27784 CTTTCCAAACAATTAA
1 CTCTCCAAACATTTAA
27800 AAAGGTGACA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
41 18 0.35
42 14 0.27
43 19 0.37
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.26
Consensus pattern (41 bp):
CTCTCCAAACATTTAATTAAAAAATGACCAATGAGAGCTAG
Found at i:27808 original size:177 final size:172
Alignment explanation
Indices: 27429--27979 Score: 538
Period size: 177 Copynumber: 3.1 Consensus size: 172
27419 TGCGAGTTAT
* * * * * * *
27429 CTCTCCTAACAATTAAAAA-GTAAAAAATATTTAAAAAATTGACCGATGAGAGCTGTCTCCCCAA
1 CTCTCCAAACAATTAAAAAGGTGACAAATATTTAAGAAAGTGACCGATGAGAGCTATCT-CTCAA
* * * * * ** *
27493 ACAGTAAATTA-AAAAAAGTGACCGATGAGAGCTATCTCTCGAAACAATTAAAAAAAAAAGTGAT
65 ACAATAAA-TAGAAAAAACTGACCGA-G-CAG---TCTCTCCAAAC-ATTTAATTAAAAAGTGAC
* * * * *
27557 CGATGAGAGCTGTCTCTCCAAACTTTAAAATAGTGACCGATAAGAGCTAT
123 CGATGAGAGCTATCTCTCCAAACTTTAAAAAAATGACCAATAAGAGCTAG
27607 CTCTCCAAACAATTAAAAAGGTGACAAATATTTAAGAAAGTGACCGATGAGAGCTATCTCTCAAA
1 CTCTCCAAACAATTAAAAAGGTGACAAATATTTAAGAAAGTGACCGATGAGAGCTATCTCTCAAA
27672 CAATTAAA-AGAAAAAACTGACCGAGCAGTCTCTCCAAACATTTAATTAAAAAGTGACCGATGAG
66 CAA-TAAATAGAAAAAACTGACCGAGCAGTCTCTCCAAACATTTAATTAAAAAGTGACCGATGAG
*
27736 AGCTATCTCTCCAAACATTTAATTAAAAAAAATGACCAATGAGAGCT-G
130 AGCTATCTCTCCAAAC---T--TT-AAAAAAATGACCAATAAGAGCTAG
*
27784 CTTTCCAAACAATTAAAAAGGTGACAAATATTTAAGAAAGTGACCGATGAGAGCTATCTCTCGAA
1 CTCTCCAAACAATTAAAAAGGTGACAAATATTTAAGAAAGTGACCGATGAGAGCTATCTCTC-AA
* * ** * * *
27849 ACAACAAATTGAAAAAGTGACTGATGAGAGCTGTCTCTCCAAAC-TTTAATTAAATAAGTAACCA
65 ACAATAAATAGAAAAA---ACTGA-CCGAGCAGTCTCTCCAAACATTTAATTAAA-AAGTGACCG
* * * * *
27913 ATGAGAGCTATCTCT-CATAACAATTAAAACAATGACCGATGAGAGCTAT
125 ATGAGAGCTATCTCTCCA-AAC-TTTAAAAAAATGACCAATAAGAGCTAG
*
27962 CTCTCCAAACAATCAAAA
1 CTCTCCAAACAATTAAAA
27980 CAATCAAACA
Statistics
Matches: 319, Mismatches: 36, Indels: 36
0.82 0.09 0.09
Matches are distributed among these distances:
172 36 0.11
173 10 0.03
175 1 0.00
176 2 0.01
177 88 0.28
178 86 0.27
179 38 0.12
181 17 0.05
182 41 0.13
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (172 bp):
CTCTCCAAACAATTAAAAAGGTGACAAATATTTAAGAAAGTGACCGATGAGAGCTATCTCTCAAA
CAATAAATAGAAAAAACTGACCGAGCAGTCTCTCCAAACATTTAATTAAAAAGTGACCGATGAGA
GCTATCTCTCCAAACTTTAAAAAAATGACCAATAAGAGCTAG
Found at i:27869 original size:42 final size:41
Alignment explanation
Indices: 27815--27978 Score: 158
Period size: 42 Copynumber: 4.0 Consensus size: 41
27805 TGACAAATAT
*
27815 TTAAGAAAGTGACCGATGAGAGCTATCTCTCGAAACAACAAA
1 TTAA-AAAGTGACCGATGAGAGCTATCTCTCCAAACAACAAA
* * ***
27857 TTGAAAAAGTGACTGATGAGAGCTGTCTCTCCAAAC-TTTAA
1 TT-AAAAAGTGACCGATGAGAGCTATCTCTCCAAACAACAAA
* * *
27898 TTAAATAAGTAACCAATGAGAGCTATCTCT-C--ATAAC-AA
1 TTAAA-AAGTGACCGATGAGAGCTATCTCTCCAAACAACAAA
*
27936 TTAAAACAATGACCGATGAGAGCTATCTCTCCAAACAATCAAA
1 TTAAAA-AGTGACCGATGAGAGCTATCTCTCCAAACAA-CAAA
27979 ACAATCAAAC
Statistics
Matches: 96, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
37 1 0.01
38 28 0.29
39 1 0.01
40 4 0.04
41 27 0.28
42 31 0.32
43 4 0.04
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (41 bp):
TTAAAAAGTGACCGATGAGAGCTATCTCTCCAAACAACAAA
Found at i:27955 original size:38 final size:38
Alignment explanation
Indices: 27815--27979 Score: 129
Period size: 38 Copynumber: 4.2 Consensus size: 38
27805 TGACAAATAT
* * *
27815 TTAAGAAAGTGACCGATGAGAGCTATCTCTCGAAACAACAAA
1 TTAA-AAAATGACCGATGAGAGCTATCTCTC--CA-AACTAA
* * *
27857 TTGAAAAAGTGACTGATGAGAGCTGTCTCTCCAAACTTTAA
1 TT-AAAAAATGACCGATGAGAGCTATCTCTCCAAAC--TAA
