Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009895.1 Corchorus capsularis cultivar CVL-1 contig09916, 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: 83490
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:5044 original size:45 final size:45
Alignment explanation
Indices: 4993--5082 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
4983 ATAAAAAGAT
4993 ACAGAATAAAGAAAAGGCCTACTGTTTCCATTACTAGGAAATATA
1 ACAGAATAAAGAAAAGGCCTACTGTTTCCATTACTAGGAAATATA
*
5038 ACAGAATTAAGAAAAGGCCTACTGTTTCCATTACTAGGAAATATA
1 ACAGAATAAAGAAAAGGCCTACTGTTTCCATTACTAGGAAATATA
5083 CTCACAACTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (45 bp):
ACAGAATAAAGAAAAGGCCTACTGTTTCCATTACTAGGAAATATA
Found at i:6108 original size:11 final size:11
Alignment explanation
Indices: 6074--6099 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6064 ACAAACAAAT
6074 AAAAAAAATTG
1 AAAAAAAATTG
6085 AAAAAAAATTG
1 AAAAAAAATTG
6096 AAAA
1 AAAA
6100 CACATTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:8812 original size:3 final size:3
Alignment explanation
Indices: 8806--8847 Score: 57
Period size: 3 Copynumber: 13.0 Consensus size: 3
8796 ACCAAAAAAA
8806 AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAAG AAAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG -AAG -AAG AAG AAG
8848 TAACAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 27 0.71
4 11 0.29
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:8826 original size:15 final size:18
Alignment explanation
Indices: 8805--8847 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 18
8795 CACCAAAAAA
8805 AAAGAAGAAG-AAG-AAG
1 AAAGAAGAAGAAAGAAAG
8821 -AAGAAGAAGAAAGAAAG
1 AAAGAAGAAGAAAGAAAG
8838 AAAGAAGAAG
1 AAAGAAGAAG
8848 TAACAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.38
16 3 0.12
17 3 0.12
18 9 0.38
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (18 bp):
AAAGAAGAAGAAAGAAAG
Found at i:16216 original size:27 final size:27
Alignment explanation
Indices: 16186--16241 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
16176 GAGGAGGAGG
16186 AGAGAAGAG-GAAGAGAGAGAAAGGGAA
1 AGAGAAGAGAG-AGAGAGAGAAAGGGAA
* *
16213 AGAGAAGAGAGGGAGAGGGAAAGGGAA
1 AGAGAAGAGAGAGAGAGAGAAAGGGAA
16240 AG
1 AG
16242 GGATGATTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (27 bp):
AGAGAAGAGAGAGAGAGAGAAAGGGAA
Found at i:16221 original size:21 final size:22
Alignment explanation
Indices: 16190--16239 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
16180 AGGAGGAGAG
16190 AAGAGGAAGAGAGAGAAAGGGA
1 AAGAGGAAGAGAGAGAAAGGGA
* *
16212 AAGA-GAAGAGAGGGAGAGGGA
1 AAGAGGAAGAGAGAGAAAGGGA
16233 AAG-GGAA
1 AAGAGGAA
16240 AGGGATGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (22 bp):
AAGAGGAAGAGAGAGAAAGGGA
Found at i:19023 original size:14 final size:14
Alignment explanation
Indices: 19004--19032 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18994 TAGAACCATC
19004 TTTTTTT-CCTTTT
1 TTTTTTTCCCTTTT
19017 TTTTTTTCCCTTTT
1 TTTTTTTCCCTTTT
19031 TT
1 TT
19033 CTTCAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTCCCTTTT
Found at i:24410 original size:24 final size:27
Alignment explanation
Indices: 24383--24438 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
24373 TTTGGTTGTC
