Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011847.1 Corchorus olitorius cultivar O-4 contig11880, 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: 47719
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1274 original size:204 final size:204
Alignment explanation
Indices: 916--1487 Score: 1037
Period size: 204 Copynumber: 2.8 Consensus size: 204
906 TTAATAACTT
916 TGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAC
1 TGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAC
* * *
981 ACATTATTATTATATATA-A-AACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTTGATTTAT
66 ACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGATTTAT
1044 TAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTT
131 TAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTT
1109 ATTTATCAA
196 ATTTATCAA
*
1118 TGGTAAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAC
1 TGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAC
1183 ACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGATTTAT
66 ACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGATTTAT
*
1248 TAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCTGATTT
131 TAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTT
1313 ATTTATCAA
196 ATTTATCAA
*
1322 TGGTGAATGTTATTAATTTTTTAAGTCGAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAC
1 TGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAC
1387 ACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGATTTAT
66 ACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGATTTAT
*
1452 TAAATT-AA--GGATCAATGTCAAACAAAATTTACAAAA
131 TAAATTAAATTAGATCAATGTCAAACAAAATTT-CAAAA
1488 GATATTAAGA
Statistics
Matches: 359, Mismatches: 8, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
201 21 0.06
202 86 0.24
203 3 0.01
204 249 0.69
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (204 bp):
TGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAAC
ACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGATTTAT
TAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCGATTT
ATTTATCAA
Found at i:1677 original size:39 final size:40
Alignment explanation
Indices: 1623--1703 Score: 130
Period size: 39 Copynumber: 2.0 Consensus size: 40
1613 TAATCTAAGA
*
1623 ATTTAATTAATGTAAGTATT-TCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTCT-AGTTATTATATATATTAC
1662 ATTTAATTAATGTAAGTATTCTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTCTAGTTATTATATATATTAC
1702 AT
1 AT
1704 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
39 30 0.77
40 9 0.23
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTCTAGTTATTATATATATTAC
Found at i:9917 original size:120 final size:124
Alignment explanation
Indices: 9763--10000 Score: 369
Period size: 126 Copynumber: 1.9 Consensus size: 124
9753 CACACCACTA
*
9763 ATAAGGTTAATGTAATTGATAGAGTCTAAC-TTTTTTTTTT-AG-A-AAGATAGAGTCTAACCTT
