Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013022.1 Corchorus olitorius cultivar O-4 contig13055, 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: 63712
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:18475 original size:19 final size:18
Alignment explanation
Indices: 18453--18488 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18443 AGGGTAGTTA
*
18453 AAAAAAAATTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
*
18471 AAAAAGAAGTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
18489 GAAAGAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAAAAAAGTGTTTTCAT
Found at i:19429 original size:19 final size:18
Alignment explanation
Indices: 19405--19440 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19395 TAAAGATTTA
19405 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
19424 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
19441 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:21511 original size:34 final size:34
Alignment explanation
Indices: 21467--21544 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 34
21457 TGTGGTTGGG
21467 GTGTAATTGAGTCGAGCTAAATC-GATACAATGTC
1 GTGTAATTGAGTCGAGCTAAATCAG-TACAATGTC
*
21501 GTGTGATTGAGTCGAGCTAAATCAGTACAATGTC
1 GTGTAATTGAGTCGAGCTAAATCAGTACAATGTC
21535 GTGTAATTGA
1 GTGTAATTGA
21545 ATTGAGTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 40 0.98
35 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.31
Consensus pattern (34 bp):
GTGTAATTGAGTCGAGCTAAATCAGTACAATGTC
Found at i:27313 original size:21 final size:22
Alignment explanation
Indices: 27277--27323 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
27267 ATGAAGAATG
27277 AAGAAAAGAATTGAAAAAGCAA
1 AAGAAAAGAATTGAAAAAGCAA
*
27299 AAGAAAA-AGTTGAAAAAGCAA
1 AAGAAAAGAATTGAAAAAGCAA
27320 AAGA
1 AAGA
27324 CGGAAGAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.68, C:0.04, G:0.19, T:0.09
Consensus pattern (22 bp):
AAGAAAAGAATTGAAAAAGCAA
Found at i:27589 original size:40 final size:39
Alignment explanation
Indices: 27498--27590 Score: 98
Period size: 40 Copynumber: 2.4 Consensus size: 39
27488 TATTGGAATG
* ** *
27498 AAAAAAAA-TTTTCTTCAAAGTGTGATCTTTTCAAACGA
1 AAAAAAAATTTTTCCTCAAAGTGCAATCTTTTCAAAAGA
***
27536 AAAAGATTTTTTTTCCTCAAAGTGCAATCTTTTCAAAAGA
1 AAAA-AAAATTTTTCCTCAAAGTGCAATCTTTTCAAAAGA
27576 AAAAAAAAGTTTTTC
1 AAAAAAAA-TTTTTC
27591 AAAAAGATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
38 4 0.10
39 2 0.05
40 36 0.86
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (39 bp):
AAAAAAAATTTTTCCTCAAAGTGCAATCTTTTCAAAAGA
Found at i:28969 original size:53 final size:53
Alignment explanation
Indices: 28804--29094 Score: 247
Period size: 53 Copynumber: 5.5 Consensus size: 53
28794 TCATTCCAAA
** * * *
28804 GAAGTTTTCA-ATGATC-AGAGTTGATCCCCAGATGA-TCTAGTGCTGTCATTTCAA
1 GAAGTTTTCAGA-GATCTA-AGTTGATCTTCAGATGACCCT-GTGCGGTC-TTTCAT
