Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008025.1 Corchorus capsularis cultivar CVL-1 contig08046, 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: 47747
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:726 original size:33 final size:33
Alignment explanation
Indices: 689--795 Score: 144
Period size: 33 Copynumber: 3.2 Consensus size: 33
679 CGCCTAGCGA
* *
689 TGGCCGGTTG-TGGCCGGACATGTCCATGTCGCG
1 TGGCCGG-TGATGGCCGGACATCTCCAAGTCGCG
*
722 TGGCCGGTGATGGCCGGGCATCTCCAAGTCGCG
1 TGGCCGGTGATGGCCGGACATCTCCAAGTCGCG
* * *
755 TGGCCGGTGTTGGCCGGACTTCTCCAAGTCGCA
1 TGGCCGGTGATGGCCGGACATCTCCAAGTCGCG
788 TGGCCGGT
1 TGGCCGGT
796 CACTAGTGCT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 2 0.03
33 64 0.97
ACGTcount: A:0.10, C:0.29, G:0.38, T:0.22
Consensus pattern (33 bp):
TGGCCGGTGATGGCCGGACATCTCCAAGTCGCG
Found at i:3032 original size:7 final size:7
Alignment explanation
Indices: 3010--3077 Score: 70
Period size: 7 Copynumber: 10.0 Consensus size: 7
3000 GAGAAAGAAG
*
3010 GAGAAGA
1 GAGAAAA
*
3017 GAAAAAA
1 GAGAAAA
3024 GAGAAAA
1 GAGAAAA
3031 GAGAAAA
1 GAGAAAA
3038 -AGAAAA
1 GAGAAAA
3044 GA-AAAA
1 GAGAAAA
*
3050 GAATAAAA
1 G-AGAAAA
3058 GAGAAAA
1 GAGAAAA
*
3065 AAGAAAA
1 GAGAAAA
3072 -AGAAAA
1 GAGAAAA
3078 TGCCACATCA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
6 17 0.32
7 31 0.58
8 5 0.09
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.01
Consensus pattern (7 bp):
GAGAAAA
Found at i:3043 original size:6 final size:6
Alignment explanation
Indices: 3020--3077 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
3010 GAGAAGAGAA
* *
3020 AAAAGAG AAAAGAG AAAAAG -AAAAG AAAAAG -AATA- AAAGAG AAAAAAG
1 AAAA-AG AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG
3068 AAAAAG AAAA
1 AAAAAG AAAA
3078 TGCCACATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
5 11 0.25
6 17 0.39
7 16 0.36
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:3046 original size:27 final size:29
Alignment explanation
Indices: 3011--3077 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 29
3001 AGAAAGAAGG
*
3011 AGAAGAGAAAAAAG-AGAAAAGAG-AAAA
1 AGAAAAGAAAAAAGAAGAAAAGAGAAAAA
*
3038 AGAAAAG-AAAAAGAATAAAAGAGAAAAA
1 AGAAAAGAAAAAAGAAGAAAAGAGAAAAA
3066 AGAAAAAGAAAA
1 AG-AAAAGAAAA
3078 TGCCACATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 6 0.18
27 14 0.41
28 6 0.18
29 5 0.15
30 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (29 bp):
AGAAAAGAAAAAAGAAGAAAAGAGAAAAA
Found at i:3415 original size:156 final size:155
Alignment explanation
Indices: 3132--3443 Score: 597
Period size: 156 Copynumber: 2.0 Consensus size: 155
3122 CATGCTGTTC
3132 ACGGGCCCAGTACCATTAGAAAAAGCCCAAGATTGAGCAACCCGAAAACGTTTGGCCATTTTTTG
1 ACGGGCCCAGTACCATTAGAAAAAGCCCAAGATTGAGCAACCCGAAAACGTTTGGCCATTTTTTG
3197 TTGCAATTGAAATGTTTGGCCCCAAATCGAGCATCACGCCAAACGTTTGGCCCCAAATTGAGCAT
66 TTGCAATTGAAATGTTTGGCCCCAAATCGAGCATCACGCCAAACGTTTGGCCCCAAATTGAGCAT
3262 TTTGCCTTAGAATGAAAGACGGTTA
131 TTTGCCTTAGAATGAAAGACGGTTA
*
3287 ACGGGCCCAGTACCATTAGAAAAAGCCCAAGATTGAGTAACCCCGAAAACGTTTGGCCATTTTTT
1 ACGGGCCCAGTACCATTAGAAAAAGCCCAAGATTGAGCAA-CCCGAAAACGTTTGGCCATTTTTT
*
3352 GTTGCAATTGAAATGTTTGGCCCCAAATCGAGCATCACGGCAAACGTTTGGCCCCAAATTGAGCA
