Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020377.1 Corchorus olitorius cultivar O-4 contig20410, 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: 81964
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:113 original size:28 final size:28
Alignment explanation
Indices: 40--214 Score: 188
Period size: 28 Copynumber: 5.8 Consensus size: 28
30 CAATCTTGGG
*
40 ATGACAACTTCTGGTGTCAATAATTTCCTCAGC
1 ATGACAACTTCTGGTGTCAATAATTT--T---T
73 ATGACAACTTCTGGTGTCAATAATTTTT
1 ATGACAACTTCTGGTGTCAATAATTTTT
101 ATGACAACTTCTGGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTC-A-ATAAT--TTT--T
*
135 ATGACAACTTCTGGTGTCAATAATTTTC
1 ATGACAACTTCTGGTGTCAATAATTTTT
* *
163 ATTACAACTTCTGGTGTCAAGATAATTTAAT
1 ATGACAACTTCTGGTGTC-A-ATAATTT-TT
194 ATGACAACTTCTGGTGTCAAT
1 ATGACAACTTCTGGTGTCAAT
215 TAAATTTAAA
Statistics
Matches: 127, Mismatches: 6, Indels: 22
0.82 0.04 0.14
Matches are distributed among these distances:
28 35 0.28
29 4 0.03
30 16 0.13
31 18 0.14
32 8 0.06
33 27 0.21
34 19 0.15
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (28 bp):
ATGACAACTTCTGGTGTCAATAATTTTT
Found at i:154 original size:62 final size:59
Alignment explanation
Indices: 73--214 Score: 230
Period size: 62 Copynumber: 2.4 Consensus size: 59
63 TTTCCTCAGC
* *
73 ATGACAACTTCTGGTGTCAATAATTTTTATGACAACTTCTGGTGTCAAGATAATAATTTGAT
1 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAG---ATAATTTAAT
*
135 ATGACAACTTCTGGTGTCAATAATTTTCATTACAACTTCTGGTGTCAAGATAATTTAAT
1 ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATTTAAT
194 ATGACAACTTCTGGTGTCAAT
1 ATGACAACTTCTGGTGTCAAT
215 TAAATTTAAA
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
59 30 0.39
62 47 0.61
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (59 bp):
ATGACAACTTCTGGTGTCAATAATTTTCATGACAACTTCTGGTGTCAAGATAATTTAAT
Found at i:7729 original size:21 final size:21
Alignment explanation
Indices: 7703--7744 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
7693 TAAACCGTGA
7703 TTCCATGAATTCAAGTCTCAC
1 TTCCATGAATTCAAGTCTCAC
7724 TTCCATGAATTCAAGTCTCAC
1 TTCCATGAATTCAAGTCTCAC
7745 GGAATCTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (21 bp):
TTCCATGAATTCAAGTCTCAC
Found at i:11823 original size:23 final size:23
Alignment explanation
Indices: 11793--11838 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
11783 AGATTTGTGG
11793 ACATTCTCTAAAGCTTTTTTTTT
1 ACATTCTCTAAAGCTTTTTTTTT
11816 ACATTCTCTAAAGCTTTTTTTTT
1 ACATTCTCTAAAGCTTTTTTTTT
11839 CTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.04, T:0.57
Consensus pattern (23 bp):
ACATTCTCTAAAGCTTTTTTTTT
Found at i:15059 original size:3 final size:3
Alignment explanation
Indices: 15053--15081 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
15043 TATTAAAGTA
15053 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
15082 AAAGTAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:18136 original size:11 final size:11
Alignment explanation
Indices: 18104--18144 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
18094 TTGTTTACCC
*
18104 TTCATTTC-AT
1 TTCATTTCTTT
18114 TTCATTTCTTT
1 TTCATTTCTTT
18125 TTC-TTTCTTT
1 TTCATTTCTTT
*
18135 TTCAATTCTT
1 TTCATTTCTT
18145 GGATCTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (11 bp):
TTCATTTCTTT
Found at i:18562 original size:18 final size:21
Alignment explanation
Indices: 18524--18562 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
