Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007131.1 Corchorus capsularis cultivar CVL-1 contig07152, 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: 28317
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:39 original size:31 final size:33
Alignment explanation
Indices: 1--77 Score: 131
Period size: 31 Copynumber: 2.4 Consensus size: 33
1 CCTGGGGCGGCACTACCGTGGTCAGG-C-CCCC
1 CCTGGGGCGGCACTACCGTGGTCAGGCCGCCCC
32 CCTGGGGCGGCACTACCGTGGTCAGGCCGCCCC
1 CCTGGGGCGGCACTACCGTGGTCAGGCCGCCCC
*
65 CCTGAGGCGGCAC
1 CCTGGGGCGGCAC
78 CGACCCTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
31 26 0.60
32 1 0.02
33 16 0.37
ACGTcount: A:0.10, C:0.42, G:0.36, T:0.12
Consensus pattern (33 bp):
CCTGGGGCGGCACTACCGTGGTCAGGCCGCCCC
Found at i:1090 original size:32 final size:32
Alignment explanation
Indices: 1046--1111 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
1036 AGGTTAGGGG
* *
1046 TCGGGTTTTGGTTTTATCGGGTTTTAGATTTT
1 TCGGGTTCTGGTTTTATCGGGTTTAAGATTTT
* *
1078 TCGGGTTCTGGTTTTTTCGGGTTTAAGTTTTT
1 TCGGGTTCTGGTTTTATCGGGTTTAAGATTTT
1110 TC
1 TC
1112 TGGTCCGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.08, C:0.09, G:0.27, T:0.56
Consensus pattern (32 bp):
TCGGGTTCTGGTTTTATCGGGTTTAAGATTTT
Found at i:1107 original size:16 final size:16
Alignment explanation
Indices: 1046--1111 Score: 78
Period size: 16 Copynumber: 4.1 Consensus size: 16
1036 AGGTTAGGGG
* *
1046 TCGGGTTTTGGTTTTA
1 TCGGGTTTTAGTTTTT
*
1062 TCGGGTTTTAGATTTT
1 TCGGGTTTTAGTTTTT
* *
1078 TCGGGTTCTGGTTTTT
1 TCGGGTTTTAGTTTTT
*
1094 TCGGGTTTAAGTTTTT
1 TCGGGTTTTAGTTTTT
1110 TC
1 TC
1112 TGGTCCGGAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.08, C:0.09, G:0.27, T:0.56
Consensus pattern (16 bp):
TCGGGTTTTAGTTTTT
Found at i:4685 original size:33 final size:33
Alignment explanation
Indices: 4585--4704 Score: 136
Period size: 33 Copynumber: 3.7 Consensus size: 33
4575 GGTTACCAGT
*
4585 TTAGATCGACGCTAAAATTATTGGGCTCTCAGC
1 TTAGATCGACGCTAAAATTATTGGACTCTCAGC
* * * * *
4618 -T-CATCGATGCTAAAATTATTGGATTATCAAC
1 TTAGATCGACGCTAAAATTATTGGACTCTCAGC
* * *
4649 TTAGATCGACGCTGAAATAACTGGACTCTCAGC
1 TTAGATCGACGCTAAAATTATTGGACTCTCAGC
*
4682 TTAGATTGACGCTAAAATTATTG
1 TTAGATCGACGCTAAAATTATTG
4705 AGTTGCCAAA
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
31 24 0.36
32 2 0.03
33 41 0.61
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (33 bp):
TTAGATCGACGCTAAAATTATTGGACTCTCAGC
Found at i:8928 original size:22 final size:22
Alignment explanation
Indices: 8903--9247 Score: 107
Period size: 22 Copynumber: 15.8 Consensus size: 22
8893 CTACCATATG
*
8903 AAATTTCGATAACCACACTATA
1 AAATTTTGATAACCACACTATA
** *
8925 AAATTTTGAT-A-C-TTCTATG
1 AAATTTTGATAACCACACTATA
** *
8944 AAATTTCAATAACCACACTATG
1 AAATTTTGATAACCACACTATA
* * * *
8966 AAACTTTGATAATCTC-CTTATG
1 AAATTTTGATAACCACAC-TATA
* **
8988 AAATTTTGATTATTACACTATA
1 AAATTTTGATAACCACACTATA
* ***
9010 AAATTTTGATAAACTTGCTATA
1 AAATTTTGATAACCACACTATA
* * *
