Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012821.1 Corchorus capsularis cultivar CVL-1 contig12842, 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: 118223
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1318 original size:23 final size:23
Alignment explanation
Indices: 1275--1318 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1265 TTGTTTTCTT
* *
1275 GAAGTTAATAATTTTATTTAAGA
1 GAAGTTAATAAATTTAGTTAAGA
1298 GAAGTTAAATAAATTT-GTTAA
1 GAAGTT-AATAAATTTAGTTAA
1319 TCAATTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (23 bp):
GAAGTTAATAAATTTAGTTAAGA
Found at i:2197 original size:21 final size:21
Alignment explanation
Indices: 2156--2197 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2146 ATAACCTTAA
*
2156 TTTTTTTATAACCTTTTTTAG
1 TTTTTTTATAACCTTTATTAG
*
2177 TTTTTTTAGTATCC-TTATTAG
1 TTTTTTTA-TAACCTTTATTAG
2198 ACGTGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.19, C:0.10, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTTTTTATAACCTTTATTAG
Found at i:26279 original size:24 final size:24
Alignment explanation
Indices: 26247--26295 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
26237 CTTTCCTCTA
26247 CAAAATCACTAGCATCATCATCAT
1 CAAAATCACTAGCATCATCATCAT
26271 CAAAATCACTAGCATCATCATCAT
1 CAAAATCACTAGCATCATCATCAT
26295 C
1 C
26296 CTCTTTGCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.31, G:0.04, T:0.24
Consensus pattern (24 bp):
CAAAATCACTAGCATCATCATCAT
Found at i:26389 original size:45 final size:45
Alignment explanation
Indices: 26325--26556 Score: 428
Period size: 45 Copynumber: 5.2 Consensus size: 45
26315 GTCCTACCCA
26325 CATTTCTACTTCCGTTCCCTATATTTCTCGAATTTAAACCCCTCT
1 CATTTCTACTTCCGTTCCCTATATTTCTCGAATTTAAACCCCTCT
*
26370 CATTTCTACTTCCGTTCCCTATATTTCTTGAATTTAAACCCCTCT
1 CATTTCTACTTCCGTTCCCTATATTTCTCGAATTTAAACCCCTCT
26415 CATTTCTACTTCCGTTCCCTATATTTCTCGAATTTAAACCCCTCT
1 CATTTCTACTTCCGTTCCCTATATTTCTCGAATTTAAACCCCTCT
*
26460 CATTTCTACTTCCGTTCCCTATGTTTCTCGAATTTAAACCCCTCT
1 CATTTCTACTTCCGTTCCCTATATTTCTCGAATTTAAACCCCTCT
* *
26505 CATTTCTACTTCTGTTCCCTATATTTCTCGAATTTAACCCCCTCT
1 CATTTCTACTTCCGTTCCCTATATTTCTCGAATTTAAACCCCTCT
26550 CATTTCT
1 CATTTCT
26557 CTCCCCTTTC
Statistics
Matches: 181, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 181 1.00
ACGTcount: A:0.19, C:0.33, G:0.05, T:0.44
Consensus pattern (45 bp):
CATTTCTACTTCCGTTCCCTATATTTCTCGAATTTAAACCCCTCT
Found at i:26442 original size:21 final size:21
Alignment explanation
Indices: 26371--26442 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
26361 AACCCCTCTC
26371 ATTTCTACTTCCGTTCCCTAT
1 ATTTCTACTTCCGTTCCCTAT
* ***** *
26392 ATTTCTTGAATTTAAACCCCTCT
1 ATTTC-T-ACTTCCGTTCCCTAT
26415 CATTTCTACTTCCGTTCCCTAT
1 -ATTTCTACTTCCGTTCCCTAT
26437 ATTTCT
1 ATTTCT
26443 CGAATTTAAA
Statistics
Matches: 34, Mismatches: 14, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
21 11 0.32
22 9 0.26
23 9 0.26
24 5 0.15
ACGTcount: A:0.18, C:0.31, G:0.04, T:0.47
Consensus pattern (21 bp):
ATTTCTACTTCCGTTCCCTAT
