Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014268.1 Corchorus olitorius cultivar O-4 contig14301, 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: 98171
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8547 original size:2 final size:2
Alignment explanation
Indices: 8540--8575 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8530 GCTTACTAAT
8540 TA TA TA TA TA 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 TA TA TA TA TA
8576 AGCGCTTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9244 original size:14 final size:14
Alignment explanation
Indices: 9221--9259 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
9211 TCAAATGTCA
*
9221 TGACTGAAGGATTT
1 TGACTAAAGGATTT
9235 TGACTAAAGGATTT
1 TGACTAAAGGATTT
9249 TGACTAAAGGA
1 TGACTAAAGGA
9260 CGCAATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.31
Consensus pattern (14 bp):
TGACTAAAGGATTT
Found at i:12353 original size:36 final size:36
Alignment explanation
Indices: 12301--12409 Score: 173
Period size: 36 Copynumber: 3.0 Consensus size: 36
12291 CCCCTATCAT
12301 GATTTTCCTTGCTCGGCTTCATCTGCTTCTTCGACG
1 GATTTTCCTTGCTCGGCTTCATCTGCTTCTTCGACG
* *
12337 GATTCTCCTTGCTCGGCTTCATCTGCTTCTTTGACG
1 GATTTTCCTTGCTCGGCTTCATCTGCTTCTTCGACG
* * *
12373 GATTTTCATTGCTCAGCTTCATCTGCTCCTTCGACG
1 GATTTTCCTTGCTCGGCTTCATCTGCTTCTTCGACG
12409 G
1 G
12410 TTCCTTTAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.10, C:0.30, G:0.19, T:0.40
Consensus pattern (36 bp):
GATTTTCCTTGCTCGGCTTCATCTGCTTCTTCGACG
Found at i:24869 original size:8 final size:8
Alignment explanation
Indices: 24858--24893 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
24848 TGTTTTTCCA
24858 TTTTTC-T
1 TTTTTCTT
24865 TTTTTCTT
1 TTTTTCTT
24873 TTTTTCTT
1 TTTTTCTT
24881 TTTTTCTT
1 TTTTTCTT
24889 TTTTT
1 TTTTT
24894 AGGAATTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTCTT
Found at i:24870 original size:15 final size:15
Alignment explanation
Indices: 24845--24884 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
24835 ACAGATTTGA
24845 TTCTGTTTTTCCATTT
1 TTCT-TTTTTCCATTT
**
24861 TTCTTTTTTCTTTTT
1 TTCTTTTTTCCATTT
24876 TTCTTTTTT
1 TTCTTTTTT
24885 TCTTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (15 bp):
TTCTTTTTTCCATTT
Found at i:24876 original size:23 final size:23
Alignment explanation
Indices: 24845--24892 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
24835 ACAGATTTGA
24845 TTCTGTTTTTCCATTTTTCTTTT
1 TTCTGTTTTTCCATTTTTCTTTT
* **
24868 TTCTTTTTTTCTTTTTTTCTTTT
1 TTCTGTTTTTCCATTTTTCTTTT
24891 TT
1 TT
24893 TAGGAATTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (23 bp):
TTCTGTTTTTCCATTTTTCTTTT
Found at i:32083 original size:21 final size:23
Alignment explanation
Indices: 32057--32106 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
32047 GGTGATCTCA
*
32057 CATAATAGAG-TT-TAACTAGAG
1 CATAATAGAGCTTATAAATAGAG
32078 CATAATAGAGCTTATAAATAGAG
1 CATAATAGAGCTTATAAATAGAG
*
32101 CTTAAT
1 CATAAT
32107 TCACCTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 2 0.08
23 13 0.52
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (23 bp):
