Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009320.1 Corchorus capsularis cultivar CVL-1 contig09341, 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: 71047
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1688 original size:850 final size:851
Alignment explanation
Indices: 1--3145 Score: 4972
Period size: 850 Copynumber: 3.7 Consensus size: 851
* * * * * * *
1 ACAAATCAGAAACACATTGATTCTTAAAAGAGTACCT-AGCAGATTCGGCAATCAGTTCATCTGG
1 ACAAATCAGAAACACATTAATTGTGAAAAGGGTA-CTGA-CGGATTTGACAATCAGTTCATCTGG
* * *
65 AACTGAAACAACCTCATTGGCATTGATAAAACCAGTTGAATCCTTCATAGGAGTAAACGTGATTG
64 AACTGAAACAACCTCAATGGCATTGATGAAAGCAGTTGAATCCTTCATAGGAGTAAACGTGATTG
*
130 TAAATGTACAATCTCGCAAGTTAAGAAGATACTTCTTGAGGATTGGGTACTGATATTGTCAAGCT
129 TAAATGTACAATCTCGCAAGTTAAAAAGATACTTCTTGAGGATTGGGTACTGATATTGTCAAGCT
195 TGAAGTTGTGGAGCAAAACATACTTGTAGGCAAAGATGGTAAATATTTTTTTGTTAAAGATCAAT
194 TGAAGTTGTGGAGCAAAACATACTTGTAGGCAAAGATGGTAAATATTTTTTTGTTAAAGATCAAT
* *
260 CCGGTCATTTTTCTGTAGAAGAAATGGAGAGGCACTCAACGTAAACAAGACCGCTTTAATTTAAA
259 CCGGTCATTTTTCAGTAGAAGAAATGGAGAGGCACTCAACGAAAACAAGACCGCTTTAATTTAAA
325 TGTGTAGGTGGCTTCTTGGGGAAAATTCAGCGTGGTTAAATATAGAGGTGAAGGAACATCGGAAG
324 TGTGTAGGTGGCTTCTTGGGGAAAATTCAGCGTGGTTAAATATAGAGGTGAAGGAACATCGGAAG
*
390 ACTA-TTCAAAAGATAATATTTCAAATGGTTCAATTACAACACCAAAGAAAATTAGAGATAAGAT
389 AC-ACTTAAAAAGATAATATTTCAAATGGTTCAATTACAACACCAAAGAAAATTAGAGATAAGAT
* * *
454 AAGGCTACTTACGAACCTGTAAAGCAACATAATAAGCCATTACTGACAGAGCAAATCTAGTAGTG
453 AAGGCTACTTGCGAACCTGTAAAGCAACATAATAAGCCATTACTGACAAAGCAAATCCAGTAGTG
* * *
519 TGGTTTCTGACCAAAATGATAATTATCTCCTTCACATGTTGCAGCAGAAGCAAGACCCATAACAT
518 TGGTTTCTGACCAAAATGATGATTATCTCCTTCACATGTTGCAGCAGAACCAAGGCCCATAACAT
*
584 TCATCCTCACTTTTCGATACCTCCCATGGAATGTATTATAAAATATTTGTATTTGCAAATATGCA
583 TCATCCTCACTTTTCGATACCTCCCATGGAATGTATTATAAAATATTTGTATTGGCAAATATGCA
649 TAATTCAAAATTCTGATAAATGAAATTATTCCTT-AAAAAGA-AACACCTGAAATTTGATTATAG
648 TAATTCAAAATTCTGATAAATGAAATTATTCCTTAAAAAAGAGAACACCTGAAATTTGATTATAG
*
712 TCTAATTACAATCTAATACTAATCAATTTTCCAGTCAAACACAGAAGAGACAGAGACTTATTTTC
713 TCTAATTACAATCTAATACTAATCAATTTTCCAGTCAAACACAGAAGAGA-A-AGACTTATTTCC
777 TAGCGTGTCGTTTTACGAGGTGATCAACGGTCCCCCCATGTTAAGCCTGTAAATGACCTGCTAAC
776 TAGCGTGTCGTTTTACGAGGTGATCAACGGTCCCCCCATGTTAAGCCTGTAAATGACCTGCTAAC
842 CATATACTTCC
841 CATATACTTCC
*
853 ACAAATCAGAAACACATTAATTGTGAAAAGGGTACTGACGGATTTGGCAATCAGTTCATCTGGAA
1 ACAAATCAGAAACACATTAATTGTGAAAAGGGTACTGACGGATTTGACAATCAGTTCATCTGGAA
* *
