Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019738.1 Corchorus olitorius cultivar O-4 contig19771, 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: 17777
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6191 original size:6 final size:6
Alignment explanation
Indices: 6180--6204 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6170 TTCTAGTGTG
6180 TATGTA TATGTA TATGTA TATGTA T
1 TATGTA TATGTA TATGTA TATGTA T
6205 TCCTCATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TATGTA
Found at i:9099 original size:29 final size:31
Alignment explanation
Indices: 9063--9129 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
9053 ATGCAATTTG
*
9063 GGATATAACGTTAC-AAAA-CAAGCACTTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
**
9092 GGATATAACGTTACGAAAAGTGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
9123 GGATATA
1 GGATATA
9130 GTCCGTTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 14 0.42
30 4 0.12
31 15 0.45
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.22
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:9285 original size:31 final size:31
Alignment explanation
Indices: 9250--9328 Score: 133
Period size: 31 Copynumber: 2.5 Consensus size: 31
9240 CTAACCGATT
9250 ATATCCTTAATTGCTTGAAATCA-AAAACGTC
1 ATATCCTTAATTGCTTGAAAT-AGAAAACGTC
*
9281 ATATCCTTAATTGCTTGAAATAGAAAACGTT
1 ATATCCTTAATTGCTTGAAATAGAAAACGTC
9312 ATATCCTTAATTGCTTG
1 ATATCCTTAATTGCTTG
9329 TTTTGTAACG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 1 0.02
31 45 0.98
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAGAAAACGTC
Found at i:9373 original size:31 final size:29
Alignment explanation
Indices: 9248--9384 Score: 130
Period size: 31 Copynumber: 4.5 Consensus size: 29
9238 CCCTAACCGA
* *
9248 TTATATCCTTAATTGCTTGAAATCAAAAACG
1 TTATATCCTTAATTGCTTG-TAT-AGAAACG
* *
9279 TCATATCCTTAATTGCTTGAAATAGAAAACG
1 TTATATCCTTAATTGCTTG-TATAG-AAACG
* * *
9310 TTATATCCTTAATTGCTTGTTTTGTAACG
1 TTATATCCTTAATTGCTTGTATAGAAACG
**
9339 TTATATCCTTAATTGCTTGTGGGAGCAAACG
1 TTATATCCTTAATTGCTTGT-ATAG-AAACG
*
9370 TTATATCCTAAATTG
1 TTATATCCTTAATTG
9385 ATTATTTGGC
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
29 24 0.26
30 4 0.04
31 63 0.69
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (29 bp):
TTATATCCTTAATTGCTTGTATAGAAACG
Found at i:10306 original size:16 final size:17
Alignment explanation
Indices: 10287--10320 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
10277 TAAAAAGTGA
*
10287 TTTAAATAAAA-TATTT
1 TTTAAAAAAAATTATTT
10303 TTTAAAAAAAATTATTT
1 TTTAAAAAAAATTATTT
10320 T
