Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011563.1 Corchorus capsularis cultivar CVL-1 contig11584, 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: 44442
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:839 original size:32 final size:33
Alignment explanation
Indices: 765--850 Score: 122
Period size: 32 Copynumber: 2.6 Consensus size: 33
755 GTCTCGTTGA
765 CCAAAATGGGCGGCAAGGCCATGGGCAAGCCAG
1 CCAAAATGGGCGGCAAGGCCATGGGCAAGCCAG
* *
798 CCAAAATGGGTGGCAAGGCCAT-GGCATGCC-G
1 CCAAAATGGGCGGCAAGGCCATGGGCAAGCCAG
*
829 CCCAAAATGGGCGGCAAAGCCA
1 -CCAAAATGGGCGGCAAGGCCA
851 ATTTTTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
31 1 0.02
32 26 0.54
33 21 0.44
ACGTcount: A:0.30, C:0.28, G:0.34, T:0.08
Consensus pattern (33 bp):
CCAAAATGGGCGGCAAGGCCATGGGCAAGCCAG
Found at i:904 original size:22 final size:23
Alignment explanation
Indices: 865--916 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
855 TTTTTAAAAA
*
865 AATTAATTAGTATTTAATTACTT
1 AATTTATTAGTATTTAATTACTT
* *
888 AGTTTATTAGT-TTTAATTAGTT
1 AATTTATTAGTATTTAATTACTT
910 AATTTAT
1 AATTTAT
917 GATTAACTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (23 bp):
AATTTATTAGTATTTAATTACTT
Found at i:1320 original size:2 final size:2
Alignment explanation
Indices: 1313--1337 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1303 ATATAAAATA
1313 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 A
1338 CTAATTAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2852 original size:16 final size:16
Alignment explanation
Indices: 2831--2889 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
2821 TGCTGAATTA
2831 CTTTGTACCGATATTG
1 CTTTGTACCGATATTG
* * *
2847 CTTTGTATATTCAATTTATG
1 CTTTG--TA-CCGATAT-TG
2867 CTTTGTACCGATATTG
1 CTTTGTACCGATATTG
2883 CTTTGTA
1 CTTTGTA
2890 TATTCAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 14 0.42
17 4 0.12
18 4 0.12
19 4 0.12
20 7 0.21
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.49
Consensus pattern (16 bp):
CTTTGTACCGATATTG
Found at i:2870 original size:20 final size:20
Alignment explanation
Indices: 2845--2905 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
2835 GTACCGATAT
2845 TGCTTTGTATATTCAATTTA
1 TGCTTTGTATATTCAATTTA
* * *
2865 TGCTTTG--TA-CCGATAT-
1 TGCTTTGTATATTCAATTTA
2881 TGCTTTGTATATTCAATTTA
1 TGCTTTGTATATTCAATTTA
2901 TGCTT
1 TGCTT
2906 AGTTTGGAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
16 7 0.23
17 4 0.13
18 4 0.13
19 4 0.13
20 12 0.39
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.52
Consensus pattern (20 bp):
TGCTTTGTATATTCAATTTA
Found at i:2873 original size:36 final size:36
Alignment explanation
Indices: 2831--2905 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
2821 TGCTGAATTA
2831 CTTTGTACCGATATTGCTTTGTATATTCAATTTATG
1 CTTTGTACCGATATTGCTTTGTATATTCAATTTATG
2867 CTTTGTACCGATATTGCTTTGTATATTCAATTTATG
1 CTTTGTACCGATATTGCTTTGTATATTCAATTTATG
2903 CTT
1 CTT
2906 AGTTTGGAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (36 bp):
CTTTGTACCGATATTGCTTTGTATATTCAATTTATG
Found at i:6869 original size:32 final size:32
Alignment explanation
Indices: 6820--6964 Score: 159
Period size: 32 Copynumber: 4.5 Consensus size: 32
6810 TTTGGTCAAA
* * * *
6820 ACCCAAACTGAACCTGAACTCGAATTAAC-CAG
1 ACCCAAATTCAACCCGAACCCGAATTAACAC-G
* * *
