Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011187.1 Corchorus capsularis cultivar CVL-1 contig11208, 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: 47451
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3913 original size:23 final size:25
Alignment explanation
Indices: 3861--3914 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
3851 GGAGTCTTTA
*
3861 TTTTTAGTAAATTGTTTGGTTTACT
1 TTTTTAATAAATTGTTTGGTTTACT
*
3886 ATTTTAATAAATT-TTT-GTTTA-T
1 TTTTTAATAAATTGTTTGGTTTACT
3908 GTTTTTA
1 -TTTTTA
3915 TGCATCATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 1 0.04
23 10 0.40
24 3 0.12
25 11 0.44
ACGTcount: A:0.24, C:0.02, G:0.11, T:0.63
Consensus pattern (25 bp):
TTTTTAATAAATTGTTTGGTTTACT
Found at i:9108 original size:15 final size:15
Alignment explanation
Indices: 9090--9118 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9080 GAAAACTCAG
9090 AAGAATCAATATCTA
1 AAGAATCAATATCTA
9105 AAGAATCAATATCT
1 AAGAATCAATATCT
9119 GAAGTATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (15 bp):
AAGAATCAATATCTA
Found at i:12508 original size:13 final size:13
Alignment explanation
Indices: 12487--12516 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12477 GAGAAGACAC
*
12487 TTTTGGGTTTTGA
1 TTTTAGGTTTTGA
12500 TTTTAGGTTTTGA
1 TTTTAGGTTTTGA
12513 TTTT
1 TTTT
12517 GGATTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.00, G:0.23, T:0.67
Consensus pattern (13 bp):
TTTTAGGTTTTGA
Found at i:15611 original size:41 final size:41
Alignment explanation
Indices: 15554--15633 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
15544 GACATCTAAT
* *
15554 TAGGGATAAAGGGAGTATAATCTTTTCCATTTTCTCTAAGG
1 TAGGGACAAAGAGAGTATAATCTTTTCCATTTTCTCTAAGG
15595 TAGGGACAAAGAGAGTATAATCTTTTCCATTTTCTCTAA
1 TAGGGACAAAGAGAGTATAATCTTTTCCATTTTCTCTAA
15634 TGTATTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (41 bp):
TAGGGACAAAGAGAGTATAATCTTTTCCATTTTCTCTAAGG
Found at i:16916 original size:11 final size:11
Alignment explanation
Indices: 16902--16933 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
16892 AATTAATATC
16902 TAATCTTCAGA
1 TAATCTTCAGA
*
16913 TAATCTCCAGA
1 TAATCTTCAGA
16924 TAATCTTCAG
1 TAATCTTCAG
16934 TTGAAATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (11 bp):
TAATCTTCAGA
Found at i:16964 original size:13 final size:13
Alignment explanation
Indices: 16926--16965 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
16916 TCTCCAGATA
* *
16926 ATCTTCAGTTGAA
1 ATCTTCTGTTGAT
*
16939 ATCTTCTGATGAT
1 ATCTTCTGTTGAT
16952 ATCTTCTGTTGAT
1 ATCTTCTGTTGAT
16965 A
1 A
16966 ATATTCTCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (13 bp):
ATCTTCTGTTGAT
Found at i:22932 original size:24 final size:24
Alignment explanation
Indices: 22887--22951 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
22877 GAGGAAAATC
* *
22887 AGTAAAACCATGATCATAAATCAT
1 AGTAAAACCAAGATAATAAATCAT
* * *
22911 AGTAAAATCAAGATAATCAATC-C
1 AGTAAAACCAAGATAATAAATCAT
22934 A--AAAACCAAGATAATAAA
1 AGTAAAACCAAGATAATAAA
22952 CCAAATCAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
21 15 0.44
23 1 0.03
24 18 0.53
ACGTcount: A:0.57, C:0.15, G:0.08, T:0.20
Consensus pattern (24 bp):
AGTAAAACCAAGATAATAAATCAT
Found at i:22955 original size:20 final size:21
Alignment explanation
Indices: 22914--22956 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
22904 AAATCATAGT
* *
22914 AAAATCAAGATAATCAATCCA
1 AAAACCAAGATAATCAAACCA
22935 AAAACCAAGATAAT-AAACCA
1 AAAACCAAGATAATCAAACCA
22955 AA
1 AA
22957 TCAGTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.63, C:0.19, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAACCAAGATAATCAAACCA
Found at i:37434 original size:37 final size:37
Alignment explanation
Indices: 37345--37434 Score: 101
Period size: 38 Copynumber: 2.4 Consensus size: 37
37335 ACTTTTTGTT
* * *
37345 TCCAATGTCCTATTTAATTTTGTCTTTTGTCTTTGTT
1 TCCAACGTCCTATTTAATTTTGTCTTTTGTCTTCGTC
* **
37382 TCTAATCGTTGTATTTAATTTTG-CTTTTTGTCTTCGTC
1 TCCAA-CGTCCTATTTAATTTTGTC-TTTTGTCTTCGTC
37420 TCCAACGTCCTATTT
1 TCCAACGTCCTATTT
37435 GGGGTTAGAT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
37 13 0.31
38 29 0.69
ACGTcount: A:0.14, C:0.19, G:0.11, T:0.56
Consensus pattern (37 bp):
TCCAACGTCCTATTTAATTTTGTCTTTTGTCTTCGTC
Found at i:37584 original size:22 final size:22
Alignment explanation
Indices: 37492--37611 Score: 102
Period size: 22 Copynumber: 5.5 Consensus size: 22
37482 TGGTCCAATT
* * *
37492 TCAAAATTTTAAAGCGAGGTTA
1 TCAAAATTTCATAGAGAGGTTA
* * *
37514 TCAAAATTACATA-ATGTGATTA
1 TCAAAATTTCATAGA-GAGGTTA
*
37536 TCAAAATTTCATAGAG-GGATCA
1 TCAAAATTTCATAGAGAGG-TTA
* *
37558 ACAAAATTTGATAGAGAGGTTA
1 TCAAAATTTCATAGAGAGGTTA
*
37580 TC-AAATTTCATAAAGAGGTTA
1 TCAAAATTTCATAGAGAGGTTA
*
37601 TCAAATTTTCA
1 TCAAAATTTCA
37612 AAATGTGATT
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
21 20 0.26
22 54 0.70
23 3 0.04
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
TCAAAATTTCATAGAGAGGTTA
Found at i:37764 original size:22 final size:22
Alignment explanation
Indices: 37736--38298 Score: 183
Period size: 22 Copynumber: 25.7 Consensus size: 22
37726 TCAGGGAGGA
*
37736 TATCAAAATTTTATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
37758 TATCAAAATTTCATAATTTA-GT
1 TATCAAAATTTCAT-ATGAAGGT
* * * *
37780 TTTCAAAATTTCAGAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
37802 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * * *
37823 AGATCAAACTTT-ATTAGGGAGAT
1 -TATCAAAATTTCA-TATGAAGGT
* *
37846 TAACAAAATTTCATATGAA-AT
1 TATCAAAATTTCATATGAAGGT
** * *
37867 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
37889 TATCAAAATTT-GTAT--A-GT
1 TATCAAAATTTCATATGAAGGT
* * * *
37907 TATTAAGATTTCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * * *
37929 TATCAAAATTTTATAGGGAGATT
1 TATCAAAATTTCATATGAAG-GT
* *
37952 TATCAAAATTTTATA-GTAAGTTT
1 TATCAAAATTTCATATG-AAG-GT
37975 TATCAAAATTTCATA-GCAAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
37997 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
38019 TATCAAAATTTCAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
38041 TACTGACAA-TTCATATGGAGGT
1 TA-TCAAAATTTCATATGAAGGT
* * * * *
38063 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
38085 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* **
38107 TATCAACATCTT-ATAGTGTTGGT
1 TATCAAAAT-TTCATA-TGAAGGT
*
38130 TATCAAAATTTCATTTGGAA-GT
1 TATCAAAATTTCATAT-GAAGGT
*
38152 TAACAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * * *
38174 CT-TCGAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
38196 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** * **
38218 TAAAAAAATTTTATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * **
38240 TCTCGAAATTCCATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
** *
38262 TATTGAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
38284 TATCAAAATTTCATA
1 TATCAAAATTTCATA
38299 AGGACGTCAT
Statistics
Matches: 399, Mismatches: 111, Indels: 62
0.70 0.19 0.11
Matches are distributed among these distances:
18 11 0.03
19 3 0.01
21 34 0.09
22 279 0.70
23 71 0.18
24 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:37958 original size:23 final size:23