* * * * * * *
28858 GAAGTTTTCAGTGATCAAAGTTGATC-CCAGATGATCCAGTGTGGTC-AT-A-
1 GAAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCAT
* * * *
28907 AAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATAACCCTGTGCGGTCTTTCAT
1 GAAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCAT
* * * *
28960 GAAGTTTTCAGAGATTTAAGTTCATCTTCAGATGACTCTATGCGGTCTTTCAT
1 GAAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCAT
*
29013 AGAAGTTTTCAGAGATCTAAGTTGAT-TTTATGATGACCCTGTGCGGTCTTTCAT
1 -GAAGTTTTCAGAGATCTAAGTTGATCTTCA-GATGACCCTGTGCGGTCTTTCAT
* ** *
29067 AAAACTTTCAGAAATCTAAGTTGATCTT
1 GAAGTTTTCAGAGATCTAAGTTGATCTT
29095 TATATAATCC
Statistics
Matches: 195, Mismatches: 32, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
49 21 0.11
50 16 0.08
51 2 0.01
52 1 0.01
53 85 0.44
54 69 0.35
55 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (53 bp):
GAAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCAT
Found at i:29034 original size:107 final size:107
Alignment explanation
Indices: 28902--29094 Score: 271
Period size: 107 Copynumber: 1.8 Consensus size: 107
28892 TCCAGTGTGG
* * * **
28902 TCATAAAAGTTTTCAGAGGTTTAAGTTGATCTTCA-GATAACCCTGTGCGGTCTTTCATGAAGTT
1 TCATAAAAGTTTTCAGAGATCTAAGTTGAT-TTCATGATAACCCTGTGCGGTCTTTCATAAAACT
* *
28966 TTCAGAGATTTAAGTTCATCTTCAGATGACTCTATGCGGTCTT
65 TTCAGAAATCTAAGTTCATCTTCAGATGACTCTATGCGGTCTT
* * *
29009 TCATAGAAGTTTTCAGAGATCTAAGTTGATTTTATGATGACCCTGTGCGGTCTTTCATAAAACTT
1 TCATAAAAGTTTTCAGAGATCTAAGTTGATTTCATGATAACCCTGTGCGGTCTTTCATAAAACTT
*
29074 TCAGAAATCTAAGTTGATCTT
66 TCAGAAATCTAAGTTCATCTT
29095 TATATAATCC
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
106 3 0.04
107 71 0.96
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (107 bp):
TCATAAAAGTTTTCAGAGATCTAAGTTGATTTCATGATAACCCTGTGCGGTCTTTCATAAAACTT
TCAGAAATCTAAGTTCATCTTCAGATGACTCTATGCGGTCTT
Found at i:29116 original size:53 final size:54
Alignment explanation
Indices: 29000--29123 Score: 126
Period size: 53 Copynumber: 2.3 Consensus size: 54
28990 GATGACTCTA
* ** * * *
29000 TGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATTTTATGATGACCCTG
1 TGCGATCTTTCATAGAAACTTTCAGAAATCTAAGTTGATTTTATGATAACCCGG
* *
29054 TGCGGTCTTTCATA-AAACTTTCAGAAATCTAAGTTGATCTTTAT-ATAATCCGG
1 TGCGATCTTTCATAGAAACTTTCAGAAATCTAAGTTGAT-TTTATGATAACCCGG
** *
29107 TGTTATCTTTCGTAGAA
1 TGCGATCTTTCATAGAA
29124 GTTTTTAGAG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
53 37 0.64
54 21 0.36
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (54 bp):
TGCGATCTTTCATAGAAACTTTCAGAAATCTAAGTTGATTTTATGATAACCCGG
Found at i:29116 original size:107 final size:106
Alignment explanation
Indices: 28902--29146 Score: 251
Period size: 107 Copynumber: 2.3 Consensus size: 106
28892 TCCAGTGTGG
* * * **
28902 TCATAAAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATAACCCTGTGCGGTCTTTCATGAAGTTT
