Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011690.1 Corchorus capsularis cultivar CVL-1 contig11711, 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: 75075
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:470 original size:33 final size:32
Alignment explanation
Indices: 433--539 Score: 142
Period size: 33 Copynumber: 3.2 Consensus size: 32
423 CGCCAAGCGA
* *
433 TGGCCGGTTGTGGCCGGACATATCCATGTCGCG
1 TGGCCGG-TGTGGCCGGGCATCTCCATGTCGCG
*
466 TGGCCGGTGATGGCCGGGCATCTCCATGTCGCA
1 TGGCCGGTG-TGGCCGGGCATCTCCATGTCGCG
* *
499 TGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCG
1 TGGCCGGTGTGGC-CGGGCATCTCCATGTCGCG
532 TGGCCGGT
1 TGGCCGGT
540 TCTCCAAGTC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
32 5 0.08
33 61 0.92
ACGTcount: A:0.10, C:0.29, G:0.38, T:0.22
Consensus pattern (32 bp):
TGGCCGGTGTGGCCGGGCATCTCCATGTCGCG
Found at i:545 original size:21 final size:21
Alignment explanation
Indices: 519--560 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
509 TGCGCGGGCA
* *
519 TCTCCAAGTCGCGTGGCCGGT
1 TCTCCAAGTCGCATGGACGGT
540 TCTCCAAGTCGCATGGACGGT
1 TCTCCAAGTCGCATGGACGGT
561 CACTTGTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.24
Consensus pattern (21 bp):
TCTCCAAGTCGCATGGACGGT
Found at i:9021 original size:30 final size:30
Alignment explanation
Indices: 8985--9052 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
8975 GTGTTTGCGA
*
8985 TGTCCC-GAGAAAGTATGTCTGATTGAGTCC
1 TGTCCCGGA-AAAGTATGTCTAATTGAGTCC
9015 TGTCCCGGAAAAGTATGTCTAATTGAGTCC
1 TGTCCCGGAAAAGTATGTCTAATTGAGTCC
9045 TGTCCCGG
1 TGTCCCGG
9053 GACAGAGTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 34 0.94
31 2 0.06
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (30 bp):
TGTCCCGGAAAAGTATGTCTAATTGAGTCC
Found at i:10323 original size:18 final size:18
Alignment explanation
Indices: 10300--10352 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
10290 ATTTCTTTTC
*
10300 TTTCTATTAGATTAGTAT
1 TTTCTATTATATTAGTAT
*
10318 TTTCTATTATATT--TTT
1 TTTCTATTATATTAGTAT
*
10334 TTTCTATTCTATTAGTAT
1 TTTCTATTATATTAGTAT
10352 T
1 T
10353 AGATTAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 14 0.48
18 15 0.52
ACGTcount: A:0.23, C:0.08, G:0.06, T:0.64
Consensus pattern (18 bp):
TTTCTATTATATTAGTAT
Found at i:10358 original size:5 final size:6
Alignment explanation
Indices: 10343--10393 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
10333 TTTTCTATTC
* *
10343 TATTAG TATTAG -ATTAG TATT-C TATT-C TATTAG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
10387 TATTAG T
1 TATTAG T
10394 TGTGATCCCG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
5 19 0.47
6 21 0.52
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:10365 original size:27 final size:27
Alignment explanation
Indices: 10335--10390 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
10325 TATATTTTTT
10335 TTCTATTCTATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTAGTA
10362 TTCTATTCTATTAGTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTAGTA
10389 TT
1 TT
10391 AGTTGTGATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54
Consensus pattern (27 bp):
TTCTATTCTATTAGTATTAGATTAGTA
Found at i:10981 original size:31 final size:32
Alignment explanation
Indices: 10929--10993 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
10919 AATTAAGAAC
10929 AATAAACTAAACTAAGGAAATCAA-TAACAATT
1 AATAAACTAAACTAAGGAAATCAATTAA-AATT
