Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006017.1 Corchorus capsularis cultivar CVL-1 contig06035, 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: 40894
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:5006 original size:15 final size:12
Alignment explanation
Indices: 4967--4996 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
4957 GCTTATAAAA
4967 TTAATAGTAGGT
1 TTAATAGTAGGT
4979 TTAATAGTAGGT
1 TTAATAGTAGGT
4991 TTAATA
1 TTAATA
4997 TGACTAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (12 bp):
TTAATAGTAGGT
Found at i:5274 original size:16 final size:16
Alignment explanation
Indices: 5253--5283 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5243 TTAAAAAATA
5253 TTACTAAATCTTTATT
1 TTACTAAATCTTTATT
*
5269 TTACTAAGTCTTTAT
1 TTACTAAATCTTTAT
5284 AATTTGTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.03, T:0.55
Consensus pattern (16 bp):
TTACTAAATCTTTATT
Found at i:6214 original size:20 final size:21
Alignment explanation
Indices: 6166--6215 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
6156 ATAACTTGAA
*
6166 AACTTTTAGGTAATCTTATTT
1 AACTTTTAGGTAAACTTATTT
6187 AACTTTTTA-GTAAAC-TATTAT
1 AAC-TTTTAGGTAAACTTATT-T
6208 AACTTTTA
1 AACTTTTA
6216 TTGTAACTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 9 0.35
21 12 0.46
22 5 0.19
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (21 bp):
AACTTTTAGGTAAACTTATTT
Found at i:6363 original size:91 final size:91
Alignment explanation
Indices: 6251--6519 Score: 502
Period size: 91 Copynumber: 3.0 Consensus size: 91
6241 ACCTTGTAAA
* * **
6251 TTTTCTTGGTAAGCTTATAAATATTTCATTAAACTTAAAACCTTTTTAAATAGTTTTCTTAAATT
1 TTTTTTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGTTTTTTAAATAGTTTTCTTAAATT
6316 TATTCAATCACCTCGTTTAAGAAATT
66 TATTCAATCACCTCGTTTAAGAAATT
6342 TTTTTTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGTTTTTTAAATAGTTTTCTTAAATT
1 TTTTTTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGTTTTTTAAATAGTTTTCTTAAATT
6407 TATTCAATCACCTCGTTTAAGAAATT
66 TATTCAATCACCTCGTTTAAGAAATT
6433 TTTTTTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGTTTTTTAAATAGTTTTCTTAAATT
1 TTTTTTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGTTTTTTAAATAGTTTTCTTAAATT
6498 TATTCAATCACCTCGTTTAAGA
66 TATTCAATCACCTCGTTTAAGA
6520 TTTTTAGTGA
Statistics
Matches: 174, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 174 1.00
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.48
Consensus pattern (91 bp):
TTTTTTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGTTTTTTAAATAGTTTTCTTAAATT
TATTCAATCACCTCGTTTAAGAAATT
Found at i:6654 original size:22 final size:22
Alignment explanation
Indices: 6611--6654 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6601 ACGAACTTTA
*
6611 TAGTAACCTTATGAAGTTTTTT
1 TAGTAACCTTATGAAGTGTTTT
6633 TAGTAACCTTATTG-AGTGTTTT
1 TAGTAACCTTA-TGAAGTGTTTT
6655 AGAAATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (22 bp):
TAGTAACCTTATGAAGTGTTTT
Found at i:6656 original size:21 final size:23
Alignment explanation
Indices: 6611--6665 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
6601 ACGAACTTTA
*
6611 TAGTAACCTTA-TGAAGTTTTTT
1 TAGTAACCTTATTGAAGTTGTTT
6633 TAGTAACCTTATTG-AG-TGTTT
1 TAGTAACCTTATTGAAGTTGTTT
* *
6654 TAGAAATCTTAT
1 TAGTAACCTTAT
6666 AAAGTAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.48
22 13 0.45
23 2 0.07
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (23 bp):
TAGTAACCTTATTGAAGTTGTTT
Found at i:7120 original size:20 final size:20