Alignment explanation
Indices: 37928--38031 Score: 104
Period size: 23 Copynumber: 4.6 Consensus size: 23
37918 CATAAGGAGG
* **
37928 TTATCAAAATTTTATAGGGAGAT
1 TTATCAAAATTTCATAGTAAGAT
* *
37951 TTATCAAAATTTTATAGTAAGTT
1 TTATCAAAATTTCATAGTAAGAT
* *
37974 TTATCAAAATTTCATAGCAAG-G
1 TTATCAAAATTTCATAGTAAGAT
* **
37996 TTATCACAATTTCATAGTGTGA-
1 TTATCAAAATTTCATAGTAAGAT
38018 TTATCAAAATTTCA
1 TTATCAAAATTTCA
38032 GAGTGTGATT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
22 30 0.43
23 39 0.57
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTCATAGTAAGAT
Found at i:38168 original size:45 final size:45
Alignment explanation
Indices: 38081--38169 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
38071 TTTCATAACG
* * * *
38081 TGGTTATCAATATATCATATGGAGGTTATCAACATCTTATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTAACAAAATCTTATAGTGT
* *
38126 TGGTTATCAAAATTTCATTTGGAAGTTAACAAAAT-TTCATAGTG
1 TGGTTATCAAAATATCATATGGAAGTTAACAAAATCTT-ATAGTG
38170 AGGTCTTCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
44 2 0.05
45 35 0.95
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTAACAAAATCTTATAGTGT
Found at i:38342 original size:62 final size:62
Alignment explanation
Indices: 38268--38420 Score: 234
Period size: 62 Copynumber: 2.5 Consensus size: 62
38258 TCGTTATTGA
* *
38268 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCTT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATAATCAT
* * *
38330 AATTTCATAGGAATGTTATCAAAATTTCATAAGGATGTCATCAAAAATAGTGTAATAATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATAATCAT
* *
38392 AATTTTAATAGGAAGGTTATCATAATTTC
1 AA-TTTCATAGGAAGGTTATCAAAATTTC
38421 GTATGAATAT
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
62 59 0.72
63 23 0.28
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (62 bp):
AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATAATCAT
Found at i:38377 original size:23 final size:22
Alignment explanation
Indices: 38330--38375 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
38320 TAATTATCTT
*
38330 AATTTCATAGGAATGTTATCAA
1 AATTTCATAGGAATGTCATCAA
38352 AATTTCATAAGG-ATGTCATCAA
1 AATTTCAT-AGGAATGTCATCAA
38374 AA
1 AA
38376 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (22 bp):
AATTTCATAGGAATGTCATCAA
Found at i:38572 original size:30 final size:31
Alignment explanation
Indices: 38513--38581 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
38503 GGGGAAACTT
*
38513 TATATTTTTCGATTGTACCCTTATTTTTAAAA
1 TATA-TTTTCAATTGTACCCTTATTTTTAAAA
38545 TATATTTTCAATTGTACCCTT-TTTTTAAAA
1 TATATTTTCAATTGTACCCTTATTTTTAAAA
*
38575 CATATTT
1 TATATTT
38582 CTAAATTGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 15 0.43
31 16 0.46
32 4 0.11
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.54
Consensus pattern (31 bp):
TATATTTTCAATTGTACCCTTATTTTTAAAA
Found at i:38589 original size:31 final size:31
Alignment explanation
Indices: 38524--38589 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
38514 ATATTTTTCG
* *
38524 ATTGTACCCTTATTTTTAAAATATATTTTCA
1 ATTGTACCCTTATTTTTAAAACATATTTTAA
38555 ATTGTACCCTT-TTTTTAAAACATATTTCTAA
1 ATTGTACCCTTATTTTTAAAACATATTT-TAA
38586 ATTG
1 ATTG
38590 CCATTACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.50
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTTAA
Found at i:39161 original size:23 final size:23
Alignment explanation
Indices: 39133--39200 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
39123 ATAGACAAAG
39133 CTCTCACAAAGGAGTTCCAAAAA
1 CTCTCACAAAGGAGTTCCAAAAA
* *
39156 CTCTCACAAAGGAGTACCAAAAG
1 CTCTCACAAAGGAGTTCCAAAAA
