Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012620.1 Corchorus capsularis cultivar CVL-1 contig12641, 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: 161749
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:629 original size:2 final size:2
Alignment explanation
Indices: 622--647 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
612 TGAATGGTGC
622 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
648 GGGATTATGC
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:4577 original size:34 final size:31
Alignment explanation
Indices: 4532--4611 Score: 101
Period size: 34 Copynumber: 2.5 Consensus size: 31
4522 TAACCTAATT
4532 AATCAAAGTTATTGCTAATCTCGCCAAAAAAAA
1 AATCAAAGTTATTGCTAAT-T-GCCAAAAAAAA
* *
4565 AATTCAAAGTTATTGCTAATTTCCAAAAAGAA
1 AA-TCAAAGTTATTGCTAATTGCCAAAAAAAA
4597 AA--AAAGTTATTGCTA
1 AATCAAAGTTATTGCTA
4612 TTTATTTTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
29 13 0.30
32 11 0.25
33 3 0.07
34 17 0.39
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (31 bp):
AATCAAAGTTATTGCTAATTGCCAAAAAAAA
Found at i:5444 original size:68 final size:68
Alignment explanation
Indices: 5330--5471 Score: 257
Period size: 68 Copynumber: 2.1 Consensus size: 68
5320 CCGTCGTACT
* *
5330 CAGGTAGAGTCTAAGACTCTTTTATGCACTAATATCTTTTATCTTAATCACATTACATGAACAAT
1 CAGGTTGAGTCTAAGACTCTTTTATGCACTAATATCTTTTACCTTAATCACATTACATGAACAAT
5395 GTG
66 GTG
*
5398 CAGGTTGAGTCTAAGACTCTTTTATGCACTAATATCTTTTACCTTAATTACATTACATGAACAAT
1 CAGGTTGAGTCTAAGACTCTTTTATGCACTAATATCTTTTACCTTAATCACATTACATGAACAAT
5463 GTG
66 GTG
5466 CAGGTT
1 CAGGTT
5472 TTTGACATAC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (68 bp):
CAGGTTGAGTCTAAGACTCTTTTATGCACTAATATCTTTTACCTTAATCACATTACATGAACAAT
GTG
Found at i:31899 original size:2 final size:2
Alignment explanation
Indices: 31892--31925 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31882 GTGATAAATG
31892 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
31926 CTTAATAACA
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:38631 original size:132 final size:132
Alignment explanation
Indices: 38394--38658 Score: 530
Period size: 132 Copynumber: 2.0 Consensus size: 132
38384 CATGAATCAA
38394 TCATCCATTTGCTGTCAAGGGTCTTGCAACTGTTCTTTATTCTTTTCCAAAATATTGGTCAAGCA
1 TCATCCATTTGCTGTCAAGGGTCTTGCAACTGTTCTTTATTCTTTTCCAAAATATTGGTCAAGCA
38459 GCCTTCATTTCTACTTTAGTTAGTCTGTAGAGTTCTATGAGTTTCTACCATCTATGAAGGAATAA
66 GCCTTCATTTCTACTTTAGTTAGTCTGTAGAGTTCTATGAGTTTCTACCATCTATGAAGGAATAA
38524 TT
131 TT
38526 TCATCCATTTGCTGTCAAGGGTCTTGCAACTGTTCTTTATTCTTTTCCAAAATATTGGTCAAGCA
1 TCATCCATTTGCTGTCAAGGGTCTTGCAACTGTTCTTTATTCTTTTCCAAAATATTGGTCAAGCA
38591 GCCTTCATTTCTACTTTAGTTAGTCTGTAGAGTTCTATGAGTTTCTACCATCTATGAAGGAATAA
66 GCCTTCATTTCTACTTTAGTTAGTCTGTAGAGTTCTATGAGTTTCTACCATCTATGAAGGAATAA
38656 TT
131 TT
38658 T
1 T
38659 GGGTGACAAA
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
132 133 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (132 bp):
TCATCCATTTGCTGTCAAGGGTCTTGCAACTGTTCTTTATTCTTTTCCAAAATATTGGTCAAGCA
GCCTTCATTTCTACTTTAGTTAGTCTGTAGAGTTCTATGAGTTTCTACCATCTATGAAGGAATAA
TT
Found at i:39889 original size:2 final size:2
Alignment explanation
