Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006572.1 Corchorus capsularis cultivar CVL-1 contig06593, 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: 54585
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:15831 original size:10 final size:10
Alignment explanation
Indices: 15802--15846 Score: 67
Period size: 9 Copynumber: 4.6 Consensus size: 10
15792 TTATCATCAA
15802 AATTAATTTTC
1 AATT-ATTTTC
15813 AATTA-TTTC
1 AATTATTTTC
15822 AATTATTTTC
1 AATTATTTTC
15832 AATTATTTT-
1 AATTATTTTC
15841 AATTAT
1 AATTAT
15847 CATTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 15 0.45
10 14 0.42
11 4 0.12
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (10 bp):
AATTATTTTC
Found at i:15831 original size:19 final size:19
Alignment explanation
Indices: 15802--15846 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
15792 TTATCATCAA
15802 AATTAATTTTCAATTATTTC
1 AATT-ATTTTCAATTATTTC
*
15822 AATTATTTTCAATTATTTT
1 AATTATTTTCAATTATTTC
15841 AATTAT
1 AATTAT
15847 CATTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTATTTTCAATTATTTC
Found at i:17248 original size:1 final size:1
Alignment explanation
Indices: 17242--17274 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
17232 AGCCTATGGC
17242 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17275 CTAGATCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18179 original size:28 final size:26
Alignment explanation
Indices: 18148--18208 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 26
18138 TTATTTTAGA
18148 CAAACTCTTAACCAATTTTAATCTCAAC
1 CAAACTCTT-A-CAATTTTAATCTCAAC
18176 CAAACTC--ACAATTTTAATCTCAAC
1 CAAACTCTTACAATTTTAATCTCAAC
*
18200 CAACCTCTT
1 CAAACTCTT
18209 CAAGATTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 22 0.73
25 1 0.03
28 7 0.23
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (26 bp):
CAAACTCTTACAATTTTAATCTCAAC
Found at i:18306 original size:34 final size:34
Alignment explanation
Indices: 18262--18331 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
18252 ATATCCACTT
18262 AACCCATAATATATAATTGGAATTGGACTAAGAA
1 AACCCATAATATATAATTGGAATTGGACTAAGAA
* * *
18296 AACCCGTAATATATAATTTGAATTGGACTAATAA
1 AACCCATAATATATAATTGGAATTGGACTAAGAA
18330 AA
1 AA
18332 ATTCAACCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (34 bp):
AACCCATAATATATAATTGGAATTGGACTAAGAA
Found at i:18360 original size:39 final size:40
Alignment explanation
Indices: 18296--18376 Score: 112
Period size: 39 Copynumber: 2.0 Consensus size: 40
18286 GGACTAAGAA
* *
18296 AACCCGTAATATATAATTTGAATTGGACTA-ATAAAAATTC
1 AACCCGTAACATATAATTGGAATTGGACTATA-AAAAATTC
*
18336 AACCCGT-ACATATAATTGGAATTGGACTTTAAAAAATTC
1 AACCCGTAACATATAATTGGAATTGGACTATAAAAAATTC
18375 AA
1 AA
18377 TTTGATTACT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (40 bp):
AACCCGTAACATATAATTGGAATTGGACTATAAAAAATTC
Found at i:18489 original size:2 final size:2
Alignment explanation
Indices: 18482--18513 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
