Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012917.1 Corchorus capsularis cultivar CVL-1 contig12938, 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: 76167
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2268 original size:54 final size:54
Alignment explanation
Indices: 2185--2367 Score: 246
Period size: 54 Copynumber: 3.4 Consensus size: 54
2175 TTACCCAATA
* **
2185 ATTAAGGTCCTCAAACACAAGGGGGTTCATCCCTAAACACAGAGGCAATTCTAT
1 ATTAAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCAATTCTAT
** *
2239 ATTAAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCACCTCTCT
1 ATTAAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCAATTCTAT
* *
2293 CA-AAAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGC-ATT-TAC
1 -ATTAAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCAATTCTAT
* *
2345 ATCAAAGTCCTCAAGCACAAGGG
1 ATTAAAGTCCTCAAACACAAGGG
2368 CATCCACATT
Statistics
Matches: 114, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
51 1 0.01
52 20 0.18
53 1 0.01
54 91 0.80
55 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.20
Consensus pattern (54 bp):
ATTAAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCAATTCTAT
Found at i:2400 original size:30 final size:30
Alignment explanation
Indices: 2322--2423 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 30
2312 AGGGTATTCA
* *
2322 TCCCTAAACACAGAGGCATTTACATCAAAG
1 TCCCTAAACACAGAGGCATCTACATTAAAG
* *
2352 T-CCTCAAGCACA-AGGGCATCCACATTAAAG
1 TCCCT-AAACACAGA-GGCATCTACATTAAAG
* *
2382 TCCCTAAACACAGAGGCATCTATACTAAAG
1 TCCCTAAACACAGAGGCATCTACATTAAAG
*
2412 TCCCCAAACACA
1 TCCCTAAACACA
2424 TATAACACAG
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
29 4 0.07
30 51 0.86
31 4 0.07
ACGTcount: A:0.39, C:0.30, G:0.13, T:0.18
Consensus pattern (30 bp):
TCCCTAAACACAGAGGCATCTACATTAAAG
Found at i:5049 original size:15 final size:16
Alignment explanation
Indices: 5017--5050 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5007 AAAGAAGAAT
*
5017 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
5033 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
5048 TAA
1 TAA
5051 GAAAACAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:6365 original size:19 final size:18
Alignment explanation
Indices: 6332--6367 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6322 TTGAAATAAT
6332 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
6350 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
6368 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:6749 original size:30 final size:30
Alignment explanation
Indices: 6715--6771 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
6705 GGAGAGGATT
*
6715 GAATCGCAAAGTCTCATGGAGATGCCAATG
1 GAATCGCAAAGCCTCATGGAGATGCCAATG
6745 GAATCGCAAAGCCTCATGGAGATGCCA
1 GAATCGCAAAGCCTCATGGAGATGCCA
6772 TTAAGATGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (30 bp):
GAATCGCAAAGCCTCATGGAGATGCCAATG
Found at i:14414 original size:30 final size:30
Alignment explanation
Indices: 14380--14439 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
14370 AAAGGAGAGG
* * *
14380 ATGGAATCGCAAAGTCTCATGGAGATGCCA
1 ATGGAATCACAAAGCCTCATAGAGATGCCA
14410 ATGGAATCACAAAGCCTCATAGAGATGCCA