1 TCATAGAAGTTTTCAGA-GATTAAGTTGATCTTCAGATAACCCTGTGCGGTCTTTCATAAAACTT
* * * * *
28967 TCAGAGATTTAAGTTCATCTTCAGATGACTCTATGCGGTCTT
65 TCAGAAATCTAAGTTCATCTTCAGATAACTCGATGCGATCTT
* *
29009 TCATAGAAGTTTTCAGAGATCTAAGTTGAT-TTTATGATGACCCTGTGCGGTCTTTCATAAAACT
1 TCATAGAAGTTTTCAGAGAT-TAAGTTGATCTTCA-GATAACCCTGTGCGGTCTTTCATAAAACT
* * * * **
29073 TTCAGAAATCTAAGTTGATCTTTATATAA-TCCGGTGTTATCTT
64 TTCAGAAATCTAAGTTCATCTTCAGATAACT-CGATGCGATCTT
* *
29116 TCGTAGAAGTTTTTAGAGATTAGAGTTGATC
1 TCATAGAAGTTTTCAGAGATTA-AGTTGATC
29147 CCTAGATGAT
Statistics
Matches: 113, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
106 8 0.07
107 105 0.93
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (106 bp):
TCATAGAAGTTTTCAGAGATTAAGTTGATCTTCAGATAACCCTGTGCGGTCTTTCATAAAACTTT
CAGAAATCTAAGTTCATCTTCAGATAACTCGATGCGATCTT
Found at i:29394 original size:215 final size:215
Alignment explanation
Indices: 28679--29576 Score: 685
Period size: 215 Copynumber: 4.2 Consensus size: 215
28669 TTGAAGTGAT
* * * * *
28679 CCAGTGCGGTCATTCCAATAAGTTTCCTT---GATCAGAGTTGAT-CCTAGATGACCCAGTGCGG
1 CCAGTGCGGTCATTCCAAGAAGTTT--TTAGAGATCAGAGTTGATCCCTACATGATCCAATGCGA
* * * * * ***
28740 TCATTCCAAGAAGTTTTTAGA-GATCAGGGTTGATCCCTACATGATCCAGTGTGGTCATTCCAAA
64 TCATTCCAAGAAGTTTTCA-ATGATCAGAGTTGATCCCCAAATGATCTAGTGCAATCATTCC-AA
* * * * * *
28804 GAAGTTTTCAATGATCAGAGTTGATCCCCAGATGATCTAGTGCTGTCATTTCAAGAAGTTTTCAG
127 GAAGTTTTCAGTGATCAGAGTTGAT-CCCAGATGATCCAGTGCGGTCATTCCAAAAAGTTTTCAA
* *
28869 TGATCAAAGTTGATC-CCAGATGAT
191 TGATCAGAGTTGATCTCCAGATGAC
* * * * * * * * ** *
28893 CCAGTGTGGTCA-T--AA-AAGTTTTCAGAGGTTTA-AGTTGAT-CTTCAGATAACCCTGTGCGG
1 CCAGTGCGGTCATTCCAAGAAGTTTTTAGA-GATCAGAGTTGATCCCT-ACATGATCCAATGCGA
* * * * ** * ** *
28952 TC-TTTCATGAAGTTTTCAGA-GATTTA-AGTTCATCTTCAGATGACTCTA-TGCGGTC-TTTCA
64 TCATTCCAAGAAGTTTTCA-ATGA-TCAGAGTTGATCCCCAAATGA-TCTAGTGCAATCATTCCA
* *** * * * *
29012 TAGAAGTTTTCAGAGATCTA-AGTTGATTTTATGATGACCCTGTGCGGTC-TTTCATAAAA-CTT
126 -AGAAGTTTTCAGTGATC-AGAGTTGATCCCA-GATGATCCAGTGCGGTCATTCCA-AAAAGTTT
* ** * * *
29074 TCAGA-AATCTA-AGTTGATCTTTATATAAT
187 TCA-ATGATC-AGAGTTGATCTCCAGATGAC
* *** * ** * *
29103 CCGGTGTTATCTTTCGTAGAAGTTTTTAGAGATTAGAGTTGATCCCTAGATGATCCAATGCGATC
1 CCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCCCTACATGATCCAATGCGATC
*
29168 ATTTCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAATGATCTAGTGCAATCATTCCAAGAAG
66 ATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAATGATCTAGTGCAATCATTCCAAGAAG
* **
29233 TTTTCAGTGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAATAAG-TTTCCTTGAT
131 TTTTCAGTGATCAGAGTTGAT-CCCAGATGATCCAGTGCGGTCATTCCAAAAAGTTTTCAATGAT
*
29297 CAGAGTTGATC-CTAGATGAC
195 CAGAGTTGATCTCCAGATGAC
* * *
29317 CCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGGGTTGATCCCTACATGATCCAGTGCGGTC
1 CCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCCCTACATGATCCAATGCGATC
* * ** *