CATAATAGAGCTTATAAATAGAG
Found at i:37042 original size:22 final size:20
Alignment explanation
Indices: 36995--37043 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
36985 TTGTCATTCT
*
36995 TCTCTCTCCCCCACTAACTC
1 TCTCTCTCCCCCACTAACTA
* *
37015 TTTCTCATCCTCCCACTCACTA
1 TCTCTC-TCC-CCCACTAACTA
37037 TCTCTCT
1 TCTCTCT
37044 TCATAAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 5 0.22
21 4 0.17
22 14 0.61
ACGTcount: A:0.14, C:0.49, G:0.00, T:0.37
Consensus pattern (20 bp):
TCTCTCTCCCCCACTAACTA
Found at i:41087 original size:3 final size:3
Alignment explanation
Indices: 41079--41142 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
41069 TTGCTTCCTT
41079 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41127 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
41143 ATATATATAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:46740 original size:30 final size:28
Alignment explanation
Indices: 46684--46760 Score: 113
Period size: 30 Copynumber: 2.7 Consensus size: 28
46674 AAAATTTATG
46684 GGTAGCTATCTTTA-TTTTTTTTAGGTA
1 GGTAGCTATCTTTATTTTTTTTTAGGTA
46711 GGTAGCTAT-TTTATTATTTTTTTCGAGGTA
1 GGTAGCTATCTTTATT-TTTTTTT--AGGTA
46741 GGTAGCTATCTTTATTTTTT
1 GGTAGCTATCTTTATTTTTT
46761 AATAGTACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
26 4 0.09
27 10 0.22
28 7 0.16
30 18 0.40
31 6 0.13
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.56
Consensus pattern (28 bp):
GGTAGCTATCTTTATTTTTTTTTAGGTA
Found at i:52444 original size:26 final size:26
Alignment explanation
Indices: 52408--52459 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
52398 ACTAATTTTA
* *
52408 TGGTAATAAAATCTCACACATAGCTT
1 TGGTAACAAAATCTCAAACATAGCTT
*
52434 TGGTAACAAAATCTCAAACCTAGCTT
1 TGGTAACAAAATCTCAAACATAGCTT
52460 AAATTACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (26 bp):
TGGTAACAAAATCTCAAACATAGCTT
Found at i:63244 original size:13 final size:13
Alignment explanation
Indices: 63226--63271 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
63216 TGTTTTTCCC
*
63226 CTGTTTCCGTTCT
1 CTGTTTTCGTTCT
*
63239 CTGTTTTTC-TGCT
1 CTG-TTTTCGTTCT
63252 CTGTTTTCGTTCT
1 CTGTTTTCGTTCT
63265 CTGTTTT
1 CTGTTTT
63272 TTCTTTAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 5 0.18
13 19 0.68
14 4 0.14
ACGTcount: A:0.00, C:0.24, G:0.15, T:0.61
Consensus pattern (13 bp):
CTGTTTTCGTTCT
Found at i:63244 original size:24 final size:25
Alignment explanation
Indices: 63212--63272 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 25
63202 CAGGTTAGTG
63212 TCTCTGTTTTTC-CCCTGTTTCCGT
1 TCTCTGTTTTTCGCCCTGTTTCCGT
* *
63236 TCTCTGTTTTTCTGCTCTGTTTTCGT
1 TCTCTGTTTTTC-GCCCTGTTTCCGT
63262 TCTCTGTTTTT
1 TCTCTGTTTTT
63273 TCTTTAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 12 0.36
26 21 0.64
ACGTcount: A:0.00, C:0.26, G:0.13, T:0.61
Consensus pattern (25 bp):
TCTCTGTTTTTCGCCCTGTTTCCGT
Found at i:63312 original size:29 final size:27
Alignment explanation
Indices: 63235--63317 Score: 64
Period size: 29 Copynumber: 3.0 Consensus size: 27
63225 CCTGTTTCCG
*
63235 TTCTCTGTTTTT-C--TGCTCTGTTTT
1 TTCTCTGTTTTTCCTTTACTCTGTTTT
