Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021944.1 Corchorus olitorius cultivar O-4 contig21977, 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: 62101
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:9369 original size:74 final size:72
Alignment explanation
Indices: 9266--9411 Score: 256
Period size: 74 Copynumber: 2.0 Consensus size: 72
9256 ACAAACTTCA
* *
9266 TTGGCATCTTGGACTTTTCAATGCTACCATATTGTTAACTTTGTTTCTTGCCATCGCGCGATTTT
1 TTGGCATCTTGGACTTTTCAATGCCACCATATTGTTAA--ATGTTTCTTGCCATCGCGCGATTTT
9331 CCTGCCCTT
64 CCTGCCCTT
9340 TTGGCATCTTGGACTTTTCAATGCCACCATATTGTTAAATGTTTCTTGCCATCGCGCGATTTTCC
1 TTGGCATCTTGGACTTTTCAATGCCACCATATTGTTAAATGTTTCTTGCCATCGCGCGATTTTCC
9405 TGCCCTT
66 TGCCCTT
9412 GTCCATCTGT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
72 33 0.47
74 37 0.53
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (72 bp):
TTGGCATCTTGGACTTTTCAATGCCACCATATTGTTAAATGTTTCTTGCCATCGCGCGATTTTCC
TGCCCTT
Found at i:11966 original size:29 final size:31
Alignment explanation
Indices: 11892--11976 Score: 120
Period size: 29 Copynumber: 2.8 Consensus size: 31
11882 TTGAGGCAAA
*
11892 ATGCTCAATTTGGTCCTAAACCTTTGATGAG
1 ATGCTCAATTTGGTCCTAAACCTTTGATGAC
*
11923 ATGCTCGATTTGGTCCTAAACCTTT-A-GAC
1 ATGCTCAATTTGGTCCTAAACCTTTGATGAC
* *
11952 CTGCTCAAATTGGTCCTAAACCTTT
1 ATGCTCAATTTGGTCCTAAACCTTT
11977 CAAAATCTGC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 24 0.49
30 1 0.02
31 24 0.49
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (31 bp):
ATGCTCAATTTGGTCCTAAACCTTTGATGAC
Found at i:11990 original size:31 final size:30
Alignment explanation
Indices: 11893--11992 Score: 112
Period size: 31 Copynumber: 3.3 Consensus size: 30
11883 TGAGGCAAAA
* **
11893 TGCTCAATTTGGTCCTAAACCTTTGATGAGA
1 TGCTCAATTTGGTCCTAAACCTTT-AAGACC
*
11924 TGCTCGATTTGGTCCTAAACCTTT-AGACC
1 TGCTCAATTTGGTCCTAAACCTTTAAGACC
* * *
11953 TGCTCAAATTGGTCCTAAACCTTTCAAAATC
1 TGCTCAATTTGGTCCTAAACCTTT-AAGACC
11984 TGCTCAATT
1 TGCTCAATT
11993 CAGTCCTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
29 24 0.41
31 34 0.59
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (30 bp):
TGCTCAATTTGGTCCTAAACCTTTAAGACC
Found at i:11999 original size:31 final size:29
Alignment explanation
Indices: 11935--12000 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
11925 GCTCGATTTG
* *
11935 GTCCTAAACCTTTAGACCTGCTCAAATTG
1 GTCCTAAACCTTTAAACCTGCTCAAATTA
*
11964 GTCCTAAACCTTTCAAAATCTGCTC-AATTCA
1 GTCCTAAACCTTT--AAACCTGCTCAAATT-A
11995 GTCCTA
1 GTCCTA
12001 TTTCAGGTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 13 0.42
30 4 0.13
31 14 0.45
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.32
Consensus pattern (29 bp):
GTCCTAAACCTTTAAACCTGCTCAAATTA
Found at i:12721 original size:21 final size:22