Indices: 39884--39908 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39874 TTAATATATA
39884 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
39909 CTTGTAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:41464 original size:24 final size:24
Alignment explanation
Indices: 41435--41481 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
41425 ATTGATAGGA
41435 TTTTTGTGTCCATGTGTGTGTTTT
1 TTTTTGTGTCCATGTGTGTGTTTT
41459 TTTTTGTGTCCATGTGTGTGTTT
1 TTTTTGTGTCCATGTGTGTGTTT
41482 CCTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.04, C:0.09, G:0.26, T:0.62
Consensus pattern (24 bp):
TTTTTGTGTCCATGTGTGTGTTTT
Found at i:41487 original size:24 final size:24
Alignment explanation
Indices: 41436--41487 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
41426 TTGATAGGAT
**
41436 TTTTGTGTCCATGTGTGTGTTTTT
1 TTTTGTGTCCATGTGTGTGTTTCC
41460 TTTTGTGTCCATGTGTGTGTTTCC
1 TTTTGTGTCCATGTGTGTGTTTCC
41484 TTTT
1 TTTT
41488 ACATGTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.04, C:0.12, G:0.23, T:0.62
Consensus pattern (24 bp):
TTTTGTGTCCATGTGTGTGTTTCC
Found at i:54472 original size:25 final size:25
Alignment explanation
Indices: 54440--54492 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
54430 AATAACATAT
*
54440 ATGATTCTTTATGTGGTTAAAATAC
1 ATGATTCTTTATATGGTTAAAATAC
54465 ATGATTCTTTATATGGTTAAAATAC
1 ATGATTCTTTATATGGTTAAAATAC
54490 ATG
1 ATG
54493 GCAGTTCCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (25 bp):
ATGATTCTTTATATGGTTAAAATAC
Found at i:55091 original size:3 final size:3
Alignment explanation
Indices: 55076--55129 Score: 76
Period size: 3 Copynumber: 18.3 Consensus size: 3
55066 TATACACATG
*
55076 ATT ATT ATAT ATT ATT ATT -TT A-T CTT ATT ATT ATT ATT ATT ATT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
55120 ATT ATT ATT A
1 ATT ATT ATT A
55130 CATAATGAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 3 0.07
3 40 0.87
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:55094 original size:32 final size:28
Alignment explanation
Indices: 55055--55132 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 28
55045 TTCACCTTCT
55055 TTATTATTGTATATACACATGATTATTATATA
1 TTATTATT-T-TAT-CACATGATTATTAT-TA
** *
55087 TTATTATTTTATCTTATTATTATTATTA
1 TTATTATTTTATCACATGATTATTATTA
*
55115 TTATTATTATTATTACAT
1 TTATTATT-TTATCACAT
55133 AATGAGAGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 10 0.26
29 17 0.44
30 3 0.08
31 1 0.03
32 8 0.21
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (28 bp):
TTATTATTTTATCACATGATTATTATTA
Found at i:59761 original size:97 final size:97
Alignment explanation
Indices: 59595--59777 Score: 323
Period size: 97 Copynumber: 1.9 Consensus size: 97
59585 TTTAAATCGA
59595 TTTCAAATAAACATGTATGGAAGCTATAATTGTAAACCACAATCAGATTTATGGAAGCATTGGTT
1 TTTCAAATAAACATGTATGGAAGCTATAATTGTAAACCACAATCAGATTTATGGAAGCATTGGTT
59660 TATAGTCTTAGTTTATTTCTTCCATACCTGTT
66 TATAGTCTTAGTTTATTTCTTCCATACCTGTT
* * *
59692 TTTCAAATAAACA-GATATGGAAGCTATAATTGTAAGCCACTATCGGATTTATGGAAGCATTGGT
1 TTTCAAATAAACATG-TATGGAAGCTATAATTGTAAACCACAATCAGATTTATGGAAGCATTGGT
59756 TTATAGTCTTAGTTTATTTCTT
65 TTATAGTCTTAGTTTATTTCTT
59778 TTGGTTGATT
