Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011704.1 Corchorus capsularis cultivar CVL-1 contig11725, 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: 58642
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:76 original size:49 final size:49
Alignment explanation
Indices: 1--278 Score: 427
Period size: 49 Copynumber: 5.7 Consensus size: 49
1 ACTTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGC
1 ACTTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGC
* * *
50 ACCTGTTTTTATCTGTTATTTCCCAAAATGCCCTTCCCGGACGGAAGGT
1 ACTTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGC
* *
99 ACTTGTTTTTATCTGTTATTTCCCAAAATGCCCTTTCCGGACGGAAGGC
1 ACTTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGC
*
148 ACTTGTTTTTATCTACTATTTCCCAAAATGCCCTTCCCGGACGGAAGGC
1 ACTTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGC
* **
197 ACTTGTTTTTATCTGCTATTT-CCAAAATGCCCTTCCCGGATGGAAGAT
1 ACTTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGC
* *
245 ACTT-ATTTTA-CTTGCTATTTCCCAAAATACCCTT
1 ACTTGTTTTTATC-TGCTATTTCCCAAAATGCCCTT
279 TCGGACCAAG
Statistics
Matches: 212, Mismatches: 15, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
46 1 0.00
47 13 0.06
48 40 0.19
49 158 0.75
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (49 bp):
ACTTGTTTTTATCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGC
Found at i:414 original size:63 final size:64
Alignment explanation
Indices: 262--424 Score: 229
Period size: 64 Copynumber: 2.6 Consensus size: 64
252 TTACTTGCTA
* * * * *
262 TTTCCCAAAATACCCTTTCGGACCAAGGGTTAGTTTTGTCACATTCTTACATTTAGGTTCTAGT
1 TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCGTCACATTCCTACATTTAAGTTCTAGT
* * * * *
326 TTTCCCAAAATGCCCTTTTGAACAAAGGGCCAGTTTCGTCACATTCCTGCATTTAAGTT-TAGT
1 TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCGTCACATTCCTACATTTAAGTTCTAGT
389 TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTT
1 TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTT
425 TATCATGTTT
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
63 36 0.42
64 49 0.58
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (64 bp):
TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCGTCACATTCCTACATTTAAGTTCTAGT
Found at i:5653 original size:26 final size:26
Alignment explanation
Indices: 5607--5657 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
5597 CATATCACAT
*
5607 CATATCCTATTAATTCGCATTAGAAC
1 CATATCCTATTAATTCACATTAGAAC
* *
5633 CATATCCTATTAGTTTACATTAGAA
1 CATATCCTATTAATTCACATTAGAA
5658 TCATGTTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (26 bp):
CATATCCTATTAATTCACATTAGAAC
Found at i:9666 original size:6 final size:6
Alignment explanation
Indices: 9650--9682 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
9640 TAAAGCAAAG
9650 TAAAT- TAAATC TAAATC TAAATC TAAATC TAAA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAA
9683 GCAGAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATC
Found at i:9694 original size:18 final size:18
Alignment explanation
Indices: 9629--9694 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 18
9619 TAAAAACAAT
* *
9629 TAAA-CTAAAAATAAAGC