* * *
27898 TTAAATAAGTAACCAATGAGAGCTATCTCT-CATAAC-AA
1 TTAAA-AAATGACCGATGAGAGCTATCTCTCCA-AACTAA
27936 TTAAAACAATGACCGATGAGAGCTATCTCTCCAAAC-AA
1 TTAAAA-AATGACCGATGAGAGCTATCTCTCCAAACTAA
*
27974 TCAAAA
1 TTAAAA
27980 CAATCAAACA
Statistics
Matches: 104, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
37 1 0.01
38 37 0.36
39 5 0.05
40 6 0.06
41 27 0.26
42 26 0.25
43 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (38 bp):
TTAAAAAATGACCGATGAGAGCTATCTCTCCAAACTAA
Found at i:27966 original size:79 final size:81
Alignment explanation
Indices: 27821--27971 Score: 200
Period size: 79 Copynumber: 1.9 Consensus size: 81
27811 ATATTTAAGA
* * * * *
27821 AAGTGACCGATGAGAGCTATCTCTCGAAACAACAAATTGAAAAAGTGACTGATGAGAGCTGTCTC
1 AAGTAACCAATGAGAGCTATCTCTC--AACAACAAATTGAAAAAATGACCGATGAGAGCTATCTC
27886 TCCAAACTTTAATTAAAT
64 TCCAAACTTTAATTAAAT
*
27904 AAGTAACCAATGAGAGCTATCTCTC-ATAAC-AATT-AAAACAATGACCGATGAGAGCTATCTCT
1 AAGTAACCAATGAGAGCTATCTCTCAACAACAAATTGAAAA-AATGACCGATGAGAGCTATCTCT
27966 CCAAAC
65 CCAAAC
27972 AATCAAAACA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
78 4 0.07
79 30 0.49
80 4 0.07
83 23 0.38
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (81 bp):
AAGTAACCAATGAGAGCTATCTCTCAACAACAAATTGAAAAAATGACCGATGAGAGCTATCTCTC
CAAACTTTAATTAAAT
Found at i:28167 original size:42 final size:41
Alignment explanation
Indices: 28107--28469 Score: 409
Period size: 37 Copynumber: 9.2 Consensus size: 41
28097 AAAAAAGTAG
* *
28107 CAAACA-TTAA-AAAAAAGTGACCAATGAGAGTTGTCTCTC
1 CAAACATTTAATAAAAAAGTGACCGATGAGAGCTGTCTCTC
* *
28146 CAAACATTTAATTAAAAAAGTGACCAATGAGAGCTATCTCTC
1 CAAACATTTAA-TAAAAAAGTGACCGATGAGAGCTGTCTCTC
* * * *
28188 GAAACAATTAA-AAAAAAGGGACTGATGAGAGCTGTCTCTC
1 CAAACATTTAATAAAAAAGTGACCGATGAGAGCTGTCTCTC
*
28228 CAAACA--T--TAAAAAAGTGACCGATGAGAGCTATCTCTC
1 CAAACATTTAATAAAAAAGTGACCGATGAGAGCTGTCTCTC
* *
28265 CAAACAATTAAAAAAAAAGTGACCGATGAGAGCTGTCTCTC
1 CAAACATTTAATAAAAAAGTGACCGATGAGAGCTGTCTCTC
*
28306 CAAACA---AA-AAAAAAGTGACCGATGAGAGCGGTCTCTC
1 CAAACATTTAATAAAAAAGTGACCGATGAGAGCTGTCTCTC
*
28343 CAAACA---AA-AAAAAAGTGACCGATGACAGCTGTCTCTC
1 CAAACATTTAATAAAAAAGTGACCGATGAGAGCTGTCTCTC
* * *
28380 CAAACATTTAATTAGAAAAGTGACCGATAAGAGCTATCTCTC
1 CAAACATTTAA-TAAAAAAGTGACCGATGAGAGCTGTCTCTC
* * *
28422 CAAACATTCAATTAAAAAAGTGATCGATGAGAG--GTTTCTC
1 CAAACATTTAA-TAAAAAAGTGACCGATGAGAGCTGTCTCTC
28462 CAAACATT
1 CAAACATT
28470 AAAAAAGTGA
Statistics
Matches: 284, Mismatches: 27, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
37 101 0.36
38 3 0.01
39 7 0.02
40 49 0.17
41 34 0.12
42 90 0.32
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (41 bp):
CAAACATTTAATAAAAAAGTGACCGATGAGAGCTGTCTCTC
Found at i:28590 original size:41 final size:42
Alignment explanation
Indices: 28487--28631 Score: 195
Period size: 41 Copynumber: 3.5 Consensus size: 42
28477 TGACAAATAT
* *
28487 TTAAGAAAGTGACCGATGAGAGCTATCTCTCCAAGCGA-TAAA
1 TTAAAAAAGTGACCGATGAGAGCTATCTCTCCAAAC-ATTAAA
* * *
28529 TTAAAAAAAGTGACTGATGAGAGCTGTCTCTCCAAACATTTAA
1 TT-AAAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTAAA
*
28572 TT-AAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTCAA
1 TTAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTAAA
*
28613 TTAAAAAAGTTACCGATGA
1 TTAAAAAAGTGACCGATGA
28632 AAGTCGCCAC
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
41 38 0.42
42 18 0.20
43 35 0.38
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (42 bp):
TTAAAAAAGTGACCGATGAGAGCTATCTCTCCAAACATTAAA
Done.