Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015626.1 Corchorus olitorius cultivar O-4 contig15659, 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: 42676
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:4171 original size:81 final size:81
Alignment explanation
Indices: 4036--4262 Score: 328
Period size: 81 Copynumber: 2.8 Consensus size: 81
4026 ACTAAGACCT
* * * * *
4036 TTCTCTTCATACTGGATTTTTTTCCTTTTGGGGCTCTTGCCATGATCATGAGGTGCCGACTTGTA
1 TTCTCTTCATACAGAAATGTTTTCCTTTTAGGGCTCTTGCCATGATCATGAGGTGCCGACTTGTA
*
4101 TCCAAAGAAGTTATCA
66 TCCAAAGAAGTCATCA
*
4117 TTCTCTTCATACAGAAATGTTTTCCTTTTAGGGCTCTTGCCATGACCATGAGGTGCCGACTTGTA
1 TTCTCTTCATACAGAAATGTTTTCCTTTTAGGGCTCTTGCCATGATCATGAGGTGCCGACTTGTA
*
4182 TCCAAAGAAGTCATCG
66 TCCAAAGAAGTCATCA
* * * * * *
4198 TTCTTTTCGTACAGAAATGTTGTCCTTTTAGGGCTCTTGCCATGATCACGAGTTGCAGACTTGTA
1 TTCTCTTCATACAGAAATGTTTTCCTTTTAGGGCTCTTGCCATGATCATGAGGTGCCGACTTGTA
4263 CCCCCAGATG
Statistics
Matches: 131, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 131 1.00
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (81 bp):
TTCTCTTCATACAGAAATGTTTTCCTTTTAGGGCTCTTGCCATGATCATGAGGTGCCGACTTGTA
TCCAAAGAAGTCATCA
Found at i:6323 original size:3 final size:3
Alignment explanation
Indices: 6315--6401 Score: 174
Period size: 3 Copynumber: 29.0 Consensus size: 3
6305 TTCTTTCTTA
6315 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6363 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6402 TATATAACAT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17263 original size:66 final size:66
Alignment explanation
Indices: 17157--17287 Score: 262
Period size: 66 Copynumber: 2.0 Consensus size: 66
17147 GACTTCCTTT
17157 TTATTGAGGTTTCTATTAGTTGCTTATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
1 TTATTGAGGTTTCTATTAGTTGCTTATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
17222 A
66 A
17223 TTATTGAGGTTTCTATTAGTTGCTTATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
1 TTATTGAGGTTTCTATTAGTTGCTTATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
17288 CAATGCTAAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (66 bp):
TTATTGAGGTTTCTATTAGTTGCTTATATTTAGTATATTTTCACATTTCCAAAAGCACAGTTAGC
A
Found at i:19072 original size:20 final size:21
Alignment explanation
Indices: 19041--19086 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
19031 GTGTTTGATA
19041 ACATGCGCTCTTGACAAGCTG
1 ACATGCGCTCTTGACAAGCTG
*
19062 ACATG-GCTCTTGACATGCTG
1 ACATGCGCTCTTGACAAGCTG
19082 ACATG
1 ACATG
19087 TATGCCACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (21 bp):
ACATGCGCTCTTGACAAGCTG
Found at i:20257 original size:11 final size:10
Alignment explanation
Indices: 20240--20295 Score: 58
Period size: 11 Copynumber: 5.2 Consensus size: 10
20230 AACTCGATTA
