Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021094.1 Corchorus olitorius cultivar O-4 contig21127, 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: 25957
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:166 original size:29 final size:28
Alignment explanation
Indices: 127--182 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
117 GTTATTCCAC
*
127 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAAT
156 GTTCTTGAGCGTTCTTGAAATTAGAAA
1 GTTCTTGAGCGTTCTTGAAATTAGAAA
183 GTTTGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAAT
Found at i:1448 original size:3 final size:3
Alignment explanation
Indices: 1436--1487 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
1426 ACTTATAAAT
1436 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1483 ATA AT
1 ATA AT
1488 TTATAATTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:8005 original size:60 final size:60
Alignment explanation
Indices: 7950--8077 Score: 170
Period size: 60 Copynumber: 2.1 Consensus size: 60
7940 TAAAATGTTT
**
7950 AAATAAGAGCT-CGATCTTTTAATTTGGCCAAATAAGGATTTAATGTTATTGAAAATACTC
1 AAATAAG-GCTCCGATCTTTTAATTTGGCCAAATAAGGACGTAATGTTATTGAAAATACTC
* * * *
8010 AAATAAGGGTCCGGTCTTTTAATTTGGCCAAATAAGGACGTAATGTT-TTCCAAAATGCTC
1 AAATAAGGCTCCGATCTTTTAATTTGGCCAAATAAGGACGTAATGTTATT-GAAAATACTC
8070 AAATAAGG
1 AAATAAGG
8078 GCCTGTCATC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
59 4 0.07
60 56 0.93
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (60 bp):
AAATAAGGCTCCGATCTTTTAATTTGGCCAAATAAGGACGTAATGTTATTGAAAATACTC
Found at i:8078 original size:60 final size:60
Alignment explanation
Indices: 7964--8078 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
7954 AAGAGCTCGA
** *
7964 TCTTTTAATTTGGCCAAATAAGGATTTAATGTTATTGAAAATACTCAAATAAGGGTCCGG
1 TCTTTTAATTTGGCCAAATAAGGACGTAATGTTATTCAAAATACTCAAATAAGGGTCCGG
*
8024 TCTTTTAATTTGGCCAAATAAGGACGTAATGTT-TTCCAAAATGCTCAAATAAGGG
1 TCTTTTAATTTGGCCAAATAAGGACGTAATGTTATT-CAAAATACTCAAATAAGGG
8079 CCTGTCATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 2 0.04
60 48 0.96
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (60 bp):
TCTTTTAATTTGGCCAAATAAGGACGTAATGTTATTCAAAATACTCAAATAAGGGTCCGG
Found at i:8593 original size:12 final size:12
Alignment explanation
Indices: 8576--8605 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
8566 GCAACATCGA
8576 TCGAATATAAGT
1 TCGAATATAAGT
8588 TCGAATATAAGT
1 TCGAATATAAGT
*
8600 TTGAAT
1 TCGAAT
8606 TATTATTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (12 bp):
TCGAATATAAGT
Found at i:9837 original size:34 final size:35
Alignment explanation
Indices: 9809--9876 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
