Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013380.1 Corchorus capsularis cultivar CVL-1 contig13401, 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: 61818
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:3296 original size:344 final size:334
Alignment explanation
Indices: 1718--3502 Score: 1420
Period size: 344 Copynumber: 5.4 Consensus size: 334
1708 ATCTCAGACA
** * * * *
1718 TTGTTTTTATAAGCATCTGAATCATGTTTCGTTTTAATTAGAAATTAATT-AGAAAAAAATG---
1 TTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA
* ** * * * *
1779 ---G-TATTAGAAGCGTGAACGGCCCTTCAATCTTTTTGGCGTTAA-AT-TATATAT-T-T-T-T
66 AACGATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGAGTTAATATATATATATATATATAT
* * * * ** * * *
1834 TATGAGTATTGTGGCTAAAAATTGAGGAAAATTATTCCGGCTCATTTTTTGCAAAATATTAGCCG
131 TATGAGTATTTTAGCCAAAAATTGAGGAAAA-AATTTTGGGTCAATTTTTGCAAAATTTTAGCCG
* * * * *
1899 AAATCGTG--TAAT-ATCACGATTTTTTTTTTGCTAAAAATGTG-TTCCGGTACCCTGG-TACAG
195 AAATCGTGTATAATCATCACG----GTTTTTGGCTAAAAACGCGTTTCGGGT-CCC-GGCT-CAG
* *
1959 TATTGCATGATTTTTGGCGCAAAGACTACTTGAGATATCC-A-ATTCATCTAATCAAATCTCAGC
253 TTTTGCATGATTTTTGGCGC-AAGACTCCTTGAGATATCCTATATTCATCTAATCAAATCTCAGC
2022 CACATTGCATTTAA-AGAT
317 CACATTGCATTTAAGA-AT
* *
2040 TT-TTTTTACAAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTTAGAAAAAATATGAA
1 TTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAA
* * * *
2104 AAACGATATGACAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTAA-ATA-ATATATATAT-T-
65 AAACGATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGAGTTAATATATATATATATATATA
* * ** ** *
2165 CTATGAGTATTTTATCCAAAAATTGAGG-AAATTTTTTTTGTC-ATATTTTGCAAAATTTTAGGC
130 TTATGAGTATTTTAGCCAAAAATTGAGGAAAAAATTTTGGGTCAAT-TTTTGCAAAATTTTAGCC
* *** * * *
2228 GAAATCGTGTACTAATCATTACGGGTTTTTTTTTTAAAAAAAAACACGTTTCGGGGCTCGGCTCA
194 GAAATCGTGTA-TAATCATCAC-GG-TTTTTGGCT----AAAAACGCGTTTCGGGTCCCGGCTCA
* * * *
2293 GTTTTGCATGATTTTTGACGTCAAGACTCCTTGAAATAT-ATATATTGATCTAATCAAATCTCAG
252 GTTTTGCATGATTTTTGGCG-CAAGACTCCTTGAGATATCCTATATTCATCTAATCAAATCTCAG
2357 CCACATTGCATTTAA-AGAT
316 CCACATTGCATTTAAGA-AT
* *
2376 TTGTTTTTACGAGCATCTAAATCTTATTTCTATTTAATTAGAAATTAATTCAGAAAAATATGAAA
1 TTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA
* * *
2441 AACAATAATAAAAGCGTGAAAAGTCCTCTAA-TTTTTT-GAGTTGAAT-TATATATATATATATA
66 AACGATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGAGTT-AATATATATATATATATATA
* * * *
2503 TTATGAGTATCTTAGACAAAAATTGAGGAAAACTATTTCT-GGTCAATTTTTGCAAAATATTA--
130 TTATGAGTATTTTAGCCAAAAATTGAGGAAAA-AATTT-TGGGTCAATTTTTGCAAAATTTTAGC
* * * * *
2565 -G---TC--G-A-AATCA-CA--GTTTTTTGCTAAAAACGCG-CTCTGCGGTCCCGGTTCAATGT
193 CGAAATCGTGTATAATCATCACGGTTTTTGGCTAAAAACGCGTTTC-G-GGTCCCGGCTCAGTTT
* * * * * *
2618 TGCATGATTTTTTGCGCCGACACTCCTTGAAATAT-CTATATT-ACTCTAACCAAATCTCATCCA
256 TGCATGATTTTTGGCG-CAAGACTCCTTGAGATATCCTATATTCA-TCTAATCAAATCTCAGCCA
* * *
2681 CAATAG-ATTTATGGAT
319 C-ATTGCATTTAAGAAT
*** * * * * * *
2697 TTG-TAAAACAAGCATCTGAATCATGTTTCGATTTAATTAAAAATT-ATCTCGGAAAATAGTAGG
1 TTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAAT-TCAGAAAA-A-TATG
* * * * * * * *
2760 AAAAATGATATTAGAAGCATGAAAAGCCCTTCAATCTTATTGGCA-TTGA-AT-TATATA-AT-T
