Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015448.1 Corchorus capsularis cultivar CVL-1 contig15469, 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: 70676
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:10453 original size:17 final size:17
Alignment explanation
Indices: 10431--10463 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
10421 CTCATAGTAG
10431 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
10448 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
10464 GATAGTGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:10731 original size:19 final size:18
Alignment explanation
Indices: 10707--10742 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10697 TGAAGATTTC
10707 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
10726 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
10743 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:15586 original size:11 final size:10
Alignment explanation
Indices: 15570--15668 Score: 75
Period size: 11 Copynumber: 9.9 Consensus size: 10
15560 GAAGTTCGTG
15570 ATTGAAGATTT
1 ATTGAAGA-TT
*
15581 ATTGAAGATA
1 ATTGAAGATT
15591 ATTTGAAGA--
1 A-TTGAAGATT
15600 ATTGAAGATTT
1 ATTGAAGA-TT
*
15611 ATTGAAGATA
1 ATTGAAGATT
15621 ATTTGAAGA--
1 A-TTGAAGATT
15630 ATTGAAGATTT
1 ATTGAAGA-TT
*
15641 ATTGAAGATA
1 ATTGAAGATT
15651 ATTTGAAGA--
1 A-TTGAAGATT
15660 ATTGAAGAT
1 ATTGAAGAT
15669 CATTAAAGAA
Statistics
Matches: 75, Mismatches: 3, Indels: 22
0.75 0.03 0.22
Matches are distributed among these distances:
8 21 0.28
9 3 0.04
10 6 0.08
11 45 0.60
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.36
Consensus pattern (10 bp):
ATTGAAGATT
Found at i:15605 original size:19 final size:19
Alignment explanation
Indices: 15581--15668 Score: 76
Period size: 19 Copynumber: 4.5 Consensus size: 19
15571 TTGAAGATTT
15581 ATTGAAGATAATTTGAAGA
1 ATTGAAGATAATTTGAAGA
*
15600 ATTGAAGAT-TTATTGAAGATA
1 ATTGAAGATAAT-TTGAAG--A
15621 ATTTGAAG--AA-TTGAAGA
1 A-TTGAAGATAATTTGAAGA
15638 TTTATTGAAGATAATTTGAAGA
1 ---ATTGAAGATAATTTGAAGA
15660 ATTGAAGAT
1 ATTGAAGAT
15669 CATTAAAGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 22
0.70 0.03 0.28
Matches are distributed among these distances:
17 1 0.02
18 1 0.02
19 36 0.64
20 1 0.02
21 4 0.07
22 13 0.23
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.35
Consensus pattern (19 bp):
ATTGAAGATAATTTGAAGA
Found at i:15690 original size:30 final size:30
Alignment explanation
Indices: 15570--15668 Score: 198
Period size: 30 Copynumber: 3.3 Consensus size: 30
15560 GAAGTTCGTG
15570 ATTGAAGATTTATTGAAGATAATTTGAAGA
1 ATTGAAGATTTATTGAAGATAATTTGAAGA
15600 ATTGAAGATTTATTGAAGATAATTTGAAGA
1 ATTGAAGATTTATTGAAGATAATTTGAAGA
15630 ATTGAAGATTTATTGAAGATAATTTGAAGA
1 ATTGAAGATTTATTGAAGATAATTTGAAGA
15660 ATTGAAGAT
1 ATTGAAGAT
15669 CATTAAAGAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.36
Consensus pattern (30 bp):
ATTGAAGATTTATTGAAGATAATTTGAAGA
Found at i:15690 original size:60 final size:60
Alignment explanation
Indices: 15570--15690 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 60
15560 GAAGTTCGTG
* * * *
15570 ATTGAAGATTTATTGAAGATAATTTGAAGAATTGAAGATTTATTGAAGATAATTTGAAGA
1 ATTGAAGATTTATTGAAGATAATTTGAAGAATTGAAGATTCATTAAAGAAAATTTCAAGA
15630 ATTGAAGATTTATTGAAGATAATTTGAAGAATTGAAGA-TCATTAAAGAAATATTTCAAGA
1 ATTGAAGATTTATTGAAGATAATTTGAAGAATTGAAGATTCATTAAAGAAA-ATTTCAAGA
15690 A
1 A
15691 GCAAGAATTG
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
59 9 0.16
60 47 0.84
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.35
