Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019257.1 Corchorus olitorius cultivar O-4 contig19290, 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: 87280
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:748 original size:14 final size:16
Alignment explanation
Indices: 729--760 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
719 ATTTTGGAAG
729 ATTATATA-ATT-TAC
1 ATTATATATATTGTAC
743 ATTATATATATTGTAC
1 ATTATATATATTGTAC
759 AT
1 AT
761 GCATTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTATATATATTGTAC
Found at i:13214 original size:1 final size:1
Alignment explanation
Indices: 13208--13267 Score: 66
Period size: 1 Copynumber: 60.0 Consensus size: 1
13198 TTTTCTTCAG
* * * * * *
13208 AAAAAAAAACAAAAAAAACAAAAAAACAAAAAAACAAAAAAACAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13268 CAATTTATCT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13223 original size:8 final size:8
Alignment explanation
Indices: 13210--13266 Score: 96
Period size: 8 Copynumber: 6.9 Consensus size: 8
13200 TTCTTCAGAA
13210 AAAAAAAC
1 AAAAAAAC
13218 AAAAAAAAC
1 -AAAAAAAC
13227 AAAAAAAC
1 AAAAAAAC
13235 AAAAAAAC
1 AAAAAAAC
13243 AAAAAAAC
1 AAAAAAAC
13251 AAAAAAAAC
1 -AAAAAAAC
13260 AAAAAAA
1 AAAAAAA
13267 ACAATTTATC
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
8 31 0.66
9 16 0.34
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:13223 original size:9 final size:9
Alignment explanation
Indices: 13209--13270 Score: 103
Period size: 9 Copynumber: 7.2 Consensus size: 9
13199 TTTCTTCAGA
13209 AAAAAAAAC
1 AAAAAAAAC
13218 AAAAAAAAC
1 AAAAAAAAC
13227 -AAAAAAAC
1 AAAAAAAAC
13235 -AAAAAAAC
1 AAAAAAAAC
13243 -AAAAAAAC
1 AAAAAAAAC
13251 AAAAAAAAC
1 AAAAAAAAC
13260 AAAAAAAAC
1 AAAAAAAAC
13269 AA
1 AA
13271 TTTATCTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
8 24 0.46
9 28 0.54
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:13232 original size:17 final size:17
Alignment explanation
Indices: 13210--13266 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
13200 TTCTTCAGAA
13210 AAAAAAACAAAAAAAAC
1 AAAAAAACAAAAAAAAC
13227 AAAAAAAC-AAAAAAAC
1 AAAAAAACAAAAAAAAC
13243 AAAAAAACAAAAAAAAC
1 AAAAAAACAAAAAAAAC
13260 AAAAAAA
1 AAAAAAA
13267 ACAATTTATC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.41
17 23 0.59
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAAAAAAAC
Found at i:16941 original size:65 final size:66
Alignment explanation
Indices: 16832--17028 Score: 260
Period size: 65 Copynumber: 3.0 Consensus size: 66
16822 CCGATTGTTT
* * * *
16832 GTTCCGCTGGGGAAACTACAGGG-GGGCCAACCATTAGGGTCTTACGGCACACGACCTGATTTAA
1 GTTCTGCTGGGGAGACTGCAGGGTGGGCCAACCACTAGGGTCTTACGGCACACGACCTGATTTAA
16896 C
66 C
* *
16897 GTTCTGCTGGGGAGACTGCAGGGTGGGCCAACCACT-GGGTCTTACGGCGCACCACCTGATTTAA
1 GTTCTGCTGGGGAGACTGCAGGGTGGGCCAACCACTAGGGTCTTACGGCACACGACCTGATTTAA