9032 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCACACTATA
* *
9054 AATTTTTTATAA-CATTC-CTATA
1 AAATTTTGATAACCA--CACTATA
* ** *
9076 AGATTTTGATAACTTTC-CTATG
1 AAATTTTGATAAC-CACACTATA
* * * *
9098 AAATTTT-AGTAAGCTCTA-AATG
1 AAATTTTGA-TAACCAC-ACTATA
* * * * *
9120 AAATTTTGGTGACCATATTATG
1 AAATTTTGATAACCACACTATA
* * *
9142 AAATTGTGATAACCACATTATG
1 AAATTTTGATAACCACACTATA
* * * *
9164 AAATTGTGATAACCTCAGTATG
1 AAATTTTGATAACCACACTATA
*
9186 AAATTTTGATAACCACATTATGA
1 AAATTTTGATAACCACACTAT-A
* ** * *
9209 AAA-TTTAATAACTTCAATATG
1 AAATTTTGATAACCACACTATA
*
9230 AAATTTTGACAACCACAC
1 AAATTTTGATAACCACAC
9248 AGAGACAACA
Statistics
Matches: 239, Mismatches: 68, Indels: 32
0.71 0.20 0.09
Matches are distributed among these distances:
19 12 0.05
20 2 0.01
21 11 0.05
22 209 0.87
23 5 0.02
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:8956 original size:41 final size:43
Alignment explanation
Indices: 8899--9020 Score: 149
Period size: 41 Copynumber: 2.9 Consensus size: 43
8889 ATAACTACCA
*
8899 TATGAAATTTCGATAACCACACTATAAAATTTTGATA-CTTC-
1 TATGAAATTTCGATAACCACACTATAAAATTTTGATATCTCCT
* * *
8940 TATGAAATTTCAATAACCACACTATGAAACTTTGATAATCTCCT
1 TATGAAATTTCGATAACCACACTATAAAATTTTGAT-ATCTCCT
* * **
8984 TATGAAATTTTGATTATTACACTATAAAATTTTGATA
1 TATGAAATTTCGATAACCACACTATAAAATTTTGATA
9021 AACTTGCTAT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 33 0.49
42 1 0.01
43 4 0.06
44 29 0.43
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (43 bp):
TATGAAATTTCGATAACCACACTATAAAATTTTGATATCTCCT
Found at i:9036 original size:44 final size:43
Alignment explanation
Indices: 8899--9197 Score: 164
Period size: 44 Copynumber: 6.9 Consensus size: 43
8889 ATAACTACCA
*
8899 TATGAAATTTCGATAACCACACTATAAAATTTTGAT--ACTTC
1 TATGAAATTTTGATAACCACACTATAAAATTTTGATAAACTTC
** * * * *
8940 TATGAAATTTCAATAACCACACTATGAAACTTTGATAATCTCC
1 TATGAAATTTTGATAACCACACTATAAAATTTTGATAAACTTC
* **
8983 TTATGAAATTTTGATTATTACACTATAAAATTTTGATAAACTTGC
1 -TATGAAATTTTGATAACCACACTATAAAATTTTGATAAACTT-C
* * * * * *
9028 TATAAAATTTTGATAACCTCCCTATGAATTTTTTAT-AACATTCC
1 TATGAAATTTTGATAACCACACTATAAAATTTTGATAAAC-TT-C
** * *
9072 TAT-AAGATTTTGATAACTTTC-CTATGAAATTTT-AGTAAGC-TC
1 TATGAA-ATTTTGATAAC-CACACTATAAAATTTTGA-TAAACTTC
* * * * * * *
9114 TAAATGAAATTTTGGTGACCATATTATGAAATTGTGATAACCACAT-
1 T--ATGAAATTTTGATAACCACACTATAAAATTTTGATAA--ACTTC
* * * *
9160 TATGAAATTGTGATAACCTCAGTATGAAATTTTGATAA
1 TATGAAATTTTGATAACCACACTATAAAATTTTGATAA
9198 CCACATTATG
Statistics
Matches: 199, Mismatches: 42, Indels: 31
0.73 0.15 0.11
Matches are distributed among these distances:
41 33 0.17
42 2 0.01
43 10 0.05
44 143 0.72
45 8 0.04
46 2 0.01
47 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (43 bp):
TATGAAATTTTGATAACCACACTATAAAATTTTGATAAACTTC
Found at i:9198 original size:44 final size:44
Alignment explanation
Indices: 9138--9246 Score: 157
Period size: 44 Copynumber: 2.5 Consensus size: 44
9128 GTGACCATAT
* * *
9138 TATGAAATTGTGATAACCACATTATG-AAATTGTGATAACCTCAG