Consensus pattern (60 bp):
ATTGAAGATTTATTGAAGATAATTTGAAGAATTGAAGATTCATTAAAGAAAATTTCAAGA
Found at i:26275 original size:33 final size:33
Alignment explanation
Indices: 26224--26292 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
26214 AGCATCTGAT
*
26224 CAGCAAAAGGTCAATGAGATGATTAATCCAAGC
1 CAGCAAAAGGTCAATGAGATGATCAATCCAAGC
* * *
26257 CAGCAAAATGTTAGTGAGATGATCAATCCAAGC
1 CAGCAAAAGGTCAATGAGATGATCAATCCAAGC
26290 CAG
1 CAG
26293 TTGAAGGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (33 bp):
CAGCAAAAGGTCAATGAGATGATCAATCCAAGC
Found at i:29479 original size:62 final size:62
Alignment explanation
Indices: 29377--29561 Score: 279
Period size: 62 Copynumber: 3.0 Consensus size: 62
29367 AACTACTTGC
*
29377 AAAGCTCGCTAAGTTAAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAAAAAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAAAAAA
*
29439 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGTTTAGGCAAAAGTTAGAGCAC----AA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAAAAAA
* * * * *
29497 AAGGCTCGTTAAGTTGAAAATCCTACGAAGGACGGCTTAGGCAAAAGTTAGAGCAAAAAAAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAAAAAA
29559 AAA
1 AAA
29562 CAAAACCAAA
Statistics
Matches: 110, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
58 52 0.47
62 58 0.53
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (62 bp):
AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAAAAAA
Found at i:29537 original size:58 final size:58
Alignment explanation
Indices: 29377--29557 Score: 263
Period size: 58 Copynumber: 3.1 Consensus size: 58
29367 AACTACTTGC
*
29377 AAAGCTCGCTAAGTTAAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAAAAAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCAC----AA
*
29439 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGTTTAGGCAAAAGTTAGAGCACAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
* * * * *
29497 AAGGCTCGTTAAGTTGAAAATCCTACGAAGGACGGCTTAGGCAAAAGTTAGAGCAAAA
1 AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
29555 AAA
1 AAA
29558 AAAACAAAAC
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
58 56 0.51
62 54 0.49
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.18
Consensus pattern (58 bp):
AAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGCACAA
Found at i:30037 original size:17 final size:17
Alignment explanation
Indices: 30015--30050 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
30005 TCTAAAGCAA
30015 CCGAACATGTCTTCAGC
1 CCGAACATGTCTTCAGC
30032 CCGAACATGTCTTCAGC
1 CCGAACATGTCTTCAGC
30049 CC
1 CC
30051 ATTCCCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.22
Consensus pattern (17 bp):
CCGAACATGTCTTCAGC
Found at i:30602 original size:59 final size:58
Alignment explanation
Indices: 30445--30667 Score: 221
Period size: 59 Copynumber: 3.9 Consensus size: 58
30435 AAGTCGATTG
* *
30445 CTTGAGCCCTGGTCAAAAGCAGATGAGCACTAGGGCAAGCGAATAATAAATTTTGATCA
1 CTTGAGCCCTGGTCGAAAGCAGA-GAGCACTAGGGCGAGCGAATAATAAATTTTGATCA
* * * * *
30504 CTTGAGCTCTAGTCG-AAG-ATGA-A-CAC-AGAGCGAGCGAATAATAAAGTTTGGTCA
1 CTTGAGCCCTGGTCGAAAGCA-GAGAGCACTAGGGCGAGCGAATAATAAATTTTGATCA
* *
30558 CTTGAGCCCTGGTTGAAAGCAGACGAGCACTAGGGCGAGCGAATAATAAATTTTGATCG
1 CTTGAGCCCTGGTCGAAAGCAGA-GAGCACTAGGGCGAGCGAATAATAAATTTTGATCA
* * * * *
30617 CTTGAGCCCTAGTCAGAAACCA-A-CGC-C-AGGACGAGCAAATAATAAATTTTG
1 CTTGAGCCCTGGTC-GAAAGCAGAGAGCACTAGGGCGAGCGAATAATAAATTTTG
30668 GTTGCTTGAG
Statistics
Matches: 136, Mismatches: 20, Indels: 20
0.77 0.11 0.11
Matches are distributed among these distances:
54 36 0.26
55 30 0.22
56 3 0.02
57 4 0.03
58 8 0.06
59 49 0.36
60 6 0.04
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.22
Consensus pattern (58 bp):
CTTGAGCCCTGGTCGAAAGCAGAGAGCACTAGGGCGAGCGAATAATAAATTTTGATCA
Found at i:30666 original size:55 final size:54
Alignment explanation
Indices: 30482--30686 Score: 180
Period size: 54 Copynumber: 3.7 Consensus size: 54
30472 CACTAGGGCA
* ** *
30482 AGCGAATAATAAATTTTGATCACTTGAGCTCTAGTCGAAGATGAAC-ACA-GAGCG
1 AGCGAATAATAAATTTTGATCACTTGAGCCCTAGTCGAA-ACCAACGCCAGGA-CG
* * * * * *
30536 AGCGAATAATAAAGTTTGGTCACTTGAGCCCTGGTTGAAAGCAGACGAGCACTAGGGCG
1 AGCGAATAATAAATTTTGATCACTTGAGCCCTAGTCGAAACCA-AC--GC-C-AGGACG
*
30595 AGCGAATAATAAATTTTGATCGCTTGAGCCCTAGTCAGAAACCAACGCCAGGACG
1 AGCGAATAATAAATTTTGATCACTTGAGCCCTAGTC-GAAACCAACGCCAGGACG
* * ** *
30650 AGCAAATAATAAATTTTGGTTGCTTGAGTCCTAGTCG
1 AGCGAATAATAAATTTTGATCACTTGAGCCCTAGTCG
30687 CTTGGGTCTT
Statistics
Matches: 123, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
53 2 0.02
54 37 0.30
55 37 0.30
56 1 0.01
57 2 0.02
58 1 0.01
59 36 0.29
60 7 0.06
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (54 bp):
AGCGAATAATAAATTTTGATCACTTGAGCCCTAGTCGAAACCAACGCCAGGACG
Found at i:33346 original size:24 final size:24
Alignment explanation
Indices: 33306--33362 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
33296 CCATTTTTTC
33306 TAAAAAAAAAAAAG-TTTGCGATT
1 TAAAAAAAAAAAAGTTTTGCGATT
* *
33329 TAAAAAAAAATTAGGTTTTGCGATT
1 TAAAAAAAAA-AAAGTTTTGCGATT
33354 TAAAAAAAA
1 TAAAAAAAA
33363 TATTTTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 10 0.33
24 2 0.07
25 18 0.60
ACGTcount: A:0.56, C:0.04, G:0.12, T:0.28
Consensus pattern (24 bp):
TAAAAAAAAAAAAGTTTTGCGATT
Found at i:36928 original size:24 final size:21
Alignment explanation
Indices: 36873--36927 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
36863 GCGCACCCTG
36873 CCGTGCCACCACCGGTCATGC
1 CCGTGCCACCACCGGTCATGC
36894 CCGTGCCACCACCGGTCATGC
1 CCGTGCCACCACCGGTCATGC
36915 CCGTGCCACCACC
1 CCGTGCCACCACC
36928 AAATCGTGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.15, C:0.51, G:0.22, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGGTCATGC
Found at i:38691 original size:11 final size:10
Alignment explanation
Indices: 38674--38723 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 10
38664 GAACTTCATA
38674 TTTGAAGATT
1 TTTGAAGATT
38684 TCTTGAAGATAT
1 T-TTGAAGAT-T
38696 TTTGAAGA--
1 TTTGAAGATT
*
38704 TTTGAAGATC
1 TTTGAAGATT
*
38714 ATTGAAGATT
1 TTTGAAGATT
38724 ATTTCAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 8 0.24
10 9 0.26
11 15 0.44
12 2 0.06
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.42
Consensus pattern (10 bp):
TTTGAAGATT
Found at i:41974 original size:77 final size:78
Alignment explanation
Indices: 41847--42140 Score: 391
Period size: 77 Copynumber: 3.8 Consensus size: 78
41837 CTGTCATGCA
* **
41847 ACGTGGTGGTGGAGAGC-TTTGTAGCCATGTGATGTTTTGGTTGCCATGATACGACATATGAAGA
1 ACGTGGTGGTGGAGACCATTTGTAGCCATGTGATACTTTGGTTGCCATGATACGACATATGAAGA
41911 TCCTTATAG-CATT
66 TCCTTAT-GCCATT
* *
41924 ACGTGGCGGTGGAGA-CATTTCTAGCCATGTGATACTTTGGTTGCCATGATACGACATATGAAGA
1 ACGTGGTGGTGGAGACCATTTGTAGCCATGTGATACTTTGGTTGCCATGATACGACATATGAAGA
41988 TCCTTATGCCATT
66 TCCTTATGCCATT
* * **
42001 ACGTAGTGGCGGAGACC-TTTGTAGCCATGTGATACTTTGGTTGCTGTGATACGACATATGAAGA
1 ACGTGGTGGTGGAGACCATTTGTAGCCATGTGATACTTTGGTTGCCATGATACGACATATGAAGA
42065 TCCTTATGCCATT
66 TCCTTATGCCATT
* * * * *
42078 ATGTGGTGGTGGAGACCTAATTTGTAGCCATGTGTTA-TTTGGGTTGTCGTGATACGGCATATG