*
39179 CTCTCACATAGGAGTTCCAAAA
1 CTCTCACAAAGGAGTTCCAAAA
39201 TAAACAAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.18
Consensus pattern (23 bp):
CTCTCACAAAGGAGTTCCAAAAA
Found at i:39485 original size:22 final size:22
Alignment explanation
Indices: 39460--39506 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
39450 CCAATGTCCT
39460 TAGTG-TGATTACCAAAATTTCA
1 TAGTGTTG-TTACCAAAATTTCA
39482 TAGTGTTGTTACCAAAATTTCA
1 TAGTGTTGTTACCAAAATTTCA
39504 TAG
1 TAG
39507 GATCAGGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TAGTGTTGTTACCAAAATTTCA
Found at i:39522 original size:24 final size:22
Alignment explanation
Indices: 39473--39553 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 22
39463 TGTGATTACC
* **
39473 AAAATTTCATAGTGT-TGTTACC
1 AAAATTTCATAG-GTAGGTTATT
39495 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGG-T-AGGTTATT
* *
39519 AAAATTTCTTAGGTTGGTTATT
1 AAAATTTCATAGGTAGGTTATT
* *
39541 GAAATTTTATAGG
1 AAAATTTCATAGG
39554 GTGGTTAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.02
22 30 0.62
23 1 0.02
24 16 0.33
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (22 bp):
AAAATTTCATAGGTAGGTTATT
Found at i:39540 original size:22 final size:22
Alignment explanation
Indices: 39512--39578 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 22
39502 CATAGGATCA
*
39512 GGTTATTAAAATTTCT-TAGGTT
1 GGTTATTAAAATTT-TATAGGGT
*
39534 GGTTATTGAAATTTTATAGGGT
1 GGTTATTAAAATTTTATAGGGT
39556 GGTTAATTATCACAATTTTATAG
1 GGTT-ATTA--A-AATTTTATAG
39579 AAAGGTTATC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.03
22 22 0.59
23 3 0.08
25 1 0.03
26 10 0.27
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.46
Consensus pattern (22 bp):
GGTTATTAAAATTTTATAGGGT
Found at i:39650 original size:22 final size:22
Alignment explanation
Indices: 39592--39650 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
39582 GGTTATCAAA
* *
39592 GAGATTATCAAAATGTCATAGC
1 GAGATTAACAAAATTTCATAGC
*
39614 GAGATT-ACAAAAATTTCATAGT
1 GAGATTAAC-AAAATTTCATAGC
*
39636 GTGATTAACAAAATT
1 GAGATTAACAAAATT
39651 CCATTAGGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 28 0.90
23 2 0.06
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (22 bp):
GAGATTAACAAAATTTCATAGC
Found at i:39768 original size:20 final size:23
Alignment explanation
Indices: 39736--39808 Score: 57
Period size: 25 Copynumber: 3.3 Consensus size: 23
39726 TAAGGAGTAC
* *
39736 CAAAATTTGATAGAAG-G-TTAT
1 CAAAATCTCATAGAAGTGATTAT
39757 C-AAATCTCATAG-AGTGATTAT
1 CAAAATCTCATAGAAGTGATTAT
*
39778 CAAAATTTCATAGATA-TCAGATTAT
1 CAAAATCTCATAGA-AGT--GATTAT
39803 CAAAAT
1 CAAAAT
39809 TTATAGGAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
19 2 0.05
20 10 0.24
21 6 0.14
22 10 0.24
23 1 0.02
24 1 0.02
25 12 0.29
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (23 bp):
CAAAATCTCATAGAAGTGATTAT
Found at i:39788 original size:22 final size:22
Alignment explanation
Indices: 39719--39991 Score: 124
Period size: 22 Copynumber: 12.5 Consensus size: 22
39709 TAAAAGTCTC
* *
39719 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
*
39739 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
*
39759 AATCTCATAGAGTGATTATCAA
1 AATTTCATAGAGTGATTATCAA
*
39781 AATTTCATAGATATCAGATTATCAA
1 AATTTCATAGA-GT--GATTATCAA
*
39806 AATTT-ATAG-G-AATTATCAA
1 AATTTCATAGAGTGATTATCAA
*
39825 AATTTCATAGTGTTG-TTATCAA
1 AATTTCATAGAG-TGATTATCAA
*
39847 AATTTCAAAACGAG-G-TTATCAA
1 AATTTC-ATA-GAGTGATTATCAA
* *
39869 AATTACATA-ATGTGATTATCAG
1 AATTTCATAGA-GTGATTATCAA
* * * *
39891 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* * *