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
96 1 0.01
97 81 0.99
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (97 bp):
TTTCAAATAAACATGTATGGAAGCTATAATTGTAAACCACAATCAGATTTATGGAAGCATTGGTT
TATAGTCTTAGTTTATTTCTTCCATACCTGTT
Found at i:66556 original size:2 final size:2
Alignment explanation
Indices: 66549--66577 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
66539 ATATCTGGCA
66549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66578 AAAGGTTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66833 original size:15 final size:15
Alignment explanation
Indices: 66813--66842 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
66803 TTGGTTACAT
*
66813 TTGCTCTGTTTTAAG
1 TTGCTCTGTCTTAAG
66828 TTGCTCTGTCTTAAG
1 TTGCTCTGTCTTAAG
66843 GTTTAACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.17, G:0.20, T:0.50
Consensus pattern (15 bp):
TTGCTCTGTCTTAAG
Found at i:67806 original size:22 final size:22
Alignment explanation
Indices: 67779--67822 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
67769 GGAGAGTTTC
*
67779 TTTTTCTTTGTTAGCATAACCT
1 TTTTTCTTTGTTAACATAACCT
67801 TTTTTCTTTGTTAACATAACCT
1 TTTTTCTTTGTTAACATAACCT
67823 GGATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.07, T:0.55
Consensus pattern (22 bp):
TTTTTCTTTGTTAACATAACCT
Found at i:70824 original size:12 final size:12
Alignment explanation
Indices: 70804--70834 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
70794 ATTGGTTGGT
70804 CCAAACCCTAAC
1 CCAAACCCTAAC
*
70816 CCTAACCCTAAC
1 CCAAACCCTAAC
70828 CCAAACC
1 CCAAACC
70835 AACACCAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.39, C:0.52, G:0.00, T:0.10
Consensus pattern (12 bp):
CCAAACCCTAAC
Found at i:71023 original size:3 final size:3
Alignment explanation
Indices: 71008--71039 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
70998 CTAAACCTAA
*
71008 AAC AAC CAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
71040 TACAAGACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:83079 original size:25 final size:24
Alignment explanation
Indices: 83044--83100 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
83034 GTTTAACACA
83044 GATAT-TC-ATGGATATATTGAACG
1 GATATATCGATGGATATATTG-ACG
83067 GATATATCGATGGATATATTGACG
1 GATATATCGATGGATATATTGACG
83091 GATATATCGA
1 GATATATCGA
83101 GGTATCGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 5 0.16
24 15 0.47
25 12 0.38
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (24 bp):
GATATATCGATGGATATATTGACG
Found at i:83083 original size:12 final size:12
Alignment explanation
Indices: 83053--83100 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
83043 AGATATTCAT
*
83053 GGATATATTGAAC
1 GGATATATCG-AC
*
83066 GGATATATCGAT
1 GGATATATCGAC
*
83078 GGATATATTGAC
1 GGATATATCGAC
83090 GGATATATCGA
1 GGATATATCGA
83101 GGTATCGATG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 21 0.70
13 9 0.30
ACGTcount: A:0.35, C:0.08, G:0.25, T:0.31
Consensus pattern (12 bp):
GGATATATCGAC
Found at i:84286 original size:10 final size:10
Alignment explanation
Indices: 84271--84312 Score: 75
Period size: 10 Copynumber: 4.2 Consensus size: 10
84261 AATTTAATAT
84271 GGATATTTAC