65 GTTGCAATTGAAATGTTTGGCCCCAAATCGAGCATCACGCCAAACGTTTGGCCCCAAATTGAGCA
3417 TTTTGCCTTAGAATGAAAGACGGTTA
130 TTTTGCCTTAGAATGAAAGACGGTTA
3443 A
1 A
3444 GTTTTTGTTT
Statistics
Matches: 154, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
155 39 0.25
156 115 0.75
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (155 bp):
ACGGGCCCAGTACCATTAGAAAAAGCCCAAGATTGAGCAACCCGAAAACGTTTGGCCATTTTTTG
TTGCAATTGAAATGTTTGGCCCCAAATCGAGCATCACGCCAAACGTTTGGCCCCAAATTGAGCAT
TTTGCCTTAGAATGAAAGACGGTTA
Found at i:4103 original size:14 final size:14
Alignment explanation
Indices: 4084--4130 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
4074 TTTTATAATT
4084 ATTTTATTTTTACC
1 ATTTTATTTTTACC
* **
4098 ATTTTA-ATTTAAA
1 ATTTTATTTTTACC
*
4111 AGTTTATTTTTACC
1 ATTTTATTTTTACC
4125 ATTTTA
1 ATTTTA
4131 CTATTTTTCA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:4131 original size:151 final size:152
Alignment explanation
Indices: 3962--4263 Score: 482
Period size: 151 Copynumber: 2.0 Consensus size: 152
3952 TTATAATTAC
*
3962 TTTATTTTTACCATTTTACAATTTTTCCTTAA-AAACTTGGATATATTAAAATTTTTTAATATAT
1 TTTATTTTTACCATTTTACAATTTTTCATTAAGAAA-TTGGATATATTAAAATTTTTTAATATAT
**
4026 AGTTTGATTATACTAAAAACTCTATTTTCATTTAATTAAATTCAATA-TTTTTATAATTATTTTA
65 AGTTTGATTATACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTTATAATTATAATA
*
4090 TTTTTACCATTTTAATTTAAAAG
130 TTTTTACAATTTTAATTTAAAAG
* *
4113 TTTATTTTTACCATTTTACTATTTTTCATTAAGATATTGGATATATTAAAATTTTTTAATATATA
1 TTTATTTTTACCATTTTACAATTTTTCATTAAGAAATTGGATATATTAAAATTTTTTAATATATA
* * * * *
4178 GTTTGATTCTATTAAAAATTCTATTTTTATTTAATTAAATTCAATATTTTTTATGATTATAATAT
66 GTTTGATTATACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTTATAATTATAATAT
4243 TTTTACAATTTTAATTTAAAA
131 TTTTACAATTTTAATTTAAAA
4264 CGTTATTGTG
Statistics
Matches: 138, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
151 101 0.73
152 37 0.27
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.54
Consensus pattern (152 bp):
TTTATTTTTACCATTTTACAATTTTTCATTAAGAAATTGGATATATTAAAATTTTTTAATATATA
GTTTGATTATACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTTATAATTATAATAT
TTTTACAATTTTAATTTAAAAG
Found at i:7921 original size:3 final size:3
Alignment explanation
Indices: 7913--7942 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
7903 ATGGACCGAA
7913 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
7943 TAAAGGAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11011 original size:13 final size:14
Alignment explanation
Indices: 10988--11031 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
10978 CCTCTGTTCC
10988 TTTTTAATTGTCCA
1 TTTTTAATTGTCCA
*
11002 TTTTT-CTTGTTCC-
1 TTTTTAATTG-TCCA
11015 TTTTTAATTGTCCA
1 TTTTTAATTGTCCA
11029 TTT
1 TTT
11032 CCCTTGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.14, C:0.16, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTTTAATTGTCCA
Found at i:11019 original size:14 final size:14
Alignment explanation
Indices: 10982--11025 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
10972 TATACTCCTC
10982 TGTTCCTTTTTAAT
1 TGTTCCTTTTTAAT
*
10996 TG-TCCATTTTT-CT
1 TGTTCC-TTTTTAAT
11009 TGTTCCTTTTTAAT
1 TGTTCCTTTTTAAT