*
24383 CACACCAT-TG-TTGA-TGGTATTATT
1 CACACCATCTGCTTGATTGGCATTATT
*
24407 CACACCATCTGCTTGATTTGCATTATT
1 CACACCATCTGCTTGATTGGCATTATT
24434 CACAC
1 CACAC
24439 TCTGATGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 8 0.30
25 2 0.07
26 4 0.15
27 13 0.48
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (27 bp):
CACACCATCTGCTTGATTGGCATTATT
Found at i:26717 original size:19 final size:19
Alignment explanation
Indices: 26693--26739 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
26683 ATTTAATATC
26693 CAAAAGCACTTTTGAAAGG
1 CAAAAGCACTTTTGAAAGG
26712 CAAAAGCACTTTTGAAAGG
1 CAAAAGCACTTTTGAAAGG
26731 CAAAAGCAC
1 CAAAAGCAC
26740 CTAAGGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (19 bp):
CAAAAGCACTTTTGAAAGG
Found at i:28209 original size:16 final size:16
Alignment explanation
Indices: 28188--28220 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28178 TATTAACTAC
28188 TGCAAAAATCTTCCAT
1 TGCAAAAATCTTCCAT
*
28204 TGCAAAAATCTTTCAT
1 TGCAAAAATCTTCCAT
28220 T
1 T
28221 CCTTGTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (16 bp):
TGCAAAAATCTTCCAT
Found at i:28341 original size:42 final size:41
Alignment explanation
Indices: 28282--28368 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 41
28272 AGGTTCACGT
28282 TTCTCTCTGGCTTGAATGCAACAATCATCTTCTCTGTTATA
1 TTCTCTCTGGCTTGAATGCAACAATCATCTTCTCTGTTATA
*
28323 TTCTCTCTGGGCTTGAATGCAGCAATCATCTTCTCTGTTATA
1 TTCTCTCT-GGCTTGAATGCAACAATCATCTTCTCTGTTATA
28365 TTCT
1 TTCT
28369 ATACAAAAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 8 0.18
42 36 0.82
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.43
Consensus pattern (41 bp):
TTCTCTCTGGCTTGAATGCAACAATCATCTTCTCTGTTATA
Found at i:28404 original size:13 final size:13
Alignment explanation
Indices: 28386--28412 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28376 AGAAAAAAAT
28386 AGACATTAAACAC
1 AGACATTAAACAC
28399 AGACATTAAACAC
1 AGACATTAAACAC
28412 A
1 A
28413 AATCACCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (13 bp):
AGACATTAAACAC
Found at i:28615 original size:18 final size:18
Alignment explanation
Indices: 28594--28629 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
28584 ACTTTTTACA
*
28594 TCTGTTTCAAGGTTTATC
1 TCTGTTTCAAGGTCTATC
28612 TCTGTTTCAAGGTCTATC
1 TCTGTTTCAAGGTCTATC
28630 GCTGCCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (18 bp):
TCTGTTTCAAGGTCTATC
Found at i:29277 original size:30 final size:30
Alignment explanation
Indices: 29233--29302 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
29223 GCCTTTGGGC
* *
29233 AATTACTCTCTCAATAAGAATTCATTGACA
1 AATTCCTCTTTCAATAAGAATTCATTGACA
29263 AATTCCTCTTTCAATAAGAATTCATTGACA
1 AATTCCTCTTTCAATAAGAATTCATTGACA
*
29293 AACTCC-CTTT
1 AATTCCTCTTT
29303 TAAGGACTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 4 0.11
30 33 0.89
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.36
Consensus pattern (30 bp):
AATTCCTCTTTCAATAAGAATTCATTGACA
Found at i:29529 original size:23 final size:23
Alignment explanation
Indices: 29503--29548 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29493 ACTAATCCAT
*
29503 AACCAAAACAAAATAAGAAATTG
1 AACCAAAACAAAAGAAGAAATTG
* *
29526 AACCAAAATAAGAGAAGAAATTG
1 AACCAAAACAAAAGAAGAAATTG