1 TAAAGCTAAATATAAATC
9646 -AAAG-TAAAT-TAAATC
1 TAAAGCTAAATATAAATC
* *
9661 TAAATCTAAATCTAAATC
1 TAAAGCTAAATATAAATC
9679 TAAAGC-AGAATATAAA
1 TAAAGCTA-AATATAAA
9695 GCAAACAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
15 5 0.13
16 10 0.26
17 6 0.15
18 18 0.46
ACGTcount: A:0.59, C:0.11, G:0.06, T:0.24
Consensus pattern (18 bp):
TAAAGCTAAATATAAATC
Found at i:11653 original size:35 final size:34
Alignment explanation
Indices: 11614--11801 Score: 129
Period size: 35 Copynumber: 5.4 Consensus size: 34
11604 AAGATTCAAG
11614 AAGTAATTTGGTAATCAACTTAATTCGGTGCAATT
1 AAGTAATTTGGTAATCAACTTAATTCGGTG-AATT
* * * * *
11649 AAGTAAATTGGTAATTAAATTAAGTAATTTGGT-AATC
1 AAGTAATTTGGTAA-TCAACT---TAATTCGGTGAATT
* * * * *
11686 AACTTAATTTGGTGTAATTAA-GTAATTTGGT--ACT
1 AA-GTAATTT-G-GTAATCAACTTAATTCGGTGAATT
11720 ---TAATTTGGTAATCAACTTAATTCGGTGTAATT
1 AAGTAATTTGGTAATCAACTTAATTCGGTG-AATT
*
11752 AAATAATTTGGTAATCAACTTAATTCGGTGCAATT
1 AAGTAATTTGGTAATCAACTTAATTCGGTG-AATT
*
11787 AAGTAAATTGGTAAT
1 AAGTAATTTGGTAAT
11802 TAAATTAAGT
Statistics
Matches: 121, Mismatches: 18, Indels: 28
0.72 0.11 0.17
Matches are distributed among these distances:
28 7 0.06
29 9 0.07
30 6 0.05
32 2 0.02
34 1 0.01
35 66 0.55
36 4 0.03
37 5 0.04
38 5 0.04
39 12 0.10
40 4 0.03
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.39
Consensus pattern (34 bp):
AAGTAATTTGGTAATCAACTTAATTCGGTGAATT
Found at i:11669 original size:21 final size:21
Alignment explanation
Indices: 11645--11684 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11635 AATTCGGTGC
11645 AATTAAGTAAATTGGTAATTA
1 AATTAAGTAAATTGGTAATTA
*
11666 AATTAAGTAATTTGGTAAT
1 AATTAAGTAAATTGGTAAT
11685 CAACTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (21 bp):
AATTAAGTAAATTGGTAATTA
Found at i:11681 original size:56 final size:56
Alignment explanation
Indices: 11614--11722 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
11604 AAGATTCAAG
11614 AAGTAATTTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATT
1 AAGTAATTTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATT
* * * *
11670 AAGTAATTTGGTAATCAACTTAATTTGGTGTAATTAAGTAATTTGGTACTTAA
1 AAGTAATTTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAA
11723 TTTGGTAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (56 bp):
AAGTAATTTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATT
Found at i:11692 original size:21 final size:21
Alignment explanation
Indices: 11645--11692 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
11635 AATTCGGTGC
*
11645 AATTAAGTAAATTGGTAATTA
1 AATTAAGTAAATTGGTAATCA
*
11666 AATTAAGTAATTTGGTAATCA
1 AATTAAGTAAATTGGTAATCA
*
11687 ACTTAA
1 AATTAA
11693 TTTGGTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (21 bp):
AATTAAGTAAATTGGTAATCA
Found at i:11729 original size:47 final size:47
Alignment explanation
Indices: 11673--11764 Score: 166
Period size: 47 Copynumber: 2.0 Consensus size: 47
11663 TTAAATTAAG
* *
11673 TAATTTGGTAATCAACTTAATTTGGTGTAATTAAGTAATTTGGTACT
1 TAATTTGGTAATCAACTTAATTCGGTGTAATTAAATAATTTGGTACT
11720 TAATTTGGTAATCAACTTAATTCGGTGTAATTAAATAATTTGGTA
1 TAATTTGGTAATCAACTTAATTCGGTGTAATTAAATAATTTGGTA