918 CTGAAACAACCTTAATGGCATTGGTGAAAGCAGTTGAATCCTTCATAGGAGTAAACGTGATTGTA
66 CTGAAACAACCTCAATGGCATTGATGAAAGCAGTTGAATCCTTCATAGGAGTAAACGTGATTGTA
* *
983 AATGAACAATCTCGCAAGTTAAAAAGATACTTCTTGAGGATTGGGTACTGATATTGTCAAGCTTA
131 AATGTACAATCTCGCAAGTTAAAAAGATACTTCTTGAGGATTGGGTACTGATATTGTCAAGCTTG
*
1048 AAGTTGTGGAGCAAAACATACTTGTAGGCAAAGATTGTAAATA-TTTTTTGTTAAAGATCAATCC
196 AAGTTGTGGAGCAAAACATACTTGTAGGCAAAGATGGTAAATATTTTTTTGTTAAAGATCAATCC
1112 GGTCATTTTTCAGTAGAAGAAATGGAGAGGCACTCAACGAAAACAAGACCGCTTTAATTTAAATG
261 GGTCATTTTTCAGTAGAAGAAATGGAGAGGCACTCAACGAAAACAAGACCGCTTTAATTTAAATG
* * *
1177 TGTAGGTGGCTTCTTGGCGAAAATTGAGCATGGTTAAATATAGAGGTGAAGGAACATCGGAAGAC
326 TGTAGGTGGCTTCTTGGGGAAAATTCAGCGTGGTTAAATATAGAGGTGAAGGAACATCGGAAGAC
* *
1242 ACTTAAAAAAATAATATTTCAAATGGTTCAATTACAACACCAAAGAAAATTAGAGAAAAGATAAG
391 ACTTAAAAAGATAATATTTCAAATGGTTCAATTACAACACCAAAGAAAATTAGAGATAAGATAAG
* * *
1307 GCTACTTGGGAACCTGTAAAGCAACATAATAAGCCATTACTGACAAAGCAAATCCAGTAGCGTTG
456 GCTACTTGCGAACCTGTAAAGCAACATAATAAGCCATTACTGACAAAGCAAATCCAGTAGTGTGG
* * * * *
1372 TTTCTGACCAAAATGATGATTATCTACTTCACATGTTGCAGCAGAACCAATGCCCGTAATATTCT
521 TTTCTGACCAAAATGATGATTATCTCCTTCACATGTTGCAGCAGAACCAAGGCCCATAACATTCA
*
1437 TCCTCACTTTTCGATACCTCCCATGGAATGTATTATAAAATATTTGTATTGGCAATTATGCATAA
586 TCCTCACTTTTCGATACCTCCCATGGAATGTATTATAAAATATTTGTATTGGCAAATATGCATAA
* *
1502 TTCAAAATTCTGATAAATGAAATTATTCTTTAAAAAAGAGACACACCTGAAATTTGATTATAGTA
651 TTCAAAATTCTGATAAATGAAATTATTCCTTAAAAAAGAGA-ACACCTGAAATTTGATTATAGTC
* * * *
1567 TAGTTACAATCTAATAATAATCAATTTTCCAGTCAAACACAGAAGAG-TAGACTTATTTCCTAAC
715 TAATTACAATCTAATACTAATCAATTTTCCAGTCAAACACAGAAGAGAAAGACTTATTTCCTAGC
* * * *
1631 GTTTCGTTTTACGAGGTGATCAATGTTCCCCCCATGTTAAGCCTGTAAATGACCTGCTAATCATA
780 GTGTCGTTTTACGAGGTGATCAACGGTCCCCCCATGTTAAGCCTGTAAATGACCTGCTAACCATA
1696 TACTTCC
845 TACTTCC
* * * *
1703 ACAAATCAGAAACACATTAATTGTGAAAAGGGTACTGGCGGATTTGACAATTAATTCATCAGGAA
1 ACAAATCAGAAACACATTAATTGTGAAAAGGGTACTGACGGATTTGACAATCAGTTCATCTGGAA
*
1768 CTGAAACAACCTCAATGGCATTGTTGAAAGCAGTTGAATCCTTCATAGGAGTAAACGTGATTGTA
66 CTGAAACAACCTCAATGGCATTGATGAAAGCAGTTGAATCCTTCATAGGAGTAAACGTGATTGTA
* *
1833 AATGTACAATCTCGCAAGTTAAAAAGATACTTCTTGAGGATTGGGTACTGATATTGTCAAACCTG
131 AATGTACAATCTCGCAAGTTAAAAAGATACTTCTTGAGGATTGGGTACTGATATTGTCAAGCTTG
1898 AAGTTGTGGAGCAAAACATACTTGTAGGCAAAGATGGTAAATATTTTTTTGTTAAAGATCAATCC
196 AAGTTGTGGAGCAAAACATACTTGTAGGCAAAGATGGTAAATATTTTTTTGTTAAAGATCAATCC
* *
1963 GGTCATTTTTCTGTAGAAGAAATGGAGAGGCACTCAACGTAAACAAGACCGCTTTAATTTAAATG