Found at i:26510 original size:24 final size:24
Alignment explanation
Indices: 26483--26557 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
26473 GTTCCCTATG
26483 TTTCTCGAATTTAAACCCCTCTCA
1 TTTCTCGAATTTAAACCCCTCTCA
* *** *
26507 TTTCT--ACTTCT-GTTCCCTAT-A
1 TTTCTCGAATT-TAAACCCCTCTCA
*
26528 TTTCTCGAATTTAACCCCCTCTCA
1 TTTCTCGAATTTAAACCCCTCTCA
26552 TTTCTC
1 TTTCTC
26558 TCCCCTTTCC
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
21 6 0.17
22 9 0.25
23 9 0.25
24 12 0.33
ACGTcount: A:0.19, C:0.33, G:0.04, T:0.44
Consensus pattern (24 bp):
TTTCTCGAATTTAAACCCCTCTCA
Found at i:32480 original size:62 final size:62
Alignment explanation
Indices: 32414--32543 Score: 145
Period size: 62 Copynumber: 2.1 Consensus size: 62
32404 TTTTGTGCAT
* ** *
32414 GTGGCATGCCACGTGTCATTTTTTGAAACATC-TGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCATGACACGTGTCACATTTTGAAACA-CGTGGCATGACACGTGTCACTTTTTGGTACAC
* * ** * * *
32476 GTGGCGTGACATGTGTCACATTTTGGTACACGTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGACACGTGTCACATTTTGAAACACGTGGCATGACACGTGTCACTTTTTGGTACAC
32538 GTGGCA
1 GTGGCA
32544 CGACTTTTTG
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 1 0.02
62 54 0.98
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (62 bp):
GTGGCATGACACGTGTCACATTTTGAAACACGTGGCATGACACGTGTCACTTTTTGGTACAC
Found at i:32492 original size:31 final size:31
Alignment explanation
Indices: 32457--32593 Score: 157
Period size: 31 Copynumber: 4.7 Consensus size: 31
32447 GGCATGCCAC
32457 GTGTCACTTTTTGGTACACGTGGCGTGACAT
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
*
32488 GTGTCACATTTTGGTACACGTGGCGTGACAT
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
*
32519 GTGTCACTTTTTGGTACATGTGGC---AC--
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
* * *
32545 --G--ACTTTTTGGTACATGTGGCATGACAC
1 GTGTCACTTTTTGGTACACGTGGCGTGACAT
*
32572 ATGTCACTTTTTGGTACACGTG
1 GTGTCACTTTTTGGTACACGTG
32594 ACATGCCACG
Statistics
Matches: 93, Mismatches: 4, Indels: 18
0.81 0.03 0.16
Matches are distributed among these distances:
22 19 0.20
24 1 0.01
25 2 0.02
28 2 0.02
29 1 0.01
31 68 0.73
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (31 bp):
GTGTCACTTTTTGGTACACGTGGCGTGACAT
Found at i:32552 original size:22 final size:22
Alignment explanation
Indices: 32524--32565 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
32514 GACATGTGTC
32524 ACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACATGTGGCACG
32546 ACTTTTTGGTACATGTGGCA
1 ACTTTTTGGTACATGTGGCA
32566 TGACACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (22 bp):
ACTTTTTGGTACATGTGGCACG
Found at i:33785 original size:17 final size:18
Alignment explanation
Indices: 33763--33799 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
33753 ACCCCTATGC
33763 AAGTAAATT-TTTTTTTT
1 AAGTAAATTATTTTTTTT
33780 AAGTAAATTAGTTTTTTTT
1 AAGTAAATTA-TTTTTTTT
33799 A
1 A
33800 GGGAACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (18 bp):
AAGTAAATTATTTTTTTT
Found at i:54142 original size:47 final size:48