11765 ATCAACTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (47 bp):
TAATTTGGTAATCAACTTAATTCGGTGTAATTAAATAATTTGGTACT
Found at i:11804 original size:16 final size:16
Alignment explanation
Indices: 11746--11806 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
11736 TTAATTCGGT
*
11746 GTAATTAAATAATTTG
1 GTAATTAAATAAATTG
* * *
11762 GTAATCAACTTAATTCG
1 GTAATTAAATAAATT-G
*
11779 GTGCAATTAAGTAAATTG
1 GT--AATTAAATAAATTG
11797 GTAATTAAAT
1 GTAATTAAAT
11807 TAAGTAAATC
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
16 18 0.53
17 3 0.09
18 3 0.09
19 10 0.29
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.38
Consensus pattern (16 bp):
GTAATTAAATAAATTG
Found at i:11807 original size:21 final size:21
Alignment explanation
Indices: 11783--11824 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11773 AATTCGGTGC
**
11783 AATTAAGTAAATTGGTAATTA
1 AATTAAGTAAATCAGTAATTA
11804 AATTAAGTAAATCAGTAATTA
1 AATTAAGTAAATCAGTAATTA
11825 GCTAAATTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (21 bp):
AATTAAGTAAATCAGTAATTA
Found at i:13740 original size:126 final size:122
Alignment explanation
Indices: 13601--13940 Score: 432
Period size: 113 Copynumber: 2.8 Consensus size: 122
13591 GAGCTAAAAA
* * *
13601 AAAATTGCAAAGAGTGTTGTACCTTGGAGTTTTAGTTGCATCTTGGGAAATATTTCCTAAGTGTT
1 AAAATTGCAAAGAGTGTTGCACCTTAGAGTTTTAGTTGCATCTTGGGAAATATTTCCTGAGTGTT
*
13666 GCACTTTAAACTTGGGTAGCACCTCAAGAGAAATATATATATATATATATATATTGCT-TTC
66 GCACTTTAAACTTGGGTAGCACCTCAA-AGAAA-ATATA-A-AGA-ATATATATTGCTCTTC
* * *
13727 AAAATTGCAAAGAGTATTGCACCTTAGAGTTTTAGTTGCATCTCGGGAAATACTTCCTGAGTGTT
1 AAAATTGCAAAGAGTGTTGCACCTTAGAGTTTTAGTTGCATCTTGGGAAATATTTCCTGAGTGTT
13792 GCACTTTAAACTTGGGTAGCACCT------AAA-A-AAAGAATATATATTGCTCTTC
66 GCACTTTAAACTTGGGTAGCACCTCAAAGAAAATATAAAGAATATATATTGCTCTTC
* * ** *
13841 -AAATTGCAAGGAGTGTTGCACCTTAGAATTTTAGTTGCATC-TCAGAGAGTATTTCCTGAGTGT
1 AAAATTGCAAAGAGTGTTGCACCTTAGAGTTTTAGTTGCATCTTGGGA-AATATTTCCTGAGTGT
*
13904 TGCACTTTAAACTTGGGTCGCACCTCAAAGAAAATAT
65 TGCACTTTAAACTTGGGTAGCACCTCAAAGAAAATAT
13941 TGTTTTCTAT
Statistics
Matches: 188, Mismatches: 16, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
112 2 0.01
113 88 0.47
114 5 0.03
115 1 0.01
116 1 0.01
117 1 0.01
118 1 0.01
119 5 0.03
120 1 0.01
126 83 0.44
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (122 bp):
AAAATTGCAAAGAGTGTTGCACCTTAGAGTTTTAGTTGCATCTTGGGAAATATTTCCTGAGTGTT
GCACTTTAAACTTGGGTAGCACCTCAAAGAAAATATAAAGAATATATATTGCTCTTC
Found at i:14214 original size:46 final size:46
Alignment explanation
Indices: 14162--14457 Score: 244
Period size: 46 Copynumber: 6.7 Consensus size: 46
14152 GAATTATATC
*
14162 CTCTTCCAACATGGTGGTGGCGCTTCCAACAGACAAAATTTATACT
1 CTCTTCCAACATGGTGGTGGCGCTTCCAACTGACAAAATTTATACT
*
14208 CTCTTCCAACATGGTGGTGGCGCTTCCAACAGACAAAATTTATACT
1 CTCTTCCAACATGGTGGTGGCGCTTCCAACTGACAAAATTTATACT
**
14254 CTC-T------T-GTGGTGGCGCTTCCAAC-GACATTATTTATACT
1 CTCTTCCAACATGGTGGTGGCGCTTCCAACTGACAAAATTTATACT
* * ** * * * *
14291 CTCCTCCAACATAGTGACGACGCTTTCAA-TTACGAGAATTTATAC-
1 CTCTTCCAACATGGTGGTGGCGCTTCCAACTGAC-AAAATTTATACT
* ** *
14336 CTTCTTCCAACATGG-GGAGAGCGCTT-CTGCTGACGAGAATTTATA-T