9799 TTTGGGTGTT
9809 TTAAGTATATGTTCTCCTTCTACTTTT-GGTACTC
1 TTAAGTATATGTTCTCCTTCTACTTTTGGGTACTC
9843 TTAAGTATATGTTCTCCTTCTACTTTT-GGTACTC
1 TTAAGTATATGTTCTCCTTCTACTTTTGGGTACTC
9877 GAGGCTGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.50
Consensus pattern (35 bp):
TTAAGTATATGTTCTCCTTCTACTTTTGGGTACTC
Found at i:16952 original size:73 final size:73
Alignment explanation
Indices: 16871--17017 Score: 258
Period size: 73 Copynumber: 2.0 Consensus size: 73
16861 ATTTAGTTTT
* * * *
16871 TATTTGTGTATTTGGTTGGTGGATGGTTTATATATGGTAGTTTCTTAGTTTAAGTTGAATTCTCA
1 TATTTGTGTATTCGGTTGATAGATGGTTTATATATGGTAGTTTCTTAGTTTAAGTTGAATTCCCA
16936 TTTAGATG
66 TTTAGATG
16944 TATTTGTGTATTCGGTTGATAGATGGTTTATATATGGTAGTTTCTTAGTTTAAGTTGAATTCCCA
1 TATTTGTGTATTCGGTTGATAGATGGTTTATATATGGTAGTTTCTTAGTTTAAGTTGAATTCCCA
17009 TTTAGATG
66 TTTAGATG
17017 T
1 T
17018 TTGGGCATTT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.22, C:0.05, G:0.23, T:0.50
Consensus pattern (73 bp):
TATTTGTGTATTCGGTTGATAGATGGTTTATATATGGTAGTTTCTTAGTTTAAGTTGAATTCCCA
TTTAGATG
Found at i:21434 original size:324 final size:319
Alignment explanation
Indices: 20920--21966 Score: 1003
Period size: 317 Copynumber: 3.2 Consensus size: 319
20910 AAATTTTTCT
* * *
20920 TCAATTCTTTGCCATAATATTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTCTT
1 TCAATTTTTTGCCAAAATATTCAGAAAAAATATATAATTCAACGCC-AAAAAATTGAAGGCT-TT
**
20985 TCACACTTCTAATGTTGTTTTTCCAATTTTTT-CGAATTTATTTCTAATTAAATCGAAACAAGAA
64 TCACACTTCTAAT-ACGTTTTTCC-ATTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAG-A
* * * *
21049 TCA-AATGCTCGTAAAAACAAATCTTTCAATCCATTGTGGCTGAGATTTAGTTAGATGAATATAG
126 TAATAATGCTCGTAAAAACAAATCCTT-AATCCAATGTGGCTGAGATTTGGTTAGATGAATATAG
*
21113 ATA-TTCAAGGAGTCTTTCTGCCAAAACTCATGCAAAA-TGAGTCGGGGCCCTGAAACGCGTTTT
190 ATATTTCAAGGAGTCTTTCTGCCAAAACTCATGCAAAACTGAGTCGGGTCCC-GAAACGCGTTTT
* * * *
21176 TAGCCAAAAACAATGATGGTTAGTACATGATTT-GG-TCT-AAAAACTGA-ACCGAACAGCTTCT
254 TAGCCAAAAACAATGATGGTTACTACACGATTTCGGATCTCAAAAACTGATA-AGAAAAG-TTCT
*
21237 T-G
317 TCC
* *
21239 TCAATTTTTTG-CAAAATATTCAGAAAAAATATATAGTTCAACGCCAAAAAGATTGACGTGCTTT
1 TCAATTTTTTGCCAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAA-ATTGAAG-GCTTT
** * *
21303 TCACGTTTCTAATACGTTTTTCCATTTTTTCCAAATTAATTAT-TAATTAAATCGAAACAAGATT
64 TCACACTTCTAATACGTTTTTCCATTTTTTCCGAATTTATT-TCTAATTAAATCGAAACAAGA--
*
21367 TAAGATTTAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAA
126 T-A-A--TA-ATGCTCGTAAAAACAAATCCTTA-ATCCAATGTGGCTGAGATTTGGTTAGATGAA
* * * * * *
21432 TATAGATATTTCAAGAAGTCTTTC-ACCAAAAATCATGCAAAATTGAGTCGGGTTTCC-AGAGCG
185 TATAGATATTTCAAGGAGTCTTTCTGCCAAAACTCATGCAAAACTGAGTCGGG-TCCCGA-AACG