1 GGATATTTAC
*
84281 GGATATTTAT
1 GGATATTTAC
84291 GGATATTTAC
1 GGATATTTAC
84301 GGATATTTAC
1 GGATATTTAC
84311 GG
1 GG
84313 TTATATCGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (10 bp):
GGATATTTAC
Found at i:84293 original size:20 final size:20
Alignment explanation
Indices: 84268--84309 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
84258 TTTAATTTAA
84268 TATGGATATTTACGGATATT
1 TATGGATATTTACGGATATT
84288 TATGGATATTTACGGATATT
1 TATGGATATTTACGGATATT
84308 TA
1 TA
84310 CGGTTATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
TATGGATATTTACGGATATT
Found at i:85262 original size:97 final size:101
Alignment explanation
Indices: 85058--85264 Score: 305
Period size: 97 Copynumber: 2.0 Consensus size: 101
85048 TATTTTACAA
85058 ATTTTTCATTTCAAGACAATATATTCTTTAATCTTTAATAGCTATAATAAATGCTTAAAGAGTGA
1 ATTTTTCATTTCAAGACAATATA----TTAATCTTTAATAGC-ATAATAAATGCTTAAAGAGTGA
85123 AACTCATAAATTGAAAAGGAAATTACTATATATGGAAGTATAT
61 AACTCATAAA-T-AAAAGGAAATTACTATATATGGAAGTATAT
*
85166 ATTTTTCATTTCAAGACAATATA-TATTCTTTAATAGC-T-ATAAATGCTTAAAGAGTGAAACTC
1 ATTTTTCATTTCAAGACAATATATTAATCTTTAATAGCATAATAAATGCTTAAAGAGTGAAACTC
*
85228 ATAAA-AAAAGGAAATTACTATATATGGTAGTATAT
66 ATAAATAAAAGGAAATTACTATATATGGAAGTATAT
85263 AT
1 AT
85265 ATATTCTGAC
Statistics
Matches: 97, Mismatches: 2, Indels: 11
0.88 0.02 0.10
Matches are distributed among these distances:
97 31 0.32
100 29 0.30
101 1 0.01
103 13 0.13
108 23 0.24
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (101 bp):
ATTTTTCATTTCAAGACAATATATTAATCTTTAATAGCATAATAAATGCTTAAAGAGTGAAACTC
ATAAATAAAAGGAAATTACTATATATGGAAGTATAT
Found at i:88318 original size:11 final size:11
Alignment explanation
Indices: 88302--88361 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
88292 GAGGTTCGTG
88302 TTTGAAGATTA
1 TTTGAAGATTA
88313 TTTGAAGA-TA
1 TTTGAAGATTA
88323 TTTTGAAG---A
1 -TTTGAAGATTA
88332 TTTGAAGATTA
1 TTTGAAGATTA
88343 -TTGAAGAATTA
1 TTTGAAG-ATTA
*
88354 TTTCAAGA
1 TTTGAAGA
88362 AGCAAGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
8 7 0.17
9 1 0.02
10 8 0.19
11 21 0.50
12 5 0.12
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:88336 original size:19 final size:18
Alignment explanation
Indices: 88312--88349 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
88302 TTTGAAGATT
*
88312 ATTTGAAGATATTTTGAAG
1 ATTTGAAGAT-TATTGAAG
88331 ATTTGAAGATTATTGAAG
1 ATTTGAAGATTATTGAAG
88349 A
1 A
88350 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (18 bp):
ATTTGAAGATTATTGAAG
Found at i:92982 original size:2 final size:2
Alignment explanation
Indices: 92975--93000 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
92965 AATAATTTGA
92975 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
93001 TCTTTATTTT
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:93853 original size:25 final size:23
Alignment explanation
Indices: 93825--93870 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
93815 TTGACATCGT
*
93825 TTTCGTTTTTCTGTTTTTTTTTTTG
1 TTTCG-TTTTC-GTTTTGTTTTTTG
93850 TTTCGTTTTCGTTTTGTTTTT
1 TTTCGTTTTCGTTTTGTTTTT
93871 GTTGCGCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 5 0.25
25 5 0.25
ACGTcount: A:0.00, C:0.09, G:0.13, T:0.78