1 C-TCTTCCAACATGGTGGTG-GCGCTTCCAACTGAC-AAAATTTATACT
* * * *
14382 CTTCTTCCAACATGGTGATAGCGCTTCCAA-TGACAAAATTTACACC
1 C-TCTTCCAACATGGTGGTGGCGCTTCCAACTGACAAAATTTATACT
* *
14428 CTTTTCCAACAGGGTGGTGGCGCTTCCAAC
1 CTCTTCCAACATGGTGGTGGCGCTTCCAAC
14458 GTAAAAAAAA
Statistics
Matches: 203, Mismatches: 29, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
37 16 0.08
38 18 0.09
39 1 0.00
44 1 0.00
45 51 0.25
46 114 0.56
47 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (46 bp):
CTCTTCCAACATGGTGGTGGCGCTTCCAACTGACAAAATTTATACT
Found at i:14272 original size:38 final size:37
Alignment explanation
Indices: 14221--14293 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
14211 TTCCAACATG
14221 GTGGTGGCGCTTCCAACAGACAAAATTTATACTCTCTT
1 GTGGTGGCGCTTCCAAC-GACAAAATTTATACTCTCTT
**
14259 GTGGTGGCGCTTCCAACGACATTATTTATACTCTC
1 GTGGTGGCGCTTCCAACGACAAAATTTATACTCTC
14294 CTCCAACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 16 0.48
38 17 0.52
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (37 bp):
GTGGTGGCGCTTCCAACGACAAAATTTATACTCTCTT
Found at i:16154 original size:3 final size:3
Alignment explanation
Indices: 16146--16170 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16136 TGGATCCACG
16146 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
16171 AATTAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:19516 original size:70 final size:68
Alignment explanation
Indices: 19365--19516 Score: 180
Period size: 70 Copynumber: 2.2 Consensus size: 68
19355 TAGGAAAGTT
* * ** * *
19365 CAACT-CTCGCCCAGATGTTGTCAACTCCGGCCAGGACTTGTGCTGTTTAGAACGGATAAAATTC
1 CAACTCCT-GCCCAGATGTTGTCAACTCCGCCCAGGACTTGTGCTGTTAAGAACACAGAAAATCC
19429 AAAA
65 AAAA
** *
19433 CAACTCCAACCCAGATGTTGTCAACTCTTGCCCAGGACTTGTGCTGTTAAGAAACACAGAAAATC
1 CAACTCCTGCCCAGATGTTGTCAACTC-CGCCCAGGACTTGTGCTGTTAAG-AACACAGAAAATC
*
19498 CAGAA
64 CAAAA
19503 CAACTCCTGCCCAG
1 CAACTCCTGCCCAG
19517 GTCTTATTGC
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
68 23 0.33
69 21 0.30
70 25 0.36
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.22
Consensus pattern (68 bp):
CAACTCCTGCCCAGATGTTGTCAACTCCGCCCAGGACTTGTGCTGTTAAGAACACAGAAAATCCA
AAA
Found at i:24962 original size:113 final size:115
Alignment explanation
Indices: 24716--24962 Score: 290
Period size: 113 Copynumber: 2.2 Consensus size: 115
24706 TGATTAAACG
* * ** * * *
24716 TGACAACTTCTGATGACAATAACGGTTTAAAATTCATTGTGTATATGGAAACTTTCGGTGTCAAT
1 TGACAACTTCTGATGTCAACAACAATTTAAAATTCATGGTGTATATGGAAACTTCCAGTGTCAAT
* *
24781 TGAAAAAAACAAAATTATGTCAACTTCTGATGCCAATTGGAAATTACTTA
66 AGAAAAAAACAAAACTATGTCAACTTCTGATGCCAATTGGAAATTACTTA
*
24831 TGACAACTTCTGATGTCAACAACAATTTAAAATTCATGGTTTATAT-GACAACTTCCAGTGTCAA
1 TGACAACTTCTGATGTCAACAACAATTTAAAATTCATGGTGTATATGGA-AACTTCCAGTGTCAA
* * *
24895 -AG-AAAAAACAAAACTAT-TATAACTTCAT-ATGTCAATTGGAAATTAGTTA
65 TAGAAAAAAACAAAACTATGT-CAACTTC-TGATGCCAATTGGAAATTACTTA
*
24944 TGATAACTTCTAGA-GTCAA
1 TGACAACTTCT-GATGTCAA
24963 TTGAAAAATA
Statistics
Matches: 114, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
112 1 0.01
113 54 0.47
114 6 0.05
115 53 0.46
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (115 bp):