* * *
21495 CGTTTATAGCC-AAAACAGTGATGGTTACTACACGATTTCGGCTAAAATTTTGCAAAAACTGATA
248 CGTTTTTAGCCAAAAACAATGATGGTTACTACACGATTTCGG-----A-TCT-CAAAAACTGATA
*
21559 AGAAAAGTTTTTCC
306 AGAAAAGTTCTTCC
* * * *
21573 ACAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAACAATTGAAGGGTTTT
1 TCAATTTTTTGCCAAAATATTCAGAAAAAATATATAATTCAACGCCAAAA-AATTGAA-GGCTTT
* *
21638 TCACACTTCAAATATCGTTTTT-CATTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATA
64 TCACACTTCTAATA-CGTTTTTCCATTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATA
* * *
21702 CA-AATACTCGTAAAAATAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGA
128 -ATAATGCTCGTAAAAACAAATCCTT-AATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGA
* * * * *
21766 TATTTCAAAGAGTTTTTATGCCAAAAAC-CATGCAAAACTGAATCGAGGTCCCGAAATGCGTTTT
191 TATTTCAAGGAGTCTTTCTGCC-AAAACTCATGCAAAACTGAGTCG-GGTCCCGAAACGCGTTTT
* ** *** ** *
21830 TAGCCAAAATCCGTGA--G---CGTACACGATTTCGG--CT-AAAAACTGACCCGAAACTTTTTT
254 TAGCCAAAAACAATGATGGTTAC-TACACGATTTCGGATCTCAAAAACTGATAAGAAA-AGTTCT
*
21887 TAC
317 TCC
* * * *
21890 TCAATTTTTTGCCACAATACTT-ACAAAAAATATATAATTCAACGCTAAAAATATTGAAGGGTTT
1 TCAATTTTTTGCCAAAATA-TTCAGAAAAAATATATAATTCAACGCCAAAAA-ATTGAA-GGCTT
21954 TTCACACTTCTAA
63 TTCACACTTCTAA
21967 AAGCTAATCC
Statistics
Matches: 610, Mismatches: 74, Indels: 90
0.79 0.10 0.12
Matches are distributed among these distances:
316 22 0.04
317 113 0.19
318 55 0.09
319 12 0.02
320 1 0.00
323 2 0.00
324 98 0.16
325 39 0.06
326 15 0.02
328 70 0.11
329 34 0.06
330 15 0.02
332 4 0.01
333 5 0.01
334 25 0.04
335 91 0.15
336 9 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (319 bp):
TCAATTTTTTGCCAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAATTGAAGGCTTTTC
ACACTTCTAATACGTTTTTCCATTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATAATA
ATGCTCGTAAAAACAAATCCTTAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTT
CAAGGAGTCTTTCTGCCAAAACTCATGCAAAACTGAGTCGGGTCCCGAAACGCGTTTTTAGCCAA
AAACAATGATGGTTACTACACGATTTCGGATCTCAAAAACTGATAAGAAAAGTTCTTCC
Found at i:22171 original size:252 final size:253
Alignment explanation
Indices: 21720--22185 Score: 604
Period size: 252 Copynumber: 1.8 Consensus size: 253
21710 CGTAAAAATA
* * * *
21720 AATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAAGAGTTTTTAT
1 AATCCTTAAATCCAATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAAGAATCTTTAT
* * * * * *
21785 GCCAAAAACCATGCAAAACTGAATCGAGGTCCCGAAATGCGTTTTTAGCCAAAATCCGTGAGCGT
66 GCCAAAAACCATACAAAACTGAACCGAGGCCCCGAAATGCGTTTTTAGCCAAAAACCATGAGAGT
* * * * * * *
21850 ACACGATTTCGGCTAAAAACTGACCCGAAACTTTTTTTACTCAATTTTTTGCCACAATACTTAC-