* *
63259 CGTTCTCTGTTTTTTCTTTAATCTGTTTT
1 --TTCTCTGTTTTTCCTTTACTCTGTTTT
* *
63288 TTGCTCTGTTTTTCCGTTTTCTCTGCTTT
1 TT-CTCTGTTTTTCC-TTTACTCTGTTTT
63317 T
1 T
63318 CATTGAATGC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
26 12 0.26
27 3 0.07
28 11 0.24
29 20 0.43
ACGTcount: A:0.02, C:0.20, G:0.12, T:0.65
Consensus pattern (27 bp):
TTCTCTGTTTTTCCTTTACTCTGTTTT
Found at i:79231 original size:49 final size:49
Alignment explanation
Indices: 79174--79299 Score: 159
Period size: 49 Copynumber: 2.6 Consensus size: 49
79164 ATTCCTAGTC
*
79174 AATCCATTTTAGAAATCGTGGATTTTATCGAGG-T-TTCATAGC-AATTGCT
1 AATCCATTTTAGAAATCGTGGAATTTATCGAGGATCTTCATAGCTAA---CT
* **
79223 AATCCATTTTAGAAATCGTGGAATTCATCGAGGATCTTCATTTCTAACT
1 AATCCATTTTAGAAATCGTGGAATTTATCGAGGATCTTCATAGCTAACT
*
79272 AATCCATTTTAGAAATCTTGGAATTTAT
1 AATCCATTTTAGAAATCGTGGAATTTAT
79300 ATATCGAGGT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
49 59 0.87
50 1 0.01
51 6 0.09
52 2 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (49 bp):
AATCCATTTTAGAAATCGTGGAATTTATCGAGGATCTTCATAGCTAACT
Found at i:79437 original size:16 final size:16
Alignment explanation
Indices: 79413--79462 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
79403 ATTATTAATC
79413 AAAAATTCCGACAAAA
1 AAAAATTCCGACAAAA
***
79429 TTGAATTCC-A-AAAA
1 AAAAATTCCGACAAAA
79443 AAAAATTCCGACAAAA
1 AAAAATTCCGACAAAA
79459 AAAA
1 AAAA
79463 TTCATTTTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 10 0.38
15 2 0.08
16 14 0.54
ACGTcount: A:0.62, C:0.16, G:0.06, T:0.16
Consensus pattern (16 bp):
AAAAATTCCGACAAAA
Found at i:79449 original size:14 final size:15
Alignment explanation
Indices: 79413--79465 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
79403 ATTATTAATC
79413 AAAAATTCCGACAAAA
1 AAAAATTCCGA-AAAA
***
79429 TTGAATTCC-AAAAA
1 AAAAATTCCGAAAAA
*
79443 AAAAATTCCGACAAA
1 AAAAATTCCGAAAAA
79458 AAAAATTC
1 AAAAATTC
79466 ATTTTTCCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
14 10 0.34
15 13 0.45
16 6 0.21
ACGTcount: A:0.58, C:0.17, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAAATTCCGAAAAA
Found at i:82407 original size:122 final size:121
Alignment explanation
Indices: 82207--82442 Score: 332
Period size: 122 Copynumber: 1.9 Consensus size: 121
82197 ACTGACGTGA
*
82207 CACTTTTTTATGGGACTTAACGAAATCCGTTAGTCAACCGTTATCAAATAATTATCCTAAAGAAA
1 CACTTTTTTATGAGACTTAACGAAATCCGTTAGTCAACCGTTATCAAATAATTATCCTAAAGAAA
* *
82272 AAAAGAAAAAAAAATA-TGTACACTTCTTATATAAAACATAATTTACAACAAATGTGG
66 AAAAGAAAAAAAAAAACCGTACACTTC-T-TATAAAACATAATTTACAACAAATGTGG
* * * * * * * *
82329 CACTTTTTTATGAGATTTAATGGAATCCTTTGGTCAACTGTTATTAAATAATTATCCTAGAGAAA
1 CACTTTTTTATGAGACTTAACGAAATCCGTTAGTCAACCGTTATCAAATAATTATCCTAAAGAAA
82394 AAAA-AGAAAAAAAAAACCGTACACTTCTTATAAAACATAATTTACAACA
66 AAAAGA-AAAAAAAAAACCGTACACTTCTTATAAAACATAATTTACAACA
82443 GACATGATCC
Statistics
Matches: 101, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
121 22 0.22
122 70 0.69
123 9 0.09
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (121 bp):
CACTTTTTTATGAGACTTAACGAAATCCGTTAGTCAACCGTTATCAAATAATTATCCTAAAGAAA
