Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010008.1 Corchorus capsularis cultivar CVL-1 contig10029, 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: 67711
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:22 original size:14 final size:14
Alignment explanation
Indices: 3--38 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1 AG
3 CCCCCCCCCCCCTC
1 CCCCCCCCCCCCTC
*
17 CCCCCCTCCCCCTC
1 CCCCCCCCCCCCTC
31 CCCTCCCC
1 CCC-CCCC
39 TCTCTCTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.00, C:0.89, G:0.00, T:0.11
Consensus pattern (14 bp):
CCCCCCCCCCCCTC
Found at i:12428 original size:60 final size:59
Alignment explanation
Indices: 12326--12460 Score: 146
Period size: 60 Copynumber: 2.3 Consensus size: 59
12316 AACATTTCTT
* ** * * * *
12326 GGGGAGAAATTGTCCCAATTTTGATAGTTTAGAGGGTGAAAGTTTCAAATTAGAAGTTCAA
1 GGGG-GAAATTGTCCCAATTTTAATAGTTTAGAGACTAAAAGTTTCAAAATAAAAATT-AA
* *
12387 GGGGGAAATTGTCCCGATTTTAATAGTTTA-ATGACTAAAAGTTTCAAAATAAAAATTTA
1 GGGGGAAATTGTCCCAATTTTAATAGTTTAGA-GACTAAAAGTTTCAAAATAAAAATTAA
*
12446 GGGGGAAAATGTCCC
1 GGGGGAAATTGTCCC
12461 TTTTGTAAGA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 16 0.25
60 43 0.68
61 4 0.06
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (59 bp):
GGGGGAAATTGTCCCAATTTTAATAGTTTAGAGACTAAAAGTTTCAAAATAAAAATTAA
Found at i:15455 original size:2 final size:2
Alignment explanation
Indices: 15442--15475 Score: 50
Period size: 2 Copynumber: 16.0 Consensus size: 2
15432 CTTAAAAATA
15442 AT AT AT AGT AT AT AT AGT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT
15476 CTTTCCATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 26 0.87
3 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:15456 original size:9 final size:9
Alignment explanation
Indices: 15442--15474 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
15432 CTTAAAAATA
15442 ATATATAGT
1 ATATATAGT
15451 ATATATAGT
1 ATATATAGT
15460 ATATATA-T
1 ATATATAGT
15468 ATATATA
1 ATATATA
15475 TCTTTCCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (9 bp):
ATATATAGT
Found at i:16421 original size:28 final size:28
Alignment explanation
Indices: 16389--16446 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
16379 TTTTTTTTTC
16389 CCGTCGATTATTTTTTGAAAAATCTGTA
1 CCGTCGATTATTTTTTGAAAAATCTGTA
16417 CCGTCGATTATTTTTTGAAAAATCTGTA
1 CCGTCGATTATTTTTTGAAAAATCTGTA
16445 CC
1 CC
16447 TTAAAAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (28 bp):
CCGTCGATTATTTTTTGAAAAATCTGTA
Found at i:16673 original size:35 final size:35
Alignment explanation
Indices: 16622--16693 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
16612 TACTATAATA
*
16622 TTAAGGGTATTTTAGTAATTGACTAGTTAAGATTT
1 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
*
16657 TTAATGGTATTTTAGTAATTGACTAATTAAGATTT
1 TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
16692 TT
1 TT
16694 GAGTTCGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.49
Consensus pattern (35 bp):
TTAAGGGTATTTTAGTAATTGACTAATTAAGATTT
Found at i:19783 original size:10 final size:12
Alignment explanation
Indices: 19760--19789 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
19750 TAAAATTAAA
19760 TTTTATATATTT
1 TTTTATATATTT
19772 TTTTAT-TATTT
1 TTTTATATATTT