1 TATGAAATTTTGATAACCACATTATGAAAATT-TAATAACCTCAA
*
9182 TATGAAATTTTGATAACCACATTATGAAAATTTAATAACTTCAA
1 TATGAAATTTTGATAACCACATTATGAAAATTTAATAACCTCAA
*
9226 TATGAAATTTTGACAACCACA
1 TATGAAATTTTGATAACCACA
9247 CAGAGACAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 54 0.92
45 5 0.08
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACATTATGAAAATTTAATAACCTCAA
Found at i:9220 original size:66 final size:66
Alignment explanation
Indices: 9117--9243 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
9107 TAAGCTCTAA
* * * * * *
9117 ATGAAATTTTGGTGACCATATTATGAAATTGTGATAACCACATTATGAAATTGTGATAACCTCAG
1 ATGAAATTTTGATAACCACATTATGAAATTGTAATAACCACAATATGAAATTGTGACAACCTCAG
9182 T
66 T
** *
9183 ATGAAATTTTGATAACCACATTATGAAAATT-TAATAACTTCAATATGAAATTTTGACAACC
1 ATGAAATTTTGATAACCACATTATG-AAATTGTAATAACCACAATATGAAATTGTGACAACC
9244 ACACAGAGAC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
66 46 0.90
67 5 0.10
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (66 bp):
ATGAAATTTTGATAACCACATTATGAAATTGTAATAACCACAATATGAAATTGTGACAACCTCAG
T
Found at i:10715 original size:11 final size:10
Alignment explanation
Indices: 10698--10748 Score: 66
Period size: 11 Copynumber: 4.8 Consensus size: 10
10688 TTAGAAAAAC
10698 ATTATATATT
1 ATTATATATT
10708 ATTTATATATT
1 A-TTATATATT
*
10719 ATTATATTAAT
1 ATTATA-TATT
10730 ATTATTATATT
1 ATTA-TATATT
10741 ATTATATA
1 ATTATATA
10749 GTCTAAAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 10 0.28
11 24 0.67
12 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTATATATT
Found at i:10723 original size:14 final size:15
Alignment explanation
Indices: 10700--10747 Score: 66
Period size: 14 Copynumber: 3.3 Consensus size: 15
10690 AGAAAAACAT
10700 TATA-TATTAT-TTA
1 TATATTATTATATTA
10713 TATATTATTATATTA
1 TATATTATTATATTA
10728 -ATATTATTATATTA
1 TATATTATTATATTA
10742 TTATAT
1 -TATAT
10748 AGTCTAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.13
14 20 0.65
15 3 0.10
16 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATTATTATATTA
Found at i:10724 original size:8 final size:8
Alignment explanation
Indices: 10698--10747 Score: 65
Period size: 8 Copynumber: 6.9 Consensus size: 8
10688 TTAGAAAAAC
10698 ATTATA-T
1 ATTATATT
10705 ATTAT-TT
1 ATTATATT
10712 A-TATATT
1 ATTATATT
10719 ATTATATT
1 ATTATATT
10727 A--ATATT
1 ATTATATT
10733 ATTATATT
1 ATTATATT
10741 ATTATAT
1 ATTATAT
10748 AGTCTAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
6 9 0.24
7 10 0.26
8 19 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTATATT
Found at i:11829 original size:30 final size:29
Alignment explanation
Indices: 11763--11834 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
11753 ACACAAAACG
**
11763 GCCAAATAAGCCCCTGAACTCTAATTGCA
1 GCCAAATAAGCCCCTGAACTCTAAAAGCA
11792 GCCAAATAAGCCCCTGAACTCTTTAAAA--A
1 GCCAAATAAGCCCCTGAACTC--TAAAAGCA
11821 GACCAAATAAGCCC
1 G-CCAAATAAGCCC
11835 TTTTCTGATG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 23 0.61
30 12 0.32
31 3 0.08