11023 TGT
1 TGT
11026 CCATTTCCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.11, C:0.16, G:0.09, T:0.64
Consensus pattern (14 bp):
TGTTCCTTTTTAAT
Found at i:11037 original size:27 final size:27
Alignment explanation
Indices: 10982--11039 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
10972 TATACTCCTC
**
10982 TGTTCCTTTTTAATTGTCCATTTTTCT
1 TGTTCCTTTTTAATTGTCCATTTCCCT
11009 TGTTCCTTTTTAATTGTCCATTTCCCT
1 TGTTCCTTTTTAATTGTCCATTTCCCT
11036 TGTT
1 TGTT
11040 TTCCAGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.10, C:0.21, G:0.09, T:0.60
Consensus pattern (27 bp):
TGTTCCTTTTTAATTGTCCATTTCCCT
Found at i:13393 original size:60 final size:60
Alignment explanation
Indices: 13306--13487 Score: 190
Period size: 60 Copynumber: 3.0 Consensus size: 60
13296 GACACTGAGA
* * * *
13306 AGAGCCCCCAAAATTTAGAGAGCAATCAGAATCAGCAAACTCAGCGATATGAACAAGAGC
1 AGAGCCCCCAAAATATAGAGAGCAATCAGAAACAACAAACTCAGCGACATGAACAAGAGC
* * * *
13366 AGAGCCCCCAAAATGTAGAGAGCAATCAGAAACAACAGAGTCTGCGACATGAACAAGAGC
1 AGAGCCCCCAAAATATAGAGAGCAATCAGAAACAACAAACTCAGCGACATGAACAAGAGC
* * * * * *
13426 AGCGCCGCCAAAATATAGAGCGCCAA--GGACAACAA-AAGAGTCAGCAACATGAACAAGAGC
1 AGAGCCCCCAAAATATAGAGAG-CAATCAGA-AACAACAA-ACTCAGCGACATGAACAAGAGC
13486 AG
1 AG
13488 GGCCGCCTCC
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.03
60 98 0.94
61 3 0.03
ACGTcount: A:0.44, C:0.24, G:0.23, T:0.10
Consensus pattern (60 bp):
AGAGCCCCCAAAATATAGAGAGCAATCAGAAACAACAAACTCAGCGACATGAACAAGAGC
Found at i:13574 original size:90 final size:90
Alignment explanation
Indices: 13421--13605 Score: 352
Period size: 90 Copynumber: 2.1 Consensus size: 90
13411 GACATGAACA
*
13421 AGAGCAGCGCCGCCAAAATATAGAGCGCCAAGGACAACAAAAGAGTCAGCAACATGAACAAGAGC
1 AGAGCAGCACCGCCAAAATATAGAGCGCCAAGGACAACAAAAGAGTCAGCAACATGAACAAGAGC
*
13486 AGGGCCGCCTCCAAGGAAAGGAGAT
66 AGGGCCACCTCCAAGGAAAGGAGAT
13511 AGAGCAGCACCGCCAAAATATAGAGCGCCAAGGACAACAAAAGAGTCAGCAACATGAACAAGAGC
1 AGAGCAGCACCGCCAAAATATAGAGCGCCAAGGACAACAAAAGAGTCAGCAACATGAACAAGAGC
13576 AGGGCCACCTCCAAGGAAAGGAGAT
66 AGGGCCACCTCCAAGGAAAGGAGAT
13601 AGAGC
1 AGAGC
13606 GCCAAGGAAA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 93 1.00
ACGTcount: A:0.42, C:0.24, G:0.27, T:0.06
Consensus pattern (90 bp):
AGAGCAGCACCGCCAAAATATAGAGCGCCAAGGACAACAAAAGAGTCAGCAACATGAACAAGAGC
AGGGCCACCTCCAAGGAAAGGAGAT
Found at i:13692 original size:60 final size:60
Alignment explanation
Indices: 13599--13714 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 60
13589 AGGAAAGGAG
13599 ATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAGCACCGCCAAAAT
1 ATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAGCACCGCCAAAAT
* *
13659 ATAGAGCTCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAGCGCCGCCA
1 ATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAGCACCGCCA
13715 GCAATATGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.41, C:0.24, G:0.28, T:0.07
Consensus pattern (60 bp):
ATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAGCACCGCCAAAAT
Found at i:13718 original size:27 final size:27
Alignment explanation
Indices: 13686--13742 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
13676 GGAGCAGAGT