1 ATGGAATCACAAAGCCTCATAGAGATGCCA
14440 TTAAGATGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (30 bp):
ATGGAATCACAAAGCCTCATAGAGATGCCA
Found at i:18809 original size:2 final size:2
Alignment explanation
Indices: 18802--18844 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
18792 AAAAGTAGAC
18802 AT AT AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18845 GGTTATTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20011 original size:43 final size:43
Alignment explanation
Indices: 19963--20047 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
19953 TCAGTGGTAC
* **
19963 GTATTATTATTCT-TTAAAATTATGCAATTTGTATCAATTATTG
1 GTATTATTATCCTCTT-AAATTACACAATTTGTATCAATTATTG
*
20006 GTATTATTATCCTCTTAAATTGCACAATTTGTATCAATTATT
1 GTATTATTATCCTCTTAAATTACACAATTTGTATCAATTATT
20048 TTATCACTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 35 0.95
44 2 0.05
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (43 bp):
GTATTATTATCCTCTTAAATTACACAATTTGTATCAATTATTG
Found at i:20493 original size:43 final size:43
Alignment explanation
Indices: 20446--20532 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
20436 TCAAAGTCAA
* * *
20446 TGGTATTGTTATTCT-TTAAAATTACACAATTTGTATCAATTAT
1 TGGTATTATTATCCTCTT-AAATCACACAATTTGTATCAATTAT
* *
20489 TGGTATTATTATCCTCTTAAATCGCACAATTTTTATCAATTAT
1 TGGTATTATTATCCTCTTAAATCACACAATTTGTATCAATTAT
20532 T
1 T
20533 TTATTACTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
43 36 0.95
44 2 0.05
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (43 bp):
TGGTATTATTATCCTCTTAAATCACACAATTTGTATCAATTAT
Found at i:20854 original size:19 final size:19
Alignment explanation
Indices: 20832--20878 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
20822 GTTATGGAAC
20832 TACTCCTAAGTTATAA-GAT
1 TACTCCTAA-TTATAAGGAT
* *
20851 TACT-CTAATTCTAAGGGT
1 TACTCCTAATTATAAGGAT
20869 TACTCCTAAT
1 TACTCCTAAT
20879 AAACTAGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 9 0.38
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (19 bp):
TACTCCTAATTATAAGGAT
Found at i:22718 original size:6 final size:6
Alignment explanation
Indices: 22707--22739 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
22697 ATCCGTTTAA
22707 TTAACT TTAACT TTAACT TTAACT TTAACT TTA
1 TTAACT TTAACT TTAACT TTAACT TTAACT TTA
22740 CATAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAACT
Found at i:27054 original size:49 final size:50
Alignment explanation
Indices: 26908--27084 Score: 275
Period size: 50 Copynumber: 3.6 Consensus size: 50
26898 AAAGAAAATT
* *
26908 GGACCTTCCGACTGGGAAGGGGCATTTTTGGAAACAAATAAAGAAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTCGGAAACAAATAAAGAAAACAG
* *
26958 GGACCTTCCGACTGGGAAGGGGCATTTTCGGAAACAAATAAAAAAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTCGGAAACAAATAAAGAAAACAG
** * *
27008 GGACCTTCCGACCGATAA-GGGCATTTTGGGAAATAAATAAAGAAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTCGGAAACAAATAAAGAAAACAG
27057 GGACCTTCCGACCGGGAAGGGGCATTTT
1 GGACCTTCCGACCGGGAAGGGGCATTTT
27085 TTTGGAATAA
Statistics
Matches: 116, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
49 44 0.38
50 72 0.62
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (50 bp):
GGACCTTCCGACCGGGAAGGGGCATTTTCGGAAACAAATAAAGAAAACAG
