Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016663.1 Corchorus olitorius cultivar O-4 contig16696, 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: 75206
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:5918 original size:22 final size:19
Alignment explanation
Indices: 5890--5932 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 19
5880 GGCAATTTTT
5890 TTCTCTCTCTCTAACTGAGAGC
1 TTCTCTCTC-CTAAC-G-GAGC
5912 TTCTCTCTCCTAACGGAGC
1 TTCTCTCTCCTAACGGAGC
5931 TT
1 TT
5933 GCCGGAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 5 0.24
22 9 0.43
ACGTcount: A:0.16, C:0.33, G:0.14, T:0.37
Consensus pattern (19 bp):
TTCTCTCTCCTAACGGAGC
Found at i:14701 original size:30 final size:30
Alignment explanation
Indices: 14665--14733 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
14655 ATCAAGCAAC
14665 CAAAGGTCCTGCACAA-GCCACTGCACCAAG
1 CAAAGGTCCTGCA-AACGCCACTGCACCAAG
*
14695 CAAAGGTCCTGCAAACTCCACTGCACCAAG
1 CAAAGGTCCTGCAAACGCCACTGCACCAAG
14725 CAAAGGTCC
1 CAAAGGTCC
14734 ACCAAGGAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.33, C:0.36, G:0.19, T:0.12
Consensus pattern (30 bp):
CAAAGGTCCTGCAAACGCCACTGCACCAAG
Found at i:15270 original size:33 final size:33
Alignment explanation
Indices: 15198--15277 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
15188 AGATTTGTAC
* * *
15198 AAATGTAAAAATTAGGTGATAGTAGATTTCTGG
1 AAATGTTAACATTAGGTGATAGAAGATTTCTGG
* *
15231 AAATGTTAACATTAGGTGATGGAAGATTTCTGT
1 AAATGTTAACATTAGGTGATAGAAGATTTCTGG
15264 AAATGTTAACATTA
1 AAATGTTAACATTA
15278 ACATAAGATG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (33 bp):
AAATGTTAACATTAGGTGATAGAAGATTTCTGG
Found at i:16306 original size:22 final size:22
Alignment explanation
Indices: 16278--16323 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
16268 GGGTTAGATC
*
16278 TCCTTTT-ATTTTCTTTTCTTTT
1 TCCTTTTCATTTT-TTTGCTTTT
16300 TCCTTTTCCATTTTTTTGCTTTT
1 TCCTTTT-CATTTTTTTGCTTTT
16323 T
1 T
16324 TTGCTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 9 0.43
24 5 0.24
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (22 bp):
TCCTTTTCATTTTTTTGCTTTT
Found at i:16335 original size:10 final size:9
Alignment explanation
Indices: 16310--16334 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16300 TCCTTTTCCA
16310 TTTTTTTGC
1 TTTTTTTGC
16319 TTTTTTTGC
1 TTTTTTTGC
16328 TTTTTTT
1 TTTTTTT
16335 TTATATTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (9 bp):
TTTTTTTGC
Found at i:23206 original size:15 final size:15
Alignment explanation
Indices: 23186--23218 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
23176 ATGGAGATTG
23186 AATTAAATTGGAGGA
1 AATTAAATTGGAGGA
23201 AATTAAATTGGAGGA
1 AATTAAATTGGAGGA
23216 AAT
1 AAT
23219 ATTGTTAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.27
Consensus pattern (15 bp):
AATTAAATTGGAGGA
Found at i:24496 original size:20 final size:21
Alignment explanation
Indices: 24467--24506 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
24457 ATGCAGCACA
24467 TTTTATTTTAATTAATTATGT
1 TTTTATTTTAATTAATTATGT
*
24488 TTTTA-TTTATTTAATTATG
1 TTTTATTTTAATTAATTATG
24507 AGTCTTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTATTTTAATTAATTATGT
Found at i:24568 original size:22 final size:23
Alignment explanation
Indices: 24540--24582 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
24530 CATTAGGATT
24540 AGGTTTTACT-TTCCTACCAGAA
1 AGGTTTTACTATTCCTACCAGAA
24562 AGGTTTTACTATTCCTACCAG
1 AGGTTTTACTATTCCTACCAG