29382 ATTCCAAAGAAGTTTTCAATGATCAGAGTTGATCCCCATATGATCTATTGCGGTCATTTCAAGAA
66 ATTCC-AAGAAGTTTTCAATGATCAGAGTTGATCCCCAAATGATCTAGTGCAATCATTCCAAGAA
* * *
29447 GTTTTTAGTGATCAGAGTTGATCCCAGATGATCTAGTGTGGTCATTCCAAAAAGTTTTCAATGAT
130 GTTTTCAGTGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAAAAGTTTTCAATGAT
*
29512 CAGAGTTGATCTCCAGATGAT
195 CAGAGTTGATCTCCAGATGAC
* * *
29533 CTAGTGCGGTCCTTCCAAGAAG-TTTTCGAAGATCAGAGTTGATC
1 CCAGTGCGGTCATTCCAAGAAGTTTTTAG-AGATCAGAGTTGATC
29577 TCCAAAAAAT
Statistics
Matches: 545, Mismatches: 104, Indels: 68
0.76 0.15 0.09
Matches are distributed among these distances:
208 1 0.00
209 23 0.04
210 61 0.11
211 47 0.09
212 24 0.04
213 6 0.01
214 141 0.26
215 192 0.35
216 50 0.09
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (215 bp):
CCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCCCTACATGATCCAATGCGATC
ATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAATGATCTAGTGCAATCATTCCAAGAAG
TTTTCAGTGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAAAAGTTTTCAATGATC
AGAGTTGATCTCCAGATGAC
Found at i:29577 original size:54 final size:53
Alignment explanation
Indices: 28675--29781 Score: 777
Period size: 54 Copynumber: 20.9 Consensus size: 53
28665 GTGTTTGAAG
* * ** *
28675 TGATCCAGTGCGGTCATTCCAATAAGTTTCCTTGATCAGAGTTGATC-CTAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAGATCAGAGTTGATCTCCAGA
* * * *
28727 TGACCCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGGGTTGATC-CCTACA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCA-AGATCAGAGTTGATCTCC-AGA
* *
28781 TGATCCAGTGTGGTCATTCCAAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGA
1 TGATCCAGTGCGGTCATTCC-AAGAAGTTTTCAA-GATCAGAGTTGATCTCCAGA
* * * * *
28836 TGATCTAGTGCTGTCATTTCAAGAAGTTTTCAGTGATCAAAGTTGATC-CCAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCA-AGATCAGAGTTGATCTCCAGA
* * * *
28889 TGATCCAGTGTGGTCA-T--AA-AAGTTTTCAGAGGTTTA-AGTTGATCTTCAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCA-A-GATCAGAGTTGATCTCCAGA
* * * * * * * *
28939 TAACCCTGTGCGGTC-TTTCATGAAGTTTTCAGAGATTTA-AGTTCATCTTCAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCA-AGA-TCAGAGTTGATCTCCAGA
* * **
28992 TGACTCTA-TGCGGTC-TTTCATAGAAGTTTTCAGAGATCTA-AGTTGAT-TTTATGA
1 TGA-TCCAGTGCGGTCATTCCA-AGAAGTTTTCA-AGATC-AGAGTTGATCTCCA-GA
* * * ** * ** *
29046 TGACCCTGTGCGGTC-TTTCATA-AAACTTTCAGAAATCTA-AGTTGATCTTTATA
1 TGATCCAGTGCGGTCATTCCA-AGAAGTTTTCA-AGATC-AGAGTTGATCTCCAGA
* * *** * ** * *
29099 TAATCCGGTGTTATCTTTCGTAGAAGTTTTTAGAGATTAGAGTTGATC-CCTAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCA-AGATCAGAGTTGATCTCC-AGA
* * * * *
29153 TGATCCAATGCGATCATTTCAAGAAGTTTTCAATGATCAGAGTTGATCCCCAAA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAA-GATCAGAGTTGATCTCCAGA
* ** * *
29207 TGATCTAGTGCAATCATTCCAAGAAGTTTTCAGTGATCAGAGTTGATCCCCAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCA-AGATCAGAGTTGATCTCCAGA
* * ** *