1 T
10321 CTTCTGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAAAAAAAATTATTT
Found at i:10450 original size:31 final size:31
Alignment explanation
Indices: 10351--10490 Score: 133
Period size: 31 Copynumber: 4.6 Consensus size: 31
10341 AGATGATAAG
* * ***
10351 CAAGCAATTTAGGATATAATGTTTTCTG-CCG
1 CAAGCAATTAAGGATATAACGTTTTC-GATTT
* ***
10382 CAAGCAATTAAGGATATAACG-TTAC-AAAA
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
*
10411 CAAGCAATTAAGGATATAACGTTTTTGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
* * *
10442 TAAGCAATTAAGGATATGATGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
10473 CAAGCAATTAAGGATATA
1 CAAGCAATTAAGGATATA
10491 GACATATAGT
Statistics
Matches: 89, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
29 21 0.24
30 5 0.06
31 63 0.71
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCGATTT
Found at i:10691 original size:29 final size:31
Alignment explanation
Indices: 10618--10684 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
10608 CCTGACGGAC
10618 TATATCCTTAATTGCTCGTTTTTCGTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
*
10649 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGTTTTTCGTAACGT
10678 TATATCC
1 TATATCC
10685 CAAATTGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGTTTTTCGTAACGT
Found at i:12011 original size:42 final size:43
Alignment explanation
Indices: 11961--12054 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
11951 AGTGCATTAC
* *
11961 CTAA-ATTCTACTC-CATCTTTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCATCTCTAGATAATTCATCAAAATAAAG
12002 CTAATATTCTACTCTTTCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTC--TCATCTCTAGATAATTCATCAAAATAAAG
12047 CTAATATT
1 CTAATATT
12055 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 9 0.19
45 34 0.72
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (43 bp):
CTAATATTCTACTCTCATCTCTAGATAATTCATCAAAATAAAG
Found at i:14423 original size:22 final size:22
Alignment explanation
Indices: 14393--14558 Score: 106
Period size: 22 Copynumber: 7.5 Consensus size: 22
14383 TCCAACGTAG
*
14393 AAATATTGATAACCACACTGCGA
1 AAAT-TTGATAACCACACTGTGA
** *
14416 AAATTTGATAACCTTATTGTG-
1 AAATTTGATAACCACACTGTGA
* *
14437 AAATTTCGATAACCTC-CTTATGA
1 AAATTT-GATAACCACAC-TGTGA
* * *
14460 AATTTTGATAACCACAGTGAGA
1 AAATTTGATAACCACACTGTGA
* *
14482 AATTTTGATAACCACACTATG-
1 AAATTTGATAACCACACTGTGA
**
14503 AAATTCTGATAACCACACAAT-A
1 AAATT-TGATAACCACACTGTGA
* * *
14525 AAGTTTTGATAACCTCAGTGTGA
1 AA-ATTTGATAACCACACTGTGA
*
14548 AATTTTGATAA
1 AAATTTGATAA
14559 TCAAATTAAA
Statistics