131 ACACGATTTCGACCAAAAACTAAACCGAAACGTTTTTTACGCAATTTTTTGCCAAAATACTTACA
21914 AAAAAATATATAATTCAACGCTAAAAATATTGAAGGGTTTTTCACACTTCTAAAAGCT
196 AAAAAATATATAATTCAACGCTAAAAATATTGAAGGGTTTTTCACACTTCTAAAAGCT
* * * *
21972 AATCCTTAAATCCATTGTGGCTGAAATTTGGTTAGATGAATATAGATGTTTCAAGGAATCTTTCT
1 AATCCTTAAATCCAATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAAGAATCTTTAT
* *
22037 GCCAAAAATCATACAAAACTGAGCCG-GGACCCCGAAATGCGTTTTTAGCCAAAAACCATGATGG
66 GCCAAAAACCATACAAAACTGAACCGAGG-CCCCGAAATGCGTTTTTAGCCAAAAACCATGA--G
* *
22101 TTAGTACATGATTTCGACCAAAAATTAAACCG-AACAGTTTTTT-CGCAATTTTTTG-CAAAATA
128 --AGTACACGATTTCGACCAAAAACTAAACCGAAAC-GTTTTTTACGCAATTTTTTGCCAAAATA
22163 -TT-CAAAAAAATATATAATTCAAC
190 CTTACAAAAAAATATATAATTCAAC
22186 ACCGAAAAGA
Statistics
Matches: 182, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
251 2 0.01
252 109 0.60
253 21 0.12
254 7 0.04
255 14 0.08
256 29 0.16
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (253 bp):
AATCCTTAAATCCAATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAAGAATCTTTAT
GCCAAAAACCATACAAAACTGAACCGAGGCCCCGAAATGCGTTTTTAGCCAAAAACCATGAGAGT
ACACGATTTCGACCAAAAACTAAACCGAAACGTTTTTTACGCAATTTTTTGCCAAAATACTTACA
AAAAAATATATAATTCAACGCTAAAAATATTGAAGGGTTTTTCACACTTCTAAAAGCT
Found at i:22685 original size:899 final size:897
Alignment explanation
Indices: 21076--22867 Score: 2455
Period size: 899 Copynumber: 2.0 Consensus size: 897
21066 CAAATCTTTC
* * *
21076 AATCCATTGTGGCTGAGATTTAGTTAGATGAATATAGATATTCAAGGAGTCTTTCTGCCAAAACT
1 AATCCATTGTGGCTGAAATTTAGTTAGATGAATATAGATATTCAAGGAATCTTTCTGCCAAAAAT
* * * *
21141 CATGCAAAATGAGTCGGGGCCCTGAAACGCGTTTTTAGCCAAAAACAATGATGGTTAGTACATGA
66 CATACAAAATGAGCCGGGACCCCGAAACGCGTTTTTAGCCAAAAACAATGATGGTTAGTACATGA
* * * *
21206 TTTGGTCTAAAAACTGAACCGAACAGCTTCTTGTCAATTTTTTGCAAAATATTCAGAAAAAATAT
131 TTTCGACCAAAAACTAAACCGAACAGCTTCTTGTCAATTTTTTGCAAAATATTCAGAAAAAATAT
* * * *
21271 ATAGTTCAACGCCAAAAAGATTGACGTGCTTTTCACGTTTCTAATACGTTTTTCCATTTTTTCCA
196 ATAATTCAACACCAAAAAGATTGACGAGCTTTTCACG----TAATACCTTTTTCCATTTTTTCCA
* * *
21336 AATTAATTATTAATTAAATCGAAACAAGATTTAAGATTTAGATGCTCGTAAAAACAAATCCTTAT
257 AATTAATTATTAATTAAATC--AACAAGA-TCAAGATTCAGATGCTCATAAAAACAAATCCTTAT
* * *
21401 ATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGAAGTCTTTCACCAAAAATC
319 ATCCAATGTGACTGACATTTGGTTCGATGAATATAGATATTTAAAGAAGTCTTTCACCAAAAATC
* * * *
21466 ATGCAAAATTGAGTCGGGTTTCCAGAGCGCGTTTATAGCCAAAACAGTGATGGTTACTACACGAT
384 ATGCAAAATTGAGTCGGGCTTCCAGAACGCGTTTATAGCCAAAACAGTGATAGTTAATACACGAT
* *
21531 TTCGGCTAAAATTTTGCAAAAACTGATAAGAAAAGTTTTTCCACAATTTTTTGCCACAATACTCA
449 TTCGGCTAAAATTTTGCAAAAACTGATAAGAAAAATTTTTCCACAATTTTTCGCCACAATACTCA
* * *
21596 GAAAAAATATATAATTCAACGCCAAAACAATTGAAGGGTTTTTCACACTTCAAATATCGTTTTTC