19783 TTTTATA
1 TTTTATA
19790 AACAATGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATATATTT
Found at i:24720 original size:13 final size:13
Alignment explanation
Indices: 24702--24728 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24692 GTGCCTCAAA
24702 AGAAAATGATCCT
1 AGAAAATGATCCT
24715 AGAAAATGATCCT
1 AGAAAATGATCCT
24728 A
1 A
24729 TAACCCTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (13 bp):
AGAAAATGATCCT
Found at i:25484 original size:16 final size:17
Alignment explanation
Indices: 25463--25495 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25453 AAAGGGTAAA
25463 TGAAA-TGAAACATATT
1 TGAAATTGAAACATATT
*
25479 TGAAATTGAATCATATT
1 TGAAATTGAAACATATT
25496 AACCCCCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (17 bp):
TGAAATTGAAACATATT
Found at i:30143 original size:18 final size:17
Alignment explanation
Indices: 30120--30155 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
30110 CTAGACCTAA
30120 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
30138 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
30155 A
1 A
30156 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:30784 original size:19 final size:18
Alignment explanation
Indices: 30747--30786 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
30737 CTCTTGAAAT
*
30747 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
30765 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
30784 AAT
1 AAT
30787 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:32709 original size:15 final size:15
Alignment explanation
Indices: 32638--32698 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
32628 CCATTATAAT
*
32638 TTTAATTAATAATTTA
1 TTTAATT-ATAATATA
* * *
32654 TTT-CTAATAATTATT
1 TTTAATTATAA-TATA
32669 TTTAGATTATAATATA
1 TTTA-ATTATAATATA
32685 TTTAATTATAATAT
1 TTTAATTATAATAT
32699 TATTATTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
14 4 0.11
15 16 0.46
16 10 0.29
17 5 0.14
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TTTAATTATAATATA
Found at i:38995 original size:49 final size:49
Alignment explanation
Indices: 38909--39345 Score: 504
Period size: 49 Copynumber: 8.9 Consensus size: 49
38899 CAATTTTCAG
* * *
38909 TTTTCACTTGCAATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
1 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* *
38958 TTTTTA-TCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCATTTA
1 TTTTTACT-TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
*
39007 TTTTTACCTG-TAATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
1 TTTTTACTTGCT-ATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* *
39056 TTTTTCACTTGCTATTTCCCAAAATGCCCTTCCTGGACGGAAGGCATTTA
1 TTTTT-ACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * *
39106 TTTTTACCTGCCATTTCCCAAAATGCCCTTCCCGGACGGAAGGTACTTA
1 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * * *
39155 -TTTTACTTGTTTTTTCCCAAAACGCCCTTCCTGGACGGAAGGCACTAA
1 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * * **
39203 TTTTTACTTGCTTTTTCCTAAAACGCCCTTCCCGGACGGAAGACACCAA
1 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * *
39252 TTTTTACTTGCCT-TTTCCTAAAACGCCCTTCCCGGACGGAAGGCGCTAA
1 TTTTTACTTG-CTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * ** * ** *