Found at i:27254 original size:95 final size:95
Alignment explanation
Indices: 26909--27393 Score: 393
Period size: 95 Copynumber: 5.0 Consensus size: 95
26899 AAGAAAATTG
* * * * * * *
26909 GACCTTCCGACTGGGAAGGGGCATTTTTGGAA-ACAAATAAAGAAAACAGGGACCTTCCGACTGG
1 GACCTTCCGACCGGGAAGGGGC-TTTTTCGAATA-AGA-GAAGAAAACTGTGACCTTCCGACCGG
* * * * * * *
26973 GAAGGGGCATTTTCGGAAACAAATAAAAAAAACAGG
63 GAAGGGGC-TTTTTGG-AA-TAAGAGAAGAAACTGT
** ** * * *
27009 GACCTTCCGACCGATAA-GGGCATTTTGGGAAATAA-ATAAAGAAAACAGGGACCTTCCGACCGG
1 GACCTTCCGACCGGGAAGGGGC-TTTTTCG-AATAAGA-GAAGAAAACTGTGACCTTCCGACCGG
* *
27072 GAAGGGGCATTTTTTTGGAATAAGTGAAGATAATTGT
63 GAAGGGGC---TTTTTGGAATAAGAGAAGA-AACTGT
* * * * * * *
27109 GACCTTCCGACCGGGAAGGGGTATTTTTTGAATAAGTGAAGATATCTGTGACCTTCCGACCTGAA
1 GACCTTCCGACCGGGAAGGGG-CTTTTTCGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGA
* *
27174 AGGGGCTTTTTGGAATAAGGGAAGAAACTAT
65 AGGGGCTTTTTGGAATAAGAGAAGAAACTGT
* * * *
27205 GACCTTTCGACCGGGAAGGGGCTTTTTGGAATATGAGAAGAAAACTGTGACCTTCCGATCGGGAA
1 GACCTTCCGACCGGGAAGGGGCTTTTTCGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGAA
* *
27270 TGGGCTTTTTCGAATAAGAGAAGAAAACTGT
66 GGGGCTTTTTGGAATAAGAGAAG-AAACTGT
* * * *
27301 GACCTTCCGACCGAGAA-GGGCTTTTTCGAATAAGAGAAGAAAACTGTGACCTTCTGACCAGGAG
1 GACCTTCCGACCGGGAAGGGGCTTTTTCGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGAA
* *
27365 GGGGCTTTTCGGGAATAAGAAAAGTAAAC
66 GGGGCTTTT-TGGAATAAGAGAAG-AAAC
27394 AACACCTTCC
Statistics
Matches: 317, Mismatches: 58, Indels: 24
0.79 0.15 0.06
Matches are distributed among these distances:
95 104 0.33
96 60 0.19
97 18 0.06
99 51 0.16
100 69 0.22
101 15 0.05
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (95 bp):
GACCTTCCGACCGGGAAGGGGCTTTTTCGAATAAGAGAAGAAAACTGTGACCTTCCGACCGGGAA
GGGGCTTTTTGGAATAAGAGAAGAAACTGT
Found at i:27269 original size:48 final size:48
Alignment explanation
Indices: 26899--27393 Score: 419
Period size: 49 Copynumber: 10.2 Consensus size: 48
26889 CAAATGTGAA
* * * *
26899 AAGAAAATTG-GACCTTCCGACTGGGAAGGGGCATTTTTGGAA-ACAAATA
1 AAGAAAACTGTGACCTTCCGACCGGGAAGGGGC-TTTTTGGAATA-AGA-G
* * * * * *
26948 AAGAAAACAGGGACCTTCCGACTGGGAAGGGGCATTTTCGGAA-ACAAATA
1 AAGAAAACTGTGACCTTCCGACCGGGAAGGGGC-TTTTTGGAATA-AGA-G
* * * ** * *
26998 AAAAAAACAGGGACCTTCCGACCGATAA-GGGCATTTTGGGAAATAA-ATA
1 AAGAAAACTGTGACCTTCCGACCGGGAAGGGGC-TTTTTGG-AATAAGA-G
* * *
27047 AAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTTTTGGAATAAGTG
1 AAGAAAACTGTGACCTTCCGACCGGGAAGGGGC---TTTTTGGAATAAGAG
* * * * *
27098 AAGATAATTGTGACCTTCCGACCGGGAAGGGGTATTTTTTGAATAAGTG
1 AAGAAAACTGTGACCTTCCGACCGGGAAGGGG-CTTTTTGGAATAAGAG
* * * * *
27147 AAGATATCTGTGACCTTCCGACCTGAAAGGGGCTTTTTGGAATAAGGG
1 AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCTTTTTGGAATAAGAG
* * *
27195 AAG-AAACTATGACCTTTCGACCGGGAAGGGGCTTTTTGGAATATGAG
1 AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCTTTTTGGAATAAGAG
* * *
27242 AAGAAAACTGTGACCTTCCGATCGGGAATGGGCTTTTTCGAATAAGAG
1 AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCTTTTTGGAATAAGAG
* *
27290 AAGAAAACTGTGACCTTCCGACCGAGAA-GGGCTTTTTCGAATAAGAG
1 AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCTTTTTGGAATAAGAG
* * * * *