514 GAAAAAATATATAATTCAACACCAAAACAATTGAAAGGTTTTTCACACTTCAAATATCGTTTTCC
21661 ATTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATACAAATACTCGTAAAAATAAATCCT
579 ATTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATACAAATACTCGTAAAAATAAATCCT
* * **
21726 TAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAAGAGTTTTTATGCCAAA
644 TAAATCCAATATGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAAGAGACTTTATGCCAAA
* *
21791 AACCATGCAAAACTGAATCGAGGTCC-CGAAATGCGTTTTTAGCCAA-AATCCGTGA-G-CGTAC
709 AACCATGCAAAACTGAATCGAGG-CCTCGAAACGCGTTTTTAGCCAATAA-CCGTGACGTAGTAC
*** * * * *
21852 ACGATTTCGGCTAA-AAACTGACCCGAAACTTTTTTTACTCAATTTTTTGCCACAATACTTACAA
772 ACGATTTCGGCTAAGAAACT-ACCC-AAA-AAATTTTACTCAAATTTTCGCCAAAATACTCACAA
* * *
21916 AAAATATATAATTCAACGCTAAAAATATTGAAGGGTTTTTCACACTTCTAAAAGCTAATCCTTA
834 AAAATATATAATTCAACGCCAAAAAGATGGAAGGGTTTTTCACACTTCTAAAAGCTAATCCTTA
* *
21980 AATCCATTGTGGCTGAAATTTGGTTAGATGAATATAGATGTTTCAAGGAATCTTTCTGCCAAAAA
1 AATCCATTGTGGCTGAAATTTAGTTAGATGAATATAGAT-ATTCAAGGAATCTTTCTGCCAAAAA
* *
22045 TCATACAAAACTGAGCCGGGACCCCGAAATGCGTTTTTAGCCAAAAACCATGATGGTTAGTACAT
65 TCATACAAAA-TGAGCCGGGACCCCGAAACGCGTTTTTAGCCAAAAACAATGATGGTTAGTACAT
* * *
22110 GATTTCGACCAAAAATTAAACCGAACAGTTTTTTCG-CAATTTTTTGCAAAATATTCA-AAAAAA
129 GATTTCGACCAAAAACTAAACCGAACAGCTTCTT-GTCAATTTTTTGCAAAATATTCAGAAAAAA
* *
22173 TATATAATTCAACACCGAAAAGATTGACGAGCTTTTCACG-AATATCCTTTTTCCATTTTTTTCT
193 TATATAATTCAACACCAAAAAGATTGACGAGCTTTTCACGTAATA-CCTTTTTCCA-TTTTTTCC
* *
22237 GAATTAATT-TCTAATTAAATC-A-AA-A-CAAGATTCAGATGCTCATAAACACAAATCCTTATA
256 AAATTAATTAT-TAATTAAATCAACAAGATCAAGATTCAGATGCTCATAAAAACAAATCCTTATA
* * *
22297 TCCAATGTGACTTACATTTGGTTCGATGAATATAGATATTTAAAGGAGTCTTTGTACCAAAAATC
320 TCCAATGTGACTGACATTTGGTTCGATGAATATAGATATTTAAAGAAGTCTTT-CACCAAAAATC
* * * * *
22362 TTGCAAAATTGAGTCGGGGCTT-CGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAATACATG
384 ATGCAAAATTGAGTC-GGGCTTCCAGAACGCGTTTATAGCC-AAAACAGTGATAGTTAATACACG
* * * *
22426 ATTTCGGCTAAAATTTTGCAAAAATTTACT-CGAAAAATTTTTCCTCAATTTTTCGCCACAATAC
447 ATTTCGGCTAAAATTTTGCAAAAACTGA-TAAGAAAAATTTTTCCACAATTTTTCGCCACAATAC
* ** *
22490 TCAGAAAAAATATATAATTCAACACCAAATA-AATTGAAAGGTTTTTTATGCTTCTAATATCGTT
511 TCAGAAAAAATATATAATTCAACACCAAA-ACAATTGAAAGGTTTTTCACACTTCAAATATCGTT
* * * *
22554 TTCCCATTATTTTCTGAATTTATTTTTAATTAAATCGAAACAAGATATAGATGCTCGTAAAAATA
575 TT-CCATT-TTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATACAAATACTCGTAAAAATA
* *
22619 AATCCTTAAATCTAATATGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTTAT
638 AATCCTTAAATCCAATATGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAAGAGACTTTAT
* *