18472 CTACTTATTA
*
18482 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18514 TAATTTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19257 original size:5 final size:6
Alignment explanation
Indices: 19243--19278 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
19233 TATATTTCTG
19243 TTTTAT TTTTAT TTTTGCAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTT--AT TTTTAT TTTTAT TTTT
19279 TTGATAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 22 0.79
8 6 0.21
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:20040 original size:17 final size:18
Alignment explanation
Indices: 19998--20046 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
19988 CTTTCACTTC
*
19998 TAATT-AATATTTATTAT
1 TAATTGAATATTTGTTAT
*
20015 TATTTGAATATTTGTT-T
1 TAATTGAATATTTGTTAT
*
20032 TAATTGAATTTTTGT
1 TAATTGAATATTTGT
20047 GATTTCTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
TAATTGAATATTTGTTAT
Found at i:20097 original size:24 final size:24
Alignment explanation
Indices: 20069--20118 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
20059 CTTATTATTT
20069 TTAAGTATTTCAAAATACATTTTG
1 TTAAGTATTTCAAAATACATTTTG
*
20093 TTAAGTATTTCAAAATATATTTTG
1 TTAAGTATTTCAAAATACATTTTG
20117 TT
1 TT
20119 CAAACGCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (24 bp):
TTAAGTATTTCAAAATACATTTTG
Found at i:28407 original size:20 final size:21
Alignment explanation
Indices: 28382--28420 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
28372 TTCGTGTTGG
28382 TTAAGTGTTTG-TTGCGTTTA
1 TTAAGTGTTTGATTGCGTTTA
28402 TTAAGTGTTTGATTGCGTT
1 TTAAGTGTTTGATTGCGTT
28421 CGTTTATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.15, C:0.05, G:0.26, T:0.54
Consensus pattern (21 bp):
TTAAGTGTTTGATTGCGTTTA
Found at i:34387 original size:2 final size:2
Alignment explanation
Indices: 34380--34416 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
34370 CTACTACTAC
34380 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34417 GTAGTAGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:35349 original size:21 final size:22
Alignment explanation
Indices: 35314--35355 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
35304 AAACTATAAT
35314 TATATATAGTATAAT-ATATTG
1 TATATATAGTATAATGATATTG
* *
35335 TATATATATTCTAATGATATT
1 TATATATAGTATAATGATATT
35356 TGCACATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (22 bp):
TATATATAGTATAATGATATTG
Found at i:36596 original size:6 final size:6
Alignment explanation
Indices: 36585--36628 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
36575 AACTAATTAA
*
36585 CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CTGTCT CTGCCT CT
1 CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CTGCCT CT
36629 TGCTTTCTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.48, G:0.16, T:0.36
Consensus pattern (6 bp):
CTGCCT
Found at i:39712 original size:35 final size:35
Alignment explanation
Indices: 39666--39732 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