39301 TTTTTACTCGCTTTTTCTTAAATTGCCCTTTTCGGACGAAAGGCA
1 TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCA
39346 AGTTCATTTT
Statistics
Matches: 342, Mismatches: 38, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
48 44 0.13
49 251 0.73
50 46 0.13
51 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (49 bp):
TTTTTACTTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
Found at i:39113 original size:99 final size:98
Alignment explanation
Indices: 38920--39295 Score: 499
Period size: 99 Copynumber: 3.8 Consensus size: 98
38910 TTTCACTTGC
* * *
38920 AATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTA-TCTGCTATTTTCCAAAATGC
1 AATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACT-TGCTATTTCCCAAAACGC
38984 CCTTCCCGGACGGAAGGCATTTATTTTTACCTGT
65 CCTTCCCGGACGGAAGGCATTTATTTTTACCTGT
*
39018 AATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTCACTTGCTATTTCCCAAAATGC
1 AATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTT-ACTTGCTATTTCCCAAAACGC
* *
39083 CCTTCCTGGACGGAAGGCATTTATTTTTACCTGC
65 CCTTCCCGGACGGAAGGCATTTATTTTTACCTGT
* * * *
39117 CATTTCCCAAAATGCCCTTCCCGGACGGAAGGTACTTA-TTTTACTTGTTTTTTCCCAAAACGCC
1 AATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTATTTCCCAAAACGCC
* * * *
39181 CTTCCTGGACGGAAGGCACTAATTTTTACTTGCT
66 CTTCCCGGACGGAAGGCATTTATTTTTACCTG-T
* * * * ** *
39215 -TTTTCCTAAAACGCCCTTCCCGGACGGAAGACACCAATTTTTACTTGCCT-TTTCCTAAAACGC
1 AATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTG-CTATTTCCCAAAACGC
39278 CCTTCCCGGACGGAAGGC
65 CCTTCCCGGACGGAAGGC
39296 GCTAATTTTT
Statistics
Matches: 250, Mismatches: 23, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
97 78 0.31
98 84 0.34
99 87 0.35
100 1 0.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.32
Consensus pattern (98 bp):
AATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTATTTCCCAAAACGCC
CTTCCCGGACGGAAGGCATTTATTTTTACCTGT
Found at i:50023 original size:20 final size:20
Alignment explanation
Indices: 49995--50032 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
49985 TTGCTATAGA
*
49995 TTTAATTTACTTTGCTTTGT
1 TTTAATTTAATTTGCTTTGT
*
50015 TTTAGTTTAATTTGCTTT
1 TTTAATTTAATTTGCTTT
50033 CTTAAAATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.08, G:0.11, T:0.66
Consensus pattern (20 bp):
TTTAATTTAATTTGCTTTGT
Found at i:51130 original size:330 final size:324
Alignment explanation
Indices: 50196--52352 Score: 1621
Period size: 330 Copynumber: 6.6 Consensus size: 324
50186 ACCGATCATC
* * * * * *
50196 AGTTTTGAATGATTTTTGGCGCCGAGACTCCTTGAAATATCTGTATTAATCTAACCAAATCTCAT
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
* * *** * * * **
50261 CCACAATGGATTTAAGGATTTG-TAAAACAAGCATCTAAATCATAATTCGATTTAATTAGAAATT
66 CCAC-TTTGATTTAA-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
** * *
50325 AATTC-GGAAAATAATGAAAAACGATATTAGAAGCCTGAAAAACCCTTCAATCTTATTGGCGTTG
129 AATTCAAAAAAAT-ATGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTT-TTGGCGTTG
* * *
50389 AATTATATA-ATTTTTATGAGTATTTTGGCAAAAAAATTAAGGAAATAA-CTTTGGAGTCAATTT
192 AATTATATATA-TTTTATGAGTATTTTGGC-TAAAAATTGA-GAAA-AATATTTGG-GTCAATTT
* * ** ** *
50452 TTGCAAAATTCTAGCCGAAATCGTGTAATAATGATCACTTTTTTTTTTTTGGCTAAAAACGCATT