261 GGTCATTTTTCAGTAGAAGAAATGGAGAGGCACTCAACGAAAACAAGACCGCTTTAATTTAAATG
2028 TGTAGGTGGCTTCTTGGGGAAAATTCAGCGTGGTTAAATATAGAGGTGAAGGAACATCGGAAGAC
326 TGTAGGTGGCTTCTTGGGGAAAATTCAGCGTGGTTAAATATAGAGGTGAAGGAACATCGGAAGAC
* * *
2093 TCTTCAAAAGATAATATTTCAAATGGTTCAATTACAACACCATAGAAAATTAGAGATAAGATAAG
391 ACTTAAAAAGATAATATTTCAAATGGTTCAATTACAACACCAAAGAAAATTAGAGATAAGATAAG
* * *
2158 GTTAC-TGCGAACCTGTAAAGCAACATAATAAGCCATTACTGACAGAGCAAATCTAGTAGTGTGG
456 GCTACTTGCGAACCTGTAAAGCAACATAATAAGCCATTACTGACAAAGCAAATCCAGTAGTGTGG
* * * *
2222 TTTCTGACAAAAATGATGATTATCTCCTTCACATGTTGCAGCAGAAACAAGGCACATAGCATTCA
521 TTTCTGACCAAAATGATGATTATCTCCTTCACATGTTGCAGCAGAACCAAGGCCCATAACATTCA
* *
2287 TCCTCACTTTTCGATACCTGCCATGGAATGTATTATTAAATATTTGTATTGGCAAATATGCATAA
586 TCCTCACTTTTCGATACCTCCCATGGAATGTATTATAAAATATTTGTATTGGCAAATATGCATAA
* *
2352 TTCAAAATTCTGATAAATGAAATTATTCCTTAAAGAAGAG-ACACC-----TTTGATTATTGTCT
651 TTCAAAATTCTGATAAATGAAATTATTCCTTAAAAAAGAGAACACCTGAAATTTGATTATAGTCT
* * *
2411 AATTACAATGC-GATACTAAACAATTTTCCAGACAAACACAGAAGAGGCAAAGACTTATTTCCTA
716 AATTACAAT-CTAATACTAATCAATTTTCCAGTCAAACACAGAAGA-G-AAAGACTTATTTCCTA
* * *
2475 GTGTGTCATTTTACGAGTTGATCAACGGTCCCCCCATGTTAAGCCTGTAAATGACCTGCTAACCA
778 GCGTGTCGTTTTACGAGGTGATCAACGGTCCCCCCATGTTAAGCCTGTAAATGACCTGCTAACCA
2540 TATACTTCC
843 TATACTTCC
* * * * *
2549 ACAAATCAGAAACACATTTATTGTGAAAAAGGTACTGGCGAATTTGACATTCAGTTCATCTGGAA
1 ACAAATCAGAAACACATTAATTGTGAAAAGGGTACTGACGGATTTGACAATCAGTTCATCTGGAA
* * * * *
2614 CAGAAACAACCTCAATGGCTTTGAAGAAAGCAGTTGAATACTTCATAGGAGTAAACATGATTGTA
66 CTGAAACAACCTCAATGGCATTGATGAAAGCAGTTGAATCCTTCATAGGAGTAAACGTGATTGTA
* * * *
2679 ACTGTACAATCTCGCAAGTTAAGAAGATACTTCTCGAGGATTGGGTACTG-TAATTGCCAAGCTT
131 AATGTACAATCTCGCAAGTTAAAAAGATACTTCTTGAGGATTGGGTACTGAT-ATTGTCAAGCTT
* * *
2743 GAAGTTATGGAGCAAAACATACTTGTAGGCAAAAATGGTAAATA-TTTTTTGTTAAAGATTAATC
195 GAAGTTGTGGAGCAAAACATACTTGTAGGCAAAGATGGTAAATATTTTTTTGTTAAAGATCAATC
* * * * *
2807 CGGTCATTTTTCACTAGAAGAAATGGAGACGCAGTCATCGAAAACCAGACCGCTTTAATTTAAAT
260 CGGTCATTTTTCAGTAGAAGAAATGGAGAGGCACTCAACGAAAACAAGACCGCTTTAATTTAAAT
* * ** * *
2872 GTGTAGATGACTTCTTGGGGAAAAACCAGTGTGGTTAAATATAAAGGTGAAGGAACATCGGAAGA
325 GTGTAGGTGGCTTCTTGGGGAAAATTCAGCGTGGTTAAATATAGAGGTGAAGGAACATCGGAAGA
* * * **
2937 CTCTTCAAAAAGATAATATTTCAAATGATTCAATTACAAAACCAAAGAAAATTAGAGCCAAGATA
390 CACTT-AAAAAGATAATATTTCAAATGGTTCAATTACAACACCAAAGAAAATTAGAGATAAGATA
* *
3002 AGCCTACTTGCGAACCTGTAAAGCAACATAATAAGCCATTGCTGACAAAGCAAATCCAGTAGTGT
454 AGGCTACTTGCGAACCTGTAAAGCAACATAATAAGCCATTACTGACAAAGCAAATCCAGTAGTGT
