Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014774.1 Corchorus capsularis cultivar CVL-1 contig14795, 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: 51766
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:4754 original size:66 final size:66
Alignment explanation
Indices: 4639--4773 Score: 245
Period size: 66 Copynumber: 2.0 Consensus size: 66
4629 CACCATCAAT
4639 TTAAACTTTAGAAAATTATAAAACTTGAACTTACTAATTTGAGTGGAATGAATGAT-AAGACCAA
1 TTAAACTTTAGAAAATTATAAAACTTGAACTTACTAATTTGAGTGGAATGAATGATAAAGACCAA
4703 A
66 A
*
4704 TTAAACTTTAGAAAATTATAAAACTTTGAACTTACTAATTTGAGTGGAATGAATGATAAAGATCA
1 TTAAACTTTAGAAAATTATAAAAC-TTGAACTTACTAATTTGAGTGGAATGAATGATAAAGACCA
4769 AA
65 AA
4771 TTA
1 TTA
4774 CGTGCTTATT
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
65 24 0.36
66 32 0.48
67 11 0.16
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (66 bp):
TTAAACTTTAGAAAATTATAAAACTTGAACTTACTAATTTGAGTGGAATGAATGATAAAGACCAA
A
Found at i:7305 original size:31 final size:31
Alignment explanation
Indices: 7267--7332 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
7257 TCGTACTAGG
*
7267 GTTTGCCACAATGTTCGATTTGGGACCAAAC
1 GTTTGCCACAATGCTCGATTTGGGACCAAAC
**
7298 GTTTGCCACAATGCTCGATTTGGGGTCAAAC
1 GTTTGCCACAATGCTCGATTTGGGACCAAAC
7329 GTTT
1 GTTT
7333 CAATTGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (31 bp):
GTTTGCCACAATGCTCGATTTGGGACCAAAC
Found at i:7477 original size:25 final size:26
Alignment explanation
Indices: 7449--7503 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
7439 AATTTAATAT
*
7449 ATTTAAAA-TTTAAAAATTATAATTA
1 ATTTAAAATTTTAAAAAATATAATTA
7474 ATTTAAAATTTTAAAAAATATAATTA
1 ATTTAAAATTTTAAAAAATATAATTA
7500 ATTT
1 ATTT
7504 GTTTAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTAAAATTTTAAAAAATATAATTA
Found at i:8733 original size:49 final size:49
Alignment explanation
Indices: 8671--9627 Score: 828
Period size: 49 Copynumber: 19.6 Consensus size: 49
8661 AAACTAGCGC
* * * * * * * *
8671 CTTCCATCTGGGAAGGGTGTTTTAGAAAAAAACAAGTAAAAATTAGTGT
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAGTGG
* * * *** * *
8720 CTTCCGTCGGGGAAGGGCACTTTGGGGAAA-AGTGGGTAAAAATAAGCGT
1 CTTCCGTCTGGGAAGGGC-GTTTTGGGAAATAGCAAGTAAAAATAAGTGG
* * * *
8769 CTTCCATAC-GGGAAGGGCCTTTTTGGAAAATAGCAAGT-AAAATAAGTGC
1 CTTCCGT-CTGGGAAGGG-CGTTTTGGGAAATAGCAAGTAAAAATAAGTGG
* * * * * * * * *
8818 CTTCCGACCGGGAAGGGCATTTTCGGAAA-AACAGGTAAAGATTAGTGC
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAGTGG
* * * * * * *
8866 CTTCCGTCCGGGAAGGGCGTTTTGGGAAA-AACAGGTAATAATCAGCGC
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAGTGG
* * * **
8914 CTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAGATAAACGG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAGTGG
* * * *
8963 CTTCCGTCCGGGAAGGGCGTTTTGGGGAGATAGCAAGCAAAAATAAATGG
1 CTTCCGTCTGGGAAGGGCGTTTT-GGGAAATAGCAAGTAAAAATAAGTGG
* ** *
9013 CTTCCGTCTGGGAAGGGCTTTTTGGGAAATAGCAAGCGAAAATAAATGG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAGTGG
9062 CTTCCGTCTGGGAAGGGCGCTTTT-GGAAATAGCAAGT-AAAATAAGTGG
1 CTTCCGTCTGGGAAGGGCG-TTTTGGGAAATAGCAAGTAAAAATAAGTGG
* * *
9110 CTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAATAAAAATAAATGG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAGTGG
* * * *
9159 CTTCCGTCTGGGAAGGGTGTTTTGGGAGATAGCACGTAAAGATGAA-TGG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAAT-AAGTGG
*
9208 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAA-TGG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAAT-AAGTGG
* *
9257 CTTCTGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAA-TGG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAAT-AAGTGG
* * * *
9306 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATACCTAGCAAAATTAA-TGG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAGTGG
* * * * * *
9354 CTTCCGTCTGGGAAGGGCATTTTAGGAAATAGCTAGCAAAAACAAATGG
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAGTGG
* * * * *
9403 CTTCCGTCTGGGAAGGGCATTTTAGGAAGA-AGCAAAT-AAAAGAAGTGC
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAA-ATAGCAAGTAAAAATAAGTGG
** * * * * *
9451 CTTCCGTCCAGGAAGGGCGTTTAGGGAAAAAGCAAATAAAAATTGAGTGC
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAA-TAAGTGG
* * * ****
9501 CTTCCGTCTGAGAAGGGCGTTTTGGGAAAAAGTTAA-TAAAAATAAACAC
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAG-CAAGTAAAAATAAGTGG
* * * ****
9550 CTTCCGTCCGGGAAGGGCGTTTTGGGAAAAAGTTAA-TAAAAATAAACAC
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAG-CAAGTAAAAATAAGTGG
* *
9599 CTTCCATCCGGGAAGGGCGTTTTGGGAAA
1 CTTCCGTCTGGGAAGGGCGTTTTGGGAAA
9628 AAGTAGGTAA
Statistics
Matches: 783, Mismatches: 107, Indels: 36
0.85 0.12 0.04
Matches are distributed among these distances:
47 9 0.01
48 213 0.27
49 458 0.58
50 101 0.13
51 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (49 bp):
CTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATAAGTGG
Found at i:9030 original size:195 final size:195
Alignment explanation
Indices: 8669--9627 Score: 857
Period size: 195 Copynumber: 4.9 Consensus size: 195
8659 TAAAACTAGC
* * * * * * * * *
8669 GCCTTCCATCTGGGAAGGGTGTTTTAGAAAAAAACAAGTAAAAATTAGTGTCTTCCGTCGGGGAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAAATGAGTGCCTTCCGTCTGGGAA
* * **** * * * * * *
8734 GGGCACTTTGGGGAAA-AGTGGGTAAAAATAAGCGTCTTCCATACGGGAAGGGCCTTTTTGGAAA
66 GGGC-GTTTTGGGAAATAACAAGTAAAAATAAACGGCTTCCGTCCGGGAAGGG-CGTTTTGGGAA
* * * * * * * *
8798 ATAGCAAG-TAAAATAAGTGCCTTCCGACCGGGAAGGGCATTTTCGGAAA-AACAGGTAAAGATT
129 ATAGCAAGCAAAAATAAATGGCTTCCGTCTGGGAAGGGCATTTTGGGAAATAGCAAGTAAAGA-T
*
8861 AGT
193 AAT
* * * * *
8864 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAA-AACAGGTAATAATCAGCGCCTTCCGTCCGGGAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAAATGAGTGCCTTCCGTCTGGGAA
* *
8928 GGGCGTTTTGGGAAATAACAAGTAAAGATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGGAGA
66 GGGCGTTTTGGGAAATAACAAGTAAAAATAAACGGCTTCCGTCCGGGAAGGGCGTTTT-GGGAAA
* *
8993 TAGCAAGCAAAAATAAATGGCTTCCGTCTGGGAAGGGCTTTTTGGGAAATAGCAAGCGAAA-ATA