20240 ATGTTCGTTT
1 ATGTTCGTTT
20250 AGTGTTCGTTT
1 A-TGTTCGTTT
*
20261 AATAGATCGTTT
1 -AT-GTTCGTTT
*
20273 ATAGCTCGTTT
1 AT-GTTCGTTT
20284 ATGTTCGTTT
1 ATGTTCGTTT
20294 AT
1 AT
20296 ATTATATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 10 0.25
11 22 0.55
12 8 0.20
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.52
Consensus pattern (10 bp):
ATGTTCGTTT
Found at i:22329 original size:23 final size:23
Alignment explanation
Indices: 22299--22350 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
22289 GGCAAGTGTC
22299 ACCCCCCAATTAAAACACTTGTA
1 ACCCCCCAATTAAAACACTTGTA
22322 ACCCCCCAATTAAAACACTTGTA
1 ACCCCCCAATTAAAACACTTGTA
22345 ACCCCC
1 ACCCCC
22351 TTTTAGAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.37, C:0.40, G:0.04, T:0.19
Consensus pattern (23 bp):
ACCCCCCAATTAAAACACTTGTA
Found at i:25190 original size:21 final size:22
Alignment explanation
Indices: 25166--25223 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 22
25156 CATTTCTTCC
*
25166 TTCTTTTAAT-TATATCTCTTT
1 TTCTTTTAATAGATATCTCTTT
25187 TTCTTTTAAATAGGATATCTCTTT
1 TTCTTTT-AATA-GATATCTCTTT
25211 TTCTTTTATATAG
1 TTCTTTTA-ATAG
25224 GATACACTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 7 0.22
22 3 0.09
23 2 0.06
24 20 0.62
ACGTcount: A:0.22, C:0.12, G:0.05, T:0.60
Consensus pattern (22 bp):
TTCTTTTAATAGATATCTCTTT
Found at i:25209 original size:24 final size:24
Alignment explanation
Indices: 25177--25227 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
25167 TCTTTTAATT
25177 ATATCTCTTTTTCTTTTAAATAGG
1 ATATCTCTTTTTCTTTTAAATAGG
*
25201 ATATCTCTTTTTCTTTTATATAGG
1 ATATCTCTTTTTCTTTTAAATAGG
25225 ATA
1 ATA
25228 CACTTTTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
ATATCTCTTTTTCTTTTAAATAGG
Found at i:27176 original size:15 final size:16
Alignment explanation
Indices: 27156--27190 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
27146 TTTTAAAATC
27156 ACAATTAAA-AAGAAA
1 ACAATTAAACAAGAAA
*
27171 ACAATTAAACTAGAAA
1 ACAATTAAACAAGAAA
27187 ACAA
1 ACAA
27191 AGCAAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (16 bp):
ACAATTAAACAAGAAA
Found at i:29566 original size:24 final size:24
Alignment explanation
Indices: 29539--29585 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
29529 AAATTCCCAT
29539 TGAAAAAAAAAGGAA-AAGAAAAAA
1 TGAAAAAAAAA-GAAGAAGAAAAAA
29563 TGAAAAAAAAAGAAGAAGAAAAA
1 TGAAAAAAAAAGAAGAAGAAAAA
29586 GGCACTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (24 bp):
TGAAAAAAAAAGAAGAAGAAAAAA
Found at i:31593 original size:22 final size:22
Alignment explanation
Indices: 31568--31617 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
31558 TGCATTTGTA
31568 AGACCTCCT-GGCACAATTTCAG
1 AGACCT-CTGGGCACAATTTCAG
*
31590 AGACCTCTGGGCACAATTTTAG
1 AGACCTCTGGGCACAATTTCAG
