Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022366.1 Corchorus olitorius cultivar O-4 contig22399, 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: 61124
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:6613 original size:18 final size:17
Alignment explanation
Indices: 6590--6625 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
6580 CTCCTCTATC
*
6590 ATGAAAACATTTTCTTTT
1 ATGAAAACAATTT-TTTT
6608 ATGAAAACAATTTTTTT
1 ATGAAAACAATTTTTTT
6625 A
1 A
6626 ATTACCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (17 bp):
ATGAAAACAATTTTTTT
Found at i:14078 original size:32 final size:32
Alignment explanation
Indices: 14037--14102 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
14027 TAATCAACAG
14037 CCAGAAAGATTAAACATATATACTTTCAATGT
1 CCAGAAAGATTAAACATATATACTTTCAATGT
14069 CCAGAAAGATTAAACATATATACTTTCAATGT
1 CCAGAAAGATTAAACATATATACTTTCAATGT
14101 CC
1 CC
14103 TTATTATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (32 bp):
CCAGAAAGATTAAACATATATACTTTCAATGT
Found at i:15566 original size:31 final size:31
Alignment explanation
Indices: 15531--15589 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
15521 CAGCCCTCAT
*
15531 GTTTAATTTTTACACTTCTTTATTCTTCTTC
1 GTTTAATTTTCACACTTCTTTATTCTTCTTC
* *
15562 GTTTAATTTTCACGCTTCTTTCTTCTTC
1 GTTTAATTTTCACACTTCTTTATTCTTC
15590 CTTTTTAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.14, C:0.22, G:0.05, T:0.59
Consensus pattern (31 bp):
GTTTAATTTTCACACTTCTTTATTCTTCTTC
Found at i:17325 original size:9 final size:9
Alignment explanation
Indices: 17311--17337 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
17301 TCCAGCCCTC
17311 TCAATTTCA
1 TCAATTTCA
17320 TCAATTTCA
1 TCAATTTCA
17329 TCAATTTCA
1 TCAATTTCA
17338 CCTTTTGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (9 bp):
TCAATTTCA
Found at i:24190 original size:54 final size:53
Alignment explanation
Indices: 24121--24724 Score: 566
Period size: 54 Copynumber: 11.6 Consensus size: 53
24111 AAATCAGAGC
* *
24121 AATTAAACTAGAGAGTAAAAGACAAAGTAAACAGAGATTAGTTTAATTCTAGGT
1 AATTAAACTAAAGAGTAAAAGA-AAAGTAAACAGAGATTAGTTTAATTCTGGGT
* * *
24175 GATTAAACTAAAGAGT--AAGAGAAG-AAGA-A-A-A-CAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAAAGTAA-ACAGAGATTAGTTTAATTCTGGGT
* * *
24222 AATTAAACTAAAAAGT--AAGAGAAG-AAGA-A-A-A-CAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAAAGTAA-ACAGAGATTAGTTTAATTCTGGGT
** **
24269 AATTAAACTAAAGAGTAAAAGAAGAAGTAAGTAGAGGCTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAA-AAGTAAACAGAGATTAGTTTAATTCTGGGT
*
24323 AATTAAACT----A--AAAAG---AGTAAACAGTA-ATTAGTTTAATTCTTGGT
1 AATTAAACTAAAGAGTAAAAGAAAAGTAAACAG-AGATTAGTTTAATTCTGGGT
*
24367 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAA-AAGTAAACAGAGATTAGTTTAATTCTGGGT
24421 AATTAAACTAAA-ATGTAAAAGAAGAAGTAAACAGTAG-TTAGTTTAATTCTGGGT
1 AATTAAACTAAAGA-GTAAAAGAA-AAGTAAACAG-AGATTAGTTTAATTCTGGGT
* * *
24475 AATTAAACTAAAAAGAGTAAAAGAAGAGTAAACAGTA-ATTAGTTTAATTCTTGAT
1 AATTAAACT--AAAGAGTAAAAGAAAAGTAAACAG-AGATTAGTTTAATTCTGGGT
* * *
