Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020031.1 Corchorus olitorius cultivar O-4 contig20064, 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: 41433
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:71 original size:23 final size:20
Alignment explanation
Indices: 23--71 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
13 TATTTCTGGG
23 TTTTTTTTTTAATCTTTTTA
1 TTTTTTTTTTAATCTTTTTA
* *
43 GATTTTCTTTTAATTTCTTTTTA
1 -TTTTTTTTTTAA--TCTTTTTA
66 TTTTTT
1 TTTTTT
72 AATAAGTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
21 10 0.45
22 4 0.18
23 8 0.36
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTTTTTTTAATCTTTTTA
Found at i:4587 original size:15 final size:14
Alignment explanation
Indices: 4562--4609 Score: 69
Period size: 15 Copynumber: 3.3 Consensus size: 14
4552 TTCTTTTCCA
4562 TTTTCCTTTTCTTT
1 TTTTCCTTTTCTTT
*
4576 TTTTCGCTTTTCTTC
1 TTTTC-CTTTTCTTT
4591 TTTTCCTTTTTCTTT
1 TTTTCC-TTTTCTTT
4606 TTTT
1 TTTT
4610 TTTCCTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
14 6 0.20
15 24 0.80
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTCCTTTTCTTT
Found at i:4602 original size:36 final size:32
Alignment explanation
Indices: 4552--4620 Score: 93
Period size: 36 Copynumber: 2.0 Consensus size: 32
4542 TTTTTTGTTT
4552 TTCTTTTCCATTTTCCTTTTCTTTTTTTCGCTTTTC
1 TTCTTTTCCATTTT-C-TTT-TTTTTTTC-CTTTTC
*
4588 TTCTTTTCCTTTTTCTTTTTTTTTTCCTTTTC
1 TTCTTTTCCATTTTCTTTTTTTTTTCCTTTTC
4620 T
1 T
4621 CCTTCTTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 7 0.22
33 8 0.25
34 3 0.09
35 1 0.03
36 13 0.41
ACGTcount: A:0.01, C:0.23, G:0.01, T:0.74
Consensus pattern (32 bp):
TTCTTTTCCATTTTCTTTTTTTTTTCCTTTTC
Found at i:4612 original size:18 final size:18
Alignment explanation
Indices: 4543--4618 Score: 66
Period size: 18 Copynumber: 4.2 Consensus size: 18
4533 TGACGTGGCT
*
4543 TTTTTGTTTTTCTTTTCC
1 TTTTTCTTTTTCTTTTCC
* *
4561 ATTTTCCTTTTCTTTT--
1 TTTTTCTTTTTCTTTTCC
**
4577 TTTCGCTTTTCTTCTTTTCC
1 TTTTTC-TTT-TTCTTTTCC
*
4597 TTTTTCTTTTTTTTTTCC
1 TTTTTCTTTTTCTTTTCC
4615 TTTT
1 TTTT
4619 CTCCTTCTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
16 3 0.07
17 2 0.05
18 32 0.73
19 3 0.07
20 4 0.09
ACGTcount: A:0.01, C:0.20, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTTCTTTTTCTTTTCC
Found at i:10875 original size:106 final size:106
Alignment explanation
Indices: 10731--10938 Score: 283
Period size: 106 Copynumber: 2.0 Consensus size: 106
10721 ATCACCATAA
* *
10731 TATTGATCTGCATAAATATCAGTTGCAAGGGAACGATTTAACTTAAGAATGAATCACTATATAAG
1 TATTGATCTGCATAAATATCAGTTGCAAAGGAACGATTTAACTTAAGAAGGAATCACTATATAAG
* *** *
10796 GAAAAACATGGATTAATAGTTAAAAAAGTATACAAAAGCAT
66 AAAAAACACACATTAATAGTTAAAAAAGTAGACAAAAGCAT
* * * *