Alignment explanation
Indices: 54089--54179 Score: 166
Period size: 47 Copynumber: 1.9 Consensus size: 48
54079 AAACAAAAAA
54089 AAATCATACAGATCTGCAAATCGAGATAATATACT-CCTCTGTTCCTT
1 AAATCATACAGATCTGCAAATCGAGATAATATACTCCCTCTGTTCCTT
*
54136 AAATCATACAGATCTGCAAATCGGGATAATATACTCCCTCTGTT
1 AAATCATACAGATCTGCAAATCGAGATAATATACTCCCTCTGTT
54180 ACTTTTTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
47 34 0.81
48 8 0.19
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (48 bp):
AAATCATACAGATCTGCAAATCGAGATAATATACTCCCTCTGTTCCTT
Found at i:59760 original size:31 final size:31
Alignment explanation
Indices: 59722--59920 Score: 161
Period size: 31 Copynumber: 6.5 Consensus size: 31
59712 TTTGGCTAAT
* *
59722 TGCTCAAATAAGGGTCTAACGTTTGTC-AAAA
1 TGCTCAAATAAGGGCCTAAC-TTTATCGAAAA
* **
59753 TGCTCAAATAAGGGTCTAAACTTT-T--AATT
1 TGCTCAAATAAGGGCCT-AACTTTATCGAAAA
*
59782 TGGC-CAAATAAGGGCCTAA-TGTTATCAAAAA
1 T-GCTCAAATAAGGGCCTAACT-TTATCGAAAA
**
59813 TGCTCAAATAAGGGCC-AGATCTTT-T--AATT
1 TGCTCAAATAAGGGCCTA-A-CTTTATCGAAAA
*
59842 TGAC-CAAATAAGGGCCTAACGTTATCGAAAA
1 TG-CTCAAATAAGGGCCTAACTTTATCGAAAA
59873 TGCTCAAATAAGGGCCTAA-TATTATCGAAAA
1 TGCTCAAATAAGGGCCTAACT-TTATCGAAAA
59904 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
59921 GGTATCAGTT
Statistics
Matches: 140, Mismatches: 11, Indels: 34
0.76 0.06 0.18
Matches are distributed among these distances:
27 1 0.01
28 7 0.05
29 34 0.24
30 9 0.06
31 83 0.59
32 5 0.04
33 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACTTTATCGAAAA
Found at i:59800 original size:29 final size:29
Alignment explanation
Indices: 59757--59860 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
59747 TCAAAATGCT
* *
59757 CAAATAAGGGTCTAAACTTTTAATTTGGC
1 CAAATAAGGGCCTAATCTTTTAATTTGGC
* * **
59786 CAAATAAGGGCCTAATGTTATCAAAAAT-GC
1 CAAATAAGGGCCTAATCTT-T-TAATTTGGC
*
59816 TCAAATAAGGGCC-AGATCTTTTAATTTGAC
1 -CAAATAAGGGCCTA-ATCTTTTAATTTGGC
59846 CAAATAAGGGCCTAA
1 CAAATAAGGGCCTAA
59861 CGTTATCGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
29 32 0.55
30 7 0.12
31 19 0.33
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGCCTAATCTTTTAATTTGGC
Found at i:59888 original size:60 final size:58
Alignment explanation
Indices: 59726--59888 Score: 227
Period size: 60 Copynumber: 2.7 Consensus size: 58
59716 GCTAATTGCT
* * * *
59726 CAAATAAGGGTCTAACGTTTGTCAAAATGCTCAAATAAGGGTCTAAACTTTTAATTTGGC
1 CAAATAAGGGCCTAACG-TTATCAAAATGCTCAAATAAGGG-CCAAACTTTTAATTTGAC
* *
59786 CAAATAAGGGCCTAATGTTATCAAAAATGCTCAAATAAGGGCCAGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTATC-AAAATGCTCAAATAAGGGCCA-AACTTTTAATTTGAC
59846 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTATC-AAAATGCTCAAATAAGGGCC
59889 TAATATTATC
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
59 6 0.06
60 87 0.94
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (58 bp):
CAAATAAGGGCCTAACGTTATCAAAATGCTCAAATAAGGGCCAAACTTTTAATTTGAC
Found at i:59990 original size:31 final size:31
Alignment explanation
Indices: 59952--60052 Score: 175