* * * * *
3067 TGTTTCTGACCAAAATGATGATTATCTTCTTTACATGTTGCAGCAAAACCAAGGCCCGTAACATT
519 GGTTTCTGACCAAAATGATGATTATCTCCTTCACATGTTGCAGCAGAACCAAGGCCCATAACATT
* *
3132 CTTCCTCAGTTTTC
584 CATCCTCACTTTTC
3146 CTCAACATCT
Statistics
Matches: 2115, Mismatches: 165, Indels: 31
0.92 0.07 0.01
Matches are distributed among these distances:
843 50 0.02
844 2 0.00
845 142 0.07
846 353 0.17
847 122 0.06
848 5 0.00
849 1 0.00
850 933 0.44
851 408 0.19
852 32 0.02
853 67 0.03
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (851 bp):
ACAAATCAGAAACACATTAATTGTGAAAAGGGTACTGACGGATTTGACAATCAGTTCATCTGGAA
CTGAAACAACCTCAATGGCATTGATGAAAGCAGTTGAATCCTTCATAGGAGTAAACGTGATTGTA
AATGTACAATCTCGCAAGTTAAAAAGATACTTCTTGAGGATTGGGTACTGATATTGTCAAGCTTG
AAGTTGTGGAGCAAAACATACTTGTAGGCAAAGATGGTAAATATTTTTTTGTTAAAGATCAATCC
GGTCATTTTTCAGTAGAAGAAATGGAGAGGCACTCAACGAAAACAAGACCGCTTTAATTTAAATG
TGTAGGTGGCTTCTTGGGGAAAATTCAGCGTGGTTAAATATAGAGGTGAAGGAACATCGGAAGAC
ACTTAAAAAGATAATATTTCAAATGGTTCAATTACAACACCAAAGAAAATTAGAGATAAGATAAG
GCTACTTGCGAACCTGTAAAGCAACATAATAAGCCATTACTGACAAAGCAAATCCAGTAGTGTGG
TTTCTGACCAAAATGATGATTATCTCCTTCACATGTTGCAGCAGAACCAAGGCCCATAACATTCA
TCCTCACTTTTCGATACCTCCCATGGAATGTATTATAAAATATTTGTATTGGCAAATATGCATAA
TTCAAAATTCTGATAAATGAAATTATTCCTTAAAAAAGAGAACACCTGAAATTTGATTATAGTCT
AATTACAATCTAATACTAATCAATTTTCCAGTCAAACACAGAAGAGAAAGACTTATTTCCTAGCG
TGTCGTTTTACGAGGTGATCAACGGTCCCCCCATGTTAAGCCTGTAAATGACCTGCTAACCATAT
ACTTCC
Found at i:8543 original size:42 final size:42
Alignment explanation
Indices: 8464--8548 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
8454 TCTACGATTG
* * * * *
8464 TTAATTTAGTTTCTTGAAAATATACCATTACATCTAAACTAT
1 TTAATTTACTTTCTTAAAAATATAACAGTACACCTAAACTAT
8506 TTAATTTACTTTCTTAAAAATATATAC-GTACACCTAAACTAT
1 TTAATTTACTTTCTTAAAAATATA-ACAGTACACCTAAACTAT
8548 T
1 T
8549 AACGACTGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
42 36 0.97
43 1 0.03
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.42
Consensus pattern (42 bp):
TTAATTTACTTTCTTAAAAATATAACAGTACACCTAAACTAT
Found at i:12152 original size:19 final size:18
Alignment explanation
Indices: 12128--12164 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
12118 TTGAAGATTT
12128 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
12147 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
12165 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:16454 original size:54 final size:54
Alignment explanation