39656 ATCAGGTTCA
39666 CTGTGCTCATGGGGCACACCGATCGAGTCTAAAAC
1 CTGTGCTCATGGGGCACACCGATCGAGTCTAAAAC
*
39701 CTGTGCTCATGGGGCACATCGATCGAGTCTAA
1 CTGTGCTCATGGGGCACACCGATCGAGTCTAA
39733 CCGAGTTCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (35 bp):
CTGTGCTCATGGGGCACACCGATCGAGTCTAAAAC
Found at i:40323 original size:20 final size:19
Alignment explanation
Indices: 40283--40320 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40273 TCTTGATGAA
*
40283 AAAATAGCCACGTGGCATT
1 AAAATAGCCACGTGGAATT
40302 AAAATAGCCACGTGGAATT
1 AAAATAGCCACGTGGAATT
40321 TAATTGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (19 bp):
AAAATAGCCACGTGGAATT
Found at i:41471 original size:19 final size:20
Alignment explanation
Indices: 41447--41485 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
41437 AATTTTTTTG
41447 GCAATAA-AATTAATT-TATA
1 GCAATAATAA-TAATTATATA
41466 GCAATAATAATAATTATATA
1 GCAATAATAATAATTATATA
41486 TATAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
GCAATAATAATAATTATATA
Found at i:41996 original size:5 final size:5
Alignment explanation
Indices: 41986--42014 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
41976 GAAAACATCT
41986 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
42015 TATTTGCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:44181 original size:334 final size:327
Alignment explanation
Indices: 42825--44148 Score: 1333
Period size: 329 Copynumber: 4.0 Consensus size: 327
42815 TCATGATGGT
* *
42825 AAAAA-TGATCCAAAAGATTTTTCCTCAATTTTTGGCA-AAAATACTCATAAAATATATATAATT
1 AAAAATTGATCC-AAAGATTTTTCCTCAATTTTTAG-ATAAAATACTCATAAAAAATATATAATT
** * * * *
42888 CAGGT-CAAAAGGATTCAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTATTCTGAATT
64 CAACTCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCATTTTT-ATATTT-TTCTAAATT
* * * * *
42952 AATTTCTAATTAAATCGAAATAAGATTCAAATGCACATAAAAACAAATTCTTAAATCCAATGTGC
127 AATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGG
* * * *
43017 CTGAGATTTGATTAGATGAATAAAGATATTTCAAGAAGTCTCGGCGACAAAAATCATGCAAAACA
191 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT
* * * * * * * * *
43082 GAGCCGTGACC-CTAAAACACGTTTTTAGCTAAAAACCGTGATGATTAGTACATGATTTCAGCTA
256 GAGTCGGGGCCTC-GAAACGCGTTTTTAGCAAAAAACCATGAT-ATTAGTACACGATTTCGGCTA
43146 AAATTTTGC
319 AAATTTTGC
* * *
43155 AAAACTTGATCTCAAAGATATTTCCTCAATTTTTTA-CTAAAAATACTCATAAAAAATATATAAT
1 AAAAATTGATC-CAAAGATTTTTCCTCAA-TTTTTAGAT-AAAATACTCATAAAAAATATATAAT
** * * * * * *
43219 TTGACTTCAAAAAGATTGAAGGGCTTTTAAC-ATTTCTAATA--A-TATT-T-TTTTTCCAAATT
63 TCAACTCCAAAAAGATTGAAGGACTTTTCACGCTTT-TAATATCATTTTTATATTTTTCTAAATT
* * * *
43278 AATTTCTAATTAAATCAAAACAAGATCCAAATGCTTGTAAAAAAAAATCCTTAAATCTAATGTGG
127 AATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATC-AATGTGG
* ** * * *
43343 ATGAGATTTGGGTAGATGAATATATATATTTCAAGGAGTCTTGGCACC-AAAATCATGCAAAACT
191 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT
* * * ** * * *
43407 GAGTC-AGGTCTCGAAACGCG-TCTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCTGCTAA
256 GAGTCGGGGCCTCGAAACGCGTTTTTAGCAAAAAACCATGAT-ATTAGTACACGATTTCGGCTAA
43470 AATTTTGC
320 AATTTTGC
* * *
43478 AAAAATTGACCCGAAAGATCTTTCCTCAATTTCTAG-TGAAAATACTCATAAAAAATATATAATT
1 AAAAATTGATCC-AAAGATTTTTCCTCAATTTTTAGAT-AAAATACTCATAAAAAATATATAATT
* * **
43542 CAA-TGCCAAGAAA-ATTGAAAGCCTTTTTCACGCTTTTAATATTGTTTTATATATTTTTCTAAA
64 CAACT-CCAA-AAAGATTGAAGGAC-TTTTCACGCTTTTAATATCATTTT-TATATTTTTCTAAA
** *
43605 TTAAAATCTAATTAAATCTAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATTCAATGT
125 TTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAA-TCAATGT
* * * *
43670 GACTGAGATTTGATTAGGTGAATACAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAA
189 GGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA
* ** * *
43735 CTAAGTTTGGGCTTCGAAACGCGTTTTTATATAGCAAAAAACCGTGATTATTAGTACACGATTTC
254 CTGAGTCGGGGCCTCGAAACGCG--TTT-T-TAGCAAAAAACCATGA-TATTAGTACACGATTTC
*
43800 GTCTAAAATTTTGC
314 GGCTAAAATTTTGC
* * * *
43814 AAAAAGTGACCCCAAA-ATTTTTCCGTCAATTTTTGGATAAAATACTTATAAAAAATATATAATT
1 AAAAATTGA-TCCAAAGATTTTTCC-TCAATTTTTAGATAAAATACTCATAAAAAATATATAATT
* *
43878 CAACTCCAAAAA-AGTT-AGAGGACTTTTCACGCTTTTAATATCATTTTTCATATTTTTTTGAAT
64 CAACTCCAAAAAGA-TTGA-AGGACTTTTCACGCTTTTAATATCATTTTT-ATATTTTTCTAAAT
* * *
43941 TATTTTTTAATTAAATCGAAACAAGATTCATATGCTCGTAAAAA-AAATCCTTAAATGCAATGTG
126 TAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAAT-CAATGTG
* ** * * *
44005 GCTGAGATTTGATTAGATGAATATAGATATTTTAAGGAGTCTCGATGCCAAATATCATACAAAAT
190 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAC
* * * **
44070 TGAGTCGGGGCCACGAAACGCATTTTCAGCAAATAAATTAT-ATATTTAGTACACGATTTCGGCT
255 TGAGTCGGGGCCTCGAAACGCGTTTTTAGCAAA-AAACCATGATA-TTAGTACACGATTTCGGCT
*
44134 AAAATTTTAC
318 AAAATTTTGC
44144 AAAAA
1 AAAAA
44149 AATATCCAGA
Statistics
Matches: 826, Mismatches: 128, Indels: 80
0.80 0.12 0.08
Matches are distributed among these distances:
321 1 0.00
322 45 0.05
323 83 0.10
324 11 0.01
325 21 0.03
326 102 0.12
327 4 0.00
328 2 0.00
329 107 0.13
330 67 0.08
331 37 0.04
332 38 0.05
333 26 0.03
334 93 0.11
335 85 0.10
336 98 0.12
337 6 0.01
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (327 bp):
AAAAATTGATCCAAAGATTTTTCCTCAATTTTTAGATAAAATACTCATAAAAAATATATAATTCA
ACTCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCATTTTTATATTTTTCTAAATTAATT
TCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCAATGTGGCTGAG
ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTC
GGGGCCTCGAAACGCGTTTTTAGCAAAAAACCATGATATTAGTACACGATTTCGGCTAAAATTTT
GC
Found at i:44194 original size:334 final size:327
Alignment explanation
Indices: 42825--44210 Score: 1342
Period size: 334 Copynumber: 4.2 Consensus size: 327
42815 TCATGATGGT
* *
42825 AAAAA-TGATCCAAAAGATTTTTCCTCAATTTTTGGCAAAAATACTCATAAAATATATATAATTC
1 AAAAATTGATCC-AAAGATTTTTCCTCAATTTTTAGCAAAAATACTCATAAAAAATATATAATTC
** * * * *
42889 AGGT-CAAAAGGATTCAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTATTCTGAATTA
65 AACTCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCATTTTT-ATATTT-TTCTAAATTA