Alignment explanation
Indices: 7083--7121 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
7073 TATTACGCTT
* *
7083 TTTTATTAACATTGTTAAGC
1 TTTTAATAACATTATTAAGC
*
7103 TTTTAATAACTTTATTAAG
1 TTTTAATAACATTATTAAG
7122 ACTGCTTTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTTAATAACATTATTAAGC
Found at i:7291 original size:21 final size:21
Alignment explanation
Indices: 7253--7310 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
7243 TTTCAATGTA
7253 TAAC-TTAGTAAGCATTTTAG
1 TAACTTTAGTAAGCATTTTAG
* *
7273 TAACTTTATTAAGCCTTTTAG
1 TAACTTTAGTAAGCATTTTAG
*
7294 TAACTTTAGAAAG-ATTT
1 TAACTTTAGTAAGCATTT
7311 ATATACTCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 7 0.22
21 25 0.78
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (21 bp):
TAACTTTAGTAAGCATTTTAG
Found at i:13154 original size:2 final size:2
Alignment explanation
Indices: 13147--13177 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
13137 ATTGTTTTAA
13147 AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
13178 GATAATCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24257 original size:19 final size:18
Alignment explanation
Indices: 24220--24259 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
24210 TTCTTGAGAT
*
24220 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
24238 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
24257 AAT
1 AAT
24260 AAATCATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:30645 original size:24 final size:24
Alignment explanation
Indices: 30601--30649 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
30591 AACCCCAATC
* *
30601 CTTAGCCATTTGCATGTAATTCTG
1 CTTAGCCACTTGCATGAAATTCTG
30625 CTTAGCCACTTG-ATTGAAATTCTG
1 CTTAGCCACTTGCA-TGAAATTCTG
30649 C
1 C
30650 CATTTCCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (24 bp):
CTTAGCCACTTGCATGAAATTCTG
Found at i:34440 original size:35 final size:34
Alignment explanation
Indices: 34295--34954 Score: 692
Period size: 35 Copynumber: 18.8 Consensus size: 34
34285 CTTAATTTTC
** * *
34295 TTTCC-TGAAATTAAGCTTGTGTCTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCT-TTTTTACCTAA
34329 TTTCCTTGAAATTAAGCCAGTCTTTCCTTTACCTAA
1 TTTCCTTGAAATTAAGCCAGTCTTT--TTTACCTAA
*
34365 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTC-TTT-TTTACCTAA
* *
34401 TTTCCTTGAAACTAAGCCAGTCCTTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGT-CTTTTTTACCTAA
* *
34436 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCT-TTTTTACCTAA
* * *
34471 TTTCCCTGAAACTAAGCCAGTCTTATTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTT-TTTTACCTAA
*
34506 TTTCCTTGAAATTAAGCCAGTCTTTTTTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTC--TTTTTTACCTAA
* * *
34542 TTTCCTTGAAACTAAGTCAGTCTTTTCTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTTTT-TTACCTAA
* *
34577 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCT-TTTTTACCTAA
* * * *
34612 TTTCCCTGGAACTAAGCCAGTCTTGTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTT-TTTTACCTAA
* * *
34647 TTTCCTTGAAATTAAGCCAATCTTCTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTTTTTTACCTAA
*
34681 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTC-TTT-TTTACCTAA
* ** * *
34717 TTTCCCTGAAATTAAGCCACACTATCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCT-TTTTTACCTAA
* * *
34752 TTTCCCTGAAACTAAGCCAGTCCTTTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGT-CTTTTTTACCTAA
* *
34787 TTTCCTTGAAATTAAGCCAGTCTATCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTCT-TTTTTACCTAA