* *
10961 AATAAAGTAAATTAA-GAAATCAATTAAAATT
1 AATAAACTAAACTAAGGAAATCAATTAAAATT
10992 AA
1 AA
10994 GAAAACCCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 14 0.47
32 16 0.53
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.25
Consensus pattern (32 bp):
AATAAACTAAACTAAGGAAATCAATTAAAATT
Found at i:13398 original size:34 final size:34
Alignment explanation
Indices: 13356--13421 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
13346 AAGATAGCAA
13356 AGAACAAAAGCCATAACAATAAACACCCATGAAT
1 AGAACAAAAGCCATAACAATAAACACCCATGAAT
* *
13390 AGAACAAAAGTCGTAACAATAAACACCCATGA
1 AGAACAAAAGCCATAACAATAAACACCCATGA
13422 TTGATCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.55, C:0.23, G:0.11, T:0.12
Consensus pattern (34 bp):
AGAACAAAAGCCATAACAATAAACACCCATGAAT
Found at i:15137 original size:15 final size:15
Alignment explanation
Indices: 15117--15146 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15107 TACTTCTATA
15117 TATTTAGATTTTGAG
1 TATTTAGATTTTGAG
15132 TATTTAGATTTTGAG
1 TATTTAGATTTTGAG
15147 GATCGCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (15 bp):
TATTTAGATTTTGAG
Found at i:16263 original size:34 final size:34
Alignment explanation
Indices: 16225--16292 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
16215 TATGTATTCA
* * *
16225 ACTAATAATAATCCATTATTATTTGAATTTAGGG
1 ACTAATAATAATCCACTATTAATTGAATATAGGG
*
16259 ACTAATAATAATTCACTATTAATTGAATATAGGG
1 ACTAATAATAATCCACTATTAATTGAATATAGGG
16293 TACAATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (34 bp):
ACTAATAATAATCCACTATTAATTGAATATAGGG
Found at i:16752 original size:40 final size:40
Alignment explanation
Indices: 16708--16783 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
16698 ATTTTCCTAC
*
16708 TGAAAGCATCATTTTCTTCTTCATTGGGCTGGGGGAGAGA
1 TGAAAGCATCATTTTCTTCTCCATTGGGCTGGGGGAGAGA
* *
16748 TGAAAGCTTTATTTTCTTCTCCATTGGGCTGGGGGA
1 TGAAAGCATCATTTTCTTCTCCATTGGGCTGGGGGA
16784 AAGTTCCTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.36
Consensus pattern (40 bp):
TGAAAGCATCATTTTCTTCTCCATTGGGCTGGGGGAGAGA
Found at i:17808 original size:31 final size:31
Alignment explanation
Indices: 17772--17838 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
17762 CAGAAAATAG
*
17772 TTTATTTGCTAAATACCAAGTTATACGTGGA
1 TTTATTTGCTAAATACCAAGTTATACATGGA
* * * *
17803 TTTATTTTCTAATTACCACGTTATTCATGGA
1 TTTATTTGCTAAATACCAAGTTATACATGGA
17834 TTTAT
1 TTTAT
17839 AAAGATGAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.46
Consensus pattern (31 bp):
TTTATTTGCTAAATACCAAGTTATACATGGA
Found at i:17944 original size:24 final size:25
Alignment explanation
Indices: 17893--17945 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
17883 AATTGTACTT
* *
17893 TATGAACCATTTTTTCTTTTTAGGTA
1 TATGAACCATTTTGTC-TTTTAAGTA
*
17919 TATGAACCATTTTGTC-TTTAATTA
1 TATGAACCATTTTGTCTTTTAAGTA
17943 TAT
1 TAT
17946 AATGCTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.38
26 15 0.62
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.53
Consensus pattern (25 bp):
TATGAACCATTTTGTCTTTTAAGTA
Found at i:27810 original size:2 final size:2
Alignment explanation
Indices: 27803--27828 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27793 GTTCTTTGTA
27803 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
27829 GTAAGTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27963 original size:23 final size:22
Alignment explanation