10837 TATTGATTTGCATAAATATCAG-TGTCAAAGGAATGATTTAGCTTAAGAAGGGATCACTATATAA
1 TATTGATCTGCATAAATATCAGTTG-CAAAGGAACGATTTAACTTAAGAAGGAATCACTATATAA
* *
10901 GAAAAAACACACATTAATAGTTTAAAGAGTAGACAAAA
65 GAAAAAACACACATTAATAGTTAAAAAAGTAGACAAAA
10939 ACATACATTA
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
105 2 0.02
106 86 0.98
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.27
Consensus pattern (106 bp):
TATTGATCTGCATAAATATCAGTTGCAAAGGAACGATTTAACTTAAGAAGGAATCACTATATAAG
AAAAAACACACATTAATAGTTAAAAAAGTAGACAAAAGCAT
Found at i:10947 original size:32 final size:32
Alignment explanation
Indices: 10903--10968 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
10893 CTATATAAGA
* *
10903 AAAAACACACATTAATAGTTTAAAGAGTAGAC
1 AAAAACACACATTAACAGTTAAAAGAGTAGAC
*
10935 AAAAACATACATTAACAGTTAAAAGAGTAGAC
1 AAAAACACACATTAACAGTTAAAAGAGTAGAC
10967 AA
1 AA
10969 TCCTGATAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (32 bp):
AAAAACACACATTAACAGTTAAAAGAGTAGAC
Found at i:14871 original size:124 final size:125
Alignment explanation
Indices: 14132--14935 Score: 812
Period size: 125 Copynumber: 6.5 Consensus size: 125
14122 CAATATATAT
* * * * * *
14132 TATACCGACGTTTGTAAATGTCGGAACAAGTTTTTCACATCAATTGA-CTCGACGTATTCCGACA
1 TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATATTCCGACA
* * * * * * * **
14196 TTTGTAAGTGTTGGTTTAGATATTATATAGGGACATTTATTAAACGTCGCTACAAAATGC
66 TCTGTAAGCGTTGGTATAGATATTATATCGTGACATTTATTAAACGTCACTATAAAAAAC
* ** * * * * *
14256 TATAACGACCCTTATAAATGTCAGAATAAGTTTTTCACATCATTTGATTTTGACGTATTCCGACA
1 TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATATTCCGACA
* * * * * * *
14321 TTTGTAAGCGTTGGTATAGATATTATATCGTGACAATTATTACATGTCACAACAAAATAC
66 TCTGTAAGCGTTGGTATAGATATTATATCGTGACATTTATTAAACGTCACTATAAAAAAC
* * * * ** **
14381 TATACCGATC-CTTGTAAATGTCGAAACAAGTTGTTCATGTCATTTGATTTCGATGTATTCCGAC
1 TATACCGA-CGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATATTCCGAC
* * * ** * * *
14445 TTTTGTAAGTGTTGGTATAGATATTATATCGTGACATTTATTAAACGTTGCAATAGAACAC
65 ATCTGTAAGCGTTGGTATAGATATTATATCGTGACATTTATTAAACGTCACTATAAAAAAC
* * * * *
14506 TTTACCGACAATTACAAATGTCGGAACAAGTTCTCCACATCATTT-ACTTTTGACATATTCCGAC
1 TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGA-TTTCGACATATTCCGAC
* * *
14570 ATCTATAAGCGTTGGTATAGATATTATATCGTGACATTTATTAGACGTCACTTTAAAAAA-
65 ATCTGTAAGCGTTGGTATAGATATTATATCGTGACATTTATTAAACGTCACTATAAAAAAC
* * *
14630 TATACCGACGATTACAAATGTCGGAACAAGTTCTTCACATCATTTCAGTTCGACA-ATTCCGACA
1 TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATATTCCGACA
* *
14694 TCTGTAAACGTTGGTATAGATATTATATCGTGACATTGATTAAACGTCACTATAAAAAAC
66 TCTGTAAGCGTTGGTATAGATATTATATCGTGACATTTATTAAACGTCACTATAAAAAAC
* * * *
14754 -ATACCGACGATTATAAATGTCGGAACAAGTTGTACAAAGT-ATTTGAGTTCGACATATTCCGAC