Matches: 113, Mismatches: 22, Indels: 17
0.74 0.14 0.11
Matches are distributed among these distances:
21 10 0.09
22 89 0.79
23 14 0.12
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (22 bp):
AAATTTGATAACCACACTGTGA
Found at i:14505 original size:66 final size:66
Alignment explanation
Indices: 14392--14558 Score: 178
Period size: 66 Copynumber: 2.5 Consensus size: 66
14382 CTCCAACGTA
* * * * ** * * *
14392 GAAATATTGATAACCACACTGCGAAAATTTGATAACCTTATTGTGAAATT-TCGATAACCTC-CT
1 GAAATTTTGATAACCACAGTGAGAAATTTTGATAACCACACTATGAAATTCT-GATAACCACAC-
*
14455 TAT
64 AAT
14458 GAAATTTTGATAACCACAGTGAGAAATTTTGATAACCACACTATGAAATTCTGATAACCACACAA
1 GAAATTTTGATAACCACAGTGAGAAATTTTGATAACCACACTATGAAATTCTGATAACCACACAA
14523 T
66 T
* *
14524 -AAAGTTTTGATAACCTCAGTGTGAAATTTTGATAA
1 GAAA-TTTTGATAACCACAGTGAGAAATTTTGATAA
14559 TCAAATTAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
65 3 0.03
66 81 0.94
67 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (66 bp):
GAAATTTTGATAACCACAGTGAGAAATTTTGATAACCACACTATGAAATTCTGATAACCACACAA
T
Found at i:14532 original size:44 final size:44
Alignment explanation
Indices: 14391--14639 Score: 139
Period size: 44 Copynumber: 5.7 Consensus size: 44
14381 GCTCCAACGT
* ** * ** ***
14391 AGAAATATTGATAACCACACTGCGAAAATTTGATAACCTTATTG
1 AGAAATTTTGATAACCACACTATGAAATTTTGATAACCACAGCA
* * * **
14435 TGAAATTTCGATAACCTC-CTTATGAAATTTTGATAACCACAGTG
1 AGAAATTTTGATAACCACAC-TATGAAATTTTGATAACCACAGCA
*
14479 AGAAATTTTGATAACCACACTATGAAATTCTGATAACCACA-CA
1 AGAAATTTTGATAACCACACTATGAAATTTTGATAACCACAGCA
* * * * * * **
14522 ATAAAGTTTTGATAACCTCAGTGTGAAATTTTGATAATCAAATTA
1 AGAAA-TTTTGATAACCACACTATGAAATTTTGATAACCACAGCA
* * * * * * **
14567 A-AAA-ATTGGTAATCGCACTCTGAATATTTTGATAACCTCCTCA
1 AGAAATTTTGATAACCACACTATGAA-ATTTTGATAACCACAGCA
*
14610 TA-AAATTTTGATAACCACACCATGAAATTT
1 -AGAAATTTTGATAACCACACTATGAAATTT
14640 CGCTAACTTC
Statistics
Matches: 157, Mismatches: 41, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
42 14 0.09
43 18 0.11
44 108 0.69
45 17 0.11
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (44 bp):
AGAAATTTTGATAACCACACTATGAAATTTTGATAACCACAGCA
Found at i:14637 original size:22 final size:22
Alignment explanation
Indices: 14456--14639 Score: 103
Period size: 22 Copynumber: 8.4 Consensus size: 22
14446 TAACCTCCTT
**
14456 ATGAAATTTTGATAACCACAGTG
1 ATGAAATTTTGATAACCACA-CC
*
14479 A-GAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* *
14500 ATGAAATTCTGATAACCACACA
1 ATGAAATTTTGATAACCACACC
* **
14522 AT-AAAGTTTTGATAACCTCAGT
1 ATGAAA-TTTTGATAACCACACC
* *
14544 GTGAAATTTTGATAATCA-A--