24583 GATTAGCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (23 bp):
AGGTTTTACTATTCCTACCAGAA
Found at i:25374 original size:30 final size:30
Alignment explanation
Indices: 25280--25356 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
25270 GAGTATGACG
25280 AGGAGGAAGATTCTGATATCTTTGTTTGTGA
1 AGGA-GAAGATTCTGATATCTTTGTTTGTGA
* * *
25311 AGGAGAATATTCCGATCTCTTTGTTTGTGA
1 AGGAGAAGATTCTGATATCTTTGTTTGTGA
25341 AGGAGAAGATTCTGAT
1 AGGAGAAGATTCTGAT
25357 TTTGTTTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 37 0.90
31 4 0.10
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.36
Consensus pattern (30 bp):
AGGAGAAGATTCTGATATCTTTGTTTGTGA
Found at i:28247 original size:22 final size:23
Alignment explanation
Indices: 28219--28261 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
28209 TAGAAGGATT
28219 AGGTTTTACT-TTCCTACCAGAA
1 AGGTTTTACTATTCCTACCAGAA
28241 AGGTTTTACTATTCCTACCAG
1 AGGTTTTACTATTCCTACCAG
28262 GATTAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (23 bp):
AGGTTTTACTATTCCTACCAGAA
Found at i:35553 original size:41 final size:39
Alignment explanation
Indices: 35491--36262 Score: 432
Period size: 41 Copynumber: 18.8 Consensus size: 39
35481 AAGACGAGAT
* *
35491 TAAACAACACCTTCCAATGAGGAAGGGCAAACTGAGAAAGG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTG-GAAA-C
* * * *
35532 TAAACAACAACTTCCGGTGAGGAAGGGCAAACTAAGAATC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACT-GGAAAC
* * *
35572 TAAACAACACCTTCC-AGTTAGGAATGACAAACTGGGAATA-
1 TAAACAACACCTTCCGA-TGAGGAAGGGCAAACT-GGAA-AC
** *
35612 TAGCCAACACCTCCCGATGAGGAAGGGCAAACTGGTAAAC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG-AAAC
35652 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAAC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG-AAAC
* *
35692 TCAACAACACCTTCCGACGAGGAAGGGCAAACTGGTAAATGC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG-AAA--C
*
35734 T-AACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG--AAAC
** * * * *
35774 GCAACAACACCTCCCGATGAGGAAGGACAAATTGGTAATTGC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG-AA--AC
* *
35816 T-GACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG-AAA--C
* * * ***
35857 T-GACAACACCTCCCGATGAGGAAGGGCAAATTGGTTTTTGC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG---AAAC
* * * *
35898 T-GACAACACCTTCCGATGAGGAATGGCAAATTGGTTAATGC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG--AA-AC
* * * *
35939 T-GACAACACCTTTCGATGATGAAGGGCAAATTGGTAAATGC
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG-AAA--C
* * * * * *
35980 T-GACAACATCTTCCTATAAGGAAGGGCAAATTGGACAAAG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG--AAAC
** * *
36020 GCAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAAA-
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG-AAAC
* * * * *
36059 TACTGACAACACCTTTCTATGAGGAAGGGCAAATTGGACAAAG
1 TA--AACAACACCTTCCGATGAGGAAGGGCAAACTGG--AAAC
** * * * *
36102 GCAACAACACCTCCCAATGAGGAAGGGCAAATTGCTAAA-
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTG-GAAAC
* * *
36141 TGCCAACAACACCTTCCGATGAGAAAGGGCAAACTGGACAAAG
1 T--AAACAACACCTTCCGATGAGGAAGGGCAAACTGG--AAAC
** *
36184 GCAACAACACCTCCCGAATCCCGATGAGGAAGGGCAAATTGGTAAATGC
1 TAAACAACACCT------T-CCGATGAGGAAGGGCAAACTGG-AAA--C
*
36233 T-GACAACACCTTCCGATGAGGAAGGGCAAA
1 TAAACAACACCTTCCGATGAGGAAGGGCAAA
36263 TTGGTAAATG
Statistics
Matches: 598, Mismatches: 93, Indels: 80
0.78 0.12 0.10
Matches are distributed among these distances:
