Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022955.1 Corchorus olitorius cultivar O-4 contig22988, 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: 91532
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2664 original size:41 final size:41
Alignment explanation
Indices: 2607--2684 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
2597 GTGACTTCTG
*
2607 TGAAGGCTATTCACTCAAAATCCAAAGCTGAATAGGACTGT
1 TGAAGGCTATTCACTCAAAATCCAAAGCTGAAGAGGACTGT
*
2648 TGAAGTCTATTCACTCAAAATCCAAAGCTGAAGAGGA
1 TGAAGGCTATTCACTCAAAATCCAAAGCTGAAGAGGA
2685 TTGTGCTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (41 bp):
TGAAGGCTATTCACTCAAAATCCAAAGCTGAAGAGGACTGT
Found at i:4742 original size:42 final size:42
Alignment explanation
Indices: 4690--4774 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
4680 TTTTCGATGG
*
4690 TGGCTGCCTGAGATGGTTGAAATTCTTT-GAAGAGGAAAGACA
1 TGGCTACCTGAGATGGTTGAAATTCTTTAG-AGAGGAAAGACA
*
4732 TGGCTACCTGAGATGGTTGAAGTTCTTTAGAGAGGAAAGACA
1 TGGCTACCTGAGATGGTTGAAATTCTTTAGAGAGGAAAGACA
4774 T
1 T
4775 AGAGGGAGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 39 0.98
43 1 0.03
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (42 bp):
TGGCTACCTGAGATGGTTGAAATTCTTTAGAGAGGAAAGACA
Found at i:13412 original size:98 final size:95
Alignment explanation
Indices: 13212--13485 Score: 478
Period size: 98 Copynumber: 2.9 Consensus size: 95
13202 AGTTATTTTG
* *
13212 TCATTTAGTCTAATCTTACCATAAATAGAAAATTATCAAAAGCTTTTTGTTTAGAAAAAAACAAA
1 TCATTTAGTCTGATCTTACCATAAATAGAAAATTGTCAAAAGCTTTTTGTTTAGAAAAAAACAAA
13277 GAGAGAGAGCCTTTCAAACGAGATGGCCAT
66 GAGAGAGAGCCTTTCAAACGAGATGGCCAT
13307 TCATTTAGTCTGATCTTACCATAAATAGAAAATTGTCAAAAGCTTTTTGTTTAGAAAAGAAAAAC
1 TCATTTAGTCTGATCTTACCATAAATAGAAAATTGTCAAAAGCTTTTTGTTTAG--AA-AAAAAC
*
13372 AAAGAGAGAGAGCCTTTCAAACGAGATGGCCTT
63 AAAGAGAGAGAGCCTTTCAAACGAGATGGCCAT
*
13405 TCATTTAGTCTGATCTTACCATAAATAGAAAATTGTCAAAAGCTTTTTATTTAG-AAAAAACAAA
1 TCATTTAGTCTGATCTTACCATAAATAGAAAATTGTCAAAAGCTTTTTGTTTAGAAAAAAACAAA
13469 GAGAGAGAGCCTTTCAA
66 GAGAGAGAGCCTTTCAA
13486 TAATTAATAA
Statistics
Matches: 172, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
94 26 0.15
95 53 0.31
97 2 0.01
98 91 0.53
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.29
Consensus pattern (95 bp):
TCATTTAGTCTGATCTTACCATAAATAGAAAATTGTCAAAAGCTTTTTGTTTAGAAAAAAACAAA
GAGAGAGAGCCTTTCAAACGAGATGGCCAT
Found at i:33417 original size:27 final size:26
Alignment explanation
Indices: 33386--33438 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
33376 GGTTAAGCTT
*
33386 CACTAACCCAACACTTCCACTTAAAAC
1 CACTAACCCAAC-CTTCCACTCAAAAC
*
33413 CACTAACCCAACCTTTCACTCAAAAC
1 CACTAACCCAACCTTCCACTCAAAAC
33439 TGGAGAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.40, C:0.42, G:0.00, T:0.19
Consensus pattern (26 bp):
CACTAACCCAACCTTCCACTCAAAAC
Found at i:42241 original size:30 final size:31
Alignment explanation
Indices: 42205--42273 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
42195 GTGCAAATGG