27337 AAGAAAACTGTGACCTTCTGACCAGGAGGGGGCTTTTCGGGAATAAGAA
1 AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCTTTT-TGGAATAAGAG
*
27386 AAGTAAAC
1 AAGAAAAC
27394 AACACCTTCC
Statistics
Matches: 383, Mismatches: 52, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
47 82 0.21
48 88 0.23
49 104 0.27
50 69 0.18
51 34 0.09
52 6 0.02
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.23
Consensus pattern (48 bp):
AAGAAAACTGTGACCTTCCGACCGGGAAGGGGCTTTTTGGAATAAGAG
Found at i:27446 original size:40 final size:40
Alignment explanation
Indices: 27388--28015 Score: 545
Period size: 40 Copynumber: 15.8 Consensus size: 40
27378 AATAAGAAAA
*
27388 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAT
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAAT
*
27428 GTGAACAACACCTTCCGGTGGGGAAGGGCAAAAC-AGGAAT
1 GTAAACAACACCTTCCGGTGGGGAAGGGC-AAACTAGGAAT
* * * *
27468 GTAAGCAACACCTTCCGGTAGGGAAGAGCAAACAAGGAAT
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAAT
*
27508 G-AAATAACACCTTCCGGTGGGGAAGGGCAAAAC-AGGAAT
1 GTAAACAACACCTTCCGGTGGGGAAGGGC-AAACTAGGAAT
* * *
27547 GTAAACAACACTTTCCAGTAGGGAAGGGCAAACTAGGAAT
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAAT
* * * *
27587 GTAAACAACTCCTTCTGGTGGGAAATGGCAAACTAGG-A-
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAAT
* *
27625 --AAACAACAACTTCCGGTAGGGAAGGGCAAAAC-AGGAAT
1 GTAAACAACACCTTCCGGTGGGGAAGGGC-AAACTAGGAAT
* * *
27663 AGAAATAGAAACCACACCTTCCGGTGGGGAAGGGCAGACT-GGAAAAA
1 -G---T--AAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG--AAT
* * * *
27710 CTAAACAACACCTTCTGGTGGGGAAGGGCAGAA-TGGGAAA
1 GTAAACAACACCTTCCGGTGGGGAAGGGCA-AACTAGGAAT
* * * *
27750 CTGAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAAA
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGG-AAT
* * *
27791 GTAAACAACACCTTTCGTTGGGGAAGGGCAAAC-AAGAAT
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAAT
* ** ** *
27830 ATAAACAACATTTTCCTACT-GGGAAGGGTAAACT-GGAAT
1 GTAAACAACACCTTCC-GGTGGGGAAGGGCAAACTAGGAAT
*** * *
27869 GGTAAACAACACCTTCCGACCGGGAAGGGC-AATTCGGAAT
1 -GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAAT
* * * *
27909 GAAAACAACACCTTCCGATAGGGAAGGGCGAACTAGGAAT
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAAT
** * *
27949 GTAATGAACACCTTCCGGTGGGGAAGGGTAAGCT-GG---
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAAT
*
27985 GAAAACAACACCTTCCGGTGGGGAAGGGCAA
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAA
28016 TTTGGGGAAA
Statistics
Matches: 481, Mismatches: 78, Indels: 62
0.77 0.13 0.10
Matches are distributed among these distances:
36 51 0.11
37 5 0.01
39 102 0.21
40 225 0.47
41 63 0.13
42 3 0.01
43 1 0.00
45 5 0.01
46 24 0.05
47 2 0.00
ACGTcount: A:0.37, C:0.19, G:0.29, T:0.15
Consensus pattern (40 bp):
GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAAT
Found at i:27544 original size:79 final size:78
Alignment explanation
Indices: 27388--28015 Score: 490
Period size: 79 Copynumber: 7.9 Consensus size: 78
27378 AATAAGAAAA
** *
27388 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATGTGAACAACACCTTCCGGTGGGGAA
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACAAGGAATG-AAACAACACCTTCCGGTGGGGAA
27453 GGGCAAAACAGGAAT
65 GGGC-AAACAGGAAT
* * * *