130 TAGCAAGCAAAAATAAATGGCTTCCGTCTGGGAAGGGCATTTTGGGAAATAGCAAG-TAAAGAT-
9057 AAT
193 AAT
* * * * *
9060 GGCTTCCGTCTGGGAAGGGCGCTTTT-GGAAATAGCAAGT-AAAATAAGTGGCTTCCGTCTGGGA
1 GCCTTCCGTCCGGGAAGGGCG-TTTTGGGAAATAACAAGTAAAAATGAGTGCCTTCCGTCTGGGA
* * * * * * *
9123 AGGGCGCTTTGGGAAATAGCAAATAAAAATAAATGGCTTCCGTCTGGGAAGGGTGTTTTGGGAGA
65 AGGGCGTTTTGGGAAATAACAAGTAAAAATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAA
* * * * *
9188 TAGCACGTAAAGATGAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGA
130 TAGCAAGCAAAAATAAATGGCTTCCGTCTGGGAAGGGCATTTTGGGAAATAGCAAGTAAAGAT-A
9253 AT
194 AT
* * * * * * *
9255 GGCTTCTGTCTGGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAATGGCTTCCGTCTGGGAA
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAAATGAGTGCCTTCCGTCTGGGAA
* * * * * * * *
9320 GGGCGTTTTGGGAAATACCTAG-CAAAATTAATGGCTTCCGTCTGGGAAGGGCATTTTAGGAAAT
66 GGGCGTTTTGGGAAATAACAAGTAAAAATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAAT
* * * *
9384 AGCTAGCAAAAACAAATGGCTTCCGTCTGGGAAGGGCATTTTAGGAAGA-AGCAAATAAAAGA-A
131 AGCAAGCAAAAATAAATGGCTTCCGTCTGGGAAGGGCATTTTGGGAA-ATAGCAAGT-AAAGATA
*
9447 GT
194 AT
* * * *
9449 GCCTTCCGTCCAGGAAGGGCGTTTAGGGAAA-AAGCAAATAAAAATTGAGTGCCTTCCGTCTGAG
1 GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAA-CAAGTAAAAA-TGAGTGCCTTCCGTCTGGG
* **
9513 AAGGGCGTTTTGGGAAA-AAGTTAA-TAAAAATAAACACCTTCCGTCCGGGAAGGGCGTTTTGGG
64 AAGGGCGTTTTGGGAAATAA--CAAGTAAAAATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGG
* * * *** * * *
9576 AAAAAGTTAA-TAAAAATAAACACCTTCCATCCGGGAAGGGCGTTTTGGGAAA
127 AAATAG-CAAGCAAAAATAAATGGCTTCCGTCTGGGAAGGGCATTTTGGGAAA
9628 AAGTAGGTAA
Statistics
Matches: 628, Mismatches: 117, Indels: 38
0.80 0.15 0.05
Matches are distributed among these distances:
193 15 0.02
194 112 0.18
195 271 0.43
196 217 0.35
197 13 0.02
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (195 bp):
GCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAAATGAGTGCCTTCCGTCTGGGAA
GGGCGTTTTGGGAAATAACAAGTAAAAATAAACGGCTTCCGTCCGGGAAGGGCGTTTTGGGAAAT
AGCAAGCAAAAATAAATGGCTTCCGTCTGGGAAGGGCATTTTGGGAAATAGCAAGTAAAGATAAT
Found at i:9242 original size:244 final size:243
Alignment explanation
Indices: 8778--9578 Score: 851
Period size: 244 Copynumber: 3.3 Consensus size: 243
8768 TCTTCCATAC
* * * * * * * *
8778 GGGAAGGGCCTTTTTGGAAAATAGCAAGTAAAATAAGTGCCTTCCGACCGGGAAGGGCATTTTCG
1 GGGAAGGG-CGTTTTGGGAAATAGCAAGAAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTCG
* * * * * * *
8843 GAAA-AACAGGTAAAGATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAA-AACAGGTAATA
65 GAAATAACAAGTAAA-ATAAGTGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAA
* ** * * * * * *
8906 ATCAGCGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAATAACAAGTAAAGATAAACGGCTTCCGTC
129 ATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAGATAGCAAGTAAAGATGAATGGCTTCCGTC
* * *
8971 CGGGAAGGGCGTTTTGGGGAGATAGCAAGCAAAAATAAATGGCTTCCGTCT
194 CGGGAAGGGCGTTTT-GGGAAATAGCAAGTAAAAATGAATGGCTTCCGTCT
* *
9022 GGGAAGGGCTTTTTGGGAAATAGCAAGCGAAAATAAATGGCTTCCGTCTGGGAAGGGCGCTTTT-