AAAAGAAAAAAAAAAACCGTACACTTCTTATAAAACATAATTTACAACAAATGTGG
Found at i:82499 original size:28 final size:28
Alignment explanation
Indices: 82458--82513 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
82448 GATCCGTAGC
* *
82458 AATTGATCTCCATTCCTAATTAATCCAT
1 AATTGATCTCCATTCCTAAGTAAACCAT
*
82486 AATTGATCTTCATTCCTAAGTAAACCAT
1 AATTGATCTCCATTCCTAAGTAAACCAT
82514 TTTAGAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (28 bp):
AATTGATCTCCATTCCTAAGTAAACCAT
Found at i:82533 original size:33 final size:33
Alignment explanation
Indices: 82486--82645 Score: 124
Period size: 33 Copynumber: 5.1 Consensus size: 33
82476 ATTAATCCAT
* * *
82486 AATTGATCTTCATTCCTAAGTAAACCATTTTAG
1 AATTCATCTTCATTCCTAACTAATCCATTTTAG
* *
82519 AATTCATCTTCATTCCTAACTGATTCATTTTAG
1 AATTCATCTTCATTCCTAACTAATCCATTTTAG
* ** *
82552 AATT--TGTAGAATT-C-GA-TAATCCA---T--
1 AATTCATCT-TCATTCCTAACTAATCCATTTTAG
* * *
82576 AATTGATCTTCATTCCTAAGTAAACCATTTTAG
1 AATTCATCTTCATTCCTAACTAATCCATTTTAG
*
82609 AATTCATCTTCATTCCTAACTGATCCATTTTAG
1 AATTCATCTTCATTCCTAACTAATCCATTTTAG
82642 AATT
1 AATT
82646 TGTAGAATTT
Statistics
Matches: 96, Mismatches: 20, Indels: 22
0.70 0.14 0.16
Matches are distributed among these distances:
24 4 0.04
25 3 0.03
26 4 0.04
27 1 0.01
28 6 0.06
29 5 0.05
30 1 0.01
31 4 0.04
32 3 0.03
33 65 0.68
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (33 bp):
AATTCATCTTCATTCCTAACTAATCCATTTTAG
Found at i:82631 original size:90 final size:90
Alignment explanation
Indices: 82478--82654 Score: 345
Period size: 90 Copynumber: 2.0 Consensus size: 90
82468 CATTCCTAAT
82478 TAATCCATAATTGATCTTCATTCCTAAGTAAACCATTTTAGAATTCATCTTCATTCCTAACTGAT
1 TAATCCATAATTGATCTTCATTCCTAAGTAAACCATTTTAGAATTCATCTTCATTCCTAACTGAT
*
82543 TCATTTTAGAATTTGTAGAATTCGA
66 CCATTTTAGAATTTGTAGAATTCGA
82568 TAATCCATAATTGATCTTCATTCCTAAGTAAACCATTTTAGAATTCATCTTCATTCCTAACTGAT
1 TAATCCATAATTGATCTTCATTCCTAAGTAAACCATTTTAGAATTCATCTTCATTCCTAACTGAT
82633 CCATTTTAGAATTTGTAGAATT
66 CCATTTTAGAATTTGTAGAATT
82655 TATCGAGGTT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.41
Consensus pattern (90 bp):
TAATCCATAATTGATCTTCATTCCTAAGTAAACCATTTTAGAATTCATCTTCATTCCTAACTGAT
CCATTTTAGAATTTGTAGAATTCGA
Found at i:83416 original size:12 final size:12
Alignment explanation
Indices: 83397--83426 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
83387 CCGTAAGTAC
83397 TGCTGCGGCTGT
1 TGCTGCGGCTGT
*
83409 TTCTGCGGCTGT
1 TGCTGCGGCTGT
83421 TGCTGC
1 TGCTGC
83427 CGCGCCTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.37, T:0.37
Consensus pattern (12 bp):
TGCTGCGGCTGT
Found at i:83680 original size:5 final size:5
Alignment explanation
Indices: 83642--83694 Score: 54
Period size: 5 Copynumber: 9.8 Consensus size: 5
83632 ACTCCACACC
83642 TATATA TATATA TATAA -ATAA TTATCATA TATAA TATAA TATAA TATAA
1 TATA-A TATA-A TATAA TATAA -TAT-A-A TATAA TATAA TATAA TATAA
83691 TATA
1 TATA
83695 TGTGTCATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
4 4 0.09
5 21 0.49
6 13 0.30
7 4 0.09
8 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:83695 original size:17 final size:16
Alignment explanation