27468 GTAAGCAACACCTTCCGGTAGGGAAGAGCAAACAAGGAATGAAATAACACCTTCCGGTGGGGAAG
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACAAGGAATGAAACAACACCTTCCGGTGGGGAAG
27533 GGCAAAACAGGAAT
66 GGC-AAACAGGAAT
* * * * * * *
27547 GTAAACAACACTTTCCAGTAGGGAAGGGCAAACTAGGAATGTAAACAACTCCTTCTGGTGGGAAA
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACAAGGAATG-AAACAACACCTTCCGGTGGGGAA
*
27612 TGGCAAACTAGG-A-
65 GGGCAAAC-AGGAAT
* * * *
27625 --AAACAACAACTTCCGGTAGGGAAGGGCAAAACAGGAATAGAAATAGAAACCACACCTTCCGGT
1 GTAAACAACACCTTCCGGTGGGGAAGGGC-AAAC----A-AGGAAT-GAAACAACACCTTCCGGT
* * *
27688 GGGGAAGGGCAGACTGGAAAAA
59 GGGGAAGGGCAAACAGG--AAT
* * **
27710 CTAAACAACACCTTCTGGTGGGGAAGGGCAGAA-TGGGAAACTG-AACAACACCTTCCGGTGGGG
1 GTAAACAACACCTTCCGGTGGGGAAGGGCA-AACAAGG-AA-TGAAACAACACCTTCCGGTGGGG
* *
27773 AAGGGCAAACTGGGAAAA
63 AAGGGCAAAC-AGG-AAT
* * * ** **
27791 GTAAACAACACCTTTCGTTGGGGAAGGGCAAACAA-GAATATAAACAACATTTTCCTACT-GGGA
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACAAGGAAT-GAAACAACACCTTCC-GGTGGGGA
* *
27854 AGGGTAAACTGGAAT
64 AGGGCAAACAGGAAT
*** * * *
27869 GGTAAACAACACCTTCCGACCGGGAAGGGCAATTC--GGAATGAAAACAACACCTTCCGATAGGG
1 -GTAAACAACACCTTCCGGTGGGGAAGGGCAA-ACAAGGAATG-AAACAACACCTTCCGGTGGGG
*
27932 AAGGGCGAACTAGGAAT
63 AAGGGCAAAC-AGGAAT
** * * * *
27949 GTAATGAACACCTTCCGGTGGGGAAGGGTAAGC-TGGGA--AAACAACACCTTCCGGTGGGGAAG
1 GTAAACAACACCTTCCGGTGGGGAAGGGCAAACAAGGAATGAAACAACACCTTCCGGTGGGGAAG
28011 GGCAA
66 GGCAA
28016 TTTGGGGAAA
Statistics
Matches: 442, Mismatches: 76, Indels: 64
0.76 0.13 0.11
Matches are distributed among these distances:
76 50 0.11
77 4 0.01
78 5 0.01
79 163 0.37
80 93 0.21
81 62 0.14
82 35 0.08
83 2 0.00
84 1 0.00
86 1 0.00
87 26 0.06
ACGTcount: A:0.37, C:0.19, G:0.29, T:0.15
Consensus pattern (78 bp):
GTAAACAACACCTTCCGGTGGGGAAGGGCAAACAAGGAATGAAACAACACCTTCCGGTGGGGAAG
GGCAAACAGGAAT
Found at i:27854 original size:39 final size:40
Alignment explanation
Indices: 27792--27965 Score: 122
Period size: 39 Copynumber: 4.4 Consensus size: 40
27782 CTGGGAAAAG
* ***
27792 TAAACAACACCTTTCGTTGGGGAAGGGCAAACAAGAAT-A
1 TAAACAACACCTTCCGACCGGGAAGGGCAAACAAGAATGA
** * * * ** *
27831 TAAACAACATTTTCCTACTGGGAAGGGTAAACTGGAATGG
1 TAAACAACACCTTCCGACCGGGAAGGGCAAACAAGAATGA
* *
27871 TAAACAACACCTTCCGACCGGGAAGGGCAATTC-GGAATGA
1 TAAACAACACCTTCCGACCGGGAAGGGCAA-ACAAGAATGA
** * *
27911 -AAACAACACCTTCCGATAGGGAAGGGCGAACTAGGAATG-
1 TAAACAACACCTTCCGACCGGGAAGGGCAAAC-AAGAATGA
**
27950 TAATGAACACCTTCCG
1 TAAACAACACCTTCCG
27966 GTGGGGAAGG
Statistics
Matches: 106, Mismatches: 24, Indels: 9
0.76 0.17 0.06
Matches are distributed among these distances:
38 1 0.01
39 54 0.51
40 50 0.47
41 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (40 bp):
TAAACAACACCTTCCGACCGGGAAGGGCAAACAAGAATGA
Found at i:28043 original size:48 final size:48
Alignment explanation
Indices: 27989--28123 Score: 173
Period size: 48 Copynumber: 2.8 Consensus size: 48
27979 AGCTGGGAAA
* *
27989 ACAACACCTTCCGGTGGGGAAGGGCAATTTGGGGAAAAGTAGACTCAG
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGGAAAAGTAGACTCAG
* * * * *
28037 ACAACACTTTCCGATGAGGAAAGGCAATTTGGGAAAAAGCAGACTTAG
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGGAAAAGTAGACTCAG
* * *
28085 ACAACACCTCCCGATGAGGAAGGGAAATTT-TGGAAAAGT