* *
42205 GTCCCTGGAGTGAACTTAGT-GAGCAATTGA
1 GTCCCTGAAGTGAACTTAATCGAGCAATTGA
* * *
42235 GTCCCTGAAGTGGAGTTAATCGAGCAATTGG
1 GTCCCTGAAGTGAACTTAATCGAGCAATTGA
42266 GTCCCTGA
1 GTCCCTGA
42274 CTCATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (31 bp):
GTCCCTGAAGTGAACTTAATCGAGCAATTGA
Found at i:46240 original size:3 final size:3
Alignment explanation
Indices: 46232--46279 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
46222 GAGGATTACC
46232 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
46280 TCTGGACAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:53634 original size:3 final size:3
Alignment explanation
Indices: 53626--53675 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
53616 GGTCATGCAT
53626 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53674 AT
1 AT
53676 GCCAAAGAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:53921 original size:3 final size:3
Alignment explanation
Indices: 53906--53947 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
53896 AATGGACAAG
53906 GCA GCA G-A GGCA GCA GCA GCA GCA GCA GCA GCA TG-A GCA GCA
1 GCA GCA GCA -GCA GCA GCA GCA GCA GCA GCA GCA -GCA GCA GCA
53948 TGAGGATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.33, C:0.29, G:0.36, T:0.02
Consensus pattern (3 bp):
GCA
Found at i:54905 original size:56 final size:57
Alignment explanation
Indices: 54790--54926 Score: 195
Period size: 56 Copynumber: 2.4 Consensus size: 57
54780 AAATCCAAAT
* * * **
54790 ATATGGCAATGGATGCGAAACTACACACTTCCTGTTCTACGAGGATTTTATTGACAA
1 ATATGGCAATGAATGAGAAAGTACACACTTCCTCCTCTACGAGGATTTTATTGACAA
**
54847 ATATGGCAATGAATGAGAAAGTACACTGTTCCTCCTCT-CGAGGATTTTATTGACAA
1 ATATGGCAATGAATGAGAAAGTACACACTTCCTCCTCTACGAGGATTTTATTGACAA
*
54903 ATATGGCAATGACTGAGAAAGTAC
1 ATATGGCAATGAATGAGAAAGTAC
54927 TATGAAGACT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
56 41 0.57
57 31 0.43
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (57 bp):
ATATGGCAATGAATGAGAAAGTACACACTTCCTCCTCTACGAGGATTTTATTGACAA
Found at i:55330 original size:29 final size:30
Alignment explanation
Indices: 55266--55334 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
55256 GAACTTTAAT
*
55266 TTTTGGCCACTCGAGCCCATAAAAACCTAA
1 TTTTGGCCAATCGAGCCCATAAAAACCTAA
55296 TTTTGGCCAATCGAGCTCC-TAAAAACCTAA
1 TTTTGGCCAATCGAGC-CCATAAAAACCTAA
55326 -TTTGGCCAA
1 TTTTGGCCAA
55335 ATAAGCCCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
29 9 0.24
30 26 0.70
31 2 0.05
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (30 bp):
TTTTGGCCAATCGAGCCCATAAAAACCTAA
Found at i:56374 original size:24 final size:23
Alignment explanation
Indices: 56317--56375 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
56307 GATATATTAG
*
56317 ATTTTAATAAATTTTTAAAATTTC
1 ATTTT-ATAAAATTTTAAAATTTC
* *
56341 ATTGTT-TAAAATTTTATAATTTT
1 ATT-TTATAAAATTTTAAAATTTC
56364 ATTTTACTAAAA
1 ATTTTA-TAAAA
56376 AATCTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 2 0.07
23 17 0.59
24 8 0.28
25 2 0.07
