Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007167.1 Corchorus capsularis cultivar CVL-1 contig07188, 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: 40172
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:2972 original size:3 final size:3
Alignment explanation
Indices: 2964--3019 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
2954 AGCCGACATT
2964 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3012 TTC TTC TT
1 TTC TTC TT
3020 TAGTTACTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:11853 original size:22 final size:22
Alignment explanation
Indices: 11811--11854 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11801 TATTCATACG
*
11811 AAATTATGATAACTTTCCTATT
1 AAATTATGATAACTTACCTATT
11833 AAATTATGATAA-TTACACTATT
1 AAATTATGATAACTTAC-CTATT
11855 TTTGACGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTATGATAACTTACCTATT
Found at i:11884 original size:62 final size:62
Alignment explanation
Indices: 11810--11961 Score: 232
Period size: 62 Copynumber: 2.5 Consensus size: 62
11800 ATATTCATAC
* * * *
11810 GAAATTATGATAACTTTCCTATTAAATTATGATAATTACACTATTTTTGACGACGTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTTGACGACGTCCTTAT
* * *
11872 GAAATTTTGATAACCTTGCTATGAAATTATAATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTTGACGACGTCCTTAT
*
11934 AAAATTTTGATAACCTTCCTATGAAATT
1 GAAATTTTGATAACCTTCCTATGAAATT
11962 TCAATAACGA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 81 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTTGACGACGTCCTTAT
Found at i:11960 original size:22 final size:22
Alignment explanation
Indices: 11935--12507 Score: 260
Period size: 22 Copynumber: 26.5 Consensus size: 22
11925 CGTCCTTATA
11935 AAATTTTGATAACCTTCCTATG
1 AAATTTTGATAACCTTCCTATG
** ** *
11957 AAATTTCAATAACGATACTATG
1 AAATTTTGATAACCTTCCTATG
* * * **
11979 GAATTTCGAGAACCTTTTTA-G
1 AAATTTTGATAACCTTCCTATG
* ** *
12000 AATTTTTTTTAACCTTCTTATG
1 AAATTTTGATAACCTTCCTATG
* *
12022 AAATTTT-ATTAACCTCCCTAAG
1 AAATTTTGA-TAACCTTCCTATG
* **
12044 GAATTTTGAGGACC-TCACTATG
1 AAATTTTGATAACCTTC-CTATG
* * *
12066 AAGTTGTGATAA-CTTCCAAATG
1 AAATTTTGATAACCTTCC-TATG
**
12088 AAATTTTGATAACCAACACTAT-
1 AAATTTTGATAACCTTC-CTATG
*
12110 AAGATGTTGATAACC-TCCATATG
1 AA-ATTTTGATAACCTTCC-TATG
* * *
12133 ATATATTGATAAGCACGT--TATG
1 AAATTTTGATAA-C-CTTCCTATG
* * *
12155 AAAATTTAAAAACC-TCCATATG
1 AAATTTTGATAACCTTCC-TATG
* * * * *
12177 -AATTGTCAGTAATC-ACACTCTG
1 AAATTTTGA-TAACCTTC-CTATG
* * *
12199 AAATTTTGATAATCATACTATG
1 AAATTTTGATAACCTTCCTATG
*
12221 AAATTGTGATAACC-TCGCTATG
1 AAATTTTGATAACCTTC-CTATG
*
12243 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGAT-AACCTTCCTATG
* * *
12266 AAATTTTGATAAATCTCCCTATA
1 AAATTTTGAT-AACCTTCCTATG
*
12289 AAATTTTGATAACC--AC-ATG
1 AAATTTTGATAACCTTCCTATG
* *
12308 AAATCTTGATAA-----CTA-C
1 AAATTTTGATAACCTTCCTATG
*
12324 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTTCCTATG
**
12346 ATTTTTTGATAACC-TCACTATG
1 AAATTTTGATAACCTTC-CTATG
* * * *
12368 AAATTTTGTTAATCTCCCTATA
1 AAATTTTGATAACCTTCCTATG
* * *
12390 AAATTTTGATCTA-CATACTATG
1 AAATTTTGAT-AACCTTCCTATG
*
12412 AAATTTTGATAACCTTCTTATG
1 AAATTTTGATAACCTTCCTATG
**
12434 AAATTTTGATAACCTTTTTATG
1 AAATTTTGATAACCTTCCTATG
*
12456 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTTCCTATG
* *
12478 AAATTTTAATATCC-TCCT-TG
1 AAATTTTGATAACCTTCCTATG
12498 AAATTTTGAT
1 AAATTTTGAT
12508 TACTCTATAA