*
31612 AAACCT
1 AGACCT
31618 TCGGATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (22 bp):
AGACCTCTGGGCACAATTTCAG
Found at i:31699 original size:167 final size:167
Alignment explanation
Indices: 31423--31767 Score: 609
Period size: 167 Copynumber: 2.1 Consensus size: 167
31413 TGCATTTATA
*
31423 AGACCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCATC
1 AGACCTCCGGGCACAATTTCAGAAACCTCCGGATATTAATTCTGATAAATCCTCCGGGTATCATC
*
31488 TCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAGTTTCAAAATGAAAACCTTGCTCAAGGTC
66 TCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTC
*
31553 GAGTTTGCATTTGTAAGACCTCCTGGCACAATTTCAG
131 GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAG
* * *
31590 AGACCTCTGGGCACAATTTTAGAAACCTTCGGATATTAATTCTGATAAATCCTCCGGGTATCATC
1 AGACCTCCGGGCACAATTTCAGAAACCTCCGGATATTAATTCTGATAAATCCTCCGGGTATCATC
*
31655 TCATTTCGTCAAGTTTTTAATCAAAGTTGCGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTC
66 TCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTC
*
31720 GAGTTTGCATTTGTAAGACCTCCGGGCGCAATTTCAG
131 GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAG
*
31757 AAACCTCCGGG
1 AGACCTCCGGG
31768 TATTAATTCT
Statistics
Matches: 168, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
167 168 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (167 bp):
AGACCTCCGGGCACAATTTCAGAAACCTCCGGATATTAATTCTGATAAATCCTCCGGGTATCATC
TCATTTCATCAAGTTTTTAATCAAAGTTGCGTTTAAGTTTCAAAATCAAAACCTTGCTCAAGGTC
GAGTTTGCATTTGTAAGACCTCCGGGCACAATTTCAG
Found at i:32015 original size:146 final size:146
Alignment explanation
Indices: 31590--32122 Score: 776
Period size: 146 Copynumber: 3.7 Consensus size: 146
31580 ACAATTTCAG
* * * *
31590 AGACCTCTGGGCACAATTTTAGAAACCT-TCGGATATTAATTCTGATAAATCCTCCGGGTATCAT
1 AGACCTCCGGGCACAATTTCAGAAACCTCT-GGGTATTAATTCTGATAAATCCTCCGGGTATCAC
* * **
31654 CTCATTTCGTCAAGTTTTTAATCAAAGTTGCGTTTAAGTTTC-AAAATCAAAACCTTGCTCAAGG
65 CTCATTTCATCAAGTTGTTAATCAAAGTTGCGTTTAAGTTTCAAAAAAAAAAACCTTGCTCAAGG
31718 TCGAGTTTGCATTTGTA
130 TCGAGTTTGCATTTGTA
* *
31735 AGACCTCCGGGCGCAATTTCAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCA--
1 AGACCTCCGGGCACAATTTCAGAAACCTCTGGGTATTAATTCTGATAAATCCTCCGGGTATCACC
* *
31798 TC---TCATCAAGTTTTTAATCAAAGTTGCGTTTAAGTCT-AAAAAAAAGAAACCTTGCTCAAGG
66 TCATTTCATCAAGTTGTTAATCAAAGTTGCGTTTAAGTTTCAAAAAAAA-AAACCTTGCTCAAGG
*
31859 TCGAGTTTGCATTTGTG
130 TCGAGTTTGCATTTGTA
*
31876 AGACCTCCGGGCACAATTTCAGAAACCTCTAGGTATTAATTCTGATAAATCCTCCGGGTATCACC
1 AGACCTCCGGGCACAATTTCAGAAACCTCTGGGTATTAATTCTGATAAATCCTCCGGGTATCACC
* *
31941 TTATTTCATCAAGTTGTTAATCAAAGTTGCATTTAAGTTTCAAAAAAAAAAACCTTGCTCAAGGT
66 TCATTTCATCAAGTTGTTAATCAAAGTTGCGTTTAAGTTTCAAAAAAAAAAACCTTGCTCAAGGT
* *
32006 CAAGTTTGCATTTGCA
131 CGAGTTTGCATTTGTA
* * * *