39 3 0.01
40 144 0.24
41 402 0.67
42 15 0.03
43 1 0.00
47 4 0.01
48 29 0.05
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (39 bp):
TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGAAAC
Found at i:35825 original size:82 final size:82
Alignment explanation
Indices: 35494--36338 Score: 874
Period size: 82 Copynumber: 10.3 Consensus size: 82
35484 ACGAGATTAA
* * * * * *
35494 ACAACACCTTCCAATGAGGAAGGGCAAACT-GAGAAAGGTAAACAACAACTTCCGGTGAGGAAGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGG-CAACAACACCTCCCGATGAGGAAGG
* * *
35558 GCAAACT--AAGAAT-CTAA
65 GCAAATTGGTA-AATGCT-G
* * *
35575 ACAACACCTTCC-AGTTAGGAATGACAAACTGGGA-ATATA-GC--CAACACCTCCCGATGAGGA
1 ACAACACCTTCCGA-TGAGGAAGGGCAAACT-GGACA-A-AGGCAACAACACCTCCCGATGAGGA
* *
35635 AGGGCAAACTGGTAAA--CTAA
62 AGGGCAAATTGGTAAATGCT-G
* ** * *
35655 ACAACACCTTCCGATGAGGAAGGGCAAACTGG-TAAACTCAACAACACCTTCCGACGAGGAAGGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
* *
35719 CAAACTGGTAAATGCTA
66 CAAATTGGTAAATGCTG
*
35736 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
*
35801 CAAATTGGTAATTGCTG
66 CAAATTGGTAAATGCTG
* * * *
35818 ACAACACCTTCCGATGAGGAAGGGCAAATTGG-TAAATGCTGACAACACCTCCCGATGAGGAAGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-AACAACACCTCCCGATGAGGAAGG
***
35882 GCAAATTGGTTTTTGCTG
65 GCAAATTGGTAAATGCTG
* * ** * * ** *
35900 ACAACACCTTCCGATGAGGAATGGCAAATTGG-TTAATGCTGACAACACCTTTCGATGATGAAGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-AACAACACCTCCCGATGAGGAAGG
35964 GCAAATTGGTAAATGCTG
65 GCAAATTGGTAAATGCTG
* * * *
35982 ACAACATCTTCCTATAAGGAAGGGCAAATTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
*
36047 CAAATTGGTAAATACTG
66 CAAATTGGTAAATGCTG
* * * *
36064 ACAACACCTTTCTATGAGGAAGGGCAAATTGGACAAAGGCAACAACACCTCCCAATGAGGAAGGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
* **
36129 CAAATTGCTAAATGCCA
66 CAAATTGGTAAATGCTG
*
36146 ACAACACCTTCCGATGAGAAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGAATCCCGATGA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACA----CC---TCCCGATGA
36211 GGAAGGGCAAATTGGTAAATGCTG
59 GGAAGGGCAAATTGGTAAATGCTG
* * * * ** *
36235 ACAACACCTTCCGATGAGGAAGGGCAAATTGG-TAAATGCTGACAACACCTCATGATGACGAAGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-AACAACACCTCCCGATGAGGAAGG
36299 GCAAATTGGTAAATGCTG
65 GCAAATTGGTAAATGCTG
* *
36317 ACAACACCTTCTGATGAAGAAG
1 ACAACACCTTCCGATGAGGAAG
36339 TTTAAATTGG
Statistics
Matches: 663, Mismatches: 76, Indels: 49
0.84 0.10 0.06
Matches are distributed among these distances:
77 1 0.00
78 2 0.00
79 3 0.00
80 89 0.13
81 66 0.10
82 419 0.63
83 8 0.01
84 1 0.00
85 2 0.00
86 2 0.00
88 5 0.01
89 65 0.10
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (82 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGG
CAAATTGGTAAATGCTG
Found at i:35851 original size:123 final size:121
Alignment explanation
Indices: 35493--36379 Score: 783
Period size: 123 Copynumber: 7.2 Consensus size: 121
35483 GACGAGATTA
* * * *
35493 AACAACACCTTCCAATGAGGAAGGGCAAACTGAG-AAAGGTAAACAACAACTTCCGGTGAGGAAG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTG-GCAAAGG-CAACAACACCTTCCGATGAGGAAG
** * * * * * *
35557 GGCAAACTAAG-AAT-CTAAACAACACCTTCC-AGTTAGGAATGACAAACTGGGAATATAGC-
64 GGCAAA-TTGGTAATGCT-GACAACACCTTCCGA-TGAGGAAGGGCAAATTGGTAA-AT-GCT
* * ***
35616 --CAACACCTCCCGATGAGGAAGGGCAAACTGGTAAACTAAACAACACCTTCCGATGAGGAAGGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGCAAAGGCAACAACACCTTCCGATGAGGAAGGG
* * * * *