Statistics
Matches: 415, Mismatches: 101, Indels: 72
0.71 0.17 0.12
Matches are distributed among these distances:
16 12 0.03
17 1 0.00
19 14 0.03
20 13 0.03
21 33 0.08
22 271 0.65
23 66 0.16
24 4 0.01
25 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTTCCTATG
Found at i:12121 original size:45 final size:45
Alignment explanation
Indices: 12059--12144 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
12049 TTGAGGACCT
* * *
12059 CACTATGAAGTTGTGATAACTTCCAAATGAAATTTTGATAACCAA
1 CACTATGAAGATGTGATAACCTCCAAATGAAATATTGATAACCAA
* *
12104 CACTAT-AAGATGTTGATAACCTCCATATGATATATTGATAA
1 CACTATGAAGATG-TGATAACCTCCAAATGAAATATTGATAA
12145 GCACGTTATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 5 0.14
45 30 0.86
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (45 bp):
CACTATGAAGATGTGATAACCTCCAAATGAAATATTGATAACCAA
Found at i:12332 original size:16 final size:17
Alignment explanation
Indices: 12288--12337 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 17
12278 ATCTCCCTAT
12288 AAAATTTTGATAACCAC
1 AAAATTTTGATAACCAC
* *
12305 ATGAAATCTTGATAACTAC
1 A--AAATTTTGATAACCAC
12324 -AAATTTTGATAACC
1 AAAATTTTGATAACC
12338 TCCCTATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
19 14 0.52
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (17 bp):
AAAATTTTGATAACCAC
Found at i:12387 original size:44 final size:43
Alignment explanation
Indices: 11935--12507 Score: 287
Period size: 44 Copynumber: 13.2 Consensus size: 43
11925 CGTCCTTATA
* ** *
11935 AAATTTTGATAACCTTCCTATGAAATTTCAATAACGATACTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAAC-CTACTATG
* * * *** * ** *
11979 GAATTTCGAGAACCTTTTTA-GAATTTTTTTTAACCTTCTTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTAC-TATG
* * **
12022 AAATTTT-ATTAACCTCCCTAAGGAATTTTGAGGACCTCACTATG
1 AAATTTTGA-TAACCTCCCTATGAAATTTTGATAACCT-ACTATG
* * * ** *
12066 AAGTTGTGATAACTTCCAAATGAAATTTTGATAACCAACACTAT-
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACC--TACTATG
* * * * *
12110 AAGATGTTGATAACCTCCATATGATATATTGATAAGC-ACGTTATG
1 AA-ATTTTGATAACCTCCCTATGAAATTTTGATAACCTAC--TATG
* * * * * * *
12155 AAAATTTAAAAACCTCCATATG-AATTGTCAGTAATCAC-ACTCTG
1 AAATTTTGATAACCTCCCTATGAAATTTTGA-TAA-C-CTACTATG
* * * *
12199 AAATTTTGATAATCAT-ACTATGAAATTGTGATAACCTCGCTATG
1 AAATTTTGATAA-CCTCCCTATGAAATTTTGATAACCT-ACTATG
* * * * *
12243 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAATCTCCCTATA
1 AAATTTTGAT-AACCTCCCTATGAAATTTTGAT-AACCT-ACTATG
* *
12289 AAATTTTGATAA-C-CAC-ATGAAATCTTGATAA-CTAC----
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTACTATG
**
12324 AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCACTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCT-ACTATG
* * * * *
12368 AAATTTTGTTAATCTCCCTATAAAATTTTGATCTACATACTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGAT-AACCTACTATG
* * **
12412 AAATTTTGATAACCTTCTTATGAAATTTTGATAACCTTTTTATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACC-TACTATG
* * * * *
12456 AAATTTTGATAACCTTCATATGAAATTTTAATATCCTCCT-TG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTACTATG
12498 AAATTTTGAT
1 AAATTTTGAT
12508 TACTCTATAA
Statistics
Matches: 399, Mismatches: 98, Indels: 66
0.71 0.17 0.12
Matches are distributed among these distances:
35 12 0.03
36 1 0.00
37 2 0.01
38 12 0.03
39 3 0.01
40 4 0.01
41 2 0.01
42 29 0.07
43 36 0.09
44 212 0.53
45 64 0.16
46 22 0.06