24530 AATTAAACTAAAGAGTAAAAGAAGAAGTGAACAGCGGTTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAA-AAGTAAACAGAGATTAGTTTAATTCTGGGT
* * *
24584 AATTAAACTAAAAAGTAAAAGAAAAAGTAAACAAAGGTTAGTTTAATTCT-GGT
1 AATTAAACTAAAGAGTAAAAG-AAAAGTAAACAGAGATTAGTTTAATTCTGGGT
* * * * *
24637 AATTAAACTATAA-ACTAGAAGAAAGAGTAAATAGTA-ATTAGTTTTATTCGGGGT
1 AATTAAACTA-AAGAGTAAAAGAAA-AGTAAACAG-AGATTAGTTTAATTCTGGGT
* *
24691 AATTGAACTAAAGAGTAAAAGAAGGAGTAAACAG
1 AATTAAACTAAAGAGTAAAAGAA-AAGTAAACAG
24725 TTTTTAGCAA
Statistics
Matches: 470, Mismatches: 44, Indels: 72
0.80 0.08 0.12
Matches are distributed among these distances:
44 31 0.07
45 1 0.00
47 74 0.16
48 7 0.01
49 5 0.01
50 12 0.03
51 7 0.01
52 8 0.02
53 55 0.12
54 218 0.46
55 39 0.08
56 12 0.03
57 1 0.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.27
Consensus pattern (53 bp):
AATTAAACTAAAGAGTAAAAGAAAAGTAAACAGAGATTAGTTTAATTCTGGGT
Found at i:24514 original size:163 final size:161
Alignment explanation
Indices: 24121--24724 Score: 648
Period size: 163 Copynumber: 3.9 Consensus size: 161
24111 AAATCAGAGC
* * * * * *
24121 AATTAAACTAGAGAGTAAAAGACAAAGTAAACAGAGATTAGTTTAATTCTAGGTGATTAAACTAA
1 AATTAAACTAAAAAGTAAAAGAAAAAGTAAACAAAGGTTAGTTTAATTCT-GGTAATTAAACTAA
* * * * * * * *
24186 AGAGTAAGAG-AAGA--AGA-A--AA-CAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAGAGA
65 AAACTAAAAGAAAGAGTAAACAGTAATTAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGA
*
24244 AGAAG--AA-A-A---CAGTTTAATTCTGGGT
130 AGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
* * ** * *
24269 AATTAAACTAAAGAGTAAAAGAAGAAGTAAGTAGAGGCTAGTTTAATTCTGGGTAA-T----T--
1 AATTAAACTAAAAAGTAAAAGAAAAAGTAAACAAAGGTTAGTTTAATTCT-GGTAATTAAACTAA
24327 AAACT--AA-AAAGAGTAAACAGTAATTAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGA
65 AAACTAAAAGAAAGAGTAAACAGTAATTAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGA
24389 AGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
130 AGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
* * *
24421 AATTAAACTAAAATGTAAAAGAAGAAGTAAACAGTA-GTTAGTTTAATTCTGGGTAATTAAACTA
1 AATTAAACTAAAAAGTAAAAGAAAAAGTAAACA-AAGGTTAGTTTAATTCT-GGTAATTAAACT-
* *
24485 AAAAGAGTAAAAG-AAGAGTAAACAGTAATTAGTTTAATTCTTGATAATTAAACTAAAGAGTAAA
63 AAAA-ACTAAAAGAAAGAGTAAACAGTAATTAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAA
* *
24549 AGAAGAAGTGAACAGCGGTTAGTTTAATTCTGGGT
127 AGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
*
24584 AATTAAACTAAAAAGTAAAAGAAAAAGTAAACAAAGGTTAGTTTAATTCTGGTAATTAAACTATA
1 AATTAAACTAAAAAGTAAAAGAAAAAGTAAACAAAGGTTAGTTTAATTCTGGTAATTAAACTAAA
* * * ** *
24649 AACTAGAAGAAAGAGTAAATAGTAATTAGTTTTATTCGGGGTAATTGAACTAAAGAGTAAAAGAA
66 AACTAAAAGAAAGAGTAAACAGTAATTAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAA
*
24714 GGAGTAAACAG
131 GAAGTAAACAG
24725 TTTTTAGCAA
Statistics
Matches: 385, Mismatches: 42, Indels: 45
0.82 0.09 0.10
Matches are distributed among these distances:
139 5 0.01
141 5 0.01
142 1 0.00
143 1 0.00
144 2 0.01
145 39 0.10
147 3 0.01
148 48 0.12
149 1 0.00
152 63 0.16
153 2 0.01
157 1 0.00