6852 ACCCAAATTCAATCTGAACCCGAATTAACATG
1 ACCCAAATTCAACCCGAACCCGAATTAACACG
*
6884 ACCCAAATTCAACCCGGACCCGAATTAACACG
1 ACCCAAATTCAACCCGAACCCGAATTAACACG
* * *
6916 ACCCAAATTCAACCCGAATCTGAATTAAC-CTT
1 ACCCAAATTCAACCCGAACCCGAATTAACAC-G
6948 ACCCAAATTCAACCCGA
1 ACCCAAATTCAACCCGA
6965 CCTGACTTAA
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
31 1 0.01
32 97 0.99
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.18
Consensus pattern (32 bp):
ACCCAAATTCAACCCGAACCCGAATTAACACG
Found at i:6892 original size:15 final size:16
Alignment explanation
Indices: 6842--6929 Score: 58
Period size: 15 Copynumber: 5.5 Consensus size: 16
6832 CCTGAACTCG
6842 AATTAACCA-GACCCA
1 AATTAACCATGACCCA
* *
6857 AATTCAATC-TGAACCCG
1 AATT-AACCATG-ACCCA
6874 AATTAA-CATGACCCA
1 AATTAACCATGACCCA
** *
6889 AATTCAACCCGGACCCG
1 AATT-AACCATGACCCA
*
6906 AATTAA-CACGACCCA
1 AATTAACCATGACCCA
6921 AATTCAACC
1 AATT-AACC
6930 CGAATCTGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
15 23 0.41
16 14 0.25
17 19 0.34
ACGTcount: A:0.41, C:0.33, G:0.09, T:0.17
Consensus pattern (16 bp):
AATTAACCATGACCCA
Found at i:6921 original size:64 final size:64
Alignment explanation
Indices: 6840--6963 Score: 178
Period size: 64 Copynumber: 1.9 Consensus size: 64
6830 AACCTGAACT
* *
6840 CGAATTAACCAGACCCAAATTCAATCTGAACCCGAATTAACATGACCCAAATTCAACCCGGACC
1 CGAATTAACCAGACCCAAATTCAACCCGAACCCGAATTAACATGACCCAAATTCAACCCGGACC
* * * *
6904 CGAATTAA-CACGACCCAAATTCAACCCGAATCTGAATTAACCTTACCCAAATTCAACCCG
1 CGAATTAACCA-GACCCAAATTCAACCCGAACCCGAATTAACATGACCCAAATTCAACCCG
6964 ACCTGACTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 2 0.04
64 51 0.96
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.19
Consensus pattern (64 bp):
CGAATTAACCAGACCCAAATTCAACCCGAACCCGAATTAACATGACCCAAATTCAACCCGGACC
Found at i:7310 original size:16 final size:16
Alignment explanation
Indices: 7285--7317 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
7275 AAGTTAATGA
*
7285 GCTAATGCCTCAATTG
1 GCTAACGCCTCAATTG
7301 GCTAACGCCTCAATTG
1 GCTAACGCCTCAATTG
7317 G
1 G
7318 GTGGAAGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (16 bp):
GCTAACGCCTCAATTG
Found at i:8363 original size:15 final size:15
Alignment explanation
Indices: 8320--8364 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
8310 TATCATCCAT
*
8320 AATATATCCTTCAAA
1 AATATATCCTTAAAA
*
8335 AATAAATCCTTTAAAA
1 AATATATCC-TTAAAA
*
8351 AATATATTCTTAAA
1 AATATATCCTTAAA
8365 TATCCTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATATCCTTAAAA
Found at i:8587 original size:19 final size:19
Alignment explanation
Indices: 8547--8588 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
8537 TTATTTATTA
*
8547 TTTATTTTAATATTATAAT
1 TTTATTTTAATATTACAAT
*
8566 TTTA-TTTATATATTACATT
1 TTTATTTTA-ATATTACAAT
8585 TTTA
1 TTTA
8589 CTTAAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTTAATATTACAAT
Found at i:10647 original size:6 final size:6
Alignment explanation
Indices: 10636--10671 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
10626 TCAACTTATC
10636 TATCTA TATC-- TATCTA TATCTA TATCTA TA-CTA TAT
1 TATCTA TATCTA TATCTA TATCTA TATCTA TATCTA TAT
10672 TAAAAAGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.15
5 5 0.19
6 18 0.67
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TATCTA
Found at i:10647 original size:10 final size:10