Alignment explanation
Indices: 12679--12725 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
12669 AGTTTCTAGG
*
12679 GTTTCTGCTGAATATGAAAATT
1 GTTTCCGCTGAATATGAAAATT
*
12701 GTTTCCGCTTAATAT-AAAATT
1 GTTTCCGCTGAATATGAAAATT
12722 GTTT
1 GTTT
12726 AAATCGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (22 bp):
GTTTCCGCTGAATATGAAAATT
Found at i:20265 original size:3 final size:3
Alignment explanation
Indices: 20257--20300 Score: 63
Period size: 3 Copynumber: 14.3 Consensus size: 3
20247 AAGGATCTTT
20257 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TATA TATA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA TTA T
20301 ACTAGTTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 30 0.77
4 7 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:21628 original size:12 final size:12
Alignment explanation
Indices: 21613--21643 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21603 CGAATTTCAA
21613 ATTCAATTCCTG
1 ATTCAATTCCTG
*
21625 ATTCATTTCCTG
1 ATTCAATTCCTG
21637 ATTCAAT
1 ATTCAAT
21644 CTTATTCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (12 bp):
ATTCAATTCCTG
Found at i:27699 original size:12 final size:12
Alignment explanation
Indices: 27674--27709 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
27664 CTTCTAATCT
27674 AAAA-TTACAAA
1 AAAAGTTACAAA
*
27685 AAAAGTTATAAA
1 AAAAGTTACAAA
27697 AAAAGTTACAAA
1 AAAAGTTACAAA
27709 A
1 A
27710 GTTATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (12 bp):
AAAAGTTACAAA
Found at i:28116 original size:68 final size:69
Alignment explanation
Indices: 28007--28140 Score: 202
Period size: 68 Copynumber: 2.0 Consensus size: 69
27997 TTGCTTGAAA
* * *
28007 ATGCATTGTCTTTATATGTGATTTTAGCATTTGGATGTAATTAATGGT-CTCTCTACC-ATTTTT
1 ATGCATTGTCTTAATATGTAATTTTAGCATTTGGATGTAATTAATGGTGCTC-CCACCAATTTTT
28070 TTCCT
65 TTCCT
28075 ATGCATTGTCTTAATATGTAATTTTAGCA-TTGAGATGTAATTAATGGTGCTCCCACCAATTTTT
1 ATGCATTGTCTTAATATGTAATTTTAGCATTTG-GATGTAATTAATGGTGCTCCCACCAATTTTT
28139 TT
65 TT
28141 TCTTATTTGT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
67 3 0.05
68 46 0.77
69 11 0.18
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.47
Consensus pattern (69 bp):
ATGCATTGTCTTAATATGTAATTTTAGCATTTGGATGTAATTAATGGTGCTCCCACCAATTTTTT
TCCT
Found at i:30018 original size:2 final size:2
Alignment explanation
Indices: 30011--30045 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
30001 TTAAAGTCCT
30011 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30046 ATTAGGAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31310 original size:112 final size:111
Alignment explanation
Indices: 31112--31336 Score: 414
Period size: 112 Copynumber: 2.0 Consensus size: 111
31102 ACAAACTGAT