32022 AGTCCTCTGGGCAGAATTTCAGAAAGCTCTGGGTATTAATTCTGATAAATCCTCCGGGTATCACC
1 AGACCTCCGGGCACAATTTCAGAAACCTCTGGGTATTAATTCTGATAAATCCTCCGGGTATCACC
* *
32087 TCATTTCGTCCAGTTGTTAATCAAAGTTGCGTTTAA
66 TCATTTCATCAAGTTGTTAATCAAAGTTGCGTTTAA
32123 TTTTTTTTCA
Statistics
Matches: 350, Mismatches: 29, Indels: 17
0.88 0.07 0.04
Matches are distributed among these distances:
140 38 0.11
141 91 0.26
143 3 0.01
145 57 0.16
146 153 0.44
147 8 0.02
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (146 bp):
AGACCTCCGGGCACAATTTCAGAAACCTCTGGGTATTAATTCTGATAAATCCTCCGGGTATCACC
TCATTTCATCAAGTTGTTAATCAAAGTTGCGTTTAAGTTTCAAAAAAAAAAACCTTGCTCAAGGT
CGAGTTTGCATTTGTA
Found at i:32421 original size:39 final size:38
Alignment explanation
Indices: 32342--32775 Score: 406
Period size: 39 Copynumber: 11.0 Consensus size: 38
32332 AATCACAATA
* *
32342 CTATTCAGGATCATTGCTTTATCAAATTAATTTCAGAATC
1 CTATTCAGGATCATTGC-TTATC-AGTTAATTTCAAAATC
*
32382 CTACTCAGGATCATTGCCATT-TCAGTTAATTTCAAAATC
1 CTATTCAGGATCATTG-C-TTATCAGTTAATTTCAAAATC
* * * *
32421 CTATTCAGGATCTTTGCCTTATCAAATCAATTTCGAAATC
1 CTATTCAGGATCATTG-CTTATC-AGTTAATTTCAAAATC
* * * *
32461 CTATAT-AGGATCATTACTTTATTAGATCAAATTTCACAATC
1 CTAT-TCAGGATCATTGC-TTATCAG-T-TAATTTCAAAATC
* *
32502 CTATTCAGGATCATTGCATCATCAGTCAATTT-AGAAATC
1 CTATTCAGGATCATTGC-TTATCAGTTAATTTCA-AAATC
* * * *
32541 CTTTTCAGGATTATTTCTTTACCAGTTAATTTCAAAATC
1 CTATTCAGGATCATTGC-TTATCAGTTAATTTCAAAATC
*
32580 CTATTCAGGATCATTGCCTTATCAGTTAATTTCGAAATC
1 CTATTCAGGATCATTG-CTTATCAGTTAATTTCAAAATC
* * *
32619 CTATTCAGGATCATTGATTTATCAGTCAATTTCAGAATC
1 CTATTCAGGATCATTG-CTTATCAGTTAATTTCAAAATC
* * * *
32658 CTATTCAGGATCATTTCTTGACCAGTTTATTTCGAAATC
1 CTATTCAGGATCATTGCTT-ATCAGTTAATTTCAAAATC
* * *
32697 CTATTCAAGATCGTTGCTTTACCAGTTAATTTCAAAAATC
1 CTATTCAGGATCATTGC-TTATCAGTTAATTTC-AAAATC
* *
32737 CTATTTAGGATCATTGTTTTATCAGTTAATTTCAAAATC
1 CTATTCAGGATCATTG-CTTATCAGTTAATTTCAAAATC
32776 TTGTTTTTGT
Statistics
Matches: 323, Mismatches: 56, Indels: 31
0.79 0.14 0.08
Matches are distributed among these distances:
38 5 0.02
39 200 0.62
40 85 0.26
41 33 0.10
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (38 bp):
CTATTCAGGATCATTGCTTATCAGTTAATTTCAAAATC
Found at i:32593 original size:78 final size:78
Alignment explanation
Indices: 32309--32775 Score: 480
Period size: 78 Copynumber: 5.9 Consensus size: 78
32299 TTAATCCTGC
* * * * * *
32309 TCAGGATCATTTCTTTACCAGTCAA--TCACAATACTATTCAGGATCATTGCTTTATCAAATTAA
1 TCAGGATCATTGCTTTACCAGTTAATTTCAAAATCCTATTCAGGATCATTGCCTTATC-AGTTAA
*
32372 TTTC-AGAATCCTAC
65 TTTCGA-AATCCTAT
* * *
32386 TCAGGATCATTGCCATTT--CAGTTAATTTCAAAATCCTATTCAGGATCTTTGCCTTATCAAATC
1 TCAGGATCATTG-C-TTTACCAGTTAATTTCAAAATCCTATTCAGGATCATTGCCTTATC-AGTT
32449 AATTTCGAAATCCTAT
63 AATTTCGAAATCCTAT
* ** * * * * *
32465 AT-AGGATCATTACTTTATTAGATCAAATTTCACAATCCTATTCAGGATCATTGCATCATCAGTC