Alignment explanation
Indices: 10632--10658 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
10622 ATCTTCAACT
10632 TATCTATCTA
1 TATCTATCTA
10642 TATCTATCTA
1 TATCTATCTA
10652 TATCTAT
1 TATCTAT
10659 ATCTATACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.52
Consensus pattern (10 bp):
TATCTATCTA
Found at i:10657 original size:16 final size:17
Alignment explanation
Indices: 10636--10671 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
10626 TCAACTTATC
10636 TATCTATATCTAT-CTA
1 TATCTATATCTATACTA
10652 TATCTATATCTATACTA
1 TATCTATATCTATACTA
10669 TAT
1 TAT
10672 TAAAAAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (17 bp):
TATCTATATCTATACTA
Found at i:13281 original size:32 final size:31
Alignment explanation
Indices: 13176--13281 Score: 124
Period size: 32 Copynumber: 3.4 Consensus size: 31
13166 CGGGCTTAAG
* **
13176 TCGGATTCGGGTTAAA-TTGGGTTGGGTTGAT
1 TCGGGTTCGGG-TAAATTTGGGTCAGGTTGAT
*
13207 TCGGGTTCAGGTTAAATTTGGGTCAGGTTGAT
1 TCGGGTTC-GGGTAAATTTGGGTCAGGTTGAT
* *
13239 TCAGGTTCGGGTAAATTTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTAAA-TTTGGGTCAGGTTGAT
13271 TCGGGTTCGGG
1 TCGGGTTCGGG
13282 CTCGGGTTGG
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
31 17 0.27
32 47 0.73
ACGTcount: A:0.17, C:0.09, G:0.37, T:0.37
Consensus pattern (31 bp):
TCGGGTTCGGGTAAATTTGGGTCAGGTTGAT
Found at i:13456 original size:20 final size:20
Alignment explanation
Indices: 13423--13461 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13413 CATAGATGAA
*
13423 ATTTTCATAAATTATTATTT
1 ATTTTCATAAATTAGTATTT
13443 ATTTTCA-AATATTAGTATT
1 ATTTTCATAA-ATTAGTATT
13462 GAATCCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTCATAAATTAGTATTT
Found at i:13500 original size:16 final size:16
Alignment explanation
Indices: 13481--13553 Score: 67
Period size: 16 Copynumber: 4.6 Consensus size: 16
13471 TTTTTTCAGG
*
13481 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGAGTTTT
*
13497 TTCGGATTCGAGTTTT
1 TTCGGGTTCGAGTTTT
* *
13513 ATCGGGTTTC-AGATTT
1 TTCGGG-TTCGAGTTTT
* **
13529 TTCGGGTTTGAACTTT
1 TTCGGGTTCGAGTTTT
13545 TTCGGGTTC
1 TTCGGGTTC
13554 AGACGGATCA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
15 2 0.04
16 40 0.89
17 3 0.07
ACGTcount: A:0.10, C:0.14, G:0.29, T:0.48
Consensus pattern (16 bp):
TTCGGGTTCGAGTTTT
Found at i:18678 original size:31 final size:31
Alignment explanation
Indices: 18643--18708 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
18633 AACTTTATGT
*
18643 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
*
18674 TTTCCAATTGTACCCTTTTTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
18705 TTTC
1 TTTC
18709 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:19092 original size:21 final size:22
Alignment explanation
Indices: 19036--19096 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
19026 TCCATGGGGA
**
19036 GGTTACCAAAATTTCATAGTGT
1 GGTTACCAAAATTTCATAAAGT
19058 GGTTACCAAAATTTCATAAAGT
1 GGTTACCAAAATTTCATAAAGT
19080 GGTTACC-AAATTTCATA
1 GGTTACCAAAATTTCATA
19097 GGATCAGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
21 10 0.27
22 27 0.73
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAAAGT
Found at i:19117 original size:24 final size:22
Alignment explanation
Indices: 18992--19142 Score: 65
Period size: 22 Copynumber: 6.8 Consensus size: 22
