Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017687.1 Corchorus olitorius cultivar O-4 contig17720, 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: 51339
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:65 original size:45 final size:45
Alignment explanation
Indices: 1--95 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
1 GCCAAGAGTCCGATGCAGAGGTAGAGGGCGAAAAAAATAAACCCC
1 GCCAAGAGTCCGATGCAGAGGTAGAGGGCGAAAAAAATAAACCCC
* *
46 GCCAAGAGTCCGATGCAGAGGTAGAGGGCGATAAAAATCAACCCC
1 GCCAAGAGTCCGATGCAGAGGTAGAGGGCGAAAAAAATAAACCCC
91 GCCAA
1 GCCAA
96 AAAGCCGTAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.38, C:0.24, G:0.28, T:0.09
Consensus pattern (45 bp):
GCCAAGAGTCCGATGCAGAGGTAGAGGGCGAAAAAAATAAACCCC
Found at i:288 original size:39 final size:40
Alignment explanation
Indices: 225--304 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
215 TTGGTTGCGG
*
225 TTGCTGCTGGAAGGTTTCTTCTGGACACGATTGGGA-CCA
1 TTGCCGCTGGAAGGTTTCTTCTGGACACGATTGGGAGCCA
*
264 TTGCCGCTTGAAGGTTTCTTCTGGACACGATTGGGAGCCA
1 TTGCCGCTGGAAGGTTTCTTCTGGACACGATTGGGAGCCA
304 T
1 T
305 GAATGGTGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 34 0.89
40 4 0.11
ACGTcount: A:0.17, C:0.21, G:0.30, T:0.31
Consensus pattern (40 bp):
TTGCCGCTGGAAGGTTTCTTCTGGACACGATTGGGAGCCA
Found at i:804 original size:13 final size:13
Alignment explanation
Indices: 786--818 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
776 ACAAGCTCAT
786 GAAAAAAAAAAGA
1 GAAAAAAAAAAGA
*
799 GAAAAAAAAACGA
1 GAAAAAAAAAAGA
812 -AAAAAAA
1 GAAAAAAA
819 CGTGGTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAAGA
Found at i:2567 original size:37 final size:37
Alignment explanation
Indices: 2525--2651 Score: 202
Period size: 37 Copynumber: 3.4 Consensus size: 37
2515 TCCAAAGTGA
* *
2525 AACAAGTCTTCATCAAAATTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
2562 AACAAGTCTCCA-CGAAAGTTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATC-AAAGTTATTCATCAAAGTTCTTC
*
2599 AACAAGTCTCCACCAAAGTTATTCATCAAAGTTCTTC
1 AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
*
2636 AACAAGTCTTCATCAA
1 AACAAGTCTCCATCAA
2652 GTTGTTCTTC
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
36 1 0.01
37 82 0.98
38 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (37 bp):
AACAAGTCTCCATCAAAGTTATTCATCAAAGTTCTTC
Found at i:2651 original size:24 final size:24
Alignment explanation
Indices: 2546--2685 Score: 92
Period size: 24 Copynumber: 5.7 Consensus size: 24
2536 ATCAAAATTA
2546 TTCATCAAAGTTCTTCAACAAGTC
1 TTCATCAAAGTTCTTCAACAAGTC
* * *
2570 TCCA-CGAAAGTTATTCATCAAAGTTC
1 TTCATC-AAAGTTCTTCAAC-AAG-TC
* * * *
2596 TTCAAC-AAG-TCTCCACCAAAGTTA
1 TTCATCAAAGTTCTTCAAC-AAG-TC
2620 TTCATCAAAGTTCTTCAACAAGTC
1 TTCATCAAAGTTCTTCAACAAGTC
* *
2644 TTCATCAAGTTGTTCTTCAACAAGTT
1 TTCATCAA--AGTTCTTCAACAAGTC
2670 TTCACTC--AGTTCTTCA
1 TTCA-TCAAAGTTCTTCA
2686 TCAAATTTTC
Statistics
Matches: 92, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
23 9 0.10
24 39 0.42
25 12 0.13
26 29 0.32