31112 GAGATTTGTGCGGTAAAGAAATTATAATTTTTTAATATATATTATTTAATTTAGTTGATAAATGA
1 GAGATTTGTGCGGTAAAGAAATTATAATTTTTTAATATATATTATTTAATTTAGTTGATAAATGA
31177 AATTACATATTAAACCATAAAAGTTAAATCTAATATTTAAAATTAA
66 AATTACATATTAAACCATAAAAGTTAAATCTAATATTTAAAATTAA
*
31223 GAGATTTGTGCGGTAAAGAAATTATAATTTTTTTGATATATATTATTTAATTTAGTTGATAAATG
1 GAGATTTGTGCGGTAAAGAAATTATAA-TTTTTTAATATATATTATTTAATTTAGTTGATAAATG
* *
31288 AAATTACATATTAAATCTTAAAAGTTAAATCTAATATTTAAAATTAA
65 AAATTACATATTAAACCATAAAAGTTAAATCTAATATTTAAAATTAA
31335 GA
1 GA
31337 AGGATATTTT
Statistics
Matches: 110, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
111 27 0.25
112 83 0.75
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (111 bp):
GAGATTTGTGCGGTAAAGAAATTATAATTTTTTAATATATATTATTTAATTTAGTTGATAAATGA
AATTACATATTAAACCATAAAAGTTAAATCTAATATTTAAAATTAA
Found at i:31846 original size:31 final size:31
Alignment explanation
Indices: 31777--31865 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 31
31767 CGACTTGTGG
* ** *
31777 CACGCCACGTGTACCAAAAAGCAACATATAT
1 CACGCCATGTGTACCAAAAAGTGACACATAT
31808 CACGCCATGTGTACCAAAAAGTGACACATGA-
1 CACGCCATGTGTACCAAAAAGTGACACAT-AT
* **
31839 CATGCCATGTGTTTCAAAAAGTGACAC
1 CACGCCATGTGTACCAAAAAGTGACAC
31866 GTGGCATGTC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 49 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (31 bp):
CACGCCATGTGTACCAAAAAGTGACACATAT
Found at i:33329 original size:84 final size:84
Alignment explanation
Indices: 33224--33430 Score: 283
Period size: 84 Copynumber: 2.4 Consensus size: 84
33214 AATAATAGAT
* *
33224 AATTGCCCCTGTATTATATATGTGTTTGGGGTCTTTGATAT-AGATGCCTCTGCATTATAAATGT
1 AATTTCCCCTGTATTATATATGTGTTTGGGGACTTTGATATGA-ATGCCTCTGCATTATAAATGT
33288 GCTTGAGGACTTTTAAAGAG
65 GCTTGAGGACTTTTAAAGAG
* * * **
33308 AATTTCCCCTGTGTTATATATGTGTTTGGAGACTTTGGTATGAATGCCTCTGTGTTATAAATGTG
1 AATTTCCCCTGTATTATATATGTGTTTGGGGACTTTGATATGAATGCCTCTGCATTATAAATGTG
*
33373 CTTGAGGACTTTTGAAGAG
66 CTTGAGGACTTTTAAAGAG
*
33392 AATATTGCCCTTGTATTATA-ATTGTGTTTGGGGACTTTG
1 AAT-TT-CCCCTGTATTATATA-TGTGTTTGGGGACTTTG
33431 GGGAGAGAGA
Statistics
Matches: 108, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
84 77 0.71
85 4 0.04
86 27 0.25
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (84 bp):
AATTTCCCCTGTATTATATATGTGTTTGGGGACTTTGATATGAATGCCTCTGCATTATAAATGTG
CTTGAGGACTTTTAAAGAG
Found at i:33383 original size:41 final size:41
Alignment explanation
Indices: 33227--33384 Score: 122
Period size: 41 Copynumber: 3.8 Consensus size: 41
33217 AATAGATAAT
* * * *
33227 TGCCCCTGTATTATATATGTGTTTGGGGTCTTTGATAT-AGA
1 TGCCCCTGTATTATAAATGTGCTTGAGGACTTTGATATGA-A
* * * * *
33268 TGCCTCTGCATTATAAATGTGCTTGAGGACTTTTAAAGAGAA
1 TGCCCCTGTATTATAAATGTGCTTGAGGACTTTGATA-TGAA
* * * * *
33310 TTTCCCCTGTGTTATATATGTGTTTG-GAGACTTTGGTATGAA
