Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016430.1 Corchorus olitorius cultivar O-4 contig16463, 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: 52274
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:6820 original size:3 final size:3
Alignment explanation
Indices: 6812--6843 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6802 CCATGTCGGA
6812 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
6844 GTAAAGGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11135 original size:74 final size:74
Alignment explanation
Indices: 11011--11155 Score: 254
Period size: 74 Copynumber: 2.0 Consensus size: 74
11001 ACTTACTGCA
*
11011 CTGAAAGTGGATCTCACTGACTTGACCGTCGGAGGAGGTCCCCCAGTCATTCGGGAGATCTCTTT
1 CTGAAAGTGGATCTCACTGACTTGACCGTCGGAGGAGGTCCCCCAATCATTCGGGAGATCTCTTT
*
11076 CTCATAGTT
66 CACATAGTT
* *
11085 CTGAAAGTGGATCTCACTGACTTGACCGTCGGAGGAGGTCTCTCAATCATTCGGGAGATCTCTTT
1 CTGAAAGTGGATCTCACTGACTTGACCGTCGGAGGAGGTCCCCCAATCATTCGGGAGATCTCTTT
11150 CACATA
66 CACATA
11156 ATTTACTCTC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (74 bp):
CTGAAAGTGGATCTCACTGACTTGACCGTCGGAGGAGGTCCCCCAATCATTCGGGAGATCTCTTT
CACATAGTT
Found at i:12322 original size:27 final size:26
Alignment explanation
Indices: 12278--12328 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
12268 TTAATTAATT
* * *
12278 AATTAAAATAAAATTAAACTAATTGA
1 AATTAAAAAAAAAATAAAATAATTGA
12304 AATTAAAAAAATAAATAAAATAATT
1 AATTAAAAAAA-AAATAAAATAATT
12329 CAATCCTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (26 bp):
AATTAAAAAAAAAATAAAATAATTGA
Found at i:31014 original size:19 final size:19
Alignment explanation
Indices: 30976--31014 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
30966 ACTGGGTCAG
* **
30976 AATATTATTATTAATTAAA
1 AATATGATTATTAAACAAA
30995 AATATGATTATTAAACAAA
1 AATATGATTATTAAACAAA
31014 A
1 A
31015 GTTTACGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AATATGATTATTAAACAAA
Found at i:35653 original size:17 final size:17
Alignment explanation
Indices: 35631--35669 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
35621 GCTGATGAAA
35631 AAAGAAACGGTTTCGAG
1 AAAGAAACGGTTTCGAG
35648 AAAG-AACGGTTTCGAG
1 AAAGAAACGGTTTCGAG
35664 AAAGAA
1 AAAGAA
35670 GAGGAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.46, C:0.10, G:0.28, T:0.15
Consensus pattern (17 bp):
AAAGAAACGGTTTCGAG
Found at i:39387 original size:6 final size:7
Alignment explanation
Indices: 39361--39386 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39351 GTCTAGTCCT
39361 AAAAAAG
1 AAAAAAG
39368 AAAAAAG
1 AAAAAAG
39375 AAAAAAG
1 AAAAAAG
39382 AAAAA
1 AAAAA
39387 GCCACCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:39686 original size:1 final size:1
Alignment explanation
Indices: 39649--39679 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
39639 TCCATTCCTC
39649 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
39680 AATTTTTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:42349 original size:10 final size:8
Alignment explanation
Indices: 42326--42351 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
42316 GAACATGGGG
42326 TGACACAC
1 TGACACAC
42334 TGACACAC
1 TGACACAC
42342 TGACACAC
1 TGACACAC
42350 TG
1 TG
42352 GTGGTAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (8 bp):
TGACACAC
Found at i:44306 original size:122 final size:122
Alignment explanation
Indices: 44104--44328 Score: 360
Period size: 122 Copynumber: 1.8 Consensus size: 122
44094 TTGCTCTGAT
* ** *
44104 TTTCCTTTTTCTGCTCTGATGGTTTCTTGATAGTGTTTCTTCTCTTCTGCAGTTGTCTCCCAATT
1 TTTCCTTTTTCTGCTCTGATGGTTTCTGGATAACGTTTCTTCTCCTCTGCAGTTGTCTCCCAATT
* * * *
44169 GGATCTGACCGTATCCTTGTGGCAGCTAGGATTGCCTTCAGATTTGTTTGTTGTAAG