18514 TATTTGTTGC
18524 ATGTCATATTATCTGAATTCA
1 ATGTCATATTATCTGAATTCA
18545 ATGT-ATATTAT-T-AATTCA
1 ATGTCATATTATCTGAATTCA
18563 TTCTCTCCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 1 0.06
20 7 0.39
21 4 0.22
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (21 bp):
ATGTCATATTATCTGAATTCA
Found at i:31882 original size:48 final size:48
Alignment explanation
Indices: 31804--31898 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
31794 TATTTCTCTA
*
31804 GGTCCCTTTCCATATCTTTTATGTATCAAACCTCAAAATTAAGAGTTT
1 GGTCCCTTTCCATATCTTTTATGTACCAAACCTCAAAATTAAGAGTTT
*
31852 GGTCTCTTTCCATATCTTTTATGTACCAAACCTCAAAATTAAGAGTT
1 GGTCCCTTTCCATATCTTTTATGTACCAAACCTCAAAATTAAGAGTT
31899 CAACATTCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (48 bp):
GGTCCCTTTCCATATCTTTTATGTACCAAACCTCAAAATTAAGAGTTT
Found at i:36301 original size:2 final size:2
Alignment explanation
Indices: 36294--36321 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36284 GCAGATTTCA
36294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36322 TTTAGGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37383 original size:31 final size:31
Alignment explanation
Indices: 37347--37512 Score: 161
Period size: 31 Copynumber: 5.4 Consensus size: 31
37337 GGTGTCCGAC
* * *
37347 GTGGCATGACATGTGTACCAAAAAGCGACAT
1 GTGGCACGCCATGTGTACCAAAAAGTGACAT
* ***
37378 GTGGCACGCCACGTGTACCAAAAACCAACAT
1 GTGGCACGCCATGTGTACCAAAAAGTGACAT
* *
37409 GAGGCACGCCACGTGTACCAAAAAGTGACAT
1 GTGGCACGCCATGTGTACCAAAAAGTGACAT
** *
37440 GTATCACGCCATGTGTACCCAAAAGTGACAT
1 GTGGCACGCCATGTGTACCAAAAAGTGACAT
* * ** * *
37471 ATGGCATGCCATGTGTTTCAAAATGTGACAC
1 GTGGCACGCCATGTGTACCAAAAAGTGACAT
*
37502 GTGGCATGCCA
1 GTGGCACGCCA
37513 CGTGCACAAA
Statistics
Matches: 111, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 111 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (31 bp):
GTGGCACGCCATGTGTACCAAAAAGTGACAT
Found at i:44028 original size:330 final size:323
Alignment explanation
Indices: 42658--45174 Score: 2042
Period size: 330 Copynumber: 7.6 Consensus size: 323
42648 TTTTAGCCAC
* * * * *
42658 AATACTCGTAAAAATTATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATAT
1 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGG-TTTTCACGCTTTTAATAT
* * * ** *
42723 CGTTTTTTTTTCTATTATTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGACCCTTG
65 CG---TTTTTCCTATT-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
*** * * * *
42788 T-TTTACAAATCCTTAAATCCAATGTGGTTGA-ATTTTGGTTAGATGAATATAGAAATTTCAATG
126 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGA-TTTGATTAGATGAATATAGATATTTCAAGG
* * * ** *
42851 AGTCTCAGCGCCAAAAATCATGCAACACTGAATCGGGGCCCCGAAATACGTTTTTAGCTAAAAAT
190 AGTCTCGGCGCCAAAAA-CATGCAAAACTG-ACCGGGGCCCCG-AACGCGTTTTTAGCCAAAAA-
* * * * * * *
42916 CGTGATTTTGACAAACATACACAATTTCGGCTAATATTTTGCAAAAATTGACCAAAAATATTTTT
251 C-TG--TGTG--ATA-TTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC-ACAAGATTTTT
*
42981 CCTCATTTTTTGTCTAA
309 CCTCA-ATTTT-TCTAA
* * * *
42998 AATACTCATAATATATATATATAATTCAACTCCAAAAAGATTGGAGGACTTTTCACGCTTTTAAT
1 AATACTCATAA-A-AAATATATAATTCAACGCCAAAAAGATTGAAGG-GTTTTCACGCTTTTAAT
* **
43063 ATCGTTTTTCATATTTTTT-AAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
63 ATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * * *
43127 AAGACAAATTCTTAAATGCAACGTGGCTGAGATTTGATTAAATGAATATAGATATTTCAAGGAGT