1 ATAAGGTTAATGTAATTGATAAAGTCTAACTTTTTTTTTTTGAGAATAAGATAGAGTCTAACCTT
*
9824 AGCAATGACTCTCTTATTTGTAATCCATCATGTAAGCTATTATGTAGGCTAAACCTTAC
66 AGCAATGACTCTCTTATTTGTAATCCATCATGTAAGCTATTATGTAAGCTAAACCTTAC
*
9883 ATAAGGTTAATGTGATT-ATAAAGTCTTAACTTTTTTTTTTTGAGAAATTAAGATAGAGTCTAAC
1 ATAAGGTTAATGTAATTGATAAAGTC-TAACTTTTTTTTTTTGAG-AA-TAAGATAGAGTCTAAC
**
9947 CTTAGCAATGACTCTCTTATTTGTAATCCATTGTGTAAGCTATTATGTAAGCTA
63 CTTAGCAATGACTCTCTTATTTGTAATCCATCATGTAAGCTATTATGTAAGCTA
10001 TTATGTAGTT
Statistics
Matches: 106, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
119 7 0.07
120 20 0.19
121 10 0.09
122 2 0.02
124 1 0.01
126 66 0.62
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (124 bp):
ATAAGGTTAATGTAATTGATAAAGTCTAACTTTTTTTTTTTGAGAATAAGATAGAGTCTAACCTT
AGCAATGACTCTCTTATTTGTAATCCATCATGTAAGCTATTATGTAAGCTAAACCTTAC
Found at i:9995 original size:12 final size:12
Alignment explanation
Indices: 9980--10007 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
9970 TAATCCATTG
9980 TGTAAGCTATTA
1 TGTAAGCTATTA
9992 TGTAAGCTATTA
1 TGTAAGCTATTA
10004 TGTA
1 TGTA
10008 GTTATACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (12 bp):
TGTAAGCTATTA
Found at i:12508 original size:20 final size:18
Alignment explanation
Indices: 12469--12504 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12459 CTAGCCCTAA
*
12469 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAAATAG
12487 AACTAGAAGAGAAAAATA
1 AACTAGAAGA-AAAAATA
12505 AGAAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (18 bp):
AACTAGAAGAAAAAATAG
Found at i:13111 original size:30 final size:31
Alignment explanation
Indices: 13072--13132 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
13062 CAATTCTTCC
*
13072 TCTTGAAATAAATCTTCAAAG-GTCTTCAAA
1 TCTTCAAATAAATCTTCAAAGAGTCTTCAAA
* *
13102 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAATCTTCAAAGAGTCTTCAAA
13133 CACGAACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (31 bp):
TCTTCAAATAAATCTTCAAAGAGTCTTCAAA
Found at i:21918 original size:14 final size:15
Alignment explanation
Indices: 21901--21940 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
21891 AGACCTTGCA
21901 AAAAAGAAGAAAA-T
1 AAAAAGAAGAAAAGT
21915 AAAAAGAAGTAAAAGT
1 AAAAAGAAG-AAAAGT
21931 AAAAAGAAGA
1 AAAAAGAAGA
21941 CCTTTAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.38
15 5 0.21
16 10 0.42
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
AAAAAGAAGAAAAGT
Found at i:27853 original size:30 final size:34
Alignment explanation
Indices: 27780--27867 Score: 112
Period size: 37 Copynumber: 2.6 Consensus size: 34
27770 TTTAAGCAAC
27780 TCCAAAAGAAGATTTTGGAAAATAAAAGTTAGGTAAT
1 TCCAAAAGAAGATTTTGGAAAATAAAAG-TA-G-AAT
27817 TCCAAAAGAAGATTTTGGAAAAT-AAAG-A-AA-
1 TCCAAAAGAAGATTTTGGAAAATAAAAGTAGAAT
*
27847 TCCAAAAGAAGGTTTTGGAAA
1 TCCAAAAGAAGATTTTGGAAA
27868 TTAATGTAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
30 20 0.40
31 2 0.04
34 1 0.02