Indices: 83645--83689 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
83635 CCACACCTAT
83645 ATATATATATATAAATA
1 ATATA-ATATATAAATA
*
83662 ATTATCATATATAATATA
1 A-TATAATATATAA-ATA
83680 ATATAATATA
1 ATATAATATA
83690 ATATATGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAATATATAAATA
Found at i:93043 original size:18 final size:18
Alignment explanation
Indices: 93020--93054 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
93010 TGGAAGCTAT
* *
93020 GGATATGATCCTTATGGA
1 GGATATAATCCCTATGGA
93038 GGATATAATCCCTATGG
1 GGATATAATCCCTATGG
93055 CTATCCTCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (18 bp):
GGATATAATCCCTATGGA
Found at i:95627 original size:335 final size:335
Alignment explanation
Indices: 93870--97320 Score: 5293
Period size: 337 Copynumber: 10.3 Consensus size: 335
93860 TGAAAAGAGG
* * * * *
93870 ACGATTTCGGCTAAAATTTTGCAAAATACAGATCCGAAAAGATTTTCCCCAATTTTTTATC-TCA
1 ACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTT-GCGACA
* * * *
93934 ATACTCGGAAAAATCATATAATTCAACGCCAAAAATATTTTAGGGTTCTTCACG-TTTTCAATAT
65 ATACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCT-AATAT
* * * *
93998 CGTTATTCCA-TTTTTTCTGTATTTATTTCTAATTAAATCGAAACAAGATTCAGATAGTCGTCAA
129 CGTTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAA
*
94062 AATAAATCCGTAAACCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGT
194 AATAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGT
94127 CTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCACGAAACGCATTTTTAGCCAAAAACCG
259 CTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCC-CGAAACGCATTTTTAGCCAAAAACCG
94192 TGATGGTTAGTAC
323 TGATGGTTAGTAC
* * * * **
94205 ACGATTTCGGCTAAAATATTGCAAAACAACTGACCCGAAAAGTTTTTACCTAATTTTAAGCGACA
1 ACGATTTCGGCTAAAATTTTGCAAAA-AACTGACCCGAAAAGATTTTCCCCAATTTTTTGCGACA
* *
94270 ATACTCAGAAAAATCATATAATTCAACGCCAAAAATATTTTAGGGGTTTTCACGCTTCTAATATC
65 ATACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATC
* * * *
94335 GTTTTTGCATTTTTTTCTGAGTTTATTTCTAATTAAAACGAAACAAGATTCAGGTACTCGTAAAA
130 GTTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAA
* *
94400 ATAAATCCGTAAACCCATTGTGGCTGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTC
195 ATAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTC
* *
94465 TTTCTGCCAAAAATCATGCAAAGCAGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTG
260 TTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTG
94530 ATGGTTAGTAC
325 ATGGTTAGTAC
** *
94541 ATTATTCCGGCTAAAATTTTGCAAAAATACTGACCCGAAAAG-TTTTACCCCAATTTTTTTGCGA
1 ACGATTTCGGCTAAAATTTTGCAAAAA-ACTGACCCGAAAAGATTTT-CCCCAA-TTTTTTGCGA
* *
94605 CAATACTCAGAAAAATCACATAATTCAATGCCGAAAATATTTTAGGGTTTTTCACGCTTCTAATA
63 CAATACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATA
* **
94670 TCATTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTTTTAA
128 TCGTTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAA
*
94735 AAATAAATCCGTAAATCCATTGTGGCCAAGAGATTTGATTAGATGAATATAGATATTTCGAGAAG
193 AAATAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAG
* *
94800 TCTTTCTGCTAAAAATCATGCAAAACTGAGTTAGGGCCCCGAAACGCATTTTTAGCCAAAAACCG
