Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014838.1 Corchorus capsularis cultivar CVL-1 contig14859, 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: 38492
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Found at i:10688 original size:33 final size:32
Alignment explanation
Indices: 10591--10731 Score: 122
Period size: 33 Copynumber: 4.3 Consensus size: 32
10581 TTGCAAAGAG
* * *
10591 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTT-GGTGTTGTTTGCGATGAAACTAAATC
** * *
10624 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
1 TGTTTTG-GTGTTGTTTGCGATGAAACTAAATC
*
10657 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
1 TGTTTT-GGTGTTGTTTGCGATGAAACTAAATC
* ** *
10690 TGTTTTGGATGCTAATTGTGATGAAAAC-AAATC
1 TGTTTTGG-TGTTGTTTGCGATG-AAACTAAATC
10723 TGTTTTGGT
1 TGTTTTGGT
10732 TGATCATAGC
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
32 4 0.04
33 81 0.90
34 5 0.06
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (32 bp):
TGTTTTGGTGTTGTTTGCGATGAAACTAAATC
Found at i:10758 original size:33 final size:33
Alignment explanation
Indices: 10711--10784 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
10701 CTAATTGTGA
* *
10711 TGAAAACAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
10744 TGCAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
10777 TGAAAATA
1 TGAAAATA
10785 GGACTGTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
Found at i:10792 original size:33 final size:33
Alignment explanation
Indices: 10722--10793 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
10712 GAAAACAAAT
* **
10722 CTGTTTTGGTTGATCATAGCATTGCAAATAATT
1 CTGTTTTGGTTGATCATAGCATTGAAAATAAGA
*
10755 CTGTTTTGGTTGATCATAGCATTGAAAATAGGA
1 CTGTTTTGGTTGATCATAGCATTGAAAATAAGA
10788 CTGTTT
1 CTGTTT
10794 CGGGTGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (33 bp):
CTGTTTTGGTTGATCATAGCATTGAAAATAAGA
Found at i:16289 original size:7 final size:7
Alignment explanation
Indices: 16277--16331 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
16267 TGGGTTTTAA
16277 TAATTAG
1 TAATTAG
16284 TAATTAG
1 TAATTAG
*
16291 CAATTAG
1 TAATTAG
16298 TAACTTA-
1 TAA-TTAG
*
16305 AAATTAG
1 TAATTAG
* *
16312 -ATTTGG
1 TAATTAG
16318 TAATTAG
1 TAATTAG
16325 TAATTAG
1 TAATTAG
16332 CAATATTTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
6 7 0.18
7 28 0.74
8 3 0.08
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.40
Consensus pattern (7 bp):
TAATTAG
Found at i:16297 original size:14 final size:14
Alignment explanation
Indices: 16278--16335 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
16268 GGGTTTTAAT
16278 AATTAGTAATTAGC
1 AATTAGTAATTAGC
*
16292 AATTAGTAACTTA-A
1 AATTAGTAA-TTAGC
* * *
16306 AATTAG-ATTTGGT
1 AATTAGTAATTAGC
16319 AATTAGTAATTAGC
1 AATTAGTAATTAGC
16333 AAT
1 AAT
16336 ATTTAGTAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
12 2 0.06
13 7 0.21
14 22 0.65
15 3 0.09
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (14 bp):
AATTAGTAATTAGC
Found at i:17132 original size:44 final size:44
Alignment explanation