29549 GTCTAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.63, C:0.11, G:0.13, T:0.13
Consensus pattern (23 bp):
AACCAAAACAAAAGAAGAAATTG
Found at i:30036 original size:27 final size:29
Alignment explanation
Indices: 29998--30070 Score: 123
Period size: 30 Copynumber: 2.6 Consensus size: 29
29988 CTCTTCAGCT
29998 TTCTTGATTTTCTT-TGTTTT-TGAAGGA
1 TTCTTGATTTTCTTGTGTTTTCTGAAGGA
30025 TTCTTGATTTTCTCTGTGTTTTCTGAAGGA
1 TTCTTGATTTTCT-TGTGTTTTCTGAAGGA
30055 TTCTTGATTTTCTTGT
1 TTCTTGATTTTCTTGT
30071 ATGTAATTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
27 13 0.30
28 1 0.02
29 9 0.21
30 20 0.47
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.59
Consensus pattern (29 bp):
TTCTTGATTTTCTTGTGTTTTCTGAAGGA
Found at i:39674 original size:20 final size:21
Alignment explanation
Indices: 39645--39685 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
39635 TAATTCAATC
*
39645 TGTTATTGGTT-GGTTAAAGT
1 TGTTACTGGTTGGGTTAAAGT
39665 TGTTACTGGTTGGGTTAAAGT
1 TGTTACTGGTTGGGTTAAAGT
39686 GGTTTGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (21 bp):
TGTTACTGGTTGGGTTAAAGT
Found at i:39699 original size:25 final size:22
Alignment explanation
Indices: 39649--39699 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 22
39639 TCAATCTGTT
*
39649 ATTGGTTGGTTAAAGTTGTTAC
1 ATTGGTTGGTTAAAGTGGTTAC
39671 --TGGTTGGGTTAAAGTGGTTTGAC
1 ATTGGTT-GGTTAAAGTGG-TT-AC
39694 ATTGGT
1 ATTGGT
39700 AACCCTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 2 0.09
23 2 0.09
25 4 0.17
ACGTcount: A:0.20, C:0.04, G:0.33, T:0.43
Consensus pattern (22 bp):
ATTGGTTGGTTAAAGTGGTTAC
Found at i:44978 original size:53 final size:53
Alignment explanation
Indices: 44898--45004 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
44888 TTGTTATCAC
* *
44898 TTCACAACAAAATTTGATTTCTCAACTGAATTTTCTTAAGAGAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTCAACTGAATTTTCTTAAAAGAAATTATAAAA
* *
44951 TTCACAACAAAATTTGATTTTTTAACTGAATTTTCTTAAAAGAAATTATAAAA
1 TTCACAACAAAATTTGATTTCTCAACTGAATTTTCTTAAAAGAAATTATAAAA
45004 T
1 T
45005 AAAACAGCCG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (53 bp):
TTCACAACAAAATTTGATTTCTCAACTGAATTTTCTTAAAAGAAATTATAAAA
Found at i:45546 original size:44 final size:44
Alignment explanation
Indices: 45483--45572 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
45473 CAGATGATAA
*
45483 GTCCCTAAATTTAAGACATTAAATTGGTAGGCTTTTAGTGATTT
1 GTCCCTAAATTTAAGACATTAAATTGGTAGGCTTTCAGTGATTT
45527 GTCCCTAAATTTAAGACATTAAATTGGTAGGCTTTCAGTGATTT
1 GTCCCTAAATTTAAGACATTAAATTGGTAGGCTTTCAGTGATTT
45571 GT
1 GT
45573 AGGAAAAAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (44 bp):
GTCCCTAAATTTAAGACATTAAATTGGTAGGCTTTCAGTGATTT
Found at i:46241 original size:60 final size:60
Alignment explanation
Indices: 46142--46502 Score: 472
Period size: 60 Copynumber: 6.0 Consensus size: 60
46132 GTGCTTCATC
* * * *
46142 TGGACCAGACCACGTTATGGATTCATCTGAACACAGGGGATCAAACTTCAGCCATGAACA
1 TGGACCAGACCAAGTTATGGATTCATCTGAATACTGGGGATCAAACTTCAGCCATGAATA
* * * *
46202 TGGACGAGACCAAGTTATGGGTTCATCTGATTACTGGGGATCAAACTTCAGCCATGAACA
1 TGGACCAGACCAAGTTATGGATTCATCTGAATACTGGGGATCAAACTTCAGCCATGAATA
* * * * *
46262 TGGACGAGACCACGTTATGGATTCATCTCAATACTGGGGATCGAACTTCAGCCATGGATA