* * *
34822 TTTCCCTGAAACTAAGCCAGTCTTGTTTTACTTAA
1 TTTCCTTGAAATTAAGCCAGTCTT-TTTTACCTAA
*
34857 TTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAG
1 TTTCCTTGAAATTAAGCCAGTC-TTT-TTTACCTAA
* * *
34893 TTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCGAG
1 TTTCCTTGAAATTAAGCCAGTC-TTT-TTTACCTAA
* * *
34929 TTTCCTTGAAACTAAACCTGTCTTTT
1 TTTCCTTGAAATTAAGCCAGTCTTTT
34955 ATCAGTCTTC
Statistics
Matches: 533, Mismatches: 73, Indels: 40
0.83 0.11 0.06
Matches are distributed among these distances:
34 49 0.09
35 294 0.55
36 184 0.35
37 6 0.01
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (34 bp):
TTTCCTTGAAATTAAGCCAGTCTTTTTTACCTAA
Found at i:34491 original size:70 final size:69
Alignment explanation
Indices: 34320--34918 Score: 867
Period size: 70 Copynumber: 8.5 Consensus size: 69
34310 CTTGTGTCTT
* * * *
34320 TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTCCTTTACCTAATTTCCTTGAAATTAAGCCAG
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTT--TTTACTTAATTTCCTTGAAATTAAGCCAG
*
34385 TCTTTTC
64 TC-TATC
34392 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCCTTTTTTACTTAATTTCCTTGAAATTAAGCCAGT
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGT-CTTTTTTACTTAATTTCCTTGAAATTAAGCCAGT
34457 CTATC
65 CTATC
*
34462 TTTACCTAGTTTCCCTGAAACTAAGCCAGTCTTATTTTACTTAATTTCCTTGAAATTAAGCCAGT
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTT-TTTTACTTAATTTCCTTGAAATTAAGCCAGT
* *
34527 CTTTTT
65 C-TATC
*
34533 TTTACCTAGTTTCCTTGAAACTAAGTCAGTCTTTTCTTACTTAATTTCCTTGAAATTAAGCCAGT
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTT-TTACTTAATTTCCTTGAAATTAAGCCAGT
34598 CTATC
65 CTATC
* * *
34603 TTTACCTAGTTTCCCTGGAACTAAGCCAGTCTTGTTTTACTTAATTTCCTTGAAATTAAGCCAAT
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTT-TTTTACTTAATTTCCTTGAAATTAAGCCAGT
34668 CT-TC
65 CTATC
* * * * * * *
34672 TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCCTGAAATTAAGCCAC
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTC-TTT-TTTACTTAATTTCCTTGAAATTAAGCCAG
*
34737 ACTATC
64 TCTATC
*
34743 TTTACCTAGTTTCCCTGAAACTAAGCCAGTCCTTTTTTACTTAATTTCCTTGAAATTAAGCCAGT
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGT-CTTTTTTACTTAATTTCCTTGAAATTAAGCCAGT
34808 CTATC
65 CTATC
*
34813 TTTACCTAGTTTCCCTGAAACTAAGCCAGTCTTGTTTTACTTAATTTCCTTGAAATTAAGCCAGT
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTT-TTTTACTTAATTTCCTTGAAATTAAGCCAGT
*
34878 CTTTTC
65 C-TATC
34884 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTT
1 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTT
34919 CTTTACCGAG
Statistics
Matches: 479, Mismatches: 37, Indels: 24
0.89 0.07 0.04
Matches are distributed among these distances:
69 35 0.07
70 251 0.52
71 161 0.34
72 28 0.06
73 4 0.01
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (69 bp):
TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTTTACTTAATTTCCTTGAAATTAAGCCAGTC
TATC
Found at i:34549 original size:141 final size:139
Alignment explanation
Indices: 34320--34954 Score: 889
Period size: 141 Copynumber: 4.5 Consensus size: 139
34310 CTTGTGTCTT
* * * * *
34320 TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTCCTTTACCTAATTTCCTTGAAATTAAGCCAG
1 TTTACCTAGTTTCCCTGAAACTAAGCCAGTCTTT--TTTACTTAATTTCCTTGAAATTAAGCCAG
34385 TCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCCTTTTTTACTTAATTTCCTTGAAATTA
64 TCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGT-CTTTTTTACTTAATTTCCTTGAAATTA
34450 AGCCAGTCTATC
128 AGCCAGTCTATC