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (43 bp):
AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTACTATG
Found at i:12638 original size:22 final size:22
Alignment explanation
Indices: 12613--12733 Score: 86
Period size: 22 Copynumber: 5.5 Consensus size: 22
12603 AATCATATTT
12613 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* *
12635 TGAAATTTTGATAACCTCTCTA
1 TGAAAATTTGATAACCTCTTTA
* * *
12657 T-AAAATTTTGTTGATCC-CTCTA
1 TGAAAA-TTTGAT-AACCTCTTTA
* * * *
12679 TGAAATTTTGATAATCACATTA
1 TGAAAATTTGATAACCTCTTTA
* * *
12701 TGTAATTTTGATAACCTCGCTT-
1 TGAAAATTTGATAACCTC-TTTA
12723 TGAAAATTTGA
1 TGAAAATTTGA
12734 AATTGGACCC
Statistics
Matches: 77, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
21 5 0.06
22 64 0.83
23 8 0.10
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:12708 original size:44 final size:44
Alignment explanation
Indices: 12588--12733 Score: 134
Period size: 44 Copynumber: 3.3 Consensus size: 44
12578 AGAAATACCA
* * * *
12588 CTATGAAATTTTGGTAATCATATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * * * * *
12632 TTATGAAATTTTGATAACCTC-TCTATAAAATTTTGTTGATCC-CT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGAT-AACCTCT
* *
12676 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* *
12720 CTTTGAAAATTTGA
1 CTATGAAATTTTGA
12734 AATTGGACCC
Statistics
Matches: 78, Mismatches: 20, Indels: 8
0.74 0.19 0.08
Matches are distributed among these distances:
43 4 0.05
44 70 0.90
45 4 0.05
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
Found at i:14280 original size:22 final size:22
Alignment explanation
Indices: 14255--14300 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
14245 ATTACACTAT
*
14255 TTTTGATGACA-TCCTTATGAAA
1 TTTTGATAACATTCC-TATGAAA
14277 TTTTGATAACATTCCTATGAAA
1 TTTTGATAACATTCCTATGAAA
14299 TT
1 TT
14301 AAGATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (22 bp):
TTTTGATAACATTCCTATGAAA
Found at i:14308 original size:62 final size:62
Alignment explanation
Indices: 14211--14362 Score: 241
Period size: 62 Copynumber: 2.5 Consensus size: 62
14201 ATATTCATAC
* * * *
14211 GAAATTATGATAACATTCCTGTTAAATTATGATAATTACACTATTTTTGATGACATCCTTAT
1 GAAATTTTGATAACATTCCTATGAAATTAAGATAATTACACTATTTTTGATGACATCCTTAT
* *
14273 GAAATTTTGATAACATTCCTATGAAATTAAGATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAACATTCCTATGAAATTAAGATAATTACACTATTTTTGATGACATCCTTAT
*
14335 GAAATTTTGATAACCTTCCTATGAAATT
1 GAAATTTTGATAACATTCCTATGAAATT
14363 TCAATAACGA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 83 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (62 bp):
GAAATTTTGATAACATTCCTATGAAATTAAGATAATTACACTATTTTTGATGACATCCTTAT
Found at i:14357 original size:22 final size:22
Alignment explanation
Indices: 14332--14934 Score: 209
Period size: 22 Copynumber: 27.9 Consensus size: 22
14322 ATGACGTCCT
14332 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
** ** *
14354 TATGAAATTTCAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
14376 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** * *
14398 TATAAAATTTTTTTTAGCCTTCT
1 TATGAAA-TTTTGATAACCTTCC
* *
14421 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
14443 TAAGGAATTTTGA-AGACC-TCAC
1 TATGAAATTTTGATA-ACCTTC-C
*
14465 TATGAAATTTTGTTAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
* **
14486 AAATGAAATTTTGATAACCAACAC
1 -TATGAAATTTTGATAACCTTC-C
*
14510 TAT-AAGATGTTGATAACC-TCC