160 8 0.02
161 63 0.16
162 13 0.03
163 130 0.34
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.27
Consensus pattern (161 bp):
AATTAAACTAAAAAGTAAAAGAAAAAGTAAACAAAGGTTAGTTTAATTCTGGTAATTAAACTAAA
AACTAAAAGAAAGAGTAAACAGTAATTAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAA
GAAGTAAACAGAGGTTAGTTTAATTCTGGGT
Found at i:24548 original size:109 final size:105
Alignment explanation
Indices: 24338--24724 Score: 483
Period size: 109 Copynumber: 3.6 Consensus size: 105
24328 AACTAAAAAG
*
24338 AGTAAACAGTAATTAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAG
1 AGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAG-AGTAAACAGA-
* *
24403 GTTAGTTTAATTCTGGGTAATTAAACTAAAATGTAAAAGAAGA
64 ATTAGTTTAATTCTTGGTAATTAAACTAAAA-GTAAAAGAAGA
*
24446 AGTAAACAGTAGTTAGTTTAATTCTGGGTAATTAAACTAAAAAGAGTAAAAGAAGAGTAAACAGT
1 AGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACT--AAAGAGTAAAAGAAGAGTAAACAG-
*
24511 AATTAGTTTAATTCTTGATAATTAAACTAAAGAGTAAAAGAAGA
63 AATTAGTTTAATTCTTGGTAATTAAACTAAA-AGTAAAAGAAGA
* *** * *
24555 AGTGAACAGCGGTTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAAAAGTAAACA-AA
1 AGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAG-AAGAGTAAACAGAA
* *
24619 GGTTAGTTTAATTC-TGGTAATTAAACTATAAACTAGAAGAA-A
65 --TTAGTTTAATTCTTGGTAATTAAACTA-AAAGTAAAAGAAGA
* * * *
24661 GAGTAAATAGTAATTAGTTTTATTCGGGGTAATTGAACTAAAGAGTAAAAGAAGGAGTAAACAG
1 -AGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAA-GAGTAAACAG
24725 TTTTTAGCAA
Statistics
Matches: 245, Mismatches: 23, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
106 5 0.02
107 81 0.33
108 60 0.24
109 82 0.33
110 17 0.07
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (105 bp):
AGTAAACAGTAATTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAGTAAACAGAAT
TAGTTTAATTCTTGGTAATTAAACTAAAAGTAAAAGAAGA
Found at i:27782 original size:35 final size:35
Alignment explanation
Indices: 27748--27866 Score: 186
Period size: 35 Copynumber: 3.4 Consensus size: 35
27738 AGTTTATTTG
*
27748 CGGAACAATGGTCTGTAATCCTTAATTTCTATT-T
1 CGGAACAATGGTTTGTAATCCTTAATTTCTATTCT
27782 GCGGAACAATGGTTTGTAATCCTTAATTTCTATTCT
1 -CGGAACAATGGTTTGTAATCCTTAATTTCTATTCT
** *
27818 CGGAATGATGGTTTGTAATCCTTAAGTTCTATTCT
1 CGGAACAATGGTTTGTAATCCTTAATTTCTATTCT
27853 CGGAACAATGGTTT
1 CGGAACAATGGTTT
27867 TATGATATGG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 76 0.99
36 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.40
Consensus pattern (35 bp):
CGGAACAATGGTTTGTAATCCTTAATTTCTATTCT
Found at i:37780 original size:11 final size:11
Alignment explanation
Indices: 37764--37789 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
37754 GTTTTAGATC
37764 TTTTCTTCTAG
1 TTTTCTTCTAG
37775 TTTTCTTCTAG
1 TTTTCTTCTAG
37786 TTTT
1 TTTT
37790 TTAGGCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:41366 original size:54 final size:53
Alignment explanation
Indices: 41297--41957 Score: 661
Period size: 54 Copynumber: 12.6 Consensus size: 53
41287 AAATCAGAGC
* * *