Period size: 31 Copynumber: 3.3 Consensus size: 31
59942 TGAGACAGAT
*
59952 CCTTATTTGAGCATTTTGGCAAACGTGAGAC
1 CCTTATTTGAGCATTTTGGCAAACGTGAGGC
*
59983 CCTTATTTGAGCATTTTAGCAAACGTGAGGC
1 CCTTATTTGAGCATTTTGGCAAACGTGAGGC
*
60014 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
1 CCTTATTTGAGCATTTTGGCAAACGTGAGGC
60045 CCTTATTT
1 CCTTATTT
60053 TGCCAAAATC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.36
Consensus pattern (31 bp):
CCTTATTTGAGCATTTTGGCAAACGTGAGGC
Found at i:60173 original size:60 final size:60
Alignment explanation
Indices: 59952--60174 Score: 193
Period size: 60 Copynumber: 3.7 Consensus size: 60
59942 TGAGACAGAT
* * * ** * *
59952 CCTTATTTGAGCATTTTGGCAAACGTGA-GACCCTTATTTGAGCATTTTAGCAAACG-TGAGGC
1 CCTTATTTGAGCATTTTGGCAAATGTTAGGA-CCTTATTTGACCA--AAATCAAA-GATCAGGC
* * **
60014 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTTG-CCAAAATCAAAGATGGGGC
1 CCTTATTTGAGCATTTTGGCAAATGTTAGGACCTTA-TTTGACCAAAATCAAAGATCAGGC
* ** * * *
60074 CCTTATTTGAGCATTTTGACAAATGTTAGGGTCTTATTTGACC-AAATTAATAGATCATGT
1 CCTTATTTGAGCATTTTGGCAAATGTTAGGACCTTATTTGACCAAAATCAA-AGATCAGGC
* *
60134 CCTTATTTGAGCATTTTGGCAAATATTAGAACCTTATTTGA
1 CCTTATTTGAGCATTTTGGCAAATGTTAGGACCTTATTTGA
60175 ATAATTAGCC
Statistics
Matches: 135, Mismatches: 21, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
59 11 0.08
60 85 0.63
62 34 0.25
63 5 0.04
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTGGCAAATGTTAGGACCTTATTTGACCAAAATCAAAGATCAGGC
Found at i:63977 original size:36 final size:36
Alignment explanation
Indices: 63937--64129 Score: 250
Period size: 36 Copynumber: 5.4 Consensus size: 36
63927 TATGTAAAGT
* * *
63937 AGCATCAGCATGATCA-ACTTCTTGTAAAGCATCATC
1 AGCATGAGCATGAGCATAC-TCTTGTGAAGCATCATC
*
63973 AGCATGAGCATGA--ACA-TCTTGTGAAGCATCATC
1 AGCATGAGCATGAGCATACTCTTGTGAAGCATCATC
* * *
64006 AGCATGGGCATGAGCATACTGTTGTGAAGCATCGTC
1 AGCATGAGCATGAGCATACTCTTGTGAAGCATCATC
* *
64042 AACATGGGCATGAGCATACTCTTGTGAAGCATCATC
1 AGCATGAGCATGAGCATACTCTTGTGAAGCATCATC
*
64078 ACCATGAGCATGAGCATACTCTTGTGAAGCATCATC
1 AGCATGAGCATGAGCATACTCTTGTGAAGCATCATC
*
64114 ATCATGAGCATGAGCA
1 AGCATGAGCATGAGCA
64130 ACATCGTCAG
Statistics
Matches: 141, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
33 28 0.20
34 1 0.01
35 3 0.02
36 109 0.77
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (36 bp):
AGCATGAGCATGAGCATACTCTTGTGAAGCATCATC
Found at i:64143 original size:24 final size:24
Alignment explanation
Indices: 64107--64153 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
64097 TCTTGTGAAG
*
64107 CATCATCATCATGAGCATGAGCAA
1 CATCATCAGCATGAGCATGAGCAA
*
64131 CATCGTCAGCATGAGCATGAGCA
1 CATCATCAGCATGAGCATGAGCA
64154 TACTCGTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (24 bp):
CATCATCAGCATGAGCATGAGCAA
Found at i:64198 original size:60 final size:58
Alignment explanation
Indices: 64080--64208 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 58
64070 GCATCATCAC
* * *
64080 CATGAGCATGAGCATACTCTTGTGAAGCATCATCATCATGAGCATGAGCAACATCGTCAG