1 TATGAA-ATTTTGATAACCTTCC
* * * *
14531 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* *
14554 TATGAAAATTTGAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
14575 ATATG-AATTGTCAGTAATC-ACAC
1 -TATGAAATTTTGA-TAACCTTC-C
* *
14598 TATGAAATTGTGATAACCTTGC
1 TATGAAATTTTGATAACCTTCC
** *
14620 TATGAAATTTTGATAAAATTTCT
1 TATGAAATTTTGAT-AACCTTCC
* * *
14643 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCTTCC
*
14666 TATAAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
14687 TTATGAAATCTTAATAA-----C
1 -TATGAAATTTTGATAACCTTCC
* *
14705 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** * *
14726 TATGATTTTTTGATAA-ATTCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
14748 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
14770 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * ***
14792 TCTGAAATTTTGA-AAACTAAAT
1 TATGAAATTTTGATAACCT-TCC
*
14814 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
14836 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
14857 --TGAAATTTTGATTA-CTTCA
1 TATGAAATTTTGATAACCTTCC
* * *
14876 TAATAAAAGTTTAATAACCTTCC
1 T-ATGAAATTTTGATAACCTTCC
* * *
14899 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
14916 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
14935 CCCCAAAAAT
Statistics
Matches: 421, Mismatches: 120, Indels: 80
0.68 0.19 0.13
Matches are distributed among these distances:
16 10 0.02
17 12 0.03
18 4 0.01
19 15 0.04
20 1 0.00
21 25 0.06
22 267 0.63
23 86 0.20
24 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:14640 original size:11 final size:11
Alignment explanation
Indices: 14624--14659 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
14614 CCTTGCTATG
14624 AAATTTTGATA
1 AAATTTTGATA
*
14635 AAATTTCTTATA
1 AAATTT-TGATA
14647 AAATTTTGATA
1 AAATTTTGATA
14658 AA
1 AA
14660 TCTCCCTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (11 bp):
AAATTTTGATA
Found at i:14893 original size:63 final size:65
Alignment explanation
Indices: 14770--14897 Score: 152
Period size: 63 Copynumber: 2.0 Consensus size: 65
14760 ATCTACATAC
* * * *
14770 TATGAAATTTTGATAACCCTCTTCTGAAATTTTGAAAACTAAATTATGAAATTTTGATAACCTTC
1 TATGAAATTTTGATAACCCTC-TCTGAAATTTTGAAAACTAAATAATAAAAGTTTAATAACCTTC
14835 A
65 A
* ** **
14836 TATGAAATTTTGAT-ATCCTC-CTGAAATTTTGATTACTTCATAATAAAAGTTTAATAACCTTC
1 TATGAAATTTTGATAACCCTCTCTGAAATTTTGAAAACTAAATAATAAAAGTTTAATAACCTTC
14898 CTAATTTGGT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
63 34 0.64
65 5 0.09
66 14 0.26
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.41
Consensus pattern (65 bp):
TATGAAATTTTGATAACCCTCTCTGAAATTTTGAAAACTAAATAATAAAAGTTTAATAACCTTCA
Found at i:15023 original size:22 final size:22
Alignment explanation
Indices: 14974--15094 Score: 100
Period size: 22 Copynumber: 5.5 Consensus size: 22
14964 AATCACATTT
* * *
14974 TGAAAATTTGATAACCTTTTTA
1 TGAAATTTTGATAACCTCTCTA
14996 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
15018 TCAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
15040 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * * *
15062 TGTAATTTTGATAACATCGCTT
1 TGAAATTTTGATAACCTCTCTA
*
15084 TAAAATTTTGA
1 TGAAATTTTGA
15095 AATTGGACCA
Statistics
Matches: 77, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
22 76 0.99
23 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:15069 original size:44 final size:44
Alignment explanation