Indices: 16372--16475 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
16362 GTCACCCGGG
* * *
16372 TGAGCTGCCCCATCATAATAACCGGGCTCAGCACCCTCTTCATAGTAACCAGCC
1 TGAGCTGCCCCATCATAATAACCGGGCTCAGCACCCCCATCATAATAACCAGCC
*
16426 TGAGCTGCCCCATCATAATAGCCGGGCTCAGCACCCCCATCATAATAACC
1 TGAGCTGCCCCATCATAATAACCGGGCTCAGCACCCCCATCATAATAACC
16476 GTGCTCAGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.27, C:0.38, G:0.16, T:0.19
Consensus pattern (54 bp):
TGAGCTGCCCCATCATAATAACCGGGCTCAGCACCCCCATCATAATAACCAGCC
Found at i:16513 original size:27 final size:27
Alignment explanation
Indices: 16382--16501 Score: 134
Period size: 27 Copynumber: 4.4 Consensus size: 27
16372 TGAGCTGCCC
16382 CATCATAATAACCGGGCTCAGCACCCT
1 CATCATAATAACCGGGCTCAGCACCCT
* * * * * *
16409 CTTCATAGTAACCAGCCTGAGCTGCCC-
1 CATCATAATAACCGGGCTCAGC-ACCCT
* *
16436 CATCATAATAGCCGGGCTCAGCACCCC
1 CATCATAATAACCGGGCTCAGCACCCT
*
16463 CATCATAATAACCGTGCTCAGCACCCT
1 CATCATAATAACCGGGCTCAGCACCCT
*
16490 CATCATAGTAAC
1 CATCATAATAAC
16502 TCGGCTGAGC
Statistics
Matches: 74, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
26 3 0.04
27 68 0.92
28 3 0.04
ACGTcount: A:0.28, C:0.37, G:0.15, T:0.20
Consensus pattern (27 bp):
CATCATAATAACCGGGCTCAGCACCCT
Found at i:17000 original size:32 final size:31
Alignment explanation
Indices: 16959--17070 Score: 118
Period size: 32 Copynumber: 3.5 Consensus size: 31
16949 GGCACAGCCA
*
16959 TGGCAAGGCCGCACCTGAGGG-ACGGCATGCCG
1 TGGCAAGGCCGC-CC-CAGGGTACGGCATGCCG
*
16991 TGGCAAGGCCGCCCCAGGGTGCGGCATGCCG
1 TGGCAAGGCCGCCCCAGGGTACGGCATGCCG
* * *
17022 TGGCAAAGCCGCCCCCAGGGTGCGGCCTGCCG
1 TGGCAAGGCCG-CCCCAGGGTACGGCATGCCG
* * *
17054 AGTCAAAGCCGCCCCAG
1 TGGCAAGGCCGCCCCAG
17071 ACGTGCGGTT
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
30 4 0.06
31 28 0.39
32 40 0.56
ACGTcount: A:0.17, C:0.37, G:0.38, T:0.09
Consensus pattern (31 bp):
TGGCAAGGCCGCCCCAGGGTACGGCATGCCG
Found at i:17019 original size:31 final size:31
Alignment explanation
Indices: 16981--17070 Score: 135
Period size: 32 Copynumber: 2.9 Consensus size: 31
16971 ACCTGAGGGA
*
16981 CGGCATGCCGTGGCAAGGCCGCCCCAGGGTG
1 CGGCATGCCGTGGCAAAGCCGCCCCAGGGTG
17012 CGGCATGCCGTGGCAAAGCCGCCCCCAGGGTG
1 CGGCATGCCGTGGCAAAGCCG-CCCCAGGGTG
* * *
17044 CGGCCTGCCGAGTCAAAGCCGCCCCAG
1 CGGCATGCCGTGGCAAAGCCGCCCCAG
17071 ACGTGCGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.16, C:0.39, G:0.37, T:0.09
Consensus pattern (31 bp):
CGGCATGCCGTGGCAAAGCCGCCCCAGGGTG
Found at i:32033 original size:4 final size:4