Indices: 17095--17182 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
17085 TTTTCAAATT
*
17095 GAACATTTTCAAT-TTAAGTAATTCCAAAAGAAGATTTTGGAAAAC
1 GAACATTTTC--TCTTAAGTAATTCCAAAAGAAGATTTTGCAAAAC
* * *
17140 GAAGATTTTCTCTTAAGTGATTCCAAAAGAAGATTTTGGAAAA
1 GAACATTTTCTCTTAAGTAATTCCAAAAGAAGATTTTGCAAAA
17183 TAAAAGTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
43 1 0.03
44 30 0.75
45 9 0.22
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (44 bp):
GAACATTTTCTCTTAAGTAATTCCAAAAGAAGATTTTGCAAAAC
Found at i:17215 original size:39 final size:43
Alignment explanation
Indices: 17107--17220 Score: 146
Period size: 44 Copynumber: 2.7 Consensus size: 43
17097 ACATTTTCAA
**
17107 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACGAAGATTTTC
1 TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACGAAGAAGTTC
* *
17150 TCTTAAGTGATTCCAAAAGAAGATTTTGGAAAA-TAA-AAGTT-
1 T-TTAAGTAATTCCAAAAGAAGATTTTGGAAAACGAAGAAGTTC
*
17191 TTTAA-TAAATCCAAAAGAAGATTTTGGAAA
1 TTTAAGTAATTCCAAAAGAAGATTTTGGAAA
17221 TTAATAAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
39 23 0.36
40 4 0.06
41 1 0.02
42 3 0.05
43 3 0.05
44 30 0.47
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (43 bp):
TTTAAGTAATTCCAAAAGAAGATTTTGGAAAACGAAGAAGTTC
Found at i:20049 original size:14 final size:14
Alignment explanation
Indices: 20004--20055 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
19994 ACAAGAGTCT
* *
20004 TTTTCAAAAAAATG
1 TTTTCAAGAAAAGG
20018 TTTTCAAGAAAAGG
1 TTTTCAAGAAAAGG
*
20032 TTTTCAA-AAATGG
1 TTTTCAAGAAAAGG
20045 ATTTTCAAGAA
1 -TTTTCAAGAA
20056 GGTTTTGAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 5 0.15
14 26 0.79
15 2 0.06
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (14 bp):
TTTTCAAGAAAAGG
Found at i:20057 original size:26 final size:25
Alignment explanation
Indices: 20011--20061 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
20001 TCTTTTTCAA
20011 AAAAATGTTTTCAAGAAAAGGTTTTC
1 AAAAATGTTTTCAAG-AAAGGTTTTC
20037 AAAAATGGATTTTCAAG-AAGGTTTT
1 AAAAAT-G-TTTTCAAGAAAGGTTTT
20062 GAGTCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 14 0.61
27 1 0.04
28 8 0.35
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (25 bp):
AAAAATGTTTTCAAGAAAGGTTTTC
Found at i:20687 original size:8 final size:7
Alignment explanation
Indices: 20668--20748 Score: 83
Period size: 7 Copynumber: 11.0 Consensus size: 7
20658 ACATTCAACT
20668 GAAAAAA
1 GAAAAAA
*
20675 -AAAAGA
1 GAAAAAA
*
20681 GAAAAAG
1 GAAAAAA
20688 GAAAAAA
1 GAAAAAA
20695 GAAAAAA
1 GAAAAAA
20702 GGAAAAAA
1 -GAAAAAA
20710 GAAAAAA
1 GAAAAAA
*
20717 AAGAAAAA
1 GA-AAAAA
20725 GAAAAAA
1 GAAAAAA
20732 TGAAAGAAA
1 -GAAA-AAA
20741 TGAAAAAA
1 -GAAAAAA
20749 CTTGGCCTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
6 5 0.08
7 30 0.48
8 20 0.32
9 8 0.13
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (7 bp):
GAAAAAA
Found at i:20700 original size:15 final size:15
Alignment explanation
Indices: 20673--20748 Score: 91
Period size: 15 Copynumber: 4.9 Consensus size: 15
20663 CAACTGAAAA
20673 AAAAAAGAGAAAAAGG