Indices: 14949--15076 Score: 132
Period size: 44 Copynumber: 2.9 Consensus size: 44
14939 AAAAATACCA
* * * **
14949 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTTT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * * *
14993 TTATGAAATTTTGATAACCTC-TCTATCAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCCCT
*
15037 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAAC
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAAC
15077 ATCGCTTTAA
Statistics
Matches: 64, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
43 1 0.02
44 62 0.97
45 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
Found at i:15238 original size:37 final size:37
Alignment explanation
Indices: 15146--15241 Score: 129
Period size: 38 Copynumber: 2.6 Consensus size: 37
15136 ATCTAAGCCC
* *
15146 AAATAGGACGTTGGAGACGAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
** * *
15183 AAATACAACGATTAGAAACAAAGACAAAAGGCAAAATT
1 AAATAGGACG-TTGGAAACAAAGACAAAAAGCAAAATT
15221 AAATAGGACGTTGGAAACAAA
1 AAATAGGACGTTGGAAACAAA
15242 AAGTCAAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 18 0.37
38 31 0.63
ACGTcount: A:0.55, C:0.11, G:0.20, T:0.14
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
Found at i:15555 original size:13 final size:13
Alignment explanation
Indices: 15537--15579 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
15527 ACTTCACATT
15537 ATAATTAGTATAG
1 ATAATTAGTATAG
15550 ATAATTAGTAT--
1 ATAATTAGTATAG
15561 AT-ATTAGTATAG
1 ATAATTAGTATAG
*
15573 ATTATTA
1 ATAATTA
15580 TTATTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.30
11 2 0.07
12 2 0.07
13 15 0.56
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (13 bp):
ATAATTAGTATAG
Found at i:15566 original size:23 final size:23
Alignment explanation
Indices: 15536--15590 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
15526 AACTTCACAT
15536 TATA-ATTAGTATAGATAATTAG
1 TATATATTAGTATAGATAATTAG
* *
15558 TATATATTAGTATAGATTATTAT
1 TATATATTAGTATAGATAATTAG
15581 TATTATATTA
1 TA-TATATTA
15591 TTATTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 4 0.14
23 18 0.62
24 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (23 bp):
TATATATTAGTATAGATAATTAG
Found at i:15581 original size:3 final size:3
Alignment explanation
Indices: 15573--15603 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
15563 ATTAGTATAG
15573 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
15604 CTAAAATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:15592 original size:14 final size:14
Alignment explanation
Indices: 15573--15600 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15563 ATTAGTATAG
15573 ATTATTATTATTAT
1 ATTATTATTATTAT
15587 ATTATTATTATTAT
1 ATTATTATTATTAT
15601 TATCTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTATTATTAT
Found at i:18643 original size:42 final size:42
Alignment explanation
Indices: 18564--18679 Score: 115
Period size: 42 Copynumber: 2.8 Consensus size: 42
18554 CTTCTCGTGC
* * * * * *
18564 AAGGTCAAAATCCAAGTCAAAATCACCCATTAATTATCGGAG
1 AAGGTCAAGATCAAAGTCAAGATCACCTATCAGTTATCGGAG
* * *
18606 AAGGTCAAGATCAAAGTCTAGATCGCCTATCAGTTATCGGCG
1 AAGGTCAAGATCAAAGTCAAGATCACCTATCAGTTATCGGAG
** * *
18648 AAGGTTGAGGTCCAAGTCAAGATCACCTATCA
1 AAGGTCAAGATCAAAGTCAAGATCACCTATCA
18680 ACTATAGACG
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
AAGGTCAAGATCAAAGTCAAGATCACCTATCAGTTATCGGAG
Found at i:23355 original size:30 final size:31
