Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017883.1 Corchorus olitorius cultivar O-4 contig17916, 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: 83324
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:3506 original size:32 final size:32
Alignment explanation
Indices: 3436--3517 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
3426 ATTTTACTAA
** *
3436 TTTCCAAAATCTCCTTTT--GAATTTCCTTAT
1 TTTCCAAAATCTCCTTTTGGGAATAACCTTAC
* *
3466 TTTTCAAAATCTCCTTTTGGGGATAACCTTAC
1 TTTCCAAAATCTCCTTTTGGGAATAACCTTAC
*
3498 TTTCCAAAATCTTCTTTTGG
1 TTTCCAAAATCTCCTTTTGG
3518 AGTTTACTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 17 0.40
32 26 0.60
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (32 bp):
TTTCCAAAATCTCCTTTTGGGAATAACCTTAC
Found at i:7329 original size:14 final size:14
Alignment explanation
Indices: 7310--7345 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
7300 TTTTCGAAAA
7310 AAATTATGGCATCG
1 AAATTATGGCATCG
*
7324 AAATTATGGCATTG
1 AAATTATGGCATCG
7338 AAATTATG
1 AAATTATG
7346 ATTAATGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.33
Consensus pattern (14 bp):
AAATTATGGCATCG
Found at i:7944 original size:21 final size:21
Alignment explanation
Indices: 7918--7960 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
7908 TGATGTATCA
*
7918 GTATGGCCGGTGGTGGCACGG
1 GTATGGCCGGTGGCGGCACGG
*
7939 GTATGGCTGGTGGCGGCACGG
1 GTATGGCCGGTGGCGGCACGG
7960 G
1 G
7961 CTTAACCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.19, G:0.53, T:0.19
Consensus pattern (21 bp):
GTATGGCCGGTGGCGGCACGG
Found at i:11042 original size:12 final size:13
Alignment explanation
Indices: 11023--11054 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
11013 GCAGCTTCCT
11023 AGAAAAACTCAAA
1 AGAAAAACTCAAA
11036 A-AAAAACTCAAA
1 AGAAAAACTCAAA
11048 AGAAAAA
1 AGAAAAA
11055 TTTGATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.75, C:0.12, G:0.06, T:0.06
Consensus pattern (13 bp):
AGAAAAACTCAAA
Found at i:15460 original size:28 final size:28
Alignment explanation
Indices: 15428--15525 Score: 124
Period size: 28 Copynumber: 3.5 Consensus size: 28
15418 CTGGATACGC
* * * *
15428 AAATGACTAAAATACCCCTGGACATGTA
1 AAATGACCAAAATGCCCCTAGACATGCA
*
15456 AAATGACCAAAATGCCCCTAGACATACA
1 AAATGACCAAAATGCCCCTAGACATGCA
* *
15484 AAATGACGAAAATGCCCCCAGACATGCA
1 AAATGACCAAAATGCCCCTAGACATGCA
*
15512 AAGTGACCAAAATG
1 AAATGACCAAAATG
15526 AGAAGTAATT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.45, C:0.24, G:0.15, T:0.15
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTAGACATGCA
Found at i:15850 original size:51 final size:51
Alignment explanation
Indices: 15779--16027 Score: 356
Period size: 51 Copynumber: 4.8 Consensus size: 51
15769 CCCAGGGAAT
*
15779 CGTCTTCCGTTTATCCTTTGAATTGTCTTCCAATTCAATCTTAAAAAGGAC
1 CGTCTTCCGTTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
15830 CGTCTTCCGTTTATCCTTTGAA-TCGTCTTCCAATTCAATCTTAAAAAGGAC
1 CGTCTTCCGTTTATCCTTTGAACT-GTCTTCCAATTCAATCTTAAAAAGGAC
* * * *
15881 CGTCTTCCGCTTCTCCTTTGAACTGTCTTCCAATTCAACCTTAAAAAAAAAGAC
1 CGTCTTCCGTTTATCCTTTGAACTGTCTTCCAATTCAATCTT---AAAAAGGAC
* *
15935 CGTCTTCCGTTTATCCCTAGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
1 CGTCTTCCGTTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