1 AAAAAAGA-AAAAAGG
20689 AAAAAAGAAAAAAGG
1 AAAAAAGAAAAAAGG
*
20704 AAAAAAGAAAAAA-A
1 AAAAAAGAAAAAAGG
*
20718 AGAAAAAGAAAAAATG
1 A-AAAAAGAAAAAAGG
20734 AAAGAAATGAAAAAA
1 AAA-AAA-GAAAAAA
20749 CTTGGCCTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
14 1 0.02
15 34 0.63
16 12 0.22
17 7 0.13
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAAAAAGG
Found at i:20708 original size:23 final size:22
Alignment explanation
Indices: 20669--20748 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 22
20659 CATTCAACTG
*
20669 AAAA-AAAAAAGAGAAAAAGGAA
1 AAAAGAAAAAAG-GAAAAAAGAA
20691 AAAAGAAAAAAGGAAAAAAGAA
1 AAAAGAAAAAAGGAAAAAAGAA
*
20713 AAAA-AAGAAAAAGAAAAAATGAA
1 AAAAGAA-AAAAGGAAAAAA-GAA
20736 AGAAATGAAAAAA
1 A-AAA-GAAAAAA
20749 CTTGGCCTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
21 2 0.04
22 28 0.56
23 11 0.22
24 3 0.06
25 4 0.08
26 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (22 bp):
AAAAGAAAAAAGGAAAAAAGAA
Found at i:20741 original size:9 final size:8
Alignment explanation
Indices: 20672--20748 Score: 63
Period size: 8 Copynumber: 9.8 Consensus size: 8
20662 TCAACTGAAA
*
20672 AAAAAAAG
1 AAAAAATG
*
20680 AGAAAAAGG
1 A-AAAAATG
20689 AAAAAA-G
1 AAAAAATG
*
20696 AAAAAAGG
1 AAAAAATG
20704 AAAAAA-G
1 AAAAAATG
20711 AAAAAA--
1 AAAAAATG
*
20717 AAGAAAAAG
1 AA-AAAATG
20726 AAAAAATG
1 AAAAAATG
20734 AAAGAAATG
1 AAA-AAATG
20743 AAAAAA
1 AAAAAA
20749 CTTGGCCTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
6 2 0.03
7 18 0.30
8 24 0.39
9 17 0.28
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (8 bp):
AAAAAATG
Found at i:21302 original size:20 final size:19
Alignment explanation
Indices: 21266--21304 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
21256 CCCTAAAATA
* *
21266 AAAATTGTTTTTGCAAAAG
1 AAAAGTGTTTTTACAAAAG
21285 AAAAGTGTTTTTCACAAAAG
1 AAAAGTGTTTTT-ACAAAAG
21305 GTTTTCGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (19 bp):
AAAAGTGTTTTTACAAAAG
Found at i:21530 original size:9 final size:9
Alignment explanation
Indices: 21518--21544 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
21508 TTAGCATTAG
21518 GGTCATTTT
1 GGTCATTTT
21527 GGTCATTTT
1 GGTCATTTT
21536 GGTCATTTT
1 GGTCATTTT
21545 CGGCACCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.56
Consensus pattern (9 bp):
GGTCATTTT
Found at i:21924 original size:14 final size:14
Alignment explanation
Indices: 21905--21932 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
21895 GCATATTAAT
21905 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
21919 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
21933 ACTACTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:22144 original size:20 final size:20
Alignment explanation
Indices: 22119--22157 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
22109 AAATACAAGG
22119 CATTTGATTTACAAATTGGA
1 CATTTGATTTACAAATTGGA
22139 CATTTGATTTACAAATTGG
1 CATTTGATTTACAAATTGG
22158 TGCTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:22728 original size:19 final size:19
Alignment explanation