41297 AATTAAACTAGAGAGTAAAAGAAGAAGTAAACAGAGACTAGTTTAATTCTGAGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGA-ATTAGTTTAATTCTGGGT
* * *
41351 AATTAAACTAAAGAGTAAGAGCAGAAG---A-A-AA-CAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAATTAGTTTAATTCTGGGT
**
41398 AATTAAACTAAAGAGT--AAGAA-AAG-AAGA-A-AA-TAGTTTAATTCCAGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAA-ACAGAATTAGTTTAATTCTGGGT
* * *
41445 AATTAAACTAAAAAGT--AAG-AGAA-TAAGA-A-AA-CAGTTTAATTATGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAA-ACAGAATTAGTTTAATTCTGGGT
* * ** *
41492 AATTAAACTAAAGAGTAAAAGAAGAAATAAGCAGAGGCTAGTTTAATTCTAGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGA-ATTAGTTTAATTCTGGGT
* * *
41546 AATAAAACTAAAAAGAGTAAAAGAAG-AGTAAATAGTAATTAGTTTAATTCTTGGT
1 AATTAAACT--AAAGAGTAAAAGAAGAAGTAAACAG-AATTAGTTTAATTCTGGGT
* * *
41601 AATTAAACTAAGGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTATGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGA-ATTAGTTTAATTCTGGGT
* * *
41655 AATTAAACTAAAAAGTAAAAGAAGAAGTAAACAGTAGTTAGTTTAATTTTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAG-AATTAGTTTAATTCTGGGT
*
41709 AATTAAACTAAAAAGAGTAAAAGAAG-AGTAAACAGTAATTAGTTTAATTCTTGGT
1 AATTAAACT--AAAGAGTAAAAGAAGAAGTAAACAG-AATTAGTTTAATTCTGGGT
* **
41764 AATTAAACTAAAGAGTAAAAGAAGAAGTGAACAAGGGTTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAAC-AGAATTAGTTTAATTCTGGGT
* *
41818 AATTAAACTAAAAAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCT-GGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGA-ATTAGTTTAATTCTGGGT
* * *
41871 AATTAAACTATAA-ACTAGAAGAA-AGAGTAAACAGTAATTAGTTTAATTCGGGGT
1 AATTAAACTA-AAGAGTAAAAGAAGA-AGTAAACAG-AATTAGTTTAATTCTGGGT
* * *
41925 AATTGAACTAAAGAGTAGAAGAAGGAGTAAACA
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACA
41958 ATTTTTAGCA
Statistics
Matches: 522, Mismatches: 55, Indels: 60
0.82 0.09 0.09
Matches are distributed among these distances:
44 3 0.01
45 3 0.01
46 1 0.00
47 101 0.19
48 1 0.00
49 4 0.01
50 5 0.01
51 5 0.01
52 2 0.00
53 76 0.15
54 224 0.43
55 67 0.13
56 30 0.06
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.26
Consensus pattern (53 bp):
AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAATTAGTTTAATTCTGGGT
Found at i:41646 original size:109 final size:107
Alignment explanation
Indices: 41297--41957 Score: 703
Period size: 109 Copynumber: 6.3 Consensus size: 107
41287 AAATCAGAGC
* **
41297 AATTAAACTAGAGAGTAAAAGAAGAAGTAAACAGAGACTAGTTTAATTCTGAGTAATTAAACTAA
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTG-GTAATTAAACTAA
* * * *
41362 AGAGTAAGAGCAGAAG---A-A--AA-CAGTTTAATTCTGGGT
65 AAAGTAAAAGAAGAAGTAAACAGTAATTAGTTTAATTCTGGGT
*
41398 AATTAAACTAAAGAGTAAGAA-AAGAAG--AA-A-A---TAGTTTAATTCCAGGTAATTAAACTA
1 AATTAAACTAAAGAGTAA-AAGAAGAAGTAAACAGAGGTTAGTTTAATT-CTGGTAATTAAACTA
* *
41455 AAAAGT--AAG-AGAA-TAAGA-A--AA-CAGTTTAATTATGGGT
64 AAAAGTAAAAGAAGAAGTAA-ACAGTAATTAGTTTAATTCTGGGT
* * * *
41492 AATTAAACTAAAGAGTAAAAGAAGAAATAAGCAGAGGCTAGTTTAATTCTAGGTAATAAAACTAA
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCT-GGTAATTAAACT-A
* *
41557 AAAGAGTAAAAGAAG-AGTAAATAGTAATTAGTTTAATTCTTGGT