Indices: 27937--27982 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
27927 TTGTAATTTG
27937 TAAATT-GTAATTTTTTAATGAAA
1 TAAATTAGTAA-TTTTT-ATGAAA
*
27960 TAAATTATTAATTTTTATGAAA
1 TAAATTAGTAATTTTTATGAAA
27982 T
1 T
27983 TTTATGCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 11 0.52
24 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
TAAATTAGTAATTTTTATGAAA
Found at i:28160 original size:4 final size:4
Alignment explanation
Indices: 28153--28199 Score: 60
Period size: 4 Copynumber: 11.5 Consensus size: 4
28143 AAAAAACGGA
*
28153 AAAG AAAGG AAAG AAAGG AAAG AAAG -AAG AAAG GAAG AAAG AAAG AA
1 AAAG AAA-G AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
28200 TGGTGTCATG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
3 3 0.08
4 27 0.71
5 8 0.21
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:28165 original size:9 final size:9
Alignment explanation
Indices: 28153--28199 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
28143 AAAAAACGGA
28153 AAAGAAAGG
1 AAAGAAAGG
28162 AAAGAAAGG
1 AAAGAAAGG
28171 AAAGAAA-G
1 AAAGAAAGG
28179 -AAGAAAGG
1 AAAGAAAGG
28187 -AAGAAA-G
1 AAAGAAAGG
28194 AAAGAA
1 AAAGAA
28200 TGGTGTCATG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.19
8 13 0.36
9 16 0.44
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (9 bp):
AAAGAAAGG
Found at i:30763 original size:21 final size:21
Alignment explanation
Indices: 30731--30784 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
30721 GGTCATGGTC
30731 CCATGCGA-TGGCGTGACTACT
1 CCATGC-ATTGGCGTGACTACT
* * * *
30752 CCTTGCTTTGGCGTGGCTCCT
1 CCATGCATTGGCGTGACTACT
30773 CCATGCATTGGC
1 CCATGCATTGGC
30785 CGGTCATATG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.11, C:0.31, G:0.28, T:0.30
Consensus pattern (21 bp):
CCATGCATTGGCGTGACTACT
Found at i:32281 original size:12 final size:12
Alignment explanation
Indices: 32261--32316 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
32251 GATCTAGAAA
32261 AAAAT-GTGTTG
1 AAAATGGTGTTG
32272 AAAATGGTGTTG
1 AAAATGGTGTTG
* *
32284 AAAATTGTTTTG
1 AAAATGGTGTTG
*
32296 AAAAAATTGTGTTG
1 --AAAATGGTGTTG
32310 AAAATGG
1 AAAATGG
32317 GTGTGCCCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
11 5 0.13
12 22 0.58
14 11 0.29
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (12 bp):
AAAATGGTGTTG
Found at i:37954 original size:21 final size:22
Alignment explanation
Indices: 37914--37957 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
37904 GTCTAAAGCA
37914 CATTTGCTAAAAGAACTTCAAT
1 CATTTGCTAAAAGAACTTCAAT
37936 CATTTGCTAAAAG-ACTTCAAT
1 CATTTGCTAAAAGAACTTCAAT
37957 C
1 C
37958 TTTCACGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (22 bp):
CATTTGCTAAAAGAACTTCAAT
Found at i:41255 original size:3 final size:3
Alignment explanation
Indices: 41247--41292 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
41237 TGCGGCATAT
41247 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
41293 AATTACTACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42753 original size:50 final size:50
Alignment explanation
Indices: 42677--42799 Score: 201
Period size: 50 Copynumber: 2.4 Consensus size: 50
42667 GGGTGAATTA
*
42677 ATTAATAATTTTATTTTCTTAACATACCTAACAATGTACTCTTCTTAGATG
1 ATTAAT-ATTTAATTTTCTTAACATACCTAACAATGTACTCTTCTTAGATG
* *
42728 ATTAATATTTAAATTTCTTAACATACCTAGCAATGTACTCTTCTTAGATG
1 ATTAATATTTAATTTTCTTAACATACCTAACAATGTACTCTTCTTAGATG