* * * * *
42953 ATTTCTAATTAAATCGAAATAAGATTCAAATGCACATAAAAACAAATTCTTAAATCCAATGTGCC
128 ATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAAT-CAATGTGGC
* * * *
43018 TGAGATTTGATTAGATGAATAAAGATATTTCAAGAAGTCTCGGCGACAAAAATCATGCAAAACAG
192 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTG
* * * * * * * * *
43083 AGCCGTGACC-CTAAAACACGTTTTTAGCTAAAAACCGTGATGATTAGTACATGATTTCAGCTAA
257 AGTCGGGGCCTC-GAAACGCGTTTTTAGCAAAAAACCATGAT-ATTAGTACACGATTTCGGCTAA
43147 AATTTTGC
320 AATTTTGC
* *
43155 AAAACTTGATCTCAAAGATATTTCCTCAATTTTTTA-CTAAAAATACTCATAAAAAATATATAAT
1 AAAAATTGATC-CAAAGATTTTTCCTCAA-TTTTTAGC-AAAAATACTCATAAAAAATATATAAT
** * * * * * *
43219 TTGACTTCAAAAAGATTGAAGGGCTTTTAAC-ATTTCTAATA--A-TATT-T-TTTTTCCAAATT
63 TCAACTCCAAAAAGATTGAAGGACTTTTCACGCTTT-TAATATCATTTTTATATTTTTCTAAATT
* * * *
43278 AATTTCTAATTAAATCAAAACAAGATCCAAATGCTTGTAAAAAAAAATCCTTAAATCTAATGTGG
127 AATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATC-AATGTGG
* ** * * *
43343 ATGAGATTTGGGTAGATGAATATATATATTTCAAGGAGTCTTGGCACC-AAAATCATGCAAAACT
191 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACT
* * * ** * * *
43407 GAGTC-AGGTCTCGAAACGCG-TCTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCTGCTAA
256 GAGTCGGGGCCTCGAAACGCGTTTTTAGCAAAAAACCATGAT-ATTAGTACACGATTTCGGCTAA
43470 AATTTTGC
320 AATTTTGC
* * * **
43478 AAAAATTGACCCGAAAGATCTTTCCTCAATTTCTAGTGAAAATACTCATAAAAAATATATAATTC
1 AAAAATTGATCC-AAAGATTTTTCCTCAATTTTTAGCAAAAATACTCATAAAAAATATATAATTC
* * **
43543 AA-TGCCAAGAAA-ATTGAAAGCCTTTTTCACGCTTTTAATATTGTTTTATATATTTTTCTAAAT
65 AACT-CCAA-AAAGATTGAAGGAC-TTTTCACGCTTTTAATATCATTTT-TATATTTTTCTAAAT
** *
43606 TAAAATCTAATTAAATCTAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATTCAATGTG
126 TAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAA-TCAATGTG
* * * *
43671 ACTGAGATTTGATTAGGTGAATACAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAAC
190 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAC
* ** * *
43736 TAAGTTTGGGCTTCGAAACGCGTTTTTATATAGCAAAAAACCGTGATTATTAGTACACGATTTCG
255 TGAGTCGGGGCCTCGAAACGCG--TTT-T-TAGCAAAAAACCATGA-TATTAGTACACGATTTCG
*
43801 TCTAAAATTTTGC
315 GCTAAAATTTTGC
* * * *
43814 AAAAAGTGACCCCAAA-ATTTTTCCGTCAATTTTT-GGATAAAATACTTATAAAAAATATATAAT
1 AAAAATTGA-TCCAAAGATTTTTCC-TCAATTTTTAGCA-AAAATACTCATAAAAAATATATAAT
* *
43877 TCAACTCCAAAAA-AGTT-AGAGGACTTTTCACGCTTTTAATATCATTTTTCATATTTTTTTGAA
63 TCAACTCCAAAAAGA-TTGA-AGGACTTTTCACGCTTTTAATATCATTTTT-ATATTTTTCTAAA
* * *
43940 TTATTTTTTAATTAAATCGAAACAAGATTCATATGCTCGTAAAAA-AAATCCTTAAATGCAATGT
125 TTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAAT-CAATGT
* ** * *
44004 GGCTGAGATTTGATTAGATGAATATAGATATTTTAAGGAGTCTCGATGCCAAATATCATACAAAA
189 GGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAA
* * * * **
44069 TTGAGTCGGGGCCACGAAACGCATTTTCAGCAAATAAATTAT-ATATTTAGTACACGATTTCGGC
254 CTGAGTCGGGGCCTCGAAACGCGTTTTTAGCAAA-AAACCATGATA-TTAGTACACGATTTCGGC
*
44133 TAAAATTTTAC
317 TAAAATTTTGC
* ** * * *