27 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.34
Consensus pattern (24 bp):
TTCATCAAAGTTCTTCAACAAGTC
Found at i:2689 original size:26 final size:26
Alignment explanation
Indices: 2634--2689 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
2624 TCAAAGTTCT
* *
2634 TCAACAAGTCTTCATCAAGTTGTTCT
1 TCAACAAGTCTTCATCAAGTTCTTCA
*
2660 TCAACAAGTTTTCACTC-AGTTCTTCA
1 TCAACAAGTCTTCA-TCAAGTTCTTCA
2686 TCAA
1 TCAA
2690 ATTTTCCACC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.38
Consensus pattern (26 bp):
TCAACAAGTCTTCATCAAGTTCTTCA
Found at i:5539 original size:30 final size:30
Alignment explanation
Indices: 5503--5567 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
5493 TGGTTTTGAA
*
5503 TTTGATTCCATTCAGTTTGCTTTTTAAGGT
1 TTTGATTCCATTCAGTTTCCTTTTTAAGGT
**
5533 TTTGATTCCATTCAGTTTCCTTTTTTGGGT
1 TTTGATTCCATTCAGTTTCCTTTTTAAGGT
5563 TTTGA
1 TTTGA
5568 AACTAGTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.55
Consensus pattern (30 bp):
TTTGATTCCATTCAGTTTCCTTTTTAAGGT
Found at i:6036 original size:87 final size:88
Alignment explanation
Indices: 5916--6089 Score: 332
Period size: 87 Copynumber: 2.0 Consensus size: 88
5906 TAGCTTCCCG
*
5916 ATTTAGCCTTAATAAAAAAAATGAAAATTGTTTAGAAATCAGGAAAAGAGGGTAATGGAGACTTT
1 ATTTAGCCTTAATAAAAAAAATGAAAATTGTTTAGAAATCAAGAAAAGAGGGTAATGGAGACTTT
5981 GAGGGTTCACAAATTAGAAGTGA
66 GAGGGTTCACAAATTAGAAGTGA
6004 ATTTAGCCTTAAT-AAAAAAATGAAAATTGTTTAGAAATCAAGAAAAGAGGGTAATGGAGACTTT
1 ATTTAGCCTTAATAAAAAAAATGAAAATTGTTTAGAAATCAAGAAAAGAGGGTAATGGAGACTTT
6068 GAGGGTTCACAAATTAGAAGTG
66 GAGGGTTCACAAATTAGAAGTG
6090 TTTAGATATA
Statistics
Matches: 85, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
87 72 0.85
88 13 0.15
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (88 bp):
ATTTAGCCTTAATAAAAAAAATGAAAATTGTTTAGAAATCAAGAAAAGAGGGTAATGGAGACTTT
GAGGGTTCACAAATTAGAAGTGA
Found at i:7775 original size:16 final size:16
Alignment explanation
Indices: 7754--7808 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
7744 CAGGTAATTT
7754 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
* *
7770 TTTCGGCTCA-TCTTGG
1 TTTCGGGTCATTC-GGG
*
7786 -TTCAGGTCATTCGGG
1 TTTCGGGTCATTCGGG
*
7801 TCTCGGGT
1 TTTCGGGT
7809 TTGCTGGGTT
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.07, C:0.22, G:0.33, T:0.38
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:7978 original size:25 final size:24
Alignment explanation
Indices: 7928--7979 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
7918 CCTTGAATTT
* *
7928 TTTAATGTTTAATTCTTAAATTTA
1 TTTAATGTTTAATTATTAAATCTA
*
7952 TTTAATGTCTTAATTATTCAATCTA
1 TTTAATGT-TTAATTATTAAATCTA
7977 TTT
1 TTT
7980 TACAATCCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.58
Consensus pattern (24 bp):
TTTAATGTTTAATTATTAAATCTA
Found at i:9509 original size:4 final size:4
Alignment explanation
Indices: 9502--9526 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9492 TTTTTTTAAC
9502 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
9527 ATTGTTGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:9556 original size:3 final size:3