42778 ATTAATATTTGAATTTTCTTAA
1 ATTAATATTT-AATTTTCTTAA
42800 AATATATTTG
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 51 0.76
51 16 0.24
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.46
Consensus pattern (50 bp):
ATTAATATTTAATTTTCTTAACATACCTAACAATGTACTCTTCTTAGATG
Found at i:43018 original size:16 final size:16
Alignment explanation
Indices: 42997--43051 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
42987 ATTTTCGGGT
42997 TCGGGTTAAATTTGGG
1 TCGGGTTAAATTTGGG
* *
43013 TCGGGTT-GATTCGGG
1 TCGGGTTAAATTTGGG
43028 TTCGGGTTAAATTTGGG
1 -TCGGGTTAAATTTGGG
*
43045 TCAGGTT
1 TCGGGTT
43052 GATTCGGGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 6 0.19
16 20 0.62
17 6 0.19
ACGTcount: A:0.15, C:0.09, G:0.38, T:0.38
Consensus pattern (16 bp):
TCGGGTTAAATTTGGG
Found at i:43027 original size:32 final size:32
Alignment explanation
Indices: 42990--43065 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
42980 TCAGACTATT
*
42990 TTCGGGTTCGGGTTAAATTTGGGTCGGGTTGA
1 TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
43022 TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
1 TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
43054 TTCGGGTTCGGG
1 TTCGGGTTCGGG
43066 CTCGGATTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.12, C:0.11, G:0.41, T:0.37
Consensus pattern (32 bp):
TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
Found at i:43240 original size:20 final size:20
Alignment explanation
Indices: 43208--43245 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43198 ATAGATGAAA
*
43208 TTTTCAGAAATTATTATTTC
1 TTTTCAGAAATTAGTATTTC
43228 TTTTCA-AATATTAGTATT
1 TTTTCAGAA-ATTAGTATT
43246 GAATTCAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTCAGAAATTAGTATTTC
Found at i:43284 original size:16 final size:16
Alignment explanation
Indices: 43265--43342 Score: 77
Period size: 16 Copynumber: 4.9 Consensus size: 16
43255 TTTTTTCAAG
43265 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
* *
43281 TTCGGGTTTC-AGATTT
1 TTCGGG-TTCGGGTTTT
* *
43297 TTCGGGTTCTGATTTT
1 TTCGGGTTCGGGTTTT
* *
43313 TTCGGGCTCGGATTTT
1 TTCGGGTTCGGGTTTT
*
43329 TTTGGGTTCGGGTT
1 TTCGGGTTCGGGTT
43343 CGGGTGGGTT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
15 3 0.06
16 44 0.88
17 3 0.06
ACGTcount: A:0.05, C:0.13, G:0.32, T:0.50
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:43301 original size:32 final size:32
Alignment explanation
Indices: 43265--43342 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
43255 TTTTTTCAAG
*
43265 TTCGGGTTCGGGTTTTTTCGGGTTTCAGA-TTT
1 TTCGGGTTCGGGTTTTTTCGGG-CTCAGATTTT
* * *
43297 TTCGGGTTCTGATTTTTTCGGGCTCGGATTTT
1 TTCGGGTTCGGGTTTTTTCGGGCTCAGATTTT
*
43329 TTTGGGTTCGGGTT
1 TTCGGGTTCGGGTT
43343 CGGGTGGGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 4 0.11
32 34 0.89
ACGTcount: A:0.05, C:0.13, G:0.32, T:0.50
Consensus pattern (32 bp):
TTCGGGTTCGGGTTTTTTCGGGCTCAGATTTT
Found at i:46787 original size:107 final size:108
Alignment explanation
Indices: 46538--46829 Score: 428
Period size: 107 Copynumber: 2.7 Consensus size: 108
46528 ACTATTATAG
* *
46538 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
46603 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACC-AAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
*
46652 TTTTATTCTATTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
46717 TTACCAAAAATTTGGATATATTAAAA-TTTTTCTAATATACAA