35679 CAAACTGGTAA-ACTCAACAACACCTTCCGACGAGGAAGGGCAAACTGGTAAATGCT
66 CAAATTGGTAATGCT-GACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCT
*
35735 AACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG-CAAAGGCAACAACACCTTCCGATGAGGAAGG
*
35800 ACAAATTGGTAATTGCTGACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCT
65 GCAAATTGGTAA-TGCTGACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCT
* * * ***** * *
35858 GACAACACCTCCCGATGAGGAAGGGCAAATTGGTTTTTGCTGACAACACCTTCCGATGAGGAATG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGCAAAGGC-AACAACACCTTCCGATGAGGAAGG
* *
35923 GCAAATTGGTTAATGCTGACAACACCTTTCGATGATGAAGGGCAAATTGGTAAATGCT
65 GCAAATTGG-TAATGCTGACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCT
* * * * * *
35981 GACAACATCTTCCTATAAGGAAGGGCAAATTGGACAAAGGCAACAACACCTCCCGATGAGGAAGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGG-CAAAGGCAACAACACCTTCCGATGAGGAAGG
* * * * *
36046 GCAAATTGGTAAATACTGACAACACCTTTCTATGAGGAAGGGCAAATTGGACAAAGGC-
65 GCAAATTGGT-AATGCTGACAACACCTTCCGATGAGGAAGGGCAAATTGG-TAAATGCT
* * * * *
36104 AACAACACCTCCCAATGAGGAAGGGCAAA-TTGCTAAATGCCAACAACACCTTCCGATGAGAAAG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGC-AAA-GGCAACAACACCTTCCGATGAGGAAG
* * * *
36168 GGCAAACTGGACAAAGGC-AACAACACCTCCCGAATCCCGATGAGGAAGGGCAAATTGGTAAATG
64 GGCAAATTGG--TAATGCTGACAACACCT------T-CCGATGAGGAAGGGCAAATTGGTAAATG
36232 CT
120 CT
* * * * * * *
36234 GACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGACAACACC-TCATGATGACGAAG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGCAAAGGC-AACAACACCTTC-CGATGAGGAAG
* * *** *
36298 GGCAAATTGGTAAATGCTGACAACACCTTCTGATGAAGAAGTTTAAATTGGTAAAAG-T
64 GGCAAATTGGT-AATGCTGACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCT
*
36356 AGACAACTCCTTCCGATGAGGAAG
1 A-ACAACACCTTCCGATGAGGAAG
36380 TTTAAATTGG
Statistics
Matches: 632, Mismatches: 99, Indels: 66
0.79 0.12 0.08
Matches are distributed among these distances:
118 2 0.00
119 3 0.00
120 62 0.10
121 63 0.10
122 45 0.07
123 343 0.54
124 16 0.03
129 13 0.02
130 83 0.13
131 2 0.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.18
Consensus pattern (121 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGGCAAAGGCAACAACACCTTCCGATGAGGAAGGG
CAAATTGGTAATGCTGACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCT
Found at i:36395 original size:41 final size:41
Alignment explanation
Indices: 35616--36393 Score: 829
Period size: 41 Copynumber: 18.9 Consensus size: 41
35606 GGAATATAGC
* * *
35616 CAACACCTCCCGATGAGGAAGGGCAAACTGGTAAA--CTAAA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCT-GA
* *
35656 CAACACCTTCCGATGAGGAAGGGCAAACTGGTAAA--CTCAA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCT-GA
* * *
35696 CAACACCTTCCGACGAGGAAGGGCAAACTGGTAAATGCTAA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
* * * *
35737 CAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-AA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGG-TAAATGCTGA
* * *
35778 CAACACCTCCCGATGAGGAAGGACAAATTGGTAATTGCTGA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
35819 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
* ***
35860 CAACACCTCCCGATGAGGAAGGGCAAATTGGTTTTTGCTGA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
* *
35901 CAACACCTTCCGATGAGGAATGGCAAATTGGTTAATGCTGA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
* *
35942 CAACACCTTTCGATGATGAAGGGCAAATTGGTAAATGCTGA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
* * * * * *