Indices: 22704--22741 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
22694 CTTTGCAGCG
22704 TGGATTTTACAATAGGAGA
1 TGGATTTTACAATAGGAGA
22723 TGGATTTTACAATAGGAGA
1 TGGATTTTACAATAGGAGA
22742 AAAGGGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (19 bp):
TGGATTTTACAATAGGAGA
Found at i:23052 original size:12 final size:12
Alignment explanation
Indices: 23037--23063 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
23027 TTGCATCATC
23037 CCATTCATCAAT
1 CCATTCATCAAT
23049 CCATTCATCAAT
1 CCATTCATCAAT
23061 CCA
1 CCA
23064 AAAAGGAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (12 bp):
CCATTCATCAAT
Found at i:24566 original size:50 final size:50
Alignment explanation
Indices: 24507--24849 Score: 286
Period size: 50 Copynumber: 6.9 Consensus size: 50
24497 ACCTTTGAAC
*
24507 AAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATG-CAATCTTCAAGT
1 AAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTC-ATCTTTAAGT
* * ** * **
24557 AAAAGATTGAATTTTTAAGTAATTAGTGAATAAAAATGAAACCTTTGGGT
1 AAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTCATCTTTAAGT
* * * *
24607 AAAAGATTGAATTTTT-AGTAATTAGTAAGTAAAAATGTCATCTCTAGGT
1 AAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTCATCTTTAAGT
* * * * **
24656 AAAAAATTGAAGTTTT-AGTAATTAGTAAGTAAAAATGTCATCTTTGGGT
1 AAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTCATCTTTAAGT
* * * * * * *
24705 AAAAGATGGAAACTTTTAA-TGATTAGTAAGTAAAGATGTCACCTTTGAGC
1 AAAAGATTG-AATTTTTAAGTAATTAGTAAATAAAGATGTCATCTTTAAGT
* * *
24755 AAAGGATTG-ATTTTTAGAGTAATTAGTAAATAGAGATGT-AACTTTTGAA-T
1 AAAAGATTGAATTTTTA-AGTAATTAGTAAATAAAGATGTCATC-TTT-AAGT
* * * *
24805 AAAAGATTGGATTTTTACAAATAATTAGTGAATAAAGATGACATC
1 AAAAGATTGAATTTTT--AAGTAATTAGTAAATAAAGATGTCATC
24850 CTGGATCATA
Statistics
Matches: 241, Mismatches: 41, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
48 6 0.02
49 81 0.34
50 125 0.52
51 8 0.03
52 18 0.07
53 3 0.01
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (50 bp):
AAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATGTCATCTTTAAGT
Found at i:24821 original size:99 final size:98
Alignment explanation
Indices: 24495--24849 Score: 331
Period size: 99 Copynumber: 3.6 Consensus size: 98
24485 AAGGAGGTCT
* * *
24495 TAACCTTTGAACAAAAGATTGAATTTTTAAGTAATTAGTAAATAAAGATG-CAATCTTCAAGTAA
1 TAACCTTTGAATAAAAGATTGAATTTTTAA-TAATTAGTAAGTAAAGATGTC-ATCTT-TAGTAA
*
24559 AAGATTGAATTTTTAAGTAATTAGTGAATAAAAATG
63 AAGATTGAATTTTTAAGTAATTAGTAAATAAAAATG
* ** * * *
24595 AAACCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAAGTAAAAATGTCATCTCTAGGTAAAA
1 TAACCTTTGAATAAAAGATTGAATTTTTAATAATTAGTAAGTAAAGATGTCATCTTTA-GTAAAA
* * *
24660 AATTGAAGTTTT-AGTAATTAGTAAGTAAAAATG
65 GATTGAATTTTTAAGTAATTAGTAAATAAAAATG
* * ** * * * * *
24693 TCATCTTTGGGTAAAAGATGGAAACTTTTAATGATTAGTAAGTAAAGATGTCACCTTTGAGCAAA
1 TAACCTTTGAATAAAAGATTG-AATTTTTAATAATTAGTAAGTAAAGATGTCATCTTT-AGTAAA
* * *
24758 GGATTG-ATTTTTAGAGTAATTAGTAAATAGAGATG
64 AGATTGAATTTTTA-AGTAATTAGTAAATAAAAATG
* * *
24793 TAACTTTTGAATAAAAGATTGGATTTTTACAAATAATTAGTGAA-TAAAGATGACATC
1 TAACCTTTGAATAAAAGATTGAATTTTT---AATAATTAGT-AAGTAAAGATGTCATC