66 GGAGCTGACCATATCCTTGTGGCAGCAAGAATTGCCTTCAGATTTGTTTGTTGTAAG
*
44226 TTTCCTTTTTCTGCTCTGATGGTTTCTGGATAACGTTTCTTCTCCTCTGCAGTTGTCTCCCCATT
1 TTTCCTTTTTCTGCTCTGATGGTTTCTGGATAACGTTTCTTCTCCTCTGCAGTTGTCTCCCAATT
*
44291 GGAGCTGAGCATATCCTTGTGGCAGCAAGAATTGCCTT
66 GGAGCTGACCATATCCTTGTGGCAGCAAGAATTGCCTT
44329 ATTGTCTCGA
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
122 93 1.00
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (122 bp):
TTTCCTTTTTCTGCTCTGATGGTTTCTGGATAACGTTTCTTCTCCTCTGCAGTTGTCTCCCAATT
GGAGCTGACCATATCCTTGTGGCAGCAAGAATTGCCTTCAGATTTGTTTGTTGTAAG
Found at i:44459 original size:20 final size:20
Alignment explanation
Indices: 44393--44459 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
44383 CATTGAGGGC
44393 CAATGTGAATTAAGGCAAGTT
1 CAATGTG-ATTAAGGCAAGTT
* * *
44414 CAATGTCATT-TGGTAAAGTT
1 CAATGTGATTAAGG-CAAGTT
**
44434 GGATGTGATTAAGGCAAGTT
1 CAATGTGATTAAGGCAAGTT
44454 CAATGT
1 CAATGT
44460 CATTTGGATG
Statistics
Matches: 34, Mismatches: 10, Indels: 5
0.69 0.20 0.10
Matches are distributed among these distances:
19 2 0.06
20 24 0.71
21 8 0.24
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.33
Consensus pattern (20 bp):
CAATGTGATTAAGGCAAGTT
Found at i:44480 original size:32 final size:32
Alignment explanation
Indices: 44432--44740 Score: 424
Period size: 32 Copynumber: 9.2 Consensus size: 32
44422 TTTGGTAAAG
44432 TTGGATGTG-ATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
44463 TTGGATGTAAATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
*
44495 TTGGATGTGAATAAAGGCAAGTTCAATGTCATTT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCA--T
44529 GGGAAAGTTGGATGTGAATTAAGGCAAGTTCAATGTCAT
1 -------TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
44568 TTGGATGTGAA-TAAGGCAAGTTCAATGTCATTT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCA--T
44601 GGGAAAGTTGGATGTGAATTAAGGCAAGTTCAATGTCAT
1 -------TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
44640 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
44672 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
44704 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
44736 TTGGA
1 TTGGA
44741 AAGTTAAATG
Statistics
Matches: 254, Mismatches: 4, Indels: 39
0.86 0.01 0.13
Matches are distributed among these distances:
31 27 0.11
32 163 0.64
33 1 0.00
34 1 0.00
39 2 0.01
40 11 0.04
41 49 0.19
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (32 bp):
TTGGATGTGAATTAAGGCAAGTTCAATGTCAT
Found at i:44564 original size:21 final size:21
Alignment explanation
Indices: 44499--44564 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
44489 TGTCATTTGG
*
44499 ATGTGAATAAAGGCAAGTTCA
1 ATGTGAATTAAGGCAAGTTCA
* ** * **
44520 ATGT-CATTTGGGAAAGTTGG
1 ATGTGAATTAAGGCAAGTTCA
44540 ATGTGAATTAAGGCAAGTTCA
1 ATGTGAATTAAGGCAAGTTCA
44561 ATGT
1 ATGT
44565 CATTTGGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (21 bp):
ATGTGAATTAAGGCAAGTTCA
Found at i:44583 original size:104 final size:104
Alignment explanation
Indices: 44395--44755 Score: 517
Period size: 104 Copynumber: 3.5 Consensus size: 104
44385 TTGAGGGCCA
44395 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGTAAAGTTGGATGTG-ATTAAGGCAAGTTCAATG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGG-AAAGTTGGATGTGAATTAAGGCAAGTTCAATG
*
44459 TCATTTGGATGTAAATTAAGGCAAGTTCAATGTCATTTGG
65 TCATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
*
44499 ATGTGAATAAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATTAAGGCAAGTTCAATG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTT-GGAAAGTTGGATGTGAATTAAGGCAAGTTCAATG
44564 TCATTTGGATGTGAA-TAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
65 TCATTTGGATGTGAATTAAGGCAAGTTCAATGTCA--T-------TTGG