35983 CAACATCTTCCTATAAGGAAGGGCAAATTGGACAAAGGC-AA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGG-TAAATGCTGA
* *
36024 CAACACCTCCCGATGAGGAAGGGCAAATTGGTAAATACTGA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
* * * * *
36065 CAACACCTTTCTATGAGGAAGGGCAAATTGGACAAAGGC-AA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGG-TAAATGCTGA
* * * **
36106 CAACACCTCCCAATGAGGAAGGGCAAATTGCTAAATGCCAA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
* * * * *
36147 CAACACCTTCCGATGAGAAAGGGCAAACTGGACAAAGGC-AA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGG-TAAATGCTGA
36188 CAACACCTCCCGAATCCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
1 CAACACCT------T-CCGATGAGGAAGGGCAAATTGGTAAATGCTGA
36236 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
* *
36277 CAACACC-TCATGATGACGAAGGGCAAATTGGTAAATGCTGA
1 CAACACCTTC-CGATGAGGAAGGGCAAATTGGTAAATGCTGA
* * *** *
36318 CAACACCTTCTGATGAAGAAGTTTAAATTGGTAAAAG-TAGA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCT-GA
* ***
36359 CAACTCCTTCCGATGAGGAAGTTTAAATTGGTAAA
1 CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAA
36394 AGTAGACAAC
Statistics
Matches: 639, Mismatches: 79, Indels: 39
0.84 0.10 0.05
Matches are distributed among these distances:
40 88 0.14
41 492 0.77
42 24 0.04
47 6 0.01
48 29 0.05
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.18
Consensus pattern (41 bp):
CAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGA
Found at i:39767 original size:25 final size:25
Alignment explanation
Indices: 39733--39781 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
39723 CCAAACAATC
*
39733 TTGAGCACTCTCGCTTGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
39758 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
39782 CAAACAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:43692 original size:2 final size:2
Alignment explanation
Indices: 43685--43715 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43675 ATATTTAGTG
43685 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43716 TTGCGCAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43839 original size:23 final size:23
Alignment explanation
Indices: 43806--43856 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
43796 TATTTGGGCC
43806 CAAGCCCAATAGCTACTAAGACT
1 CAAGCCCAATAGCTACTAAGACT
*
43829 CAAGCCTAATAGCTACTAAGACT
1 CAAGCCCAATAGCTACTAAGACT
43852 CAAGC
1 CAAGC
43857 TTATAAGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.29, G:0.14, T:0.18
Consensus pattern (23 bp):
CAAGCCCAATAGCTACTAAGACT
Found at i:48418 original size:18 final size:19
Alignment explanation
Indices: 48395--48434 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
48385 TTCTTGAAAT
48395 AATTCTTC-AATAGTCTTC
1 AATTCTTCAAATAGTCTTC
*
48413 AATTCTTCAAATTGTCTTC
1 AATTCTTCAAATAGTCTTC
48432 AAT
1 AAT
48435 AAATCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAATAGTCTTC
Found at i:64828 original size:438 final size:434
Alignment explanation
Indices: 63875--64896 Score: 1280
Period size: 438 Copynumber: 2.3 Consensus size: 434
63865 AATCGAAATC
* * * *
63875 ACAAAATTTCAAAAGTATTTTTTAGAATTGAAACATGAAAATTAGCTTTTGAGTCTTTCATGAAA
1 ACAAAATTTCAGAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCTTTCATGAAA
* * * * * *
63940 GTTGTAGATCATAAAATTACCTTTTAATAGACACCTGAATTACCTTAATTGCATAAATAGAACAA
66 GTTGTAGATCATGAAATTACCTTTTAATAGACA-TTGAATCACCTTAATCGGACAAATAGAAC-A
* *
64005 AGAAAATAAAAAAAAATGAAGCGTTAAATCGAGTAAGATAGAATTTGTAAAGGACTAAGTAGCAT