1 ATGAAATTTTGATAACCACACC
* ** * * *
14563 ATTAAAAAATTGGTAATCGCACTC
1 A-TGAAATTTTGATAACCACAC-C
*
14587 -TGAATATTTTGATAACCTC-CTC
1 ATGAA-ATTTTGATAACCACAC-C
*
14609 ATAAAATTTTGATAACCACACC
1 ATGAAATTTTGATAACCACACC
14631 ATGAAATTT
1 ATGAAATTT
14640 CGCTAACTTC
Statistics
Matches: 124, Mismatches: 26, Indels: 23
0.72 0.15 0.13
Matches are distributed among these distances:
20 12 0.10
21 6 0.05
22 89 0.72
23 17 0.14
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.32
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:14852 original size:22 final size:22
Alignment explanation
Indices: 14827--14936 Score: 89
Period size: 22 Copynumber: 5.0 Consensus size: 22
14817 TAAAATTTCA
14827 ATAACCTTCGTATGAAATTTTG
1 ATAACCTTCGTATGAAATTTTG
* **
14849 ATAACATTTTTATGAAATTTTG
1 ATAACCTTCGTATGAAATTTTG
* *
14871 GTAATC-TCTGTATGAAATTTTG
1 ATAACCTTC-GTATGAAATTTTG
* * *
14893 ATAA-CTACATTATGAAGTTTTG
1 ATAACCTTC-GTATGAAATTTTG
* * *
14915 ATAACCTCCATATGAAGTTTTG
1 ATAACCTTCGTATGAAATTTTG
14937 GTAATTACAG
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
21 2 0.03
22 65 0.93
23 3 0.04
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
ATAACCTTCGTATGAAATTTTG
Found at i:14897 original size:66 final size:67
Alignment explanation
Indices: 14819--14981 Score: 152
Period size: 66 Copynumber: 2.4 Consensus size: 67
14809 TCACACTATA
* * *** *
14819 AAATTTCAATAACCTTCGTATGAAATTTTGATAACATTTTTATGAAATTTTGGTAATCT-CTGTA
1 AAATTTTAATAACCTTCCTATGAAATTTTGATAACATCCATATGAAATTTTGGTAAT-TACAGTA
14883 T-G
65 TGG
* * * * * *
14885 AAATTTTGATAA-CTACATTATGAAGTTTTGATAACCTCCATATGAAGTTTTGGTAATTACAGTA
1 AAATTTTAATAACCTTC-CTATGAAATTTTGATAACATCCATATGAAATTTTGGTAATTACAGTA
14949 TGG
65 TGG
* * *
14952 AATTTTTAATAACTTTCCTATGTAATTTTG
1 AAATTTTAATAACCTTCCTATGAAATTTTG
14982 GCTTGATTGT
Statistics
Matches: 75, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
65 4 0.05
66 48 0.64
67 21 0.28
68 2 0.03
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (67 bp):
AAATTTTAATAACCTTCCTATGAAATTTTGATAACATCCATATGAAATTTTGGTAATTACAGTAT
GG
Found at i:14906 original size:44 final size:44
Alignment explanation
Indices: 14798--14957 Score: 135
Period size: 44 Copynumber: 3.6 Consensus size: 44
14788 CGTTCTAATT
* * ** *
14798 AATTTTGATAA-TCACACTATAAAATTTCAATAACCTTCGTATGA
1 AATTTTGATAACT-ACATTATGAAATTTTGATAACCTCCGTATGA
** * * *
14842 AATTTTGATAAC-ATTTTTATGAAATTTTGGTAATCTCTGTATGA
1 AATTTTGATAACTA-CATTATGAAATTTTGATAACCTCCGTATGA
* *
14886 AATTTTGATAACTACATTATGAAGTTTTGATAACCTCCATATGA
1 AATTTTGATAACTACATTATGAAATTTTGATAACCTCCGTATGA
* * * * *