13686 CAGCAACATGAACAAGAGCAGCGCCGC
1 CAGCAACATGAACAAGAGCAGCGCCGC
*
13713 CAGCAATATGAACAAGAGCAGCGCCGC
1 CAGCAACATGAACAAGAGCAGCGCCGC
13740 CAG
1 CAG
13743 GATATAGAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.32, G:0.26, T:0.05
Consensus pattern (27 bp):
CAGCAACATGAACAAGAGCAGCGCCGC
Found at i:13724 original size:87 final size:87
Alignment explanation
Indices: 13626--13801 Score: 280
Period size: 87 Copynumber: 2.0 Consensus size: 87
13616 GGAGCAGAGT
*
13626 CAGCAACATGAACAAGAGCAGCACCGCCAAAATATAGAGCTCCAAGGAAAGGAGCAGAGTCAGCA
1 CAGCAACATGAACAAGAGCAGCACCGCCAAAATATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCA
* *
13691 ACATGAACAAGAGCAGCGCCGC
66 ACATGAAAAAGAGCAGCACCGC
* * ** *
13713 CAGCAATATGAACAAGAGCAGCGCCGCCAGGATATAGAGCGCCAAGGAAAGGAGCGGAGTCAGCA
1 CAGCAACATGAACAAGAGCAGCACCGCCAAAATATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCA
13778 ACATGAAAAAGAGCAGCACCGC
66 ACATGAAAAAGAGCAGCACCGC
13800 CA
1 CA
13802 AAATATAGAG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.40, C:0.26, G:0.27, T:0.07
Consensus pattern (87 bp):
CAGCAACATGAACAAGAGCAGCACCGCCAAAATATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCA
ACATGAAAAAGAGCAGCACCGC
Found at i:13782 original size:147 final size:139
Alignment explanation
Indices: 13594--13991 Score: 557
Period size: 138 Copynumber: 2.8 Consensus size: 139
13584 CTCCAAGGAA
*
13594 AGGAGATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAGCACCGCCAAAAT
1 AGGATATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAGCACCGCCAAAAT
* *
13659 ATAGAGCTCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAGCGCCGCCAGCAATATGA
66 ATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCA--GACG--A-C---ATGA
*
13724 ACAAGAGCAGCGCCGCC
123 ACAAGAGCAGCACCGCC
* *
13741 AGGATATAGAGCGCCAAGGAAAGGAGCGGAGTCAGCAACATGAAAAAGAGCAGCACCGCCAAAAT
1 AGGATATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAGCACCGCCAAAAT
13806 ATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCA-ACGACATGAACAAGAGC
66 ATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAGACGACATGAACAAGAGC
13870 AGCACCGCC
131 AGCACCGCC
** * * ** * * *
13879 AAAATATAGAGCACCAACGAATA-CTGCAGAGTCAGCAATATGAACAAGAGCAGCGCCGCCAGAA
1 AGGATATAGAGCGCCAAGGAA-AGGAGCAGAGTCAGCAACATGAACAAGAGCAGCACCGCCAAAA
*
13943 TATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAAAAAGAGCAG
65 TATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAG
13992 TGTCGCCAAA
Statistics
Matches: 231, Mismatches: 18, Indels: 12
0.89 0.07 0.05
Matches are distributed among these distances:
138 118 0.51
139 1 0.00
141 1 0.00
142 1 0.00
144 2 0.01
147 108 0.47
ACGTcount: A:0.42, C:0.23, G:0.28, T:0.08
Consensus pattern (139 bp):
AGGATATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAGCACCGCCAAAAT
ATAGAGCGCCAAGGAAAGGAGCAGAGTCAGCAACATGAACAAGAGCAGACGACATGAACAAGAGC
AGCACCGCC
Found at i:13808 original size:60 final size:60
Alignment explanation
Indices: 13713--13852 Score: 226
Period size: 60 Copynumber: 2.3 Consensus size: 60
13703 GCAGCGCCGC
* * ** *
13713 CAGCAATATGAACAAGAGCAGCGCCGCCAGGATATAGAGCGCCAAGGAAAGGAGCGGAGT
1 CAGCAACATGAACAAGAGCAGCACCGCCAAAATATAGAGCGCCAAGGAAAGGAGCAGAGT
*
13773 CAGCAACATGAAAAAGAGCAGCACCGCCAAAATATAGAGCGCCAAGGAAAGGAGCAGAGT