1 -TGCCCCTGTATTATAAATGTGCTTGAG-GACTTTGATATGAA
* *
33352 TGCCTCTGTGTTATAAATGTGCTTGAGGACTTT
1 TGCCCCTGTATTATAAATGTGCTTGAGGACTTT
33385 TGAAGAGAAT
Statistics
Matches: 89, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
41 56 0.63
42 6 0.07
43 27 0.30
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.41
Consensus pattern (41 bp):
TGCCCCTGTATTATAAATGTGCTTGAGGACTTTGATATGAA
Found at i:35852 original size:11 final size:11
Alignment explanation
Indices: 35836--35860 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
35826 AGACACAACC
35836 AAACAAAAAGA
1 AAACAAAAAGA
35847 AAACAAAAAGA
1 AAACAAAAAGA
35858 AAA
1 AAA
35861 TCAGGCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAACAAAAAGA
Found at i:38683 original size:52 final size:51
Alignment explanation
Indices: 38595--38743 Score: 246
Period size: 52 Copynumber: 2.9 Consensus size: 51
38585 TTAATAAAAA
*
38595 AGTTTTCAAAGTATCCAATTTAGCTC-TTTTTCAAATTGGGAAAGTTCCCATC
1 AGTTTTTAAAGTATCCAATTTAGC-CATTTTT-AAATTGGGAAAGTTCCCATC
38647 AGTTTTTAAAGTATCCAATTTAGCCAATTTTTAAATTGGGAAAGTTCCCATC
1 AGTTTTTAAAGTATCCAATTTAGCC-ATTTTTAAATTGGGAAAGTTCCCATC
38699 AGTTTTTAAAGTATCCAATTTAGCCAGTTTTTAAATTGGGAAAGT
1 AGTTTTTAAAGTATCCAATTTAGCCA-TTTTTAAATTGGGAAAGT
38744 CCCCGTCATT
Statistics
Matches: 93, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
51 2 0.02
52 86 0.92
53 5 0.05
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (51 bp):
AGTTTTTAAAGTATCCAATTTAGCCATTTTTAAATTGGGAAAGTTCCCATC
Found at i:38730 original size:25 final size:25
Alignment explanation
Indices: 38646--38733 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
38636 AAGTTCCCAT
38646 CAGTTTTTAAAGTATCCAATTTAGC
1 CAGTTTTTAAAGTATCCAATTTAGC
* * **** * **
38671 CAATTTTTAAATTGGGAAAGTTCCC
1 CAGTTTTTAAAGTATCCAATTTAGC
38696 ATCAGTTTTTAAAGTATCCAATTTAGC
1 --CAGTTTTTAAAGTATCCAATTTAGC
38723 CAGTTTTTAAA
1 CAGTTTTTAAA
38734 TTGGGAAAGT
Statistics
Matches: 43, Mismatches: 18, Indels: 4
0.66 0.28 0.06
Matches are distributed among these distances:
25 27 0.63
27 16 0.37
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (25 bp):
CAGTTTTTAAAGTATCCAATTTAGC
Found at i:41329 original size:72 final size:72
Alignment explanation
Indices: 41212--41417 Score: 315
Period size: 72 Copynumber: 2.9 Consensus size: 72
41202 ACTAGTACTG
* *
41212 AGGATTGTGCGAAGGACTACCAAATGTGGGAACTACCTCGGCTACAATCGCAACG-AGAAGGATG
1 AGGATTGTGCGAAGGACTACCAAATGTGGGAACTGCCTTGGCTACAATCGCAACGAAGAA-GATG
41276 ATCATGTA
65 ATCATGTA
*
41284 AGGATTGTGCGAAGGACTACCAAATGTGGGAACTGCCTTGGCTACAATCGCAATGAAGAAGATGA
1 AGGATTGTGCGAAGGACTACCAAATGTGGGAACTGCCTTGGCTACAATCGCAACGAAGAAGATGA
*
41349 TTATGTA
66 TCATGTA
** * * *
41356 AGGATTGTGCGAAGGACCGCCAAATGAGGGAATTGCCTTGGCTACAATCGCAATGAAGAAGA
1 AGGATTGTGCGAAGGACTACCAAATGTGGGAACTGCCTTGGCTACAATCGCAACGAAGAAGA