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTTTATAAAATTTTAAAATTTC
Found at i:62460 original size:2 final size:2
Alignment explanation
Indices: 62453--62478 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62443 GAAGACATGC
62453 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
62479 GCGGGGTATC
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):
AT
Found at i:64340 original size:51 final size:50
Alignment explanation
Indices: 64252--64354 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 50
64242 TTTTATATAT
*
64252 ATATATACTATATATTATTTTAGTTACTAGGGAAATTACTAAAATGCCAA
1 ATATATACTATATATTATTTTAGTTACTAGGGAAATTACTAAAAGGCCAA
64302 ATATATACTATATATTATTTTTAGTTACTAGGGAAATTACTAAAAGGCCAA
1 ATATATACTATATATTA-TTTTAGTTACTAGGGAAATTACTAAAAGGCCAA
64353 AT
1 AT
64355 TGAGGATTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 17 0.33
51 34 0.67
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.38
Consensus pattern (50 bp):
ATATATACTATATATTATTTTAGTTACTAGGGAAATTACTAAAAGGCCAA
Found at i:69277 original size:22 final size:22
Alignment explanation
Indices: 69248--69367 Score: 115
Period size: 22 Copynumber: 5.5 Consensus size: 22
69238 TGAATATTTT
*
69248 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTACCA
*
69270 TATTAAATTTTGATAA-TCACGC-
1 TATGAAATTTTGATAACT-AC-CA
69292 TATGAAATTTTGATAAACT-CCA
1 TATGAAATTTTGAT-AACTACCA
*
69314 TATGAAATTGTGATAAACTA-CA
1 TATGAAATTTTGAT-AACTACCA
* *
69336 TATGAAAATTTGATAATCTAAC-
1 TATGAAATTTTGATAA-CTACCA
69358 TATGAAATTT
1 TATGAAATTT
69368 CAATAAACCT
Statistics
Matches: 84, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.05
22 75 0.89
23 4 0.05
24 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACCA
Found at i:69322 original size:44 final size:45
Alignment explanation
Indices: 69248--69366 Score: 129
Period size: 44 Copynumber: 2.7 Consensus size: 45
69238 TGAATATTTT
* * * * *
69248 TATGAAATTTTGAT-AACTACCCTATTAAATTTTGATAATC-ACGC
1 TATGAAATTTTGATAAACTACCATATGAAATTGTGATAAACTAC-A
69292 TATGAAATTTTGATAAACT-CCATATGAAATTGTGATAAACTACA
1 TATGAAATTTTGATAAACTACCATATGAAATTGTGATAAACTACA
* * *
69336 TATGAAAATTTGATAATCTAAC-TATGAAATT
1 TATGAAATTTTGATAAACTACCATATGAAATT
69367 TCAATAAACC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
44 57 0.89
45 7 0.11
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (45 bp):
TATGAAATTTTGATAAACTACCATATGAAATTGTGATAAACTACA
Found at i:69399 original size:21 final size:21
Alignment explanation
Indices: 69248--69435 Score: 78
Period size: 22 Copynumber: 8.6 Consensus size: 21
69238 TGAATATTTT
*
69248 TATGAAATTTTGATAA-CTACCC
1 TATGAAATTTTG-TAACCT-TCC
* * *
69270 TATTAAATTTTGATAATC-ACGC
1 TATGAAATTTTG-TAACCTTC-C
*
69292 TATGAAATTTTGATAAAC-TCC
1 TATGAAATTTTG-TAACCTTCC
* * * *
69313 ATATGAAATTGTGATAAACTACA
1 -TATGAAATTTTG-TAACCTTCC
* * **
69336 TATGAAAATTTGATAATCTAAC
1 TATGAAATTTTG-TAACCTTCC
**
69358 TATGAAATTTCAATAAACCTTCC
1 TATGAAATTT-TGT-AACCTTCC
*
69381 AATGAAATTTTGTAACCTTCC
1 TATGAAATTTTGTAACCTTCC
* *
69402 TATG-ATTTTTGCTAACCTCCC