64 AAA-AGTAAAAGAAGAAGTAAACAGTAATTAGTTTAATTCTGGGT
* *
41601 AATTAAACTAAGGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTATGGGTAATTAAACTAA
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCT-GGTAATTAAACTAA
* *
41666 AAAGTAAAAGAAGAAGTAAACAGTAGTTAGTTTAATTTTGGGT
65 AAAGTAAAAGAAGAAGTAAACAGTAATTAGTTTAATTCTGGGT
*
41709 AATTAAACTAAAAAGAGTAAAAGAAG-AGTAAACAGTA-ATTAGTTTAATTCTTGGTAATTAAAC
1 AATTAAACT--AAAGAGTAAAAGAAGAAGTAAACAG-AGGTTAGTTTAATTC-TGGTAATTAAAC
* * **
41772 TAAAGAGTAAAAGAAGAAGTGAACAAG-GGTTAGTTTAATTCTGGGT
62 TAAAAAGTAAAAGAAGAAGTAAAC-AGTAATTAGTTTAATTCTGGGT
* *
41818 AATTAAACTAAAAAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGTAATTAAACTATA
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGTAATTAAACTAAA
* * *
41883 AACTAGAAGAA-AGAGTAAACAGTAATTAGTTTAATTCGGGGT
66 AAGTAAAAGAAGA-AGTAAACAGTAATTAGTTTAATTCTGGGT
* * *
41925 AATTGAACTAAAGAGTAGAAGAAGGAGTAAACA
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACA
41958 ATTTTTAGCA
Statistics
Matches: 481, Mismatches: 44, Indels: 64
0.82 0.07 0.11
Matches are distributed among these distances:
91 4 0.01
92 2 0.00
93 2 0.00
94 69 0.14
95 2 0.00
96 1 0.00
97 2 0.00
98 2 0.00
99 2 0.00
100 1 0.00
101 44 0.09
102 6 0.01
103 3 0.01
105 5 0.01
106 9 0.02
107 100 0.21
108 61 0.13
109 148 0.31
110 18 0.04
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.26
Consensus pattern (107 bp):
AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGTAATTAAACTAAA
AAGTAAAAGAAGAAGTAAACAGTAATTAGTTTAATTCTGGGT
Found at i:41699 original size:163 final size:161
Alignment explanation
Indices: 41297--41958 Score: 769
Period size: 163 Copynumber: 4.2 Consensus size: 161
41287 AAATCAGAGC
* ** * *
41297 AATTAAACTAGAGAGTAAAAGAAGAAGTAAACAGAGACTAGTTTAATTCTGAGTAATTAAACTAA
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACA-AGGTTAGTTTAATTATGGGTAATTAAACTAA
* * * *
41362 AGAGTAAGAGCAGAAG--AA-A-A---CAGTTTAATTCTGGGTAATTAAACT-AAAGAGTAAGAA
65 AAAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAAGAGTAA-AA
* **
41419 -AAGA--AGA-A--AA-TAGTTTAATTCCAGGT
129 GAAGAGTAAACAGTAATTAGTTTAATTCTTGGT
* * * *
41445 AATTAAACTAAAAAGTAAGAGAATAAG--AA-AA---CAGTTTAATTATGGGTAATTAAACTAAA
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAGGTTAGTTTAATTATGGGTAATTAAACTAAA
* * * * * *
41504 GAGTAAAAGAAGAAATAAGCAGAGGCTAGTTTAATTCTAGGTAATAAAACTAAAAAGAGTAAAAG
66 AAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGTAATTAAACT-AAAAGAGTAAAAG
*
41569 AAGAGTAAATAGTAATTAGTTTAATTCTTGGT
130 AAGAGTAAACAGTAATTAGTTTAATTCTTGGT
*
41601 AATTAAACTAAGGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTATGGGTAATTAAACTAA
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACA-AGGTTAGTTTAATTATGGGTAATTAAACTAA
*
41666 AAAGTAAAAGAAGAAGTAAACAGTA-GTTAGTTTAATTTTGGGTAATTAAACTAAAAAGAGTAAA
65 AAAGTAAAAGAAGAAGTAAACAG-AGGTTAGTTTAATTCTGGGTAATTAAACT-AAAAGAGTAAA
41730 AGAAGAGTAAACAGTAATTAGTTTAATTCTTGGT
128 AGAAGAGTAAACAGTAATTAGTTTAATTCTTGGT
* *
41764 AATTAAACTAAAGAGTAAAAGAAGAAGTGAACAAGGGTTAGTTTAATTCTGGGTAATTAAACTAA