1 ACGTGGTGGTGGAGACC--ATTTGTAGCCATGTGATACTTT-GGTTGCCATGATACGACATATG
42141 GCCACATGGG
Statistics
Matches: 193, Mismatches: 17, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
76 2 0.01
77 152 0.79
78 1 0.01
79 3 0.02
80 35 0.18
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (78 bp):
ACGTGGTGGTGGAGACCATTTGTAGCCATGTGATACTTTGGTTGCCATGATACGACATATGAAGA
TCCTTATGCCATT
Found at i:42976 original size:17 final size:18
Alignment explanation
Indices: 42934--42977 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
42924 TAGATTGCTA
42934 ATGATTA-TG-ATGTTGG
1 ATGATTATTGAATGTTGG
*
42950 AT-ATTTTTGAATGTT-G
1 ATGATTATTGAATGTTGG
42966 ATGATTATTGAA
1 ATGATTATTGAA
42978 CGACATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 3 0.13
16 7 0.30
17 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.48
Consensus pattern (18 bp):
ATGATTATTGAATGTTGG
Found at i:44255 original size:25 final size:26
Alignment explanation
Indices: 44222--44283 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
44212 AAAACACAAC
* *
44222 AACAACACCAAATTTAGCT-AAAAAA
1 AACAGCACCAAAGTTAGCTCAAAAAA
* *
44247 AATAGCACCAAAGTTAGCTCAATAAA
1 AACAGCACCAAAGTTAGCTCAAAAAA
44273 AACAG-ACCAAA
1 AACAGCACCAAA
44284 ACAGTTTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 22 0.71
26 9 0.29
ACGTcount: A:0.56, C:0.21, G:0.08, T:0.15
Consensus pattern (26 bp):
AACAGCACCAAAGTTAGCTCAAAAAA
Found at i:47227 original size:13 final size:13
Alignment explanation
Indices: 47194--47237 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
47184 AATTCTGCCT
*
47194 ATATATATATA-T
1 ATATATATATAGG
47206 ATATAATATATAGG
1 ATAT-ATATATAGG
*
47220 ATATATATGTAGG
1 ATATATATATAGG
47233 ATATA
1 ATATA
47238 GAAACTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 4 0.14
13 20 0.71
14 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (13 bp):
ATATATATATAGG
Found at i:47442 original size:31 final size:31
Alignment explanation
Indices: 47368--47442 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 31
47358 TCCAAAATTA
* * *
47368 TTAGTGGGGTCAATACTATAAAATTTTCATT
1 TTAGTGGGGTCAATACAATAAAACTTTCAAT
* * *
47399 TTAAT-GGGTCAATAGAATAAACCTTTCAAT
1 TTAGTGGGGTCAATACAATAAAACTTTCAAT
47429 TTAGTGGGGTCAAT
1 TTAGTGGGGTCAAT
47443 TAGTAATTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 24 0.67
31 12 0.33
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (31 bp):
TTAGTGGGGTCAATACAATAAAACTTTCAAT
Found at i:47470 original size:12 final size:11
Alignment explanation
Indices: 47455--47494 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
47445 GTAATTTGTC
47455 CTATTTTTTTT
1 CTATTTTTTTT
*
47466 CCTATTTCATTTT
1 -CTATTT-TTTTT
47479 CTATTTTTTTT
1 CTATTTTTTTT
47490 CTATT
1 CTATT
47495 AATAAATGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.36
12 12 0.48
13 4 0.16
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.72
Consensus pattern (11 bp):
CTATTTTTTTT
Found at i:50930 original size:27 final size:29
Alignment explanation
Indices: 50859--50936 Score: 79
Period size: 27 Copynumber: 2.7 Consensus size: 29
50849 TAAAGATCCA
*
50859 AAAAAAATCCCTTATGTTTTTCTTTGGGGAC
1 AAAATAATCCCTTATG--TTTCTTTGGGGAC
**
50890 AAAATAATTTCTTATGTTT-TTT-GGGAC
1 AAAATAATCCCTTATGTTTCTTTGGGGAC
* *
50917 AAATTAATCCCTTACGTTTC
1 AAAATAATCCCTTATGTTTC
50937 AAAATTGGAC
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 20 0.51
28 3 0.08
29 3 0.08
31 13 0.33
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42
Consensus pattern (29 bp):
AAAATAATCCCTTATGTTTCTTTGGGGAC