Alignment explanation
Indices: 9543--9653 Score: 213
Period size: 3 Copynumber: 37.0 Consensus size: 3
9533 GTTGTTGTTG
*
9543 TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9591 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9639 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
9654 ATTTCTAATT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 106 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:9993 original size:33 final size:32
Alignment explanation
Indices: 9936--10054 Score: 125
Period size: 32 Copynumber: 3.7 Consensus size: 32
9926 ATCCAGACGC
* * *
9936 GGAGGCGTCTCCAGAGGGTGCCCCACCACGGG
1 GGAGGCATCCCCAGGGGGTGCCCCACCACGGG
9968 GTGAGGCATCCCCAGGGGGCT-CCCCACCACGGG
1 G-GAGGCATCCCCAGGGGG-TGCCCCACCACGGG
* *
10001 GGAAGGCGT-CCCAGGGGGTGCCCCACCACAGG
1 GG-AGGCATCCCCAGGGGGTGCCCCACCACGGG
* * *
10033 GGAGGCTTCCCCACGGGTTGCC
1 GGAGGCATCCCCAGGGGGTGCC
10055 TCGTCCATGT
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
31 6 0.08
32 35 0.47
33 32 0.43
34 1 0.01
ACGTcount: A:0.15, C:0.36, G:0.39, T:0.10
Consensus pattern (32 bp):
GGAGGCATCCCCAGGGGGTGCCCCACCACGGG
Found at i:10025 original size:32 final size:31
Alignment explanation
Indices: 9936--10043 Score: 128
Period size: 33 Copynumber: 3.4 Consensus size: 31
9926 ATCCAGACGC
*
9936 GGAGGCGTCTCCAGAGGGTGCCCCACCACGGG
1 GGAGGCGTC-CCAGGGGGTGCCCCACCACGGG
*
9968 GTGAGGCATCCCCAGGGGGCT-CCCCACCACGGG
1 G-GAGGCGT-CCCAGGGGG-TGCCCCACCACGGG
*
10001 GGAAGGCGTCCCAGGGGGTGCCCCACCACAGG
1 GG-AGGCGTCCCAGGGGGTGCCCCACCACGGG
*
10033 GGAGGCTTCCC
1 GGAGGCGTCCC
10044 CACGGGTTGC
Statistics
Matches: 66, Mismatches: 5, Indels: 11
0.80 0.06 0.13
Matches are distributed among these distances:
31 9 0.14
32 24 0.36
33 31 0.47
34 2 0.03
ACGTcount: A:0.16, C:0.36, G:0.39, T:0.09
Consensus pattern (31 bp):
GGAGGCGTCCCAGGGGGTGCCCCACCACGGG
Found at i:10091 original size:3 final size:3
Alignment explanation
Indices: 10083--10120 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
10073 CCCCAAAGGG
10083 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
10121 CAGAGAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:10966 original size:240 final size:240
Alignment explanation
Indices: 10543--11007 Score: 824
Period size: 240 Copynumber: 1.9 Consensus size: 240
10533 CCCATGGGCG
* * *
10543 AGGCGCCCCGTGGGGACGTCTCCCCCCGTGGTCGGGCACCCCCTGGGGACGCTCTGGGTCAACAG
1 AGGCGCCCCGTGGGGACGCCTCCCCCCGTGGTCGGGCACCCCCTGGGGACGCCCCGGGTCAACAG
* * *
10608 CCCCAACTTTCCCAATAACTCGTTAAATTTGCATTTTTCTTACCTTGTCAAATGTCGACGGCACG
66 CCCCAACTATCCCAATAACTCGTTAAATTTGCATTTTTCTTACCTTGTCAAATGTCGACGACACA
*
10673 TTATCGTCCATTTCCGGAGTTCTCGGGCTGTTCCACATTGGTGATTGGCTTGAAAATTTGAGTTT
131 TTATCGTCCATTTCCGGAGTTCTCGGGCTGTTCCACATTGGTGATTGGCTTGAAAATTTGAGATT
10738 TTTAGTTTGAAGGTTTTAGAGGAAAATGAAAGCTTCAACATTTTT
196 TTTAGTTTGAAGGTTTTAGAGGAAAATGAAAGCTTCAACATTTTT
*
10783 AGGCGCCTCC-TGGGGATGCCTCCCCCCGTGGTCGGGCACCCCCTGGGGACGCCCCGGGTCAACA
1 AGGCGCC-CCGTGGGGACGCCTCCCCCCGTGGTCGGGCACCCCCTGGGGACGCCCCGGGTCAACA