1 GGGAAGGGCGTTTTGGGAAATAGCAAG-AAAAATAAATGGCTTCCGTCTGGGAAGGGCG-TTTTC
* * *
9086 GGAAATAGCAAGTAAAATAAGTGGCTTCCGTCTGGGAAGGGCGCTTTGGGAAATAGCAAATAAAA
64 GGAAATAACAAGTAAAATAAGTGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAA
* *
9151 ATAAATGGCTTCCGTCTGGGAAGGGTGTTTTGGGAGATAGCACGTAAAGATGAATGGCTTCCGTC
129 ATAAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAGATAGCAAGTAAAGATGAATGGCTTCCGTC
* * *
9216 TGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAGATGAATGGCTTCTGTCT
194 CGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATGAATGGCTTCCGTCT
* * *
9266 GGGAAGGGCGCTTTGGGAAATAGCAAGTAAAAATGAATGGCTTCCGTCTGGGAAGGGCGTTTTGG
1 GGGAAGGGCGTTTTGGGAAATAGCAAG-AAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTCG
* * * * * * *
9331 GAAATACCTAGCAAAATTAA-TGGCTTCCGTCTGGGAAGGGCATTTTAGGAAATAGCTAGCAAAA
65 GAAATAACAAGTAAAA-TAAGTGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAA
* * * * *
9395 ACAAATGGCTTCCGTCTGGGAAGGGCATTTTAGGAAGA-AGCAAATAAA-A-GAAGTGCCTTCCG
129 ATAAATGGCTTCCGTCTGGGAAGGGCGTTTT-GGGAGATAGCAAGTAAAGATGAA-TGGCTTCCG
* * * * * *
9457 TCCAGGAAGGGCGTTTAGGGAAAAAGCAAATAAAAATTGAGTGCCTTCCGTCT
192 TCCGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAA-TGAATGGCTTCCGTCT
* * * * *** * *
9510 GAGAAGGGCGTTTTGGGAAAAAGTTAATAAAAATAAACACCTTCCGTCCGGGAAGGGCGTTTTGG
1 GGGAAGGGCGTTTTGGGAAATAG-CAAGAAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTCG
9575 GAAA
65 GAAA
9579 AAGTTAATAA
Statistics
Matches: 473, Mismatches: 74, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
242 3 0.01
243 61 0.13
244 312 0.66
245 97 0.21
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (243 bp):
GGGAAGGGCGTTTTGGGAAATAGCAAGAAAAATAAATGGCTTCCGTCTGGGAAGGGCGTTTTCGG
AAATAACAAGTAAAATAAGTGGCTTCCGTCTGGGAAGGGCGTTTTGGGAAATAGCAAGTAAAAAT
AAATGGCTTCCGTCTGGGAAGGGCGTTTTGGGAGATAGCAAGTAAAGATGAATGGCTTCCGTCCG
GGAAGGGCGTTTTGGGAAATAGCAAGTAAAAATGAATGGCTTCCGTCT
Found at i:19549 original size:22 final size:22
Alignment explanation
Indices: 19524--19566 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19514 ACCGCTGTTC
19524 ACTTTTCTCTTGAATGATTTCA
1 ACTTTTCTCTTGAATGATTTCA
* *
19546 ACTTTTGTCTTGGATGATTTC
1 ACTTTTCTCTTGAATGATTTC
19567 GGTAAACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (22 bp):
ACTTTTCTCTTGAATGATTTCA
Found at i:22352 original size:45 final size:45
Alignment explanation
Indices: 22303--22419 Score: 114
Period size: 45 Copynumber: 2.6 Consensus size: 45
22293 AAGACCTCAA
* * *
22303 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAACGC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAACGC
* * * *
22348 TATGAGATGTTGATAACCTCCATATGATATATTGATAACC-ATGT
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACGC
* *
22392 TATGAAAAT-TTAAAAACCTCCATATGAA
1 TATG-AAATGTTGATAACCTCCATATGAA
22420 TTGTTACTAA
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
44 25 0.42
45 34 0.58
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACGC
Found at i:22382 original size:22 final size:22
Alignment explanation
Indices: 22251--22419 Score: 87