* * * *
15986 CGTCTTCCGCTTATCCCTAGAACTGTCTTCCAATTCACTCTT
1 CGTCTTCCGTTTATCCTTTGAACTGTCTTCCAATTCAATCTT
16028 CTGGATATCT
Statistics
Matches: 181, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
50 1 0.01
51 134 0.74
52 1 0.01
54 45 0.25
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.36
Consensus pattern (51 bp):
CGTCTTCCGTTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGAC
Found at i:15975 original size:105 final size:102
Alignment explanation
Indices: 15779--16022 Score: 364
Period size: 105 Copynumber: 2.4 Consensus size: 102
15769 CCCAGGGAAT
* * * *
15779 CGTCTTCCGTTTATCCTTTGAATTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGTTTAT
1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAACCTTAAAAAAGACCGTCTTCCGTTTAT
* *
15844 CCTTTGAATCGTCTTCCAATTCAATCTTAAAAAGGAC
66 CCCTAGAATCGTCTTCCAATTCAATCTTAAAAAGGAC
*
15881 CGTCTTCCGCTTCTCCTTTGAACTGTCTTCCAATTCAACCTTAAAAAAAAAGACCGTCTTCCGTT
1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAACCTT---AAAAAAGACCGTCTTCCGTT
15946 TATCCCTAGAA-CTGTCTTCCAATTCAATCTTAAAAAGGAC
63 TATCCCTAGAATC-GTCTTCCAATTCAATCTTAAAAAGGAC
* *
15986 CGTCTTCCGCTTATCCCTAGAACTGTCTTCCAATTCA
1 CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCA
16023 CTCTTCTGGA
Statistics
Matches: 128, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
102 38 0.30
104 1 0.01
105 89 0.70
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (102 bp):
CGTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAACCTTAAAAAAGACCGTCTTCCGTTTAT
CCCTAGAATCGTCTTCCAATTCAATCTTAAAAAGGAC
Found at i:24115 original size:28 final size:28
Alignment explanation
Indices: 24084--24181 Score: 133
Period size: 28 Copynumber: 3.5 Consensus size: 28
24074 CTGGATACGC
* * *
24084 AAATGACTAAAATACCCCCGGACATATA
1 AAATGACCAAAATGCCCCCGGACATACA
* *
24112 AAATGACCAAAATGCCCCTGGACATGCA
1 AAATGACCAAAATGCCCCCGGACATACA
*
24140 AAATGACCAAAATGCCCCCGGACATGCA
1 AAATGACCAAAATGCCCCCGGACATACA
*
24168 AAGTGACCAAAATG
1 AAATGACCAAAATG
24182 AGAAGTAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCCGGACATACA
Found at i:24161 original size:56 final size:55
Alignment explanation
Indices: 24063--24181 Score: 157
Period size: 56 Copynumber: 2.1 Consensus size: 55
24053 CTTGAAGTGG
* * * *
24063 CCAAAATCCCCCTGGATACGCAAATGACTAAAATACCCCCGGACATATAAAATGA
1 CCAAAATGCCCCTGGACACGCAAATGACCAAAATACCCCCGGACATACAAAATGA
* * * *
24118 CCAAAATGCCCCTGGACATGCAAAATGACCAAAATGCCCCCGGACATGCAAAGTGA
1 CCAAAATGCCCCTGGACACGC-AAATGACCAAAATACCCCCGGACATACAAAATGA
24174 CCAAAATG
1 CCAAAATG
24182 AGAAGTAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
55 18 0.33
56 37 0.67
ACGTcount: A:0.40, C:0.29, G:0.16, T:0.14
Consensus pattern (55 bp):
CCAAAATGCCCCTGGACACGCAAATGACCAAAATACCCCCGGACATACAAAATGA
Found at i:25857 original size:22 final size:21
Alignment explanation
Indices: 25813--25890 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 21
25803 CCCCTTAACT
*
25813 TTAACCTTCCTA-ATGCTTAC
1 TTAACCTTCCAAGATGCTTAC
25833 TTAACCTTCCAAGCAT-CATTAC
1 TTAACCTTCCAAG-ATGC-TTAC
*
25855 TTAAAACCTTCC-TGATGCTTAC
1 TT--AACCTTCCAAGATGCTTAC
25877 TTAACCTTCCAAGA
1 TTAACCTTCCAAGA
25891 CATGAACTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
20 19 0.40
21 3 0.06
22 16 0.33
23 2 0.04
24 8 0.17