14930 AGTTTTGGTAATTACAGTATGGAATTTT
1 AATTTTGATAACTACATTATGAAATTTT
14958 TAATAACTTT
Statistics
Matches: 90, Mismatches: 23, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
43 1 0.01
44 88 0.98
45 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (44 bp):
AATTTTGATAACTACATTATGAAATTTTGATAACCTCCGTATGA
Found at i:14950 original size:22 final size:22
Alignment explanation
Indices: 14836--14957 Score: 88
Period size: 22 Copynumber: 5.5 Consensus size: 22
14826 AATAACCTTC
**
14836 GTATGAAATTTTGATAAC-ATTT
1 GTATGAAATTTTGATAACTA-CA
* * *
14858 TTATGAAATTTTGGTAATCT-CT
1 GTATGAAATTTTGATAA-CTACA
14880 GTATGAAATTTTGATAACTACA
1 GTATGAAATTTTGATAACTACA
* * *
14902 TTATGAAGTTTTGATAACCTCCA
1 GTATGAAATTTTGATAA-CTACA
* * *
14925 -TATGAAGTTTTGGTAATTACA
1 GTATGAAATTTTGATAACTACA
*
14946 GTATGGAATTTT
1 GTATGAAATTTT
14958 TAATAACTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
21 5 0.06
22 71 0.88
23 5 0.06
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (22 bp):
GTATGAAATTTTGATAACTACA
Found at i:16926 original size:22 final size:22
Alignment explanation
Indices: 16899--17562 Score: 256
Period size: 22 Copynumber: 29.7 Consensus size: 22
16889 TCTTAATTAC
*
16899 TATGAAATTTTGGTGACCTCCA
1 TATGAAATTTTGGTAACCTCCA
*
16921 TATGAAATTTTGGTAACCT-GA
1 TATGAAATTTTGGTAACCTCCA
*
16942 CTATGAAATTTTGGTGACCT-CA
1 -TATGAAATTTTGGTAACCTCCA
* **
16964 CTATGAAATTTCGGTAA-CTTGA
1 -TATGAAATTTTGGTAACCTCCA
*
16986 CTATTAAATTTTGGTAACCTTCC-
1 -TATGAAATTTTGGTAACC-TCCA
* *
17009 CATGAGATTTTGGTAA-CTCCA
1 TATGAAATTTTGGTAACCTCCA
* *
17030 CTATGAAACTTTTGGCAACCTCCC
1 -TATGAAA-TTTTGGTAACCTCCA
*
17054 TATGAAATTTTGGTAACC-CCC
1 TATGAAATTTTGGTAACCTCCA
* * *
17075 GATGAAATTTTGTTAACC-CCGC
1 TATGAAATTTTGGTAACCTCC-A
* * *
17097 TATTAAATTTCGGTTACCT-CA
1 TATGAAATTTTGGTAACCTCCA
*
17118 CTATGAAATTTCGGTAACCTCCCA
1 -TATGAAATTTTGGTAACCT-CCA
* *
17142 -ATAAAATTTTGGTAACCTCCC
1 TATGAAATTTTGGTAACCTCCA
* * *
17163 TATGAAATTTTAGTAATCTCAA
1 TATGAAATTTTGGTAACCTCCA
* *
17185 TGTGAAATTTTGATAA--TCACA
1 TATGAAATTTTGGTAACCTC-CA
* **
17206 -ATAAAAAATTGGTAA--TCGCA
1 TATGAAATTTTGGTAACCTC-CA
* *
17226 CTATGAAAATTTTGATAACCTCCT
1 -TATG-AAATTTTGGTAACCTCCA
* * *
17250 TATAAAATTTTGATAACC-ACA
1 TATGAAATTTTGGTAACCTCCA
* * *
17271 CTATGAAATTTCGCTAACTTCCCTA
1 -TATGAAATTTTGGTAACCT-CC-A
* * * *
17296 TGGGAATGAAATTGTGATATCCTCTA
1 T----ATGAAATTTTGGTAACCTCCA
** *
17322 TATGTAACATTTTCATAACCTCCT
1 TATG-AA-ATTTTGGTAACCTCCA
*
17346 TATGAAATTTTGTTAACCTTCC-
1 TATGAAATTTTGGTAACC-TCCA
* *
17368 TA-GAAAATTTTGATAACCTCCCTCCC
1 TATG-AAATTTTGGTAA----CCTCCA
* * *
17394 TATGAAATTTTGTTAACGTTC-