Alignment explanation
Indices: 32026--32050 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
32016 ATATATATAT
32026 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
32051 CATTGCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:35690 original size:51 final size:46
Alignment explanation
Indices: 35571--35686 Score: 214
Period size: 46 Copynumber: 2.5 Consensus size: 46
35561 TAAAACGCTT
* *
35571 AAATTGTGTTAGTCGTGTCGTGTCATGTTTGGGCTACACACTTATA
1 AAATCGTGTTAGTCGTGTCGTGTCATGTTTGGACTACACACTTATA
35617 AAATCGTGTTAGTCGTGTCGTGTCATGTTTGGACTACACACTTATA
1 AAATCGTGTTAGTCGTGTCGTGTCATGTTTGGACTACACACTTATA
35663 AAATCGTGTTAGTCGTGTCGTGTC
1 AAATCGTGTTAGTCGTGTCGTGTC
35687 GTGTACATGA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (46 bp):
AAATCGTGTTAGTCGTGTCGTGTCATGTTTGGACTACACACTTATA
Found at i:37384 original size:23 final size:23
Alignment explanation
Indices: 37358--37412 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
37348 AGACAAAGGC
*
37358 TGTTTTGCTGTTGAAAATGTTGT
1 TGTTTTGCTGTTCAAAATGTTGT
37381 TGTTTTGCTGTTCAAAATGTTGT
1 TGTTTTGCTGTTCAAAATGTTGT
*
37404 TATTTTGCT
1 TGTTTTGCT
37413 TATTTGTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.16, C:0.07, G:0.22, T:0.55
Consensus pattern (23 bp):
TGTTTTGCTGTTCAAAATGTTGT
Found at i:39079 original size:12 final size:12
Alignment explanation
Indices: 39062--39086 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39052 GTTTTCTCTA
39062 ACACAGGTTTGT
1 ACACAGGTTTGT
39074 ACACAGGTTTGT
1 ACACAGGTTTGT
39086 A
1 A
39087 TCTCCTTTAC
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:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (12 bp):
ACACAGGTTTGT
Found at i:43269 original size:21 final size:21
Alignment explanation
Indices: 43245--43293 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
43235 CAGCTGGGGG
* * *
43245 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
43266 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
43287 CCCATGT
1 CCCATGT
43294 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:51426 original size:437 final size:430
Alignment explanation
Indices: 50448--51445 Score: 1172
Period size: 435 Copynumber: 2.3 Consensus size: 430
50438 TTTCAAAAGT
* * *
50448 ATTTTTTGGAATTGAAACATTAAAATTAGCTTTTGAG-TCTTTCAT-AAAAGTTAG-AGATCATA
1 ATTTTTTAGAATTAAAACATTAAAATTAGCTTTTGAGTTC-TTCATGAAAA-TT-GTAGATCATG
* * * * * *
50510 AAATTACCTTTTTATAAACACCTGAATTACCTTAATTGGATAAATAGAACAAAGAAAATAAAAAA
