Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007907.1 Corchorus capsularis cultivar CVL-1 contig07928, 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: 63923
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:5127 original size:46 final size:46
Alignment explanation
Indices: 5060--5153 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
5050 CTGAATCTGA
*
5060 CCAATAGACCTTGATCTCTGCGGAGAAGGATTAATATGCACATTGC
1 CCAATAGACCATGATCTCTGCGGAGAAGGATTAATATGCACATTGC
*
5106 CCAATAGACCATGATCTCTGCGGAGAAGGATTATTATGCACATTGC
1 CCAATAGACCATGATCTCTGCGGAGAAGGATTAATATGCACATTGC
5152 CC
1 CC
5154 GTTCATCACT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (46 bp):
CCAATAGACCATGATCTCTGCGGAGAAGGATTAATATGCACATTGC
Found at i:6618 original size:60 final size:60
Alignment explanation
Indices: 6520--6637 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
6510 TCAACAATTC
* * *
6520 GGGCCGATTCATTCATTCCAACATCATCTTGACAAACGCTATTAGGGACCTCTATATTTT
1 GGGCAGATTCATTCATTCCAACATCATCTCGACAAACGCTATCAGGGACCTCTATATTTT
* *
6580 GGGCAGATTCATTCA-TCCTAACATCATCTCGACCAACGCTATCATGGACCTCTATATT
1 GGGCAGATTCATTCATTCC-AACATCATCTCGACAAACGCTATCAGGGACCTCTATATT
6638 CATATGATCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 3 0.06
60 49 0.94
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (60 bp):
GGGCAGATTCATTCATTCCAACATCATCTCGACAAACGCTATCAGGGACCTCTATATTTT
Found at i:8415 original size:6 final size:6
Alignment explanation
Indices: 8404--8442 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
8394 ATTAATTTGC
*
8404 TTTAGA TTTAGA TCTAGA TTTAGA TTTAGA TTTA-A TTTA
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTA
8443 CTTTGCTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (6 bp):
TTTAGA
Found at i:8767 original size:33 final size:34
Alignment explanation
Indices: 8722--8788 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
8712 TCCAAGAATT
8722 AGTTTTTATTTTTTCCG-TTTTTTCTAAAAAAAA
1 AGTTTTTATTTTTTCCGATTTTTTCTAAAAAAAA
* *
8755 AGTTTTTCTTTTTTTCGATTTTTTCTAAAAAAAA
1 AGTTTTTATTTTTTCCGATTTTTTCTAAAAAAAA
8789 TATTTGCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 15 0.48
34 16 0.52
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (34 bp):
AGTTTTTATTTTTTCCGATTTTTTCTAAAAAAAA
Found at i:17231 original size:14 final size:12
Alignment explanation
Indices: 17202--17234 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17192 TTAATTCATT
17202 TATATATAATAA
1 TATATATAATAA
17214 TATATGATAATAA
1 TATAT-ATAATAA
17227 -ATATATAA
1 TATATATAA
17235 ACTAATTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 9 0.45
13 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
TATATATAATAA
Found at i:17782 original size:166 final size:168
Alignment explanation
Indices: 17305--17792 Score: 560
Period size: 173 Copynumber: 2.9 Consensus size: 168
17295 TAGTCATTTG
* *
17305 TCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAAAATCAAAAGTTAGGACATT
1 TCAATTGAGAAATGACCAAAAAG-TTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
* *
17370 TAAGTAATCTGCCAAGTAGGCAAAGAC-AATAAAAATTAGTTCTCTAGCTCATCATCAATCCTTG
65 TAAGTAATCTGCCAAGTAGGAAAAGACGAA-AAAAATTAGTTCTCTAGCTCCTCATCAATCCTTG
* * * * *
17434 ATGGGGATCTTTTATTAATTCCTAATTCCATTATTCTATTCAAA
129 GTGGGGATCTTTTAGTAATTCC-AA-T-CA-TACTCCATTAAAA
* *