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (21 bp):
TTAACCTTCCAAGATGCTTAC
Found at i:27010 original size:27 final size:27
Alignment explanation
Indices: 26950--27015 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
26940 TCGAATTAAT
* *
26950 GAACAAAATATAAACTAATTTTTTTCA
1 GAACAAAATAGAAACTAATTTTATTCA
*
26977 CAA-AAAATAGAAACTAAATTTTATT-A
1 GAACAAAATAGAAACT-AATTTTATTCA
*
27003 GAACAAAAAAGAA
1 GAACAAAATAGAA
27016 CAAAAATGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
26 14 0.44
27 18 0.56
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.27
Consensus pattern (27 bp):
GAACAAAATAGAAACTAATTTTATTCA
Found at i:30491 original size:1 final size:1
Alignment explanation
Indices: 30485--30510 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
30475 TAATCAAAGG
30485 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
30511 CTATGGAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30986 original size:18 final size:18
Alignment explanation
Indices: 30963--31002 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
30953 AAGGAAAATC
**
30963 AGAAAATAGAATCGAAGA
1 AGAAAATAGAAAAGAAGA
30981 AGAAAATAGAAAAGAAGA
1 AGAAAATAGAAAAGAAGA
30999 AGAA
1 AGAA
31003 GAGAGTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.68, C:0.03, G:0.23, T:0.07
Consensus pattern (18 bp):
AGAAAATAGAAAAGAAGA
Found at i:31826 original size:15 final size:15
Alignment explanation
Indices: 31806--31836 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31796 GAGAACAGGA
31806 TTTGAAAAAACCTTT
1 TTTGAAAAAACCTTT
*
31821 TTTGAAAACACCTTT
1 TTTGAAAAAACCTTT
31836 T
1 T
31837 ATTGCTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (15 bp):
TTTGAAAAAACCTTT
Found at i:34879 original size:27 final size:26
Alignment explanation
Indices: 34837--34968 Score: 122
Period size: 27 Copynumber: 4.8 Consensus size: 26
34827 AGTGAACTTA
**
34837 AAATGACCAACGTGCCTCT-AAGTATGC
1 AAATGACCAAAATGCC-CTGAA-TATGC
* * **
34864 AAATGACCAAAATGCCCTTAGTATAA
1 AAATGACCAAAATGCCCTGAATATGC
*
34890 AAATGACCAAAATGCCCCTGAACATGC
1 AAATGACCAAAATG-CCCTGAATATGC
*
34917 AAATGACCAAAATACCCTTGAATATGCC
1 AAATGACCAAAATGCCC-TGAATATG-C
34945 AAAATGACCAAAATGCCCCTGAAT
1 -AAATGACCAAAATG-CCCTGAAT
34969 GACCCTAATG
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
26 22 0.26
27 42 0.49
28 1 0.01
29 18 0.21
30 3 0.03
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.20
Consensus pattern (26 bp):
AAATGACCAAAATGCCCTGAATATGC
Found at i:34966 original size:56 final size:53
Alignment explanation
Indices: 34860--34967 Score: 162
Period size: 56 Copynumber: 2.0 Consensus size: 53
34850 GCCTCTAAGT
* *
34860 ATGCAAATGACCAAAATGCCCTTAGTATAAAAATGACCAAAATGCCCCTGAAC
1 ATGCAAATGACCAAAATACCCTTAATATAAAAATGACCAAAATGCCCCTGAAC
*
34913 ATGCAAATGACCAAAATACCCTTGAATATGCCAAAATGACCAAAATGCCCCTGAA
1 ATGCAAATGACCAAAATACCCTT-AATAT--AAAAATGACCAAAATGCCCCTGAA
34968 TGACCCTAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
53 22 0.45
54 4 0.08
56 23 0.47
ACGTcount: A:0.44, C:0.25, G:0.13, T:0.19
Consensus pattern (53 bp):
ATGCAAATGACCAAAATACCCTTAATATAAAAATGACCAAAATGCCCCTGAAC
Found at i:37925 original size:30 final size:31
Alignment explanation
Indices: 37860--37931 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
37850 ATCTAATTTT
* *
37860 ATCCTGAATTGACACAACCCGATAACGTTAT