24850 CTGGATCATA
Statistics
Matches: 204, Mismatches: 41, Indels: 18
0.78 0.16 0.07
Matches are distributed among these distances:
98 42 0.21
99 80 0.39
100 60 0.29
102 20 0.10
103 2 0.01
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34
Consensus pattern (98 bp):
TAACCTTTGAATAAAAGATTGAATTTTTAATAATTAGTAAGTAAAGATGTCATCTTTAGTAAAAG
ATTGAATTTTTAAGTAATTAGTAAATAAAAATG
Found at i:25795 original size:55 final size:55
Alignment explanation
Indices: 25688--25996 Score: 528
Period size: 55 Copynumber: 5.6 Consensus size: 55
25678 GATCAGTCCG
* * *
25688 AATAGTAATCAGTTAATCAGTAATTAAAGTAAAAAGAGATTAATTAGAGTCAAAGT
1 AATAGTAATCAGTAAATCAGTAATT-AAGTAAAAAGAGATTAATCAGAGTCAAGGT
25744 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
* *
25799 AATAGTAATTAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
* *
25854 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAAGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
25909 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
* *
25964 AATAGTAATCAGTAAATCAGTAATCAGGTAAAA
1 AATAGTAATCAGTAAATCAGTAATTAAGTAAAA
25997 GGTTAGTAAT
Statistics
Matches: 242, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
55 218 0.90
56 24 0.10
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (55 bp):
AATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
Found at i:26358 original size:43 final size:42
Alignment explanation
Indices: 26309--26639 Score: 180
Period size: 43 Copynumber: 7.7 Consensus size: 42
26299 GTAATTAGTA
26309 AAGAGTAAAATAGTAATCAGTAAAAAGTACGAA-GGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTA--AATGGTAATCAAC
* **
26352 AAGAGTAAAATAGTAGTCAGTAAAAAGTAAATGGTAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAATGGTAATCAAC
* * **
26394 AAGAGTAAAATAGT-A--A-T---AAGTAAAAGGAAATCAGT
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAATGGTAATCAAC
* * * * * **
26429 AAGAGTAAAA-AGGTGATCAGTAGAGAGTAAAAAGCTAATCAGT
1 AAGAGTAAAATA-GTAATCAGTAAAAAGT-AAATGGTAATCAAC
* * * *
26472 AAGAAGTAAAA-GGTAATCAGTAAAAAGCAAAAGGCAATCAGTA-
1 AAG-AGTAAAATAGTAATCAGTAAAAAGTAAATGGTAATCA--AC
* * * * *
26515 AAAAGTAAAAGAGTAATCAGTAAAAAAGAGCAGAAAAATAGTAATCAGTAA
1 AAGAGTAAAATAGTAATCAGT---AAA-A--AG-TAAATGGTAATCA--AC
* * *
26566 AAGAGTAAAATGGTAATCAGCAAAAAGTAAGAGGGTAATCAAC
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAA-ATGGTAATCAAC
* *
26609 AAGAGTAAAATAGAAATCAGTACAAAGTAAA
1 AAGAGTAAAATAGTAATCAGTAAAAAGTAAA
26640 GAATAATCAA
Statistics
Matches: 230, Mismatches: 35, Indels: 47
0.74 0.11 0.15
Matches are distributed among these distances:
34 1 0.00
35 28 0.12
36 1 0.00
38 2 0.01
39 2 0.01
41 2 0.01
42 43 0.19
43 93 0.40
44 9 0.04
45 10 0.04
46 3 0.01
47 2 0.01
48 3 0.01
49 2 0.01
50 12 0.05
51 17 0.07
ACGTcount: A:0.55, C:0.07, G:0.21, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAATAGTAATCAGTAAAAAGTAAATGGTAATCAAC
Found at i:26389 original size:64 final size:64
Alignment explanation
Indices: 26259--26639 Score: 268
Period size: 64 Copynumber: 5.9 Consensus size: 64
26249 AATAGCATGC
* * * * * *