1 TATGAAATTTTG-TAACCTTCC
*
69423 TATGAGATTTTGT
1 TATGAAATTTTGT
69436 TAATCTCCCT
Statistics
Matches: 131, Mismatches: 27, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
20 6 0.05
21 26 0.20
22 83 0.63
23 16 0.12
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGTAACCTTCC
Found at i:69406 original size:66 final size:65
Alignment explanation
Indices: 69248--69406 Score: 171
Period size: 66 Copynumber: 2.4 Consensus size: 65
69238 TGAATATTTT
* * * **
69248 TATGAAATTTTGATAACTACCCTATTAAATTTTGATAATCACGCTATGAAATTTTGATAAACTCC
1 TATGAAATTTTGATAACTA-CCTATGAAAATTTGATAATCACACTATGAAATTTCAATAAACTCC
69313 A
65 A
* *
69314 TATGAAATTGTGATAAACTACATATGAAAATTTGATAATCTA-ACTATGAAATTTCAATAAACCT
1 TATGAAATTTTGAT-AACTACCTATGAAAATTTGATAATC-ACACTATGAAATTTCAATAAA-C-
69378 TCCA
62 TCCA
*
69382 -ATGAAATTTTG-TAACCTTCCTATGA
1 TATGAAATTTTGATAA-CTACCTATGA
69407 TTTTTGCTAA
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
65 2 0.03
66 55 0.71
67 17 0.22
68 4 0.05
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.36
Consensus pattern (65 bp):
TATGAAATTTTGATAACTACCTATGAAAATTTGATAATCACACTATGAAATTTCAATAAACTCCA
Found at i:69434 original size:42 final size:43
Alignment explanation
Indices: 69373--69454 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
69363 AATTTCAATA
* *
69373 AACCTTCCAATGAAATTTTG-TAACCTTCCTATGATTTTTGCT
1 AACCTCCCAATGAAATTTTGTTAACCTCCCTATGATTTTTGCT
* * * *
69415 AACCTCCCTATGAGATTTTGTTAATCTCCCTATTATTTTT
1 AACCTCCCAATGAAATTTTGTTAACCTCCCTATGATTTTT
69455 TTATACTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 17 0.52
43 16 0.48
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (43 bp):
AACCTCCCAATGAAATTTTGTTAACCTCCCTATGATTTTTGCT
Found at i:69455 original size:22 final size:22
Alignment explanation
Indices: 69388--69447 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
69378 TCCAATGAAA
*
69388 TTTTG-TAACCTTCCTATGA-T
1 TTTTGCTAACCTCCCTATGAGT
*
69408 TTTTGCTAACCTCCCTATGAGA
1 TTTTGCTAACCTCCCTATGAGT
* *
69430 TTTTGTTAATCTCCCTAT
1 TTTTGCTAACCTCCCTAT
69448 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.15
21 13 0.38
22 16 0.47
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (22 bp):
TTTTGCTAACCTCCCTATGAGT
Found at i:71127 original size:1 final size:1
Alignment explanation
Indices: 71121--71147 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
71111 TAGACGTTAG
71121 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
71148 ATTAATTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:75540 original size:4 final size:4
Alignment explanation
Indices: 75531--75566 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
75521 CCTTTATTTT
75531 AATA AATA AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA
75567 CCTTAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:86751 original size:100 final size:106
Alignment explanation
Indices: 86609--86850 Score: 311
Period size: 100 Copynumber: 2.3 Consensus size: 106
86599 AATTTTAATT
*