63 AAATTACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAAAATAAAAAA
* *
50575 GAAATGAAGCGTTAAATCGAATAAGATAGAATTTGAAAATGACTAAGTAGCAAAATAAAAAAGCA
128 -AAAT--A-CGTTAAATAGAATAAGATAGAATTTGAAAAGGACTAAGTAGCAAAATAAAAAAGCA
* * * *
50640 TTAGGGTCATTTGATAACTAATTCAAAAAGAAAATATTTCTTAATGGATATCTTGAAACATAAAA
189 TGAGGGTCATTTGATAAATAATCCAAAAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAA
* * * *
50705 ATTCCCTTTTAAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAACGT
254 ATTCCCTTTTAAACCCTTCATGAAACTCGCAAATCAAATTAACTTTCGGGTCCTTCATGAAACAT
* * * * *
50770 AGATCATACAGTACCTTTTAACCAACACTTGAATAATTTTAATCGGAAATGTGGATCGAAAAATT
319 AAATCATACAATACCTTTTAACCAACACTTCAATAACTTCAATCGGAAATGTGGATCGAAAAATT
* * * * *
50835 ATATGATATTAAATAGATCAACAATCGAAACGATCAAATTTAGGAAGC
384 ATAAGAAATTAAATAGACCAACAATCAAAACCATCAAATTTAGG-AGC
* * * * * *
50883 ATTTTTTTGAATTAAAACATAAAAATTTGCTTTTAAGTCCTTCATGAAAGTTGTAGATCATGAAA
1 ATTTTTTAGAATTAAAACATTAAAATTAGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAA
*
50948 TTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAGAATAATAAAAAAAA
66 TTACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAA-AATAAAAAAAA
* * * *
51013 AT-C-TTAAACATTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAA-TA
130 ATACGTT-AA-A-TAGAATAAGATAGAATTTGAAAAGGACTAAGTAGCA-AAA-TA-AAAAAGCA
* * *
51075 TGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAA
189 TGAGGGTCATTTGATAAATAATCCAAA-AAGAAAATATTTCTTAATGGAGATCTTGAAACATAAA
* * * *
51140 AATTCCCTTTTGAACCCTTCATGAAACTCGCAAATCAAGTTTAGCTTTCTGGTCCTTCATGAAAA
253 AATTCCCTTTTAAACCCTTCATGAAACTCGCAAATCAA-ATTAACTTTCGGGTCCTTCATG-AAA
* ** *
51205 TCATAAATCATGCAATAACCTTTTAACTGACACTTCAATAACTTCAATCGGACATGTGGA-CGAA
316 -CATAAATCATACAAT-ACCTTTTAACCAACACTTCAATAACTTCAATCGGAAATGTGGATCGAA
* * *
51269 AAATTATAAGAAATTAAATTGACCGACAATCAAAACCA-CAAAATTTCGG-GC
379 AAATTATAAGAAATTAAATAGACCAACAATCAAAACCATC-AAATTTAGGAGC
* * * *
51320 ATTTTTTAGAATCAAAATATTAAAATTGGCTTTTGAGTTCTGCATGAAAATTGTAGATCATGAAA
1 ATTTTTTAGAATTAAAACATTAAAATTAGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAA
* * * *
51385 TTACCTTTTAATAGACACTTGAATCACCTTACTCAGACAAATAGAA-AAA-AAAATACAAAAA
66 TTACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAAAATAAAAAAA
51446 TAAAAGGCAA
Statistics
Matches: 480, Mismatches: 67, Indels: 33
0.83 0.12 0.06
Matches are distributed among these distances:
430 2 0.00
431 3 0.01
432 1 0.00
433 31 0.06
434 13 0.03
435 128 0.27
436 89 0.19
437 118 0.25
438 4 0.01