18982 GTCTCTATGT
* * *
18992 GGTTATCAAAATTTCATAAGAA
1 GGTTATTAAAATTTCATACGTA
* * ** *
19014 GGTTATTATAATTCCATGGGGA
1 GGTTATTAAAATTTCATACGTA
** *
19036 GGTTACCAAAATTTCATA-GTGT
1 GGTTATTAAAATTTCATACGT-A
** *
19058 GGTTACCAAAATTTCATAAAGT-
1 GGTTATTAAAATTTCAT-ACGTA
** *
19080 GGTTA-CCAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATACG-T-A
* *
19103 GGTTATTAAAATTTCTTACGTT
1 GGTTATTAAAATTTCATACGTA
*
19125 GGTTATTGAAATTTCATA
1 GGTTATTAAAATTTCATA
19143 AGGTGATTAA
Statistics
Matches: 100, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
20 2 0.02
21 12 0.12
22 67 0.67
23 7 0.07
24 12 0.12
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (22 bp):
GGTTATTAAAATTTCATACGTA
Found at i:19320 original size:22 final size:22
Alignment explanation
Indices: 19272--19576 Score: 75
Period size: 22 Copynumber: 13.8 Consensus size: 22
19262 CTTCATCGGG
*
19272 AGGTTATCAAAATTTTATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
*
19294 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
*
19316 AGGTTAT-AAAAGTCTCAATTTCAT-A
1 AGGTTATCAAAA-TTTC-A--T-ATGA
* * *
19341 AGGAGTACCAAAATTTGATA-GA
1 AGG-TTATCAAAATTTCATATGA
* *
19363 AGATTATC-AAATCTCATA-G-
1 AGGTTATCAAAATTTCATATGA
* * **
19382 AGTGATTATCGAAATTTTATAAAAA
1 AG-G-TTATCAAAATTTCAT-ATGA
19407 TAGGATTATCAAAATTT-ATATGA
1 -AGG-TTATCAAAATTTCATATGA
**
19430 AAATTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
** * * *
19452 TTGTTATCAAGATTTCA-AAGCG
1 AGGTTATCAAAATTTCATATG-A
*
19474 AGGTTATCAAAATTACATAATG-
1 AGGTTATCAAAATTTCAT-ATGA
* *
19496 TGATTATC-AAATTTCATA-GA
1 AGGTTATCAAAATTTCATATGA
* ** * *
19516 GGGGCAACAAAATTT--TATAA
1 AGGTTATCAAAATTTCATATGA
*
19536 AGATGTTATCAAAATTTCATA-AA
1 AG--GTTATCAAAATTTCATATGA
*
19559 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
19577 AAATGTGATT
Statistics
Matches: 207, Mismatches: 46, Indels: 60
0.66 0.15 0.19
Matches are distributed among these distances:
19 5 0.02
20 16 0.08
21 41 0.20
22 97 0.47
23 9 0.04
24 8 0.04
25 19 0.09
26 8 0.04
27 4 0.02
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:19415 original size:25 final size:26
Alignment explanation
Indices: 19385--19433 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
19375 CTCATAGAGT
*
19385 GATTATCGAAATTT-TATAAAAATAG
1 GATTATCAAAATTTATATAAAAATAG
*
19410 GATTATCAAAATTTATATGAAAAT
1 GATTATCAAAATTTATATAAAAAT
19434 TATCAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (26 bp):
GATTATCAAAATTTATATAAAAATAG
Found at i:19513 original size:21 final size:22
Alignment explanation
Indices: 19410--19600 Score: 98
Period size: 22 Copynumber: 8.8 Consensus size: 22
19400 ATAAAAATAG
*
19410 GATTATCAAAATTT-AT-ATGAA
1 GATTATCAAAATTTCATAATG-T
* *
19431 AATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAATG-T
* *
19454 G-TTATCAAGATTTCA-AA-GC
1 GATTATCAAAATTTCATAATGT
*
19473 GAGGTTATCAAAATTACATAATGT
1 GA--TTATCAAAATTTCATAATGT
* *
19497 GATTATC-AAATTTCATAGAGGG
1 GATTATCAAAATTTCATA-ATGT
* *
19519 GCA--A-CAAAATTTTATAAAGAT
1 G-ATTATCAAAATTTCATAATG-T
* *
19540 G-TTATCAAAATTTCATAAAGA
1 GATTATCAAAATTTCATAATGT
* * *
19561 GGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAATGT
19583 GATTA-CAAAAATTTCATA
1 GATTATC-AAAATTTCATA
19601 GTGGTATTTC
Statistics
Matches: 128, Mismatches: 26, Indels: 31
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.01