41418 GGGCCATGGG
Statistics
Matches: 125, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
72 121 0.97
73 4 0.03
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.20
Consensus pattern (72 bp):
AGGATTGTGCGAAGGACTACCAAATGTGGGAACTGCCTTGGCTACAATCGCAACGAAGAAGATGA
TCATGTA
Found at i:47888 original size:35 final size:35
Alignment explanation
Indices: 47847--47991 Score: 182
Period size: 35 Copynumber: 4.1 Consensus size: 35
47837 ATGACATAGC
* *
47847 CCCCAAGCGTTGAATGATGAAGGAGTTGCCGGAGT
1 CCCCAAGTGTTGAATGATGAAGGAGTTGCTGGAGT
* * * *
47882 ACCCAAGTGTTAAATGATGAAAGAATTGCTGGAGT
1 CCCCAAGTGTTGAATGATGAAGGAGTTGCTGGAGT
*
47917 CCCCAAGTGTTGAATGATGAAGGGGTTGCTGGAGT
1 CCCCAAGTGTTGAATGATGAAGGAGTTGCTGGAGT
* * * * *
47952 CCCCAAATGTCGAATGATGAAGGGGTTGCTGCAGC
1 CCCCAAGTGTTGAATGATGAAGGAGTTGCTGGAGT
47987 CCCCA
1 CCCCA
47992 GGTGCTAAAT
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 95 1.00
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (35 bp):
CCCCAAGTGTTGAATGATGAAGGAGTTGCTGGAGT
Found at i:53730 original size:41 final size:41
Alignment explanation
Indices: 53679--53826 Score: 156
Period size: 41 Copynumber: 3.5 Consensus size: 41
53669 TGCACCTGAA
*
53679 TTATATATGTGTTTGGGTACTTTGATATAG-ATGCCTCTGTG
1 TTATAAATGTGTTTGGG-ACTTTGATATAGAATGCCTCTGTG
* * * * *
53720 TTATAAATGTGCTTGAGGACTTTTAGAGAGAATTGCCCCTGTG
1 TTATAAATGTGTTTG-GGACTTTGATATAGAA-TGCCTCTGTG
* *
53763 TTATAAATGTGTTTGGGAATTTTGGTAT-GAATGCCTCTGTG
1 TTATAAATGTGTTTGGG-ACTTTGATATAGAATGCCTCTGTG
*
53804 TTATAAATGTGCTTGAGGACTTT
1 TTATAAATGTGTTTG-GGACTTT
53827 TGAAGAGAAT
Statistics
Matches: 87, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
41 49 0.56
42 10 0.11
43 28 0.32
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (41 bp):
TTATAAATGTGTTTGGGACTTTGATATAGAATGCCTCTGTG
Found at i:53767 original size:43 final size:42
Alignment explanation
Indices: 53710--53853 Score: 168
Period size: 41 Copynumber: 3.4 Consensus size: 42
53700 TTGATATAGA
*
53710 TGCCTCTGTGTTATAAATGTGCTTGAGGACTTTTAGAGAGAAT
1 TGCCCCTGTGTTATAAATGTGCTTGAGGACTTTT-GAGAGAAT
* *
53753 TGCCCCTGTGTTATAAATGTGTTTG-GGAATTTTG-GTATGAA-
1 TGCCCCTGTGTTATAAATGTGCTTGAGGACTTTTGAG-A-GAAT
*
53794 TGCCTCTGTGTTATAAATGTGCTTGAGGACTTTTGAAGAGAATAT
1 TGCCCCTGTGTTATAAATGTGCTTGAGGACTTTTG-AGAG-A-AT
*
53839 TGCCCTTGTGTTATA
1 TGCCCCTGTGTTATA
53854 GTTGTGTTTA
Statistics
Matches: 85, Mismatches: 8, Indels: 14
0.79 0.07 0.13
Matches are distributed among these distances:
40 1 0.01
41 25 0.29
42 19 0.22
43 25 0.29
44 2 0.02
45 13 0.15
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.40
Consensus pattern (42 bp):
TGCCCCTGTGTTATAAATGTGCTTGAGGACTTTTGAGAGAAT
Found at i:53807 original size:84 final size:86
Alignment explanation
Indices: 53679--53872 Score: 263