1 TATGAAATTTTGGTAACCTCCA
* *
17415 TAAT-TAATTTTGATAA--TCACA
1 T-ATGAAATTTTGGTAACCTC-CA
* **** * *
17436 CTATAAAATTGCAATAACCTTCG
1 -TATGAAATTTTGGTAACCTCCA
* * ***
17459 TATGAAATTTTGATAACATTTT
1 TATGAAATTTTGGTAACCTCCA
*
17481 TATGAAATTTTGGTAACCTCTA
1 TATGAAATTTTGGTAACCTCCA
* *
17503 TATGAAATTTTGATAA-CTACA
1 TATGAAATTTTGGTAACCTCCA
* *
17524 TTATGAAGTTTTGATAACCTCCA
1 -TATGAAATTTTGGTAACCTCCA
*
17547 TATGAAGTTTTGGTAA
1 TATGAAATTTTGGTAA
17563 TTACGGTATG
Statistics
Matches: 492, Mismatches: 103, Indels: 94
0.71 0.15 0.14
Matches are distributed among these distances:
19 1 0.00
20 20 0.04
21 46 0.09
22 321 0.65
23 40 0.08
24 26 0.05
25 6 0.01
26 17 0.03
27 2 0.00
28 13 0.03
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGGTAACCTCCA
Found at i:16946 original size:44 final size:44
Alignment explanation
Indices: 16897--17562 Score: 306
Period size: 44 Copynumber: 14.9 Consensus size: 44
16887 TTTCTTAATT
* *
16897 ACTATGAAATTTTGGTGACCTCCATATGAAATTTTGGTAACCTG
1 ACTATGAAATTTTGGTAACCTCCATATGAAATTTTGGTAACCTC
* * * *
16941 ACTATGAAATTTTGGTGACCT-CACTATGAAATTTCGGTAACTTG
1 ACTATGAAATTTTGGTAACCTCCA-TATGAAATTTTGGTAACCTC
* * *
16985 ACTATTAAATTTTGGTAACCTTCC-CATGAGATTTTGGTAA-CTCC
1 ACTATGAAATTTTGGTAACC-TCCATATGAAATTTTGGTAACCT-C
* *
17029 ACTATGAAACTTTTGGCAACCTCCCTATGAAATTTTGGTAACC-C
1 ACTATGAAA-TTTTGGTAACCTCCATATGAAATTTTGGTAACCTC
* * * * * * *
17073 CCGATGAAATTTTGTTAACC-CCGCTATTAAATTTCGGTTACCTC
1 ACTATGAAATTTTGGTAACCTCC-ATATGAAATTTTGGTAACCTC
* *
17117 ACTATGAAATTTCGGTAACCTCCCA-ATAAAATTTTGGTAACCTC
1 ACTATGAAATTTTGGTAACCT-CCATATGAAATTTTGGTAACCTC
* * * * * *
17161 CCTATGAAATTTTAGTAATCTCAATGTGAAATTTTGATAA--TC
1 ACTATGAAATTTTGGTAACCTCCATATGAAATTTTGGTAACCTC
* * ** *
17203 ACAATAAAAAATTGGTAA--TCGCACTATGAAAATTTTGATAACCTC
1 ACTATGAAATTTTGGTAACCTC-CA-TATG-AAATTTTGGTAACCTC
* * * * * *
17248 -CTTATAAAATTTTGATAACC-ACACTATGAAATTTCGCTAACTTC
1 AC-TATGAAATTTTGGTAACCTCCA-TATGAAATTTTGGTAACCTC
* * * * * **
17292 CCTATGGGAATGAAATTGTGATATCCTCTATATGTAACATTTTCATAACCTC
1 AC--T----ATGAAATTTTGGTAACCTCCATATG-AA-ATTTTGGTAACCTC
* *
17344 -CTTATGAAATTTTGTTAACCTTCC-TA-GAAAATTTTGATAACCTCCCTC
1 AC-TATGAAATTTTGGTAACC-TCCATATG-AAATTTTGGTAA----CCTC
* * * * * * * *
17392 CCTATGAAATTTTGTTAACGTTC-TAAT-TAATTTTGATAATCAC
1 ACTATGAAATTTTGGTAACCTCCAT-ATGAAATTTTGGTAACCTC
* **** * * * * *
17435 ACTATAAAATTGCAATAACCTTCGTATGAAATTTTGATAACATT
1 ACTATGAAATTTTGGTAACCTCCATATGAAATTTTGGTAACCTC
** * *
17479 TTTATGAAATTTTGGTAACCTCTATATGAAATTTTGATAA-CTAC
1 ACTATGAAATTTTGGTAACCTCCATATGAAATTTTGGTAACCT-C
* * * *
17523 ATTATGAAGTTTTGATAACCTCCATATGAAGTTTTGGTAA