39913 AATTTTATAAAGAGGTAATTGTCAA
1 AATTTCAT--AGA-GTGATTATCAA
* * *
39938 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* * *
39960 ATTTTCA-AAATGTTATTA-CAAA
1 AATTTCATAGA-GTGATTATC-AA
39982 AATTTCATAG
1 AATTTCATAG
39992 TGGTATTTCT
Statistics
Matches: 189, Mismatches: 40, Indels: 45
0.69 0.15 0.16
Matches are distributed among these distances:
19 16 0.08
20 23 0.12
21 16 0.08
22 92 0.49
23 7 0.04
24 9 0.05
25 26 0.14
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:40097 original size:20 final size:20
Alignment explanation
Indices: 40072--40123 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
40062 TTATGAAGTA
40072 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
40092 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
40112 ATCACAATTTCA
1 ATCAAAATTTCA
40124 TAGTTTAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:40317 original size:23 final size:23
Alignment explanation
Indices: 40280--40359 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
40270 CATAAGAAAG
40280 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* * *
40303 TTTTCAGAATTTTAT-GGGAAGAT
1 TTATCAAAATTTTATAGGG-AGGT
* *
40326 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGGGAGGT
*
40348 TTATCACAATTT
1 TTATCAAAATTT
40360 CATAATGTGG
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
22 14 0.30
23 30 0.65
24 2 0.04
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:40352 original size:22 final size:21
Alignment explanation
Indices: 40072--40496 Score: 141
Period size: 22 Copynumber: 19.7 Consensus size: 21
40062 TTATGAAGTA
*
40072 ATCAAAATTTCA-AGGAGGAT
1 ATCAAAATTTCATAGGAGGTT
* *
40092 ATCAAAATTTCA-GGGAGGAT
1 ATCAAAATTTCATAGGAGGTT
* *
40112 ATCACAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG--GAGGTT
* *
40134 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATAGGA-GGTT
* ***
40156 ATCAAAATTTCATAGTATGCAG
1 ATCAAAATTTCATAGGA-GGTT
*
40178 ATCAAAATTTCATAGCGAGATT
1 ATCAAAATTTCATAG-GAGGTT
* ** *
40200 AACAAAATTTCATAATAAGGGT
1 ATCAAAATTTCAT-AGGAGGTT
** *
40222 ATCAAAAAATCATAGGGAGATT
1 ATCAAAATTTCATA-GGAGGTT
*
40244 ATCAAAA-TT--T-GTA-GTT
1 ATCAAAATTTCATAGGAGGTT
* * * *
40260 ATCAAGAGTTCATAAGAAAGTT
1 ATCAAAATTTCAT-AGGAGGTT
*
40282 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA-GGAGG-TT
* * * * *
40305 TTCAGAATTTTATGGGAAGATTT
1 ATCAAAATTTCATAGG-AG-GTT
40328 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAG-GAGGTT
* * *
40350 ATCACAATTTCATAATGTGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* * * *
40372 ATCAAAATGTCAGAGTGTGATT
1 ATCAAAATTTCATAG-GAGGTT
*
40394 A-CTAACAA-TTCATATGGAGCTT
1 ATC-AA-AATTTCATA-GGAGGTT
* * * * * *
40416 TTTAAATTTTCGTAACGTGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* *
40438 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATA-GGAGGTT
* * *
40460 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-G-AGGTT
40483 ATCAAAATTTCATA
1 ATCAAAATTTCATA
40497 TTGAGTTCTT
Statistics
Matches: 292, Mismatches: 83, Indels: 57
0.68 0.19 0.13
Matches are distributed among these distances:
16 8 0.03
17 4 0.01
19 2 0.01
20 31 0.11
21 11 0.04
22 181 0.62
23 54 0.18
24 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGGTT
Found at i:40567 original size:21 final size:22
Alignment explanation
Indices: 40522--40568 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
40512 TTCTTTATGG
* * *
40522 AGGTTAACAAATTTTCATAAGA
1 AGGTTAAAAAAATTTCATAAAA
40544 AGGTTAAAAAAATTT-ATAAAA
1 AGGTTAAAAAAATTTCATAAAA
40565 AGGT
1 AGGT
40569 ACTCGAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAAA
Done.