ACGTcount: A:0.39, C:0.31, G:0.12, T:0.18
Consensus pattern (29 bp):
GCCAAATAAGCCCCTGAACTCTAAAAGCA
Found at i:12741 original size:34 final size:34
Alignment explanation
Indices: 12698--12815 Score: 200
Period size: 34 Copynumber: 3.5 Consensus size: 34
12688 TATAAAGTTG
12698 ATATCAGGACCAATTGTTGGGTCCTGATGGAGGA
1 ATATCAGGACCAATTGTTGGGTCCTGATGGAGGA
12732 ATATCAGGACCAATTGTTGGGTCCTGATGGAGGA
1 ATATCAGGACCAATTGTTGGGTCCTGATGGAGGA
* * *
12766 ATATCAGGACCAATTGTTGGGTCCTAATGGCGGT
1 ATATCAGGACCAATTGTTGGGTCCTGATGGAGGA
*
12800 ATATCAGGATCAATTG
1 ATATCAGGACCAATTG
12816 ATAAGCTCCC
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 80 1.00
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (34 bp):
ATATCAGGACCAATTGTTGGGTCCTGATGGAGGA
Found at i:15354 original size:24 final size:24
Alignment explanation
Indices: 15327--15373 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
15317 CATATATTTG
* * *
15327 TTAATTTTGATCATCTGCGCAACT
1 TTAATTTTAATCACCCGCGCAACT
15351 TTAATTTTAATCACCCGCGCAAC
1 TTAATTTTAATCACCCGCGCAAC
15374 GTAGCGCGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.36
Consensus pattern (24 bp):
TTAATTTTAATCACCCGCGCAACT
Found at i:20030 original size:41 final size:41
Alignment explanation
Indices: 19894--20465 Score: 378
Period size: 41 Copynumber: 13.9 Consensus size: 41
19884 ACAAGAAGAG
* *
19894 TAAACAACACCTTCCGATGAGGAAGGGCAAGACAT--G-AATG
1 TAAACAACACCTTCCGATGGGGAAGGGCAA-AC-TGGGAAATC
* * * * *
19934 TAGACAACACCTTCCGGTAGGGAAGGGCAAACTAGG-AATG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATC
* * *
19974 TAAACAACACCTTCTGGTGGGGAAGGGTAAAAC-GGGAAATC
1 TAAACAACACCTTCCGATGGGGAAGGG-CAAACTGGGAAATC
* * * * * *
20015 TAAACAACACATTCTGGTGGGGAAGAGCAGAAC-AGGAAAAC
1 TAAACAACACCTTCCGATGGGGAAGGGCA-AACTGGGAAATC
20056 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATGTAGAC
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAA--T---C
* * *
20102 TTAGACAACATCTTCCGATGGGGAAGGGCAAACTGGGAAAAC
1 -TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATC
20144 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAAAGAC
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAT-----C
* * *
20190 TTAAGCAACACCTTCCG--GTGG-A--G--AA--GGGAAAAC
1 -TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATC
20223 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATGTAGAC
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAA--T---C
* * * * *
20269 TTAGACAACAGCTTCCGGTAGGGAAGGGCAAACTGGGAAAAC
1 -TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATC
* * ** *
20311 TAAACAATACCTTCCGACGGGGGAAGGGCAAAC-AAG-AATGAG
1 TAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAAAT--C
** *
20353 TAAACAACACCTTCCGATGGGGAAGGGCAAAC-AAG-AATG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATC
* * ** * *
20392 TAAATAATACCTTCCGACCGGGAAGGGCAAAC-AGG-AATG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATC
*
20431 TAAACAACACCTTCCGACT-GGGAAGGACAAACTGG
1 TAAACAACACCTTCCGA-TGGGGAAGGGCAAACTGG
20466 AAAACGTAGA
Statistics