86609 TTAATTT-GGGTTAAACTTAGTG-AATTAGTTTTATAATATATTTCTAAAACCCTATAACAAT-A
1 TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATAATATATTTCTAAAACCCTATAACAATAA
* *
86671 TTATTAATTATGGAATTTATCCTT-AA-AAT-AAAA-AAAA
66 TTATTAATTATGAAATTTACCCTTAAATAATAAAAATAAAA
* * * *
86708 -TAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAATCCTATAACAATAA
1 TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATAATATATTTCTAAAACCCTATAACAAT-A
*
86772 ATTATTAATTTTGAAATTTACCCTTAAATTAATAAAAATAAAA
65 ATTATTAATTATGAAATTTACCCTTAAA-TAATAAAAATAAAA
*
86815 TTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTT
1 --TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTT
86851 TGTTATGGAT
Statistics
Matches: 122, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
98 6 0.05
99 14 0.11
100 35 0.29
102 22 0.18
103 2 0.02
105 3 0.02
106 4 0.03
107 4 0.03
110 32 0.26
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.42
Consensus pattern (106 bp):
TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATAATATATTTCTAAAACCCTATAACAATAA
TTATTAATTATGAAATTTACCCTTAAATAATAAAAATAAAA
Found at i:87427 original size:62 final size:59
Alignment explanation
Indices: 87307--87754 Score: 434
Period size: 62 Copynumber: 7.4 Consensus size: 59
87297 TTTAAATTTA
* *
87307 ATTGACACCAGAAGTTGTCATATTAAATTATCTTGACATCAGAAGTTGTCAT-AGAAATT
1 ATTGACACCAGAAGTTGTCATATCAAATTAT-TTGACACCAGAAGTTGTCATGAGAAATT
* *
87366 ATTGACACCAGAAGTTGTTATATTATATTATTATTTTGACACCAGAAGTTGTCATGA-AAATT
1 ATTGACACCAGAAGTTGTCATATCA-A--ATTA-TTTGACACCAGAAGTTGTCATGAGAAATT
* *
87428 ATTGACACCAGAAATTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCAT-AAAAATT
1 ATTGACACCAGAAGTTGTCATATC-AA--ATTAT-TTGACACCAGAAGTTGTCATGAGAAATT
* * *
87490 ATTGACATCAGAAGTTGTCATATCAAATTA-TT-ACACCAGAAGTTGTCATAATAAATT
1 ATTGACACCAGAAGTTGTCATATCAAATTATTTGACACCAGAAGTTGTCATGAGAAATT
* *
87547 ATCTTGACATCAGAAGTTGTCATA-GAAATTA-TTGACACCAGAAGTTGTCAT-ATGATATTATT
1 A--TTGACACCAGAAGTTGTCATATCAAATTATTTGACACCAGAAGTTGTCATGA-GA-A--ATT
* *
87609 ATTTTGACACCAGAAATTGT-A-ATGAAAATTA-TTGACACCAGAAGTTGTCATGA-AAATT
1 A--TTGACACCAGAAGTTGTCATAT-CAAATTATTTGACACCAGAAGTTGTCATGAGAAATT
* *
87667 ATTGACACCAAAAGTTGTCATATCAAATTATTATCTTGACACCAAAAGTTGTCATGCTGAAGAAA
1 ATTGACACCAGAAGTTGTCATATC-AA--ATTAT-TTGACACCAGAAGTTGTCA---TG-AGAAA
87732 TT
58 TT
*
87734 ATGGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
87755 CATAAGATTG
Statistics
Matches: 338, Mismatches: 20, Indels: 54
0.82 0.05 0.13
Matches are distributed among these distances:
56 32 0.09
57 10 0.03
58 17 0.05
59 67 0.20
60 8 0.02
61 6 0.02
62 167 0.49
63 4 0.01
65 2 0.01
66 1 0.00
67 24 0.07
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (59 bp):
ATTGACACCAGAAGTTGTCATATCAAATTATTTGACACCAGAAGTTGTCATGAGAAATT
Found at i:87688 original size:90 final size:88
Alignment explanation
Indices: 87307--87759 Score: 390
Period size: 90 Copynumber: 5.0 Consensus size: 88
87297 TTTAAATTTA
* * * *
87307 ATTGACACCAGAAGTTGTCATAT-TAAATTATCTTGACATCAGAAGTTGTCAT-AGAAATTATTG