1 CATGAGCATGAGCATACTCGTGTGAAGCATCATCATCATAAGCAT--GCAACAGCGTCAG
**
64140 CATGAGCATGAGCATACTCGTGTGAAGCATCATCATCACCATAAGCAT-CCTCAGCGTCAG
1 CATGAGCATGAGCATACTCGTGTGAAGCATCATCAT---CATAAGCATGCAACAGCGTCAG
64200 CATGAGCAT
1 CATGAGCAT
64209 CAACGTCCTC
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
60 53 0.87
63 8 0.13
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (58 bp):
CATGAGCATGAGCATACTCGTGTGAAGCATCATCATCATAAGCATGCAACAGCGTCAG
Found at i:77647 original size:3 final size:3
Alignment explanation
Indices: 77639--77668 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
77629 TTTTTGGGGG
*
77639 TTA TTA TTA ATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
77669 ACTAGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:78975 original size:2 final size:2
Alignment explanation
Indices: 78968--79006 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
78958 TATAATGAAG
78968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
79007 ATAATCAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:79855 original size:31 final size:32
Alignment explanation
Indices: 79800--79907 Score: 98
Period size: 32 Copynumber: 3.4 Consensus size: 32
79790 AAATCCAATG
79800 TGGCAATGCCAC-ATCATC-GATTTGGTCA-AAA
1 TGGCAATGCCACGAT-ATCAG-TTTGGTCAGAAA
* * **
79831 TGGCAATGGCACTATATCAGTTTGGT-ATGACG
1 TGGCAATGCCACGATATCAGTTTGGTCA-GAAA
* **
79863 TGGCAATGCCACGATATCAGTTTGGTCTGACG
1 TGGCAATGCCACGATATCAGTTTGGTCAGAAA
79895 TGGCAATGCCACG
1 TGGCAATGCCACG
79908 TCAACGGCAT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
30 1 0.02
31 20 0.30
32 45 0.68
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (32 bp):
TGGCAATGCCACGATATCAGTTTGGTCAGAAA
Found at i:79869 original size:32 final size:32
Alignment explanation
Indices: 79831--79907 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
79821 TTGGTCAAAA
* *
79831 TGGCAATGGCACTATATCAGTTTGGTATGACG
1 TGGCAATGCCACGATATCAGTTTGGTATGACG
*
79863 TGGCAATGCCACGATATCAGTTTGGTCTGACG
1 TGGCAATGCCACGATATCAGTTTGGTATGACG
79895 TGGCAATGCCACG
1 TGGCAATGCCACG
79908 TCAACGGCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (32 bp):
TGGCAATGCCACGATATCAGTTTGGTATGACG
Found at i:81939 original size:4 final size:4
Alignment explanation
Indices: 81932--81970 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
81922 TATATATATA
*
81932 TATG TATG TATG TATG TATG CATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
81971 ATATAGGTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:85832 original size:5 final size:5
Alignment explanation
Indices: 85822--85868 Score: 78
Period size: 5 Copynumber: 9.6 Consensus size: 5
85812 TTTTTCTGGC
*
85822 AAAA- AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
85869 TTTGTCATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
4 4 0.10
5 37 0.90
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:97034 original size:33 final size:33
Alignment explanation
Indices: 96992--97058 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
96982 ACTACTAAAT
*
96992 CGGATTCATTTGGAAGTTTGAGGGCATATCAGA