1 -TCAGGATCATTGCTTTACCAG-T-TAATTTCAAAATCCTATTCAGGATCATTGCCTTATCAGTT
* *
32529 AATTTAGAAATCCTTT
63 AATTTCGAAATCCTAT
* *
32545 TCAGGATTATTTCTTTACCAGTTAATTTCAAAATCCTATTCAGGATCATTGCCTTATCAGTTAAT
1 TCAGGATCATTGCTTTACCAGTTAATTTCAAAATCCTATTCAGGATCATTGCCTTATCAGTTAAT
32610 TTCGAAATCCTAT
66 TTCGAAATCCTAT
* * * * * * *
32623 TCAGGATCATTGATTTATCAGTCAATTTCAGAATCCTATTCAGGATCATT-TCTTGACCAGTTTA
1 TCAGGATCATTGCTTTACCAGTTAATTTCAAAATCCTATTCAGGATCATTGCCTT-ATCAGTTAA
32687 TTTCGAAATCCTAT
65 TTTCGAAATCCTAT
* * * **
32701 TCAAGATCGTTGCTTTACCAGTTAATTTCAAAAATCCTATTTAGGATCATTGTTTTATCAGTTAA
1 TCAGGATCATTGCTTTACCAGTTAATTTC-AAAATCCTATTCAGGATCATTGCCTTATCAGTTAA
*
32766 TTTCAAAATC
65 TTTCGAAATC
32776 TTGTTTTTGT
Statistics
Matches: 327, Mismatches: 49, Indels: 26
0.81 0.12 0.06
Matches are distributed among these distances:
77 23 0.07
78 140 0.43
79 95 0.29
80 38 0.12
81 31 0.09
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (78 bp):
TCAGGATCATTGCTTTACCAGTTAATTTCAAAATCCTATTCAGGATCATTGCCTTATCAGTTAAT
TTCGAAATCCTAT
Found at i:32643 original size:117 final size:118
Alignment explanation
Indices: 32309--32775 Score: 497
Period size: 117 Copynumber: 4.0 Consensus size: 118
32299 TTAATCCTGC
* * *
32309 TCAGGATCATTTCTTTACCAGTCAA--TCACAATACTATTCAGGATCATTGCTTTATCAAATTAA
1 TCAGGATCATTTCTTTACCAGTCAATTTCAAAATCCTATTCAGGATCATTGCTTTATC-AGTTAA
* * *
32372 TTTCAGAATCCTACTCAGGATCATTGCCATT-TCAGTTAATTTCA-AAATCCTAT
65 TTTCACAATCCTATTCAGGATCATTG-CATTATCAGTCAATTTCAGAAATCCTAT
* * * * * *
32425 TCAGGATC-TTTGCCTTATCAAATCAATTTCGAAATCCTATAT-AGGATCATTACTTTATTAGAT
1 TCAGGATCATTT-CTTTA-CCAGTCAATTTCAAAATCCTAT-TCAGGATCATTGCTTTATCAG-T
* * *
32488 CAAATTTCACAATCCTATTCAGGATCATTGCATCATCAGTCAATTT-AGAAATCCTTT
62 -TAATTTCACAATCCTATTCAGGATCATTGCATTATCAGTCAATTTCAGAAATCCTAT
* * *
32545 TCAGGATTATTTCTTTACCAGTTAATTTCAAAATCCTATTCAGGATCATTGCCTTATCAGTTAAT
1 TCAGGATCATTTCTTTACCAGTCAATTTCAAAATCCTATTCAGGATCATTGCTTTATCAGTTAAT
32610 TTCGA-AATCCTATTCAGGATCATTG-ATTTATCAGTCAATTTCAG-AATCCTAT
66 TTC-ACAATCCTATTCAGGATCATTGCA-TTATCAGTCAATTTCAGAAATCCTAT
* ** * * * *
32662 TCAGGATCATTTCTTGACCAGTTTATTTCGAAATCCTATTCAAGATCGTTGCTTTACCAGTTAAT
1 TCAGGATCATTTCTTTACCAGTCAATTTCAAAATCCTATTCAGGATCATTGCTTTATCAGTTAAT
* * ** *
32727 TTCAAAAATCCTATTTAGGATCATTGTTTTATCAGTTAATTTCA-AAATC
66 TTC-ACAATCCTATTCAGGATCATTGCATTATCAGTCAATTTCAGAAATC
32776 TTGTTTTTGT
Statistics
Matches: 295, Mismatches: 39, Indels: 32
0.81 0.11 0.09
Matches are distributed among these distances:
115 3 0.01
116 13 0.04
117 113 0.38
118 44 0.15
119 63 0.21
120 56 0.19
121 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (118 bp):
TCAGGATCATTTCTTTACCAGTCAATTTCAAAATCCTATTCAGGATCATTGCTTTATCAGTTAAT
TTCACAATCCTATTCAGGATCATTGCATTATCAGTCAATTTCAGAAATCCTAT
Found at i:33107 original size:24 final size:24