252 TTGCAAAATTTTAGCCGAAATCGT-TACTAACCATCAC-----GGTTTTTGGCTAAAAACGCGTT
*
50517 TCGGGACCCCGACCA
311 TCGGG-CCCCGACTA
* * * * * * *
50532 AGTTTTGCATGATTTTTGGTGCCAAAAAGTTCTTTGAGATATCCATATTCATCTAATCAAATCTT
1 AGTTTTGCATGATTTTTGGCGCC-AAGA-CTCCTTGAAATATCTATATTCATCTAATCAAATCTC
** * * *
50597 AGTTACATTGATTTAAGAATTTGTTTTTACAAGTATCTGAATCTTGTTTCGATTTAATTAGAAAT
64 AGCCACTTTGATTTAAG-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
** * * * * * *
50662 TAATTCAAAAAAATATGAAAAATAATATTAAAAGTGTGAAGAGTCCTTCAATCTTTTTAGCGTTA
128 TAATTCAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATC-TTTTGGCGTTG
* * * * ** * * *
50727 AATTATATATATTTCATGAGTATTTTAGCCAAAAATTGTGGAAATTTTTTTTGGTCATTTTTTTT
192 AATTATATATATTTTATGAGTATTTTGGCTAAAAATTG-AGAAAAATATTTGGGTCA--ATTTTT
* *
50792 GTAAAATTTTAGCCGAAATCGTCTACTAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGAC
254 GCAAAATTTTAGCCGAAATCGT-TACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGG-C
*
50857 CCCGACTT
317 CCCGACTA
** * * * * *
50865 AGTTTTGCAT-ATTTTTGGCATCGAGACTCCTTAAAATATCTATATTCATGTAATCAAATCCCAA
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
*
50929 CCACTTTGATTTTAAGATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
66 CCACTTTGA-TTTAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * * *
50994 ATTCAAAAAACATATGAAAAACGATGTTAAAAGCGTGAAGAGTCCTCCAATATATTTGGCGTTTA
130 ATTCAAAAAA-ATATGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCT-TTTGGCGTTGA
* * *
51059 ATTACATATATTCTATGAGTATTATGGCTAAAAATTGAGAAAAAATATTTCGGGTCAATTTTTGC
193 ATTATATATATTTTATGAGTATTTTGGCTAAAAATTGAG-AAAAATATTT-GGGTCAATTTTTGC
* * * * * *
51124 AAAATTTTAGCCGAATTCG-T-GT-ACCATTATGGTTTTTTTTTTGGCTAAAAACGCATTCTGGG
256 AAAATTTTAGCCGAAATCGTTACTAACCATCACGG-----TTTTTGGCTAAAAACGCGTT-TCGG
* ** *
51186 GCACCGGGTC
315 GCCCCGACTA
* * * * * * * * *
51196 AGTCTTCCATGATTTTTTGTGGCAACACTCCTTGAAATATCTATATTCATCAAACCAAATCTTAG
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
* * * * * *
51261 CCAC----A-TT-AGA------TTTA--AGCATTTGAATCATATCTCAATTTAATTAGAAATGAA
66 CCACTTTGATTTAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * *
51312 TTTGAAAAAAAATAGGAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAATCCTTTT-GCTATTG
131 -TT-CAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAAT-CTTTTGGC-GTTG
* * * * *
51376 AATTATATACT-TTTTACGAGTATTGTGGCTAAAAATTGAGAAAATTAATTTGGATCAGTTTTTG
192 AATTATATA-TATTTTATGAGTATTTTGGCTAAAAATTGAGAAAAAT-ATTTGGGTCAATTTTTG
* * *
51440 CAAAAATTTAGCCGAAATCG-T-GT-ACCATCATGGTTTTTTAGG-TAAAAACGCGTTTCGGGGC
255 CAAAATTTTAGCCGAAATCGTTACTAACCATCACGG-TTTTT-GGCTAAAAACGCGTTTC-GGGC
** *
51501 CCTAAGTA
317 CCCGACTA
* * * *
51509 AGTGTTTGCATGATTTTTGGCGGCAAGATTCCTT--AATATATATATTCATCTAATCTAATCTCA
1 AGT-TTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCA
* ** * *
51572 GCCACTTTGCGTTTAAGGATTTGTTTTTACGAGTTTCTAAATCTTGTTTCGATTTAATCAGAAAT
65 GCCACTTTG-ATTTAA-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * ***
51637 TAATTTTGAAATAAAATAGGAAAAATGATATTAGAAGCGTGAAAAAGGATTTCAAT-TGTTTGGC
128 TAA--TTCAAA-AAAATATGAAAAACGATATTAGAAGCGTG-AAAAGCCCTTCAATCT-TTTGGC
* * * * * * * *
51701 GTTGAATTATATATGTTGTATGAGTGTTTTCGTTAGAAATTGAGGAAAAATATTTCGGGTCGATG
188 GTTGAATTATATATATTTTATGAGTATTTTGGCTAAAAATTGA-GAAAAATATTT-GGGTCAATT
*** * * *
51766 TTTGCTGGA-TTTAGCCGAAATCGGGTACTAACCATCAC-GTTTTTCGGCTAAAAACGTGTTCCG