34462 TTTACCTAGTTTCCCTGAAACTAAGCCAGTCTTATTTTACTTAATTTCCTTGAAATTAAGCCAGT
1 TTTACCTAGTTTCCCTGAAACTAAGCCAGTCTT-TTTTACTTAATTTCCTTGAAATTAAGCCAGT
* *
34527 CTTTTTTTTACCTAGTTTCCTTGAAACTAAGTCAGTCTTTTCTTACTTAATTTCCTTGAAATTAA
65 CTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTT-TTACTTAATTTCCTTGAAATTAA
34592 GCCAGTCTATC
129 GCCAGTCTATC
* *
34603 TTTACCTAGTTTCCCTGGAACTAAGCCAGTCTTGTTTTACTTAATTTCCTTGAAATTAAGCCAAT
1 TTTACCTAGTTTCCCTGAAACTAAGCCAGTCTT-TTTTACTTAATTTCCTTGAAATTAAGCCAGT
* * * * * *
34668 C--TTCTTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTCTTTACCTAGTTTCCCTGAAATTA
65 CTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTC-TTT-TTTACTTAATTTCCTTGAAATTA
**
34731 AGCCACACTATC
128 AGCCAGTCTATC
34743 TTTACCTAGTTTCCCTGAAACTAAGCCAGTCCTTTTTTACTTAATTTCCTTGAAATTAAGCCAGT
1 TTTACCTAGTTTCCCTGAAACTAAGCCAGT-CTTTTTTACTTAATTTCCTTGAAATTAAGCCAGT
* *
34808 C-TATCTTTACCTAGTTTCCCTGAAACTAAGCCAGTCTTGTTTTACTTAATTTCCTTGAAATTAA
65 CTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTT-TTTTACTTAATTTCCTTGAAATTAA
*
34872 GCCAGTCTTTTC
129 GCCAGTC-TATC
* ** * * * *
34884 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTCTTTACCGAGTTTCCTTGAAACTAAACCTG
1 TTTACCTAGTTTCCCTGAAACTAAGCCAGTC-TTT-TTTACTTAATTTCCTTGAAATTAAGCCAG
34949 TCTTTT
64 TCTTTT
34955 ATCAGTCTTC
Statistics
Matches: 441, Mismatches: 41, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
139 29 0.07
140 126 0.29
141 229 0.52
142 54 0.12
143 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (139 bp):
TTTACCTAGTTTCCCTGAAACTAAGCCAGTCTTTTTTACTTAATTTCCTTGAAATTAAGCCAGTC
TTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTTTACTTAATTTCCTTGAAATTAAGC
CAGTCTATC
Found at i:34970 original size:11 final size:11
Alignment explanation
Indices: 34956--35137 Score: 138
Period size: 11 Copynumber: 16.6 Consensus size: 11
34946 CTGTCTTTTA
*
34956 TCAGTCTTCTT
1 TCAGTCTTATT
*
34967 TCAGTCTGATT
1 TCAGTCTTATT
*
34978 TCAGT-TTAGTA
1 TCAGTCTTA-TT
*
34989 TCAGT-TTTTT
1 TCAGTCTTATT
*
34999 TAAGTC-TATTT
1 TCAGTCTTA-TT
*
35010 TCAGTCTAATT
1 TCAGTCTTATT
* *
35021 TCAGTATTCTT
1 TCAGTCTTATT
*
35032 TCAGTCTGATT
1 TCAGTCTTATT
*
35043 TCAGT-TTCATA
1 TCAGTCTT-ATT
*
35054 TCAGTCTTATA
1 TCAGTCTTATT
*
35065 TCAGTCTAATT
1 TCAGTCTTATT
* *
35076 TCAGTCTAATA
1 TCAGTCTTATT
*
35087 TCAGTCTTTTT
1 TCAGTCTTATT
*
35098 TCAGTCTAATT
1 TCAGTCTTATT
* *
35109 TCAGTCTTCTA
1 TCAGTCTTATT
*
35120 TCAGTCTAATT
1 TCAGTCTTATT
35131 TCAGTCT
1 TCAGTCT
35138 AACTTTGCCT
Statistics
Matches: 133, Mismatches: 32, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
10 9 0.07
11 121 0.91
12 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (11 bp):
TCAGTCTTATT
Found at i:34981 original size:22 final size:22
Alignment explanation
Indices: 34956--35137 Score: 165
Period size: 22 Copynumber: 8.3 Consensus size: 22
34946 CTGTCTTTTA
*
34956 TCAGTCTTCTTTCAGTCTGATT
1 TCAGTCTTCTTTCAGTCTAATT
* * **
34978 TCAGT-TTAGTATCAGT-TTTTT
1 TCAGTCTT-CTTTCAGTCTAATT
*
34999 TAAGTCTAT-TTTCAGTCTAATT
1 TCAGTCT-TCTTTCAGTCTAATT
* *
35021 TCAGTATTCTTTCAGTCTGATT
1 TCAGTCTTCTTTCAGTCTAATT
* * *
35043 TCAGT-TTCATATCAGTCTTATA
1 TCAGTCTTC-TTTCAGTCTAATT
** *
35065 TCAGTCTAATTTCAGTCTAATA
1 TCAGTCTTCTTTCAGTCTAATT
*
35087 TCAGTCTTTTTTCAGTCTAATT
1 TCAGTCTTCTTTCAGTCTAATT
*
35109 TCAGTCTTCTATCAGTCTAATT
1 TCAGTCTTCTTTCAGTCTAATT
35131 TCAGTCT
1 TCAGTCT
35138 AACTTTGCCT
Statistics
Matches: 130, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
21 19 0.15
22 109 0.84
23 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (22 bp):