1 TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACA-TCATTTGATTTCGACATATTCCGAC
** * * * * * *
14817 ATCTGTAAATGTTGTTATAAATATTATATCGTGACATTTATTAAATGTCGCTATAAAATAT
65 ATCTGTAAGCGTTGGTATAGATATTATATCGTGACATTTATTAAACGTCACTATAAAAAAC
* * * * * * * * *
14878 TATACCAACGCTTACAAATGTCGAAACAATTTATTCGCATCAATGGATTTCGACATAT
1 TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATAT
14936 GTAAGCGTTG
Statistics
Matches: 573, Mismatches: 97, Indels: 19
0.83 0.14 0.03
Matches are distributed among these distances:
123 110 0.19
124 153 0.27
125 309 0.54
126 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (125 bp):
TATACCGACGATTATAAATGTCGGAACAAGTTCTTCACATCATTTGATTTCGACATATTCCGACA
TCTGTAAGCGTTGGTATAGATATTATATCGTGACATTTATTAAACGTCACTATAAAAAAC
Found at i:17811 original size:13 final size:13
Alignment explanation
Indices: 17795--17819 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17785 CAAAGTTTAA
17795 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
17808 AAAAAAGAAAAA
1 AAAAAAGAAAAA
17820 TATAAGAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:19812 original size:2 final size:2
Alignment explanation
Indices: 19805--19838 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19795 AACCCACTCA
19805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19839 TCATATGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20302 original size:2 final size:2
Alignment explanation
Indices: 20295--20320 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20285 TCTTTTTAAC
20295 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
20321 GGTAGAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25741 original size:428 final size:425
Alignment explanation
Indices: 24934--26544 Score: 1859
Period size: 428 Copynumber: 3.8 Consensus size: 425
24924 CGTTTACCCT
* *
24934 AAACGTTGTCATAAATGTCGGAGAAGTCTAT-TTAAAAG-AGACGTTTGTT-AAAAATGTCGCAT
1 AAACGTTGTTATAAATGTCGGAAAAGTCTATCTT-AAAGCA-ACGTTTGTTGAAAAATGTCGCAT
* * * * * *
24996 GATTGAACAACGTTTGAGATAAACGTATCAACAAACGTCGCAAAAGCCTAAACAAGAGCGACACT
64 GATTGAACGACATTTGAGA-AAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACACA
* * * * * *
25061 ATTAAAAAAATGTCACTC-AGTTTAAAAAAGAGTCGCAATG-TACTGCGATATTTATTAAAATAT
128 ATT-AAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAA-GATATTACGACATTTATTAAAATGT
* * * * *
25124 CATATTTTAAAACGACGTTT-TATAACAACGTTTTTATAAATGTTGGAAAAGTTTATCTTAAAGC
191 CAT-TTATAAAACGACGTTTCCATAA-AACGTTGTTATAAATGTCGGAAAAGTATATCTTAAAGC
* * * * * *
25188 GACGTTTCTTGATAAATGTCGCATGATTGAACGGCATTTGAGAAACACGTCGCTACAAACGTCGC
254 GACGTTTGTT-AAAAATGTCGCATGATTGAACGACGTTTGAGAAAAACGT-GTTACAAACGTCGC
* *
25253 AAAAGCATAAACAAGAGCGGCGTTATTAAAAAATGTCACTCAGTTTAAAAAAGAGTCGCAATGTA
317 AAAAGCATAAACAAGAGCGACGTTATTAAAAAATGTCACTCAATTTAAAAAAGAGTCGCAA-GTA