66 TTACCAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* **
46759 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTA-
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAATTACTTTAT
46822 TTTTACCA
64 TTTTACCA
46830 TTTTAATTTA
Statistics
Matches: 168, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
106 1 0.01
107 69 0.41
108 31 0.18
109 42 0.25
110 3 0.02
111 2 0.01
114 20 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (108 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:62549 original size:6 final size:6
Alignment explanation
Indices: 62538--62570 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
62528 GTTTCTTTAT
62538 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTT
62571 GGAGTGAGAG
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:0.00, C:0.15, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTTGC
Found at i:64094 original size:1 final size:1
Alignment explanation
Indices: 64088--64116 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
64078 ATACTAACTC
64088 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
64117 GCAATCACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:66468 original size:11 final size:11
Alignment explanation
Indices: 66425--66462 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
66415 TTTGTATTCA
*
66425 AAATAAATTAT
1 AAATTAATTAT
66436 CAAA-TAATTAT
1 -AAATTAATTAT
66447 AAATTAATTAT
1 AAATTAATTAT
66458 AAATT
1 AAATT
66463 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:66703 original size:16 final size:16
Alignment explanation
Indices: 66679--66713 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
66669 ATTTTCTTTT
66679 TCTCCATATTCTATTG
1 TCTCCATATTCTATTG
* *
66695 TCTCTATATTCTCTTG
1 TCTCCATATTCTATTG
66711 TCT
1 TCT
66714 TTTCCATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.26, G:0.06, T:0.54
Consensus pattern (16 bp):
TCTCCATATTCTATTG
Found at i:66965 original size:13 final size:13
Alignment explanation
Indices: 66947--66976 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
66937 TAATCCAAAT
*
66947 TTTAAAATTATTA
1 TTTAAAATTATAA
66960 TTTAAAATTATAA
1 TTTAAAATTATAA
66973 TTTA
1 TTTA
66977 TTACTAATAT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTAAAATTATAA
Found at i:67000 original size:16 final size:17
Alignment explanation
Indices: 66957--67014 Score: 66
Period size: 16 Copynumber: 3.4 Consensus size: 17
66947 TTTAAAATTA
*
66957 TTATTTAAAATTATAAT
1 TTATTTATAATTATAAT
66974 TTA-TTACTAA-TATAAT
1 TTATTTA-TAATTATAAT
66990 TTATTTATAATTATTAAT
1 TTATTTATAATTA-TAAT
*
67008 ATATTTA
1 TTATTTA
67015 AATGAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 15 0.43
17 10 0.29
18 10 0.29
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTTATAATTATAAT
Found at i:67152 original size:75 final size:76
Alignment explanation
Indices: 67061--67210 Score: 239
Period size: 77 Copynumber: 2.0 Consensus size: 76
67051 TGATATCAGG
*
67061 TAATTAAAGG-TATTTTTAATAGGAGGTAACCCTCTCCTTTTCCATAATCCCGCCCCGTCCATCA
1 TAATTAAAGGTTATTTTTAATAGGAGGTAACCCTCTCCTTTTCCATAATCCCACCCCGTCCATCA
67125 CAGGATTCGTC
66 CAGGATTCGTC
* * * *
67136 TAATTAAAGGTTTTTTTTTAATAGGAGGTAGCCCTCTCCTTTTCCATAATCTCACCCTGTCCATC
1 TAATTAAAGG-TTATTTTTAATAGGAGGTAACCCTCTCCTTTTCCATAATCCCACCCCGTCCATC
67201 ACAGGATTCG
65 ACAGGATTCG
67211 AACGCGAGAC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
75 10 0.15
77 58 0.85
