Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014342.1 Corchorus capsularis cultivar CVL-1 contig14363, 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: 56834
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:1605 original size:33 final size:33
Alignment explanation
Indices: 1529--1652 Score: 144
Period size: 33 Copynumber: 3.7 Consensus size: 33
1519 TAGACAAAGG
* *
1529 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGGTTGTGGCCGGACAT-GCCCAT
** *
1562 GTCGTTTGGCCGGTTGTAGCCGGACATGCCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGCCCAT
*
1595 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTG-TGGCCGGACATGCCCAT
1628 GTCGCGTGGCCGGTCTTGTGGCCGG
1 GTCGCGTGGCCGG--TTGTGGCCGG
1653 TGTTGCGCGG
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
32 6 0.08
33 62 0.81
35 7 0.09
36 2 0.03
ACGTcount: A:0.08, C:0.27, G:0.42, T:0.23
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTGGCCGGACATGCCCAT
Found at i:5558 original size:5 final size:5
Alignment explanation
Indices: 5548--5581 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
5538 CTGGTCGAAA
*
5548 TTTAT TTTAT TTTAT TTTAT TTTTT TTCTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT-TAT TTT
5582 TCGATATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:5689 original size:9 final size:8
Alignment explanation
Indices: 5655--5688 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
5645 GAATCAACTA
5655 TGAATTTT
1 TGAATTTT
*
5663 TGAAGTTTC
1 TGAA-TTTT
5672 TGAATTTT
1 TGAATTTT
5680 TGAATTTT
1 TGAATTTT
5688 T
1 T
5689 TCAAGCAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:6670 original size:33 final size:33
Alignment explanation
Indices: 6594--6717 Score: 144
Period size: 33 Copynumber: 3.7 Consensus size: 33
6584 TAGACAAAGG
* *
6594 GTCGCGTGGCCGGTTGTGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGGTTGTGGCCGGACAT-GCCCAT
** *
6627 GTCGTTTGGCCGGTTGTAGCCGGACATGCCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGCCCAT
*
6660 GTCGCGTGGCCGG-TGATGGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTG-TGGCCGGACATGCCCAT
6693 GTCGCGTGGCCGGTCTTGTGGCCGG
1 GTCGCGTGGCCGG--TTGTGGCCGG
6718 TGTTGCGCGG
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
32 6 0.08
33 62 0.81
35 7 0.09
36 2 0.03
ACGTcount: A:0.08, C:0.27, G:0.42, T:0.23
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTGGCCGGACATGCCCAT
Found at i:13917 original size:20 final size:20
Alignment explanation
Indices: 13894--13931 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13884 GGCGCAGCAC
13894 CAATTTGCAAATCAAATGTT
1 CAATTTGCAAATCAAATGTT
*
13914 CAATTTGTAAATCAAATG
1 CAATTTGCAAATCAAATG
13932 CCTTGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (20 bp):
CAATTTGCAAATCAAATGTT
Found at i:14134 original size:14 final size:14
Alignment explanation
Indices: 14115--14142 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14105 TGATAGTAAT
14115 CTAAATGGACTAAA
1 CTAAATGGACTAAA
14129 CTAAATGGACTAAA
1 CTAAATGGACTAAA
14143 ATTAATATGC
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:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
CTAAATGGACTAAA
Found at i:14808 original size:48 final size:48
Alignment explanation
Indices: 14750--14908 Score: 153
Period size: 47 Copynumber: 3.4 Consensus size: 48
14740 AAAACCTGTT
*
14750 GACCAACTTTGGTCACTAAATTGAAAATTCGCATGGAAGCGAGAGAAA
1 GACCAACTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAGAAA
* * **
14798 GACCATCTTTGGTCACTAACTTGCCAACTCGCATGGAAGCGAGAG-AA
1 GACCAACTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAGAAA
** * * * ** * **
14845 TCCCAACTTTGGCCACTGATTTGCTATCTCGTGTGGAAGCGAGA-AAA
1 GACCAACTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAGAAA
14892 GACCATA-TTTGGTCACT
1 GACCA-ACTTTGGTCACT
14909 TAACTTATGT
Statistics
Matches: 91, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
47 50 0.55
48 41 0.45
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (48 bp):
GACCAACTTTGGTCACTAAATTGAAAACTCGCATGGAAGCGAGAGAAA
Found at i:15119 original size:69 final size:69
Alignment explanation
Indices: 15007--15178 Score: 299
Period size: 69 Copynumber: 2.5 Consensus size: 69
14997 CTGAACTCGA
* * * *
15007 CTTATGGAAAAGCCCCTGAATGCTTGGATGAAACCAAATCTTAAACTCTCTCGCGTGGAAGCGAT
1 CTTATGGAAAAGCCTCTG-CTGCTTGGATGGAACCAAATCTTAAACTCTCTCGCGTGGAAGCGAG
15072 TTTAG
65 TTTAG
15077 CTTATGGAAAAGCCTCTGCTGCTTGGATGGAACCAAATCTTAAACTCTCTCGCGTGGAAGCGAGT
1 CTTATGGAAAAGCCTCTGCTGCTTGGATGGAACCAAATCTTAAACTCTCTCGCGTGGAAGCGAGT
15142 TTAG
66 TTAG
15146 CTTATGGAAAAGCCTCTGCTGCTTGGATGGAAC
1 CTTATGGAAAAGCCTCTGCTGCTTGGATGGAAC
15179 TGACTCGCAT
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
69 81 0.83
70 17 0.17
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (69 bp):
CTTATGGAAAAGCCTCTGCTGCTTGGATGGAACCAAATCTTAAACTCTCTCGCGTGGAAGCGAGT
TTAG
Found at i:16108 original size:50 final size:50
Alignment explanation
Indices: 16051--16157 Score: 135
Period size: 50 Copynumber: 2.1 Consensus size: 50
16041 TAAAACGCCC
* **
16051 TTTGAAAAGCAGACTTTGA-TCTTGGACTCACAAATGGAATGCAATCTTAT
1 TTTGAAAAGC-GAATTTGAGTAATGGACTCACAAATGGAATGCAATCTTAT
* * * *
16101 TTTGAAAATCGAATTTTAGTAATGGACTCACAAATGGAGTGCCATCTTAT
1 TTTGAAAAGCGAATTTGAGTAATGGACTCACAAATGGAATGCAATCTTAT
16151 TTTGAAA
1 TTTGAAA
16158 CTTGTTGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
49 6 0.12
50 43 0.88
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (50 bp):
TTTGAAAAGCGAATTTGAGTAATGGACTCACAAATGGAATGCAATCTTAT
Found at i:16817 original size:20 final size:20
Alignment explanation
Indices: 16789--16834 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
16779 TCACTCTTCC
*
16789 TTTCACTTTCATTTTCAATT
1 TTTCACTTTCACTTTCAATT
*
16809 TTTCCCTTTCACTTTCAA-T
1 TTTCACTTTCACTTTCAATT
16828 TTTCACT
1 TTTCACT
16835 CTTTTTTCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.17, C:0.26, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTCACTTTCACTTTCAATT
Found at i:20747 original size:21 final size:22
Alignment explanation
Indices: 20722--20769 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
20712 CGCACTAAGT
*
20722 TTGATTTGAAT-TTGAAAAC-C
1 TTGATTTAAATCTTGAAAACTC
20742 TCTGA-TTAAATCTTGAAAACTC
1 T-TGATTTAAATCTTGAAAACTC
20764 TTGATT
1 TTGATT
20770 ACCAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
20 6 0.26
21 14 0.61
22 3 0.13
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (22 bp):
TTGATTTAAATCTTGAAAACTC
Found at i:20883 original size:20 final size:23
Alignment explanation
Indices: 20860--20905 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 23
20850 CATCTTTTTA
20860 TTTTTCTGA-TTTT-TTC-ATTT
1 TTTTTCTGAGTTTTCTTCGATTT
*
20880 TTTTTTTGAGTTTTCTTCGATTT
1 TTTTTCTGAGTTTTCTTCGATTT
20903 TTT
1 TTT
20906 CCTTGACCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 4 0.18
22 3 0.14
23 7 0.32
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (23 bp):
TTTTTCTGAGTTTTCTTCGATTT
Found at i:20902 original size:23 final size:21
Alignment explanation
Indices: 20855--20905 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
20845 TATTGCATCT
20855 TTTTATTTTTCTGATTTTTTCA
1 TTTT-TTTTTCTGATTTTTTCA