63 AAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGG-AGTTAATATATATATATATAT
* * * * * * *
2820 -T-TTATGAGTATTGTGGCTAAAAATTGAGGAAATAACTTTTGAGTCCATTTTTGTAAAATTTTA
127 ATATTATGAGTATTTTAGCCAAAAATTGAGGAAA-AAATTTTGGGTCAATTTTTGCAAAATTTTA
* * * *
2883 GCCGAAATCATGTGATAATCATCACGGTTTTTGGCTAAAAACGCGTTCCGTGGCCCCGGCTAAGT
191 GCCGAAATCGTGT-ATAATCATCACGGTTTTTGGCTAAAAACGCGTTTCG-GGTCCCGGCTCAGT
* ** * *
2948 TTTGCATGACTTTTGGCGTCAAGACTATTTGAGATATCCT-TATTCATCTAACCAAATC-CTAGT
254 TTTGCATGATTTTTGGCG-CAAGACTCCTTGAGATATCCTATATTCATCTAATCAAATCTC-AGC
* * *
3011 TACATCGGATTTAAGAAT
317 CACATTGCATTTAAGAAT
* *
3029 TTGTTTTTATGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAACATGAAA
1 TTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA
* *
3094 AATGATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGAATTAAATTATATATATATATATAT
66 AACGATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGAGTT-AA-TATATATATATATATAT
* **
3159 ATTATGAGTATTTTATCCAAAAATTGACGGAAAAAATTTATGGGTCGTTTTTTGCAAAATTTTAG
129 ATTATGAGTATTTTAGCCAAAAATTGA-GGAAAAAATTT-TGGGTCAATTTTTGCAAAATTTTAG
* * * * *
3224 CCGAAATCGTGTACTAATTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGAGATCTCGACTT
192 CCGAAATCGTGTA-TAA-T---CATCACGGTTTTTGGCTAAAAACGCGTTTCG-GGTCCCGGCTC
* * *
3289 AGTTTTGCTTGATTTTTGGCGCTGAGACTCCTT-AGAATAT-CTATATTTATCTAATCAAATCTC
251 AGTTTTGCATGATTTTTGGCGC-AAGACTCCTTGAG-ATATCCTATATTCATCTAATCAAATCTC
* *
3352 AGCCACATTGAATTTAAGGAT
314 AGCCACATTGCATTTAAGAAT
*
3373 TT-TATTTTACGAGCATCTAAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAA
1 TTGT-TTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAA
* * *
3437 AAACAATAATAAAAGCGTGAAAAGTCCTCTAA-TTTTTT-GAGTTGAATTATATATATATATATA
65 AAACGATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGAGTT-AA-TATATATATATATATA
3500 TAT
128 TAT
3503 ATATATATAT
Statistics
Matches: 1175, Mismatches: 194, Indels: 168
0.76 0.13 0.11
Matches are distributed among these distances:
317 1 0.00
318 47 0.04
319 6 0.01
320 51 0.04
321 122 0.10
322 42 0.04
323 14 0.01
324 12 0.01
325 2 0.00
326 1 0.00
328 2 0.00
329 12 0.01
330 75 0.06
331 50 0.04
332 122 0.10
333 49 0.04
334 14 0.01
335 54 0.05
336 101 0.09
337 54 0.05
338 25 0.02
339 31 0.03
340 61 0.05
341 4 0.00
342 26 0.02
343 12 0.01
344 184 0.16
345 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (334 bp):
TTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAA
AACGATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGAGTTAATATATATATATATATATAT
TATGAGTATTTTAGCCAAAAATTGAGGAAAAAATTTTGGGTCAATTTTTGCAAAATTTTAGCCGA
AATCGTGTATAATCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGTCCCGGCTCAGTTTTGCAT
GATTTTTGGCGCAAGACTCCTTGAGATATCCTATATTCATCTAATCAAATCTCAGCCACATTGCA
TTTAAGAAT
Found at i:3489 original size:2 final size:2
Alignment explanation
Indices: 3484--3512 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3474 TGAGTTGAAT
3484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3513 TTTATGAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9800 original size:41 final size:41
Alignment explanation
Indices: 9713--9800 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 41
9703 AAGATTTCCT