128 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
* * * * * *
43192 CTCGACGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCAAAAAACAGT
193 CTCGGCGCCAAAAA-CATGCAAAACTGA-CCGGGGCCCCG-AACGCGTTTTTAGCCAAAAACTGT
* * * ** * * * * **
43257 AATAGTTAGTACACGATTTTTGTTAAAATTTTGC-TAAATGTGACCAGAAAAAATTTCCTCAATT
255 -GT-GATATTACACGATTTCGGCTAAAATTTTGCAAAAAT-TGACCACAAGATTTTTCCTCAA-T
43321 TTTGTCTAA
316 TTT-TCTAA
* * * * * * * *
43330 AATACTCATGAAATATATATAATTTAACGCCAAAGAGATTGGAGGACTGTTCACGCTTTTCATAT
1 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGG-GTTTTCACGCTTTTAATAT
* * * * *
43395 CGTTTTTCATATTTTTTATGAATTAATTTCTAATTAAATCAAAACAAGATTCAAATGTTCGTAAA
65 CGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * * *
43460 AACAAATCCTTAAATACAATGTGACTGAGAGTTGATTAGATGAATATGGATATCTCAAGGAGTCT
130 AACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT
** * * * * * *
43525 TAGCGCAAAAAATAATGTAAAACTTACCCGGGGCCCTGGAACGCGTGTTTAGCCAAAAACCATGA
195 CGGCGCCAAAAA-CATGCAAAACTGA-CCGGGGCCC-CGAACGCGTTTTTAGCCAAAAA-C-TG-
* * * *
43590 TGATTAATATTACATGATTTCGGCTAAAGTTTTACAAAAATTGACCGGA-AAGATTTTTCCTCAA
254 TG--TGATATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACC--ACAAGATTTTTCCTCAA
43654 TTTTTGGCT-A
315 TTTTT--CTAA
* *
43664 AATACTCATAAAAAATATATAATTCAATGCCAAAAATATTGAAGGGTTCTT-ACGCTTCTATATA
1 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTT-TTCACGC-T-T-T-TA
* * * * *
43728 ATATTGTTTTTCCTA-CTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCG
61 ATATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
** * * *
43792 TAAAAACAAATTTTTAAATCCAATGTGGCTGAAATTTGATTAGATGAATATAAATATTTCAAGAA
126 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGA
* * *
43857 GTCTTGGCGTCTAAAAA-ATGCAAAACTGACTCGGGGCCCCAGAACGCGTTTTTAGCTAAAAA-T
191 GTCTCGGCG-CCAAAAACATGCAAAACTGAC-CGGGGCCCC-GAACGCGTTTTTAGCCAAAAACT
* * * * *
43920 GTCGTGATGTTACATGATTTCGACTAATATTTTGCAAAAATTGAACCACAATATTTTTCCTCAAT
253 GT-GTGATATTACACGATTTCGGCTAAAATTTTGCAAAAATTG-ACCACAAGATTTTTCCTCAAT
* *
43985 TTTATCCAC
316 TTT-TCTAA
* *
43994 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATAT
1 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGG-TTTTCACGCTTTTAATAT
* * *
44059 CGTTTTTCCTATTTTTTTTCTGAATTAATTTCTAATTAAATCAAAACATGATT-AGATGCTTGTA
65 CGTTTTTCCTA--TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * * * * * *
44123 AAAAC-AATGGCTGAGAT----T-TGG-TTAGATGTGTATATATAT-ATATATATATATGTATAT
128 AAAACAAAT-CCTTAAATCCAATGTGGCTGAGATTTG-AT-TAGATGA-ATATAGATAT-T-T-C
* * ** * **
44180 AGAGGACTCTCGACGTAAAAAACTCATGCAAAACTGA-AGTGGGCCTTGGAACGCGTTTTTAGCC
186 A-AGGAGTCTCGGCGCCAAAAA--CATGCAAAACTGACCG-GGGCC-CCGAACGCGTTTTTAGCC
* * *
44244 AAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTACAAAAATTGACC-CGAGAGATAT
246 AAAAACTGTG-TGA-TATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAC-A-AGATTT
* *
44308 TTCCTCAATTTTTAGCCAC
307 TTCCTCAATTTTT--CTAA
*
44327 AATACTCATAAAAAATATATAATTCAACGCCTAAAAGATTGAAGGGTTTTTCACGCTTTTAATAT
1 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGG-TTTTCACGCTTTTAATAT
** *
44392 CGTTTTTAATATTTTTTCTGAAATTAATTTCTAATTTAATCGAAACAAGATTCAGATGCTCGTGA
65 CGTTTTTCCTATTTTTTCTG-AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-A
* * * * * *
44457 AAAA-AAATCTTTAAAT-GATATGTAGCTAAGATATT-ATTAGATGAATATTGGTATTTCAAGGA
128 AAAACAAATCCTTAAATCCA-ATGTGGCTGAGAT-TTGATTAGATGAATATAGATATTTCAAGGA