Found at i:51154 original size:29 final size:29
Alignment explanation
Indices: 51095--51174 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
51085 TTAATACCCA
*
51095 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAATAATCCCTTATG--TTTCTTTTGGGAC
51126 AAAATAATCCCTTATG-TTCTTTTAGGGAC
1 AAAATAATCCCTTATGTTTCTTTT-GGGAC
* * *
51155 AAATTAATCCCGTAGGTTTC
1 AAAATAATCCCTTATGTTTC
51175 AAAATTGAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
28 7 0.16
29 18 0.42
30 3 0.07
31 15 0.35
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (29 bp):
AAAATAATCCCTTATGTTTCTTTTGGGAC
Found at i:51940 original size:11 final size:11
Alignment explanation
Indices: 51920--51954 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
51910 TTGACAACGC
51920 AACAAAAACAA
1 AACAAAAACAA
*
51931 AACGAAAACAA
1 AACAAAAACAA
51942 AACAAAAACAA
1 AACAAAAACAA
51953 AA
1 AA
51955 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:53459 original size:29 final size:31
Alignment explanation
Indices: 53414--53485 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
53404 TTGAATTGTG
* *
53414 AGGGATTAATTTGTCCC-AAA-AAAAATATA
1 AGGGATTATTTTATCCCAAAAGAAAAATATA
53443 AGGGATTATTTTATCCCAAAAGAAAAATATA
1 AGGGATTATTTTATCCCAAAAGAAAAATATA
*
53474 AGGGATTTTTTT
1 AGGGATTATTTT
53486 GGTATTTAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 15 0.39
30 3 0.08
31 20 0.53
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.33
Consensus pattern (31 bp):
AGGGATTATTTTATCCCAAAAGAAAAATATA
Found at i:53718 original size:31 final size:28
Alignment explanation
Indices: 53650--53727 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
53640 GCTCACTTTG
* * *
53650 AAACGTAAGTGATTAATTTGTCCTAAAA
1 AAACATAAGAGATTATTTTGTCCTAAAA
*
53678 ATACATAAGAGATTATTTTGTCCTAAAAGAA
1 AAACATAAGAGATTATTTTGTCCT--AA-AA
*
53709 AAACATAAGAGATTTTTTT
1 AAACATAAGAGATTATTTT
53728 AGATATTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 20 0.49
30 2 0.05
31 19 0.46
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.35
Consensus pattern (28 bp):
AAACATAAGAGATTATTTTGTCCTAAAA
Found at i:56327 original size:21 final size:20
Alignment explanation
Indices: 56301--56347 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
56291 TTGTAATCTC
56301 TAATTA-TTGATTAATAAAAAA
1 TAATTATTTGA-TAA-AAAAAA
*
56322 TGATTATTTGATAAAAAAAA
1 TAATTATTTGATAAAAAAAA
56342 TAATTA
1 TAATTA
56348 GAATGAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 11 0.48
21 8 0.35
22 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (20 bp):
TAATTATTTGATAAAAAAAA
Found at i:68284 original size:13 final size:13
Alignment explanation
Indices: 68239--68285 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
68229 ATCATTTTTA
68239 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
68252 CT-TTTTACTAATT
1 CTCTTTT-CTTACT
68265 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
68279 CTCTTTT
1 CTCTTTT
68286 ATTTATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:68300 original size:29 final size:28
Alignment explanation
Indices: 68236--68313 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
68226 TTTATCATTT
*
68236 TTACTCTTTTCTTACTCT-TTTTACTAA
1 TTACACTTTTCTTACTCTCTTTTACTAA
* * *
68263 TTACTCTTTTCTTACTCTCTTTTATTTA
1 TTACACTTTTCTTACTCTCTTTTACTAA
68291 TTACCAC-TTT-TTACTCTTCTTTT
1 TTA-CACTTTTCTTACTC-TCTTTT
68314 TTCTTATACT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 24 0.53
28 19 0.42
29 2 0.04
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (28 bp):
TTACACTTTTCTTACTCTCTTTTACTAA