Alignment explanation
Indices: 23307--23364 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
23297 ATGTTTTTCG
23307 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCTTATTTTTAAAACATATTTCCA
23338 ATTGTACCCTT-TTTTTAAAACATATTT
1 ATTGTACCCTTATTTTTAAAACATATTT
23365 ATAAATTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTCCA
Found at i:23372 original size:31 final size:31
Alignment explanation
Indices: 23307--23373 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
23297 ATGTTTTTCG
*
23307 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCTTATTTTTAAAACATATTTCAA
*
23338 ATTGTACCCTT-TTTTTAAAACATATTTATAA
1 ATTGTACCCTTATTTTTAAAACATATTT-CAA
23369 ATTGT
1 ATTGT
23374 CATTACTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTCAA
Found at i:24465 original size:22 final size:21
Alignment explanation
Indices: 24440--24905 Score: 137
Period size: 22 Copynumber: 21.0 Consensus size: 21
24430 TGATCCTTAT
24440 AATTTCATGAGGAAGTTATCAA
1 AATTTCAT-AGGAAGTTATCAA
* ** *
24462 AATTCCATAGCGTGGTTACCAA
1 AATTTCATAG-GAAGTTATCAA
24484 AATTTCATATGGAAGTTATCAA
1 AATTTCATA-GGAAGTTATCAA
*
24506 AATTTCATGGGAAGGTTATCAA
1 AATTTCATAGGAA-GTTATCAA
* * **
24528 AATATCATAATGTGGTTA-CAAA
1 AATTTCAT-AGGAAGTTATC-AA
*
24550 AATTTCATAGGATCAGGTTATTAA
1 AATTTCATAGGA--A-GTTATCAA
* **
24574 AATTTCTTAGGAAGGTTATTGA
1 AATTTCATAGGAA-GTTATCAA
24596 AATTTCAGT-GTG--GTTATCAA
1 AATTTCA-TAG-GAAGTTATCAA
** **
24616 AATTTTTTAGTGTGGTTATCAA
1 AATTTCATAG-GAAGTTATCAA
** * *
24638 CTTTTCATATGAAGGTTATAAAA
1 AATTTCATAGGAA-GTTAT-CAA
* * * *
24661 GTCTCAATTTTATAAGGAG-TACCAA
1 -----AATTTCATAGGAAGTTATCAA
* *
24686 AATTTGATA-GAAGGTAATC-A
1 AATTTCATAGGAA-GTTATCAA
* * *
24706 AATCTCATA-GAGTGATTATCAG
1 AATTTCATAGGA-AG-TTATCAA
24728 AATTTCATAGAGATCAGATTATCAA
1 AATTTCATAG-GA--AG-TTATCAA
*
24753 AATTT-ATAGGAAGATTATCGA
1 AATTTCATAGGAAG-TTATCAA
**
24774 AATTTCATAGTGTTGTTATCAA
1 AATTTCATAG-GAAGTTATCAA
* *
24796 AATTTCAAAGCAAGGTTATCAA
1 AATTTCATAGGAA-GTTATCAA
*
24818 AATTACATAATGTG-A-TTATCAA
1 AATTTCAT-A-G-GAAGTTATCAA
* * *
24840 AATTTCATA-GAGGGTCAACAA
1 AATTTCATAGGA-AGTTATCAA
* *
24861 AATTTTATAGAGAGGTTATCAA
1 AATTTCATAG-GAAGTTATCAA
* *
24883 AATTTCATAAAGAGGTTATCAA
1 AATTTCAT-AGGAAGTTATCAA
24905 A
1 A
24906 TTTTTGAAAT
Statistics
Matches: 329, Mismatches: 74, Indels: 82
0.68 0.15 0.17
Matches are distributed among these distances:
18 1 0.00
19 3 0.01
20 34 0.10
21 44 0.13
22 182 0.55
23 14 0.04
24 25 0.08
25 15 0.05
26 2 0.01
27 1 0.00
28 8 0.02
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (21 bp):
AATTTCATAGGAAGTTATCAA
Found at i:24512 original size:66 final size:68
Alignment explanation
Indices: 24440--24592 Score: 192
Period size: 66 Copynumber: 2.3 Consensus size: 68
24430 TGATCCTTAT
* *
24440 AATTTCATGAGGAA-GTTATCAAAAT-TCCATAGCGTGGTTACCAAAATTTCATATGGA-A-GTT
1 AATTTCATGAGGAAGGTTATCAAAATAT-CATAACGTGGTTACAAAAATTTCATA-GGACAGGTT
24501 ATCAA
64 ATCAA
*
24506 AATTTCATG-GGAAGGTTATCAAAATATCATAATGTGGTTACAAAAATTTCATAGGATCAGGTTA
1 AATTTCATGAGGAAGGTTATCAAAATATCATAACGTGGTTACAAAAATTTCATAGGA-CAGGTTA
*
24570 TTAA
65 TCAA
*
24574 AATTTC-TTAGGAAGGTTAT
1 AATTTCATGAGGAAGGTTAT
24593 TGAAATTTCA
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
65 7 0.09
66 43 0.57
67 3 0.04
68 23 0.30
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (68 bp):
AATTTCATGAGGAAGGTTATCAAAATATCATAACGTGGTTACAAAAATTTCATAGGACAGGTTAT
CAA