Period size: 22 Copynumber: 7.7 Consensus size: 22
22241 AATTTTTTTT
* * * *
22251 TAACCTTCTTATGAAATTTGGT
1 TAACCTCCATATGAAATTTTGA
* * *
22273 TAACCTCCCTA-GGATTTTTGA
1 TAACCTCCATATGAAATTTTGA
*
22294 -AGACCTCAATATGAAATTTTGA
1 TA-ACCTCCATATGAAATTTTGA
*
22316 TAACTTCCCA-ATGAAATTTTGA
1 TAACCT-CCATATGAAATTTTGA
* * *
22338 TAACCAACGC-TATGAGATGTTGA
1 TAACC-TC-CATATGAAATTTTGA
* *
22361 TAACCTCCATATGATATATTGA
1 TAACCTCCATATGAAATTTTGA
** * *
22383 TAACCAT-GTTATGAAAATTTAA
1 TAACC-TCCATATGAAATTTTGA
*
22405 AAACCTCCATATGAA
1 TAACCTCCATATGAA
22420 TTGTTACTAA
Statistics
Matches: 109, Mismatches: 28, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
20 1 0.01
21 15 0.14
22 73 0.67
23 20 0.18
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (22 bp):
TAACCTCCATATGAAATTTTGA
Found at i:22471 original size:22 final size:22
Alignment explanation
Indices: 22446--22733 Score: 162
Period size: 22 Copynumber: 13.5 Consensus size: 22
22436 TATCATACTC
*
22446 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAATCTCACTA
* * **
22468 TGAAATTGTGATAACCTTGCTA
1 TGAAATTTTGATAATCTCACTA
22490 TGAAATTTTGATAAATCTTC-CTA
1 TGAAATTTTGAT-AATC-TCACTA
* * *
22513 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AATCTCACTA
* * *
22536 TAAAATTTTGATAACTTTC-TTA
1 TGAAATTTTGATAA-TCTCACTA
*
22558 TGAAATCTTGATAAT-T-AC--
1 TGAAATTTTGATAATCTCACTA
* * *
22576 --AAATTTTAATAACCTCCCTA
1 TGAAATTTTGATAATCTCACTA
* * *
22596 TG-ATTTTTGATAACCTCATTA
1 TGAAATTTTGATAATCTCACTA
* *
22617 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAATCTCACTA
* *
22639 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAATCT-CACTA
*
22661 TGAAATTTTGATAACCTTCA-TA
1 TGAAATTTTGATAATC-TCACTA
*
22683 TGAAATTTTGAT-ATCCTC-C-C
1 TGAAATTTTGATAAT-CTCACTA
22703 TG-AATTTTGAT-ATCCTC-CT-
1 TGAAATTTTGATAAT-CTCACTA
22722 TGAAATTTTGAT
1 TGAAATTTTGAT
22734 TACCTCATAA
Statistics
Matches: 210, Mismatches: 37, Indels: 40
0.73 0.13 0.14
Matches are distributed among these distances:
16 10 0.05
17 1 0.00
18 1 0.00
19 18 0.09
20 12 0.06
21 25 0.12
22 99 0.47
23 42 0.20
24 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAATCTCACTA
Found at i:22570 original size:45 final size:45
Alignment explanation
Indices: 22448--22571 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 45
22438 TCATACTCTG
* ** *
22448 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTTGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
*
22492 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTATA
* *
22538 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
22572 TTACAAATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
44 11 0.16
45 31 0.46
46 25 0.37
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:22618 original size:59 final size:61
Alignment explanation
Indices: 22515--22631 Score: 150
Period size: 59 Copynumber: 2.0 Consensus size: 61
22505 TCTTCCTATA
* *
22515 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTATGAAATCTTGATAATTAC
1 AAATTTTAATAAACCTCCCTATAAAATTTTGATAACTCTCTTATGAAATCTTGATAATTAC