Consensus pattern (23 bp):
TTTCGTTTTCGTTTTGTTTTTTG
Found at i:97709 original size:12 final size:12
Alignment explanation
Indices: 97692--97718 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
97682 TTGTTTTCTT
97692 TTGATCTCATAG
1 TTGATCTCATAG
97704 TTGATCTCATAG
1 TTGATCTCATAG
97716 TTG
1 TTG
97719 TTAAATTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (12 bp):
TTGATCTCATAG
Found at i:102584 original size:22 final size:22
Alignment explanation
Indices: 102556--102876 Score: 137
Period size: 22 Copynumber: 14.5 Consensus size: 22
102546 TTAATCAAAC
*
102556 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
102578 CAAAATTTCATAGTG-TGGTTA-
1 CAAAATTTCATAG-GAAGGTTAT
*
102599 CTAAAATTTCATATGG-AGATTAT
1 C-AAAATTTCATA-GGAAGGTTAT
** *
102622 CAAAACGTCATAGTATA-GTTAT
1 CAAAATTTCATAGGA-AGGTTAT
* * *
102644 CAAAATTTCATA-CAGACGTTAC
1 CAAAATTTCATAGGA-AGGTTAT
**
102666 CAAAATTT--TAAAAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * * *
102686 CAAATTTTCTTA-GAGTGGTTAA
1 CAAAATTTCATAGGA-AGGTTAT
*
102708 CAAAATTTCATACGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * * *
102730 C-GAATTTTATAGTG-TGCTTAT
1 CAAAATTTCATAG-GAAGGTTAT
102751 CAAAATTTCATAGGGAGGGAGGTTAT
1 CAAAATTTCATA-GGA---AGGTTAT
* * * * *
102777 CAAAGTTACCTAGGGAGGTTTAA
1 CAAAATTTCATAGGAAGG-TTAT
*
102800 CAAAATTTCATAGGAAGATTA-
1 CAAAATTTCATAGGAAGGTTAT
*
102821 CAAAAATTTTAT-GGAGAGGTTAT
1 C-AAAATTTCATAGGA-AGGTTAT
* * *
102844 CAAAATTACAT-GAAGAGGATAT
1 CAAAATTTCATAGGA-AGGTTAT
*
102866 CACAATTTCAT
1 CAAAATTTCAT
102877 TCTCATAGGG
Statistics
Matches: 225, Mismatches: 51, Indels: 46
0.70 0.16 0.14
Matches are distributed among these distances:
20 14 0.06
21 24 0.11
22 147 0.65
23 24 0.11
25 2 0.01
26 14 0.06
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:102736 original size:44 final size:43
Alignment explanation
Indices: 102678--102762 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
102668 AAATTTTAAA
* *
102678 AAGGTTATCAAATTTTCTTAGAGTGGTTAACAAAATTTCATACG
1 AAGGTTATCAAATTTT-ATAGAGTGCTTAACAAAATTTCATACG
* * *
102722 AAGGTTATCGAATTTTATAGTGTGCTTATCAAAATTTCATA
1 AAGGTTATCAAATTTTATAGAGTGCTTAACAAAATTTCATA
102763 GGGAGGGAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 21 0.58
44 15 0.42
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (43 bp):
AAGGTTATCAAATTTTATAGAGTGCTTAACAAAATTTCATACG
Found at i:102993 original size:22 final size:22
Alignment explanation
Indices: 102980--103041 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
102970 TTTATAGTAT
102980 GATTATCAAAATTTCATACGGA
1 GATTATCAAAATTTCATACGGA
* * **
103002 GATTATTAAAATTTCACATTGA
1 GATTATCAAAATTTCATACGGA
* *
103024 GGTTATCAGAATTTCATA
1 GATTATCAAAATTTCATA
103042 GTGTCGTTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (22 bp):
GATTATCAAAATTTCATACGGA
Found at i:103091 original size:18 final size:19
Alignment explanation
Indices: 103068--103123 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 19
103058 TCCACAATAT
103068 GGTTATCAAATTTTCAT-A
1 GGTTATCAAATTTTCATGA
*
103086 GGTTATCGAAATTTAATAATGA
1 GGTTATC-AAATTT--TCATGA
103108 GGTTATCAAATTTTCA
1 GGTTATCAAATTTTCA
103124 AAGTGTGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 7 0.22