1 CAGCAACATGAACAAGAGCAGCACCGCCAAAATATAGAGCGCCAAGGAAAGGAGCAGAGT
13833 CAGCAACATGAACAAGAGCA
1 CAGCAACATGAACAAGAGCA
13853 ACGACATGAA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.42, C:0.22, G:0.29, T:0.07
Consensus pattern (60 bp):
CAGCAACATGAACAAGAGCAGCACCGCCAAAATATAGAGCGCCAAGGAAAGGAGCAGAGT
Found at i:13860 original size:78 final size:78
Alignment explanation
Indices: 13778--13930 Score: 236
Period size: 78 Copynumber: 2.0 Consensus size: 78
13768 GGAGTCAGCA
* * *
13778 ACATGAAAAAGAGCAGCACCGCCAAAATATAGAGCGCCAAGGAA-AGGAGCAGAGTCAGCAACAT
1 ACATGAAAAAGAGCAGCACCGCCAAAATATAGAGCACCAACGAATA-CAGCAGAGTCAGCAACAT
13842 GAACAAGAGCAACG
65 GAACAAGAGCAACG
* * *
13856 ACATGAACAAGAGCAGCACCGCCAAAATATAGAGCACCAACGAATACTGCAGAGTCAGCAATATG
1 ACATGAAAAAGAGCAGCACCGCCAAAATATAGAGCACCAACGAATACAGCAGAGTCAGCAACATG
13921 AACAAGAGCA
66 AACAAGAGCA
13931 GCGCCGCCAG
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
78 67 0.99
79 1 0.01
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.08
Consensus pattern (78 bp):
ACATGAAAAAGAGCAGCACCGCCAAAATATAGAGCACCAACGAATACAGCAGAGTCAGCAACATG
AACAAGAGCAACG
Found at i:13938 original size:60 final size:60
Alignment explanation
Indices: 13856--14115 Score: 315
Period size: 60 Copynumber: 4.3 Consensus size: 60
13846 AAGAGCAACG
* * *
13856 ACATGAACAAGAGCAGCACCGCCAAAATATAGAGCACCAACGAATACTGCAGAGTCAGCA
1 ACATGAACAAGAGCAGCGCCGCCAAAATATAGAGCACCAAGGAATACAGCAGAGTCAGCA
* * * *
13916 ATATGAACAAGAGCAGCGCCGCCAGAATATAGAGCGCCAAGGAA-AGGAGCAGAGTCAGCA
1 ACATGAACAAGAGCAGCGCCGCCAAAATATAGAGCACCAAGGAATA-CAGCAGAGTCAGCA
* * * * * * *
13976 ACATGAAAAAGAGCAGTGTCGCCAAAATATAGAGCGCCAAGGAAAAGAGCAGAGTCAGGA
1 ACATGAACAAGAGCAGCGCCGCCAAAATATAGAGCACCAAGGAATACAGCAGAGTCAGCA
* * * * ** *
14036 AGATGAACAAGAGCAGCGGCACCGAAATATAGAGCAGGAAGGAATACAACAGAGTCAGCA
1 ACATGAACAAGAGCAGCGCCGCCAAAATATAGAGCACCAAGGAATACAGCAGAGTCAGCA
14096 ACATGAACAAGAGCAGCGCC
1 ACATGAACAAGAGCAGCGCC
14116 AAGGAAAACA
Statistics
Matches: 170, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
59 1 0.01
60 168 0.99
61 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.27, T:0.09
Consensus pattern (60 bp):
ACATGAACAAGAGCAGCGCCGCCAAAATATAGAGCACCAAGGAATACAGCAGAGTCAGCA
Found at i:18027 original size:14 final size:14
Alignment explanation
Indices: 18008--18035 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17998 GAATAGATGG
18008 TTTAAATTTAATTA
1 TTTAAATTTAATTA
18022 TTTAAATTTAATTA
1 TTTAAATTTAATTA
18036 AAATCTAATA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAAATTTAATTA
Found at i:23032 original size:41 final size:41
Alignment explanation
Indices: 22984--23095 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 41
22974 TGGTAATTCA
*
22984 AAGGTGACAATTTCTGGTGTCAACA-GTAATTATAATTTACC
1 AAGGTGACAACTTCTGGTGTCAA-AGGTAATTATAATTTACC
** * *
23025 GGGGTGAC-ACTTCTGATGTCAAAGGTAATTTTAATTTACC
1 AAGGTGACAACTTCTGGTGTCAAAGGTAATTATAATTTACC
**
23065 AAAATGACAACTTCTGGTGTCAAAGGTAATT
1 AAGGTGACAACTTCTGGTGTCAAAGGTAATT
23096 TTCAATATTA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.02
40 31 0.53
41 27 0.46
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (41 bp):
AAGGTGACAACTTCTGGTGTCAAAGGTAATTATAATTTACC