1 TGGACCAGACCAAGTTATGGATTCATCTGAATACTGGGGATCAAACTTCAGCCATGAATA
* * * *
46322 TGTACC-GTACCAAGTTGTGGATTCATCTGCATACTGGGGATCAAACTTCAGCCATGGATA
1 TGGACCAG-ACCAAGTTATGGATTCATCTGAATACTGGGGATCAAACTTCAGCCATGAATA
* ** * *
46382 TGTACCCTACCAAGTTATGGATTCATCTCAATACTGGGGATCAAACTTCAGCCATGGATA
1 TGGACCAGACCAAGTTATGGATTCATCTGAATACTGGGGATCAAACTTCAGCCATGAATA
* * * *
46442 TGTACCACACCAAGTTATGGATTCATCTGATTACTGGGGATCAAACTTCGGCCATGAATA
1 TGGACCAGACCAAGTTATGGATTCATCTGAATACTGGGGATCAAACTTCAGCCATGAATA
46502 T
1 T
46503 ATACCTAAAC
Statistics
Matches: 269, Mismatches: 30, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
59 1 0.00
60 268 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (60 bp):
TGGACCAGACCAAGTTATGGATTCATCTGAATACTGGGGATCAAACTTCAGCCATGAATA
Found at i:53144 original size:3 final size:3
Alignment explanation
Indices: 53138--53186 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
53128 ATTAATATAC
53138 ATA ATA ATA ATA TATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53183 ATA A
1 ATA A
53187 CATAAAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:55321 original size:6 final size:6
Alignment explanation
Indices: 55304--55343 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
55294 CATGTATAAG
* *
55304 TGTACA TGTATA TATATA TGTATA TGTATA TGTATA TGTA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTA
55344 AAGAAAGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (6 bp):
TGTATA
Found at i:64398 original size:28 final size:28
Alignment explanation
Indices: 64358--64431 Score: 148
Period size: 28 Copynumber: 2.6 Consensus size: 28
64348 TCTTAGACAT
64358 ATTATTTGAAATTTATTTTTTTGGCATC
1 ATTATTTGAAATTTATTTTTTTGGCATC
64386 ATTATTTGAAATTTATTTTTTTGGCATC
1 ATTATTTGAAATTTATTTTTTTGGCATC
64414 ATTATTTGAAATTTATTT
1 ATTATTTGAAATTTATTT
64432 ATGAGAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.27, C:0.05, G:0.09, T:0.58
Consensus pattern (28 bp):
ATTATTTGAAATTTATTTTTTTGGCATC
Found at i:66464 original size:125 final size:125
Alignment explanation
Indices: 66242--66485 Score: 479
Period size: 125 Copynumber: 2.0 Consensus size: 125
66232 GCCGGTCGGA
66242 CCGGTTAAATCGGGAACCGATGGCATGTCCGGTCCTTGAAGGTGTGGGAACCGCGGTTAATCAAC
1 CCGGTTAAATCGGGAACCGATGGCATGTCCGGTCCTTGAAGGTGTGGGAACCGCGGTTAATCAAC
66307 ATGGTCAACAACCGTGAAAAAACCGGTTGGACCGGCGGTTGAACCGGGTTTGACGACCGG
66 ATGGTCAACAACCGTGAAAAAACCGGTTGGACCGGCGGTTGAACCGGGTTTGACGACCGG
*
66367 CCGGTTAAATCGGGAACCGATGGCATGTCCGGTCCTTGAAGGTGTGGGAACCGCGGTTAGTCAAC
1 CCGGTTAAATCGGGAACCGATGGCATGTCCGGTCCTTGAAGGTGTGGGAACCGCGGTTAATCAAC
66432 ATGGTCAACAACCGTGAAAAAACCGGTTGGACCGGCGGTTGAACCGGGTTTGAC
66 ATGGTCAACAACCGTGAAAAAACCGGTTGGACCGGCGGTTGAACCGGGTTTGAC
66486 TGGATAAAAC
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 118 1.00
ACGTcount: A:0.25, C:0.23, G:0.33, T:0.20
Consensus pattern (125 bp):
CCGGTTAAATCGGGAACCGATGGCATGTCCGGTCCTTGAAGGTGTGGGAACCGCGGTTAATCAAC
ATGGTCAACAACCGTGAAAAAACCGGTTGGACCGGCGGTTGAACCGGGTTTGACGACCGG
Found at i:66884 original size:23 final size:22
Alignment explanation
Indices: 66848--66912 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
66838 GAAGACCTCA
*
66848 ATATGAAATTTTGATAACCAAC
1 ATATGAAATATTGATAACCAAC
* * **
66870 ACTATGAGATGTTGATAACCTCC
1 A-TATGAAATATTGATAACCAAC