36 4 0.08
37 23 0.46
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.24
Consensus pattern (34 bp):
TCCAAAAGAAGATTTTGGAAAATAAAAGTAGAAT
Found at i:35779 original size:331 final size:329
Alignment explanation
Indices: 35141--35949 Score: 902
Period size: 331 Copynumber: 2.4 Consensus size: 329
35131 ATACTATACA
* * * *
35141 TCATCTAACCAAATCTC-AGCACCATTGGATTTAAAAATTTGTTTTTATGAGCATCTGAATCTTA
1 TCATCTAATCAAATCTCAACCA-CATTGGATTTAAGAATTT-TTTTTAAGAGCATCTGAATCTTA
* * * *
35205 TTTCGATTTAATTAGAAATTAATTAAGAAAAAAATAAGAAATACGATATTAAAAGCATAAAAAAA
64 TTTCGATTTAATTAGAAATTAATT-TGGAAAAAATAGGAAA-ACGATATTAAAA-CGT--AAAAA
* *
35270 TCCTCCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTAGGAGAA
124 GCCTCCAATCTTTTTGGCATTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTAGGAGAA
* * * * * *
35335 ATCTTTCGTATCAATTTTTGCGACATTTTAGCAGAAATCCTGTATTAACAAACCATCACGGTTTT
189 ATCTTTCGGATCAATTTTTACAACATTTTAGCAGAAATCATGTAATAAC-AACCATCACAGTTTT
* ** * **
35400 TGGCTAAAAACGAGTTCCAGGGACCTGGCTCAATTTTGCATGATTTTTGACTCCAAGACTATTTG
253 TAGCTAAAAACGAGTTCCAGGGACCTGGCTCAATTTCACATGATTTTTGACGCCAAGACTACATG
35465 AAATAT-CTATAT
318 AAATATAC-ATAT
* * * * *
35477 TCATCTAATCTAATCTCAACCACATTGGATTTAAGGATTTTTCTTACGAGCATCTGAATCTTGTT
1 TCATCTAATCAAATCTCAACCACATTGGATTTAAGAATTTTTTTTAAGAGCATCTGAATCTTATT
* *
35542 TCGATTTAATTAGAAATT-ATTTGGAAAAAATAGGAAAACGATATTAGAAACGTCAAAAGCCATT
66 TCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAACGATATTA-AAACGTAAAAAGCC-TC
*
35606 CAATCTTTTTGGCATTGAATTATATATTGTTTATGAGTATTTTAGCCAAAAATTGCGGA-AATAT
129 CAATCTTTTTGGCATTGAATTATATATT-TTTATGAGTATTTTAGCCAAAAATT-AGGAGAA-AT
* * * * *
35670 CTTTCGGGTCAATTTTTACAAGATTTTAGCCGAAATTATGTAATAATC-A-TATCACAGTTTTTA
191 CTTTCGGATCAATTTTTACAACATTTTAGCAGAAATCATGTAATAA-CAACCATCACAGTTTTTA
** * * * * *
35733 GCT-AAAA-GAGCATT-TTGGGGCCTCGGCTCAGTTTCACATTATTTTTGGCGCCAAGACTCCAT
255 GCTAAAAACGAG--TTCCAGGGACCT-GGCTCAATTTCACATGATTTTTGACGCCAAGACTACAT
*
35795 GAGATATACATAT
317 GAAATATACATAT
* * *
35808 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTTTTTTAAAAGCATCTGAATCTTCTT
1 TCATCTAATCAAATCTCAACCACATTGGATTTAAGAATTTTTTTTAAGAGCATCTGAATCTTATT
* * *
35873 TCGATTTAATTGGAAATTAATTTAG-AAAAATATGAAAAACGATATTAAAAACG-AGAAAAGTCC
66 TCGATTTAATTAGAAATTAATTTGGAAAAAATA-GGAAAACGATATT-AAAACGTA-AAAAG-CC
35936 TCCAATCTTTTTGG
127 TCCAATCTTTTTGG
35950 TGTTAAACAT
Statistics
Matches: 403, Mismatches: 54, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
329 3 0.01
330 16 0.04
331 165 0.41
332 80 0.20
333 61 0.15
334 4 0.01
335 40 0.10
336 31 0.08
337 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (329 bp):
TCATCTAATCAAATCTCAACCACATTGGATTTAAGAATTTTTTTTAAGAGCATCTGAATCTTATT
TCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAACGATATTAAAACGTAAAAAGCCTCCA
ATCTTTTTGGCATTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTAGGAGAAATCTTTC
GGATCAATTTTTACAACATTTTAGCAGAAATCATGTAATAACAACCATCACAGTTTTTAGCTAAA