Found at i:23733 original size:31 final size:31
Alignment explanation
Indices: 23668--23742 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
23658 TTTAGTAATG
*
23668 ACAATTTAGAAATATGTTTTTTAAAAAAAGGGT
1 ACAATTGA-AAATATG-TTTTTAAAAAAAGGGT
23701 ACAATTGAAAATATG-TTTTAAAAATAAGGGT
1 ACAATTGAAAATATGTTTTTAAAAA-AAGGGT
*
23732 ACAATCGAAAA
1 ACAATTGAAAA
23743 ACATAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 9 0.23
31 16 0.41
32 7 0.18
33 7 0.18
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (31 bp):
ACAATTGAAAATATGTTTTTAAAAAAAGGGT
Found at i:24035 original size:43 final size:43
Alignment explanation
Indices: 23979--24094 Score: 198
Period size: 43 Copynumber: 2.7 Consensus size: 43
23969 CACAACTCCG
* *
23979 GCCAAAAAAAAAAAGGGGACATAACAATTCCTTTGTGCCAACT
1 GCCAAAGAGAAAAAGGGGACATAACAATTCCTTTGTGCCAACT
24022 GCCAAAGAGAAAAAGGGGACATAACAATTCCTTTGTGCCAACT
1 GCCAAAGAGAAAAAGGGGACATAACAATTCCTTTGTGCCAACT
*
24065 GCCAAAGAGAAAAAGGGGACATTAC-ATTCC
1 GCCAAAGAGAAAAAGGGGACATAACAATTCC
24095 ATACTTTAAG
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
42 5 0.07
43 65 0.93
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (43 bp):
GCCAAAGAGAAAAAGGGGACATAACAATTCCTTTGTGCCAACT
Found at i:27891 original size:170 final size:170
Alignment explanation
Indices: 27607--27947 Score: 648
Period size: 170 Copynumber: 2.0 Consensus size: 170
27597 ACTCCCTTTA
27607 TACCTTTTTATAAGTCCCATTTTAGAAAGCTTTTTTTGTCCCAAAATATAAGTCCTTTCTAAACC
1 TACCTTTTTATAAGTCCCATTTTAGAAAGCTTTTTTTGTCCCAAAATATAAGTCCTTTCTAAACC
*
27672 CAATACATATTTAAAAGTTATTAATAACTAGCCTTGGAAATAGTAAGGTAGTTAAGAAAGTGAGA
66 CAATACATATTTAAAAGTTATTAATAACTAGCCTTGGAAATAATAAGGTAGTTAAGAAAGTGAGA
27737 AGGATGAGAGAA-AATGAGTAGAAGAAAGAAAATAACTAAC
131 AGGATGAGA-AAGAATGAGTAGAAGAAAGAAAATAACTAAC
*
27777 TACCTTTTTATAAGTCCCCTTTTAGAAAGCTTTTTTTGTCCCAAAATATAAGTCCTTTCTAAACC
1 TACCTTTTTATAAGTCCCATTTTAGAAAGCTTTTTTTGTCCCAAAATATAAGTCCTTTCTAAACC
27842 CAATACATATTTAAAAGTTATTAATAACTAGCCTTGGAAATAATAAGGTAGTTAAGAAAGTGAGA
66 CAATACATATTTAAAAGTTATTAATAACTAGCCTTGGAAATAATAAGGTAGTTAAGAAAGTGAGA
27907 AGGATGAGAAAGAATGAGTAGAAGAAAGAAAATAACTAAC
131 AGGATGAGAAAGAATGAGTAGAAGAAAGAAAATAACTAAC
27947 T
1 T
27948 TTACAGAGGG
Statistics
Matches: 168, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
169 2 0.01
170 166 0.99
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.30
Consensus pattern (170 bp):
TACCTTTTTATAAGTCCCATTTTAGAAAGCTTTTTTTGTCCCAAAATATAAGTCCTTTCTAAACC
CAATACATATTTAAAAGTTATTAATAACTAGCCTTGGAAATAATAAGGTAGTTAAGAAAGTGAGA
AGGATGAGAAAGAATGAGTAGAAGAAAGAAAATAACTAAC
Found at i:32883 original size:27 final size:27
Alignment explanation
Indices: 32845--32918 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
32835 ATGTTGCAGG
**
32845 GCAGAATTCCCATCCTCCAAAGGTTGA
1 GCAGAATTCCCATCCTCCAAAGGCCGA
32872 GCAGAATTCCCATCCTCCAAAGGCCGA
1 GCAGAATTCCCATCCTCCAAAGGCCGA
* *
32899 GCCGAATTCTCATCCTCCAA
1 GCAGAATTCCCATCCTCCAA
32919 GGGCAGAGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.28, C:0.35, G:0.16, T:0.20
Consensus pattern (27 bp):
GCAGAATTCCCATCCTCCAAAGGCCGA
Found at i:34719 original size:31 final size:31
Alignment explanation
Indices: 34681--34814 Score: 116