* * *
9713 CGTTTGAAATCTGTCTCAAAGTGGTTTGCTTTCCTTCTTCAA
1 CGTTTAAAATCTGTCTCAAAGAGGTTTGCTTTCATTCTTC-A
*
9755 CGTTTAAAATCTGTCT-TAAGAGGTTTGCCTTTTCATTCTTC-
1 CGTTTAAAATCTGTCTCAAAGAGGTTTG-C-TTTCATTCTTCA
9796 CGTTT
1 CGTTT
9801 TGCTCCCTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 14 0.35
42 16 0.40
43 10 0.25
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (41 bp):
CGTTTAAAATCTGTCTCAAAGAGGTTTGCTTTCATTCTTCA
Found at i:10154 original size:15 final size:15
Alignment explanation
Indices: 10110--10154 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
10100 TCCTTATGTG
10110 CCCGGGTCAATCACT
1 CCCGGGTCAATCACT
* *
10125 CCC--TTCACT-ACT
1 CCCGGGTCAATCACT
10137 CCCGGGTCAATCACT
1 CCCGGGTCAATCACT
10152 CCC
1 CCC
10155 TCACCAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 6
0.70 0.12 0.18
Matches are distributed among these distances:
12 6 0.26
13 4 0.17
14 4 0.17
15 9 0.39
ACGTcount: A:0.18, C:0.47, G:0.13, T:0.22
Consensus pattern (15 bp):
CCCGGGTCAATCACT
Found at i:10636 original size:54 final size:54
Alignment explanation
Indices: 10554--10656 Score: 188
Period size: 54 Copynumber: 1.9 Consensus size: 54
10544 TTCTTTTCTT
*
10554 TCCTTTCAGTACTCCAACTATGAGTTTTTGAAGGTAGAGGATGTGAAGGTAGGG
1 TCCTTTCAGTACTCCAACTATGAGTTTTTGAAGGTAAAGGATGTGAAGGTAGGG
*
10608 TCCTTTCAGTACTCCAACTATGAGTTTTTTAAGGTAAAGGATGTGAAGG
1 TCCTTTCAGTACTCCAACTATGAGTTTTTGAAGGTAAAGGATGTGAAGG
10657 CAATTCCGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (54 bp):
TCCTTTCAGTACTCCAACTATGAGTTTTTGAAGGTAAAGGATGTGAAGGTAGGG
Found at i:10861 original size:55 final size:55
Alignment explanation
Indices: 10777--10886 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
10767 ATGGCTCACC
* *
10777 GTGACAATGAAAGTGTCATAGTAATTGACTTTTGTGAAGAAGTAAATTGAAGGCT
1 GTGACAATAAAAGTGTCATACTAATTGACTTTTGTGAAGAAGTAAATTGAAGGCT
*
10832 GTGACAATAAAAGTGTCATACTAATTGACTTTTGTGAAGAAGTAGATTGAAGGCT
1 GTGACAATAAAAGTGTCATACTAATTGACTTTTGTGAAGAAGTAAATTGAAGGCT
10887 TGGGGATTGG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (55 bp):
GTGACAATAAAAGTGTCATACTAATTGACTTTTGTGAAGAAGTAAATTGAAGGCT
Found at i:12809 original size:38 final size:38
Alignment explanation
Indices: 12758--12833 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
12748 TCTGCCGATC
12758 TCATTGCGGTTCCATCGCACCATTGTTTGAAGATGGAA
1 TCATTGCGGTTCCATCGCACCATTGTTTGAAGATGGAA
12796 TCATTGCGGTTCCATCGCACCATTGTTTGAAGATGGAA
1 TCATTGCGGTTCCATCGCACCATTGTTTGAAGATGGAA
12834 GAACTTAGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (38 bp):
TCATTGCGGTTCCATCGCACCATTGTTTGAAGATGGAA
Found at i:12890 original size:17 final size:17
Alignment explanation
Indices: 12868--12922 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
12858 ATCACCCCCC
*
12868 AGATCACTAGTGATCAA
1 AGATCACCAGTGATCAA
12885 AGATCACCAGTGATGC-A
1 AGATCACCAGTGAT-CAA
*
12902 AGATCACCGGTGATCAA
1 AGATCACCAGTGATCAA
12919 AGAT
1 AGAT
12923 TACATGGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 1 0.03
17 32 0.94
18 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (17 bp):
AGATCACCAGTGATCAA
Found at i:13063 original size:20 final size:20
Alignment explanation
Indices: 13040--13088 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