1 ATCCTGAATTGACACAACCCGATAACGGTAC
** *
37891 ATCCTGAATTGACACAAGTC-ATAACGGTGC
1 ATCCTGAATTGACACAACCCGATAACGGTAC
37921 ATCCTGAATTG
1 ATCCTGAATTG
37932 CATTTTCGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (31 bp):
ATCCTGAATTGACACAACCCGATAACGGTAC
Found at i:39401 original size:33 final size:34
Alignment explanation
Indices: 39362--39425 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
39352 AAAAGATAAT
*
39362 AAAAAATTACCAAAG-AATCGAGATTTTGCCAAA
1 AAAAAATTACCAAAGAAATCAAGATTTTGCCAAA
**
39395 AAAAAATTACCTGAGAAATCAAGATTTTGCC
1 AAAAAATTACCAAAGAAATCAAGATTTTGCC
39426 TAATAATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 13 0.48
34 14 0.52
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.23
Consensus pattern (34 bp):
AAAAAATTACCAAAGAAATCAAGATTTTGCCAAA
Found at i:39989 original size:29 final size:27
Alignment explanation
Indices: 39953--40050 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 27
39943 ACCTAAGGGT
39953 ATTTTGGTCATTTTCAAAAATCCAGGGGC
1 ATTTTGGTCATTTTC--AAATCCAGGGGC
*
39982 ATTTTGGTCATTTTTCACATCCAGGGGC
1 ATTTTGGTCA-TTTTCAAATCCAGGGGC
* *
40010 ATTTTGGTCATTTTTACA-CCTAGGGGGC
1 ATTTTGGTCATTTTCAAATCC-A-GGGGC
*
40038 ATTTTAGTCATTT
1 ATTTTGGTCATTT
40051 GTGCTTCAGG
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
26 2 0.03
27 8 0.13
28 38 0.60
29 10 0.16
30 5 0.08
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.41
Consensus pattern (27 bp):
ATTTTGGTCATTTTCAAATCCAGGGGC
Found at i:40204 original size:21 final size:20
Alignment explanation
Indices: 40176--40224 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
40166 TGTTGTGTTC
**
40176 TTTTGCATATTTGTATCACA
1 TTTTGCATATTAATATCACA
*
40196 TTTTCGCATATTAATTTCACA
1 TTTT-GCATATTAATATCACA
40217 TTTTGCAT
1 TTTTGCAT
40225 TTACATAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTTGCATATTAATATCACA
Found at i:56453 original size:2 final size:2
Alignment explanation
Indices: 56446--56474 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
56436 TGTTGGTAAT
56446 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
56475 TAATTGAAAG
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:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:61162 original size:21 final size:22
Alignment explanation
Indices: 61123--61163 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
61113 TCAATCCTTT
**
61123 AGGAATGCAAGAGGGATTTCAA
1 AGGAATGCAAGAGCCATTTCAA
61145 AGGAA-GCAAGAGCCATTTC
1 AGGAATGCAAGAGCCATTTC
61164 CACGAAGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.39, C:0.15, G:0.29, T:0.17
Consensus pattern (22 bp):
AGGAATGCAAGAGCCATTTCAA
Found at i:63722 original size:21 final size:21
Alignment explanation
Indices: 63693--63733 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
63683 TTACCTTTGT
63693 TCATAAA-TTCACTCACTTCAA
1 TCATAAATTTCACT-ACTTCAA
*
63714 TCATCAATTTCACTACTTCA
1 TCATAAATTTCACTACTTCA
63734 TCACTTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (21 bp):
TCATAAATTTCACTACTTCAA
Found at i:65366 original size:65 final size:65
Alignment explanation
Indices: 65257--65386 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
65247 GGAAAAATTG
* *
65257 GTCCTACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
65322 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