* * * *
22576 AAATTTTAAT-AACCTCCCTAT-GATTTTTGATAAC-CTCATTATGAAATTTTGTTAAT
1 AAATTTTAATAAACCTCCCTATAAAATTTTGATAACTCTC-TTATGAAATCTTGATAAT
22632 CTCCCTATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 2 0.04
59 27 0.55
60 11 0.22
61 9 0.18
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.43
Consensus pattern (61 bp):
AAATTTTAATAAACCTCCCTATAAAATTTTGATAACTCTCTTATGAAATCTTGATAATTAC
Found at i:22710 original size:19 final size:20
Alignment explanation
Indices: 22683--22733 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
22673 AACCTTCATA
22683 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
22703 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
22722 TGAAATTTTGAT
1 TGAAATTTTGAT
22734 TACCTCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:22867 original size:22 final size:22
Alignment explanation
Indices: 22842--22885 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
22832 TGTAATAACA
22842 TTGAAAAATTGATAACCTCTTT
1 TTGAAAAATTGATAACCTCTTT
**
22864 TTGAAATTTTGATAACCTCTTT
1 TTGAAAAATTGATAACCTCTTT
22886 ATAAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (22 bp):
TTGAAAAATTGATAACCTCTTT
Found at i:22914 original size:22 final size:22
Alignment explanation
Indices: 22850--23057 Score: 105
Period size: 22 Copynumber: 9.4 Consensus size: 22
22840 CATTGAAAAA
* * *
22850 TTGATAACCTCTTTTTGAAATT
1 TTGATAACCCCTCTATGAAATT
* * *
22872 TTGATAACCTCTTTATAAAATT
1 TTGATAACCCCTCTATGAAATT
* *
22894 TTGTTGACCCCTCTATGAAATT
1 TTGATAACCCCTCTATGAAATT
* * * * ** *
22916 CTAATAATCACAGTATGTAATT
1 TTGATAACCCCTCTATGAAATT
* * * *
22938 TTGATAATCTCGCTTTGAAATT
1 TTGATAACCCCTCTATGAAATT
** *
22960 TTGATAACAACACTATGAAATT
1 TTGATAACCCCTCTATGAAATT
* **
22982 TTGATAATCTTTCTAT-AAATT
1 TTGATAACCCCTCTATGAAATT
* *
23003 TTGATAATCCGATCTCTATGAAATA
1 TTGATAA-CC--CCTCTATGAAATT
* * *
23028 TTGATAATCACTCTATGAGA-T
1 TTGATAACCCCTCTATGAAATT
23049 TTGATAACC
1 TTGATAACC
23058 TTCTATCAAA
Statistics
Matches: 141, Mismatches: 41, Indels: 9
0.74 0.21 0.05
Matches are distributed among these distances:
21 20 0.14
22 103 0.73
24 7 0.05
25 11 0.08
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TTGATAACCCCTCTATGAAATT
Found at i:23044 original size:68 final size:63
Alignment explanation
Indices: 22934--23063 Score: 147
Period size: 68 Copynumber: 2.0 Consensus size: 63
22924 CACAGTATGT
* *
22934 AATTTTGATAATCTCGCTTTGAAATTTTGATAACAACACTATGAAATTTTGATAATCTTTCTATA
1 AATTTTGATAATCTCGCTTTGAAATATTGATAACAACACTATGAAA-TTTGATAA-CCTTCTATA
* *
22999 AATTTTGATAATC-CGATCTCTATGAAATATTGATAATC-ACTCTATGAGATTTGATAACCTTCT
1 AATTTTGATAATCTCG--CT-T-TGAAATATTGATAA-CAACACTATGAAATTTGATAACCTTCT
23062 AT
61 AT
23064 CAAACTTTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
64 2 0.04
65 13 0.23
66 9 0.16
67 9 0.16
68 22 0.39
69 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (63 bp):
AATTTTGATAATCTCGCTTTGAAATATTGATAACAACACTATGAAATTTGATAACCTTCTATA
Found at i:23054 original size:21 final size:23
Alignment explanation