26259 AATCAGTAAAAAGTAAAAAGG-CATCTAAAAGGGTAAAATGGTAATTAGTAAAGAGTAAAATAGT
1 AATCAGTAAAAAGTAAAAAGGTAATC-AAAAGAGTAAAATAGTAATCAGTAAAAAGTAAAATGGT
** *
26323 AATCAGTAAAAAGTACGAAGGTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAAGT-AAATGGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAA-AAGAGTAAAATAGTAATCAGTAAAAAGTAAAATGGT
* * * * *
26387 AATCAGT-AAGAGTAAAATA-GTAAT----A-AGTAAAA-GGAAATCAGT-AAGAGTAAAAAGGT
1 AATCAGTAAAAAGTAAAA-AGGTAATCAAAAGAGTAAAATAGTAATCAGTAAAAAGTAAAATGGT
* * * * * * *
26443 GATCAGTAGAGAGTAAAAAGCTAATCAGTAAGAAGTAAAA-GGTAATCAGTAAAAAGCAAAA-GG
1 AATCAGTAAAAAGTAAAAAGGTAATCA-AAAG-AGTAAAATAGTAATCAGTAAAAAGTAAAATGG
*
26506 C
64 T
*
26507 AATCAGTAAAAAGT-AAAAGAGTAATCAGTAAAAAAGAGCAGAAAAATAGTAATCAGTAAAAGAG
1 AATCAGTAAAAAGTAAAAAG-GTAATC------AAA-AG-AGTAAAATAGTAATCAGTAAAA-AG
26571 TAAAATGGT
56 TAAAATGGT
* * * * *
26580 AATCAGCAAAAAGTAAGAGGGTAATCAACAAGAGTAAAATAGAAATCAGTACAAAGTAAA
1 AATCAGTAAAAAGTAAAAAGGTAATCAA-AAGAGTAAAATAGTAATCAGTAAAAAGTAAA
26640 GAATAATCAA
Statistics
Matches: 250, Mismatches: 40, Indels: 53
0.73 0.12 0.15
Matches are distributed among these distances:
55 5 0.02
56 20 0.08
57 20 0.08
58 1 0.00
62 1 0.00
63 17 0.07
64 69 0.28
65 40 0.16
66 19 0.08
67 4 0.02
68 1 0.00
69 1 0.00
70 9 0.04
71 13 0.05
72 6 0.02
73 21 0.08
74 3 0.01
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.18
Consensus pattern (64 bp):
AATCAGTAAAAAGTAAAAAGGTAATCAAAAGAGTAAAATAGTAATCAGTAAAAAGTAAAATGGT
Found at i:26392 original size:21 final size:21
Alignment explanation
Indices: 26294--26673 Score: 151
Period size: 21 Copynumber: 17.8 Consensus size: 21
26284 TAAAAGGGTA
* *
26294 AAATGGTAATTAGTAAAGAGT
1 AAATGGTAATCAGTAAAAAGT
*
26315 AAAATAGTAATCAGTAAAAAGT
1 -AAATGGTAATCAGTAAAAAGT
*
26337 ACGAA-GGTAATCA--ACAAGAGT
1 A--AATGGTAATCAGTA-AAAAGT
* *
26358 AAAATAGTAGTCAGTAAAAAGT
1 -AAATGGTAATCAGTAAAAAGT
*
26380 AAATGGTAATCAGT-AAGAGT
1 AAATGGTAATCAGTAAAAAGT
*
26400 -AA----AAT-AGTAATAAGT
1 AAATGGTAATCAGTAAAAAGT
* * *
26415 AAAAGGAAATCAGT-AAGAGT
1 AAATGGTAATCAGTAAAAAGT
* * * *
26435 AAAAAGGTGATCAGTAGAGAGT
1 -AAATGGTAATCAGTAAAAAGT
* * *
26457 AAAAAGCTAATCAGTAAGAAGT
1 -AAATGGTAATCAGTAAAAAGT
* *
26479 AAAAGGTAATCAGTAAAAAGC
1 AAATGGTAATCAGTAAAAAGT
* *
26500 AAAAGGCAATCAGTAAAAAGT
1 AAATGGTAATCAGTAAAAAGT
* *
26521 AAAAGAGTAATCAGTAAAAAAGAGCAGAA
1 AAATG-GTAATCAGT---AAA-A--AG-T
*
26550 AAATAGTAATCAGTAAAAGAGT
1 AAATGGTAATCAGTAAAA-AGT
*
26572 AAAATGGTAATCAGCAAAAAGT
1 -AAATGGTAATCAGTAAAAAGT
* *
26594 AAGAGGGTAATCA--ACAAGAGT
1 AA-ATGGTAATCAGTA-AAAAGT
* * *
26615 AAAATAGAAATCAGTACAAAGT
1 -AAATGGTAATCAGTAAAAAGT
* *
26637 AAA-GAATAATCAATAAAATAGT
1 AAATG-GTAATCAGTAAAA-AGT
*
26659 -AATGGTAATTAGTAA
1 AAATGGTAATCAGTAA
26674 TTCAGTAAAA
Statistics
Matches: 274, Mismatches: 51, Indels: 67
0.70 0.13 0.17
Matches are distributed among these distances:
14 3 0.01
15 7 0.03
16 2 0.01
19 2 0.01
20 16 0.06
21 117 0.43
22 83 0.30
23 22 0.08
24 1 0.00
25 6 0.02
26 1 0.00
28 11 0.04
29 3 0.01
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.19
Consensus pattern (21 bp):
AAATGGTAATCAGTAAAAAGT