1 ACTATGAAATTTTGGTAACCTCCATATGAAATTTTGGTAA
17563 TTACGGTATG
Statistics
Matches: 478, Mismatches: 104, Indels: 80
0.72 0.16 0.12
Matches are distributed among these distances:
40 2 0.00
41 1 0.00
42 19 0.04
43 63 0.13
44 250 0.52
45 50 0.10
46 21 0.04
47 16 0.03
48 22 0.05
49 1 0.00
50 19 0.04
51 4 0.01
52 10 0.02
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (44 bp):
ACTATGAAATTTTGGTAACCTCCATATGAAATTTTGGTAACCTC
Found at i:16972 original size:66 final size:66
Alignment explanation
Indices: 16897--17281 Score: 307
Period size: 66 Copynumber: 5.8 Consensus size: 66
16887 TTTCTTAATT
* * * *
16897 ACTATGAAATTTTGGTGACCTCCATATGAAATTTTGGTAACCTGACTATGAAATTTTGGTGACCT
1 ACTATGAAATTTTGGTAACCTCCATATGAAATTTTGGTAACCTCACAATGAAATTTTGGTAACCT
16962 C
66 C
* ** * * *
16963 ACTATGAAATTTCGGTAA-CTTGACTATTAAATTTTGGTAACCTTC-CCATGAGATTTTGGTAA-
1 ACTATGAAATTTTGGTAACCTCCA-TATGAAATTTTGGTAACC-TCACAATGAAATTTTGGTAAC
17025 CTCC
64 CT-C
* * * * *
17029 ACTATGAAACTTTTGGCAACCTCCCTATGAAATTTTGGTAACC-CCCGATGAAATTTTGTTAACC
1 ACTATGAAA-TTTTGGTAACCTCCATATGAAATTTTGGTAACCTCACAATGAAATTTTGGTAACC
*
17093 CC
65 TC
* * * * * * *
17095 GCTATTAAATTTCGGTTACCT-CACTATGAAATTTCGGTAACCTCCCAATAAAATTTTGGTAACC
1 ACTATGAAATTTTGGTAACCTCCA-TATGAAATTTTGGTAACCTCACAATGAAATTTTGGTAACC
17159 TC
65 TC
* * * * * * * ** * *
17161 CCTATGAAATTTTAGTAATCTCAATGTGAAATTTTGATAA--TCACAATAAAAAATTGGTAATCG
1 ACTATGAAATTTTGGTAACCTCCATATGAAATTTTGGTAACCTCACAATGAAATTTTGGTAACCT
17224 C
66 C
* * * * * *
17225 ACTATGAAAATTTTGATAACCTCCTTATAAAATTTTGATAACCACACTATGAAATTT
1 ACTATG-AAATTTTGGTAACCTCCATATGAAATTTTGGTAACCTCACAATGAAATTT
17282 CGCTAACTTC
Statistics
Matches: 248, Mismatches: 58, Indels: 25
0.75 0.18 0.08
Matches are distributed among these distances:
64 25 0.10
65 59 0.24
66 126 0.51
67 36 0.15
68 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (66 bp):
ACTATGAAATTTTGGTAACCTCCATATGAAATTTTGGTAACCTCACAATGAAATTTTGGTAACCT
C
Found at i:17573 original size:44 final size:43
Alignment explanation
Indices: 17481--17604 Score: 124
Period size: 44 Copynumber: 2.8 Consensus size: 43
17471 ATAACATTTT
* * * *
17481 TATGAAATTTTGGTAACCTCTATATGAAATTTTGATAACTACAT
1 TATGAAATTTTGATAACCTCCATATG-AATTTTGGTAACTACAG
* * *
17525 TATGAAGTTTTGATAACCTCCATATGAAGTTTTGGTAATTACGG
1 TATGAAATTTTGATAACCTCCATATGAA-TTTTGGTAACTACAG
* *
17569 TATGAAAATTTAATAACCATCC-TATGTAATTTTGGT
1 TATGAAATTTTGATAACC-TCCATATG-AATTTTGGT
17605 TTGATTGTCA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
43 2 0.03
44 60 0.90
45 5 0.07
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTCCATATGAATTTTGGTAACTACAG
Done.