17478 TCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
1 TCAATTGAGAAATGACCAAAAAG-TTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
* * * ** *
17543 TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAA-AAGTTGTCTAACTCCAAAATCAAGCCTTG
65 TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCC-TCATCAATCCTTG
* *
17607 GTAGGGATCTTTTGGTAATTCC-A-C-TACTCCATTAAAA
129 GTGGGGATCTTTTAGTAATTCCAATCATACTCCATTAAAA
* *
17644 TCAATTGAGAAATGACCAAAAAGTCTAATTTTTTAATCACCTCAAGAATCAAAAGTTAGGGA-AT
1 TCAATTGAGAAATGACCAAAAAGT-TAATTATTTAATCCCCTCAAGAATCAAAAGTTA-GGACAT
* * * * * *
17708 TTAGGTAAT-TGATCATGT-GTGAAAAGACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCCG
64 TTAAGTAATCTG-CCAAGTAG-GAAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCATCAATCCT
*
17771 GGGTGGGGATCTTTTAGTAATT
127 TGGTGGGGATCTTTTAGTAATT
17793 TCCCTATGTG
Statistics
Matches: 270, Mismatches: 38, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
165 4 0.01
166 117 0.43
167 14 0.05
168 1 0.00
171 1 0.00
172 11 0.04
173 120 0.44
174 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (168 bp):
TCAATTGAGAAATGACCAAAAAGTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATTT
AAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAGCTCCTCATCAATCCTTGGT
GGGGATCTTTTAGTAATTCCAATCATACTCCATTAAAA
Found at i:19527 original size:41 final size:41
Alignment explanation
Indices: 19475--19585 Score: 152
Period size: 41 Copynumber: 2.7 Consensus size: 41
19465 AGGGTCGAAT
*
19475 GACTTGGTCTTGAATTGATAATTTAATTCAAGGGTCTT-GAC
1 GACTTGATCTTGAATTGATAATTTAATTCAAGGGT-TTCGAC
* * *
19516 GACTTGATCTTGAATTGATGACTTAATTCAAGGGTTTCGAT
1 GACTTGATCTTGAATTGATAATTTAATTCAAGGGTTTCGAC
**
19557 GACTCAATCTTGAATTGATAATTTAATTC
1 GACTTGATCTTGAATTGATAATTTAATTC
19586 TGTTGCCGCA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 2 0.03
41 59 0.97
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.40
Consensus pattern (41 bp):
GACTTGATCTTGAATTGATAATTTAATTCAAGGGTTTCGAC
Found at i:22090 original size:41 final size:41
Alignment explanation
Indices: 22019--22257 Score: 302
Period size: 41 Copynumber: 5.9 Consensus size: 41
22009 ATTTGATTTG
* **
22019 ATTTGATTCAAGGG--TCGAATGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCG-ATGACTTAATCTTGAATTGATA
* * ** *
22059 ATTTAATTCAAGGGTCTTGACGACTTGGTCTTGAATTGATG
1 ATTTAATTCAAGGGTCTCGATGACTTAATCTTGAATTGATA
* * *
22100 ACTTAATTCAAGGGTTTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTAATCTTGAATTGATA
* ** *
22141 ATTTAATTCAAGGGTCTCCATGACTTTTTCTTAAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTAATCTTGAATTGATA
*
22182 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
1 ATTTAATTCAAGGGTCTCGATGACTTAATCTTGAATTGATA
*
22223 ATTTAATTCAAGGGTCTCGATGACTCAATCTTGAA
1 ATTTAATTCAAGGGTCTCGATGACTTAATCTTGAA
22258 CAAACGAAAA
Statistics
Matches: 173, Mismatches: 24, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
40 13 0.08
41 158 0.91
42 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (41 bp):
ATTTAATTCAAGGGTCTCGATGACTTAATCTTGAATTGATA
Found at i:22178 original size:123 final size:122
Alignment explanation
Indices: 22019--22257 Score: 343
Period size: 123 Copynumber: 2.0 Consensus size: 122
22009 ATTTGATTTG
* * * *
22019 ATTTGATTCAAGGGTCGAATGACTTGGTCTTGAATTGATAATTTAATTCAAGGGTCTTGACGACT