Found at i:68370 original size:21 final size:21
Alignment explanation
Indices: 68346--68460 Score: 85
Period size: 21 Copynumber: 5.4 Consensus size: 21
68336 ACTCTTTGAA
*
68346 TTACTGATCACCTTTTACTCT
1 TTACTGATTACCTTTTACTCT
68367 TTACTGATTA-CTATTTGACTC-
1 TTACTGATTACCT-TTT-ACTCT
* ** *
68388 TTACTAATTATCAATTTGCTC-
1 TTACTGATTA-CCTTTTACTCT
* *
68409 TTACTGGTTACTATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
*
68430 TTACTGATTACTTTTTTACTCT
1 TTACTGATTAC-CTTTTACTCT
68452 TTACTGATT
1 TTACTGATT
68461 TTACTCTTTA
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.04
21 58 0.75
22 16 0.21
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (21 bp):
TTACTGATTACCTTTTACTCT
Found at i:68452 original size:42 final size:43
Alignment explanation
Indices: 68358--68460 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 43
68348 ACTGATCACC
68358 TTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTATCA
1 TTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTATCA
* * * * * *
68401 ATTTGCTC-TTACTGGTTACTATTTTACTCTTACTGATTA-CTT
1 TTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTATC-A
68443 TTTTACTCTTTACTGATT
1 TTTTACTCTTTACTGATT
68461 TTACTCTTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.02
42 34 0.69
43 14 0.29
ACGTcount: A:0.21, C:0.18, G:0.07, T:0.53
Consensus pattern (43 bp):
TTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTATCA
Found at i:68464 original size:16 final size:16
Alignment explanation
Indices: 68443--68476 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
68433 CTGATTACTT
68443 TTTTACTCTTTACTGA
1 TTTTACTCTTTACTGA
68459 TTTTACTCTTTACTGA
1 TTTTACTCTTTACTGA
68475 TT
1 TT
68477 ACCTTCTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTTACTCTTTACTGA
Found at i:68559 original size:15 final size:14
Alignment explanation
Indices: 68526--68560 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
68516 TATTTTACTC
*
68526 TTTACTGATTATCT
1 TTTACTGATTATAT
68540 TTTACTGATTATTAT
1 TTTACTGATTA-TAT
68555 TTTACT
1 TTTACT
68561 CTTTATCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (14 bp):
TTTACTGATTATAT
Found at i:68610 original size:22 final size:22
Alignment explanation
Indices: 68585--68832 Score: 105
Period size: 22 Copynumber: 11.8 Consensus size: 22
68575 TCTTTACCAG
*
68585 TTACC-TTCTTACTTTTTAATGA
1 TTACCATT-TTACTCTTTAATGA
*
68607 TTACCATTTTACTCTTTACTGA
1 TTACCATTTTACTCTTTAATGA
* * *
68629 TTACCATTTTGCTC-TCATTGA
1 TTACCATTTTACTCTTTAATGA
* *
68650 TTACCATTTTGCTC-TTACTGA
1 TTACCATTTTACTCTTTAATGA
* *
68671 TTACTATTTTAC-CTTTTACTGA
1 TTACCATTTTACTC-TTTAATGA
* * *
68693 TTATCA--TTACTTTTTATTGA
1 TTACCATTTTACTCTTTAATGA
* * **
68713 TTACC-TTTTACTATTTCATTCT
1 TTACCATTTTACTCTTT-AATGA
* * *
68735 TTACTGATTAT-CT-TTTACTGA
1 TTAC-CATTTTACTCTTTAATGA
*
68756 TTACTATTTTACTC-TT--T-A
1 TTACCATTTTACTCTTTAATGA
* * *
68774 -T--CATCTTACTCTTTACTGG
1 TTACCATTTTACTCTTTAATGA
* * *
68793 TTACCTTCTTACTTTTTAATGA
1 TTACCATTTTACTCTTTAATGA
*
68815 TTACCATTTTACTTTTTA
1 TTACCATTTTACTCTTTA
68833 CCATTCTTCC
Statistics
Matches: 175, Mismatches: 33, Indels: 36
0.72 0.14 0.15
Matches are distributed among these distances:
15 8 0.05
16 2 0.01
17 1 0.01
18 2 0.01
19 1 0.01
20 21 0.12
21 52 0.30
22 81 0.46
23 4 0.02
24 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.54
Consensus pattern (22 bp):
TTACCATTTTACTCTTTAATGA
Found at i:68652 original size:21 final size:21
Alignment explanation
Indices: 68604--68700 Score: 113
Period size: 21 Copynumber: 4.5 Consensus size: 21
68594 TACTTTTTAA
*
68604 TGATTACCATTTTACTCTTTAC