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAA-GGTTAGTTTAATTATGGGTAATTAAACTAA
* * *
41829 AAAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCT-GGTAATTAAACTATAA-ACTAGAAG
65 AAAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAAGAGTAAAAG
**
41892 AAAGAGTAAACAGTAATTAGTTTAATTCGGGGT
130 -AAGAGTAAACAGTAATTAGTTTAATTCTTGGT
* * *
41925 AATTGAACTAAAGAGTAGAAGAAGGAGTAAACAA
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAA
41959 TTTTTAGCAA
Statistics
Matches: 444, Mismatches: 43, Indels: 41
0.84 0.08 0.08
Matches are distributed among these distances:
141 37 0.08
143 1 0.00
144 2 0.00
145 2 0.00
146 2 0.00
148 45 0.10
149 2 0.00
150 13 0.03
152 2 0.00
153 1 0.00
155 2 0.00
156 37 0.08
158 2 0.00
159 1 0.00
160 7 0.02
161 63 0.14
162 14 0.03
163 210 0.47
164 1 0.00
ACGTcount: A:0.49, C:0.06, G:0.20, T:0.26
Consensus pattern (161 bp):
AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAGGTTAGTTTAATTATGGGTAATTAAACTAAA
AAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAAGAGTAAAAGA
AGAGTAAACAGTAATTAGTTTAATTCTTGGT
Found at i:43135 original size:22 final size:22
Alignment explanation
Indices: 43103--43243 Score: 105
Period size: 22 Copynumber: 6.5 Consensus size: 22
43093 TAAATATTTT
43103 TATG-AATTTTGATAACTACCC
1 TATGAAATTTTGATAACTACCC
* * **
43124 TATTAAATTTTGATAATTATGC
1 TATGAAATTTTGATAACTACCC
* *
43146 TATGAAATTCTGATAATTA-CC
1 TATGAAATTTTGATAACTACCC
*
43167 TATGAAATTGTT-ATAAACT-CCA
1 TATGAAATT-TTGAT-AACTACCC
*
43189 TATGAAATTTTGATAACTTA-AC
1 TATGAAATTTTGATAAC-TACCC
* *
43211 TATGAAATTTTAATAAACCT-TCC
1 TATGAAATTTTGAT-AA-CTACCC
43234 TATGAAATTT
1 TATGAAATTT
43244 GCAATCTTCG
Statistics
Matches: 96, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
21 20 0.21
22 61 0.64
23 14 0.15
24 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCC
Found at i:43169 original size:43 final size:42
Alignment explanation
Indices: 43103--43243 Score: 128
Period size: 43 Copynumber: 3.2 Consensus size: 42
43093 TAAATATTTT
* * *
43103 TATG-AATTTTGATAACTACCCTATTAAATTTTGATAATTA-TGC-
1 TATGAAATTTTGATAATTA-CCTATGAAATTTT-ATAA--ACTCCA
*
43146 TATGAAATTCTGATAATTACCTATGAAATTGTTATAAACTCCA
1 TATGAAATTTTGATAATTACCTATGAAATT-TTATAAACTCCA
*
43189 TATGAAATTTTGATAACTTAACTATGAAATTTTAATAAACCTTCC-
1 TATGAAATTTTGATAA-TTACCTATGAAATTTT-ATAAA-C-TCCA
43234 TATGAAATTT
1 TATGAAATTT
43244 GCAATCTTCG
Statistics
Matches: 84, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 35 0.42
44 32 0.38
45 11 0.13
46 3 0.04
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (42 bp):
TATGAAATTTTGATAATTACCTATGAAATTTTATAAACTCCA
Found at i:43227 original size:44 final size:44
Alignment explanation
Indices: 43145--43243 Score: 132
Period size: 44 Copynumber: 2.2 Consensus size: 44
43135 GATAATTATG
* *
43145 CTATGAAATTCTGATAATTACCTATGAAATTGTTATAAA-C-TC
1 CTATGAAATTTTGATAATTAACTATGAAATTGTTATAAACCTTC
43187 CATATGAAATTTTGATAACTTAACTATGAAATT-TTAATAAACCTTC
1 C-TATGAAATTTTGATAA-TTAACTATGAAATTGTT-ATAAACCTTC
43233 CTATGAAATTT
1 CTATGAAATTT
43244 GCAATCTTCG