19 8 0.25
21 9 0.28
22 8 0.25
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (19 bp):
GGTTATCAAATTTTCATGA
Found at i:103133 original size:22 final size:21
Alignment explanation
Indices: 103024--103144 Score: 72
Period size: 22 Copynumber: 5.7 Consensus size: 21
103014 TTCACATTGA
*
103024 GGTTATCAGAA-TTTCATAGTGT
1 GGTTATCA-AATTTTCA-AATGT
* * * *
103046 CGTTATCAAAATTCCACAATAT
1 GGTTATCAAATTTTCA-AATGT
*
103068 GGTTATCAAATTTTC--AT-A
1 GGTTATCAAATTTTCAAATGT
* *
103086 GGTTATCGAAA-TTTAATAATGA
1 GGTTATC-AAATTTTCA-AATGT
103108 GGTTATCAAATTTTCAAAGTGT
1 GGTTATCAAATTTTCAAA-TGT
103130 GGTTATCAATATTTT
1 GGTTATCAA-ATTTT
103145 TACGTTGGAG
Statistics
Matches: 78, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
18 10 0.13
19 5 0.06
21 9 0.12
22 49 0.63
23 5 0.06
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (21 bp):
GGTTATCAAATTTTCAAATGT
Found at i:110575 original size:21 final size:21
Alignment explanation
Indices: 110550--110596 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
110540 AGCCCTAGCG
*
110550 AACAACCTCAGATTCTAAAGC
1 AACAACCACAGATTCTAAAGC
**
110571 AACAATGACAGATTCTAAAGC
1 AACAACCACAGATTCTAAAGC
110592 AACAA
1 AACAA
110597 TTACTTCGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.49, C:0.23, G:0.11, T:0.17
Consensus pattern (21 bp):
AACAACCACAGATTCTAAAGC
Found at i:110597 original size:21 final size:21
Alignment explanation
Indices: 110558--110597 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
110548 CGAACAACCT
110558 CAGATTCTAAAGCAACAATGA
1 CAGATTCTAAAGCAACAATGA
110579 CAGATTCTAAAGCAACAAT
1 CAGATTCTAAAGCAACAAT
110598 TACTTCGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.20
Consensus pattern (21 bp):
CAGATTCTAAAGCAACAATGA
Found at i:116055 original size:23 final size:23
Alignment explanation
Indices: 116029--116073 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
116019 CGGTTTCAAC
116029 CTGGAGATTTGCATTTTCGTTTT
1 CTGGAGATTTGCATTTTCGTTTT
116052 CTGGAGATTTGCATTTTCGTTT
1 CTGGAGATTTGCATTTTCGTTT
116074 GATGTTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.13, G:0.22, T:0.51
Consensus pattern (23 bp):
CTGGAGATTTGCATTTTCGTTTT
Found at i:116150 original size:18 final size:19
Alignment explanation
Indices: 116126--116179 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
116116 AGAGAGATTC
116126 TTTTGAACTGGAAAAACGA
1 TTTTGAACTGGAAAAACGA
*
116145 -TTTGAACTGCTGCAAAACGA
1 TTTTGAACTG--GAAAAACGA
*
116165 TTTTGAACTGCAAAA
1 TTTTGAACTGGAAAA
116180 TTGAAATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 9 0.31
19 3 0.10
20 8 0.28
21 9 0.31
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (19 bp):
TTTTGAACTGGAAAAACGA
Found at i:116169 original size:21 final size:20
Alignment explanation
Indices: 116126--116179 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
116116 AGAGAGATTC
116126 TTTTGAACTG-GAAAAACGA
1 TTTTGAACTGCGAAAAACGA
*
116145 -TTTGAACTGCTGCAAAACGA
1 TTTTGAACTGC-GAAAAACGA
116165 TTTTGAACTGC-AAAA
1 TTTTGAACTGCGAAAA
116180 TTGAAATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 9 0.30
19 3 0.10
20 8 0.27
21 10 0.33
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (20 bp):