* * * *
25318 CTGCGATATTTATTAAAATATCATATTTTAAAACGACGTTTTATAA
381 -TGCGACATTTATTAAAATGTCATATTTTAAAACGACGTTTCAGAA
* * * * * ** * *
25364 CAACGTTTTTATAAATGTTGGAAAAGTCTATCTTAAAGCGACATTTGTTGATTAATGTCACTTGA
1 AAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATGA
* * * **
25429 TTGAACGACATTTGAGAAACACGTCGCTACAAACGTTGCAAAAGCATAAACTAGAGCGACATTAT
66 TTGAACGACATTTGAGAAA-ACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACACAAT
* * * *
25494 TAAAAAACGTCACTCAA-ATTAAAAAAGAGTCGCAAGGTATTGCGACATTTATCAAAATGTCATT
130 TAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCATT
* * * * * *
25558 T-TAAAAACGACGTTTCCCT-AAACGTTGTTATAAATGTCGGAGAAGTATGT-TCTAAGGCAACA
195 TAT-AAAACGACGTTTCCATAAAACGTTGTTATAAATGTCGGAAAAGTATATCT-TAAAGCGACG
* * * *
25620 TTTGTTAAAAAACGTCGCATGATTAAACGACGTTTAAGAAAAATGTAGTTACAAACGTCGCACAA
258 TTTGTT-AAAAATGTCGCATGATTGAACGACGTTTGAGAAAAACGT-GTTACAAACGTCGCA-AA
* * *
25685 A-CATAAACTAGAGCGACATTATTAAAAAATGTCACTCAATTTAAAAAAGTGTCGCAAGGTGATG
320 AGCATAAACAAGAGCGACGTTATTAAAAAATGTCACTCAATTTAAAAAAGAGTCGCAA-GT-ATG
* * *
25749 TGACATTTATTAAAATGTCATATATTAAAACGACGTTTCGGAA
383 CGACATTTATTAAAATGTCATATTTTAAAACGACGTTTCAGAA
*
25792 AAACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATGA
1 AAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATGA
* * * * *
25857 TTGAACGACGTTTGAGAAAACGTCTCTACAAATGTCGCAAAAGTATAAAAAAGAGCGATACAATT
66 TTGAACGACATTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACACAATT
* * * *
25922 AAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATTTTACAACGTTGATTAAAATGTCATTT
131 AAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCATTT
* *
25987 ATTAAATGACGTTTCCGA-AAAACGTTGTTATAAATGTCGGAAAAG-ACTATCTTAAAGCGACGT
196 ATAAAACGACGTTTCC-ATAAAACGTTGTTATAAATGTCGGAAAAGTA-TATCTTAAAGCGACGT
* *
26050 TTGTTCAAAAATGTTGCATGATTGAACGACGTTTGAG-AAAACGTCTCTACAAACGTCGCAAAAG
259 TTGTT-AAAAATGTCGCATGATTGAACGACGTTTGAGAAAAACGTGT-TACAAACGTCGCAAAAG
* * ** * * * * *
26114 TATAAGCAAGAGCGACGCAATTAAAAAACGTCACTCAATTTTAAAAAGGAGTCACAAGATTTTAC
322 CATAAACAAGAGCGACGTTATTAAAAAATGTCACTCAA-TTTAAAAAAGAGTCGCAAG--TATGC
* * *
26179 GACGTTTATTAAGATGTCAT-TTATT-AAACGACGTTTCCGAA
384 GACATTTATTAAAATGTCATATT-TTAAAACGACGTTTCAGAA
*
26220 AAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTAAAAAAAATGTCGCAT
1 AAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTT--GAAAAATGTCGCAT
* *
26285 GATTGAACGACATTTGAGAAAACGTCTCTACAAACGTCGCAAAAGTATAAACAAGAGCGACGCAA
64 GATTGAACGACATTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACACAA
* **
26350 TTAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATTTTACGATGTTTATTAAAATGTCAT
129 TTAAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCAT
* * * * * *
26415 TTATTAAATGACGTTTCCCTAAAACGTTGTTATAAATGTTGGAAAAGTCTATCTTAAAGCGAGGT