29261 TGATCCAGTGCGGTCATTCCAATAAGTTTCCTTGATCAGAGTTGATC-CTAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAGATCAGAGTTGATCTCCAGA
* * * *
29313 TGACCCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGGGTTGATC-CCTACA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCA-AGATCAGAGTTGATCTCC-AGA
* *
29367 TGATCCAGTGCGGTCATTCCAAAGAAGTTTTCAATGATCAGAGTTGATCCCCATA
1 TGATCCAGTGCGGTCATTCC-AAGAAGTTTTCAA-GATCAGAGTTGATCTCCAGA
* * * * *
29422 TGATCTATTGCGGTCATTTCAAGAAGTTTTTAGTGATCAGAGTTGATC-CCAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCA-AGATCAGAGTTGATCTCCAGA
* * *
29475 TGATCTAGTGTGGTCATTCCAAAAAGTTTTCAATGATCAGAGTTGATCTCCAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAA-GATCAGAGTTGATCTCCAGA
* * *
29529 TGATCTAGTGCGGTCCTTCCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAAA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTC-AAGATCAGAGTTGATCTCCAGA
** * *
29583 AAATTCGGTGCGG----T-C----A-TTTT-AAGATCAGAGTTGATCTCCAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAGATCAGAGTTGATCTCCAGA
* ** * *
29625 TGATCCGGTGCGGTCATTTTATGAAGTTTTCGATGATCAGA-TTCGATCTCCAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTC-AAGATCAGAGTT-GATCTCCAGA
* ** *
29679 TGATTCAGTGCGGTTGTTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAGA
1 TGATCCAGTGCGGTCATTCCAAGAAGTTTTC-AAGATCAGAGTTGATCTCCAGA
* ** * * *
29733 TGATCCGGTGCGGTCATTTTAAGAAGTTTTTGATGATCATAGTTGATCT
1 TGATCCAGTGCGGTCATTCCAAGAAG-TTTTCAAGATCAGAGTTGATCT
29782 TCAATTTGAT
Statistics
Matches: 859, Mismatches: 146, Indels: 98
0.78 0.13 0.09
Matches are distributed among these distances:
42 31 0.04
44 4 0.00
45 1 0.00
46 1 0.00
49 19 0.02
50 22 0.03
51 1 0.00
52 65 0.08
53 188 0.22
54 428 0.50
55 95 0.11
56 4 0.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (53 bp):
TGATCCAGTGCGGTCATTCCAAGAAGTTTTCAAGATCAGAGTTGATCTCCAGA
Found at i:29608 original size:42 final size:42
Alignment explanation
Indices: 29561--29645 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
29551 GAAGTTTTCG
*
29561 AAGATCAGAGTTGATCTCCAAAAAATTCGGTGCGGTCATTTT
1 AAGATCAGAGTTGATCTCCAAAAAATCCGGTGCGGTCATTTT
* **
29603 AAGATCAGAGTTGATCTCCAGATGATCCGGTGCGGTCATTTT
1 AAGATCAGAGTTGATCTCCAAAAAATCCGGTGCGGTCATTTT
29645 A
1 A
29646 TGAAGTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
AAGATCAGAGTTGATCTCCAAAAAATCCGGTGCGGTCATTTT
Found at i:29702 original size:150 final size:149
Alignment explanation
Indices: 29456--29756 Score: 426
Period size: 150 Copynumber: 2.0 Consensus size: 149
29446 AGTTTTTAGT
* *
29456 GATCAGAGTTGATCCCAGATGATCTAGTGTGGTCATTCCAAAAAGTTTTCAATGATCAGAGTTGA
1 GATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAAAAGTTTTCAATGATCAGAGTTGA
29521 TCTCCAGATGATCTAGTGCGGTCCTTCCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAAAAAA
66 TCTCCAGATGATCTAGTGCGGTCCTTCCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAAAAAA
*
29586 TTCGGTGCGGTCATTTTAA