Found at i:26409 original size:35 final size:35
Alignment explanation
Indices: 26370--26438 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
26360 AATAGTAGTC
* *
26370 AGTAAAAAGTAAATGGTAATCAGTAAGAGTAAAAT
1 AGTAAAAAGTAAAAGGAAATCAGTAAGAGTAAAAT
*
26405 AGTAATAAGTAAAAGGAAATCAGTAAGAGTAAAA
1 AGTAAAAAGTAAAAGGAAATCAGTAAGAGTAAAA
26439 AGGTGATCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (35 bp):
AGTAAAAAGTAAAAGGAAATCAGTAAGAGTAAAAT
Found at i:26536 original size:15 final size:15
Alignment explanation
Indices: 26518--26573 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
26508 ATCAGTAAAA
26518 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* *
26533 AGTAAAAAAG--AGC
1 AGTAAAAGAGTAATC
* *
26546 AGAAAAATAGTAATC
1 AGTAAAAGAGTAATC
26561 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
26574 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 10 0.31
15 22 0.69
ACGTcount: A:0.59, C:0.05, G:0.20, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:28763 original size:64 final size:64
Alignment explanation
Indices: 28691--29000 Score: 421
Period size: 64 Copynumber: 4.9 Consensus size: 64
28681 AGTTTTTAAG
28691 AGTTGATCGGAAGACGATCTTGGTAAGAAATTAACCAGAAGATGGTTTCTCAAGAGTTTTCAGA
1 AGTTGATCGGAAGACGATCTTGGTAAGAAATTAACCAGAAGATGGTTTCTCAAGAGTTTTCAGA
* * * *
28755 AGTTGATCGGAAGACGATCTTGGTAAGAAATTAACCAGAAGATAGTTTCTCAAGGGCTTTCGGA
1 AGTTGATCGGAAGACGATCTTGGTAAGAAATTAACCAGAAGATGGTTTCTCAAGAGTTTTCAGA
* * *
28819 AGTTGATCGGAAGACGATCTTGGTAAGAAATTAGCCAGAAGATGTTTTCTCAAGAGTTTTCAAA
1 AGTTGATCGGAAGACGATCTTGGTAAGAAATTAACCAGAAGATGGTTTCTCAAGAGTTTTCAGA
* * * *
28883 AGTCGATCGGAAGACGATCTT-GTCAAG-AAGTACATCTGAAGATGGTTTCTCAAGAGTTTTCAG
1 AGTTGATCGGAAGACGATCTTGGT-AAGAAATTA-ACCAGAAGATGGTTTCTCAAGAGTTTTCAG
28946 A
64 A
* * * * *
28947 AGTTGAACGGAAGACGATTTTGTTAAGAAA-TATACCGGAAGACGGTTTC-CAAGA
1 AGTTGATCGGAAGACGATCTTGGTAAGAAATTA-ACCAGAAGATGGTTTCTCAAGA
29001 AAAAACTTTA
Statistics
Matches: 216, Mismatches: 26, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
63 11 0.05
64 202 0.94
65 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (64 bp):
AGTTGATCGGAAGACGATCTTGGTAAGAAATTAACCAGAAGATGGTTTCTCAAGAGTTTTCAGA
Found at i:35443 original size:13 final size:13
Alignment explanation
Indices: 35421--35451 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
35411 GGCAACCCAA
35421 TTTTAATTTTAAT
1 TTTTAATTTTAAT
*
35434 TTTTAGTTTTAAT
1 TTTTAATTTTAAT
35447 TTTTA
1 TTTTA
35452 TTTAGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:36803 original size:27 final size:27
Alignment explanation
Indices: 36773--36844 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
36763 GGGTCACCTA
36773 GGGGCATTTTGGTCATTTTC-ACATTCC
1 GGGGCATTTTGGTCATTTTCTACATT-C
* *
36800 GGGGCATTTTAGTCA-TTTCTGCATTC
1 GGGGCATTTTGGTCATTTTCTACATTC
*
36826 AGGGCATTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
36845 GAGTCCACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 18 0.46
27 21 0.54
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.43
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTTCTACATTC
Done.