194 TTATAAAACGACGTTTCCATAAAACGTTGTTATAAATGTCGGAAAAGTATATCTTAAAGCGACGT
* * * * * *
26480 TTGTTAAAAATGTCGCATGATTGAACGACGTTAGACAAAAATGTCTCTACAAATGTCGTAAAAGC
259 TTGTTAAAAATGTCGCATGATTGAACGACGTTTGAGAAAAACGTGT-TACAAACGTCGCAAAAGC
26545 GTGAGCAATA
Statistics
Matches: 1011, Mismatches: 142, Indels: 56
0.84 0.12 0.05
Matches are distributed among these distances:
427 58 0.06
428 415 0.41
429 152 0.15
430 318 0.31
431 68 0.07
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (425 bp):
AAACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATGA
TTGAACGACATTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACACAATT
AAAAAACGTCACTCAATTTTAAAAAAGAGTCGCAAGATATTACGACATTTATTAAAATGTCATTT
ATAAAACGACGTTTCCATAAAACGTTGTTATAAATGTCGGAAAAGTATATCTTAAAGCGACGTTT
GTTAAAAATGTCGCATGATTGAACGACGTTTGAGAAAAACGTGTTACAAACGTCGCAAAAGCATA
AACAAGAGCGACGTTATTAAAAAATGTCACTCAATTTAAAAAAGAGTCGCAAGTATGCGACATTT
ATTAAAATGTCATATTTTAAAACGACGTTTCAGAA
Found at i:26028 original size:214 final size:214
Alignment explanation
Indices: 24871--26544 Score: 1829
Period size: 215 Copynumber: 7.8 Consensus size: 214
24861 TAAAATTTAG
* * * * * ** **
24871 AAAGAGTCGCAAGGTACTGCGACGTTTATTAAAAAAGACACGTATTTAAACGACGTTTACC-CTA
1 AAAGAGTCGCAAGATATTGCGACATTTATT-AAAATGTCATTTA-TTAAACGACGTTT-CCGAAA
* *
24935 AACGTTGTCATAAATGTCGGAGAAGTCTAT-TTAAAAG-AGACGTTTGTT-AAAAATGTCGCATG
63 AACGTTGTTATAAATGTCGGAAAAGTCTATCTT-AAAGCA-ACGTTTGTTGAAAAATGTCGCATG
* * * *
24997 ATTGAACAACGTTTGAGATAAACGTATCAACAAACGTCGCAAAAGCCTAAACAAGAGCGACACTA
126 ATTGAACGACGTTTGAGA-AAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACACTA
* *
25062 TTAAAAAAATGTCACTC-AGTTTAAA
190 TT-AAAAAACGTCACTCAATTTTAAA
* * * *** *
25087 AAAGAGTCGCAATG-TACTGCGATATTTATTAAAATATCATATT-TTAAAACGACGTTTTATAAC
1 AAAGAGTCGCAA-GATATTGCGACATTTATTAAAATGTCAT-TTATT-AAACGACGTTTCCGAAA
* * * * * *
25150 AACGTTTTTATAAATGTTGGAAAAGTTTATCTTAAAGCGACGTTTCTTGATAAATGTCGCATGAT
63 AACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATGAT
* * * * **
25215 TGAACGGCATTTGAGAAACACGTCGCTACAAACGTCGCAAAAGCATAAACAAGAGCGGCGTTATT
128 TGAACGACGTTTGAGAAA-ACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACACTATT
* *
25280 AAAAAATGTCACTC-AGTTTAAA
192 AAAAAACGTCACTCAATTTTAAA
* * * *** *
25302 AAAGAGTCGCAATG-TACTGCGATATTTATTAAAATATCATATT-TTAAAACGACGTTTTATAAC
1 AAAGAGTCGCAA-GATATTGCGACATTTATTAAAATGTCAT-TTATT-AAACGACGTTTCCGAAA
* * * * ** * *
25365 AACGTTTTTATAAATGTTGGAAAAGTCTATCTTAAAGCGACATTTGTTGATTAATGTCACTTGAT
63 AACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATGAT
* * * * *
25430 TGAACGACATTTGAGAAACACGTCGCTACAAACGTTGCAAAAGCATAAACTAGAGCGACATTATT
128 TGAACGACGTTTGAGAAA-ACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACACTATT
*
25495 AAAAAACGTCACTCAA-ATTAAA