65387 AATAGCAAGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.21, C:0.31, G:0.27, T:0.22
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
Found at i:65609 original size:21 final size:21
Alignment explanation
Indices: 65582--65671 Score: 162
Period size: 21 Copynumber: 4.3 Consensus size: 21
65572 TAGACAATTG
*
65582 CAATGAGCTTGAAACCTTCTC
1 CAATGAGCTTGGAACCTTCTC
*
65603 AAATGAGCTTGGAACCTTCTC
1 CAATGAGCTTGGAACCTTCTC
65624 CAATGAGCTTGGAACCTTCTC
1 CAATGAGCTTGGAACCTTCTC
65645 CAATGAGCTTGGAACCTTCTC
1 CAATGAGCTTGGAACCTTCTC
65666 CAATGA
1 CAATGA
65672 ACTCCTAGCA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (21 bp):
CAATGAGCTTGGAACCTTCTC
Found at i:70566 original size:28 final size:26
Alignment explanation
Indices: 70524--70580 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 26
70514 CCGCTTAATT
*
70524 AAATTTGCTTCTTCATTTTCTACCCA
1 AAATTTGCTTCTTCATTTTCGACCCA
*
70550 AAATTTGTTCTTCTTCATTTTCGACTCA
1 AAATTTG--CTTCTTCATTTTCGACCCA
70578 AAA
1 AAA
70581 GCAAAAAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 7 0.26
28 20 0.74
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.46
Consensus pattern (26 bp):
AAATTTGCTTCTTCATTTTCGACCCA
Found at i:74269 original size:76 final size:75
Alignment explanation
Indices: 74104--74409 Score: 312
Period size: 76 Copynumber: 4.0 Consensus size: 75
74094 AGTTGTCGGA
* * * * * *
74104 TGAGTGACGTCTGCGTGGACACTCAGCGTCATTGAGAGTGAGACGGGGGCGCCAGTTTAAGCACT
1 TGAGTG-CATCTGCGTGGACGCTCAGCCTCACT--GAG-G-GACGGGGGCGCCAGTCTAGGCACT
*
74169 CAGCCGTGGGATGAG
61 CAGCCGTAGGATGAG
* * * * * *
74184 T--G-GCGTCTGCGTGGACGCTCAGCCTCATTCACGGACGGGGGTGCCAATCTAGGCACTCAGCC
1 TGAGTGCATCTGCGTGGACGCTCAGCCTCACTGAGGGACGGGGGCGCCAGTCTAGGCACTCAGCC
74246 GTAGGATGAG
66 GTAGGATGAG
* * *
74256 TGAGATGCATCTGCGTGGACGCTCTGCCTCACTGAGGGACAGGGGCGCCAGTCTAGGCACTTAGC
1 TGAG-TGCATCTGCGTGGACGCTCAGCCTCACTGAGGGACGGGGGCGCCAGTCTAGGCACTCAGC
*
74321 CGTTGGATGAG
65 CGTAGGATGAG
* * ** *
74332 TGAGTGGCATCTACGTGGACGCTCAGCCTCACTGAGGGACGGGGGCACCAGTCTATCCACTTAGC
1 TGAGT-GCATCTGCGTGGACGCTCAGCCTCACTGAGGGACGGGGGCGCCAGTCTAGGCACTCAGC
* *
74397 TGTGGGATGAG
65 CGTAGGATGAG
74408 TG
1 TG
74410 GCGTCTAGGC
Statistics
Matches: 194, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
72 35 0.18
73 1 0.01
74 2 0.01
75 1 0.01
76 152 0.78
77 1 0.01
78 1 0.01
80 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.36, T:0.21
Consensus pattern (75 bp):
TGAGTGCATCTGCGTGGACGCTCAGCCTCACTGAGGGACGGGGGCGCCAGTCTAGGCACTCAGCC
GTAGGATGAG
Found at i:74416 original size:30 final size:30
Alignment explanation
Indices: 74382--74439 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
74372 GGGGGCACCA
* * *
74382 GTCTATCCACTTAGCTGTGGGATGAGTGGC
1 GTCTAGCCACTCAGCCGTGGGATGAGTGGC
* *
74412 GTCTAGGCACTCAGCCGTTGGATGAGTG
1 GTCTAGCCACTCAGCCGTGGGATGAGTG
74440 AGTGGCATCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.17, C:0.21, G:0.34, T:0.28
Consensus pattern (30 bp):
GTCTAGCCACTCAGCCGTGGGATGAGTGGC
Found at i:74499 original size:106 final size:106
Alignment explanation
Indices: 74306--74502 Score: 322
Period size: 106 Copynumber: 1.9 Consensus size: 106
74296 AGGGGCGCCA
*
74306 GTCTAGGCACTTAGCCGTTGGATGAGTGAGTGGCATCTACGTGGACGCTCAGCCTCACTGAGGGA
1 GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTACGTGGACGCTCAGCCTCACTGAGGGA