Found at i:24618 original size:66 final size:64
Alignment explanation
Indices: 24440--24620 Score: 163
Period size: 66 Copynumber: 2.7 Consensus size: 64
24430 TGATCCTTAT
**
24440 AATTTCATGAGGAA-GTTATCAAAAT-TCCATAGCGTGGTTACCAAAATTTCATATGGAAGTTAT
1 AATTTCAT-AGGAAGGTTATCAAAATAT-CA-AATGTGGTTA-CAAAATTTCATATGGAAGTTAT
24503 CAA
62 CAA
*
24506 AATTTCATGGGAAGGTTATCAAAATATCATAATGTGGTTACAAAAATTTCATA-GGATCAGGTTA
1 AATTTCATAGGAAGGTTATCAAAATATCA-AATGTGGTTAC-AAAATTTCATATGGA--A-GTTA
*
24570 TTAA
61 TCAA
* ** * *
24574 AATTTCTTAGGAAGGTTATTGAAATTTC-AGTGTGGTTATCAAAATTT
1 AATTTCATAGGAAGGTTATCAAAATATCAAATGTGGTTA-CAAAATTT
24621 TTTAGTGTGG
Statistics
Matches: 98, Mismatches: 10, Indels: 14
0.80 0.08 0.11
Matches are distributed among these distances:
65 8 0.08
66 57 0.58
67 3 0.03
68 30 0.31
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (64 bp):
AATTTCATAGGAAGGTTATCAAAATATCAAATGTGGTTACAAAATTTCATATGGAAGTTATCAA
Found at i:24864 original size:87 final size:87
Alignment explanation
Indices: 24773--24936 Score: 199
Period size: 87 Copynumber: 1.9 Consensus size: 87
24763 AAGATTATCG
* **
24773 AAATTTCATAGTGTTGTTATCAAAATTTC--AAAGCAAGGTTATCAAA-ATTACATAATGTGATT
1 AAATTTCATAGAGAGGTTATCAAAATTTCATAAAG--AGGTTATCAAATATTACA-AATGTGATT
*
24835 ATCAAAATTTCATAGAGGGTCAACA
63 ACCAAAATTTCATAGAGGGTCAACA
* * **
24860 AAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTTGAAATGTGATTACC
1 AAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATATTACAAATGTGATTACC
*
24925 AAATTTTCATAG
66 AAAATTTCATAG
24937 TGGTATTTCT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
87 58 0.89
88 3 0.05
89 4 0.06
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (87 bp):
AAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATATTACAAATGTGATTACC
AAAATTTCATAGAGGGTCAACA
Found at i:25152 original size:29 final size:29
Alignment explanation
Indices: 25084--25153 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 29
25074 GGCCTAATGT
* * *
25084 CCAAATTGGGTCTAAACTTTTCCAAACTTG
1 CCAAATTGAGTCTAAACCTTT-CAAACATG
*
25114 CTCAATTTGAGTCTAAACCTTT-AAACATG
1 C-CAAATTGAGTCTAAACCTTTCAAACATG
25143 ACCAAATTGAG
1 -CCAAATTGAG
25154 CCTGAACATT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
29 14 0.42
30 2 0.06
31 17 0.52
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.31
Consensus pattern (29 bp):
CCAAATTGAGTCTAAACCTTTCAAACATG
Found at i:26740 original size:78 final size:78
Alignment explanation
Indices: 26568--26796 Score: 333
Period size: 78 Copynumber: 3.0 Consensus size: 78
26558 TTATAGTTTT
* * ***
26568 ACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATA-CCTTTATAA--A-TA-AAAATAC
1 ACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCC-TTATAACTATTATATTTTAC
*
26628 CATTTTACTATTTT
65 CATTTTACTATTTC
* *
26642 ACTCAACTAAAAACTCTATTTTTATATAACTAAACCTAATATCCTTATAACTATTATATTTTACC
1 ACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACC
26707 ATTTTACTATTTC
66 ATTTTACTATTTC
*
26720 ACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATTCTTATAACTATTATATTTTACC
1 ACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACC
26785 ATTTTACTATTT
66 ATTTTACTATTT
26797 TAATTAAAAA
Statistics
Matches: 139, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
74 43 0.31
75 2 0.01
76 1 0.01
77 2 0.01
78 91 0.65
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (78 bp):
ACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACC
ATTTTACTATTTC
Done.