* *
10847 GCCCCAACTATCCCAATAACTCGTTAAATTTGCATTTTTCTTACCTTGTTAGATGTCGACGACAC
65 GCCCCAACTATCCCAATAACTCGTTAAATTTGCATTTTTCTTACCTTGTCAAATGTCGACGACAC
10912 ATTATCGTCCATTTCCGGAGTTCTCGGGCTGTTCCACATTGGTGATTGGCTTGAAAATTTGAGAT
130 ATTATCGTCCATTTCCGGAGTTCTCGGGCTGTTCCACATTGGTGATTGGCTTGAAAATTTGAGAT
10977 TTTTAGTTTGAAGGTTTTAGAGGAAAATGAA
195 TTTTAGTTTGAAGGTTTTAGAGGAAAATGAA
11008 GCAAAGGGCA
Statistics
Matches: 214, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
240 212 0.99
241 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (240 bp):
AGGCGCCCCGTGGGGACGCCTCCCCCCGTGGTCGGGCACCCCCTGGGGACGCCCCGGGTCAACAG
CCCCAACTATCCCAATAACTCGTTAAATTTGCATTTTTCTTACCTTGTCAAATGTCGACGACACA
TTATCGTCCATTTCCGGAGTTCTCGGGCTGTTCCACATTGGTGATTGGCTTGAAAATTTGAGATT
TTTAGTTTGAAGGTTTTAGAGGAAAATGAAAGCTTCAACATTTTT
Found at i:17035 original size:53 final size:54
Alignment explanation
Indices: 16947--17050 Score: 192
Period size: 53 Copynumber: 1.9 Consensus size: 54
16937 CTACCCTTCT
*
16947 TTGTGAATTTTTTGTTTTATTGTTGGGATTGATTTGTTCAATTTAATTTACAAA
1 TTGTGAATTTTTTGTTTTATTATTGGGATTGATTTGTTCAATTTAATTTACAAA
17001 TTGTGAATTTTTTGTTTTATTATT-GGATTGATTTGTTCAATTTAATTTAC
1 TTGTGAATTTTTTGTTTTATTATTGGGATTGATTTGTTCAATTTAATTTAC
17051 CATCTATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 26 0.53
54 23 0.47
ACGTcount: A:0.23, C:0.04, G:0.15, T:0.58
Consensus pattern (54 bp):
TTGTGAATTTTTTGTTTTATTATTGGGATTGATTTGTTCAATTTAATTTACAAA
Found at i:17415 original size:20 final size:20
Alignment explanation
Indices: 17382--17419 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
17372 TTCTCTACTA
*
17382 ATCTTTTTATCAAATCTTCCT
1 ATCTTTTGATCAAA-CTTCCT
17403 ATCTTTTGA-CAAACTTC
1 ATCTTTTGATCAAACTTC
17420 TGCTAACGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 4 0.25
21 8 0.50
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (20 bp):
ATCTTTTGATCAAACTTCCT
Found at i:17885 original size:2 final size:2
Alignment explanation
Indices: 17878--17946 Score: 58
Period size: 2 Copynumber: 36.5 Consensus size: 2
17868 CGACCGAATA
* *
17878 AT AT AT AT AT AT AT A- AC A- AT AT AT AT TT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
17917 AT CT GAT A- AT AT AT TT AT AT AT AT A- AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
17947 AATAATATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
1 5 0.09
2 49 0.89
3 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17918 original size:29 final size:26
Alignment explanation
Indices: 17878--17958 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 26
17868 CGACCGAATA
17878 ATATATATATATATAACAATATATATTT
1 ATATATATATATAT-A-AATATATATTT
**
17906 ATAT-TATATATATCTGATAATATATTT
1 ATATATATATATAT-AAAT-ATATATTT
17933 ATATATATA-ATATAAATA-ATATTT
1 ATATATATATATATAAATATATATTT
17957 AT
1 AT
17959 TTTTAAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
24 8 0.17
25 1 0.02
26 4 0.09
27 25 0.54
28 8 0.17
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (26 bp):
ATATATATATATATAAATATATATTT
Found at i:17940 original size:31 final size:31