44612 ATGTGAATTAAGGCAAGTTCAATGTCA--T------TTGGATGTGAATTAAGGCAAGTTCAATGT
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGAAAGTTGGATGTGAATTAAGGCAAGTTCAATGT
44669 CATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
66 CATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
**
44708 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGAAAGTTAAATGTGAAT
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGAAAGTTGGATGTGAAT
44756 GTGCCGCGTG
Statistics
Matches: 232, Mismatches: 5, Indels: 40
0.84 0.02 0.14
Matches are distributed among these distances:
96 31 0.13
98 1 0.00
103 1 0.00
104 114 0.49
105 53 0.23
106 1 0.00
111 1 0.00
113 30 0.13
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (104 bp):
ATGTGAATTAAGGCAAGTTCAATGTCATTTGGAAAGTTGGATGTGAATTAAGGCAAGTTCAATGT
CATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
Found at i:44608 original size:20 final size:20
Alignment explanation
Indices: 44585--44643 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
44575 TGAATAAGGC
44585 AAGTTCAATGTCATTTGGGA
1 AAGTTCAATGTCATTTGGGA
** * ** *
44605 AAGTTGGATGTGAATTAAGGC
1 AAGTTCAATGT-CATTTGGGA
44626 AAGTTCAATGTCATTTGG
1 AAGTTCAATGTCATTTGG
44644 ATGTGAATTA
Statistics
Matches: 27, Mismatches: 11, Indels: 2
0.68 0.28 0.05
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (20 bp):
AAGTTCAATGTCATTTGGGA
Found at i:44616 original size:72 final size:72
Alignment explanation
Indices: 44463--44755 Score: 469
Period size: 72 Copynumber: 4.2 Consensus size: 72
44453 TCAATGTCAT
* *
44463 TTGGATGTAAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATAAAGGCAAGTTCAATGTCATT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCATT
44528 TGGGAAAG
66 T-GGAAAG
44536 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAA-TAAGGCAAGTTCAATGTCATT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCATT
44600 TGGGAAAG
66 T-GGAAAG
44608 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCA--
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCATT
44671 T------
66 TGGAAAG
44672 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCATT
1 TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCATT
44737 TGGAAAG
66 TGGAAAG
**
44744 TTAAATGTGAAT
1 TTGGATGTGAAT
44756 GTGCCGCGTG
Statistics
Matches: 207, Mismatches: 4, Indels: 19
0.90 0.02 0.08
Matches are distributed among these distances:
64 63 0.30
66 1 0.00
71 1 0.00
72 81 0.39
73 61 0.29
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (72 bp):
TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGTCATT
TGGAAAG
Found at i:44636 original size:21 final size:21
Alignment explanation
Indices: 44572--44636 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 21
44562 TGTCATTTGG
44572 ATGTGAA-TAAGGCAAGTTCA
1 ATGTGAATTAAGGCAAGTTCA
* ** * **
44592 ATGT-CATTTGGGAAAGTTGG
1 ATGTGAATTAAGGCAAGTTCA
44612 ATGTGAATTAAGGCAAGTTCA
1 ATGTGAATTAAGGCAAGTTCA
44633 ATGT
1 ATGT
44637 CATTTGGATG
Statistics
Matches: 31, Mismatches: 12, Indels: 3
0.67 0.26 0.07
Matches are distributed among these distances:
19 1 0.03
20 16 0.52
21 14 0.45
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.31
Consensus pattern (21 bp):
ATGTGAATTAAGGCAAGTTCA
Found at i:44691 original size:177 final size:168
Alignment explanation
Indices: 44395--44740 Score: 568
Period size: 177 Copynumber: 2.0 Consensus size: 168
44385 TTGAGGGCCA
*
44395 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGTAAAGTTGGATGTGATTAAGGCAAGTTCAATGT
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGATTAAGGCAAGTTCAATGT
44460 CATTTGGATGTAAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATAAAGGCAAGTTCAATGTC
66 CATTTGGATGTAAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATAAAGGCAAGTTCAATGTC
44525 ATTTGGGAAAGTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
131 A--T-------TTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
44572 ATGTGAA-TAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGAATTAAGGCAAGTTCAATG
1 ATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTG-ATTAAGGCAAGTTCAATG
* *
44636 TCATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATTAAGGCAAGTTCAATGT
65 TCATTTGGATGTAAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATAAAGGCAAGTTCAATGT
44701 CATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
130 CATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
44740 A
1 A
44741 AAGTTAAATG
Statistics
Matches: 165, Mismatches: 3, Indels: 11
0.92 0.02 0.06
Matches are distributed among these distances:
168 37 0.22
175 1 0.01
176 37 0.22
177 90 0.55
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (168 bp):
ATGTGAATTAAGGCAAGTTCAATGTCATTTGGGAAAGTTGGATGTGATTAAGGCAAGTTCAATGT
CATTTGGATGTAAATTAAGGCAAGTTCAATGTCATTTGGATGTGAATAAAGGCAAGTTCAATGTC
ATTTGGATGTGAATTAAGGCAAGTTCAATGTCATTTGG
Found at i:45001 original size:12 final size:12
Alignment explanation
Indices: 44984--45016 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
44974 TTTTGTTTCA
44984 TCTGTTTGTATT
1 TCTGTTTGTATT
44996 TCTGTTTGTATT
1 TCTGTTTGTATT
*
45008 TCAGTTTGT
1 TCTGTTTGT
45017 GATGCTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.18, T:0.64
Consensus pattern (12 bp):
TCTGTTTGTATT
Found at i:47303 original size:27 final size:27
Alignment explanation
Indices: 47273--47324 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
47263 TACATGCTGT
*
47273 GAAATTCCGTTAAATATTTATGAAATG
1 GAAATTCCATTAAATATTTATGAAATG
47300 GAAATTCCATTAAATATTTATGAAA
1 GAAATTCCATTAAATATTTATGAAA
47325 ACGGGCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (27 bp):
GAAATTCCATTAAATATTTATGAAATG
Found at i:50292 original size:333 final size:332
Alignment explanation
Indices: 48893--50818 Score: 2573
Period size: 333 Copynumber: 5.9 Consensus size: 332
48883 TTTCGCCGTT
* * *
48893 GAAAAATTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAACATGACGCCAAAAAG
1 GAAAATTTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAACTTAACGCCAAAAAG
* *
48958 ATTCAAGGATTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTCTG----AA--T-TAATT--
66 ATTCGAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAA
*
49014 -T-----CAAGATTCAAATGCTTGTAAAAACAAATCCTCAAATGCAACGTGGCTAAGGTTTTTAT
131 ATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTCAAATGCAACGTGGCTAA-GTTTTTAT
* * *
49073 TAGATAAATATAGATATTTCAAGGATTCTTGACGCCAAAAATCATGCAAAATTGAGCCGGGA-CC
195 TAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCC
* * * **
49137 CGAAGCGCGTTTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTTTACTAAAATTTTGCAAAA
260 CGAAACGCGTTTTTAGCCAAAAACCGTGATGG-TAGTACACGATTTTGGCTAAAATTTTGCAAAA
49202 AATGACCGC
324 AATGACCGC
* * * *
49211 TAAAATGTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAACCTAACGGCAAAAAG
1 GAAAATTTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAACTTAACGCCAAAAAG
* *
49276 ATTTGAGGACTTTTCATGCTTTTAATATCATTTTTCATATTTTTTCTGAATTAATTTCTAATTAA
66 ATTCGAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAA
* * * *
49341 ATTGAAACAAGATTCATATGCTCGTAAAAACAAATCCTCAAATGCAATGTGGCTAAGTTTTTAAT
131 ATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTCAAATGCAACGTGGCTAAGTTTTTATT
* * * * *
49406 AGGTGAATATAGATATTTCAAGGAGTTTTGCCGCCAAAAATCATGCAAAACTGAGTCGGGTCCCC
196 AGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCC
* * * *
49471 GAAACGCCATTTTTTTTTGCCAAAAACTGTGATGGTTAGTACACGATTTTGGCTAATA-TTTG--
261 GAAACG-C---GTTTTTAGCCAAAAACCGTGATGG-TAGTACACGATTTTGGCTAAAATTTTGCA
*