Indices: 22904--23055 Score: 111
Period size: 22 Copynumber: 6.8 Consensus size: 23
22894 TTGTTGACCC
* *
22904 CTCTATGAAATTCTAATAATC-A
1 CTCTATGAAATTTTGATAATCAA
** * *
22926 CAGTATGTAATTTTGATAATC-T
1 CTCTATGAAATTTTGATAATCAA
* *
22948 CGCTTTGAAATTTTGATAA-CAA
1 CTCTATGAAATTTTGATAATCAA
* *
22970 CACTATGAAATTTTGATAATC-T
1 CTCTATGAAATTTTGATAATCAA
* *
22992 TTCTAT-AAATTTTGATAATCCGAT
1 CTCTATGAAATTTTGATAAT-C-AA
*
23016 CTCTATGAAATATTGATAATC-A
1 CTCTATGAAATTTTGATAATCAA
*
23038 CTCTATGAGA-TTTGATAA
1 CTCTATGAAATTTTGATAA
23056 CCTTCTATCA
Statistics
Matches: 103, Mismatches: 21, Indels: 13
0.75 0.15 0.09
Matches are distributed among these distances:
21 21 0.20
22 62 0.60
23 1 0.01
24 7 0.07
25 12 0.12
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (23 bp):
CTCTATGAAATTTTGATAATCAA
Found at i:23124 original size:22 final size:23
Alignment explanation
Indices: 23095--23149 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
23085 AAATTGAAAC
*
23095 TTTT-ATAACCTTCA-TATAAAA
1 TTTTGATAACCTACACTATAAAA
23116 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
23138 TTTTGATAACCT
1 TTTTGATAACCT
23150 CCCCATGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:23347 original size:22 final size:22
Alignment explanation
Indices: 23319--23392 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
23309 ACCTGATCCT
*
23319 ATGAAATTTTGGTAACCGCACC
1 ATGAAATTTTGGTAACCACACC
*
23341 ATGAAATTTTGGTAACCACACT
1 ATGAAATTTTGGTAACCACACC
* * * *
23363 ACGGAATTTTGATAACCTC-CTC
1 ATGAAATTTTGGTAACCACAC-C
23385 ATGAAATT
1 ATGAAATT
23393 ATAATAACCA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 1 0.02
22 41 0.98
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGGTAACCACACC
Found at i:23399 original size:22 final size:22
Alignment explanation
Indices: 23374--23424 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
23364 CGGAATTTTG
23374 ATAACC-TCCTCATGAAATTATA
1 ATAACCAT-CTCATGAAATTATA
* * *
23396 ATAACCATCTTATGAAATTTTG
1 ATAACCATCTCATGAAATTATA
23418 ATAACCA
1 ATAACCA
23425 CATAGAGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (22 bp):
ATAACCATCTCATGAAATTATA
Found at i:23621 original size:19 final size:20
Alignment explanation
Indices: 23590--23627 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
23580 TAGTGACATT
23590 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
23609 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
23628 AGCAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:24759 original size:1 final size:1
Alignment explanation
Indices: 24753--24796 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
24743 CCATTAATGT
24753 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24797 GCAGTTGAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:42469 original size:27 final size:27
Alignment explanation
Indices: 42431--42498 Score: 136
Period size: 27 Copynumber: 2.5 Consensus size: 27
42421 AGGAAGCATC
42431 GTTTTTATTTTTTTGTTTTAGTCTTTA
1 GTTTTTATTTTTTTGTTTTAGTCTTTA
42458 GTTTTTATTTTTTTGTTTTAGTCTTTA