1 ATTTAATTCAAGGGTCCAATGACTTGGTCTTAAATTGATAATTTAATTCAAGGGTCTCGACGACT
*** * *
22084 TGGTCTTGAATTGATGACTTAATTCAAGGGTTTCGATGACTCAATCTTGAATTGATA
66 CAATCTTGAATTGATAACTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
* ** *
22141 ATTTAATTCAAGGGTCTCCATGACTTTTTCTTAAATTGATAATTTAATTCAAGGGTCTCGATGAC
1 ATTTAATTCAAGGGTC-CAATGACTTGGTCTTAAATTGATAATTTAATTCAAGGGTCTCGACGAC
*
22206 TCAATCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAATCTTGAA
65 TCAATCTTGAATTGATAACTTAATTCAAGGGTCTCGATGACTCAATCTTGAA
22258 CAAACGAAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
122 15 0.15
123 87 0.85
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (122 bp):
ATTTAATTCAAGGGTCCAATGACTTGGTCTTAAATTGATAATTTAATTCAAGGGTCTCGACGACT
CAATCTTGAATTGATAACTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATA
Found at i:25227 original size:3 final size:3
Alignment explanation
Indices: 25219--25244 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25209 ATTCAGAATC
25219 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
25245 CTTTTTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:28645 original size:66 final size:66
Alignment explanation
Indices: 28565--28698 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
28555 AGATTCGTAC
28565 AAGCCATATTTTCTCAATTAAATTTAATTTATGGATACTATATATATGAAGTTAAAGACCTAAAT
1 AAGCCATATTTTCTCAATTAAATTTAATTTATGGATACTATATATATGAAGTTAAAGACCTAAAT
28630 A
66 A
28631 AAGCCATATTTTCTCAATTAAATTTAATTTATGGATACTATATATATGAAGTTAAAGACCTAAAT
1 AAGCCATATTTTCTCAATTAAATTTAATTTATGGATACTATATATATGAAGTTAAAGACCTAAAT
28696 A
66 A
28697 AA
1 AA
28699 AAGATGAAGA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.37
Consensus pattern (66 bp):
AAGCCATATTTTCTCAATTAAATTTAATTTATGGATACTATATATATGAAGTTAAAGACCTAAAT
A
Found at i:38485 original size:12 final size:12
Alignment explanation
Indices: 38468--38492 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38458 AACCGTCTTA
38468 AAAAAAAAAAAG
1 AAAAAAAAAAAG
38480 AAAAAAAAAAAG
1 AAAAAAAAAAAG
38492 A
1 A
38493 CAAATAGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:45496 original size:15 final size:16
Alignment explanation
Indices: 45459--45501 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
45449 AAGTTTTATG
*
45459 ATTATAAAT-AATGAT
1 ATTATAATTAAATGAT
45474 ATTATAATTAAAT-AT
1 ATTATAATTAAATGAT
45489 ATTATAATCTAAA
1 ATTATAAT-TAAA
45502 AATAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTATAATTAAATGAT
Found at i:45748 original size:22 final size:22
Alignment explanation
Indices: 45720--45768 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
45710 CAGCTTCCTT
45720 AGATACAGCAGCCCGATACCTC
1 AGATACAGCAGCCCGATACCTC
45742 AGATACAGCAGCCCGATACCTC
1 AGATACAGCAGCCCGATACCTC
45764 AGATA
1 AGATA
45769 GAGAGTAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.33, G:0.18, T:0.14
Consensus pattern (22 bp):
AGATACAGCAGCCCGATACCTC
Found at i:47375 original size:35 final size:35
Alignment explanation
Indices: 47307--48472 Score: 1247
Period size: 35 Copynumber: 33.7 Consensus size: 35
47297 TTCTTACTAA
* * * *
47307 ACTTAATTACCCTGAACTAAGTCGATCAATGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
47342 GCTTGATTACCCTGAATTAAGTT-ATTTATTGACTT
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* * *
47377 ACTTAATTACCCTGGATTTAAGTCGATTACTGACTC