AACGAGTTCCAGGGACCTGGCTCAATTTCACATGATTTTTGACGCCAAGACTACATGAAATATAC
ATAT
Found at i:37514 original size:331 final size:327
Alignment explanation
Indices: 36374--37590 Score: 1159
Period size: 331 Copynumber: 3.7 Consensus size: 327
36364 TTTGGCGCCG
* * * * *
36374 ACACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATTTAAGGATTTGTT
1 ACACTCCATGAAATATCCATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATATGTT
* * * *
36439 TTTACGAGCATTTGAATCTTATTTTGATTTAATTAGAAATTAATTC--AAAAAA-ATGAAAAATG
66 TTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACG
* * * * *
36501 ATATTAAAAGCATGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTACATATTTTTATGAGTATTA
131 ATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTT
* * * * *
36566 TGGCTAAAAATTGAGGAAATATCTTTCGGATCAATTTTTGCAAAAATTTTAGCCGAAATCGTGCA
196 TAGCCAAAAATTGA-GAAATAT-TTTCGGGTCAATTTTTGC-AAAATATTAGCCGAAATCGTGTA
* * * * * *
36631 ATAATCATCACG-GTTTTTG-GCT-AAAACACATTCCGG-G-CCC-GGTTCAATTTTGAATGATT
258 A-AATC-GCA-GTATTTTTGTGCTAAAAACACGTTCAGGAGCCCCAGG-CCAATTTTGCATGA-T
* *
36690 TTTGGCGTCA
318 TTTGACGGCA
* * * * *
36700 AGACTCCTTGAAATATCTATATTCATCTAACCAAA--T---CC-CA--G----T---CAT-TGTT
1 ACACTCCATGAAATATCCATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATATGTT
* * * *
36749 TTTAC-AGGCATTAGAATCATGTTTCGTTTTAATTAGAAAATAATTCGGAAAAAA-AGGAAAAAC
66 TTTACGA-GCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAAC
* *
36812 GATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGTGTTGAATTATATATTTTTTATTAGTAT
130 GATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTAT
* * ** * *
36877 TGTGGATAAAAATTGAGGAAAAATATTCTGGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGT
194 TTTAGCCAAAAATTGA-GAAATATTTTC-GGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGT
* * * *
36942 AACATCGCAGTTTTTTTTGCTTTAGCTAAAAACACGTTCCGGAGCCCCGGGCCAATTTTGCATGA
257 AAAATCGCAG-TATTTTTG---T-GCTAAAAACACGTTCAGGAGCCCCAGGCCAATTTTGCATGA
37007 TTTTGACGGCA
317 TTTTGACGGCA
* * * *
37018 ACACTCCATGAAATATCTATATTCATCTAATGAAATCTCAGCCACATTGGATTTAAGGATTTGTT
1 ACACTCCATGAAATATCCATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATATGTT
* * * * *
37083 TTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAGTTAATTCGGGAAAAGTAGGAAAAACG
66 TTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACG
* *
37148 ATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTGAATTATAAACTTTTTATGAGTATT
131 ATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATT
* *
37213 TTAGCCAAAAATTGATGAAATATCTTTCCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
195 TTAGCCAAAAATTGA-GAAATAT-TTTCGGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTA
* ** * * *
37278 ATAATCATCACG-ATTTTTG-GCTAAAAAGGCGTTCAAGG-GCCCCAGGTCAGTTTTGCATTATT
258 A-AATC-GCA-GTATTTTTGTGCTAAAAACACGTTC-AGGAGCCCCAGGCCAATTTTGCATGATT
*
37340 TTTAC-GCTA
319 TTGACGGC-A
* * * * *
37349 AGACTCCTTTAGATATCCATATTCATCTAATCAAATCTCAGTCACATTGCATTTAAGGATATGTT
1 ACACTCCATGAAATATCCATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATATGTT
*** * *
37414 TTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTTATAAAAAATATGAAAAATG
66 TTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACG
* ** * *
37479 ATA-TAAACAGCGTGAAAAGTCC-TCTAATCTTTTTGGCGTTAAATTATATATATTTCATGAGTA
131 ATATTAGA-AGCGTGAAAAACCCTTC-AATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTA
* *
37542 TTTTAGCCAAAAATTGAGAAAATAATTTTTGGGGTCATTTTTTGCAAAA
193 TTTTAGCCAAAAATTGAG-AAAT-A-TTTTCGGGTCAATTTTTGCAAAA
37591 ATGCGTTTCG
Statistics
Matches: 744, Mismatches: 101, Indels: 86
0.80 0.11 0.09
Matches are distributed among these distances:
309 2 0.00
310 44 0.06
311 11 0.01
312 84 0.11
313 46 0.06
314 1 0.00
316 3 0.00
317 13 0.02
318 42 0.06
319 15 0.02
320 5 0.01
321 2 0.00
323 2 0.00
324 3 0.00
326 33 0.04
330 10 0.01
331 217 0.29
332 22 0.03
333 3 0.00
334 47 0.06
335 124 0.17
336 12 0.02
337 2 0.00
338 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (327 bp):
ACACTCCATGAAATATCCATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATATGTT
TTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACG
ATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTT
TAGCCAAAAATTGAGAAATATTTTCGGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTAAAA
TCGCAGTATTTTTGTGCTAAAAACACGTTCAGGAGCCCCAGGCCAATTTTGCATGATTTTGACGG
CA
Found at i:38221 original size:333 final size:331
Alignment explanation
Indices: 37587--38684 Score: 876
Period size: 330 Copynumber: 3.3 Consensus size: 331
37577 CATTTTTTGC
* * * * * *
37587 AAAAATGCGTTTCGGGGCCCCGACTCA-GTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAAT
1 AAAAACGCGTATCGGGACCCCGGCTAAGGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
* * * * * ** *
37651 AACTATATTAATCTAACCAAATCTCAACCGCATTAGATTTAAGGATCTGTA-AAATA--AGCTTC
66 ATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGAT-T-TATTTATACGAGCATC
* * * *
37713 TGAATCATGTTTCTATTTAATTAGAAATTAATTCGGAAAATAATAGGAAAAACAATATCAGAAGC
129 TGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAATAATA-CAAAAACAATATCAAAAGC
* * * * *
37778 ATGAAAAGCAATTCAATCTTTTTGGCATTGAATTATATAATTTTTATGAGTATTGTGGCTAAAAA
193 ATGAAAAGCAATCCAATCTTTTTGGCATTAAATTATATAATTTTTATAAGTATTGTAGCAAAAAA
* *
37843 TTGAAAAAATAACTTTCGAGTCAATTTTTGCAAAGTTCTAGCCGAAATCGTGTAATAATCATCAC
258 TTGAAAAAATAACTTTCAAGTCAATTTTTACAAAGTTCTAGCCGAAATCGTGT-ATAA--ATCAC
37908 -AGTTATTTGACT
320 GA-TTATTTGACT
* * * * *
37920 AAAAACGTGT-TCTGGGGCCCTGGCT-AGGTTTTGCATGATTTTTGGCGCCAAGACTCTTTGACA
1 AAAAACGCGTATC-GGGACCCCGGCTAAGGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAA
* ** * * *
37983 TATCCATATTCATCTAATTAAATCTCAGCTACATTGGATTTAAGAATTTATTTTTACGAGCATCT
65 TATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTATACGAGCATCT
* * *
38048 GAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAT-AT-CAAAAACGAA-ATTAAAAGCG