* * * * *
44519 GTCTCGACGCCAAAAATCATACAAAACTGAGCCGGGTCCCTGAAACGCGTTTTTAGCCAAAAACA
191 GTCTCGGCGCCAAAAA-CATGCAAAACTGA-CCGGGGCCCCG-AACGCGTTTTTAGCCAAAAACT
* ** *
44584 GTGATGATTATTACACGATTTTGGCTAAAATTTTGCAAAAAAAAAAGACC-CAAAAATTTTTTCC
253 GTG-TGA-TATTACACGATTTCGGCTAAAATTTTGC---AAAAATTGACCAC-AAGA-TTTTTCC
* *
44648 TAAATTTTTGGATAA
311 TCAATTTTT--CTAA
* * * * * * *
44663 ATTACTCATAAAATATAAATAATTTAACGACAAAAAGATT-AGAGGACTTTTCACGCTTTTGATA
1 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGA-AGG-GTTTTCACGCTTTTAATA
* * **
44727 TCGTTTTTCTTA-TTTTTCTGAATTAATTTCCAATTAAATCGAAACAAGATTCAGATGCTTTTAA
64 TCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-A
* * *
44791 AAAAAAAATTCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATGGATATCTT-AAGGAG
128 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT-TTCAAGGAG
* ** * * ** *
44855 TCTTGGTACCAAAAATCATGCAAAACTCAGCCAGCACCCCAGAACG-TTTTTTAGCCAAAAACTG
192 TCTCGGCGCCAAAAA-CATGCAAAACTGA-CCGGGGCCCC-GAACGCGTTTTTAGCCAAAAACTG
* * *
44919 TG-GATTATTACACGATATCGGCTAAAATTTTGTAAAAATTTACC-CGAAAGATATTTT-CTCAA
254 TGTGA-TATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAC--AAGAT-TTTTCCTCAA
44981 TTTCTTACTAA
315 TTT-TT-CTAA
* * * * * * * *
44992 AATACTTATAAAAAAATATATATTTAAATGCCAAAAAGGTTGAAGGGCTTTTGAC-TTTTCTGAT
1 AATACTCAT-AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGG-TTTTCACGCTTT-TAAT
* * * *
45056 ATCGTTTTCCCTA-TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCATATGCTTGTA
63 ATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* *
45120 AAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAAATAT
128 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
45175 ATATATATAT
Statistics
Matches: 1788, Mismatches: 296, Indels: 197
0.78 0.13 0.09
Matches are distributed among these distances:
323 6 0.00
324 6 0.00
325 14 0.01
326 1 0.00
327 17 0.01
328 9 0.01
329 113 0.06
330 327 0.18
331 185 0.10
332 158 0.09
333 195 0.11
334 149 0.08
335 148 0.08
336 203 0.11
337 72 0.04
338 112 0.06
339 15 0.01
340 11 0.01
341 1 0.00
342 46 0.03
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (323 bp):
AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTCACGCTTTTAATATC
GTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
ACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC
GGCGCCAAAAACATGCAAAACTGACCGGGGCCCCGAACGCGTTTTTAGCCAAAAACTGTGTGATA
TTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCACAAGATTTTTCCTCAATTTTTCTAA
Found at i:45439 original size:56 final size:60
Alignment explanation
Indices: 45372--45489 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 60
45362 TATCCGTTTC
*
45372 CTTTCACACAAT-AAATGTTA-TA-AA-AAATGATATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAAATGTTAGTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
* *
45428 CTTTCACACAATAAAATGTTAGTATAATAAATCCTATCCCCCTATTTCTACTTAATTATT
1 CTTTCACACAATAAAATGTTAGTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
45488 CT
1 CT
45490 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
56 12 0.22
57 8 0.15
58 2 0.04
59 2 0.04
60 31 0.56
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (60 bp):
CTTTCACACAATAAAATGTTAGTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
Found at i:45773 original size:59 final size:56
Alignment explanation
Indices: 45680--45796 Score: 180
Period size: 59 Copynumber: 2.0 Consensus size: 56