439 54 0.11
440 37 0.08
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (430 bp):
ATTTTTTAGAATTAAAACATTAAAATTAGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAA
TTACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAAAATAAAAAAAAA
TACGTTAAATAGAATAAGATAGAATTTGAAAAGGACTAAGTAGCAAAATAAAAAAGCATGAGGGT
CATTTGATAAATAATCCAAAAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAATTCCCT
TTTAAACCCTTCATGAAACTCGCAAATCAAATTAACTTTCGGGTCCTTCATGAAACATAAATCAT
ACAATACCTTTTAACCAACACTTCAATAACTTCAATCGGAAATGTGGATCGAAAAATTATAAGAA
ATTAAATAGACCAACAATCAAAACCATCAAATTTAGGAGC
Found at i:58227 original size:75 final size:75
Alignment explanation
Indices: 58137--58283 Score: 285
Period size: 75 Copynumber: 2.0 Consensus size: 75
58127 ACGTGAGTCC
*
58137 CAGTGTGGGTTCCCAACTTAACTCGGATTCATTAGCCATGGAGCCATTTTTAATGCTGGAAACAA
1 CAGTGTGGGTTCCCAACTTAACTCAGATTCATTAGCCATGGAGCCATTTTTAATGCTGGAAACAA
58202 GCCAAATTTA
66 GCCAAATTTA
58212 CAGTGTGGGTTCCCAACTTAACTCAGATTCATTAGCCATGGAGCCATTTTTAATGCTGGAAACAA
1 CAGTGTGGGTTCCCAACTTAACTCAGATTCATTAGCCATGGAGCCATTTTTAATGCTGGAAACAA
58277 GCCAAAT
66 GCCAAAT
58284 AAATTTGCCG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (75 bp):
CAGTGTGGGTTCCCAACTTAACTCAGATTCATTAGCCATGGAGCCATTTTTAATGCTGGAAACAA
GCCAAATTTA
Found at i:59157 original size:83 final size:83
Alignment explanation
Indices: 59018--59186 Score: 338
Period size: 83 Copynumber: 2.0 Consensus size: 83
59008 ATCTGCCAAA
59018 TTAAGAAAACAAGAGGGTGAGAGATATTTGCAGCTACTCTTAGAATATTACACAGAAATCTGCAG
1 TTAAGAAAACAAGAGGGTGAGAGATATTTGCAGCTACTCTTAGAATATTACACAGAAATCTGCAG
59083 GGTTTTTTTAACTTGCAT
66 GGTTTTTTTAACTTGCAT
59101 TTAAGAAAACAAGAGGGTGAGAGATATTTGCAGCTACTCTTAGAATATTACACAGAAATCTGCAG
1 TTAAGAAAACAAGAGGGTGAGAGATATTTGCAGCTACTCTTAGAATATTACACAGAAATCTGCAG
59166 GGTTTTTTTAACTTGCAT
66 GGTTTTTTTAACTTGCAT
59184 TTA
1 TTA
59187 GATAAAGGTC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (83 bp):
TTAAGAAAACAAGAGGGTGAGAGATATTTGCAGCTACTCTTAGAATATTACACAGAAATCTGCAG
GGTTTTTTTAACTTGCAT
Found at i:63401 original size:9 final size:9
Alignment explanation
Indices: 63379--63422 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
63369 TCTTCTGCGT
63379 TTTTCTTTC
1 TTTTCTTTC
*
63388 TTTTTCTTTG
1 -TTTTCTTTC
63398 TTTTC-TTC
1 TTTTCTTTC
63406 TTTTCTTTC
1 TTTTCTTTC
*
63415 CTTTCTTT
1 TTTTCTTT
63423 TCTGTTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
8 7 0.23
9 15 0.50
10 8 0.27
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTTCTTTC
Done.