TCAGTCTTCTTTCAGTCTAATT
Found at i:35045 original size:33 final size:33
Alignment explanation
Indices: 34954--35139 Score: 203
Period size: 33 Copynumber: 5.7 Consensus size: 33
34944 ACCTGTCTTT
* * *
34954 TATCAGTCTTCTTTCAGTCTGATTTCAGTTTAG
1 TATCAGTCTTCTTTCAGTCTAATTTCAGTCTAA
* * *
34987 TATCAGT-TTTTTTAAGTCTATTTTCAGTCTAA
1 TATCAGTCTTCTTTCAGTCTAATTTCAGTCTAA
* * * * *
35019 TTTCAGTATTCTTTCAGTCTGATTTCAGTTTCA
1 TATCAGTCTTCTTTCAGTCTAATTTCAGTCTAA
* *
35052 TATCAGTCTTATATCAGTCTAATTTCAGTCTAA
1 TATCAGTCTTCTTTCAGTCTAATTTCAGTCTAA
* **
35085 TATCAGTCTTTTTTCAGTCTAATTTCAGTCTTC
1 TATCAGTCTTCTTTCAGTCTAATTTCAGTCTAA
**
35118 TATCAGTCTAATTTCAGTCTAA
1 TATCAGTCTTCTTTCAGTCTAA
35140 CTTTGCCTAA
Statistics
Matches: 126, Mismatches: 26, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
32 25 0.20
33 101 0.80
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48
Consensus pattern (33 bp):
TATCAGTCTTCTTTCAGTCTAATTTCAGTCTAA
Found at i:35305 original size:40 final size:40
Alignment explanation
Indices: 35259--35346 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
35249 TTTAATTTCT
* *
35259 ATTAAGTCTTTTGACCGCTGTTTTTACTTAATTT-TGATGA
1 ATTAAGTCTTCTGACCACTGTTTTTACTTAATTTCT-ATGA
**
35299 ATTAAGTCTTCTGAGTACTGTTTTTACTTAATTTCTATGA
1 ATTAAGTCTTCTGACCACTGTTTTTACTTAATTTCTATGA
35339 ATTAAGTC
1 ATTAAGTC
35347 CTCAACTATG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 42 0.98
41 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (40 bp):
ATTAAGTCTTCTGACCACTGTTTTTACTTAATTTCTATGA
Found at i:35394 original size:39 final size:41
Alignment explanation
Indices: 35350--35435 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 41
35340 TTAAGTCCTC
35350 AACTATGCTT-ACTTTATTAACCACCCTGG-TTAAAACTTT
1 AACTATGCTTCACTTTATTAACCACCCTGGATTAAAACTTT
* * * * *
35389 AACTATGTTTCCCTTTCTTAATCTCCCTGGATTAAAACTTT
1 AACTATGCTTCACTTTATTAACCACCCTGGATTAAAACTTT
*
35430 GACTAT
1 AACTAT
35436 CTTTTAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 9 0.23
40 15 0.38
41 15 0.38
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (41 bp):
AACTATGCTTCACTTTATTAACCACCCTGGATTAAAACTTT
Found at i:38585 original size:41 final size:41
Alignment explanation
Indices: 38528--38609 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
38518 CATTTTTGTG
38528 TACTTGTAGTTATTCAATTCATGGTCTCCTTTTATTCTAAA
1 TACTTGTAGTTATTCAATTCATGGTCTCCTTTTATTCTAAA
38569 TACTTGTAGTTATTCAATTCATGGTCTCCTTTTATTCTAAA
1 TACTTGTAGTTATTCAATTCATGGTCTCCTTTTATTCTAAA
38610 AAAAATCAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (41 bp):
TACTTGTAGTTATTCAATTCATGGTCTCCTTTTATTCTAAA
Found at i:38937 original size:16 final size:16
Alignment explanation
Indices: 38916--38948 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
38906 ACATCCTATA
38916 AGCCCATAAAATAAAT
1 AGCCCATAAAATAAAT
38932 AGCCCATAAAATAAAT
1 AGCCCATAAAATAAAT
38948 A
1 A
38949 ATTCCAAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.18, G:0.06, T:0.18
Consensus pattern (16 bp):
AGCCCATAAAATAAAT
Found at i:40370 original size:27 final size:29
Alignment explanation
Indices: 40308--40363 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
40298 TAAAAGTACA
*
40308 AAATTGGTTCCTCAAGTGGAGCGAAAATAGC
1 AAATTGGTCCCTCAAGTGGA--GAAAATAGC
40339 AAATTGGTCCCTCAAGT-GA-AAAATA
1 AAATTGGTCCCTCAAGTGGAGAAAATA
40364 TGAAATTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
30 2 0.08
31 16 0.67
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.23
Consensus pattern (29 bp):
AAATTGGTCCCTCAAGTGGAGAAAATAGC
Done.