20 4 0.03
21 37 0.29
22 78 0.61
23 5 0.04
24 3 0.02
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (22 bp):
GATTATCAAAATTTCATAATGT
Found at i:19527 original size:86 final size:86
Alignment explanation
Indices: 19437--19601 Score: 208
Period size: 86 Copynumber: 1.9 Consensus size: 86
19427 TGAAAATTAT
** * * * *
19437 CAAAATTTCATAGTGTTGTTATCAAGATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATT
19501 ATC-AAATTTCATAGAGGGGCAA
65 A-CAAAATTTCATAGAGGGGCAA
* * *
19523 CAAAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
19588 CAAAAATTTCATAG
66 C-AAAATTTCATAG
19602 TGGTATTTCT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
85 1 0.01
86 53 0.79
87 13 0.19
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (86 bp):
CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CAAAATTTCATAGAGGGGCAA
Found at i:19765 original size:22 final size:22
Alignment explanation
Indices: 19739--20192 Score: 172
Period size: 22 Copynumber: 20.7 Consensus size: 22
19729 TCAGTGAGGA
19739 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
19761 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
19783 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
19805 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
*
19826 AGATCAAAATTTCATAATG-AGGT
1 -TATCAAAATTTCAT-ATGAAGGT
* ** * * *
19849 AATCAAAAAATCATAGGGAGCT
1 TATCAAAATTTCATATGAAGGT
*
19871 TATCAAAATTT-GTAT--A-GT
1 TATCAAAATTTCATATGAAGGT
* * *
19889 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
19911 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * * *
19934 TATTAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
19957 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
19979 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
20001 TATCAAAATTTTAAAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
20023 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
** * *
20045 T-TTTAAATTT-TTATAAAGTGGT
1 TATCAAAATTTCATATGAA--GGT
* *
20067 TATCAATATATCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
20089 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
20112 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
20134 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
20156 CT-TCAAAATTCCTTA-GCGAGGT
1 -TATCAAAATTTCATATG-AAGGT
*
20178 TAACAAAATTTCATA
1 TATCAAAATTTCATA
20193 AGTTAAAAGA
Statistics
Matches: 323, Mismatches: 75, Indels: 68
0.69 0.16 0.15
Matches are distributed among these distances:
18 11 0.03
19 3 0.01
20 7 0.02
21 17 0.05
22 210 0.65
23 67 0.21
24 8 0.02
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:19941 original size:23 final size:23
Alignment explanation
Indices: 19910--20013 Score: 104
Period size: 23 Copynumber: 4.6 Consensus size: 23
19900 CATAAGAAAG
19910 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* * *
19933 TTATTAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
* *
19956 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
* * * * *
19978 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
20000 TTATCAAAATTTTA
1 TTATCAAAATTTTA
20014 AAGTGTGATT
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
21 1 0.01
22 29 0.43
23 37 0.55
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:21618 original size:21 final size:22
Alignment explanation