22684 GCCAAAAACCATGCAAAACTGAGTCGAGGCCTCGAAACGCGTTTTTAGCCAATAACCGTTATCGT
703 GCCAAAAACCATGCAAAACTGAATCGAGGCCTCGAAACGCGTTTTTAGCCAATAACCGTGA-CG-
* *
22749 TAGTACACGATTTCGGCTAAGAACCTACCCAAAAAATTTTCCTCAAATTTTCGCCAAAATACTCA
766 TAGTACACGATTTCGGCTAAGAAACTACCCAAAAAATTTTACTCAAATTTTCGCCAAAATACTCA
* * *
22814 TAAAAAATATATAATTCAATGCCAAAAAGATGGAAGGGTTTTTCACGCTTCTAA
831 CAAAAAATATATAATTCAACGCCAAAAAGATGGAAGGGTTTTTCACACTTCTAA
22868 TATCGTTTTT
Statistics
Matches: 782, Mismatches: 86, Indels: 43
0.86 0.09 0.05
Matches are distributed among these distances:
895 79 0.10
896 39 0.05
897 139 0.18
898 10 0.01
899 164 0.21
900 6 0.01
901 83 0.11
902 28 0.04
903 22 0.03
904 41 0.05
905 73 0.09
906 97 0.12
907 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (897 bp):
AATCCATTGTGGCTGAAATTTAGTTAGATGAATATAGATATTCAAGGAATCTTTCTGCCAAAAAT
CATACAAAATGAGCCGGGACCCCGAAACGCGTTTTTAGCCAAAAACAATGATGGTTAGTACATGA
TTTCGACCAAAAACTAAACCGAACAGCTTCTTGTCAATTTTTTGCAAAATATTCAGAAAAAATAT
ATAATTCAACACCAAAAAGATTGACGAGCTTTTCACGTAATACCTTTTTCCATTTTTTCCAAATT
AATTATTAATTAAATCAACAAGATCAAGATTCAGATGCTCATAAAAACAAATCCTTATATCCAAT
GTGACTGACATTTGGTTCGATGAATATAGATATTTAAAGAAGTCTTTCACCAAAAATCATGCAAA
ATTGAGTCGGGCTTCCAGAACGCGTTTATAGCCAAAACAGTGATAGTTAATACACGATTTCGGCT
AAAATTTTGCAAAAACTGATAAGAAAAATTTTTCCACAATTTTTCGCCACAATACTCAGAAAAAA
TATATAATTCAACACCAAAACAATTGAAAGGTTTTTCACACTTCAAATATCGTTTTCCATTTTTT
CTGAATTTATTTCTAATTAAATCGAAACAAGATACAAATACTCGTAAAAATAAATCCTTAAATCC
AATATGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAAGAGACTTTATGCCAAAAACCATG
CAAAACTGAATCGAGGCCTCGAAACGCGTTTTTAGCCAATAACCGTGACGTAGTACACGATTTCG
GCTAAGAAACTACCCAAAAAATTTTACTCAAATTTTCGCCAAAATACTCACAAAAAATATATAAT
TCAACGCCAAAAAGATGGAAGGGTTTTTCACACTTCTAAAAGCTAATCCTTA
Found at i:22985 original size:322 final size:319
Alignment explanation
Indices: 21972--23033 Score: 1133
Period size: 332 Copynumber: 3.3 Consensus size: 319
21962 TCTAAAAGCT
* * * * *
21972 AATCCTTAAATCCATTGTGGCTGAAATTTGGTTAGATGAATATAGATGTTTCAAGGA-ATCTTTC
1 AATCCTTAAATCCAATGTGGCGGACATTTGGTTAGATGAATATAGATATTTCAAGGAGA-CTTTA
* * * * * *
22036 TGCCAAAAATCATACAAAACTGAGCCGGGACCCCGAAATGCGTTTTTAGCCAAAAACCATGATGG
65 TGCCAAAAATCATGCAAAACTGAGTCGGG-CCTCGAAACGCGTTTTTAGCCAAAAACCGTGATAG
* * * * * * * *
22101 TTAGTACATGATTTCGACCAA-AAATTAAACCGAACAGTTTTTTCGCAATTTTTTG-CAAAATAT
129 TTAGTACATGATTTCGGCTAAGAAATT--ACCGAAAAATTTTTCCTCAATTTTTCGCCAAAATAC
* * * * *
22164 TCAAAAAAATATATAATTCAACACCGAAAAGATTGACGAGCTTTTCACG-----AATATCCTTTT
192 TCAAAAAAATATATAATTCAACACCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTT
*
22224 TCCATTTTTTTCTGAATTAATTTCTAATTAAATCA-AAACAAGATTCAGATGCTCATAAACACA
257 TCCATTTTTTTCTGAATTAATTTCTAATTAAAT-AGAAACAAGATTCAGATGCTCATAAAAACA