44144 AAAAAAAT-ATCCAGATTATTTTTTTTTCCTCAATTTTTAGCCATAATACTTAT-AAAAATATAT
1 -AAAAATTGATCCA-A--A--GATTTTTCCTCAATTTTTAGCAAAAATACTCATAAAAAATATAT
44207 AATT
60 AATT
44211 TATATAATTA
Statistics
Matches: 874, Mismatches: 135, Indels: 91
0.79 0.12 0.08
Matches are distributed among these distances:
321 1 0.00
322 44 0.05
323 83 0.09
324 11 0.01
325 21 0.02
326 102 0.12
327 4 0.00
328 2 0.00
329 110 0.13
330 64 0.07
331 44 0.05
332 40 0.05
333 40 0.05
334 112 0.13
335 94 0.11
336 97 0.11
337 5 0.01
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Consensus pattern (327 bp):
AAAAATTGATCCAAAGATTTTTCCTCAATTTTTAGCAAAAATACTCATAAAAAATATATAATTCA
ACTCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCATTTTTATATTTTTCTAAATTAATT
TCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCAATGTGGCTGAG
ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTC
GGGGCCTCGAAACGCGTTTTTAGCAAAAAACCATGATATTAGTACACGATTTCGGCTAAAATTTT
GC
Found at i:44501 original size:15 final size:16
Alignment explanation
Indices: 44483--44576 Score: 79
Period size: 16 Copynumber: 5.9 Consensus size: 16
44473 GTTGGGTGGG
*
44483 TTCGGG-TTCGGGTTA
1 TTCGGGTTTCGGGTCA
44498 TTCGGGTTTCGGGTCA
1 TTCGGGTTTCGGGTCA
*
44514 TTCAGGTCTT-GGGTCA
1 TTCGGGT-TTCGGGTCA
* *
44530 TACGGGTCTT-AGGTCAA
1 TTCGGGT-TTCGGGTC-A
*
44547 TT-GGGTTCCGGGTCA
1 TTCGGGTTTCGGGTCA
*
44562 TTCGGGTCTCGGGTC
1 TTCGGGTTTCGGGTC
44577 TACCGGGTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
15 10 0.16
16 50 0.78
17 4 0.06
ACGTcount: A:0.10, C:0.19, G:0.36, T:0.35
Consensus pattern (16 bp):
TTCGGGTTTCGGGTCA
Found at i:44591 original size:32 final size:30
Alignment explanation
Indices: 44484--44591 Score: 81
Period size: 32 Copynumber: 3.4 Consensus size: 30
44474 TTGGGTGGGT
* *
44484 TCGGGTTCGGGTTATTCGGGTTTCGGGTCA
1 TCGGGTTCGGGTCATTCGGGTCTCGGGTCA
* * * **
44514 TTCAGGTCTTGGGTCATACGGGTCTTAGGTCAA
1 -TCGGGT-TCGGGTCATTCGGGTCTCGGGTC-A
*
44547 TTGGGTTCCGGGTCATTCGGGTCTCGGGTCTA
1 TCGGGTT-CGGGTCATTCGGGTCTCGGGTC-A
*
44579 CCGGGTCTCGGGT
1 TCGGGT-TCGGGT
44592 TGGACGGATT
Statistics
Matches: 57, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
31 6 0.11
32 49 0.86
33 2 0.04
ACGTcount: A:0.09, C:0.20, G:0.37, T:0.33
Consensus pattern (30 bp):
TCGGGTTCGGGTCATTCGGGTCTCGGGTCA
Found at i:44858 original size:42 final size:42
Alignment explanation
Indices: 44812--44893 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
44802 TAGATATTAA
*
44812 TTTTGAATATTAAATACATAATTGATTATCAGGTGAGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
*
44854 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTA
44894 TGTGTCAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:45449 original size:16 final size:16
Alignment explanation
Indices: 45428--45575 Score: 122
Period size: 16 Copynumber: 9.2 Consensus size: 16
45418 GGTTCACTTC
*
45428 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
*
45444 TCGGGTCATACGGGTCT
1 TCGGGTCATTCGGGT-T
*
45461 T-GGGTCACTCGGGTT
1 TCGGGTCATTCGGGTT
*
45476 ACGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