1 ATTGACACCAGAAGTTGTCATATCAAAATTAT-TTGACACCAGAAATTGTAATGAGAAATTATTG
*
87370 ACACCAGAAGTTGTTATATTATATTATT
65 ACACCAGAAGTTGTCATA-TA-A--ATT
* *
87398 ATTTTGACACCAGAAGTTGTC--ATGAAAATTA-TTGACACCAGAAATTGTCATATCA-AATTAT
1 A--TTGACACCAGAAGTTGTCATATCAAAATTATTTGACACCAGAAATTGT-A-ATGAGAA--AT
*
87459 TATCTTGACACCAGAAGTTGTCATAAAAATT
60 TA--TTGACACCAGAAGTTGTCATATAAATT
* * * * *
87490 ATTGACATCAGAAGTTGTCATATC-AAATTA-TT-ACACCAGAAGTTGTCATAATAAATTATCTT
1 ATTGACACCAGAAGTTGTCATATCAAAATTATTTGACACCAGAAATTGTAATGAGAAATTA--TT
* *
87552 GACATCAGAAGTTGTCATAGAAATT
64 GACACCAGAAGTTGTCATATAAATT
* *
87577 ATTGACACCAGAAGTTGTCATATGATATTATTATTTTGACACCAGAAATTGTAATGA-AAATTAT
1 ATTGACACCAGAAGTTGTCATATCA-A-AATTA-TTTGACACCAGAAATTGTAATGAGAAATTAT
87641 TGACACCAGAAGTTGTCATGA-AAATT
63 TGACACCAGAAGTTGTCAT-ATAAATT
* *
87667 ATTGACACCAAAAGTTGTCATATCAAATTATTATCTTGACACCA-AAAGTTGTCATGCTGAAGAA
1 ATTGACACCAGAAGTTGTCATATCAAA--ATTAT-TTGACACCAGAAA-TTGT-A--ATG-AGAA
*
87731 ATTATGGACACCAGAAGTTGTCATCATAA
58 ATTATTGACACCAGAAGTTGTCAT-ATAA
87760 GATTGGAATT
Statistics
Matches: 306, Mismatches: 26, Indels: 55
0.79 0.07 0.14
Matches are distributed among these distances:
87 53 0.17
88 3 0.01
89 8 0.03
90 113 0.37
91 13 0.04
92 24 0.08
93 37 0.12
94 6 0.02
95 27 0.09
96 22 0.07
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (88 bp):
ATTGACACCAGAAGTTGTCATATCAAAATTATTTGACACCAGAAATTGTAATGAGAAATTATTGA
CACCAGAAGTTGTCATATAAATT
Found at i:87718 original size:211 final size:208
Alignment explanation
Indices: 87311--87721 Score: 630
Period size: 211 Copynumber: 1.9 Consensus size: 208
87301 AATTTAATTG
*
87311 ACACCAGAAGTTGTCATATTAAATTATCTTGACATCAGAAGTTGTCATAGAAATTATTGACACCA
1 ACACCAGAAGTTGTCATAATAAATTATCTTGACATCAGAAGTTGTCATAGAAATTATTGACACCA
* * * *
87376 GAAGTTGTTATATTATATTATTATTTTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAA
66 GAAGTTGTCATATGATATTATTATTTTGACACCAGAAATTGTAATGAAAATTATTGACACCAGAA
* * *
87441 ATTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATAAAAATTATTGACATCAGAAGTT
131 ATTGTCA-ATCAAA-TATTA-CTTGACACCAAAAGTTGTCATAAAAATTATTGACACCAAAAGTT
87506 GTCATATCAAATTATT
193 GTCATATCAAATTATT
87522 ACACCAGAAGTTGTCATAATAAATTATCTTGACATCAGAAGTTGTCATAGAAATTATTGACACCA
1 ACACCAGAAGTTGTCATAATAAATTATCTTGACATCAGAAGTTGTCATAGAAATTATTGACACCA
87587 GAAGTTGTCATATGATATTATTATTTTGACACCAGAAATTGTAATGAAAATTATTGACACCAGAA
66 GAAGTTGTCATATGATATTATTATTTTGACACCAGAAATTGTAATGAAAATTATTGACACCAGAA
* *
87652 GTTGTC-ATGAAA-ATTA-TTGACACCAAAAGTTGTCATATCAAATTATTATCTTGACACCAAAA
131 ATTGTCAATCAAATATTACTTGACACCAAAAGTTGTCATA--AAA--ATTA--TTGACACCAAAA
87714 GTTGTCAT
190 GTTGTCAT
87722 GCTGAAGAAA
Statistics
Matches: 184, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
205 20 0.11
207 7 0.04
209 9 0.05
211 148 0.80
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (208 bp):
ACACCAGAAGTTGTCATAATAAATTATCTTGACATCAGAAGTTGTCATAGAAATTATTGACACCA
GAAGTTGTCATATGATATTATTATTTTGACACCAGAAATTGTAATGAAAATTATTGACACCAGAA
ATTGTCAATCAAATATTACTTGACACCAAAAGTTGTCATAAAAATTATTGACACCAAAAGTTGTC
ATATCAAATTATT
Done.