* *
74371 CGGGGGCACCAGTCTATCCACTTAGCTGTGGGATGAGTGGC
66 CGGGGGCACCAGTATAGCCACTTAGCTGTGGGATGAGTGGC
* *
74412 GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTGCGTGGACGCTCTGCCTCACTGAGGGA
1 GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTACGTGGACGCTCAGCCTCACTGAGGGA
** *
74477 CGGGGGTTCCAGTATAGGCACTTAGC
66 CGGGGGCACCAGTATAGCCACTTAGC
74503 CGTTAGTTGA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 83 1.00
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.23
Consensus pattern (106 bp):
GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTACGTGGACGCTCAGCCTCACTGAGGGA
CGGGGGCACCAGTATAGCCACTTAGCTGTGGGATGAGTGGC
Found at i:74538 original size:182 final size:182
Alignment explanation
Indices: 74231--74568 Score: 543
Period size: 182 Copynumber: 1.9 Consensus size: 182
74221 GGGGTGCCAA
74231 TCTAGGCACTCAGCCGTAGGATGAGTGAGATGCATCTGCGTGGACGCTCTGCCTCACTGAGGGAC
1 TCTAGGCACTCAGCCGTAGGATGAGTGAGATGCATCTGCGTGGACGCTCTGCCTCACTGAGGGAC
* * * *
74296 AGGGGCGCCAGTCTAGGCACTTAGCCGTTGGATGAGTGAGTGGCATCTACGTGGACGCTCAGCCT
66 AGGGGCGCCAGTATAGGCACTTAGCCGTTAGATGAGTAAGTGGCATCTACGTGGACGCTCAACCT
*
74361 CACTGAGGGACGGGGGCACCAGTCTATCCACTTAGCTGTGGGATGAGTGGCG
131 CACTAAGGGACGGGGGCACCAGTCTATCCACTTAGCTGTGGGATGAGTGGCG
*
74413 TCTAGGCACTCAGCCGTTGGATGAGTGAG-TGGCATCTGCGTGGACGCTCTGCCTCACTGAGGGA
1 TCTAGGCACTCAGCCGTAGGATGAGTGAGAT-GCATCTGCGTGGACGCTCTGCCTCACTGAGGGA
* ** * * *
74477 CGGGGGTTCCAGTATAGGCACTTAGCCGTTAGTTGAGTAAGTGGCATCTGCGTGGACGCTCAACT
65 CAGGGGCGCCAGTATAGGCACTTAGCCGTTAGATGAGTAAGTGGCATCTACGTGGACGCTCAACC
*
74542 TCACTAAGGGACGGGGGCGCCAGTCTA
130 TCACTAAGGGACGGGGGCACCAGTCTA
74569 GACACTCCGC
Statistics
Matches: 142, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
181 1 0.01
182 141 0.99
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.22
Consensus pattern (182 bp):
TCTAGGCACTCAGCCGTAGGATGAGTGAGATGCATCTGCGTGGACGCTCTGCCTCACTGAGGGAC
AGGGGCGCCAGTATAGGCACTTAGCCGTTAGATGAGTAAGTGGCATCTACGTGGACGCTCAACCT
CACTAAGGGACGGGGGCACCAGTCTATCCACTTAGCTGTGGGATGAGTGGCG
Found at i:74643 original size:258 final size:254
Alignment explanation
Indices: 74164--74673 Score: 657
Period size: 258 Copynumber: 2.0 Consensus size: 254
74154 GCCAGTTTAA
* *
74164 GCACTCAGCCGTGGGATGAGTGGCGTCTGCGTGGACGCTCAGCCTCATTCACGGACGGGGGTGCC
1 GCACTCAGCCGTGGGATGAGTGGCATCTGCGTGGACGCTCAGCCTCACTCACGGACGGGGGTGCC
* * ** *
74229 AATCTAGGCACTCAGCCGTAGGATGAGTGAGATGCATCTGCGTGGACGCTCTGCCTCACTGAGGG
66 AATATAGGCACTCAGCCGTAGGATGAGTAAGATGCATCTGCGTGGACGCTCAACCTCACTAAGGG
* * *
74294 ACAGGGGCGCCAGTCTAGGCACTTAGCCGTTGGATGAGTGAGTGGCATCTACGTGGACGCTCAGC
131 ACAGGGGCGCCAGTCTAGACACTCAGCCGTTGGATGAGTGAGTGGCATCTACATGGACGCTCAGC
* * ** * *
74359 CTCACTGAGGGACGGGGGCACCAGTCTATCCACTTAGCTGTGGGATGAGTGGCGTCTAG
196 CTAACTGAGGGACGAGGGCACCAGTCTAGACACTCAGCCGTGGGATGAGTGGCGTCTAG
* * *
74418 GCACTCAGCCGTTGGATGAGTGAGTGGCATCTGCGTGGACGCTCTGCCTCACTGAGGGACGGGGG
1 GCACTCAGCCG-TGG--GA-TGAGTGGCATCTGCGTGGACGCTCAGCCTCACTCACGGACGGGGG
* * * * *
74483 TTCCAGTATAGGCACTTAGCCGTTA-GTTGAGTAAG-TGGCATCTGCGTGGACGCTCAACTTCAC
62 TGCCAATATAGGCACTCAGCCG-TAGGATGAGTAAGAT-GCATCTGCGTGGACGCTCAACCTCAC
* * * *
74546 TAAGGGACGGGGGCGCCAGTCTAGACACTCCGCCGTTGGATGAGTGAGTGGCATCTGCATGGATG
125 TAAGGGACAGGGGCGCCAGTCTAGACACTCAGCCGTTGGATGAGTGAGTGGCATCTACATGGACG