20877 TTTTTTTTT-TGAGTTTTCTTCGA
1 TTTTTTTTTCTGA-TTTT-TTC-A
20900 TTTTTT
1 TTTTTT
20906 CCTTGACCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.12
21 9 0.35
22 7 0.27
23 7 0.27
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.75
Consensus pattern (21 bp):
TTTTTTTTTCTGATTTTTTCA
Found at i:20911 original size:23 final size:21
Alignment explanation
Indices: 20869--20911 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
20859 ATTTTTCTGA
**
20869 TTTTTTCATTTTTTTTTTGAG
1 TTTTTTCATTTTTTCCTTGAG
20890 TTTTCTTCGATTTTTTCCTTGA
1 TTTT-TTC-ATTTTTTCCTTGA
20912 CCTCTACTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 3 0.17
23 11 0.61
ACGTcount: A:0.09, C:0.12, G:0.09, T:0.70
Consensus pattern (21 bp):
TTTTTTCATTTTTTCCTTGAG
Found at i:23424 original size:19 final size:19
Alignment explanation
Indices: 23400--23438 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
23390 GAACCCCTTT
23400 TCTCCTATTGTAAAATCCA
1 TCTCCTATTGTAAAATCCA
23419 TCTCCTATTGTAAAATCCA
1 TCTCCTATTGTAAAATCCA
23438 T
1 T
23439 GCTGCAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (19 bp):
TCTCCTATTGTAAAATCCA
Found at i:23934 original size:262 final size:261
Alignment explanation
Indices: 23453--23976 Score: 994
Period size: 262 Copynumber: 2.0 Consensus size: 261
23443 CAAAGTGCCT
* *
23453 CTTCAAATTTGTTTCTTGAATTCAAAGTTGCTTGCTGCATATGAATTAGTTTTGTACCTTGAACT
1 CTTCAAATTTGTTTCTTGAATTCAAAGTTGCTTGCTGCATATGAATCAGTTTTGTACCCTGAACT
*
23518 TCAGAATTCATAACTTCTTCAATTCAGCTCCAAATTGTGTGTTTTTGTAGGGTATGGAAAACTTG
66 TCAGAATTCATAACTTCTTCAATTCAGCTCCAAATTGTGTGTTTTTGCAGGGTATGGAAAACTTG
23583 GAGAGTGCACTTCAACTTCCATGAAGACCACTTTGTCAAACAGAGTCGTCTTGGGTGCCAAATTT
131 GAGAGTGCACTTCAACTTCCATGAAGACCACTTTGTCAAACAGAGTCGTCTTGGGTGCCAAATTT
23648 GAAGTTTTCTCTGGCTGCAACTGCTGTCTAGAATTTCTGCGATTTTTGGAGGCCTAGACTGCGGG
196 GAAGTTTTCTCTGGCTGCAACTGCTGTCTAGAATTTCTGCGATTTTTGGAGGCCTAGACTGCGGG
23713 G
261 G
23714 CTTCAAATTTGTTTCTTGAATTCAAAGTTGCTTGCTGCATATGAATCAGTTTTGTACCCTGAACT
1 CTTCAAATTTGTTTCTTGAATTCAAAGTTGCTTGCTGCATATGAATCAGTTTTGTACCCTGAACT
*
23779 TCAGAATTCATAACTTCTTCAATTCAGCTCCAAATTGTGTGTTCTTTGCAGGGTATGGAAAGCTT
66 TCAGAATTCATAACTTCTTCAATTCAGCTCCAAATTGTGTGTT-TTTGCAGGGTATGGAAAACTT
23844 GGAGAGTGCACTTCAACTTCCATGAAGACCACTTTGTCAAACAGAGTCGTCTTGGGTGCCAAATT
130 GGAGAGTGCACTTCAACTTCCATGAAGACCACTTTGTCAAACAGAGTCGTCTTGGGTGCCAAATT
*
23909 TGAAGTTTTCTCTGGCTGCAACTGCTGTCTAGAATTTCTGCGATTTTTGGAGGCCTGGACTGCGG
195 TGAAGTTTTCTCTGGCTGCAACTGCTGTCTAGAATTTCTGCGATTTTTGGAGGCCTAGACTGCGG
23974 GG
260 GG
23976 C
1 C
23977 CCATATCACC
Statistics
Matches: 257, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
261 106 0.41
262 151 0.59
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (261 bp):
CTTCAAATTTGTTTCTTGAATTCAAAGTTGCTTGCTGCATATGAATCAGTTTTGTACCCTGAACT
TCAGAATTCATAACTTCTTCAATTCAGCTCCAAATTGTGTGTTTTTGCAGGGTATGGAAAACTTG
GAGAGTGCACTTCAACTTCCATGAAGACCACTTTGTCAAACAGAGTCGTCTTGGGTGCCAAATTT
GAAGTTTTCTCTGGCTGCAACTGCTGTCTAGAATTTCTGCGATTTTTGGAGGCCTAGACTGCGGG
G
Found at i:24460 original size:14 final size:14
Alignment explanation
Indices: 24441--24468 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24431 TGTTAGTAAT
24441 CTAAATGGACTAAA
1 CTAAATGGACTAAA
24455 CTAAATGGACTAAA
1 CTAAATGGACTAAA
24469 ATCAATATGC
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:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
CTAAATGGACTAAA
Found at i:25078 original size:2 final size:2
Alignment explanation
Indices: 25065--25127 Score: 74
Period size: 2 Copynumber: 31.5 Consensus size: 2
25055 ATGGATCTTC
* * * *