*
66893 ATATGATATATTGATAACCA
1 ATATGAAATATTGATAACCA
66913 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
ATATGAAATATTGATAACCAAC
Found at i:67037 original size:23 final size:22
Alignment explanation
Indices: 66964--67065 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 22
66954 TCGCATTCTG
* * *
66964 AAATTTTGAT-AATCACACTAT
1 AAATTTTGATAAACCTCCCTAT
* *
66985 GAAATTGTGAT-AACCTCGCTAT
1 -AAATTTTGATAAACCTCCCTAT
* *
67007 GAAATTTTGATAAATCTTCCTAT
1 -AAATTTTGATAAACCTCCCTAT
67030 AAAGTTTTGATAAACCTCCCTAT
1 AAA-TTTTGATAAACCTCCCTAT
67053 AAAATTTTGATAA
1 -AAATTTTGATAA
67066 CTTTCTTATG
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
22 30 0.45
23 34 0.51
24 3 0.04
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAAACCTCCCTAT
Found at i:67142 original size:22 final size:22
Alignment explanation
Indices: 66832--67273 Score: 188
Period size: 22 Copynumber: 20.4 Consensus size: 22
66822 TTTCCTAAGG
*
66832 AATTTTGA-AGACCTCAATATGA
1 AATTTTGATA-ACCTCACTATGA
*
66854 AATTTTGATAACCAACACTATGA
1 AATTTTGATAACC-TCACTATGA
* *
66877 GATGTTGATAACCTC-CATATGA
1 AATTTTGATAACCTCAC-TATGA
* * * **
66899 TATATTGATAACCACGTTATGA
1 AATTTTGATAACCTCACTATGA
* * *
66921 AAATTTAAAAACCTC-CATATG-
1 AATTTTGATAACCTCAC-TATGA
* * * *
66942 AATTGTT-AGTAATCGCATTCTGA
1 AATT-TTGA-TAACCTCACTATGA
* *
66965 AATTTTGATAATCACACTATGA
1 AATTTTGATAACCTCACTATGA
* *
66987 AATTGTGATAACCTCGCTATGA
1 AATTTTGATAACCTCACTATGA
*
67009 AATTTTGATAAATCTTC-CTAT-A
1 AATTTTGAT-AA-CCTCACTATGA
* *
67031 AAGTTTTGATAAACCTCCCTATAA
1 AA-TTTTGAT-AACCTCACTATGA
* *
67055 AATTTTGATAACTTTC-TTATGA
1 AATTTTGATAAC-CTCACTATGA
*
67077 AATCTTGATAA-CT-AC----A
1 AATTTTGATAACCTCACTATGA
*
67093 AATTTTGATAACCTCCCTATGA
1 AATTTTGATAACCTCACTATGA
** *
67115 TTTTTTGATAACCTCATTATGA
1 AATTTTGATAACCTCACTATGA
* ** * *
67137 AATTTTGTTATTCTCCCTATAA
1 AATTTTGATAACCTCACTATGA
* *
67159 AATTTTGATCTACAT-ACTATGA
1 AATTTTGAT-AACCTCACTATGA
* * *
67181 GATTTGGATAACCCTC-TTATGA
1 AATTTTGATAA-CCTCACTATGA
* * *
67203 AAATTTGA-AAACTAAACTATGA
1 AATTTTGATAACCT-CACTATGA
* *
67225 AATTTTGATATCCTC-C-CTGA
1 AATTTTGATAACCTCACTATGA
**
67245 AATTTTGATATTCTC-CT-TGA
1 AATTTTGATAACCTCACTATGA
67265 AATTTTGAT
1 AATTTTGAT
67274 TACTCCATAA
Statistics
Matches: 314, Mismatches: 76, Indels: 62
0.69 0.17 0.14
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
20 33 0.11
21 9 0.03
22 195 0.62
23 57 0.18
24 6 0.02
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACCTCACTATGA
Found at i:67247 original size:20 final size:20
Alignment explanation
Indices: 67222--67273 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
67212 AACTAAACTA
67222 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
* *
67242 TGAAATTTTGATATTCTCCT
1 TGAAATTTTGATATCCTCCC
67262 TGAAATTTTGAT
1 TGAAATTTTGAT
67274 TACTCCATAA
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:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:67431 original size:22 final size:22
Alignment explanation
Indices: 67381--67432 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
67371 TCACATTTTG
*
67381 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGAGAACCTCTTTAT
*
67402 GAAATTTTGAGAACCTCTTTAT
1 AAAATTTTGAGAACCTCTTTAT
67424 AAAATTTTG
1 AAAATTTTG