TGACAACTTCTGATGTCAACAACAATTTAAAATTCATGGTGTATATGGAAACTTCCAGTGTCAAT
AGAAAAAAACAAAACTATGTCAACTTCTGATGCCAATTGGAAATTACTTA
Found at i:27266 original size:103 final size:103
Alignment explanation
Indices: 27087--27295 Score: 409
Period size: 103 Copynumber: 2.0 Consensus size: 103
27077 GAGAAGAGAG
27087 GAACCCGCAAACTGGAAAATAATAGTTTCCTAGCCGCCGACCATGCACCGAGAGCTCCTCCCCTT
1 GAACCCGCAAACTGGAAAATAATAGTTTCCTAGCCGCCGACCATGCACCGAGAGCTCCTCCCCTT
27152 CAATTCACCGGCATAGAGAGAAACATCACAAACCCAAT
66 CAATTCACCGGCATAGAGAGAAACATCACAAACCCAAT
*
27190 GAACCCGCAGACTGGAAAATAATAGTTTCCTAGCCGCCGACCATGCACCGAGAGCTCCTCCCCTT
1 GAACCCGCAAACTGGAAAATAATAGTTTCCTAGCCGCCGACCATGCACCGAGAGCTCCTCCCCTT
27255 CAATTCACCGGCATAGAGAGAAACATCACAAACCCAAT
66 CAATTCACCGGCATAGAGAGAAACATCACAAACCCAAT
27293 GAA
1 GAA
27296 GCATCAGATT
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.34, C:0.33, G:0.17, T:0.16
Consensus pattern (103 bp):
GAACCCGCAAACTGGAAAATAATAGTTTCCTAGCCGCCGACCATGCACCGAGAGCTCCTCCCCTT
CAATTCACCGGCATAGAGAGAAACATCACAAACCCAAT
Found at i:29752 original size:23 final size:23
Alignment explanation
Indices: 29726--29772 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
29716 TCATAACCGA
29726 GTGACCCGAGACCCGAATGACCT
1 GTGACCCGAGACCCGAATGACCT
* *
29749 GTGACCCGAGACCTGTATGACCT
1 GTGACCCGAGACCCGAATGACCT
29772 G
1 G
29773 AAACTCGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.23, C:0.32, G:0.28, T:0.17
Consensus pattern (23 bp):
GTGACCCGAGACCCGAATGACCT
Found at i:42276 original size:21 final size:21
Alignment explanation
Indices: 42231--42277 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
42221 TTCAAAATAA
* *
42231 AATAAAAACTACCCATTTTAG
1 AATAAAAACTACCCAATATAG
42252 -ATAAAAACTACCCAATATAG
1 AATAAAAACTACCCAATATAG
42272 AATAAA
1 AATAAA
42278 TACAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.55, C:0.17, G:0.04, T:0.23
Consensus pattern (21 bp):
AATAAAAACTACCCAATATAG
Found at i:42351 original size:17 final size:18
Alignment explanation
Indices: 42308--42349 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
42298 ATATTATTTT
42308 AAAAAAACTACCTATTAA
1 AAAAAAACTACCTATTAA
*
42326 AAAAAAACTATCTATTAA
1 AAAAAAACTACCTATTAA
42344 AAAAAA
1 AAAAAA
42350 CTGTCACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAAAACTACCTATTAA
Found at i:43932 original size:23 final size:24
Alignment explanation
Indices: 43864--43936 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
43854 AGGCATTGCC
* *
43864 CTGA-TTTTAGGCTTGCTCAGTTT
1 CTGAGTTTTAGGCATGCTCTGTTT
*
43887 CTGAGTTTTAGGCATGCTATGTTT
1 CTGAGTTTTAGGCATGCTCTGTTT
43911 CTGAGTTTTA-GCATGCTCTGTTT
1 CTGAGTTTTAGGCATGCTCTGTTT
43934 CTG
1 CTG
43937 TTAAATGTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.42
24 26 0.58
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.47
Consensus pattern (24 bp):
CTGAGTTTTAGGCATGCTCTGTTT
Found at i:47623 original size:12 final size:12
Alignment explanation
Indices: 47494--47625 Score: 140
Period size: 12 Copynumber: 11.0 Consensus size: 12
47484 TTCACCATCC
* *
47494 CTTTCTGCAGCT
1 CTTTCTTCAACT
47506 CTTTCTTCAACT
1 CTTTCTTCAACT
*
47518 CTTTCTTCAACC
1 CTTTCTTCAACT
*
47530 CTTAT-TTCAAAT