Period size: 84 Copynumber: 2.3 Consensus size: 86
53669 TGCACCTGAA
* *
53679 TTATATATGTGTTTGGGTACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTT
1 TTATAAATGTGTTTGGGAACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTT
53744 --AGAGAGA-ATTGCCCCTGTG
66 GAAGAGA-ATATTGCCCCTGTG
* *
53763 TTATAAATGTGTTTGGGAATTTTGGTAT-GAATGCCTCTGTGTTATAAATGTGCTTGAGGACTTT
1 TTATAAATGTGTTTGGGAACTTTGATATAG-ATGCCTCTGTGTTATAAATGTGCTTGAGGACTTT
*
53827 TGAAGAGAATATTGCCCTTGTG
65 TGAAGAGAATATTGCCCCTGTG
**
53849 TTATAGTTGTGTTTAGGG-ACTTTG
1 TTATAAATGTGTTT-GGGAACTTTG
53873 GGGAGAGAGA
Statistics
Matches: 97, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
83 1 0.01
84 59 0.61
85 1 0.01
86 33 0.34
87 3 0.03
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.42
Consensus pattern (86 bp):
TTATAAATGTGTTTGGGAACTTTGATATAGATGCCTCTGTGTTATAAATGTGCTTGAGGACTTTT
GAAGAGAATATTGCCCCTGTG
Found at i:56265 original size:23 final size:23
Alignment explanation
Indices: 56239--56282 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
56229 TTTTGTGTTC
*
56239 TTGAGTTCTTTGGAAAATGATCT
1 TTGAGTTCTTAGGAAAATGATCT
56262 TTGAGTTCTTAGGAAAATGAT
1 TTGAGTTCTTAGGAAAATGAT
56283 AGTTTTGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (23 bp):
TTGAGTTCTTAGGAAAATGATCT
Found at i:56391 original size:24 final size:23
Alignment explanation
Indices: 56359--56411 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
56349 AGTGAAATCA
*
56359 TTTTT-AAATATTTTAGCTTTTAT
1 TTTTTAAAATATTTTA-CTATTAT
56382 TTTTTAAAATATTTTACTATTAT
1 TTTTTAAAATATTTTACTATTAT
56405 TATTTTA
1 T-TTTTA
56412 GAGATTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTTAAAATATTTTACTATTAT
Found at i:61466 original size:17 final size:17
Alignment explanation
Indices: 61444--61478 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
61434 CTGTACTACT
61444 AACTAATTGTTTATACC
1 AACTAATTGTTTATACC
61461 AACTAATTGTTTATACC
1 AACTAATTGTTTATACC
61478 A
1 A
61479 TGATTTACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (17 bp):
AACTAATTGTTTATACC
Found at i:61661 original size:18 final size:17
Alignment explanation
Indices: 61638--61675 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
61628 CCCAAATTAC
61638 TTATGGAAATTAGGGAAA
1 TTATGGAAATTA-GGAAA
61656 TTATGGAAATTAGGAAA
1 TTATGGAAATTAGGAAA
61673 TTA
1 TTA
61676 AATGAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32
Consensus pattern (17 bp):
TTATGGAAATTAGGAAA
Found at i:61673 original size:8 final size:9
Alignment explanation
Indices: 61642--61675 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
61632 AATTACTTAT
61642 GGAAATTAG
1 GGAAATTAG
*
61651 GGAAATTAT
1 GGAAATTAG
61660 GGAAATTA-
1 GGAAATTAG
61668 GGAAATTA
1 GGAAATTA
61676 AATGAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (9 bp):
GGAAATTAG
Done.