Alignment explanation
Indices: 17879--17946 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
17869 GACCGAATAA
*
17879 TATATATATATATAACAATATATATTTATAT
1 TATATATATATATAACAATATATATATATAT
* * *
17910 TATATATATCTGATAA-TATATTTATATATAT
1 TATATATATAT-ATAACAATATATATATATAT
*
17941 AATATA
1 TATATA
17947 AATAATATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (31 bp):
TATATATATATATAACAATATATATATATAT
Found at i:19458 original size:25 final size:27
Alignment explanation
Indices: 19418--19472 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
19408 AAATGTTAAA
*
19418 TCAATTGTTATATTCTGAATTTCTT-T
1 TCAATTGTAATATTCTGAATTTCTTAT
19444 TCAATTG-AATATTCTGAATTTCTTAT
1 TCAATTGTAATATTCTGAATTTCTTAT
19470 TCA
1 TCA
19473 TTCCGAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (27 bp):
TCAATTGTAATATTCTGAATTTCTTAT
Found at i:23001 original size:74 final size:74
Alignment explanation
Indices: 22876--23023 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
22866 ACTTCACAGG
*
22876 CTACTATCTTTTAGATGAATGTCATTTTCCTGCATCAAATTGAACAGCTTAATAAACAAAGAAGC
1 CTACTATCTTTTAGATGAATGTCATTTTCCTGCATCAAATTGAACAACTTAATAAACAAAGAAGC
22941 AACAACCAA
66 AACAACCAA
22950 CTACTATCTTTTAGATGAATGTCATTTTCCTGCATCAAATTGAACAACTTAATAAACAAAGAAGC
1 CTACTATCTTTTAGATGAATGTCATTTTCCTGCATCAAATTGAACAACTTAATAAACAAAGAAGC
23015 AACAACCAA
66 AACAACCAA
23024 GTTCACTTTT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.28
Consensus pattern (74 bp):
CTACTATCTTTTAGATGAATGTCATTTTCCTGCATCAAATTGAACAACTTAATAAACAAAGAAGC
AACAACCAA
Found at i:23871 original size:2 final size:2
Alignment explanation
Indices: 23813--23854 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
23803 ATATTAGTTT
* *
23813 TA TA TA TT TA TA TA TA TA CA TA -A TA TA 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 TA TA TA
23854 T
1 T
23855 TTTTAAATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24223 original size:41 final size:42
Alignment explanation
Indices: 24149--24232 Score: 143
Period size: 41 Copynumber: 2.0 Consensus size: 42
24139 TAAGTCTTTA
*
24149 TATCTTGGAATTCATCTGGTTCTTAAATTGATTCAATACATT
1 TATCTTGGAATTCATCTGGTTCTTAAATCGATTCAATACATT
*
24191 TATCTTGGAATTCAT-TTGTTCTTAAATCGATTCAATACATT
1 TATCTTGGAATTCATCTGGTTCTTAAATCGATTCAATACATT
24232 T
1 T
24233 CTATTTCAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 25 0.62
42 15 0.38
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (42 bp):
TATCTTGGAATTCATCTGGTTCTTAAATCGATTCAATACATT
Found at i:25654 original size:2 final size:2
Alignment explanation
Indices: 25647--25672 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25637 ATGTTGTAAA
25647 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
25673 TTGACTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27063 original size:16 final size:15
Alignment explanation
Indices: 27042--27079 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
27032 TTATTTTTTA
27042 TTTTTCTTAT-TTAAT
1 TTTTTCTTATATT-AT
27057 TTGTTTCTTATATTAT
1 TT-TTTCTTATATTAT
27073 TTTTTCT
1 TTTTTCT