130 GAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAATAATACAAAAAC-AATATCAAAAGCA
* * ** *
38110 TGAAAAATC-CTCCAATCTTTTTGGTGTTAAATTATAT-ATATTTTATAAGTATTTTAGCAAAAA
194 TG-AAAAGCAATCCAATCTTTTTGGCATTAAATTATATAAT-TTTTATAAGTATTGTAGCAAAAA
* ** * *
38173 ATTGACAGAAATATTTTTCAAGTCATTTTTTTACAAAATT-TCAGCCGAAATCGTGTATAAATCA
257 ATTGA-AAAAATAACTTTCAAGTCA-ATTTTTACAAAGTTCT-AGCCGAAATCGTGTATAAATCA
* **
38237 CGATTTTTTGGTT
319 CGATTATTTGACT
* * ** *
38250 AAAAACGCGTATCGGGACCCCGGGTAAGTTTTTGCAT-ATTTTTTGTTG-CAAAACTCCTTGAAA
1 AAAAACGCGTATCGGGACCCCGGCTAAGGTTTTGCATGA-TTTTTGGCGCCAAGACTCCTTGAAA
* * *
38313 TATCTATATTCATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTATACGAGCATTT
65 TATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTATACGAGCATCT
* * ** * * **
38378 GAATCATGTTTCGATTTAATTA-AAATTAATT-TGAAAAAAATAGGGAAAACAATATTAGAAGTG
130 GAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAATAATA-CAAAAACAATATCAAAAGCA
* ** * * * * * * *
38441 TGAGAAGCCCTTCAATCTTTTTTTGGCGTTGAATTATAT-ATTTTTTTGAGTATTGTGGCTAAAA
194 TGAAAAGCAATCCAATC--TTTTTGGCATTAAATTATATAATTTTTATAAGTATTGTAGCAAAAA
** * * * * * * ** *
38505 ATTGAGAAAAAT-A-TTTCGGGTCAAGTTTTGCAAAATTTTAGCAGAAATCTTGTA-CCATCATG
257 ATTGA-AAAAATAACTTTCAAGTCAATTTTTACAAAGTTCTAGCCGAAATCGTGTATAAATCACG
* * *
38567 GTTTTTTGGCT
321 ATTATTTGACT
* * * * * ** * *
38578 AAAAACGCGTTATTGAG-CCCTGTGC-CA-GTGTTGCATGATTTTTGTTGTCAAGACTCCTTAAA
1 AAAAACGCG-TATCGGGACCCCG-GCTAAGGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-GA
* * * *
38640 ATATATTTCTATTCATCTAACAAAATCTCAGCCACATTGTATTTA
63 A-ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTA
38685 TTAGAAGCGT
Statistics
Matches: 623, Mismatches: 113, Indels: 61
0.78 0.14 0.08
Matches are distributed among these distances:
327 16 0.03
328 44 0.07
329 43 0.07
330 175 0.28
331 106 0.17
332 61 0.10
333 135 0.22
334 43 0.07
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (331 bp):
AAAAACGCGTATCGGGACCCCGGCTAAGGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
ATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTATTTATACGAGCATCTG
AATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAATAATACAAAAACAATATCAAAAGCATG
AAAAGCAATCCAATCTTTTTGGCATTAAATTATATAATTTTTATAAGTATTGTAGCAAAAAATTG
AAAAAATAACTTTCAAGTCAATTTTTACAAAGTTCTAGCCGAAATCGTGTATAAATCACGATTAT
TTGACT
Found at i:38912 original size:257 final size:254
Alignment explanation
Indices: 38451--39064 Score: 921
Period size: 257 Copynumber: 2.4 Consensus size: 254
38441 TGAGAAGCCC
* * * * *
38451 TTCAATCTTTTTTTGGCGTTGAATTATATATTTTTT-TGAGTATTGTGGCTAAAAATTGA-GAAA
1 TTCAAT-TTTTTTTGGCGTTGAATTATATATTTTTTATGACTATTTTCGCTAGAAATCGAGGAAA
**
38514 AATATTTCGGGTCAAGTTTTGCAAAATTTTAGCAGAAATCTTGTACCATCATGGTTTTTTGGCTA
65 AATATTTCGGGTCATTTTTTGC-AAATTTTAGCAGAAATCTTGTACCATCATGGTTTTTTGGCTA
* ** *
38579 AAAACGCGTTATTGAGCCCTGTGCCAGTGTTGCATGATTTTTGTTGTCAAGACTCCTTAAAATAT
129 AAAACCCGTTACGGAGCCCTGTGCCAGTGTTGCATGATTTTTGTTGCCAAGACTCCTTAAAATAT