45670 TATATGTTTC
*
45680 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATTTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
* *
45736 CTTTTACACAATAAATGTTAGTATAATAAATCCTATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATG-T--TATAATAAATCATATCCCCCTATCTCTACTTAATTATT
45795 CT
1 CT
45797 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
56 16 0.29
57 1 0.02
59 38 0.69
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
Found at i:45922 original size:42 final size:42
Alignment explanation
Indices: 45863--45943 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
45853 TAAGGATCAG
45863 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
45905 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
45944 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:49295 original size:11 final size:11
Alignment explanation
Indices: 49281--49318 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
49271 ATTCATAACA
49281 AATTTATAATT
1 AATTTATAATT
49292 AATTTATAATT
1 AATTTATAATT
49303 -ATTTGATAATT
1 AATTT-ATAATT
*
49314 TATTT
1 AATTT
49319 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:50802 original size:29 final size:31
Alignment explanation
Indices: 50756--50832 Score: 122
Period size: 29 Copynumber: 2.5 Consensus size: 31
50746 TGATACCAAA
*
50756 TTGTAAGTAGAGGGACCAAATTGA-CAGTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
*
50786 TTGT-AGTAGAGGGACCAAATTGATCCCTTT
1 TTGTAAGTAGAGGGACCAAATTGATCACTTT
50816 TTGTAAGTAGAGGGACC
1 TTGTAAGTAGAGGGACC
50833 TGTACGGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 19 0.44
30 12 0.28
31 12 0.28
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (31 bp):
TTGTAAGTAGAGGGACCAAATTGATCACTTT
Found at i:50828 original size:31 final size:31
Alignment explanation
Indices: 50728--50832 Score: 126
Period size: 31 Copynumber: 3.5 Consensus size: 31
50718 CAGATTCTAT
* ***
50728 TAAGTAGAGGGACTC-AATTGATACCAAATTG
1 TAAGTAGAGGGAC-CAAATTGATCCCTTTTTG
**
50759 TAAGTAGAGGGACCAAATTGA-CAGTTTTTG
1 TAAGTAGAGGGACCAAATTGATCCCTTTTTG
50789 T-AGTAGAGGGACCAAATTGATCCCTTTTTG
1 TAAGTAGAGGGACCAAATTGATCCCTTTTTG
50819 TAAGTAGAGGGACC
1 TAAGTAGAGGGACC
50833 TGTACGGTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 19 0.30
30 13 0.21
31 31 0.49
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (31 bp):
TAAGTAGAGGGACCAAATTGATCCCTTTTTG
Found at i:72256 original size:31 final size:31
Alignment explanation
Indices: 72216--72276 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
72206 AGTTCAAGAG
* *
72216 CTTTTTTTTTTTGGTTCAAGAGCTTTTCTTT
1 CTTTCTTTTTTTGGTTCAACAGCTTTTCTTT
**
72247 CTTTCTTTTTTTTTTTCAACAGCTTTTCTT
1 CTTTCTTTTTTTGGTTCAACAGCTTTTCTT
72277 AGTATCTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.10, C:0.16, G:0.08, T:0.66
Consensus pattern (31 bp):
CTTTCTTTTTTTGGTTCAACAGCTTTTCTTT
Found at i:72285 original size:31 final size:32
Alignment explanation
Indices: 72219--72285 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
72209 TCAAGAGCTT
* * *
72219 TTTTTTTTTGGTTCAAGAGCTTTTCTTTCTTTC
1 TTTTTTTTT-GTTCAACAGCTTTTCTTACTATC
*
72252 TTTTTTTTT-TTCAACAGCTTTTCTTAGTATC
1 TTTTTTTTTGTTCAACAGCTTTTCTTACTATC
72283 TTT
1 TTT
72286 AATTATGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 21 0.70
33 9 0.30
ACGTcount: A:0.12, C:0.15, G:0.09, T:0.64
Consensus pattern (32 bp):
TTTTTTTTTGTTCAACAGCTTTTCTTACTATC
Done.