45492 TAGGGTTA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
* * *
45508 ACGGATCATTCGGGTC
1 TCGGGTCATTCGGGTT
*
45524 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
*
45540 TCGGGTCA-TCTGGTT
1 TCGGGTCATTCGGGTT
* * *
45555 TGCAGGTAATTCGGGTC
1 T-CGGGTCATTCGGGTT
45572 TCGG
1 TCGG
45576 ATTGGGCGGA
Statistics
Matches: 103, Mismatches: 23, Indels: 12
0.75 0.17 0.09
Matches are distributed among these distances:
15 9 0.09
16 84 0.82
17 10 0.10
ACGTcount: A:0.11, C:0.19, G:0.36, T:0.34
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:45567 original size:48 final size:47
Alignment explanation
Indices: 45426--45575 Score: 160
Period size: 48 Copynumber: 3.1 Consensus size: 47
45416 CGGGTTCACT
* * *
45426 TCTCGGGTTATTCGGGTTTCGGGTCATACGGGTCTTG-GGTCACTCGGG
1 TCTCGGGTCATTCGGGTTTCGGGTCAT-CTGGT-TTGCGGTCATTCGGG
* * * *
45474 T-TACGGGTCATTCGGGTTTAGGGTTATCTGGGTTACGGATCATTCGGG
1 TCT-CGGGTCATTCGGGTTTCGGGTCATCTGGTTTGCGG-TCATTCGGG
* *
45522 TCTCGGGTCATTCGGGTCTCGGGTCATCTGGTTTGCAGGTAATTCGGG
1 TCTCGGGTCATTCGGGTTTCGGGTCATCTGGTTTGC-GGTCATTCGGG
45570 TCTCGG
1 TCTCGG
45576 ATTGGGCGGA
Statistics
Matches: 84, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
46 2 0.02
47 6 0.07
48 73 0.87
49 3 0.04
ACGTcount: A:0.11, C:0.19, G:0.36, T:0.34
Consensus pattern (47 bp):
TCTCGGGTCATTCGGGTTTCGGGTCATCTGGTTTGCGGTCATTCGGG
Found at i:46287 original size:38 final size:40
Alignment explanation
Indices: 46244--46323 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 40
46234 AATATGTCCG
*
46244 TAAAAATTAAATCCTTTA-A-AAATATTCTTAAATATCCT
1 TAAAAAATAAATCCTTTACACAAATATTCTTAAATATCCT
*
46282 TAAAAAATAAATCCTTTACACTATATATTCTTAAATATCCT
1 TAAAAAATAAATCCTTTACAC-AAATATTCTTAAATATCCT
46323 T
1 T
46324 CAACAATCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 17 0.46
39 1 0.03
41 19 0.51
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (40 bp):
TAAAAAATAAATCCTTTACACAAATATTCTTAAATATCCT
Found at i:46869 original size:84 final size:82
Alignment explanation
Indices: 46728--47010 Score: 363
Period size: 84 Copynumber: 3.4 Consensus size: 82
46718 CTCTCTCCCC
* * *
46728 AAAGTCCCCAAGCACATATATAACACAGGGCAACTCTCTTTTTAAAGTCCTCAAGCACATTTATA
1 AAAGTCCTCAAACACAT-TATAACACAGGGCAACTCTC-TTTAAAAGTCCTCAAGCACATTTATA
*
46793 ACACAGAGACATCCATATT
64 ACACAGAGACATCTATATT
* *
46812 AAAGTCCTCAAACACAATTATAACACAGGGGCAATTCTCTCTAAAAGTCCTCAAGCACATTTATA
1 AAAGTCCTCAAACAC-ATTATAACACA-GGGCAACTCTCTTTAAAAGTCCTCAAGCACATTTATA
46877 ACACAGAGACATCTATATT
64 ACACAGAGACATCTATATT
* * * * *
46896 AAAGTCCTCAAGCACAATTATAACACATGGGCACCTCTCTTTCAAAGTCTTTAAGCACATTTATA
1 AAAGTCCTCAAACAC-ATTATAACACA-GGGCAACTCTCTTTAAAAGTCCTCAAGCACATTTATA
*
46961 ACACAGAGACATCTATATC
64 ACACAGAGACATCTATATT
*
46980 AAAGTCC-CTAAACACA-TGTAACACAAGGGCA
1 AAAGTCCTC-AAACACATTATAACAC-AGGGCA
47011 TTCTCTACAT
Statistics
Matches: 178, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
82 12 0.07
83 3 0.02
84 151 0.85
85 12 0.07
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.24