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.35
Consensus pattern (76 bp):
TAATTAAAGGTTATTTTTAATAGGAGGTAACCCTCTCCTTTTCCATAATCCCACCCCGTCCATCA
CAGGATTCGTC
Found at i:69876 original size:109 final size:105
Alignment explanation
Indices: 69758--69995 Score: 327
Period size: 106 Copynumber: 2.2 Consensus size: 105
69748 AAAAGAATCT
*
69758 AGCAAGAAGAAAATTGCAGCACATTCAACCCACAAATTCAACCCGCAAGGAA-AAAATTGCAGCA
1 AGCAAGAAGAAAATTGCAGCACATTCAACCCACAAATTCAA-CCG--A-GAAGAAAATTACAGCA
* * *
69822 CATACATCAAGAAGAAAATTCCATTACCCACAAGAAAAAACAT-T
62 CATACAGCAACAAGAAAATTCCATTACCCACAAG-AAAAACATCC
69866 ATGCAAGAAGAAAATTGCAGCACATTCAACCCACAAATTCAACCGAGAAGAAAATTACAGCACAT
1 A-GCAAGAAGAAAATTGCAGCACATTCAACCCACAAATTCAACCGAGAAGAAAATTACAGCACAT
* * *
69931 CCAGCAACAAGAAAATTCTATTACCCACAAGGAAAACATCC
65 ACAGCAACAAGAAAATTCCATTACCCACAAGAAAAACATCC
**
69972 AGCAAGAAGAAAATTAAAGCACAT
1 AGCAAGAAGAAAATTGCAGCACAT
69996 CCAGCCAGAA
Statistics
Matches: 118, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
105 31 0.26
106 43 0.36
108 4 0.03
109 40 0.34
ACGTcount: A:0.49, C:0.24, G:0.13, T:0.15
Consensus pattern (105 bp):
AGCAAGAAGAAAATTGCAGCACATTCAACCCACAAATTCAACCGAGAAGAAAATTACAGCACATA
CAGCAACAAGAAAATTCCATTACCCACAAGAAAAACATCC
Found at i:71396 original size:27 final size:28
Alignment explanation
Indices: 71337--71404 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 28
71327 ATCCAGGGGT
* *
71337 ATTTTGGTCATTTTCACATCATAGGGGC
1 ATTTTGGTCATTTGCACATCATAGGGAC
* *
71365 ATTTTGGTCATTTGCATAT-TTAGGGAC
1 ATTTTGGTCATTTGCACATCATAGGGAC
*
71392 ATTTTGGTAATTT
1 ATTTTGGTCATTT
71405 TTAGTACACC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 18 0.51
28 17 0.49
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.46
Consensus pattern (28 bp):
ATTTTGGTCATTTGCACATCATAGGGAC
Found at i:71529 original size:24 final size:24
Alignment explanation
Indices: 71497--71547 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
71487 CTTTTGGCAT
*
71497 TTTTTGCATCCCAATATTCTTGCA
1 TTTTGGCATCCCAATATTCTTGCA
*
71521 TTTTGGCATCTCAATATTCTTGCA
1 TTTTGGCATCCCAATATTCTTGCA
71545 TTT
1 TTT
71548 CAGTCACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTTGGCATCCCAATATTCTTGCA
Found at i:72293 original size:26 final size:26
Alignment explanation
Indices: 72210--72285 Score: 143
Period size: 26 Copynumber: 2.9 Consensus size: 26
72200 CATTAAAGGG
72210 AACAAGGAACATGCAAGGGGCTGTGA
1 AACAAGGAACATGCAAGGGGCTGTGA
*
72236 AACAAGGAACATACAAGGGGCTGTGA
1 AACAAGGAACATGCAAGGGGCTGTGA
72262 AACAAGGAACATGCAAGGGGCTGT
1 AACAAGGAACATGCAAGGGGCTGT
72286 CAAGCAAGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.39, C:0.16, G:0.33, T:0.12
Consensus pattern (26 bp):
AACAAGGAACATGCAAGGGGCTGTGA
Found at i:73814 original size:6 final size:6
Alignment explanation
Indices: 73803--73838 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
73793 TTTTATAGCA
73803 TTTATT TTTATT TTTATT TTTA-- -TTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
73839 CAGCGCATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
3 3 0.11
6 24 0.89
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:73828 original size:15 final size:15
Alignment explanation
Indices: 73810--73838 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
73800 GCATTTATTT
73810 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
73825 TTATTTTTATTTTT
1 TTATTTTTATTTTT
73839 CAGCGCATGC
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Done.