1 ACAACACCTTCCGATGAGGAAGGGCAATTTGGGGAAAAGT
28124 GGAAACAAGA
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
47 6 0.08
48 67 0.92
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (48 bp):
ACAACACCTTCCGATGAGGAAGGGCAATTTGGGGAAAAGTAGACTCAG
Found at i:28698 original size:50 final size:49
Alignment explanation
Indices: 28621--28939 Score: 292
Period size: 50 Copynumber: 6.4 Consensus size: 49
28611 AATTTTCCAA
* * * * * *
28621 TTCAATCCCTTTACTTAAAGATTTCATTTTTA-TTCCAATTTTATCAAAAG
1 TTCAAT-CTTTTACTCAAAGGTCTCATTTTTATTTACAA-ATTATCAAAAG
* * *
28671 TTCAATCTTTTAATTCAAAGGTCTCATTTTTCACTTACAAATTTATCAAGA-
1 TTCAATCTTTT-ACTCAAAGGTCTCATTTTT-ATTTACAAA-TTATCAAAAG
* * *
28722 TTCAATCTTTTACTTAAAGATCTCATTTTTACTTACAAATTAATCAAAAGG
1 TTCAATCTTTTACTCAAAGGTCTCATTTTTATTTACAAATT-ATCAAAA-G
* * *** *
28773 TTCGATCTTTTACTTAATCTTCTCATTTTTATTTACAAATTACTTAAAAG
1 TTCAATCTTTTACTCAAAGGTCTCATTTTTATTTACAAATTA-TCAAAAG
* *
28823 TTCGATCTTTT-CTCAAAGGT-TACATCTTTATTTACAAATTA--AAAAG
1 TTCAATCTTTTACTCAAAGGTCT-CATTTTTATTTACAAATTATCAAAAG
* *
28869 TTCAATCTTTTACTCAAAGGT-TACATCTTTATTTACAAATTATTCAAATG
1 TTCAATCTTTTACTCAAAGGTCT-CATTTTTATTTACAAATTA-TCAAAAG
28919 TTCAATCTTTTACTCAAAGGT
1 TTCAATCTTTTACTCAAAGGT
28940 TACATCTTTA
Statistics
Matches: 231, Mismatches: 25, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
46 15 0.06
47 30 0.13
48 3 0.01
49 42 0.18
50 75 0.32
51 53 0.23
52 13 0.06
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (49 bp):
TTCAATCTTTTACTCAAAGGTCTCATTTTTATTTACAAATTATCAAAAG
Found at i:28993 original size:50 final size:51
Alignment explanation
Indices: 28939--29041 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 51
28929 TACTCAAAGG
*
28939 TTACATCTTTATCATAAATCAA-TCAAAAATTTCATCTTCTAAAATAAAAA
1 TTACATCTTTATCATAAATCAATTAAAAAATTTCATCTTCTAAAATAAAAA
* * * * *
28989 TTACATTTTTATTATAAGTCAATTAAAAAATTTCATCTTTTAACATAAAAA
1 TTACATCTTTATCATAAATCAATTAAAAAATTTCATCTTCTAAAATAAAAA
29040 TT
1 TT
29042 TCACCTTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 19 0.41
51 27 0.59
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.41
Consensus pattern (51 bp):
TTACATCTTTATCATAAATCAATTAAAAAATTTCATCTTCTAAAATAAAAA
Found at i:29039 original size:21 final size:21
Alignment explanation
Indices: 29014--29071 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
29004 AAGTCAATTA
29014 AAAAATTTCATCTTTTAACAT
1 AAAAATTTCATCTTTTAACAT
* *
29035 AAAAATTTCACCTTTTTACAT
1 AAAAATTTCATCTTTTAACAT
* *
29056 AAAGATTACAT-TTTTA
1 AAAAATTTCATCTTTTA
29072 TTACAAGTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAAATTTCATCTTTTAACAT
Found at i:29080 original size:72 final size:72
Alignment explanation
Indices: 28963--29109 Score: 231
Period size: 72 Copynumber: 2.0 Consensus size: 72
28953 TAAATCAATC
* *
28963 AAAAATTTCATCTTCTAAAATAAAAATTACATTTTTATTATAAGTCAATTAAAAAATTTCATCTT
1 AAAAATTTCACCTTCTAAAATAAAAATTACATTTTTATTACAAGTCAATTAAAAAATTTCATCTT
29028 TTAACAT
66 TTAACAT
* * * *
29035 AAAAATTTCACCTTTTTACATAAAGATTACATTTTTATTACAAGTCAATTAAAAAATTTCATCTT
1 AAAAATTTCACCTTCTAAAATAAAAATTACATTTTTATTACAAGTCAATTAAAAAATTTCATCTT
*
29100 TTAATAT
66 TTAACAT
29107 AAA
1 AAA
29110 GATTACATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (72 bp):