1 ACTTAATTACCCT-GAATTAAGTTGATTACTGACTT
*
47413 ACTTAATTACCCTAAATTAAAGTTGATTACTGAC-T
1 ACTTAATTACCCTGAATT-AAGTTGATTACTGACTT
* *
47448 -C--AATTA-CCTGAATTAAGTTTATTTCTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
47479 ACTTAATTACCCTAAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
47514 ACTCAATTACCCTGAACTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
47549 ACTTAATTACCCTGAATTAAGTT-ACTCATTGAAC-T
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTG-ACTT
* * * *
47584 ACTTAATTAACCTGAATTAAGTT-ACTTATTAACTC
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* *
47619 ACTTAATTACCCTGAAGTAAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAA-TTAAGTTGATTACTGACTT
*
47655 ACTCAATTACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
47690 ACTTAATTACCCTGAATTAAGTTGATTCCCGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
47725 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
47760 ACTCAATTACCCTGAACTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
47795 ACTTAATTACCCTGAATTAAGTT-ACTCATTGAAC-T
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTG-ACTT
* * *
47830 ACTTAATTACCCTGAATTAAGTT-ACTTATTAACTC
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
47865 ACTTAATTACCCTGAATTAAAGTTGATTACTGA-TT
1 ACTTAATTACCCTGAATT-AAGTTGATTACTGACTT
*
47900 CACTCAATTACCCTGAATTAAGTTGATTACTGACTT
1 -ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
47936 ACTTAATTACCCTAAATTAAGTTGATTACCGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * **
47971 ACTTAATTACCATGAACTAAGTTGATTACCAACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
48006 ACTTAATTACCCTGAATTAAGTTAATTACCGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
48041 ACTTAATTACCCTGAATTAAGTTAATTACCGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
48076 ACTTAATTACCCTGAATTAAGTTGATTACCGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
48111 ACTTAATTACCCCGAATTAAGTTGATTACCGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
48146 ACTTAATTACCCTGAATTAAGTTAATTACCGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
48181 ACTTAATTACCCTGAATTAGGTTGATTA-T---TG
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * * *
48212 GCTTAATTACCCTGAATTAAGTTAATTACTAAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * * * * *
48247 TCTTAATTACTCTGAATTAAATTAATAACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * * *
48282 ACTTGATTACCCTGAATTAAGTTAATTATTGACTA
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
48317 ACTTAGTTACTCTGAATTAAGTT-A--CCT-A-TT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* **
48347 GGCTTAATTACCCTGAATTAAGTT-ACCAACTGACTT
1 -ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* ** * *
48383 ACTCAATTACCCTGAATTAAG-CCACTAACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
*
48418 ACTTAATTACCCTGAATTAAGCT-ACTTACT-A---
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
48449 ACTTAATTACCCTGAATTAAGTTG
1 ACTTAATTACCCTGAATTAAGTTG
48473 CTTATTATGA
Statistics
Matches: 980, Mismatches: 117, Indels: 71
0.84 0.10 0.06
Matches are distributed among these distances:
30 14 0.01
31 78 0.08
32 8 0.01
34 17 0.02
35 753 0.77
36 107 0.11
37 3 0.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
Found at i:47965 original size:19 final size:19
Alignment explanation
Indices: 47660--48208 Score: 184