TTTTGAACTGCGAAAAACGA
Found at i:132892 original size:33 final size:33
Alignment explanation
Indices: 132833--132934 Score: 154
Period size: 33 Copynumber: 3.1 Consensus size: 33
132823 GCTCTTACAA
*
132833 ACAATGAAG-TTGCGGGCCTTCATCACGCCGTTT
1 ACAATGAAGTTTACGGGCCTTCATCACGCC-TTT
*
132866 -CAATGAAGTTTACGGGTCTTCATCACGCCTTT
1 ACAATGAAGTTTACGGGCCTTCATCACGCCTTT
*
132898 ACAATGAAGTTCACGGGCCTTCATCACGCCTTT
1 ACAATGAAGTTTACGGGCCTTCATCACGCCTTT
132931 ACAA
1 ACAA
132935 GTTGAGCAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (33 bp):
ACAATGAAGTTTACGGGCCTTCATCACGCCTTT
Found at i:134234 original size:30 final size:30
Alignment explanation
Indices: 134200--134261 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
134190 AAGTTAAAAG
134200 CAAACAAGAGATATTCAATTCAAGCACACA
1 CAAACAAGAGATATTCAATTCAAGCACACA
134230 CAAACAAGAGATATTCAATTCAAGCACACA
1 CAAACAAGAGATATTCAATTCAAGCACACA
134260 CA
1 CA
134262 TATTTCTCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.50, C:0.24, G:0.10, T:0.16
Consensus pattern (30 bp):
CAAACAAGAGATATTCAATTCAAGCACACA
Found at i:136411 original size:20 final size:20
Alignment explanation
Indices: 136388--136426 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
136378 ATGATGATAA
*
136388 ATGATGGAATGCAA-TGAAAC
1 ATGATGAAAT-CAAGTGAAAC
136408 ATGATGAAATCAAGTGAAA
1 ATGATGAAATCAAGTGAAA
136427 AGCTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.49, C:0.08, G:0.23, T:0.21
Consensus pattern (20 bp):
ATGATGAAATCAAGTGAAAC
Found at i:142908 original size:65 final size:66
Alignment explanation
Indices: 142655--142921 Score: 518
Period size: 66 Copynumber: 4.0 Consensus size: 66
142645 ATTTGTTTAC
142655 TCTTTTCCTCTTTAACTTTTTTCAGGAAACCCTGATATGAATGGATTGTAGAGTCTTTATATATC
1 TCTTTTCCTC-TTAACTTTTTTCAGGAAACCCTGATATGAATGGATTGTAGAGTCTTTATATATC
142720 TA
65 TA
142722 TCTTTTCCTCTTAACTTTTTTCAGGAAACCCTGATATGAATGGATTGTAGAGTCTTTATATATCT
1 TCTTTTCCTCTTAACTTTTTTCAGGAAACCCTGATATGAATGGATTGTAGAGTCTTTATATATCT
142787 A
66 A
142788 TCTTTTCCTCTTAACTTTTTTCAGGAAACCCTGATATGAATGGATTGTAGAGTCTTTATATATCT
1 TCTTTTCCTCTTAACTTTTTTCAGGAAACCCTGATATGAATGGATTGTAGAGTCTTTATATATCT
142853 A
66 A
142854 TCTTTTCCTCTTAACTTTTTTCA-GAAACCCTGATATGAATGGATTGTAGAGTCTTTATATATCT
1 TCTTTTCCTCTTAACTTTTTTCAGGAAACCCTGATATGAATGGATTGTAGAGTCTTTATATATCT
142918 A
66 A
142919 TCT
1 TCT
142922 GTTTGGTTTC
Statistics
Matches: 200, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
65 45 0.22
66 145 0.73
67 10 0.05
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (66 bp):
TCTTTTCCTCTTAACTTTTTTCAGGAAACCCTGATATGAATGGATTGTAGAGTCTTTATATATCT
A
Found at i:145510 original size:30 final size:30
Alignment explanation
Indices: 145476--145538 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
145466 TCTCACGGAA
* *
145476 TGTGAGTTTTCTTTGTAATTTATTTGTTTG
1 TGTGAATTTTCTTTGTAATTTATATGTTTG
145506 TGTGAATTTTCTTTGTAATTTATATGTTTG
1 TGTGAATTTTCTTTGTAATTTATATGTTTG
145536 TGT
1 TGT
145539 ATTTAGCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.03, G:0.19, T:0.62
Consensus pattern (30 bp):
TGTGAATTTTCTTTGTAATTTATATGTTTG
Found at i:147052 original size:20 final size:21
Alignment explanation