16961 C
66 C
* * *
16962 GTCCCT-CTAGGGAGACTGCA-GGTCGGCCAACCACTAGGGTCTTACGGCACACTG-CCTGATTT
1 GT-TCTGCTGGGGAGACTGCAGGGTGGGCCAACCACTAGGGTCTTACGGCACAC-GACCTGATTT
17024 AAC
64 AAC
17027 GT
1 GT
17029 CCCTCTTGGG
Statistics
Matches: 117, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
64 14 0.12
65 90 0.77
66 13 0.11
ACGTcount: A:0.21, C:0.28, G:0.29, T:0.21
Consensus pattern (66 bp):
GTTCTGCTGGGGAGACTGCAGGGTGGGCCAACCACTAGGGTCTTACGGCACACGACCTGATTTAA
C
Found at i:17106 original size:48 final size:48
Alignment explanation
Indices: 17051--17311 Score: 346
Period size: 48 Copynumber: 5.4 Consensus size: 48
17041 GTGCCTATAA
17051 CCTCTTTGGGGAGCTTGTGGCATTCCCTCTTTGGGGAGCTTAGCATTC
1 CCTCTTTGGGGAGCTTGTGGCATTCCCTCTTTGGGGAGCTTAGCATTC
*
17099 CCTCTTTGGGGAGCTTGAGGCATTCCCTCTTTGGGGAGCTTGTAGCATTC
1 CCTCTTTGGGGAGCTTGTGGCATTCCCTCTTTGGGGAGC-T-TAGCATTC
* *
17149 CCTCTTTGGGGAGC--CTGACATTCCCTCTTTGGGGAGCTTAAGGCATTC
1 CCTCTTTGGGGAGCTTGTGGCATTCCCTCTTTGGGGAGCTT-A-GCATTC
* * * * *
17197 CCTCTTTCGGGAACTTGAGGTATTCCCTCTTTGGGGAGCTTGGCATTC
1 CCTCTTTGGGGAGCTTGTGGCATTCCCTCTTTGGGGAGCTTAGCATTC
* *
17245 CCTCTTTGGGGAGCTTGTGACATTCCCTCTTTGGGGAACTTGAGGCATTC
1 CCTCTTTGGGGAGCTTGTGGCATTCCCTCTTTGGGGAGCTT-A-GCATTC
* *
17295 CCTATTTCGGGAGCTTG
1 CCTCTTTGGGGAGCTTG
17312 ATGGGAGCGC
Statistics
Matches: 185, Mismatches: 20, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
46 1 0.01
47 2 0.01
48 117 0.63
49 1 0.01
50 64 0.35
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.34
Consensus pattern (48 bp):
CCTCTTTGGGGAGCTTGTGGCATTCCCTCTTTGGGGAGCTTAGCATTC
Found at i:17147 original size:73 final size:72
Alignment explanation
Indices: 17051--17311 Score: 380
Period size: 73 Copynumber: 3.6 Consensus size: 72
17041 GTGCCTATAA
* *
17051 CCTCTTTGGGGAGCTTGTGGCATTCCCTCTTTGGGGAGCTTAGCATTCCCTCTTTGGGGAGCTTG
1 CCTCTTTGGGGAACTTGAGGCATTCCCTCTTTGGGGAGCTT-GCATTCCCTCTTTGGGGAGCTTG
17116 AGGCATTC
65 AGGCATTC
* *
17124 CCTCTTTGGGGAGCTTGTA-GCATTCCCTCTTTGGGGAGCCTGACATTCCCTCTTTGGGGAGCTT
1 CCTCTTTGGGGAACTTG-AGGCATTCCCTCTTTGGGGAGCTTG-CATTCCCTCTTTGGGGAGCTT
*
17188 AAGGCATTC
64 GAGGCATTC
* *
17197 CCTCTTTCGGGAACTTGAGGTATTCCCTCTTTGGGGAGCTTGGCATTCCCTCTTTGGGGAGCTTG
1 CCTCTTTGGGGAACTTGAGGCATTCCCTCTTTGGGGAGCTT-GCATTCCCTCTTTGGGGAGCTTG
* *
17262 TGACATTC
65 AGGCATTC
* *
17270 CCTCTTTGGGGAACTTGAGGCATTCCCTATTTCGGGAGCTTG
1 CCTCTTTGGGGAACTTGAGGCATTCCCTCTTTGGGGAGCTTG
17312 ATGGGAGCGC
Statistics
Matches: 170, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
72 3 0.02
73 166 0.98
74 1 0.01
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.34
Consensus pattern (72 bp):
CCTCTTTGGGGAACTTGAGGCATTCCCTCTTTGGGGAGCTTGCATTCCCTCTTTGGGGAGCTTGA
GGCATTC
Found at i:17312 original size:25 final size:25
Alignment explanation
Indices: 17051--17312 Score: 367
Period size: 25 Copynumber: 10.7 Consensus size: 25
17041 GTGCCTATAA
*
17051 CCTCTTTGGGGAGCTTGTGGCATTC