1 CGGATTCATTTGGAAGTTTGAGGGCAGATCAGA
97025 CGGATTCATTTGGAAGTTTGAGGGCAGATCAGA
1 CGGATTCATTTGGAAGTTTGAGGGCAGATCAGA
97058 C
1 C
97059 TTGTTCCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.28
Consensus pattern (33 bp):
CGGATTCATTTGGAAGTTTGAGGGCAGATCAGA
Found at i:103263 original size:30 final size:30
Alignment explanation
Indices: 103182--103273 Score: 132
Period size: 30 Copynumber: 3.1 Consensus size: 30
103172 TTGTGGTGGG
* *
103182 TTCTGAATCGTCTGGGCTTGGTTAGGTACA
1 TTCTGACTCGTCTGGGCTTGGTTGGGTACA
103212 TTCTGACTCGTCTGGGCTTGGTTGGGTACA
1 TTCTGACTCGTCTGGGCTTGGTTGGGTACA
* *
103242 TTCTGACTCGTCT-GACTTTGGTTGGGGACA
1 TTCTGACTCGTCTGGGC-TTGGTTGGGTACA
103272 TT
1 TT
103274 TAATATTTGA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
29 2 0.04
30 55 0.96
ACGTcount: A:0.13, C:0.18, G:0.30, T:0.38
Consensus pattern (30 bp):
TTCTGACTCGTCTGGGCTTGGTTGGGTACA
Found at i:115887 original size:20 final size:20
Alignment explanation
Indices: 115862--115901 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
115852 GAGGAATGGA
115862 TGTAAAAAATTAGATCTAGG
1 TGTAAAAAATTAGATCTAGG
115882 TGTAAAAAATTAGATCTAGG
1 TGTAAAAAATTAGATCTAGG
115902 GGCTGAGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (20 bp):
TGTAAAAAATTAGATCTAGG
Found at i:116072 original size:31 final size:31
Alignment explanation
Indices: 116037--116120 Score: 150
Period size: 31 Copynumber: 2.7 Consensus size: 31
116027 CCTCAGTAGA
* *
116037 CCGCACACAGGGGGCGGCCTTGGCAAGCAAG
1 CCGCACACTGGGGTCGGCCTTGGCAAGCAAG
116068 CCGCACACTGGGGTCGGCCTTGGCAAGCAAG
1 CCGCACACTGGGGTCGGCCTTGGCAAGCAAG
116099 CCGCACACTGGGGTCGGCCTTG
1 CCGCACACTGGGGTCGGCCTTG
116121 CCACGGCAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.18, C:0.33, G:0.37, T:0.12
Consensus pattern (31 bp):
CCGCACACTGGGGTCGGCCTTGGCAAGCAAG
Found at i:116601 original size:27 final size:27
Alignment explanation
Indices: 116565--116630 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
116555 TGGTCAACCG
* *
116565 GGTTACTATGATCAGGGTGTTGAGCCC
1 GGTTATTATGATCAGGGTGCTGAGCCC
** * **
116592 GGTTATTATGATGGGGGTGCTGGGTTC
1 GGTTATTATGATCAGGGTGCTGAGCCC
116619 GGTTATTATGAT
1 GGTTATTATGAT
116631 GGGGCAGCTC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.17, C:0.11, G:0.36, T:0.36
Consensus pattern (27 bp):
GGTTATTATGATCAGGGTGCTGAGCCC
Found at i:116747 original size:53 final size:54
Alignment explanation
Indices: 116620--116755 Score: 247
Period size: 54 Copynumber: 2.5 Consensus size: 54
116610 GCTGGGTTCG
116620 GTTATTATGATGGGGCAGCTCAGGCGGGTTACCATGATAATAATGCTGACCCCC
1 GTTATTATGATGGGGCAGCTCAGGCGGGTTACCATGATAATAATGCTGACCCCC
116674 GTTATTATGATGGGGCAGCTCAGGCGGGTTACCATGATAATAATGC-GACCCCC
1 GTTATTATGATGGGGCAGCTCAGGCGGGTTACCATGATAATAATGCTGACCCCC
* *
116727 GTTATTATGATAGGGCAGCTCAGTCGGGT
1 GTTATTATGATGGGGCAGCTCAGGCGGGT
116756 GACTTTGATC
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 34 0.43
54 46 0.57
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (54 bp):
GTTATTATGATGGGGCAGCTCAGGCGGGTTACCATGATAATAATGCTGACCCCC
Done.