13030 ATCACCTGCC
13040 AAGATCACCACAGGTGATCA
1 AAGATCACCACAGGTGATCA
13060 AAGATCACCACAGGTGATCA
1 AAGATCACCACAGGTGATCA
13080 AAGATCACC
1 AAGATCACC
13089 CCCAACCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.41, C:0.27, G:0.18, T:0.14
Consensus pattern (20 bp):
AAGATCACCACAGGTGATCA
Found at i:16144 original size:13 final size:13
Alignment explanation
Indices: 16128--16176 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
16118 ACGTCATCCT
16128 GTTGACTTTGACA
1 GTTGACTTTGACA
* *
16141 GTTGACTTTTTATA
1 GTTGAC-TTTGACA
16155 GTTGACTTTGATC-
1 GTTGACTTTGA-CA
16168 GTTGACTTT
1 GTTGACTTT
16177 TTGGTTGACC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.18, C:0.12, G:0.20, T:0.49
Consensus pattern (13 bp):
GTTGACTTTGACA
Found at i:19248 original size:3 final size:3
Alignment explanation
Indices: 19240--19306 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
19230 TACATTCATG
*
19240 TTA TTA TTA TTA TTA TCA TTA -TA TTA -TA TTA -TA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
19283 TTA CTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
19307 ATTTTATATT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 6 0.11
3 48 0.86
4 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:21294 original size:5 final size:5
Alignment explanation
Indices: 21284--21309 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
21274 TAATTGTCTC
21284 TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT T
21310 TTTCGTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:25722 original size:18 final size:18
Alignment explanation
Indices: 25699--25787 Score: 124
Period size: 18 Copynumber: 4.9 Consensus size: 18
25689 TGTACAGGCA
*
25699 GATGTTCCACTACCGCAG
1 GATGTTCCACTGCCGCAG
*
25717 GATGTTCTACTGCCGCAG
1 GATGTTCCACTGCCGCAG
*
25735 GATGTTCCACTGCTGCAG
1 GATGTTCCACTGCCGCAG
* * *
25753 AATGTTCCATTACCGCAG
1 GATGTTCCACTGCCGCAG
25771 GATGTTCCACTGCCGCA
1 GATGTTCCACTGCCGCA
25788 AGAACCTTTG
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (18 bp):
GATGTTCCACTGCCGCAG
Found at i:30716 original size:114 final size:114
Alignment explanation
Indices: 30464--30827 Score: 545
Period size: 114 Copynumber: 3.2 Consensus size: 114
30454 AGGGTCCTAA
* * *
30464 ACGCCGCTAAATGGAAGCGTCTGAACCTAAAGACGCCG-CTATCTTTAATTTTTCTCCGAGAAAG
1 ACGCCGCTAAATGGAGGCGTCTGTACCTCAAGACGCCGTC-ATCTTTAATTTTTCTCCGAGAAAG
* *
30528 GCAAATTGGGCAAAAAAAGAAGGCTAAAAGTTAGCGGCGTCTTGTCCCCAG
65 GCAAATTGGG-TAAAAAAGAAGGCTAAAAGATAGCGGCGTCTTGTCCCCAG
*
30579 ACGCCGCTAAATGGAGGCGTCTGTACCTCAAGATGCCGTCATCTTTAATTTTTCTCCGAGAAAGG
1 ACGCCGCTAAATGGAGGCGTCTGTACCTCAAGACGCCGTCATCTTTAATTTTTCTCCGAGAAAGG
*
30644 CAAATTCGGTAAAAAAGAAGGCTAAAAGATAGCGGCGTCTTGTCCCCAG
66 CAAATTGGGTAAAAAAGAAGGCTAAAAGATAGCGGCGTCTTGTCCCCAG
* **
30693 ACGCCGCTAAATAGG-GGCATCTGTACCTCAAGACGTTGTCATCTTTAATTTTTCTCCGAGAAAG
1 ACGCCGCTAAAT-GGAGGCGTCTGTACCTCAAGACGCCGTCATCTTTAATTTTTCTCCGAGAAAG
* * * * *
30757 GCAAATTGGGTAAAAAATAAAGCTAAAATATAGCGGCATCTTG-CCCTAG
65 GCAAATTGGGTAAAAAAGAAGGCTAAAAGATAGCGGCGTCTTGTCCCCAG
30806 ACGCCGCTAAATGGAGGCGTCT
1 ACGCCGCTAAATGGAGGCGTCT
30828 TAGGTTACAA
Statistics
Matches: 228, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