Consensus pattern (82 bp):
AAAGTCCTCAAACACATTATAACACAGGGCAACTCTCTTTAAAAGTCCTCAAGCACATTTATAAC
ACAGAGACATCTATATT
Found at i:46996 original size:41 final size:41
Alignment explanation
Indices: 46727--46986 Score: 243
Period size: 43 Copynumber: 6.2 Consensus size: 41
46717 TCTCTCTCCC
* * * * *
46727 CAAAGTCCCCAAGCACATATATAACACAG-GGCAACTCTCTTTT
1 CAAAGTCCTCAAGCACATTTATAACACAGAGAC-A-TCT-ATAT
* *
46770 TAAAGTCCTCAAGCACATTTATAACACAGAGACATCCATAT
1 CAAAGTCCTCAAGCACATTTATAACACAGAGACATCTATAT
* * * * * * *
46811 TAAAGTCCTCAAACACAATTATAACACAGGGGCAATTCTCTCT
1 CAAAGTCCTCAAGCACATTTATAACACAGAGAC-A-TCTATAT
*
46854 AAAAGTCCTCAAGCACATTTATAACACAGAGACATCTATAT
1 CAAAGTCCTCAAGCACATTTATAACACAGAGACATCTATAT
* * * * * *
46895 TAAAGTCCTCAAGCACAATTATAACACATGGGCACCTCTCTTT
1 CAAAGTCCTCAAGCACATTTATAACACA-GAG-ACATCTATAT
* *
46938 CAAAGTCTTTAAGCACATTTATAACACAGAGACATCTATAT
1 CAAAGTCCTCAAGCACATTTATAACACAGAGACATCTATAT
46979 CAAAGTCC
1 CAAAGTCC
46987 CTAAACACAT
Statistics
Matches: 176, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
41 76 0.43
42 8 0.05
43 90 0.51
44 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.25
Consensus pattern (41 bp):
CAAAGTCCTCAAGCACATTTATAACACAGAGACATCTATAT
Found at i:50175 original size:83 final size:79
Alignment explanation
Indices: 50022--50175 Score: 254
Period size: 79 Copynumber: 1.9 Consensus size: 79
50012 ACCTTATTTA
*
50022 AAAAATGTAAATATATATAGAGCTCTAATACACATATATTGTCGCAAACATTAATAAAAACATTC
1 AAAAATGTAAATATATATAGAGCTCTAATACACATATATTGTCGCAAACATTAAAAAAAACATTC
50087 ACATAAACGTTGAT
66 ACATAAACGTTGAT
50101 AAAAATGTAAATATATATAGAGCTCTAATACACATATATTAATTGTCGCAAACATTAAAAAAAAC
1 AAAAATGTAAATATATATAGAGCTCTAATACAC--ATA-T-ATTGTCGCAAACATTAAAAAAAAC
*
50166 ATTCCCATAA
62 ATTCACATAA
50176 TGAATTGCGA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
79 33 0.48
81 3 0.04
82 1 0.01
83 32 0.46
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (79 bp):
AAAAATGTAAATATATATAGAGCTCTAATACACATATATTGTCGCAAACATTAAAAAAAACATTC
ACATAAACGTTGAT
Found at i:52734 original size:40 final size:38
Alignment explanation
Indices: 52673--52749 Score: 118
Period size: 40 Copynumber: 2.0 Consensus size: 38
52663 GAAAAAGGAC
*
52673 ATATGAAACTATTTTTTTGTTGCTGGAAGATGTATGAA
1 ATATGAAACTATTTTTTTGTTGCTGGAAAATGTATGAA
*
52711 ATATGAAACTGTTATTTTTTGTTGCTGGAAAATGTATGA
1 ATATGAAACT-AT-TTTTTTGTTGCTGGAAAATGTATGA
52750 GCTATAACCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 10 0.29
39 1 0.03
40 24 0.69
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (38 bp):
ATATGAAACTATTTTTTTGTTGCTGGAAAATGTATGAA
Found at i:53635 original size:20 final size:20
Alignment explanation
Indices: 53589--53635 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
53579 AAACCAAGTG
*
53589 GGGCGCAAAGCTTGCCGCAT
1 GGGCGCCAAGCTTGCCGCAT
53609 GGGCGCCAAGCTTGCCGCAT
1 GGGCGCCAAGCTTGCCGCAT
53629 GGGCGCC
1 GGGCGCC
53636 CTGCGCCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.34, G:0.38, T:0.13
Consensus pattern (20 bp):
GGGCGCCAAGCTTGCCGCAT
Done.