131 TCCGGTGCGGTCATTTTAA
* ** ** *
29605 GATCAGAGTTGATCTCCAGATGATCCGGTGCGGTCATTTTATGAAGTTTTCGATGATCAGA-TTC
1 GATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTCCAAAAAGTTTTCAATGATCAGAGTT-
** * *
29669 GATCTCCAGATGAT-TCAGTGCGGTTGTTTCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAGA
64 GATCTCCAGATGATCT-AGTGCGGTCCTTCCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAAA
**
29733 TGATCCGGTGCGGTCATTTTAA
128 AAATCCGGTGCGGTCATTTTAA
29755 GA
1 GA
29757 AGTTTTTGAT
Statistics
Matches: 134, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
149 17 0.13
150 117 0.87
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (149 bp):
GATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAAAAGTTTTCAATGATCAGAGTTGA
TCTCCAGATGATCTAGTGCGGTCCTTCCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAAAAAA
TCCGGTGCGGTCATTTTAA
Found at i:29759 original size:204 final size:203
Alignment explanation
Indices: 29402--29781 Score: 498
Period size: 204 Copynumber: 1.9 Consensus size: 203
29392 AGTTTTCAAT
* * * *
29402 GATCAGAGTTGATCCCCATATGATCTATTGCGGTCATTTCAAGAAGTTTTTAGTGATCAGAGTTG
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTGAGTGATCAGAGTTG
*
29467 ATCCCAGATGATCTAGTGTGGTCATTCCAAAAAGTTTTCAATGATCAGAGTTGATCTCCAGATGA
66 ATCCCAGATGATCTAGTGCGGTCATTCCAAAAAGTTTTCAATGATCAGAGTTGATCTCCAGATGA
* *
29532 TCTAGTGCGGTCCTTCCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAAAAAATTCGGTGCGGT
131 TCCAGTGCGGTCATTCCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAAAAAATTCGGTGCGGT
29597 CATTTTAA
196 CATTTTAA
* * * *
29605 GATCAGAGTTGATCTCCAGATGATCCGGTGCGGTCATTTTATGAAGTTTTCGA-TGATCAGA-TT
1 GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTT-GAGTGATCAGAGTT
** * *
29668 CGATCTCCAGATGAT-TCAGTGCGGTTGTTTCAAGAAGTTTTCGAA-GATCAGAGTTGATCTCCA
65 -GATC-CCAGATGATCT-AGTGCGGTCATTCCAAAAAGTTTTC-AATGATCAGAGTTGATCTCCA
* ** * * *
29731 GATGATCCGGTGCGGTCATTTTAAGAAGTTTTTGATGATCATAGTTGATCT
126 GATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGAAGATCAGAGTTGATCT
29782 TCAATTTGAT
Statistics
Matches: 151, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
202 2 0.01
203 56 0.37
204 91 0.60
205 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (203 bp):
GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTGAGTGATCAGAGTTG
ATCCCAGATGATCTAGTGCGGTCATTCCAAAAAGTTTTCAATGATCAGAGTTGATCTCCAGATGA
TCCAGTGCGGTCATTCCAAGAAGTTTTCGAAGATCAGAGTTGATCTCCAAAAAATTCGGTGCGGT
CATTTTAA
Found at i:31071 original size:38 final size:38
Alignment explanation
Indices: 31020--31098 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
31010 TTTCAGTGAC
*
31020 TGATCGAAATTTCGGGACTCGCTGAATGTCTCTGAGGA
1 TGATCGAAATTTCGAGACTCGCTGAATGTCTCTGAGGA
31058 TGATCGAAATTTCGAGACTCGCTGAATGTCTCTGAGGA
1 TGATCGAAATTTCGAGACTCGCTGAATGTCTCTGAGGA
31096 TGA
1 TGA
31099 GAAGGTTTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (38 bp):