1 GTTTTTATTTTTTTGTTTTAGTCTTTA
42485 GTTTTTATTTTTTT
1 GTTTTTATTTTTTT
42499 TTTATTCTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.76
Consensus pattern (27 bp):
GTTTTTATTTTTTTGTTTTAGTCTTTA
Found at i:42484 original size:7 final size:7
Alignment explanation
Indices: 42431--42496 Score: 57
Period size: 7 Copynumber: 9.9 Consensus size: 7
42421 AGGAAGCATC
42431 GTTTTTA
1 GTTTTTA
* *
42438 TTTTTTT
1 GTTTTTA
42445 G-TTTTA
1 GTTTTTA
*
42451 GTCTTTA
1 GTTTTTA
42458 GTTTTTA
1 GTTTTTA
* *
42465 TTTTTTT
1 GTTTTTA
42472 G-TTTTA
1 GTTTTTA
*
42478 GTCTTTA
1 GTTTTTA
42485 GTTTTTA
1 GTTTTTA
42492 -TTTTT
1 GTTTTT
42497 TTTTTATTCT
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
6 15 0.33
7 30 0.67
ACGTcount: A:0.11, C:0.03, G:0.11, T:0.76
Consensus pattern (7 bp):
GTTTTTA
Found at i:42496 original size:20 final size:20
Alignment explanation
Indices: 42454--42496 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
42444 TGTTTTAGTC
* *
42454 TTTAGTTTTTATTTTTTTGT
1 TTTAGTCTTTATTTTTATGT
42474 TTTAGTCTTTAGTTTTTAT-T
1 TTTAGTCTTTA-TTTTTATGT
42494 TTT
1 TTT
42497 TTTTTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.12, C:0.02, G:0.09, T:0.77
Consensus pattern (20 bp):
TTTAGTCTTTATTTTTATGT
Found at i:43084 original size:15 final size:15
Alignment explanation
Indices: 43064--43094 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43054 TCATCACTGG
43064 AACCCAATACATAGA
1 AACCCAATACATAGA
*
43079 AACCCAATATATAGA
1 AACCCAATACATAGA
43094 A
1 A
43095 CATAGAACAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.23, G:0.06, T:0.16
Consensus pattern (15 bp):
AACCCAATACATAGA
Found at i:48243 original size:20 final size:20
Alignment explanation
Indices: 48218--48258 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
48208 AATCCTCTGC
48218 TTTCTCTGTATCTACTATAA
1 TTTCTCTGTATCTACTATAA
48238 TTTCTCTGTATCTACTATAA
1 TTTCTCTGTATCTACTATAA
48258 T
1 T
48259 AAAAAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTCTCTGTATCTACTATAA
Found at i:50072 original size:30 final size:30
Alignment explanation
Indices: 50019--50132 Score: 147
Period size: 30 Copynumber: 3.8 Consensus size: 30
50009 CCATCACGCG
* * **
50019 TGTACCAAAAAATGACACATGACACACCATG
1 TGTACC-AAAAATGACACGTGACACGCCACA
*
50050 TGTACCAAAAATAACACGTGACACGCCACA
1 TGTACCAAAAATGACACGTGACACGCCACA
* *
50080 TGTACCAAAAATGACACGTGGCATGCCACA
1 TGTACCAAAAATGACACGTGACACGCCACA
*
50110 TGTACAAAAAATGACACGTGACA
1 TGTACCAAAAATGACACGTGACA
50133 TGTCACGTAT
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 67 0.92
31 6 0.08
ACGTcount: A:0.43, C:0.25, G:0.16, T:0.16
Consensus pattern (30 bp):
TGTACCAAAAATGACACGTGACACGCCACA
Found at i:50859 original size:21 final size:21
Alignment explanation
Indices: 50833--50874 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
50823 TGGGGAAGGA
* *
50833 ACCGAAATCAATTCGATAGTT
1 ACCGAAATCAATACAATAGTT
50854 ACCGAAATCAATACAATAGTT
1 ACCGAAATCAATACAATAGTT
50875 GCTTCTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (21 bp):
ACCGAAATCAATACAATAGTT
Done.