25065 AT AT AG AT AT AT AT AT AT AT AT GT AT TT TT CAT 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
25108 AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT A
25128 AATAAGAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
1 1 0.02
2 51 0.96
3 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:28468 original size:30 final size:30
Alignment explanation
Indices: 28432--28489 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
28422 CATCTTCAAG
28432 TCCATGATAAGTCCTT-CGCGCATCATTCAC
1 TCCATGATAAG-CCTTGCGCGCATCATTCAC
*
28462 TCCATGATAAGCCTTGGGCGCATCATTC
1 TCCATGATAAGCCTTGCGCGCATCATTC
28490 CCCCCTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.29
Consensus pattern (30 bp):
TCCATGATAAGCCTTGCGCGCATCATTCAC
Found at i:31089 original size:19 final size:18
Alignment explanation
Indices: 31065--31101 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
31055 CTTTGAATGA
*
31065 AATTCTGTTTTGTTTTTTG
1 AATTCTGATTT-TTTTTTG
31084 AATTCTGATTTTTTTTTG
1 AATTCTGATTTTTTTTTG
31102 GATTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.14, C:0.05, G:0.14, T:0.68
Consensus pattern (18 bp):
AATTCTGATTTTTTTTTG
Found at i:38791 original size:23 final size:23
Alignment explanation
Indices: 38761--38807 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
38751 CAACCGGCCA
38761 CAACCGGCCATCGCATGGAGCAT
1 CAACCGGCCATCGCATGGAGCAT
*
38784 CAACCGGCCATCGCATGGGGCAT
1 CAACCGGCCATCGCATGGAGCAT
38807 C
1 C
38808 CGCACACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.36, G:0.28, T:0.13
Consensus pattern (23 bp):
CAACCGGCCATCGCATGGAGCAT
Found at i:39963 original size:33 final size:33
Alignment explanation
Indices: 39892--39995 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 33
39882 CTATGATCAA
** * *
39892 CCAAAACAGA-TTTGTTTTCATCACAATTAGCAT
1 CCAAAACAGATTTTGTTTT-ATCACAAACAACAC
*
39925 ACAAAACAGATTTTGTTTTATCACAAACAACAC
1 CCAAAACAGATTTTGTTTTATCACAAACAACAC
* * * *
39958 CCAAAACAGATTTAGTGTCATCGCAAACAACAC
1 CCAAAACAGATTTTGTTTTATCACAAACAACAC
*
39991 TCAAA
1 CCAAA
39996 TTAGGTTTAG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 51 0.86
34 8 0.14
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (33 bp):
CCAAAACAGATTTTGTTTTATCACAAACAACAC
Found at i:40005 original size:33 final size:33
Alignment explanation
Indices: 39926--40031 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
39916 AATTAGCATA
* * * *
39926 CAAAACAGATTTTGTTTTATCACAAACAACACC
1 CAAAACAGATTTAGTATCATCGCAAACAACACC
* *
39959 CAAAACAGATTTAGTGTCATCGCAAACAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACC
** * *
39992 CAAATTAGGTTTAGTATCATCGCAAACAACATC
1 CAAAACAGATTTAGTATCATCGCAAACAACACC
*
40025 TAAAACA
1 CAAAACA
40032 CTATTTGCAA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCGCAAACAACACC
Found at i:46101 original size:15 final size:15
Alignment explanation
Indices: 46077--46119 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
46067 AATCCAAGTT
*
46077 GCTCATCTTCTTGTG
1 GCTCATCTTCTGGTG
*
46092 GCTTATCTTCTGGTG
1 GCTCATCTTCTGGTG
46107 GCTCATCTTCTGG
1 GCTCATCTTCTGG
46120 CTTGTCAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.07, C:0.26, G:0.23, T:0.44
Consensus pattern (15 bp):
GCTCATCTTCTGGTG
Found at i:47037 original size:142 final size:142
Alignment explanation
Indices: 46781--47062 Score: 537
Period size: 142 Copynumber: 2.0 Consensus size: 142
46771 AAAATTCTTC
*
46781 ATTAATTTCCCTTCAGGTAGACCGTGGTCAACAAAGAACTGACACATCCAATTGAATCTATCCCA
1 ATTAATTTCCCTTCAGGTAGACCATGGTCAACAAAGAACTGACACATCCAATTGAATCTATCCCA
**
46846 ATAGTAAAACCATGTTTCATGAGGGTATTGTCGACAAGAAAGAACTTCCTTTTGAACAGCACGTA