Indices: 21592--21635 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
21582 AAAACTCGGG
21592 ATTACTAAATACCG-TCCCAAA
1 ATTACTAAATACCGCTCCCAAA
**
21613 ATTACTAGCTACCGCTCCCAAA
1 ATTACTAAATACCGCTCCCAAA
21635 A
1 A
21636 GACATTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.39, C:0.32, G:0.07, T:0.23
Consensus pattern (22 bp):
ATTACTAAATACCGCTCCCAAA
Found at i:25991 original size:16 final size:16
Alignment explanation
Indices: 25968--26011 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
25958 CGGGCTCGGG
*
25968 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTAATT
*
25984 TTGGGTTCGGGTAATT
1 TCGGGTTCGGGTAATT
26000 TCGGGTTCGGGT
1 TCGGGTTCGGGT
26012 TTGGGCGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.11, G:0.41, T:0.41
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:27943 original size:3 final size:3
Alignment explanation
Indices: 27937--27976 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
27927 TAAAACAGAG
27937 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
27977 AACATTTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:28121 original size:30 final size:31
Alignment explanation
Indices: 28069--28166 Score: 119
Period size: 31 Copynumber: 3.1 Consensus size: 31
28059 TGTAATATCA
*
28069 CTAAACTTTCAAATTGAGGACATTTTA-CCT
1 CTAAACTTTCAAATTCAGGACATTTTACCCT
*
28099 TTCAAACTTTCAAA-TCAGGACATTTTACCCT
1 CT-AAACTTTCAAATTCAGGACATTTTACCCT
* *
28130 CTAAACTTTTCAAATTACAAGACATTTTACCCC
1 CTAAAC-TTTCAAATT-CAGGACATTTTACCCT
28163 CTAA
1 CTAA
28167 CGACTGGAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
30 17 0.29
31 22 0.38
32 1 0.02
33 18 0.31
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (31 bp):
CTAAACTTTCAAATTCAGGACATTTTACCCT
Found at i:35803 original size:20 final size:21
Alignment explanation
Indices: 35768--35816 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
35758 AAAAAATAAC
* *
35768 AATTATAAAGTAAAGC-AATTA
1 AATTA-AAAATAAAGCAAAGTA
35789 AATTAAAAATAAAGCAAAGTA
1 AATTAAAAATAAAGCAAAGTA
35810 AATTAAA
1 AATTAAA
35817 TCTAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.24
Consensus pattern (21 bp):
AATTAAAAATAAAGCAAAGTA
Found at i:41856 original size:22 final size:23
Alignment explanation
Indices: 41828--41870 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
41818 CCCTCTCCCT
41828 TTCCTTTCTCTTT-CTTCTTTCA
1 TTCCTTTCTCTTTCCTTCTTTCA
*
41850 TTCCTTTCTTTTTCCTTCTTT
1 TTCCTTTCTCTTTCCTTCTTT
41871 TTCTTAGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (23 bp):
TTCCTTTCTCTTTCCTTCTTTCA
Found at i:41957 original size:19 final size:20
Alignment explanation
Indices: 41933--41970 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41923 GGCTATCTAC
*
41933 AATACCC-AATTTTATTTGT
1 AATACCCAAATTTCATTTGT
41952 AATACCCAAATTTCATTTG
1 AATACCCAAATTTCATTTG
41971 ACAAAGCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.42
Consensus pattern (20 bp):
AATACCCAAATTTCATTTGT
Found at i:42109 original size:24 final size:24
Alignment explanation
Indices: 42085--42130 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
42075 TAATCATTGT
*
42085 TTTTATTTTAT-TTTTTAATTATG
1 TTTTATTTTATGCTTTTAATTATG
*
42108 TTTTGTTTTATGCTTTTAATTAT
1 TTTTATTTTATGCTTTTAATTAT
42131 AACTAGTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.72
Consensus pattern (24 bp):
TTTTATTTTATGCTTTTAATTATG
Done.