67433 TTGACCCCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 3 0.11
22 24 0.89
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (22 bp):
AAAATTTTGAGAACCTCTTTAT
Found at i:67450 original size:22 final size:22
Alignment explanation
Indices: 67379--67451 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
67369 AATCACATTT
* * * *
67379 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGAGAACCCCTCTA
* *
67401 TGAAATTTTGAGAACCTCTTTA
1 TGAAATTTTGAGAACCCCTCTA
* *
67423 TAAAATTTTGTTG-ACCCCTCTA
1 TGAAATTTTG-AGAACCCCTCTA
67445 TGAAATT
1 TGAAATT
67452 CTGATAATCA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 42 0.98
23 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGAGAACCCCTCTA
Found at i:67491 original size:22 final size:22
Alignment explanation
Indices: 67463--67515 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
67453 TGATAATCAT
* *
67463 ATTTTGATAACCT-CGCTTTGAA
1 ATTTTGATAA-CTGCACTATGAA
67485 ATTTTGATAACTGCACTATGAA
1 ATTTTGATAACTGCACTATGAA
67507 ATTTTGATA
1 ATTTTGATA
67516 TTCTTCCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (22 bp):
ATTTTGATAACTGCACTATGAA
Found at i:67688 original size:22 final size:22
Alignment explanation
Indices: 67637--67762 Score: 96
Period size: 22 Copynumber: 5.7 Consensus size: 22
67627 ATAACATTCA
* **
67637 TATGAAATTTTGATAACCACAT
1 TATGAAATTTTGATAACCTCCC
* *
67659 TGTAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* *
67681 CATGAAATATT-AGTAACCT-CC
1 TATGAAATTTTGA-TAACCTCCC
* * *
67702 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAACCTCCC
*
67725 TATGAAATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCTCCC
*
67747 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
67763 TCTCTTTGAT
Statistics
Matches: 80, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
21 5 0.06
22 71 0.89
23 4 0.05
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:67711 original size:44 final size:44
Alignment explanation
Indices: 67663--67762 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 44
67653 CCACATTGTA
* *
67663 AAATTTTGATAACCTCCCCATGAAA-TATTAGTAACCTC-CTAATG
1 AAATTTTGATAACCACACCATGAAATTATTA-TAACCTCGCT-ATG
* * *
67707 AAATTTTGTTAACCACACTATGAAATTCTTATAACCTCGCTATG
1 AAATTTTGATAACCACACCATGAAATTATTATAACCTCGCTATG
*
67751 ACATTTTGATAA
1 AAATTTTGATAA
67763 TCTCTTTGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
44 41 0.87
45 6 0.13
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (44 bp):
AAATTTTGATAACCACACCATGAAATTATTATAACCTCGCTATG
Found at i:68668 original size:38 final size:37
Alignment explanation
Indices: 68626--68703 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 37
68616 CATTGAAGAT
68626 AAAGACAAAAAGCAAAATTAAATACAACGATTGGAAAC
1 AAAGACAAAAAGCAAAATTAAATACAACG-TTGGAAAC
* **
68664 AAAGACAAAAGGCAAAATTAAATAGGACGTTGGAAAC
1 AAAGACAAAAAGCAAAATTAAATACAACGTTGGAAAC
68701 AAA
1 AAA
68704 AAGTCAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
37 11 0.30
38 26 0.70
ACGTcount: A:0.59, C:0.12, G:0.17, T:0.13
Consensus pattern (37 bp):
AAAGACAAAAAGCAAAATTAAATACAACGTTGGAAAC
Found at i:69430 original size:22 final size:22
Alignment explanation
Indices: 69399--69471 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
69389 CTCTCTTCCT
69399 TTTTAATTGTCCCTTTTAACTA