Period size: 31 Copynumber: 4.4 Consensus size: 31
34671 TTAATTTGAC
* *
34681 CAAATAAGGGCCTAACATTATTGAAAAGGCT
1 CAAATAAGGGCCTAACGTTATCGAAAAGGCT
* * * * *
34712 CAAATAAGGACCCGATC-TT-T-TAATATGG-T
1 CAAATAAGG-GCCTAACGTTATCGAA-AAGGCT
* *
34741 CAAATAAGGGCCTAA-GTTATCAAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAAGGCT
* *
34771 CAAATAAGGGTCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAAGGCT
34802 CAAATAAGGGCCT
1 CAAATAAGGGCCT
34815 GGTGTCAGTT
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
28 5 0.06
29 15 0.18
30 21 0.26
31 37 0.45
32 4 0.05
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAAGGCT
Found at i:34719 original size:60 final size:59
Alignment explanation
Indices: 34650--34779 Score: 188
Period size: 60 Copynumber: 2.2 Consensus size: 59
34640 TGTCAAAATA
* **
34650 CTCAAATAAGGACCCGATCTTTTAATTTGACCAAATAAGGGCCTAACATTATTGAAAAGG
1 CTCAAATAAGGACCCGATCTTTTAATATGACCAAATAAGGGCCTAA-ATTATCAAAAAGG
** * *
34710 CTCAAATAAGGACCCGATCTTTTAATATGGTCAAATAAGGGCCTAAGTTATCAAAAATG
1 CTCAAATAAGGACCCGATCTTTTAATATGACCAAATAAGGGCCTAAATTATCAAAAAGG
34769 CTCAAATAAGG
1 CTCAAATAAGG
34780 GTCTAACGTT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
59 20 0.32
60 43 0.68
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (59 bp):
CTCAAATAAGGACCCGATCTTTTAATATGACCAAATAAGGGCCTAAATTATCAAAAAGG
Found at i:34748 original size:29 final size:29
Alignment explanation
Indices: 34651--34749 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
34641 GTCAAAATAC
* *
34651 TCAAATAAGGACCCGATCTTTTAATTTGA
1 TCAAATAAGGACCCGATCTTTTAATATGG
* * * * *
34680 CCAAATAAGG-GCCTAACATTATTGAA-AAGG
1 TCAAATAAGGACCCGATC-TT-TT-AATATGG
34710 CTCAAATAAGGACCCGATCTTTTAATATGG
1 -TCAAATAAGGACCCGATCTTTTAATATGG
34740 TCAAATAAGG
1 TCAAATAAGG
34750 GCCTAAGTTA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
28 4 0.08
29 23 0.44
30 8 0.15
31 13 0.25
32 4 0.08
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (29 bp):
TCAAATAAGGACCCGATCTTTTAATATGG
Found at i:34776 original size:30 final size:31
Alignment explanation
Indices: 34740--34814 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
34730 TTTAATATGG
34740 TCAAATAAGGGCCTAA-GTTATCAAAAATGC
1 TCAAATAAGGGCCTAACGTTATCAAAAATGC
* *
34770 TCAAATAAGGGTCTAACGTTATCGAAAATGC
1 TCAAATAAGGGCCTAACGTTATCAAAAATGC
34801 TCAAATAAGGGCCT
1 TCAAATAAGGGCCT
34815 GGTGTCAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 15 0.37
31 26 0.63
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (31 bp):
TCAAATAAGGGCCTAACGTTATCAAAAATGC
Found at i:34876 original size:31 final size:30
Alignment explanation
Indices: 34841--35006 Score: 137
Period size: 31 Copynumber: 5.5 Consensus size: 30
34831 ACGCGTGAGA
34841 TAGGCCCTTATTTGAGCATTTTGACAAACGT
1 TAGGCCCTTATTTGAGCATTTT-ACAAACGT
** * *
34872 TAGGCCCTTATTTG-GCCAAATT-C-AATGA
1 TAGGCCCTTATTTGAG-CATTTTACAAACGT
* *
34900 TCGAGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAG-GCCCTTATTTGAGCATTTT-ACAAACGT
**
34932 TAGGCCCTTATTTG-GCCAAATTA-AAA-GAT
1 TAGGCCCTTATTTGAG-CATTTTACAAACG-T
*
34961 CAGGCCCTTATTTGAGCATTTTATCAAACGT
1 TAGGCCCTTATTTGAGCATTTTA-CAAACGT
*
34992 TAAGCCCTTATTTGA
1 TAGGCCCTTATTTGA
35007 ACAATTAGCC
Statistics