66 ATAGTAAAACCACATTTCATGAGGGTATTGTCGACAAGAAAGAACTTCCTTTTGAACAGCACGTA
46911 TCCTTCGCTCTG
131 TCCTTCGCTCTG
46923 ATTAATTTCCCTTCAGGTAGACCATGGTCAACAAAGAACTGACACATCCAATTGAATCTATCCCA
1 ATTAATTTCCCTTCAGGTAGACCATGGTCAACAAAGAACTGACACATCCAATTGAATCTATCCCA
46988 ATAGTAAAACCACATTTCATGAGGGTATTGTCGACAAGAAAGAACTTCCTTTTGAACAGCACGTA
66 ATAGTAAAACCACATTTCATGAGGGTATTGTCGACAAGAAAGAACTTCCTTTTGAACAGCACGTA
47053 TCCTTCGCTC
131 TCCTTCGCTC
47063 CCTTGCTTCT
Statistics
Matches: 137, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 137 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (142 bp):
ATTAATTTCCCTTCAGGTAGACCATGGTCAACAAAGAACTGACACATCCAATTGAATCTATCCCA
ATAGTAAAACCACATTTCATGAGGGTATTGTCGACAAGAAAGAACTTCCTTTTGAACAGCACGTA
TCCTTCGCTCTG
Found at i:47248 original size:23 final size:23
Alignment explanation
Indices: 47220--47282 Score: 92
Period size: 22 Copynumber: 2.7 Consensus size: 23
47210 CGCAAACCCT
47220 AATTTTTTTAAAAAAAATCGC-A
1 AATTTTTTTAAAAAAAATCGCAA
*
47242 AATTTTTTAAAAAAAAATCGCAA
1 AATTTTTTTAAAAAAAATCGCAA
*
47265 AATTTTTTTTAGAAAAAA
1 AA-TTTTTTTAAAAAAAA
47283 CGGAAAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 20 0.56
23 3 0.08
24 13 0.36
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (23 bp):
AATTTTTTTAAAAAAAATCGCAA
Found at i:48749 original size:30 final size:30
Alignment explanation
Indices: 48713--48771 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
48703 TGTCTTCAAG
48713 TCCATGATAAGTCCTT-GGCGCATCATTCCT
1 TCCATGATAAG-CCTTGGGCGCATCATTCCT
48743 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATGATAAGCCTTGGGCGCATCATTCC
48772 CTCCCCCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.20, C:0.31, G:0.19, T:0.31
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCT
Found at i:52287 original size:21 final size:21
Alignment explanation
Indices: 52263--52311 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
52253 CAACTGGGGG
* * *
52263 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
52284 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
52305 CCCATGT
1 CCCATGT
52312 CCTCCAGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:53798 original size:24 final size:26
Alignment explanation
Indices: 53770--53819 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
53760 CATTATAATG
53770 AATAAATAAAT-AAAAT-ATCAATTA
1 AATAAATAAATCAAAATAATCAATTA
*
53794 AATAAATAAATCATAATAATCAATTA
1 AATAAATAAATCAAAATAATCAATTA
53820 GAACATGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.48
25 4 0.17
26 8 0.35
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (26 bp):
AATAAATAAATCAAAATAATCAATTA
Found at i:53855 original size:24 final size:25
Alignment explanation
Indices: 53815--53875 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
53805 CATAATAATC
53815 AATTAGAACATGATCAATT-AGAACAA
1 AATTA-AACATGATCAATTGA-AACAA
*
53841 AATTAAACAT-ATCAATTGAAACAG
1 AATTAAACATGATCAATTGAAACAA
*
53865 AATTATACATG
1 AATTAAACATG
53876 TGTATGTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 20 0.65
25 6 0.19
26 5 0.16
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.26
Consensus pattern (25 bp):
AATTAAACATGATCAATTGAAACAA
Found at i:56060 original size:17 final size:17
Alignment explanation
Indices: 56033--56065 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
56023 TTTTCTAACA
56033 TGTTTCTTCTT-TTCCC
1 TGTTTCTTCTTCTTCCC
56049 TGTTTCCTTCTTCTTCC
1 TGTTT-CTTCTTCTTCC
56066 TCTTGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.00, C:0.33, G:0.06, T:0.61
Consensus pattern (17 bp):
TGTTTCTTCTTCTTCCC
Done.