Period size: 16 Copynumber: 31.2 Consensus size: 19
47650 GACTCACTCA
47660 ATTACCCTGAATTAAGTTG
1 ATTACCCTGAATTAAGTTG
* * *
47679 ATTA--CTGACTT-ACTTA
1 ATTACCCTGAATTAAGTTG
47695 ATTACCCTGAATTAAGTTG
1 ATTACCCTGAATTAAGTTG
* * *
47714 ATT-CCC-GACTT-ACTTA
1 ATTACCCTGAATTAAGTTG
47730 ATTACCCTGAATTAAGTTG
1 ATTACCCTGAATTAAGTTG
* * * **
47749 ATTA--CTG-ACTCACTCA
1 ATTACCCTGAATTAAGTTG
*
47765 ATTACCCTGAACTAAGTTG
1 ATTACCCTGAATTAAGTTG
* * * *
47784 ATTA--CTG-ACTCACTTA
1 ATTACCCTGAATTAAGTTG
47800 ATTACCCTGAATTAAGTT-
1 ATTACCCTGAATTAAGTTG
* ** * * *
47818 ACT-CATTGAACT-ACTTA
1 ATTACCCTGAATTAAGTTG
47835 ATTACCCTGAATTAAGTT-
1 ATTACCCTGAATTAAGTTG
* * * * *
47853 ACTTA---TTAACTCACTTA
1 A-TTACCCTGAATTAAGTTG
47870 ATTACCCTGAATTAAAGTTG
1 ATTACCCTGAATT-AAGTTG
* * **
47890 ATTA--CTG-ATTCACTCA
1 ATTACCCTGAATTAAGTTG
47906 ATTACCCTGAATTAAGTTG
1 ATTACCCTGAATTAAGTTG
* * *
47925 ATTA--CTGACTT-ACTTA
1 ATTACCCTGAATTAAGTTG
*
47941 ATTACCCTAAATTAAGTTG
1 ATTACCCTGAATTAAGTTG
* * *
47960 ATTA-CC-GACTT-ACTTA
1 ATTACCCTGAATTAAGTTG
* *
47976 ATTACCATGAACTAAGTTG
1 ATTACCCTGAATTAAGTTG
* *
47995 ATTA-CC--AACTT-ACTTA
1 ATTACCCTGAA-TTAAGTTG
*
48011 ATTACCCTGAATTAAGTTA
1 ATTACCCTGAATTAAGTTG
* * *
48030 ATTA-CC-GACTT-ACTTA
1 ATTACCCTGAATTAAGTTG
*
48046 ATTACCCTGAATTAAGTTA
1 ATTACCCTGAATTAAGTTG
* * *
48065 ATTA-CC-GACTT-ACTTA
1 ATTACCCTGAATTAAGTTG
48081 ATTACCCTGAATTAAGTTG
1 ATTACCCTGAATTAAGTTG
* * *
48100 ATTA-CC-GACTT-ACTTA
1 ATTACCCTGAATTAAGTTG
*
48116 ATTACCCCGAATTAAGTTG
1 ATTACCCTGAATTAAGTTG
* * *
48135 ATTA-CC-GACTT-ACTTA
1 ATTACCCTGAATTAAGTTG
*
48151 ATTACCCTGAATTAAGTTA
1 ATTACCCTGAATTAAGTTG
* * *
48170 ATTA-CC-GACTT-ACTTA
1 ATTACCCTGAATTAAGTTG
*
48186 ATTACCCTGAATTAGGTTG
1 ATTACCCTGAATTAAGTTG
48205 ATTA
1 ATTA
48209 TTGGCTTAAT
Statistics
Matches: 379, Mismatches: 101, Indels: 100
0.65 0.17 0.17
Matches are distributed among these distances:
16 111 0.29
17 74 0.20
18 77 0.20
19 110 0.29
20 7 0.02
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (19 bp):
ATTACCCTGAATTAAGTTG
Found at i:49812 original size:135 final size:134
Alignment explanation
Indices: 49564--49861 Score: 418
Period size: 135 Copynumber: 2.2 Consensus size: 134
49554 GAAAGACTTG
* * * ** *
49564 GAGGGG-AAAACCAACAACTGCTTGGTGTCCAGCCCGGTGCTCTGCCTTTTCAACAAGTTAACTA
1 GAGGGGCAAAACCAACAACTGCTTGGTG-CCAGCACAGTCCTCTGCCCCTTCAACAAGTTAACCA
* *
49628 TCAGGTGAACAACCCACAAGTCATGGCTGAGATTGGTCTCATCGATGAAAGGCTTGGGGGGCAAG
65 TCAGGTGAACAACCAACAAGTCATGGCTGAGATTGGTCTCATCGATGAAAGACTTGGGGGGCAAG
49693 AACTC
130 AACTC
*
49698 GAGGGGCAAAACCAACAACTGCTTGGTGCCAGGCACAGTCCTCTTCCCCTTCAACAAGTTAACCA
1 GAGGGGCAAAACCAACAACTGCTTGGTGCCA-GCACAGTCCTCTGCCCCTTCAACAAGTTAACCA
* * * * *
49763 TCAGGTGAACAATCAACAGGTCATGGCTTAGGTTGGTCTCATCGATGAAAGATTTGGGGGGCAAG
65 TCAGGTGAACAACCAACAAGTCATGGCTGAGATTGGTCTCATCGATGAAAGACTTGGGGGGCAAG
*
49828 GACTC
130 AACTC
* *
49833 GAGGGGCAAAACCAACAGCCGCTTGGTGC
1 GAGGGGCAAAACCAACAACTGCTTGGTGC
49862 TCTGCCTCTA
Statistics
Matches: 145, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
134 9 0.06
135 136 0.94
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.20
Consensus pattern (134 bp):
GAGGGGCAAAACCAACAACTGCTTGGTGCCAGCACAGTCCTCTGCCCCTTCAACAAGTTAACCAT
CAGGTGAACAACCAACAAGTCATGGCTGAGATTGGTCTCATCGATGAAAGACTTGGGGGGCAAGA
ACTC
Done.