AAAAATTTCACCTTCTAAAATAAAAATTACATTTTTATTACAAGTCAATTAAAAAATTTCATCTT
TTAACAT
Found at i:41976 original size:17 final size:16
Alignment explanation
Indices: 41943--41977 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
41933 CGCAAACCCT
*
41943 AATTTTTTTTTTTCAC
1 AATTTTTTTTTTGCAC
41959 AATTTTTTTTTTCGCAC
1 AATTTTTTTTTT-GCAC
41976 AA
1 AA
41978 AGCAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.23, C:0.14, G:0.03, T:0.60
Consensus pattern (16 bp):
AATTTTTTTTTTGCAC
Found at i:43633 original size:19 final size:18
Alignment explanation
Indices: 43599--43636 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
43589 CTTGAAATAT
43599 TTCTTCAATGATCTTCAA
1 TTCTTCAATGATCTTCAA
*
43617 TTCTTCAAATTATCTTCAA
1 TTCTTC-AATGATCTTCAA
43636 T
1 T
43637 AAATCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (18 bp):
TTCTTCAATGATCTTCAA
Found at i:52140 original size:18 final size:17
Alignment explanation
Indices: 52117--52152 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
52107 CTCAACCTAA
52117 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
52135 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
52152 A
1 A
52153 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:52772 original size:19 final size:18
Alignment explanation
Indices: 52739--52774 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
52729 TTGAAATAAT
52739 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
52757 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
52775 TAAATATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:60997 original size:19 final size:18
Alignment explanation
Indices: 60964--61000 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
60954 TTGAAATAAT
60964 TCTTCAATGGTCTTCAAG
1 TCTTCAATGGTCTTCAAG
*
60982 TCTTCAAATTGTCTTCAAG
1 TCTTC-AATGGTCTTCAAG
61001 AATTTGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.41
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAG
Found at i:70690 original size:13 final size:14
Alignment explanation
Indices: 70672--70700 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
70662 ATAATTGGAC
70672 TTTGCATTCAT-CA
1 TTTGCATTCATGCA
70685 TTTGCATTCATGCA
1 TTTGCATTCATGCA
70699 TT
1 TT
70701 GAGTGGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:72448 original size:15 final size:15
Alignment explanation
Indices: 72408--72448 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
72398 GGACGACACA
*
72408 ATTGGAGGTGCTGCT
1 ATTGGAGGTGGTGCT
72423 ATTGGAGGTGGTGCT
1 ATTGGAGGTGGTGCT
* *
72438 GTTGGAAGTGG
1 ATTGGAGGTGG
72449 CACCGTTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.15, C:0.07, G:0.46, T:0.32
Consensus pattern (15 bp):
ATTGGAGGTGGTGCT
Found at i:74847 original size:55 final size:53
Alignment explanation
Indices: 74788--75069 Score: 254
Period size: 55 Copynumber: 5.2 Consensus size: 53
74778 AATAGCTTGA
*
74788 TCCTGATGGTGTTGCCTTCAACTTATCATTCAGATCATCTGGACCAAAATATTGG
1 TCCTGATGGTGTTGCCTTCAAATTA-CATTCAGATCATCTGGACCAAAA-ATTGG
* * * * *
74843 TCCTGATGGTGTTGTCAATTAAAAATTAC--TCAAATCAT-TGGGACTAATAAATTGA
1 TCCTGATGGTGTTG-C-CTT-CAAATTACATTCAGATCATCT-GGACCAA-AAATTGG
*
74898 TCCTGAT-GTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAAAAAATTGG
1 TCCTGATGGTGTTGCCTTCAAATTA-CATTCAGATCATCTGGACC-AAAAATTGG
* * * * *
74952 TCCTGATGGTGTTGTCAATTAAAAATTAC--TCAAATCATC-GAGACTAATAAATTGA
1 TCCTGATGGTGTTG-C-CTT-CAAATTACATTCAGATCATCTG-GACCAA-AAATTGG
*
75007 TCCTGATGGTGTTGCCTTCAATTTACCATTCAGATCATCTGGACCAAAAAATTGG
1 TCCTGATGGTGTTGCCTTCAAATTA-CATTCAGATCATCTGGACC-AAAAATTGG
75062 TCCTGATG
1 TCCTGATG
75070 ATGTAACAAA
Statistics
Matches: 182, Mismatches: 24, Indels: 42
0.73 0.10 0.17
Matches are distributed among these distances:
51 5 0.03
52 8 0.04
53 4 0.02
54 36 0.20
55 106 0.58
56 7 0.04
57 6 0.03
58 10 0.05
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (53 bp):
TCCTGATGGTGTTGCCTTCAAATTACATTCAGATCATCTGGACCAAAAATTGG
Found at i:74987 original size:109 final size:110
Alignment explanation
Indices: 74784--75069 Score: 520
Period size: 109 Copynumber: 2.6 Consensus size: 110
74774 GATAAATAGC
* *
74784 TTGATCCTGATGGTGTTGCCTTCAACTTATCATTCAGATCATCTGGACCAAAATATTGGTCCTGA
1 TTGATCCTGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAAAAAATTGGTCCTGA
* *
74849 TGGTGTTGTCAATTAAAAATTACTCAAATCATTGGGACTAATAAA
66 TGGTGTTGTCAATTAAAAATTACTCAAATCATCGAGACTAATAAA
74894 TTGATCCTGAT-GTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAAAAAATTGGTCCTGA
1 TTGATCCTGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAAAAAATTGGTCCTGA
74958 TGGTGTTGTCAATTAAAAATTACTCAAATCATCGAGACTAATAAA
66 TGGTGTTGTCAATTAAAAATTACTCAAATCATCGAGACTAATAAA
*
75003 TTGATCCTGATGGTGTTGCCTTCAATTTACCATTCAGATCATCTGGACCAAAAAATTGGTCCTGA
1 TTGATCCTGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAAAAAATTGGTCCTGA
75068 TG
66 TG
75070 ATGTAACAAA
Statistics
Matches: 170, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
109 105 0.62
110 65 0.38
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (110 bp):
TTGATCCTGATGGTGTTGCCTTCAATTTATCATTCAGATCATCTGGACCAAAAAATTGGTCCTGA
TGGTGTTGTCAATTAAAAATTACTCAAATCATCGAGACTAATAAA
Found at i:75395 original size:21 final size:22
Alignment explanation
Indices: 75350--75398 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
75340 TAAAATTGGT
*
75350 AATCA-AGAGTTTTCAAGATTT
1 AATCAGAGAGTTTTCAAGATTA
75371 AATCAGAG-GTTTTCAA-ATTCA
1 AATCAGAGAGTTTTCAAGATT-A
75392 AATCAGA
1 AATCAGA
75399 TTTAGTGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 20 0.80
22 2 0.08
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (22 bp):
AATCAGAGAGTTTTCAAGATTA
Found at i:76091 original size:50 final size:50
Alignment explanation
Indices: 76015--76167 Score: 227
Period size: 50 Copynumber: 3.1 Consensus size: 50
76005 CGTTTCGACA
** * *
76015 GAAACAAATTAAGAAAACAGGAACCTTCCAACCAGGAAGGGGCATTTTTG
1 GAAACAAACAAAGAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTGG
76065 GAAACAAACAAAGAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTGG
1 GAAACAAACAAAGAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTGG
* * *
76115 GAAACAAACAAAGGAAACCA-GGACCTTCCGACCGGGAAGGGGCATTTTGG
1 GAAACAAACAAA-GAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTGG
76165 GAA
1 GAA
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 89 0.94
51 6 0.06
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.14
Consensus pattern (50 bp):
GAAACAAACAAAGAAAACAGGGACCTTCCAACCAGGAAGGGGCATTTTGG
Done.