1 CTT-TCTTCAACT
47542 CTTTCTTCAACT
1 CTTTCTTCAACT
*
47554 ATTTCTTCAACT
1 CTTTCTTCAACT
* *
47566 CTTTCTTGAACC
1 CTTTCTTCAACT
*
47578 CTTTCTTGAACT
1 CTTTCTTCAACT
* *
47590 CTTTCTTGAACC
1 CTTTCTTCAACT
*
47602 CTTTCTTCAACC
1 CTTTCTTCAACT
*
47614 CTTTCATCAACT
1 CTTTCTTCAACT
47626 GGATCTGGAG
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
11 1 0.01
12 101 0.98
13 1 0.01
ACGTcount: A:0.19, C:0.32, G:0.04, T:0.45
Consensus pattern (12 bp):
CTTTCTTCAACT
Found at i:48823 original size:16 final size:16
Alignment explanation
Indices: 48798--48833 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
48788 GGTTAATGGG
48798 TTTTTATTTTATTTTC
1 TTTTTATTTTATTTTC
* *
48814 TTTTTCTTTTTTTTTC
1 TTTTTATTTTATTTTC
48830 TTTT
1 TTTT
48834 GCCGCTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.08, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTATTTTATTTTC
Found at i:55706 original size:12 final size:12
Alignment explanation
Indices: 55689--55713 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55679 AACTCATGCC
55689 GTGGGTTCCCTT
1 GTGGGTTCCCTT
55701 GTGGGTTCCCTT
1 GTGGGTTCCCTT
55713 G
1 G
55714 CTTCTTGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.36, T:0.40
Consensus pattern (12 bp):
GTGGGTTCCCTT
Found at i:56767 original size:29 final size:32
Alignment explanation
Indices: 56734--56795 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
56724 GTTCTAAGTT
*
56734 TGGTTTCTTT-TCA-ATG-CTATCTCATTTAA
1 TGGTTTCTTTAGCATATGACTATCTCATTTAA
* *
56763 TGGTTTGTTTAGCATATGACTATGTCATTTAA
1 TGGTTTCTTTAGCATATGACTATCTCATTTAA
56795 T
1 T
56796 CAATAGGGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 9 0.33
30 2 0.07
31 3 0.11
32 13 0.48
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.50
Consensus pattern (32 bp):
TGGTTTCTTTAGCATATGACTATCTCATTTAA
Found at i:57618 original size:6 final size:6
Alignment explanation
Indices: 57599--57637 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
57589 TTCAAGCTGC
*
57599 ATCACA ATCGCA ATCACA ATCACA ATCACA ATCACA ATC
1 ATCACA ATCACA ATCACA ATCACA ATCACA ATCACA ATC
57638 TTGCCAACAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.46, C:0.33, G:0.03, T:0.18
Consensus pattern (6 bp):
ATCACA
Found at i:57692 original size:38 final size:38
Alignment explanation
Indices: 57636--57826 Score: 292
Period size: 38 Copynumber: 5.0 Consensus size: 38
57626 ACAATCACAA
* *
57636 TCTTGCCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCGCGGGTCCAC
*
57674 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCGCGGGTCCAC
* *
57712 TCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCTAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCGCGGGTCCAC
* * *
57750 TTTTACCAGCAGTTTAACCCCCTGAGGCGTGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCGCGGGTCCAC
* *
57788 TCTTACCATCAGTTTAACCCCCTGAGGCGCGGTTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCGCGGGTCCAC
57826 T
1 T
57827 ATGCACAGCC
Statistics
Matches: 141, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 141 1.00
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.25
Consensus pattern (38 bp):
TCTTACCAACAGTTTAACCCCCTGAGGCGCGGGTCCAC
Done.