* * *
74611 CTCTGCCTAAGTGAGGGAC-AGGGCTCCCAGTCTAGACACTCAGCCGTGGGATGAGTGGCGTCT
190 CTCAGCCTAACTGAGGGACGAGGGC-ACCAGTCTAGACACTCAGCCGTGGGATGAGTGGCGTCT
74674 GCGTGGACGC
Statistics
Matches: 218, Mismatches: 31, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
254 11 0.05
255 3 0.01
257 7 0.03
258 195 0.89
259 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (254 bp):
GCACTCAGCCGTGGGATGAGTGGCATCTGCGTGGACGCTCAGCCTCACTCACGGACGGGGGTGCC
AATATAGGCACTCAGCCGTAGGATGAGTAAGATGCATCTGCGTGGACGCTCAACCTCACTAAGGG
ACAGGGGCGCCAGTCTAGACACTCAGCCGTTGGATGAGTGAGTGGCATCTACATGGACGCTCAGC
CTAACTGAGGGACGAGGGCACCAGTCTAGACACTCAGCCGTGGGATGAGTGGCGTCTAG
Found at i:74814 original size:223 final size:224
Alignment explanation
Indices: 74412--74891 Score: 608
Period size: 223 Copynumber: 2.1 Consensus size: 224
74402 GATGAGTGGC
*
74412 GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTGCGTGGACGCTCTGCCTCACTGAGGGA
1 GTCTAGGCACTCAGCCG-TGG--GA-TGAGTGGCATCTGCGTGGACGCTCAGCCTCACTGAGGGA
* * *
74477 CGGGGGTTCCAGTATAGGCACTTAGCCGTTAGTTGAGTAAGTGGCATCTGCGTGGACGCTCAACT
62 CGGGGGTACCAGTATAGGCACTTAGCCGTTAGTGGAGTAAGTGGCATCTGCGTGGACGCTCAACC
* * *
74542 TCACTAAGGGACGGGGGCGCCAGTCTAGACACTCCGCCGTTGGATGAGTGAGTGGCATCTGCATG
127 TCACTAAGGGACGGGGGCGCCAGTCTAGACACTCAGCCGTTGAATGAGTGAGTGGCATCTGCATA
*
74607 GATGCTCTGCCTAAGTGAGGGACAGGGCTCCCA
192 GACGCTCTGCCTAAGTGAGGGACAGGGCTCCCA
* * *
74640 GTCTAGACACTCAGCCGTGGGATGAGTGGCGTCTGCGTGGACGCTCAGCCTCAATTGAGTGAGAC
1 GTCTAGGCACTCAGCCGTGGGATGAGTGGCATCTGCGTGGACGCTCAGCCTC-ACTGAG-G-GAC
* * * * **
74705 GGGGGTACCAGTCTAGGCACTTAGCCG-T-G-GGA-TGAGTGGCGTTTGCGTGGACGCTCTGCCT
63 GGGGGTACCAGTATAGGCACTTAGCCGTTAGTGGAGTAAGTGGCATCTGCGTGGACGCTCAACCT
* * * * *
74766 CATTCAGGGACGGGGGTGCCAGTTTAGGCACTCAGCCGTTGAATGAGTGAGTGGCATCTGCATAG
128 CACTAAGGGACGGGGGCGCCAGTCTAGACACTCAGCCGTTGAATGAGTGAGTGGCATCTGCATAG
* * ** * *
74831 ACGCTCTGCCTCATTGAGGGATGGGGGTGCCA
193 ACGCTCTGCCTAAGTGAGGGACAGGGCTCCCA
*
74863 GTCTAGGCACTCAGCCGCGGGATGAGTGG
1 GTCTAGGCACTCAGCCGTGGGATGAGTGG
74892 GGCGTCCCTT
Statistics
Matches: 219, Mismatches: 30, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
223 132 0.60
224 30 0.14
225 8 0.04
226 2 0.01
227 31 0.14
228 16 0.07
ACGTcount: A:0.19, C:0.24, G:0.36, T:0.22
Consensus pattern (224 bp):
GTCTAGGCACTCAGCCGTGGGATGAGTGGCATCTGCGTGGACGCTCAGCCTCACTGAGGGACGGG
GGTACCAGTATAGGCACTTAGCCGTTAGTGGAGTAAGTGGCATCTGCGTGGACGCTCAACCTCAC
TAAGGGACGGGGGCGCCAGTCTAGACACTCAGCCGTTGAATGAGTGAGTGGCATCTGCATAGACG
CTCTGCCTAAGTGAGGGACAGGGCTCCCA
Found at i:74888 original size:76 final size:76
Alignment explanation
Indices: 74412--74890 Score: 542
Period size: 76 Copynumber: 6.4 Consensus size: 76
74402 GATGAGTGGC
*
74412 GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTGCGTGGACGCTCTGCCTCACTGAGGGA
1 GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTGCGTGGACGCTCTGCCTCATTGAGGGA
*
74477 CGGGGGTTCCA
66 CGGGGGTGCCA
* * * * * ** * * *
74488 GTATAGGCACTTAGCCGTTAGTTGAGTAAGTGGCATCTGCGTGGACGCTCAACTTCACTAAGGGA
1 GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTGCGTGGACGCTCTGCCTCATTGAGGGA
*
74553 CGGGGGCGCCA
66 CGGGGGTGCCA
* * * * * *
74564 GTCTAGACACTCCGCCGTTGGATGAGTGAGTGGCATCTGCATGGATGCTCTGCCTAAGTGAGGGA
1 GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTGCGTGGACGCTCTGCCTCATTGAGGGA
* * *