27080 AACTAGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 12 0.57
17 2 0.10
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTTCTTATATTAT
Found at i:27228 original size:96 final size:93
Alignment explanation
Indices: 27105--27300 Score: 329
Period size: 96 Copynumber: 2.1 Consensus size: 93
27095 AGTAAATAGG
27105 AATTAATAATTATGTTATTAGTGATTGTTGGTATATTATCATTTGATTAGTGTTAGTGATTAAGT
1 AATTAATAATTATGTTATTAGTGATTGTTGGTATATTATCATTTGATTAGTGTTAGTGATTAAGT
*
27170 ATTGATAATTAGTAATATTAGAATGTCATTT
66 ATTG---ATTAGTAATATTAGAAAGTCATTT
* *
27201 GATTAATAATTATGTTATTAGTGATTGTTGGTATATTATCTTTTGATTAGTGTTAGTGATTAAGT
1 AATTAATAATTATGTTATTAGTGATTGTTGGTATATTATCATTTGATTAGTGTTAGTGATTAAGT
*
27266 ATTGATTAGTAATATTAGAAAGTTATTT
66 ATTGATTAGTAATATTAGAAAGTCATTT
27294 AATTAAT
1 AATTAAT
27301 TATTGGAATT
Statistics
Matches: 95, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
93 28 0.29
96 67 0.71
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (93 bp):
AATTAATAATTATGTTATTAGTGATTGTTGGTATATTATCATTTGATTAGTGTTAGTGATTAAGT
ATTGATTAGTAATATTAGAAAGTCATTT
Found at i:28154 original size:30 final size:31
Alignment explanation
Indices: 28120--28185 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
28110 TATAGGATTT
28120 ATTTGTCCCAAAA-AAAAAGTTAAGGGGCCA
1 ATTTGTCCCAAAATAAAAAGTTAAGGGGCCA
** * *
28150 ATTTGTCCCAAAATGGATAGTTAAGGGGCTA
1 ATTTGTCCCAAAATAAAAAGTTAAGGGGCCA
28181 ATTTG
1 ATTTG
28186 GGTATTAAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (31 bp):
ATTTGTCCCAAAATAAAAAGTTAAGGGGCCA
Found at i:28397 original size:83 final size:84
Alignment explanation
Indices: 28309--28508 Score: 285
Period size: 83 Copynumber: 2.4 Consensus size: 84
28299 TAGATTTTTA
* * * *
28309 ATATAGATTTTGATACCTTAAGCTAATTTTAATAGTATTCATTTTCTCTCACTTATGGTTTAAAT
1 ATATAGATTTAGGTACCTTAAGCTAATTTTAATAGTATTCATTTTCTCTCACCTAGGGTTTAAAT
*
28374 TTCATGTCAC-CATTTTAT
66 TTCATGTCACACATATTAT
* * * *
28392 GTATAGATTTAGGTATCTTAAGCTAATTTTAATGGTATTCATTTTTTCTCACCTAGGGTTTAAAT
1 ATATAGATTTAGGTACCTTAAGCTAATTTTAATAGTATTCATTTTCTCTCACCTAGGGTTTAAAT
28457 TTCATGTCACACATATTAT
66 TTCATGTCACACATATTAT
* * *
28476 ATATAGATTTAGGTAGCTTAAGTTAATTCTAAT
1 ATATAGATTTAGGTACCTTAAGCTAATTTTAAT
28509 GTGACATAGG
Statistics
Matches: 103, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
83 67 0.65
84 36 0.35
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (84 bp):
ATATAGATTTAGGTACCTTAAGCTAATTTTAATAGTATTCATTTTCTCTCACCTAGGGTTTAAAT
TTCATGTCACACATATTAT
Found at i:30846 original size:107 final size:106
Alignment explanation
Indices: 30594--30873 Score: 324
Period size: 103 Copynumber: 2.7 Consensus size: 106
30584 TTTTCTAACT
* ** * * * *
30594 CTTAAAATAAAATTTTAATTTTAA-TTAGGGTTAAACTTGGTG-AATTAGTTATATATTTTATTT
1 CTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTT
* *
30657 CT-AAAACCCTATAACAATATTATTAATTATGGAATTTACC
66 CTAAAAACCCTATAACAATATAATTAATTATGAAATTTACC
* * *
30697 CTTAAAATACAAA-AAAA--CTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGT-TTCTTATT
1 CTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATT-TTATT