192 AAAAAACGTCACTCAATTTTAAA
* * * **
25517 AAAGAGTCGCAAGGTATTGCGACATTTATCAAAATGTCATTT-TAAAAACGACGTTTCC-CTAAA
1 AAAGAGTCGCAAGATATTGCGACATTTATTAAAATGTCATTTAT-TAAACGACGTTTCCGAAAAA
* * * * * * *
25580 CGTTGTTATAAATGTCGGAGAAGTATGT-TCTAAGGCAACATTTGTTAAAAAACGTCGCATGATT
65 CGTTGTTATAAATGTCGGAAAAGTCTATCT-TAAAGCAACGTTTGTTGAAAAATGTCGCATGATT
* * * * * *
25644 AAACGACGTTTAAGAAAAATGTAGT-TACAAACGTCGCACAAA-CATAAACTAGAGCGACATTAT
129 GAACGACGTTTGAG-AAAACGT-CTCTACAAACGTCGCA-AAAGCATAAACAAGAGCGACACTAT
*
25707 TAAAAAATGTCACTCAA-TTTAAA
191 TAAAAAACGTCACTCAATTTTAAA
* * * * *
25730 AAAGTGTCGCAAGGTGA-TGTGACATTTATTAAAATGTCATATATTAAAACGACGTTTCGGAAAA
1 AAAGAGTCGCAAGAT-ATTGCGACATTTATTAAAATGTCATTTATT-AAACGACGTTTCCGAAAA
*
25794 ACGTTGCTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATGATT
64 ACGTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATGATT
* * * * *
25859 GAACGACGTTTGAGAAAACGTCTCTACAAATGTCGCAAAAGTATAAAAAAGAGCGATACAATTAA
129 GAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACACTATTAA
25924 AAAACGTCACTCAATTTTAAA
194 AAAACGTCACTCAATTTTAAA
* * * * * *
25945 AAAGAGTCGCAAGATTTTACAACGTTGATTAAAATGTCATTTATTAAATGACGTTTCCGAAAAAC
1 AAAGAGTCGCAAGATATTGCGACATTTATTAAAATGTCATTTATTAAACGACGTTTCCGAAAAAC
* * * *
26010 GTTGTTATAAATGTCGGAAAAGACTATCTTAAAGCGACGTTTGTTCAAAAATGTTGCATGATTGA
66 GTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATGATTGA
* * * *
26075 ACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGTATAAGCAAGAGCGACGCAATTAAAA
131 ACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACACTATTAAAA
26140 AACGTCACTCAATTTTAAA
196 AACGTCACTCAATTTTAAA
* * * * * *
26159 AAGGAGTCACAAGATTTTACGACGTTTATTAAGATGTCATTTATTAAACGACGTTTCCGAAAAAC
1 AAAGAGTCGCAAGATATTGCGACATTTATTAAAATGTCATTTATTAAACGACGTTTCCGAAAAAC
*
26224 GTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTAAAAAAAATGTCGCATGATT
66 GTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTT--GAAAAATGTCGCATGATT
* * * *
26289 GAACGACATTTGAGAAAACGTCTCTACAAACGTCGCAAAAGTATAAACAAGAGCGACGCAATTAA
129 GAACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACACTATTAA
26354 AAAACGTCACTCAATTTTAAA
194 AAAACGTCACTCAATTTTAAA
* * ** * **
26375 AAAGAGTCGCAAGATTTTACGATGTTTATTAAAATGTCATTTATTAAATGACGTTTCCCTAAAAC
1 AAAGAGTCGCAAGATATTGCGACATTTATTAAAATGTCATTTATTAAACGACGTTTCCGAAAAAC
* * *
26440 GTTGTTATAAATGTTGGAAAAGTCTATCTTAAAGCGAGGTTTGTT-AAAAATGTCGCATGATTGA
66 GTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATGATTGA
* * * * *
26504 ACGACGTTAGACAAAAATGTCTCTACAAATGTCGTAAAAGC
131 ACGACGTTTGA-GAAAACGTCTCTACAAACGTCGCAAAAGC
26545 GTGAGCAATA
Statistics
Matches: 1278, Mismatches: 153, Indels: 56
0.86 0.10 0.04
Matches are distributed among these distances:
212 1 0.00
213 187 0.15
214 369 0.29
215 422 0.33
216 298 0.23