258 TCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCG
94865 TGATGGTTAGTAC
323 TGATGGTTAGTAC
* * * **
94878 ACGATTTCGGCTAAAATTTTACAAAAAACAGACCCGAAAAGATTGTCCCCAATTTTTTGCCTCAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCGACAA
* *
94943 TACTCAGAAAAATCACATAACTCAACGCGAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCG
66 TACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCG
* *
95008 TTTTT-C--------CTGAATTTAGTTCTAATCAAATCGAAACAAGATTCAGATACTCGTAAAAA
131 TTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA
* * *
95064 TAAATCTGTAACTCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTTT
196 TAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCT
* * *
95129 TTTTGCCAAAAATCATGCAAAACTGAGTCA-GGTCCCGAAACGCATTTTTAGCCAAAAACTGTGA
261 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTGA
95193 TGGTTAGTAC
326 TGGTTAGTAC
95203 ACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAA-ATTTTACCCCAATTTTTTGCGACA
1 ACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGATTTT-CCCCAATTTTTTGCGACA
95267 ATACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATC
65 ATACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATC
* * *
95332 GTTTTTCCATTTTTTTCTAAATTTATTTCTAATTAAATCGAAACAAGATTTAGATTCTCGTAAAA
130 GTTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAA
*
95397 ATAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTGGATGAATATAGATATTTCGAGAAGTC
195 ATAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTC
*
95462 TTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACAGTG
260 TTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTG
**
95527 ATGGTTAGTTT
325 ATGGTTAGTAC
* * * **
95538 ACGATTTCGGCTAAAATTTTACAAAAAACCGACCCGAAAAGATTGTCCCCAATTTTTTGCCTCAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCGACAA
95603 TACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTT-ACGCTTCTAATATCG
66 TACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCG
*
95667 --TTT---TTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTAAGATACTCGTAAAAA
131 TTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA
* * *
95727 TAAATGCGTAAACCCATTGTGGCTGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCT
196 TAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCT
* * * *
95792 TTCTGCCAAAAACCATGCAAAACTGAGTCAGGGCCTCGAAACCCATTTTTAGCCAAAAACCGTAA
261 TTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTGA
95857 TGGTTAGTAC
326 TGGTTAGTAC
* *
95867 ACGATTTCGGCTAAAATTTTGCAAAAAAACTGACCAGAAAAGTTTTTCCCCAATTTTTTGCGACA
1 ACGATTTCGGCTAAAATTTTGC-AAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCGACA
95932 ATACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATC
65 ATACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATC
* *
95997 ATTTTTCC--TTTTTTCTGAATTTATTTCTAATTAAATCAAAACAAGATTCAGATACTCGTAAAA
130 GTTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAA
* * *
96060 ATAAATCCGTAAATCCATTGTGGCTGAGATATTTCG-TTAGATAAATTATATAGATATTTCGAGA
195 ATAAATCCGTAAATCCATTGTGGCCGAGAGATTT-GATTAGAT-GA--ATATAGATATTTCGAGA
* * * *
96124 AGTCTTTCTGCCAAAACTAATGCAAAGCTGAGTCAGGGCCCCGAAACGCATTTTTAGCAAAAAAC