129 A-AAAAT--AAAAAAATAAAGCGTTAAATCGAGTAAGATAGAATTTGTAAAGGACTAAATAGCAT
* * * *
64070 AAAATAGAAAAGTAAGAGGGTCATCTGATAACTAATTCAAATAAGAAAATATTTCTTAATAGATA
191 AAAATAGAAAAATAAGAGGGTCATCTGATAAATAATCCAAATAAGAAAATATTTCTTAATAGAGA
* *
64135 TCTTGAAACAAAAAAATTCCCTTTTGAACCTTTCATGAAACCCGCAGATCAAATTAACTTTCGGG
256 TCTTGAAACAAAAAAATTCCCTTTTGAACCCTTCATGAAACCCGCAGATCAAATTAACTTTCAGG
* * * * * *
64200 TTCTTCATGAAAGTCGTAGATCATATAGTAACCTTTTAACCGACACTTGAACAACTTTAATCGGA
321 TCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAACAACTTCAATCGGA
* ** * *
64265 CATGTGGATCAAAAATTATATGGTATTAAATAAACCAACAATCGAAACG
386 CATGTGGATCAAAAATTATACGAAATTAAATAAACCAACAAGCGAAAAG
* * * * *
64314 ACCAAATTTAAGAAGCATTTTTTTGAATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAA
1 ACAAAATTTCAGAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCTTTCATGAAA
* * *
64379 GTTGTAGATCATGAAATTATCATTTAATAGACATATGAATCAACTTAATCGGACAAATAGAACAA
66 GTTGTAGATCATGAAATTACCTTTTAATAGACAT-TGAATCACCTTAATCGGACAAATAGAACAA
* * * *
64444 ATAATAAAAAAATAAATC-TTAAA-CGTTAGATTAAGATAGAATTTGTAAAGGATTAAATAGTAT
130 AAAATAAAAAAATAAAGCGTTAAATCG--AG--TAAGATAGAATTTGTAAAGGACTAAATAGCAT
* * * * * *
64507 AAAGTAGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGA
191 AAAATAGAAAAATAAGAGGGTCATCTGATAAATAATCCAAATAAGAAAATATTTCTTAATAGAGA
* * * *
64572 TCTTGAAGCATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGCAGATCAAATTTAGCTTTCAG
256 TCTTGAAACAAAAAAATTCCCTTTTGAACCCTTCATGAAACCCGCAGATCAAA-TTAACTTTCAG
* * * *
64637 GTCCTTCATGAAAGTTGTAAATCATGCAATAACCTTTTAACCGACATTTCAATAACTTCAATCGG
320 GTCCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAACAACTTCAATCGG
** **
64702 ACATGTGGA-CAAAAAATTATACGAAATTAAATTGACCGGCAAGC-AAAAG
385 ACATGTGGATC-AAAAATTATACGAAATTAAATAAACCAACAAGCGAAAAG
* * * * *
64751 TACAAAATTTCGGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTTTTCATGAA
1 -ACAAAATTTCAGAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCTTTCATGAA
* *
64816 AATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTTAATGGGACAAATAGAA-A
65 AGTTGTAGATCATGAAATTACCTTTTAATAGACA-TTGAATCACCTTAATCGGACAAATAGAACA
*
64880 AAAAATACAAAAATAAA
129 AAAAATAAAAAAATAAA
64897 AGCCAACGCG
Statistics
Matches: 499, Mismatches: 75, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
433 2 0.00
434 5 0.01
435 13 0.03
437 158 0.32
438 211 0.42
439 110 0.22
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (434 bp):
ACAAAATTTCAGAAGCATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCTTTCATGAAA
GTTGTAGATCATGAAATTACCTTTTAATAGACATTGAATCACCTTAATCGGACAAATAGAACAAA
AAATAAAAAAATAAAGCGTTAAATCGAGTAAGATAGAATTTGTAAAGGACTAAATAGCATAAAAT
AGAAAAATAAGAGGGTCATCTGATAAATAATCCAAATAAGAAAATATTTCTTAATAGAGATCTTG
AAACAAAAAAATTCCCTTTTGAACCCTTCATGAAACCCGCAGATCAAATTAACTTTCAGGTCCTT
CATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAACAACTTCAATCGGACATGT
GGATCAAAAATTATACGAAATTAAATAAACCAACAAGCGAAAAG
Found at i:67534 original size:15 final size:15
Alignment explanation
Indices: 67510--67596 Score: 120
Period size: 15 Copynumber: 5.7 Consensus size: 15
67500 GATAACTTTC
*
67510 CAGCACTTTAGTATT
1 CAGCATTTTAGTATT
67525 CAGCATTTTAGTATT
1 CAGCATTTTAGTATT
67540 CAGCATTTTAGTATT
1 CAGCATTTTAGTATT
*
67555 CAACATTTTAGTATT
1 CAGCATTTTAGTATT
*
67570 CAACATTTTAAGTATT
1 CAGCATTTT-AGTATT
* *
67586 TAGAATTTTAG
1 CAGCATTTTAG
67597 GTTTCAAAGG
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
15 54 0.82
16 12 0.18
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (15 bp):
CAGCATTTTAGTATT
Done.