TGATCGAAATTTCGAGACTCGCTGAATGTCTCTGAGGA
Found at i:44444 original size:4 final size:4
Alignment explanation
Indices: 44435--44502 Score: 64
Period size: 4 Copynumber: 17.0 Consensus size: 4
44425 CAAACTGTTT
* * * * * * * *
44435 TATA TATA TACA TATA CATA TACA TATA CATA CATA TACA TACA TACA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
44483 TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA
44503 ATCCTAACTA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (4 bp):
TATA
Found at i:44449 original size:6 final size:6
Alignment explanation
Indices: 44435--44498 Score: 69
Period size: 6 Copynumber: 10.7 Consensus size: 6
44425 CAAACTGTTT
*
44435 TATATA TATACA TATACA TATACA TATAC- -ATACA TATACA TACATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA T--ATACA
* *
44483 TATATA TATATA TATA
1 TATACA TATACA TATA
44499 TATAATCCTA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
4 4 0.08
6 42 0.81
8 6 0.12
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (6 bp):
TATACA
Found at i:44495 original size:10 final size:10
Alignment explanation
Indices: 44435--44502 Score: 64
Period size: 10 Copynumber: 6.8 Consensus size: 10
44425 CAAACTGTTT
44435 TATATATATA
1 TATATATATA
* *
44445 CATATACATA
1 TATATATATA
* *
44455 TACATATACA
1 TATATATATA
* *
44465 TACATATACA
1 TATATATATA
* *
44475 TACATACATA
1 TATATATATA
44485 TATATATATA
1 TATATATATA
44495 TATATATA
1 TATATATA
44503 ATCCTAACTA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 48 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (10 bp):
TATATATATA
Found at i:55735 original size:21 final size:22
Alignment explanation
Indices: 55695--55745 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
55685 AATTAAAGTA
55695 AAAATAAAAATAAATAAGCAAG
1 AAAATAAAAATAAATAAGCAAG
* * *
55717 AAAATAATAA-AATTAAGCAAC
1 AAAATAAAAATAAATAAGCAAG
*
55738 AAGATAAA
1 AAAATAAA
55746 TAAATACACC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.16
Consensus pattern (22 bp):
AAAATAAAAATAAATAAGCAAG
Found at i:55750 original size:21 final size:21
Alignment explanation
Indices: 55702--55750 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
55692 GTAAAAATAA
*
55702 AAATAAA-TAAGCAAGAAAAT
1 AAATAAATTAAGCAACAAAAT
*
55722 -AATAAAATTAAGCAACAAGAT
1 AAAT-AAATTAAGCAACAAAAT
55743 AAATAAAT
1 AAATAAAT
55751 ACACCAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 15 0.62
22 3 0.12
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.18
Consensus pattern (21 bp):
AAATAAATTAAGCAACAAAAT
Found at i:60135 original size:13 final size:13
Alignment explanation
Indices: 60117--60143 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
60107 AAACGGAAAA
60117 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
60130 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
60143 T
1 T
60144 TCAGTTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Done.