112 2 0.01
113 23 0.10
114 133 0.58
115 69 0.30
116 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (114 bp):
ACGCCGCTAAATGGAGGCGTCTGTACCTCAAGACGCCGTCATCTTTAATTTTTCTCCGAGAAAGG
CAAATTGGGTAAAAAAGAAGGCTAAAAGATAGCGGCGTCTTGTCCCCAG
Found at i:45127 original size:20 final size:20
Alignment explanation
Indices: 45089--45127 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
45079 TAAGAAAACA
*
45089 TAAAACAAAATATATTATTG
1 TAAAACAAAATATACTATTG
45109 TAAAA-AAAATAATACTATT
1 TAAAACAAAAT-ATACTATT
45128 AGAGAGGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
TAAAACAAAATATACTATTG
Found at i:56144 original size:3 final size:3
Alignment explanation
Indices: 56136--56160 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
56126 AAGGAAGAAA
56136 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
56161 CAACAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:60286 original size:70 final size:69
Alignment explanation
Indices: 60211--60435 Score: 279
Period size: 70 Copynumber: 3.1 Consensus size: 69
60201 TAACTACAAT
*
60211 AGTAAAATTGTAAAATATAATAGTATAAGGATAATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTATAAGGAT-ATTAGATTTAATTATATAAAAATAGAGTTTTT
60276 AGTTG
65 AGTTG
60281 AGTAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-A-T----T-GTAAAATATAATAG-TATAAGGATATTAGATTTAATTATATAAAAATA
60346 GAGTTTTTAGTTG
57 GAGTTTTTAGTTG
* * * * * * *
60359 AATAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATTGTAAAATATAAT-AGTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
60424 AGTTG
65 AGTTG
60429 AGTAAAA
1 AGTAAAA
60436 CTATAAAAAC
Statistics
Matches: 136, Mismatches: 9, Indels: 20
0.82 0.05 0.12
Matches are distributed among these distances:
70 63 0.46
71 4 0.03
72 1 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 4 0.03
78 52 0.38
79 9 0.07
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (69 bp):
AGTAAAATTGTAAAATATAATAGTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTTA
GTTG
Found at i:60302 original size:78 final size:76
Alignment explanation
Indices: 60208--60443 Score: 333
Period size: 78 Copynumber: 3.1 Consensus size: 76
60198 TTTTAACTAC
*
60208 AATAGTAAAATTGTAAAATATAATAGTATAAGGATAATTAGATTTAATTATATAAAAATTGAGTT
1 AATAGTAAAA-TGTAAAATATAATAGTATAAGGAT-ATTAGATTTAATTATATAAAAATAGAGTT
60273 TTTAGTTGAGTAA
64 TTTAGTTGAGTAA
60286 AATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATAGAGTT
1 AATAGTAAAAT-GTAAAATATAATAG-TATAAGGATATTAGATTTAATTATATAAAAATAGAGTT
*
60351 TTTAGTTGAATAA
64 TTTAGTTGAGTAA
* * *
60364 AATAGTAAAA--T-AAA-ATAAT--TATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTT
1 AATAGTAAAATGTAAAATATAATAGTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
60423 TAGTTGAGTAA
66 TAGTTGAGTAA
60434 AACTA-TAAAA
1 AA-TAGTAAAA
60444 ACCTAAACAA
Statistics
Matches: 149, Mismatches: 6, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
70 54 0.36
71 2 0.01
73 5 0.03
74 3 0.02
75 1 0.01
77 1 0.01
78 74 0.50
79 9 0.06
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.36
Consensus pattern (76 bp):
AATAGTAAAATGTAAAATATAATAGTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
TAGTTGAGTAA
Done.