1 TGATTACCATTTTGCTC-TTAC
* *
68626 TGATTACCATTTTGCTCTCAT
1 TGATTACCATTTTGCTCTTAC
68647 TGATTACCATTTTGCTCTTAC
1 TGATTACCATTTTGCTCTTAC
* * *
68668 TGATTACTATTTTACCTTTTAC
1 TGATTACCATTTT-GCTCTTAC
*
68690 TGATTATCATT
1 TGATTACCATT
68701 ACTTTTTATT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 33 0.52
22 31 0.48
ACGTcount: A:0.22, C:0.21, G:0.07, T:0.51
Consensus pattern (21 bp):
TGATTACCATTTTGCTCTTAC
Found at i:68742 original size:29 final size:33
Alignment explanation
Indices: 68679--68758 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 33
68669 GATTACTATT
*
68679 TTACCTTTTACTGATTATCATTACTTTTTATTGA
1 TTACCTTTTACTGATTATCATTAC-TTTTACTGA
68713 TTACCTTTTACT-ATT-TCATT-C-TTTACTGA
1 TTACCTTTTACTGATTATCATTACTTTTACTGA
*
68742 TTATCTTTTACTGATTA
1 TTACCTTTTACTGATTA
68759 CTATTTTACT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 18 0.43
30 3 0.07
31 1 0.02
32 5 0.12
33 3 0.07
34 12 0.29
ACGTcount: A:0.23, C:0.16, G:0.05, T:0.56
Consensus pattern (33 bp):
TTACCTTTTACTGATTATCATTACTTTTACTGA
Found at i:68753 original size:14 final size:14
Alignment explanation
Indices: 68704--68768 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 14
68694 TATCATTACT
* *
68704 TTTTATTGATTACC
1 TTTTACTGATTATC
68718 TTTTACT-ATT-TC
1 TTTTACTGATTATC
68730 ATTCTTTACTGATTATC
1 --T-TTTACTGATTATC
*
68747 TTTTACTGATTACTA
1 TTTTACTGATTA-TC
68762 TTTTACT
1 TTTTACT
68769 CTTTATCATC
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
12 1 0.02
13 3 0.07
14 18 0.43
15 15 0.36
16 3 0.07
17 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.05, T:0.58
Consensus pattern (14 bp):
TTTTACTGATTATC
Found at i:68766 original size:29 final size:28
Alignment explanation
Indices: 68698--68768 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
68688 ACTGATTATC
*
68698 ATTACT-TTTTATTGATTACCTTTTACT
1 ATTACTATTTTACTGATTACCTTTTACT
* *
68725 ATTTC-ATTCTTTACTGATTATCTTTTACT
1 ATTACTA-T-TTTACTGATTACCTTTTACT
68754 GATTACTATTTTACT
1 -ATTACTATTTTACT
68769 CTTTATCATC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
27 4 0.11
28 1 0.03
29 24 0.69
30 5 0.14
31 1 0.03
ACGTcount: A:0.23, C:0.15, G:0.04, T:0.58
Consensus pattern (28 bp):
ATTACTATTTTACTGATTACCTTTTACT
Found at i:68861 original size:72 final size:72
Alignment explanation
Indices: 68756--68935 Score: 183
Period size: 72 Copynumber: 2.5 Consensus size: 72
68746 CTTTTACTGA
* *
68756 TTACTATTTTACTCTTTA-TCATCTTACTCTTTACTGGTTACC-TTCTTACTTTTTAATGATTAC
1 TTACCATTTTACTCTTTACT-A-ATTACTCTTTACTGGTTACCATTCTT-C-TTTTAATGATTAC
68819 -CATTTTAC-TTT
62 TC--TTTACTTTT
* ** *
68830 TTACCATTCTT-C-CTTTACTGATTACTCTTTACTTTTTACCATTCTTCTTTTACTGATTACTCT
1 TTACCATT-TTACTCTTTACTAATTACTCTTTACTGGTTACCATTCTTCTTTTAATGATTACTCT
68893 TTACTTTT
65 TTACTTTT
* *
68901 TTATCATTTTACTCTTTACTAATTACTCCTTACTG
1 TTACCATTTTACTCTTTACTAATTACTCTTTACTG
68936 ATTATTCTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
70 7 0.08
71 23 0.26
72 38 0.43
73 10 0.11
74 9 0.10
75 2 0.02
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.55
Consensus pattern (72 bp):
TTACCATTTTACTCTTTACTAATTACTCTTTACTGGTTACCATTCTTCTTTTAATGATTACTCTT
TACTTTT
Found at i:68864 original size:35 final size:37
Alignment explanation
Indices: 68732--68934 Score: 183
Period size: 37 Copynumber: 5.6 Consensus size: 37
68722 ACTATTTCAT
** *
68732 TCTTTACTGATTA-TCTTTTACTGATTACTATT-TTAC
1 TCTTTACTGATTACTC-TTTACTTTTTACCATTCTTAC
* **
68768 TCTTTATCAT-CTTACTCTTTACTGGTTACC-TTCTTAC
1 TCTTTA-C-TGATTACTCTTTACTTTTTACCATTCTTAC
* *
68805 TTTTTAATGATTAC-CATTTTACTTTTTACCATTCTT-C