Matches: 105, Mismatches: 18, Indels: 24
0.71 0.12 0.16
Matches are distributed among these distances:
28 6 0.06
29 38 0.36
30 4 0.04
31 51 0.49
32 6 0.06
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (30 bp):
TAGGCCCTTATTTGAGCATTTTACAAACGT
Found at i:34917 original size:60 final size:60
Alignment explanation
Indices: 34838--35005 Score: 261
Period size: 60 Copynumber: 2.8 Consensus size: 60
34828 ATGACGCGTG
*
34838 AGAT-AGGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTCAA
1 AGATCAGGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAA
* *
34897 TGATC-GAGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAA
1 AGATCAG-GCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAA
*
34957 AGATCAGGCCCTTATTTGAGCATTTT-ATCAAACGTTAAGCCCTTATTTG
1 AGATCAGGCCCTTATTTGAGCATTTTGA-CAAACGTTAGGCCCTTATTTG
35006 AACAATTAGC
Statistics
Matches: 99, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
59 4 0.04
60 94 0.95
61 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (60 bp):
AGATCAGGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAA
Found at i:34972 original size:29 final size:29
Alignment explanation
Indices: 34873--34974 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 29
34863 GACAAACGTT
* *
34873 AGGCCCTTATTTGGCCAAATTCAATGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
** * *
34902 -GAGCCCTTATTTGAG-CATTTTGGCAAACG-TT
1 AG-GCCCTTATTTG-GCCAAATT---AAAAGATC
34933 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
34962 AGGCCCTTATTTG
1 AGGCCCTTATTTG
34975 AGCATTTTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
28 5 0.09
29 29 0.52
30 2 0.04
31 16 0.29
32 4 0.07
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:35374 original size:24 final size:26
Alignment explanation
Indices: 35336--35396 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
35326 TATTTTGTTC
*
35336 CATTGCATTCGACATAA-T-TCATTA
1 CATTGCATTCTACATAATTCTCATTA
35360 CA-TGACATTCTACATAATTCTCATTA
1 CATTG-CATTCTACATAATTCTCATTA
35386 CATTGCATTCT
1 CATTGCATTCT
35397 GAATCATTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.06
24 13 0.41
25 1 0.03
26 14 0.44
27 2 0.06
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (26 bp):
CATTGCATTCTACATAATTCTCATTA
Found at i:46243 original size:16 final size:16
Alignment explanation
Indices: 46222--46272 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
46212 CTGGAGCTTA
46222 TGAAAAAAGTGTTGTT
1 TGAAAAAAGTGTTGTT
*
46238 TG-AAAAA--GCTG-T
1 TGAAAAAAGTGTTGTT
*
46250 TGAAAAAAGTGTTGTA
1 TGAAAAAAGTGTTGTT
46266 TGAAAAA
1 TGAAAAA
46273 GCTGGTAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
12 3 0.11
13 8 0.29
15 8 0.29
16 9 0.32
ACGTcount: A:0.45, C:0.02, G:0.24, T:0.29
Consensus pattern (16 bp):
TGAAAAAAGTGTTGTT
Found at i:46256 original size:28 final size:28
Alignment explanation
Indices: 46222--46276 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
46212 CTGGAGCTTA
*
46222 TGAAAAAAGTGTTGTTTGAAAAAGCTGT
1 TGAAAAAAGTGTTGTATGAAAAAGCTGT
46250 TGAAAAAAGTGTTGTATGAAAAAGCTG
1 TGAAAAAAGTGTTGTATGAAAAAGCTG
46277 GTAGATTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.29
Consensus pattern (28 bp):
TGAAAAAAGTGTTGTATGAAAAAGCTGT
Done.