* * *
30758 TCTAAAAACCCTATAATAATA-AATTAAAGTTTTGAAATTTATC
65 TCTAAAAACCCTATAACAATATAATT-AA-TTATGAAATTTACC
30801 CTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATATTTTAT
1 CTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAG-TTT-TATATTTTAT
30866 TTCTAAAA
64 TTCTAAAA
30874 CTCTATACTA
Statistics
Matches: 147, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
100 3 0.02
101 17 0.12
102 23 0.16
103 29 0.20
104 23 0.16
105 4 0.03
107 29 0.20
108 3 0.02
109 14 0.10
110 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (106 bp):
CTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTT
CTAAAAACCCTATAACAATATAATTAATTATGAAATTTACC
Found at i:36208 original size:104 final size:104
Alignment explanation
Indices: 36026--36253 Score: 332
Period size: 103 Copynumber: 2.2 Consensus size: 104
36016 GTAAAAAAAA
*
36026 TTATTTTTATTTTAAGGGTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTTAGAAATAAA
1 TTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAA-TTATTGTTATAGGGTTTTAGAAATAAA
* *
36091 ATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATT
65 ACATAAAACTAA-TTCACTAAGTTTAGCCCAAATTAAAACT
* *
36132 TTATTTTTATTTTAAGGGTAAATTCCATAATTAATGA-TATTGTTATAGGGTTTTAGAAATAAAA
1 TTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAATTATTGTTATAGGGTTTTAGAAATAAAA
* * *
36196 CATATAACTAATTCGCTAAGTTTAGTCCAAATTAAAACT
66 CATAAAACTAATTCACTAAGTTTAGCCCAAATTAAAACT
** *
36235 AAAATTTTATTTTAAGGGT
1 TTATTTTTATTTTAAGGGT
36254 TAGAAAAATT
Statistics
Matches: 111, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
103 41 0.37
104 36 0.32
106 34 0.31
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (104 bp):
TTATTTTTATTTTAAGGGTAAATTCCAAAATTAATAATTATTGTTATAGGGTTTTAGAAATAAAA
CATAAAACTAATTCACTAAGTTTAGCCCAAATTAAAACT
Found at i:38095 original size:21 final size:21
Alignment explanation
Indices: 38054--38094 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
38044 ACAGTTCTTC
*
38054 TGGGTGTTTTTTGTTTCTTTT
1 TGGGTATTTTTTGTTTCTTTT
38075 TGGGTA-TTTTT-TTTCTTTT
1 TGGGTATTTTTTGTTTCTTTT
38094 T
1 T
38095 TGTTTTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 5 0.26
21 5 0.26
ACGTcount: A:0.02, C:0.05, G:0.20, T:0.73
Consensus pattern (21 bp):
TGGGTATTTTTTGTTTCTTTT
Found at i:39009 original size:30 final size:30
Alignment explanation
Indices: 38973--39038 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
38963 AGACTGGCAT
38973 GATCAATGGGCTCCGACCTTCTCCTTTGAA
1 GATCAATGGGCTCCGACCTTCTCCTTTGAA
39003 GATCAATGGGCTCCGACCTTCTCCTTTGAA
1 GATCAATGGGCTCCGACCTTCTCCTTTGAA
39033 GATCAA
1 GATCAA
39039 CAAAGACTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (30 bp):
GATCAATGGGCTCCGACCTTCTCCTTTGAA
Found at i:43236 original size:14 final size:15
Alignment explanation
Indices: 43217--43245 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43207 TAGTGCATTG
43217 GATTATT-TCTGTCT
1 GATTATTATCTGTCT
43231 GATTATTATCTGTCT
1 GATTATTATCTGTCT
43246 AAATTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (15 bp):
GATTATTATCTGTCT
Done.