217 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (214 bp):
AAAGAGTCGCAAGATATTGCGACATTTATTAAAATGTCATTTATTAAACGACGTTTCCGAAAAAC
GTTGTTATAAATGTCGGAAAAGTCTATCTTAAAGCAACGTTTGTTGAAAAATGTCGCATGATTGA
ACGACGTTTGAGAAAACGTCTCTACAAACGTCGCAAAAGCATAAACAAGAGCGACACTATTAAAA
AACGTCACTCAATTTTAAA
Found at i:37920 original size:28 final size:29
Alignment explanation
Indices: 37862--37918 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
37852 ATTATATTAT
*** * *
37862 TTTTATTTTTTATATTTTTTTTGGATAAA
1 TTTTATTTTTTATATTACATTAGAATAAA
37891 TTTTATTTTTTATATTACATTAGAATAA
1 TTTTATTTTTTATATTACATTAGAATAA
37919 TTAATCACTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (29 bp):
TTTTATTTTTTATATTACATTAGAATAAA
Found at i:38131 original size:3 final size:3
Alignment explanation
Indices: 38118--38180 Score: 103
Period size: 3 Copynumber: 21.3 Consensus size: 3
38108 ACTTCTATAC
38118 TTA TATA TTA TTA TTA TTA -TA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38162 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
38181 ATAATAGCAA
Statistics
Matches: 57, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.07
3 50 0.88
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:39353 original size:10 final size:10
Alignment explanation
Indices: 39338--39384 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
39328 AAGTCTTTTT
39338 GAGTTAATTA
1 GAGTTAATTA
39348 GAGTTAATTA
1 GAGTTAATTA
*
39358 -AGGTTAATTT
1 GA-GTTAATTA
*
39368 GGGTTAATTA
1 GAGTTAATTA
39378 GAGTTAA
1 GAGTTAA
39385 CCTTTGTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 1 0.03
10 30 0.97
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.40
Consensus pattern (10 bp):
GAGTTAATTA
Found at i:39424 original size:69 final size:70
Alignment explanation
Indices: 39351--39491 Score: 266
Period size: 69 Copynumber: 2.0 Consensus size: 70
39341 TTAATTAGAG
39351 TTAATTAAGGTTAATTTGGGTTAATTAGAGTTAACCTTTGTTAATTGGTGACTTTGATTTTCCC-
1 TTAATTAAGGTTAATTTGGGTTAATTAGAGTTAACCTTTGTTAATTGGTGACTTTGATTTTCCCA
39415 TACTA
66 TACTA
*
39420 TTAATTAAGGTTAATTTGGGTTAATTATAGTTAACCTTTGTTAATTGGTGACTTTGATTTTCCCA
1 TTAATTAAGGTTAATTTGGGTTAATTAGAGTTAACCTTTGTTAATTGGTGACTTTGATTTTCCCA
39485 TACTA
66 TACTA
39490 TT
1 TT
39492 TCCTATTCAT
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 63 0.90
70 7 0.10
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (70 bp):
TTAATTAAGGTTAATTTGGGTTAATTAGAGTTAACCTTTGTTAATTGGTGACTTTGATTTTCCCA
TACTA
Found at i:40494 original size:2 final size:2
Alignment explanation
Indices: 40477--40519 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
40467 ATGTTTGTTA
* *
40477 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40519 A
1 A
40520 CACACTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Done.