251 TTTGCAAAATTTTAGCCGAAATC-GTTACTAACCATCACGGTTTTT-GGCTAAAAACGCGTTTCG
*
51829 GTG-CCCGACTC
314 G-GCCCCGACTA
* * * *
51840 AGTTTTTCATGATTTTTGGTGCCAAGACTTCTTGAAATATCTATATTCATCTAACCAAATCTCAG
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
* * * *
51905 CCACATTAGATTTAAGAATATATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAATT
66 CCAC-TTTGATTTAAG-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * * * * * *
51970 AATTCTAAAAAA-AGGAAGAACAATATTAGAAGCGTTACAAA-CCCTTCAATTTTTTTG-ATACT
129 AATTCAAAAAAATATGAAAAACGATATTAGAAGCGTGA-AAAGCCCTTCAATCTTTTGGCGT--T
* * * * * *
52032 GAATTACATATTTTTTATGAGTATTTTAGC---CAATTGAG-GAAATACCTTTTGAGTCAATTTT
191 GAATTATATATATTTTATGAGTATTTTGGCTAAAAATTGAGAAAAATA---TTTGGGTCAATTTT
* * * * *
52093 TGCAAAATTTTAGCTGAAATCGTATATTAACCATCACGGTTTTTGGCTAAAAACACATTACAGGG
253 TGCAAAATTTTAGCCGAAATCGT-TACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGG
* *
52158 CCACGACTC
316 CCCCGACTA
* * * * *
52167 TGTTTTGCATGATTTTTGGCGCCGAGACTTCTTGAAATATCTTTATTCATCTAATCAAATCTCAA
1 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
* * * *
52232 CCACATTGGATTTAATGATTT-ATTTTATGTGCAT-TCGAATCTTGTTTCGATTTAATTAGAAAT
66 CCAC-TTTGATTTAA-GATTTGTTTTTACGAGCATCT-GAATCTTGTTTCGATTTAATTAGAAAT
* * * *
52295 TAATTTAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAAT-TTTTG
128 TAATTCA-AAAAAATATGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTG
52353 AGTATTTTTG
Statistics
Matches: 1453, Mismatches: 285, Indels: 175
0.76 0.15 0.09
Matches are distributed among these distances:
312 30 0.02
313 27 0.02
314 26 0.02
317 79 0.05
318 80 0.06
319 13 0.01
320 2 0.00
323 5 0.00
324 1 0.00
325 23 0.02
326 97 0.07
327 115 0.08
328 111 0.08
329 88 0.06
330 176 0.12
331 139 0.10
332 157 0.11
333 51 0.04
336 26 0.02
337 31 0.02
338 168 0.12
339 8 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (324 bp):
AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
CCACTTTGATTTAAGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
TTCAAAAAAATATGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTGGCGTTGAATT
ATATATATTTTATGAGTATTTTGGCTAAAAATTGAGAAAAATATTTGGGTCAATTTTTGCAAAAT
TTTAGCCGAAATCGTTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGCCCCGACTA
Found at i:57978 original size:42 final size:42
Alignment explanation
Indices: 57904--58015 Score: 203
Period size: 42 Copynumber: 2.7 Consensus size: 42
57894 TGTGTATAAC
57904 AATAT-TATGTGTAC-A-ATATATATATATAATTAATTTCTA
1 AATATATATGTGTACAATATATATATATATAATTAATTTCTA
57943 AATATATATGTGTACAATATATATATATATAATTAATTTCTA
1 AATATATATGTGTACAATATATATATATATAATTAATTTCTA
57985 AATATATATGTGTACAATATATATATATATA
1 AATATATATGTGTACAATATATATATATATA
58016 GGTATAAGAA
Statistics
Matches: 70, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
39 5 0.07
40 9 0.13
41 1 0.01
42 55 0.79
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (42 bp):
AATATATATGTGTACAATATATATATATATAATTAATTTCTA
Found at i:58102 original size:3 final size:3
Alignment explanation
Indices: 58094--58131 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
58084 TGAAAAATAA
58094 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
58132 AATAACACCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.