Alignment explanation
Indices: 33076--33126 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
33066 TCTTTTAATT
33076 ATATCTCTTTTTCTTTTAAATAGG
1 ATATCTCTTTTTCTTTTAAATAGG
*
33100 ATATCTCTTTTTCTTTTATATAGG
1 ATATCTCTTTTTCTTTTAAATAGG
33124 ATA
1 ATA
33127 CACTTTTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
ATATCTCTTTTTCTTTTAAATAGG
Found at i:35221 original size:3 final size:3
Alignment explanation
Indices: 35213--35248 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
35203 CCCTGCCTGA
* *
35213 ATT ATT ATT ATT GTT TTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35249 TTCTTAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:39680 original size:27 final size:27
Alignment explanation
Indices: 39623--39722 Score: 89
Period size: 27 Copynumber: 3.7 Consensus size: 27
39613 AAGTGAACCT
*
39623 AAAATGACCAAAATG-CCCT-TTGTGC
1 AAAATGACCAAAATGCCCCTGATGTGC
39648 AAAAATGACCAAAATGCCCCTGGATGTGC
1 -AAAATGACCAAAATGCCCCT-GATGTGC
* * * **
39677 -AAATGACTAATATGCCCCTGAATATAA
1 AAAATGACCAAAATGCCCCTG-ATGTGC
*
39704 AAAATGACCAAAATACCCC
1 AAAATGACCAAAATGCCCC
39723 CTAGATGACC
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
26 16 0.27
27 24 0.40
28 15 0.25
29 5 0.08
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGATGTGC
Found at i:39804 original size:3 final size:3
Alignment explanation
Indices: 39796--39905 Score: 211
Period size: 3 Copynumber: 36.3 Consensus size: 3
39786 GGGTGTCTAC
39796 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39844 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
39890 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
39906 TAGTTTGAAT
Statistics
Matches: 106, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 103 0.97
4 3 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40751 original size:33 final size:32
Alignment explanation
Indices: 40698--40764 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
40688 AAATAAGCCA
*
40698 TTTTTATTTTCAAGCAAAGGGAAGGTTCCCATT
1 TTTTTATTTTCAAG-AAAGGGAAAGTTCCCATT
40731 TTTTTAGTTTTACAAG-AAGGGAAAGTTCCCATT
1 TTTTTA-TTTT-CAAGAAAGGGAAAGTTCCCATT
40764 T
1 T
40765 CCAGTTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 23 0.74
34 4 0.13
35 4 0.13
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (32 bp):
TTTTTATTTTCAAGAAAGGGAAAGTTCCCATT
Found at i:41418 original size:3 final size:3
Alignment explanation
Indices: 41410--41483 Score: 121
Period size: 3 Copynumber: 24.0 Consensus size: 3
41400 AAATAACAAG
41410 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
41458 ATT ATT ATT ATAT ACT ATAT ATT ATT
1 ATT ATT ATT AT-T ATT AT-T ATT ATT
41484 TTTAGTGACT
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
3 62 0.93
4 5 0.07
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.