49533 AAAAATTACCGC
321 AAAAATGACCGC
* * * *
49545 G-AAA-----TGCTCAATTTTTGGATAAAATACTCATAATATATATATAACATAACACCAAAAAG
1 GAAAATTTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAACTTAACGCCAAAAAG
* *
49604 ATTCGAGAACTTTTCATGCTTTTAATATCGTTTTTTATATTTTTTCTGAATTAATTTCTAATTAA
66 ATTCGAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAA
* * * *
49669 ATCGAAACAAGATTCAAATGCTCGTAAAAA-AAAACCTCAAATGAAATGTGGCTAAGTTTATATT
131 ATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTCAAATGCAACGTGGCTAAGTTTTTATT
* * * * *
49733 ATATGAATATAGATATTTCAAGGAGCCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGTCCCC
196 AGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCC
* * * *
49798 GAAACGCCTTTTTTTGCCAAAAACC--GA--G-CGTACACGATTTTGGCTAAAATTTTGCAGAAA
261 GAAACG-CGTTTTTAGCCAAAAACCGTGATGGTAGTACACGATTTTGGCTAAAATTTTGCAAAAA
*
49858 ATAACCGC
325 ATGACCGC
* * *
49866 GAAAAATTTTTGCTCAATTTTCGGATAAAATACTCATAAAATATATATAACTTAACGCCAAAAAG
1 GAAAATTTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAACTTAACGCCAAAAAG
49931 ATTCGAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAA
66 ATTCGAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAA
* *
49996 ATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATT
131 ATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTCAAATGCAACGTGGCTAAGTTTTTATT
* *
50061 AGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGTCTCC
196 AGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCC
* *
50126 GAAACGCGTTTTTAGCCAAAAACCGTGATGGTAGTACACGATTTTGGGTAAAACTTTGCAAAAAA
261 GAAACGCGTTTTTAGCCAAAAACCGTGATGGTAGTACACGATTTTGGCTAAAATTTTGCAAAAAA
* *
50191 GTTACGGC
326 -TGACCGC
* * * *
50199 GAAAATTTTTTCCTCAATTTTTGGATAAAAAACTCATAAAATATAAATAATTTAACGCCAAAAAC
1 GAAAATTTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAACTTAACGCCAAAAAG
* *
50264 ATTGGAGGACTTTTCATGCTTTTAATATCATTTTTCATATTTTTTCTGAATTAATTTCTAATTAA
66 ATTCGAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAA
* *
50329 ATCGAAAAAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAACGTGGCTAAGTTTTTATT
131 ATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTCAAATGCAACGTGGCTAAGTTTTTATT
* * * * *
50394 AGATGAGTATTGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAATTGAGCCCGGACTCC
196 AGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCC
* *
50459 GAAGCGCGTTTTTAGCCAAAAACC---A---T-G-ACACGATTTTGACTAAAATTTTGCAAAAAA
261 GAAACGCGTTTTTAGCCAAAAACCGTGATGGTAGTACACGATTTTGGCTAAAATTTTGCAAAAAA
*
50516 TGACCGT
326 TGACCGC
* *
50523 GAAAATTTTTTCCTC-ATTCTTTGGAAAAAATTACTCATAATATATATATATATAACTTAACGAC
1 GAAAATTTTTTCCTCAATT-TTTGGATAAAA-TACTCAT-A-A-A-ATATATATAACTTAACGCC
* *
50587 AAAAATATTTGAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCT
60 AAAAAGATTCGAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCT
* * * *
50652 AATTAAATCGAAACAAGATTCAAATGCTTGTAAAAATAAATCCTTAAATGCAACGTGGCTAAATT
125 AATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTCAAATGCAACGTGGCTAAGTT
* * * * **
50717 TTAATTAGATGAATATAAATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAATTAAGCTAG
190 TTTATTAGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGG
*
50782 GACCCCGAAACGCGTTTGTAGCCAAAAACCGTGATGG
255 GACCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG
50819 CTAAGCCAGC
Statistics
Matches: 1434, Mismatches: 126, Indels: 79
0.87 0.08 0.05
Matches are distributed among these distances:
318 122 0.09
319 4 0.00
320 1 0.00
321 11 0.01
322 7 0.00
323 3 0.00
324 46 0.03
325 38 0.03
326 2 0.00
327 258 0.18
328 237 0.17
329 226 0.16
330 1 0.00
331 1 0.00
332 91 0.06
333 329 0.23
334 12 0.01
336 4 0.00
337 41 0.03
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (332 bp):
GAAAATTTTTTCCTCAATTTTTGGATAAAATACTCATAAAATATATATAACTTAACGCCAAAAAG
ATTCGAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAA
ATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTCAAATGCAACGTGGCTAAGTTTTTATT
AGATGAATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGACCCC
GAAACGCGTTTTTAGCCAAAAACCGTGATGGTAGTACACGATTTTGGCTAAAATTTTGCAAAAAA
TGACCGC
Found at i:52176 original size:336 final size:335
Alignment explanation
Indices: 51233--52273 Score: 1678
Period size: 337 Copynumber: 3.1 Consensus size: 335
51223 TTTTAGTAAC
* * * * *
51233 GTACACGGTTTTGGCTAAAATTTGGCAAAAAATTA-C-CGAAAAATTTTTCCTCAAATTTTGGAT
1 GTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTTTTCCTCAATTTTTGGAA
* * * * * * * *
51296 AAAATACTAATAA-A-ATATACATAATTTAATGCCAAAAACATTGGAGGACTTTTCATGCTTTTA
66 AAAATACTCATAATATATATATATAACTTAACGACAAAAAGATTCGAGGATTTTTCATGCTTTTA
*
51359 ATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATTGAAACAAGATTCAAATGCTCG
131 ATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCG
51424 TAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAGTATAGATATTTCAAGGA
196 TAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAGTATAGATATTTCAAGGA
51489 GTCTTGACGCCAAAAATCCTGCAAAACTGAGCCGGGACTCCGAAGCGCGTTTTTAGTCAAAAACC
261 GTCTTGACGCCAAAAATCCTGCAAAACTGAGCCGGGACTCCGAAGCGCGTTTTTAGTCAAAAACC
51554 GTGATGGTTA
326 GTGATGGTTA
51564 GTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTTTTCCTCAATTTTTGGAA
1 GTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTTTTCCTCAATTTTTGGAA
51629 AAAATACTCATAATATATATATATAAAACTTAACGACAAAAAGATTCGAGGATTTTTCATGCTTT
66 AAAATACTCATAATATATATATAT--AACTTAACGACAAAAAGATTCGAGGATTTTTCATGCTTT
*
51694 TAATATCGTTTTTCATATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCT
129 TAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCT
*
51759 CGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATCAGATGAGTATAGATATTTCAAG
194 CGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAGTATAGATATTTCAAG
51824 GAGTCTTGACGCCAAAAATCCTGCAAAACTGAGCCGGGACTCCGAAGCGCGTTTTTAGTCAAAAA
259 GAGTCTTGACGCCAAAAATCCTGCAAAACTGAGCCGGGACTCCGAAGCGCGTTTTTAGTCAAAAA
51889 CCGTGATGGTTA
324 CCGTGATGGTTA
51901 GTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTTTTCCTCAATTTTTGGAA
1 GTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTTTTCCTCAATTTTTGG-A
*
51966 AAAAATACTCATAATATATATATATAACTTAACGACAAAAAGATTCGAGGATTTTTCATGGTTTT
65 AAAAATACTCATAATATATATATATAACTTAACGACAAAAAGATTCGAGGATTTTTCATGCTTTT
* * *
52031 AATATCGTTTTTCATATTTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGACTCAAATTCTC
130 AATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTC
* * * *
52096 GTAAAAACAAATCCTTAAATGCAACGTGGCTAAATTTTAATTAGATGAATATAGATATTTCAAGG
195 GTAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAGTATAGATATTTCAAGG
* * * * * * *
52161 AGTCTTGACGCCAAAAATCATGCAAAACTTAGCAGGGTC-CTCGAAACGCGTTTTTTGCCAAAAA
260 AGTCTTGACGCCAAAAATCCTGCAAAACTGAGCCGGGACTC-CGAAGCGCGTTTTTAGTC---AA
52225 AAACCGTGATGGTTA
321 AAACCGTGATGGTTA
52240 GTACACGATTTTGGTCTAAAATTTTAGTCAAAAA
1 GTACACGATTTTGG-CTAAAATTTT-G-CAAAAA
52274 T
Statistics
Matches: 663, Mismatches: 33, Indels: 17
0.93 0.05 0.02
Matches are distributed among these distances:
331 32 0.05
332 1 0.00
333 37 0.06
334 1 0.00
335 8 0.01
336 210 0.32
337 300 0.45
338 26 0.04
339 31 0.05
340 10 0.02
341 1 0.00
342 6 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (335 bp):
GTACACGATTTTGGCTAAAATTTTGCAAAAAATGACCGCGAAAAATTTTTCCTCAATTTTTGGAA
AAAATACTCATAATATATATATATAACTTAACGACAAAAAGATTCGAGGATTTTTCATGCTTTTA
ATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCG
TAAAAACAAATCCTTAAATGCAATGTGGCTAAGTTTTTATTAGATGAGTATAGATATTTCAAGGA
GTCTTGACGCCAAAAATCCTGCAAAACTGAGCCGGGACTCCGAAGCGCGTTTTTAGTCAAAAACC
GTGATGGTTA
Done.