* * * *
38644 ATTTCTATTCATCTAACAAAATCTCAGCCACATTGTATTTATTAGAAGCGTGAAAAAGGCT
194 ATCTATATTCATCTAACAAAATATCAGCCACATTGTATTTATTAGAAGCATGAAAAAGGCT
** *
38705 TTCAATTTTTTTTTACGTTGAATTTTATATTTTTTATGACTATTTTCGCTAGAAATCGAGGAAAA
1 TTCAATTTTTTTTGGCGTTGAATTATATATTTTTTATGACTATTTTCGCTAGAAATCGAGGAAAA
*
38770 ATATTTCGGGTCATTTTTTGCAAAGTTTTAGCAGAAATCTTGTACCATCATGGTTTTTTTTTGCT
66 ATATTTCGGGTCATTTTTTGCAAA-TTTTAGCAGAAATCTTGTACCATCATGG--TTTTTTGGCT
*
38835 AAAAACCCGTTACGGGGCCCTGTGCCAGTGTTGCATGATTTTTGTTGCCAAGACTCCTTAAAATA
128 AAAAACCCGTTACGGAGCCCTGTGCCAGTGTTGCATGATTTTTGTTGCCAAGACTCCTTAAAATA
* *
38900 TATCTATATTCATCTAACCAAATATCAGTCACATTGTATTTATTAGAAGCATGAAAAAGGCT
193 TATCTATATTCATCTAACAAAATATCAGCCACATTGTATTTATTAGAAGCATGAAAAAGGCT
*
38962 TTCAA-TTTTTTTGGCGTTGAATTATATATTTTGTATGACTATTTTCGCTAGAAATCGAGGAAAA
1 TTCAATTTTTTTTGGCGTTGAATTATATATTTTTTATGACTATTTTCGCTAGAAATCGAGGAAAA
*
39026 ATATTTCGGGTCAATTTTTGTG-AAATTTTAGCCGAAATC
66 ATATTTCGGGTC-ATTTTT-TGCAAATTTTAGCAGAAATC
39065 GCATACTAAC
Statistics
Matches: 326, Mismatches: 27, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
253 26 0.08
254 27 0.08
255 52 0.16
256 80 0.25
257 139 0.43
258 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (254 bp):
TTCAATTTTTTTTGGCGTTGAATTATATATTTTTTATGACTATTTTCGCTAGAAATCGAGGAAAA
ATATTTCGGGTCATTTTTTGCAAATTTTAGCAGAAATCTTGTACCATCATGGTTTTTTGGCTAAA
AACCCGTTACGGAGCCCTGTGCCAGTGTTGCATGATTTTTGTTGCCAAGACTCCTTAAAATATAT
CTATATTCATCTAACAAAATATCAGCCACATTGTATTTATTAGAAGCATGAAAAAGGCT
Found at i:43394 original size:41 final size:43
Alignment explanation
Indices: 43311--43409 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 43
43301 TAGCCAAAAA
* * * *
43311 CCCCATGCACATATATAACACAGGGGCAACTCTTTCTAAAAGT
1 CCCCAAGCACATATATAACACAGAGGCAACTCATACTAAAAGT
* *
43354 CCCCAAGCACATATATAACACAGAGGCATC-CATAC-CAAAGT
1 CCCCAAGCACATATATAACACAGAGGCAACTCATACTAAAAGT
* *
43395 CCCTAAACACATATA
1 CCCCAAGCACATATA
43410 ACATCTCTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 18 0.38
42 3 0.06
43 27 0.56
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.19
Consensus pattern (43 bp):
CCCCAAGCACATATATAACACAGAGGCAACTCATACTAAAAGT
Found at i:46954 original size:15 final size:16
Alignment explanation
Indices: 46930--46969 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
46920 AGAGGTTGAA
*
46930 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
46945 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
46961 AGAAAACAA
1 AGAAAACAA
46970 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:47549 original size:16 final size:15
Alignment explanation
Indices: 47511--47552 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
47501 ACAGAGGTTG
47511 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
47526 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
47541 ACTAGAAAACAA
1 AC-AGAAAACAA
47553 AGCAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.