Matches: 434, Mismatches: 60, Indels: 76
0.76 0.11 0.13
Matches are distributed among these distances:
32 15 0.03
33 1 0.00
34 3 0.01
35 1 0.00
37 1 0.00
38 7 0.02
39 66 0.15
40 66 0.15
41 148 0.34
42 32 0.07
44 1 0.00
45 3 0.01
46 3 0.01
47 87 0.20
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (41 bp):
TAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATC
Found at i:20128 original size:47 final size:44
Alignment explanation
Indices: 19937--20600 Score: 345
Period size: 41 Copynumber: 15.5 Consensus size: 44
19927 ATGAATGTAG
* * * *
19937 ACAACACCTTCCGGTAGGGAAGGGCAAACTAGG-AAT-G--TAA
1 ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAGACTTA
* * * *
19977 ACAACACCTTCTGGTGGGGAAGGGTAAAAC-GGGAAAT---CTAA
1 ACAACACCTTCCGATGGGGAAGGG-CAAACTGGGAAATAGACTTA
* * * * * *
20018 ACAACACATTCTGGTGGGGAAGAGCAGAAC-AGG-AA-A-ACTAA
1 ACAACACCTTCCGATGGGGAAGGGCA-AACTGGGAAATAGACTTA
20059 ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATGTAGACTTA
1 ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAA--TAGACTTA
* *
20105 GACAACATCTTCCGATGGGGAAGGGCAAACTGGG-AA-A-ACTAA
1 -ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAGACTTA
20147 ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAAAGACTTA
1 ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAAT--AGACTTA
* *
20193 AGCAACACCTTCCG--GTGG-A--G--AA--GGG-AA-A-ACTAA
1 A-CAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAGACTTA
20226 ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATGTAGACTTA
1 ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAA--TAGACTTA
* * * *
20272 GACAACAGCTTCCGGTAGGGAAGGGCAAACTGGG-AA-A-ACTAA
1 -ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAGACTTA
* * ** * *
20314 ACAATACCTTCCGACGGGGGAAGGGCAAAC-AAG-AAT-GAGTAA
1 ACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAAATAGACTTA
** *
20356 ACAACACCTTCCGATGGGGAAGGGCAAAC-AAG-AAT-G--TAA
1 ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAGACTTA
* * ** * *
20395 ATAATACCTTCCGACCGGGAAGGGCAAAC-AGG-AAT-G--TAA
1 ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAGACTTA
* *
20434 ACAACACCTTCCGACT-GGGAAGGACAAACTGGAAAACGTAGACTTA
1 ACAACACCTTCCGA-TGGGGAAGGGCAAACTGGGAAA--TAGACTTA
* * **
20480 TTCAACACCTTCCGACGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTA
1 -ACAACACCTT-C--CGATGGGGAAGGGCAAACTGGG--AAA-TAGACTTA
** **
20531 GACAACACCTTCCGATGACGAAGGGCAATTTGGGAAAAAGTAGACTTA
1 -ACAACACCTTCCGATGGGGAAGGGCAAACTGGG--AAA-TAGACTTA
*
20579 GACAACACCTTCCGATGAGGAA
1 -ACAACACCTTCCGATGGGGAA
20601 AGACAATTTG
Statistics
Matches: 514, Mismatches: 58, Indels: 96
0.77 0.09 0.14
Matches are distributed among these distances:
32 12 0.02
33 5 0.01
34 4 0.01
35 1 0.00
37 3 0.01
38 3 0.01
39 63 0.12
40 33 0.06
41 137 0.27
42 45 0.09
43 3 0.01
44 2 0.00
45 6 0.01
46 19 0.04
47 83 0.16
48 57 0.11
49 1 0.00
50 16 0.03
51 18 0.04
52 3 0.01
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (44 bp):
ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAGACTTA
Found at i:20151 original size:88 final size:88
Alignment explanation
Indices: 19934--20384 Score: 475
Period size: 88 Copynumber: 5.4 Consensus size: 88
19924 GACATGAATG
* * ** * *
19934 TAGACAACACCTTCCGGTAGGGAAGGGCAAACTAGG-AATGTAAACAACACCTTCTGGTGGGGAA
1 TAGACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAA
*
19998 GGGTAAAAC-GGGAAA--T---C-
66 GGG-CAAACTGGGAAATGTAGACT
* * * * *
20015 TAAACAACACATTCTGGTGGGGAAGAGCAGAAC-AGGAAAACTAAACAACACCTTCCGATGGGGA
1 TAGACAACACCTTCCGGTGGGGAAGGGCA-AACTGGGAAAACTAAACAACACCTTCCGATGGGGA
20079 AGGGCAAACTGGGAAATGTAGACT
65 AGGGCAAACTGGGAAATGTAGACT
* *
20103 TAGACAACATCTTCCGATGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAA
1 TAGACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAA
**
20168 GGGCAAACTGGGAAATAAAGACT
66 GGGCAAACTGGGAAATGTAGACT
20191 TA-AGCAACACCTTCCGGT--GG-A--G--AA--GGGAAAACTAAACAACACCTTCCGATGGGGA
1 TAGA-CAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGA
20246 AGGGCAAACTGGGAAATGTAGACT
65 AGGGCAAACTGGGAAATGTAGACT
* * * *
20270 TAGACAACAGCTTCCGGTAGGGAAGGGCAAACTGGGAAAACTAAACAATACCTTCCGACGGGGGA
1 TAGACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGA-TGGGGA
**
20335 AGGGCAAAC-AAG-AATG-AG---
65 AGGGCAAACTGGGAAATGTAGACT
* *
20353 TAAACAACACCTTCCGATGGGGAAGGGCAAAC
1 TAGACAACACCTTCCGGTGGGGAAGGGCAAAC
20385 AAGAATGTAA
Statistics
Matches: 316, Mismatches: 32, Indels: 42
0.81 0.08 0.11
Matches are distributed among these distances:
79 68 0.22
80 1 0.00
81 35 0.11
82 37 0.12
83 29 0.09
84 2 0.01
85 1 0.00
86 6 0.02
87 9 0.03
88 114 0.36
89 14 0.04
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.14
Consensus pattern (88 bp):
TAGACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAACTAAACAACACCTTCCGATGGGGAA
GGGCAAACTGGGAAATGTAGACT
Found at i:20234 original size:32 final size:32
Alignment explanation
Indices: 20195--20255 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
20185 AAGACTTAAG
*
20195 CAACACCTTCCGGTGGAGAAGGGAAAACTAAA
1 CAACACCTTCCGATGGAGAAGGGAAAACTAAA
* *
20227 CAACACCTTCCGATGGGGAAGGGCAAACT
1 CAACACCTTCCGATGGAGAAGGGAAAACT
20256 GGGAAATGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.36, C:0.25, G:0.26, T:0.13
Consensus pattern (32 bp):
CAACACCTTCCGATGGAGAAGGGAAAACTAAA
Found at i:20269 original size:79 final size:79
Alignment explanation
Indices: 20049--20302 Score: 323
Period size: 79 Copynumber: 3.1 Consensus size: 79
20039 GAGCAGAACA
** *
20049 GGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATGTAGACTTAGACAACATC
1 GGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAAAGACTTAGACAACACC
*
20114 TTCCGATGGGGAAGGGCAAACTG
66 TTCC-----GGTAGGG--AA--G
20137 GGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAAAGACTTA-AGCAACAC
1 GGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAAAGACTTAGA-CAACAC
20201 CTTCCGGT-GGAGAAG
65 CTTCCGGTAGG-GAAG
** *
20216 GGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATGTAGACTTAGACAACAGC
1 GGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAAAGACTTAGACAACACC
20281 TTCCGGTAGGGAAG
66 TTCCGGTAGGGAAG
*
20295 GGCAAACT
1 GGAAAACT
20303 GGGAAAACTA
Statistics
Matches: 154, Mismatches: 8, Indels: 17
0.86 0.04 0.09
Matches are distributed among these distances:
79 79 0.51
80 3 0.02
81 2 0.01
82 2 0.01
83 3 0.02
87 1 0.01
88 64 0.42
ACGTcount: A:0.37, C:0.20, G:0.28, T:0.15
Consensus pattern (79 bp):
GGAAAACTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAATAAAGACTTAGACAACACC
TTCCGGTAGGGAAG
Found at i:20406 original size:39 final size:40
Alignment explanation
Indices: 20311--20462 Score: 202
Period size: 39 Copynumber: 3.8 Consensus size: 40
20301 CTGGGAAAAC
* *
20311 TAAACAATACCTTCCGACGGGGGAAGGGCAAACAAGAATGAG
1 TAAACAACACCTTCCGACTGGGGAAGGGCAAACAAGAAT--G
20353 TAAACAACACCTTCCGA-TGGGGAAGGGCAAACAAGAATG
1 TAAACAACACCTTCCGACTGGGGAAGGGCAAACAAGAATG
* * * *
20392 TAAATAATACCTTCCGAC-CGGGAAGGGCAAACAGGAATG
1 TAAACAACACCTTCCGACTGGGGAAGGGCAAACAAGAATG
*
20431 TAAACAACACCTTCCGACT-GGGAAGGACAAAC
1 TAAACAACACCTTCCGACTGGGGAAGGGCAAAC
20463 TGGAAAACGT
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
39 63 0.64
41 20 0.20
42 16 0.16
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.13
Consensus pattern (40 bp):
TAAACAACACCTTCCGACTGGGGAAGGGCAAACAAGAATG
Found at i:20454 original size:78 final size:80
Alignment explanation
Indices: 20311--20462 Score: 229
Period size: 78 Copynumber: 1.9 Consensus size: 80
20301 CTGGGAAAAC
*
20311 TAAACAATACCTTCCGACGGGGGAAGGGCAAACAAGAATGAGTAAACAACACCTTCCGATGGGGA
1 TAAACAATACCTTCCGACGCGGGAAGGGCAAACAAGAAT-AGTAAACAACACCTTCCGATGGGGA
*
20376 AGGGCAAACAAGAATG
65 AGGACAAACAAGAATG
* *
20392 TAAATAATACCTTCCGAC-CGGGAAGGGCAAACAGGAAT-GTAAACAACACCTTCCGACT-GGGA
1 TAAACAATACCTTCCGACGCGGGAAGGGCAAACAAGAATAGTAAACAACACCTTCCGA-TGGGGA
20454 AGGACAAAC
65 AGGACAAAC
20463 TGGAAAACGT
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
78 30 0.45
79 1 0.02
80 18 0.27
81 17 0.26
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.13
Consensus pattern (80 bp):
TAAACAATACCTTCCGACGCGGGAAGGGCAAACAAGAATAGTAAACAACACCTTCCGATGGGGAA
GGACAAACAAGAATG
Found at i:20566 original size:48 final size:48
Alignment explanation
Indices: 20434--20633 Score: 251
Period size: 48 Copynumber: 4.1 Consensus size: 48
20424 AGGAATGTAA
** * *
20434 ACAACACCTTCCGACTG-GGAAGGACAAACT-GGAAAACGTAGACTTAT
1 ACAACACCTTCCGA-TGAGGAAGGACAATTTGGGAAAAAGTAGACTTAG
* *
20481 TCAACACCTTCCGACGATGAGGAAGGGCAATTTGGGAAAAAGTAGACTTAG
1 ACAACACCTT-C--CGATGAGGAAGGACAATTTGGGAAAAAGTAGACTTAG
* *
20532 ACAACACCTTCCGATGACGAAGGGCAATTTGGGAAAAAGTAGACTTAG
1 ACAACACCTTCCGATGAGGAAGGACAATTTGGGAAAAAGTAGACTTAG
* *
20580 ACAACACCTTCCGATGAGGAAAGACAATTTGGGAAAAAGCAGACTTAG
1 ACAACACCTTCCGATGAGGAAGGACAATTTGGGAAAAAGTAGACTTAG
*
20628 ATAACA
1 ACAACA
20634 TTGATATGAG
Statistics
Matches: 135, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
47 9 0.07
48 86 0.64
49 2 0.01
50 14 0.10
51 24 0.18
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (48 bp):
ACAACACCTTCCGATGAGGAAGGACAATTTGGGAAAAAGTAGACTTAG
Done.