Indices: 147024--147068 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
147014 ATCTAAGTAC
147024 TTGGGGAAAGGCCGT-ATTAG
1 TTGGGGAAAGGCCGTGATTAG
* *
147044 TTGGTGAAAGGCCGTGTTTAG
1 TTGGGGAAAGGCCGTGATTAG
147065 TTGG
1 TTGG
147069 AGACAGGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.20, C:0.09, G:0.40, T:0.31
Consensus pattern (21 bp):
TTGGGGAAAGGCCGTGATTAG
Found at i:147466 original size:34 final size:34
Alignment explanation
Indices: 147405--147543 Score: 212
Period size: 34 Copynumber: 4.2 Consensus size: 34
147395 GTTTCATCGG
* *
147405 CCCTGCCCAGTGGG-T-T-ATAATAACTGGAAGG
1 CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
147436 CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
*
147470 CCATGCCCAGTGGGTTGTGAAAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
* *
147504 CCCTGTCCAGTGGGTTGTGATAATAACTGGAAGA
1 CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
147538 CCCTGC
1 CCCTGC
147544 TAACGGGTTA
Statistics
Matches: 98, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
31 14 0.14
32 1 0.01
33 1 0.01
34 82 0.84
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (34 bp):
CCCTGCCCAGTGGGTTGTGAAAATAACTGGAAGA
Found at i:155529 original size:30 final size:30
Alignment explanation
Indices: 155493--155553 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
155483 TTAGTAAGAT
155493 ATTAAAATTTGAGGGAATAAGAGGAAAGTC
1 ATTAAAATTTGAGGGAATAAGAGGAAAGTC
155523 ATTAAAATTTGAGGGAATAAGAGGAAAGTC
1 ATTAAAATTTGAGGGAATAAGAGGAAAGTC
155553 A
1 A
155554 AGATAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.03, G:0.26, T:0.23
Consensus pattern (30 bp):
ATTAAAATTTGAGGGAATAAGAGGAAAGTC
Found at i:158137 original size:21 final size:21
Alignment explanation
Indices: 158113--158152 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
158103 AATCAAAATT
158113 GAGTGAGTCCAATATGAAAAC
1 GAGTGAGTCCAATATGAAAAC
*
158134 GAGTGAGTCCAATTTGAAA
1 GAGTGAGTCCAATATGAAA
158153 GCAATTGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (21 bp):
GAGTGAGTCCAATATGAAAAC
Found at i:161376 original size:66 final size:65
Alignment explanation
Indices: 161296--161428 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 65
161286 ACCAAAAGAA
* * **
161296 TTACAAATAAAATATAGTCTATGGCAATACTTAATATTTTTTTGTTTTGTAATTAGAATATCTAA
1 TTACAAATAAAATATAGTCTATGGAAATACTTAATATTTTTATGTTTAAT-ATTAGAATATCTAA
161361 T
65 T
*
161362 TTACAAATAAAATATAGTCTATGGAAATACTTAATATTTTTATGTTTAATATTATAATATCTAAT
1 TTACAAATAAAATATAGTCTATGGAAATACTTAATATTTTTATGTTTAATATTAGAATATCTAAT
161427 TT
1 TT
161429 TTTTTGTTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
65 16 0.26
66 46 0.74
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.46
Consensus pattern (65 bp):
TTACAAATAAAATATAGTCTATGGAAATACTTAATATTTTTATGTTTAATATTAGAATATCTAAT
Found at i:161573 original size:21 final size:21
Alignment explanation
Indices: 161549--161588 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
161539 GTTCTTCTTT
161549 AAGGTTACTAAAAAA-GTTAAA
1 AAGGTTA-TAAAAAATGTTAAA
161570 AAGGTTATAAAAAATGTTA
1 AAGGTTATAAAAAATGTTA
161589 TAGTATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.55, C:0.03, G:0.15, T:0.28
Consensus pattern (21 bp):
AAGGTTATAAAAAATGTTAAA
Done.