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
42 1 0.02
43 17 0.34
44 18 0.36
45 11 0.22
46 3 0.06
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (44 bp):
CTATGAAATTTTGATAATTAACTATGAAATTGTTATAAACCTTC
Found at i:43569 original size:45 final size:45
Alignment explanation
Indices: 43519--43607 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
43509 AATCTATTCT
*
43519 GGTTTAACTCTTATAGTATAATTATACATTTAAAAATTCAACTCC
1 GGTTTAACTCTTATAGTATAATTATACATTTAAAAATCCAACTCC
** * *
43564 GGTTTAGTTCTTATAGTATGATTATACGTTTAAAAATCCAACTC
1 GGTTTAACTCTTATAGTATAATTATACATTTAAAAATCCAACTC
43608 GTTTGAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (45 bp):
GGTTTAACTCTTATAGTATAATTATACATTTAAAAATCCAACTCC
Found at i:44028 original size:30 final size:30
Alignment explanation
Indices: 43992--44050 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
43982 GTAAGATTTA
43992 AACTTAACATTAAATCATAAATAAATAATC
1 AACTTAACATTAAATCATAAATAAATAATC
44022 AACTTAACATTAAATCATAAATAAATAAT
1 AACTTAACATTAAATCATAAATAAATAAT
44051 AGTATATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (30 bp):
AACTTAACATTAAATCATAAATAAATAATC
Found at i:52314 original size:133 final size:133
Alignment explanation
Indices: 52065--52311 Score: 408
Period size: 133 Copynumber: 1.9 Consensus size: 133
52055 ATTTTAATAT
*
52065 ATATATATCTAAGTTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAATAGATACAAGGATATT
1 ATATATATATAAGTTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAATAGATACAAGGATATT
*
52130 GAATTTAATTAAATAAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAATT
66 GAATTTAATCAAATAAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAATT
52195 CTA
131 CTA
* * * *
52198 ATATATATATAATTTTTTTAATTAAATTAGTAAAATGGTAAAAATTAAATAGTTATAAGGATATT
1 ATATATATATAAGTTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAATAGATACAAGGATATT
*
52263 -AGATTTAATCAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
66 GA-ATTTAATCAAATAAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAA
52312 AGTTTAGACA
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
132 35 0.33
133 71 0.67
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (133 bp):
ATATATATATAAGTTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAATAGATACAAGGATATT
GAATTTAATCAAATAAAAAATAGAATTTTTAGTTGAGTAAAACTATAAAAGTATATTTAAAAATT
CTA
Found at i:55060 original size:4 final size:4
Alignment explanation
Indices: 55051--55077 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
55041 TTTTCTTTTT
55051 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
55078 TTTTCAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:57351 original size:21 final size:21
Alignment explanation
Indices: 57308--57354 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
57298 AGGGATCGAG
*
57308 CTGGGCGCTGAGCCTTGTCGC
1 CTGGGCGCTGAGCATTGTCGC
*
57329 CTGGGCGCTGAGGCATT-TTGC
1 CTGGGCGCTGA-GCATTGTCGC
57350 CTGGG
1 CTGGG
57355 TGCCCAGCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.06, C:0.28, G:0.40, T:0.26
Consensus pattern (21 bp):
CTGGGCGCTGAGCATTGTCGC
Done.