256 AGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAAC
* *
96189 CTTGATGATTAGTAC
321 CGTGATGGTTAGTAC
*** * * *
96204 TTTATTTCGGCTAAAATTTTACAAAAAAACTGACCCGAAAAGTTTTTTCCCAATTTTTTGCGACA
1 ACGATTTCGGCTAAAATTTTGC-AAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCGACA
*
96269 ATACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTTACGCTTCTAATATC
65 ATACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATC
*
96334 GTTTTTCCATTTTTTTCTGAATTTATTCCTAATTAAATCGAAACAAGATTCA-AGTACTCGTAAA
130 GTTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGA-TACTCGTAAA
* *
96398 AATAAATGCGTAAACCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGT
194 AATAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGT
* * *
96463 CTTTCTGCCAAAAAT-ATGCAAAACTAAGTCACGGCCCCGAAACTCATTTTTAGCCAAAAACCGT
259 CTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGT
*
96527 GATGGTTAGAAC
324 GATGGTTAGTAC
* *
96539 ACGATTTCGGCTAAAATATTGAAAAAAACTGACCCGAAAAG-TTTTACCCCAATTTTTTGCGACA
1 ACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGATTTT-CCCCAATTTTTTGCGACA
* * *
96603 ATACTCAGAAAAATCACATAATTCAATGCCGAAAATATTTTAGGTTTTTTCACGCTTCTAATATC
65 ATACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATC
* * *
96668 GTTTTTTCATTTTTTTTCTGAATTTATTTCTAATTAAATCGAAAAAAGATTCAGATACTTGTAAA
130 GTTTTTCCA-TTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAA
*
96733 AATAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGGAGT
194 AATAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGT
* *
96798 CTTTCTGCCAAAAATCATGCAAAACTGAGTTAGGGCCCCAAAACGCATTTTTAGCCAAAAACCGT
259 CTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGT
*
96863 GATGGTTATTAC
324 GATGGTTAGTAC
* * * * * * ** *
96875 ACGATTTCGGCTAAGATATTGGAAAAAACAGACCCGAAAAGATTTTTCCCAATTTCTTGCCTCCA
1 ACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCGACAA
* *
96940 TACTCAGAAAAATCATATAATTCGACGACCAAAACAATATTTTAGGGTTTTTCACGCTTCTAATA
66 TACTCAGAAAAATCACATAATTCAACG-CC-AAA-AATATTTTAGGGTTTTTCACGCTTCTAATA
*
97005 TCGTTTTTCC-TTTTTTTCTGAATTTATTTCTAATTAAATCGAATCAAGATTCAGATACTCGTAA
128 TCGTTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAA
97069 AAATAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAG
193 AAATAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAG
* *
97134 TCTTTCTGCCAAAAATCATTCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACTG
258 TCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCG
97199 TGATGGTTAGTAC
323 TGATGGTTAGTAC
* **
97212 ACGATTTCGGCTAAAATTTTGCAAAAAACTGACACGAAAAGATTTTCCCCAATTTTTTGCCTCAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCGACAA
* *
97277 TACTCAGAAAAATCATATAATTCGACGACCAAAATAATATTTTA
66 TACTCAGAAAAATCACATAATTCAACG-CC-AAA-AATATTTTA
97321 TTGTGAATTT
Statistics
Matches: 2851, Mismatches: 223, Indels: 82
0.90 0.07 0.03
Matches are distributed among these distances:
324 4 0.00
325 165 0.06
326 135 0.05
329 204 0.07
330 86 0.03
331 14 0.00
332 3 0.00
333 7 0.00
334 346 0.12
335 449 0.16
336 357 0.13
337 951 0.33
338 5 0.00
339 125 0.04
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (335 bp):
ACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGATTTTCCCCAATTTTTTGCGACAA
TACTCAGAAAAATCACATAATTCAACGCCAAAAATATTTTAGGGTTTTTCACGCTTCTAATATCG
TTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAA
TAAATCCGTAAATCCATTGTGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCT
TTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTGA
TGGTTAGTAC
Found at i:98082 original size:334 final size:336
Alignment explanation
Indices: 97327--98170 Score: 1331
Period size: 336 Copynumber: 2.5 Consensus size: 336
97317 TTTATTGTGA
*
97327 ATTTATTTATAATTAAATCGAAACAACATTCAGATACTCGTAAAAATAAATCCGTAAACCCATTG
1 ATTTATTTATAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAACCCATTG
* * * **
97392 TGGCCGAGAGATTTAATTAGATAAATATAGATATTTCGAAAAGTCTTTCTGCCAAAAATGTTGCA
66 TGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCA
* * * *
97457 AAACTGAGTCATGGCCACGAAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTATACGATTTTC
131 AAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTTC
* * * * *
97522 GGCTAAAATTTTGCAAAAAACAGACGCGAAAAGTTTTTCCCTAATTTTTTGCGTCAATACTCAGA
196 GGCAAAAATTTTGCAAAAAACAGACACGAAAAGATTTTCCCCAATTTTTTGCCTCAATACTCAGA
* * * *
97587 AAAATCATATAATTCAACGCCAAAAATTTTTTAGAGGTTTTTCACGCTTCTAATATCGTTTTTCC
261 AAAATCATATAATTCAACGCCAAAAAATTTTTAGAGGTTTCTCACGCATCTAATATCGTTATTCC
97652 ATTTTTTCTGT
326 ATTTTTTCTGT
* * *
97663 ATTTGTTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAACGCATTG
1 ATTTATTTATAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAACCCATTG
*
97728 TGGCCGAGAGATTTGATTAGATGAATATAGATATTTAGAGAAGTCTTTCTGCCAAAAATCATGCA
66 TGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCA
* * *
97793 AACCTAAGACAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTGATAGTTAGTACACGA-TTTC
131 AAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTTC
*
97857 GGCAAAAATTTTGCAAAAAACTGACACGAAAAGATTTTCCCCAATTTTTTGCCTCAATACTCAGA
196 GGCAAAAATTTTGCAAAAAACAGACACGAAAAGATTTTCCCCAATTTTTTGCCTCAATACTCAGA
*
97922 AAAATCATATAATTCAATGCCAAAAAATTTTTAG-GGTTTCTCACGCATCTAATATCGTTATTCC
261 AAAATCATATAATTCAACGCCAAAAAATTTTTAGAGGTTTCTCACGCATCTAATATCGTTATTCC
97986 ATTTTTTCTGT
326 ATTTTTTCTGT
* * * *
97997 ATTTATTTATAATTAAGTCGATACAAGATTCAGATACTCGTCAAAATAAATCCGTAAACCCATTA
1 ATTTATTTATAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAACCCATTG
*
98062 TAGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCC-AAAATCATGCA
66 TGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCA
*
98126 AAACTGAGTTAGGGCCCC-AAACGACA-TTTTAGCC-AAAACCGTGAT
131 AAACTGAGTCAGGGCCCCGAAACG-CATTTTTAGCCAAAAACCGTGAT
98171 G
Statistics
Matches: 466, Mismatches: 41, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
331 11 0.02
332 13 0.03
333 27 0.06
334 147 0.32
335 95 0.20
336 173 0.37
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (336 bp):
ATTTATTTATAATTAAATCGAAACAAGATTCAGATACTCGTAAAAATAAATCCGTAAACCCATTG
TGGCCGAGAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCA
AAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTTC
GGCAAAAATTTTGCAAAAAACAGACACGAAAAGATTTTCCCCAATTTTTTGCCTCAATACTCAGA
AAAATCATATAATTCAACGCCAAAAAATTTTTAGAGGTTTCTCACGCATCTAATATCGTTATTCC
ATTTTTTCTGT
Done.