1 TTTTAATTGTCCCTTTTAACTA
* * * *
69421 TTTTATTTGT-TCTCTTCA-T-
1 TTTTAATTGTCCCTTTTAACTA
*
69440 TTTTAATTGTCCCTTTTAGCTA
1 TTTTAATTGTCCCTTTTAACTA
*
69462 TTTTATTTGT
1 TTTTAATTGT
69472 TTAAGAAAAG
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 9 0.24
20 5 0.13
21 6 0.16
22 18 0.47
ACGTcount: A:0.16, C:0.15, G:0.07, T:0.62
Consensus pattern (22 bp):
TTTTAATTGTCCCTTTTAACTA
Found at i:69435 original size:41 final size:41
Alignment explanation
Indices: 69390--69472 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
69380 ATATACTCTC
*
69390 TCTCTTCCTTTTTAATTGTCCCTTTTAACTATTTTATTTGT
1 TCTCTTCATTTTTAATTGTCCCTTTTAACTATTTTATTTGT
*
69431 TCTCTTCATTTTTAATTGTCCCTTTTAGCTATTTTATTTGT
1 TCTCTTCATTTTTAATTGTCCCTTTTAACTATTTTATTTGT
69472 T
1 T
69473 TAAGAAAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.14, C:0.18, G:0.06, T:0.61
Consensus pattern (41 bp):
TCTCTTCATTTTTAATTGTCCCTTTTAACTATTTTATTTGT
Found at i:74081 original size:20 final size:20
Alignment explanation
Indices: 74053--74111 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
74043 CAAATTTTGG
*
74053 AAGGGTTATTAACACTTATA
1 AAGGGTTATTAAGACTTATA
* * * *
74073 AAGGCTTATCAAGTCTTATG
1 AAGGGTTATTAAGACTTATA
74093 AAGGGTTATTAAGACTTAT
1 AAGGGTTATTAAGACTTAT
74112 TGAAGCAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (20 bp):
AAGGGTTATTAAGACTTATA
Found at i:77199 original size:6 final size:6
Alignment explanation
Indices: 77192--77232 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
77182 TAAATATATG
*
77192 ATTATG ATTATC ATTATC ATTATC ATTATC ATTATC ATTAT
1 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTAT
77233 AGTTAGTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.51
Consensus pattern (6 bp):
ATTATC
Found at i:77600 original size:25 final size:25
Alignment explanation
Indices: 77572--77622 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
77562 ATAAATATAA
* *
77572 TTTAATTTAAGTACATACAAAATTG
1 TTTAATTCAAGTACATAAAAAATTG
*
77597 TTTAATTCAAGTGCATAAAAAATTG
1 TTTAATTCAAGTACATAAAAAATTG
77622 T
1 T
77623 ATAGTAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (25 bp):
TTTAATTCAAGTACATAAAAAATTG
Found at i:78314 original size:24 final size:20
Alignment explanation
Indices: 78259--78301 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
78249 GGTAAGAAAA
*
78259 TAAAACACATTATTATTACT
1 TAAAATACATTATTATTACT
78279 TAAAATACATTATTATTACT
1 TAAAATACATTATTATTACT
78299 TAA
1 TAA
78302 TTAAATATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAATACATTATTATTACT
Found at i:82344 original size:3 final size:3
Alignment explanation
Indices: 82336--82394 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
82326 ACTCTTATAC
82336 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
82384 ATA ATA ATA AT
1 ATA ATA ATA AT
82395 CTAAAATCGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:83058 original size:16 final size:16
Alignment explanation
Indices: 83034--83069 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
83024 TGGTCGTGTC
*
83034 ATTATAAATAGAGACA
1 ATTAAAAATAGAGACA
83050 ATTAAAAATAGAGACA
1 ATTAAAAATAGAGACA
83066 ATTA
1 ATTA
83070 GGTAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.25
Consensus pattern (16 bp):
ATTAAAAATAGAGACA
Done.