* * ** * * * *
22287 AATCCTTATATCCAATGTGACTTACATTTGGTTCGATGAATATAGATATTTAAAGGAGTCTTTGT
1 AATCCTTAAATCCAATGTGGCGGACATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTTAT
* * * * *
22352 ACCAAAAATCTTGCAAAATTGAGTCGGGGCTTCGGAACGCGTTTTTAGCCAAAAACCGTGATAGT
66 GCCAAAAATCATGCAAAACTGAGTC-GGGCCTCGAAACGCGTTTTTAGCCAAAAACCGTGATAGT
*
22417 TAATACATGATTTCGGCTAAAATTTTGCAAAAATTTACTCGAAAAATTTTTCCTCAATTTTTCGC
130 TAGTACATGATTTCGGCT--AA----G---AAA-TTAC-CGAAAAATTTTTCCTCAATTTTTCGC
* * * *
22482 CACAATACTCAGAAAAAATATATAATTCAACACCAAATAA-ATTGAAAGGTTTTTTATGCTTCTA
184 CAAAATACTCA-AAAAAATATATAATTCAACACCAAA-AAGATTGAAGGGTTTTTCACGCTTCTA
* * * * *
22546 ATATCGTTTTCCCATTATTTTCTGAATTTATTTTTAATTAAATCGAAACAAGATAT-AGATGCTC
247 ATATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAATTAAATAGAAACAAGAT-TCAGATGCTC
* *
22610 GTAAAAATA
311 ATAAAAACA
* * * *
22619 AATCCTTAAATCTAATATGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTTAT
1 AATCCTTAAATCCAATGTGGCGGACATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTTAT
* * * *
22684 GCCAAAAACCATGCAAAACTGAGTCGAGGCCTCGAAACGCGTTTTTAGCCAATAACCGTTATCGT
66 GCCAAAAATCATGCAAAACTGAGTCG-GGCCTCGAAACGCGTTTTTAGCCAAAAACCGTGATAGT
* ** * * *
22749 TAGTACACGATTTCGGCTAAGAACCTACCCAAAAAATTTTCCTCAAATTTTCGCCAAAATACTCA
130 TAGTACATGATTTCGGCTAAGAAATTACCGAAAAATTTTTCCTCAATTTTTCGCCAAAATACTCA
** *
22814 TAAAAAATATATAATTCAATGCCAAAAAGATGGAAGGGTTTTTCACGCTTCTAATATCGTTTTTT
195 -AAAAAATATATAATTCAACACCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCG-TTTTT
** * *
22879 TAATTTTTTTCTGAATCAATTTCTAATTAAATAGAAACAAGATTCAGATTCTCATAAAAACA
258 CCATTTTTTTCTGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCATAAAAACA
*
22941 AATCCTTAAATCCAATGTGGCAGGA-ATTTGGTTCA-ATGAATATAGATATTTCAAGGAGTCTTT
1 AATCCTTAAATCCAATGTGGC-GGACATTTGGTT-AGATGAATATAGATATTTCAAGGAGACTTT
* **
23004 ACGCCAAAAATCATGCAAATTTGAGTCGGG
64 ATGCCAAAAATCATGCAAAACTGAGTCGGG
23034 ACTAAAAACT
Statistics
Matches: 617, Mismatches: 100, Indels: 54
0.80 0.13 0.07
Matches are distributed among these distances:
315 119 0.19
316 3 0.00
317 2 0.00
320 2 0.00
321 85 0.14
322 135 0.22
323 5 0.01
324 2 0.00
325 23 0.04
326 12 0.02
327 36 0.06
328 2 0.00
330 2 0.00
331 1 0.00
332 187 0.30
333 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (319 bp):
AATCCTTAAATCCAATGTGGCGGACATTTGGTTAGATGAATATAGATATTTCAAGGAGACTTTAT
GCCAAAAATCATGCAAAACTGAGTCGGGCCTCGAAACGCGTTTTTAGCCAAAAACCGTGATAGTT
AGTACATGATTTCGGCTAAGAAATTACCGAAAAATTTTTCCTCAATTTTTCGCCAAAATACTCAA
AAAAATATATAATTCAACACCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA
TTTTTTTCTGAATTAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCATAAAAACA
Done.