1 TCTTTACTGATTACTC--TTTACTTTTTACCATTCTTAC
68842 -CTTTACTGATTACTCTTTACTTTTTACCATTCTT-C
1 TCTTTACTGATTACTCTTTACTTTTTACCATTCTTAC
*
68877 T-TTTACTGATTACTCTTTACTTTTTTATCATT-TTAC
1 TCTTTACTGATTACTCTTTAC-TTTTTACCATTCTTAC
* *
68913 TCTTTACTAATTACTCCTTACT
1 TCTTTACTGATTACTCTTTACT
68935 GATTATTCTT
Statistics
Matches: 141, Mismatches: 13, Indels: 26
0.78 0.07 0.14
Matches are distributed among these distances:
35 43 0.30
36 36 0.26
37 54 0.38
38 8 0.06
ACGTcount: A:0.20, C:0.22, G:0.03, T:0.55
Consensus pattern (37 bp):
TCTTTACTGATTACTCTTTACTTTTTACCATTCTTAC
Found at i:68919 original size:86 final size:86
Alignment explanation
Indices: 68819--68976 Score: 230
Period size: 86 Copynumber: 1.8 Consensus size: 86
68809 TAATGATTAC
* * * *
68819 CATTTTACTTTTTAC-CATT-CTTCCTTTACTGATTACTCTTTACTTTTTACCATTCTTCTTTTA
1 CATTTTACTCTTTACTAATTAC-TCC-TTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTA
68882 CTGATTACTCTTTACTTTTTTAT
64 CTGATTACTCTTTACTTTTTTAT
* *
68905 CATTTTACTCTTTACTAATTACTCCTTACTGATTATTCTTTACTCTTTACCATTTTTCCTTTACT
1 CATTTTACTCTTTACTAATTACTCCTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACT
68970 GATTACT
66 GATTACT
68977 GTCTTGAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
86 57 0.89
87 6 0.09
88 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.56
Consensus pattern (86 bp):
CATTTTACTCTTTACTAATTACTCCTTACTGATTACTCTTTACTCTTTACCATTCTTCCTTTACT
GATTACTCTTTACTTTTTTAT
Found at i:69192 original size:55 final size:55
Alignment explanation
Indices: 69122--69375 Score: 409
Period size: 55 Copynumber: 4.6 Consensus size: 55
69112 CTCTTAATTA
* *
69122 CTGATTAATCTCTTTTTACTGATTTACTGATTGACTGATTACCATTATCTTGACT
1 CTGATTAATCTCTTTTTACTGATTTACTGATTGACTGATTACCATCACCTTGACT
*
69177 CTGATTAATCTCTTTTTACTGATTTACTAATTGACTGATTACCATCACCTTGACT
1 CTGATTAATCTCTTTTTACTGATTTACTGATTGACTGATTACCATCACCTTGACT
*
69232 CTGATTAACCTCTTTTTACTGATTTACTGATTGACTGATTACCATCACCTTGACT
1 CTGATTAATCTCTTTTTACTGATTTACTGATTGACTGATTACCATCACCTTGACT
* * **
69287 CTTGATTAACCTCTTTTTACTGATTTATTGATTGACTGATTACCATTGCCTTGACT
1 C-TGATTAATCTCTTTTTACTGATTTACTGATTGACTGATTACCATCACCTTGACT
* *
69343 TTGATTAATCTCTTTCTACTGATTTACTGATTG
1 CTGATTAATCTCTTTTTACTGATTTACTGATTG
69376 CCCCTTTTTA
Statistics
Matches: 186, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
55 135 0.73
56 51 0.27
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (55 bp):
CTGATTAATCTCTTTTTACTGATTTACTGATTGACTGATTACCATCACCTTGACT
Found at i:69348 original size:111 final size:110
Alignment explanation
Indices: 69122--69375 Score: 409
Period size: 111 Copynumber: 2.3 Consensus size: 110
69112 CTCTTAATTA
* * *
69122 CTGATTAATCTCTTTTTACTGATTTACTGATTGACTGATTACCATTATCTTGACTCTGATTAATC
1 CTGATTAATCTCTTTTTACTGATTTACTGATTGACTGATTACCATCACCTTGACTCTGATTAACC
69187 TCTTTTTACTGATTTACTAATTGACTGATTACCATCACCTTGACT
66 TCTTTTTACTGATTTACTAATTGACTGATTACCATCACCTTGACT
*
69232 CTGATTAACCTCTTTTTACTGATTTACTGATTGACTGATTACCATCACCTTGACTCTTGATTAAC
1 CTGATTAATCTCTTTTTACTGATTTACTGATTGACTGATTACCATCACCTTGACTC-TGATTAAC
* * **
69297 CTCTTTTTACTGATTTATTGATTGACTGATTACCATTGCCTTGACT
65 CTCTTTTTACTGATTTACTAATTGACTGATTACCATCACCTTGACT
* *
69343 TTGATTAATCTCTTTCTACTGATTTACTGATTG
1 CTGATTAATCTCTTTTTACTGATTTACTGATTG
69376 CCCCTTTTTA
Statistics
Matches: 132, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
110 53 0.40
111 79 0.60
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (110 bp):
CTGATTAATCTCTTTTTACTGATTTACTGATTGACTGATTACCATCACCTTGACTCTGATTAACC
TCTTTTTACTGATTTACTAATTGACTGATTACCATCACCTTGACT
Done.