74629 CAGGGCTCCCA
66 CGGGGGTGCCA
* * *
74640 GTCTAGACACTCAGCCG-TGG--GA-TGAGTGGCGTCTGCGTGGACGCTCAGCCTCAATTGAGTG
1 GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTGCGTGGACGCTCTGCCTC-ATTGAG-G
*
74701 AGACGGGGGTACCA
64 -GACGGGGGTGCCA
* * * *
74715 GTCTAGGCACTTAGCCG-TGG--GA-TGAGTGGCGTTTGCGTGGACGCTCTGCCTCATTCAGGGA
1 GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTGCGTGGACGCTCTGCCTCATTGAGGGA
74776 CGGGGGTGCCA
66 CGGGGGTGCCA
* * * *
74787 GTTTAGGCACTCAGCCGTTGAATGAGTGAGTGGCATCTGCATAGACGCTCTGCCTCATTGAGGGA
1 GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTGCGTGGACGCTCTGCCTCATTGAGGGA
*
74852 TGGGGGTGCCA
66 CGGGGGTGCCA
**
74863 GTCTAGGCACTCAGCCGCGGGATGAGTG
1 GTCTAGGCACTCAGCCGTTGGATGAGTG
74891 GGGCGTCCCT
Statistics
Matches: 337, Mismatches: 59, Indels: 14
0.82 0.14 0.03
Matches are distributed among these distances:
72 52 0.15
73 10 0.03
74 6 0.02
75 63 0.19
76 206 0.61
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.22
Consensus pattern (76 bp):
GTCTAGGCACTCAGCCGTTGGATGAGTGAGTGGCATCTGCGTGGACGCTCTGCCTCATTGAGGGA
CGGGGGTGCCA
Found at i:75589 original size:151 final size:149
Alignment explanation
Indices: 75225--75696 Score: 525
Period size: 153 Copynumber: 3.2 Consensus size: 149
75215 TTGATAGGGT
* *
75225 TCATGCCCCCCAAGTGTCCTGTCCCGGATCGGT-GCTTCGCCGAGGCGGAGGTCTCCGTGGGAGA
1 TCATGCCCCCCAAGTGTCCTGCCCCAGATCGGTGGC-TCGCCGAGGCGGAGGTCTCCGTGGGAGA
** * * * * * *
75289 CACTCGTCAACTTTTGACTGAATTGTTACGCGGCCGTATTCGTCCGACTGGGGGTTCAAGTGGGC
65 TGCTCGTCAAC-TTTGACTG-ATTATTA-GTGACCGTGTTCGTCCGATTGGGGGTTCAAGTGGGG
* *
75354 AGGTTGATCTGTGTTGTTGTCAGGC
127 AGGTTG--CTGTGTTGTTGACAAGC
* * * ** * **
75379 TCATG-CCCCCAAGTGTCCTGCCCTAGATCGGTGTCTTGTTGAGGCAGAGGTCTTTGTGGGAGAT
1 TCATGCCCCCCAAGTGTCCTGCCCCAGATCGGTGGCTCGCCGAGGCGGAGGTCTCCGTGGGAGAT
* * * * *
75443 GCTCATCAGCTTGTGATTGGATTATTAGGTGACCGCGTTCTTCCGATTGGGGGTTCAAGTGGGGA
66 GCTCGTCAACTT-TGACT-GATTATTA-GTGACCGTGTTCGTCCGATTGGGGGTTCAAGTGGGGA
*
75508 GGTTGCTCTG-TGTTGACAAGC
128 GGTTGCTGTGTTGTTGACAAGC
75529 TCATGCCCCCCAAGTGTCCTGCCCCAGATCGGTGGCTCGCCGAGGCGGAGGTCTCCGTGGGAGAT
1 TCATGCCCCCCAAGTGTCCTGCCCCAGATCGGTGGCTCGCCGAGGCGGAGGTCTCCGTGGGAGAT
* *
75594 GCTCGTCAAC----ACT-A-TACTT-GT-ATCATGTTCGTCCGATTGGGGGTTCAAGTGGGGAGG
66 GCTCGTCAACTTTGACTGATTA-TTAGTGACCGTGTTCGTCCGATTGGGGGTTCAAGTGGGGAGG
75651 TTGCTGTGTTGTTGACAAGC
130 TTGCTGTGTTGTTGACAAGC
75671 TCATGCCCCCCAAGTGTCCTGCCCCA
1 TCATGCCCCCCAAGTGTCCTGCCCCA
75697 TATCAGCGTA
Statistics
Matches: 269, Mismatches: 43, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
141 39 0.14
142 39 0.14
143 2 0.01
144 3 0.01
146 2 0.01
150 14 0.05
151 63 0.23
152 2 0.01
153 98 0.36
154 7 0.03
ACGTcount: A:0.15, C:0.25, G:0.32, T:0.28
Consensus pattern (149 bp):
TCATGCCCCCCAAGTGTCCTGCCCCAGATCGGTGGCTCGCCGAGGCGGAGGTCTCCGTGGGAGAT
GCTCGTCAACTTTGACTGATTATTAGTGACCGTGTTCGTCCGATTGGGGGTTCAAGTGGGGAGGT
TGCTGTGTTGTTGACAAGC
Found at i:81681 original size:18 final size:19
Alignment explanation
Indices: 81658--81695 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
81648 GGTGAAGATG
*
81658 AGGAAGGAAGAAGAA-AAT
1 AGGAAGAAAGAAGAAGAAT
81676 AGGAAGAAAGAAGAAGAAT
1 AGGAAGAAAGAAGAAGAAT
81695 A
1 A
81696 AGGAGGGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.32, T:0.05
Consensus pattern (19 bp):
AGGAAGAAAGAAGAAGAAT
Done.