1 CCTCTTTGGGGAGCTTGAGGCATTC
17076 CCTCTTTGGGGAGCTT-A-GCATTC
1 CCTCTTTGGGGAGCTTGAGGCATTC
17099 CCTCTTTGGGGAGCTTGAGGCATTC
1 CCTCTTTGGGGAGCTTGAGGCATTC
17124 CCTCTTTGGGGAGCTTGTA-GCATTC
1 CCTCTTTGGGGAGCTTG-AGGCATTC
*
17149 CCTCTTTGGGGAGCCTGA--CATTC
1 CCTCTTTGGGGAGCTTGAGGCATTC
*
17172 CCTCTTTGGGGAGCTTAAGGCATTC
1 CCTCTTTGGGGAGCTTGAGGCATTC
* * *
17197 CCTCTTTCGGGAACTTGAGGTATTC
1 CCTCTTTGGGGAGCTTGAGGCATTC
17222 CCTCTTTGGGGAGCTT--GGCATTC
1 CCTCTTTGGGGAGCTTGAGGCATTC
* *
17245 CCTCTTTGGGGAGCTTGTGACATTC
1 CCTCTTTGGGGAGCTTGAGGCATTC
*
17270 CCTCTTTGGGGAACTTGAGGCATTC
1 CCTCTTTGGGGAGCTTGAGGCATTC
* *
17295 CCTATTTCGGGAGCTTGA
1 CCTCTTTGGGGAGCTTGA
17313 TGGGAGCGCA
Statistics
Matches: 212, Mismatches: 18, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
23 65 0.31
24 2 0.01
25 144 0.68
26 1 0.00
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.34
Consensus pattern (25 bp):
CCTCTTTGGGGAGCTTGAGGCATTC
Found at i:17650 original size:100 final size:100
Alignment explanation
Indices: 17522--17837 Score: 506
Period size: 100 Copynumber: 3.2 Consensus size: 100
17512 TAAGGGCGCA
* * *
17522 CGCCAGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAAATGGTGCTCGGCCTGATTGCCC
1 CGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCC
* * * *
17587 CCCAGTAGGGGAATTATTGCAGAGAATGAGGCATC
66 CCAAGTGGGGGAATTACTGCAGAGAATGAGGCGTC
* * * *
17622 CGCCGGTCTTACGGCCCATCATGCGGTCTTACGGCCGAGAAAGATGGCGTTCGGCCTGATAGCCC
1 CGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCC
*
17687 CCAAGTGGGGGAATTAGTGCAGAGAATGAGGCGTC
66 CCAAGTGGGGGAATTACTGCAGAGAATGAGGCGTC
17722 CGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCC
1 CGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCC
*
17787 CCAAGTGGGGGAATTACTGTAGAGAATGAGGCGTC
66 CCAAGTGGGGGAATTACTGCAGAGAATGAGGCGTC
*
17822 TGCCGGTCTTACGGCC
1 CGCCGGTCTTACGGCC
17838 GAGAAAGATG
Statistics
Matches: 198, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 198 1.00
ACGTcount: A:0.20, C:0.27, G:0.33, T:0.20
Consensus pattern (100 bp):
CGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCC
CCAAGTGGGGGAATTACTGCAGAGAATGAGGCGTC
Found at i:17762 original size:50 final size:49
Alignment explanation
Indices: 17608--17762 Score: 113
Period size: 50 Copynumber: 3.1 Consensus size: 49
17598 AATTATTGCA
* *
17608 GAGAATGAGGCATCCGCCGGTCTTACGGCCCATCATGCGGTCTTACGGCC
1 GAGAATGAGGCGTCCGCCGGTCTTACGGCCC-TCATGGGGTCTTACGGCC
* * ** * ** *
17658 GAGAAAGATGGCGTTCGGCC--TGATA--GCCCCCAAGTGGGGGAATTA-GTGCA
1 GAGAATGA-GGCG-TCCGCCGGTCTTACGGCCCTC-A-T-GGGGTCTTACG-GCC
17708 GAGAATGAGGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCC
1 GAGAATGAGGCGTCCGCCGGTCTTACGGCCC-TCATGGGGTCTTACGGCC
17758 GAGAA
1 GAGAA
17763 AGATGGCGCT
Statistics
Matches: 75, Mismatches: 18, Indels: 24
0.64 0.15 0.21
Matches are distributed among these distances:
47 1 0.01
48 10 0.13
49 6 0.08
50 42 0.56
51 5 0.07
52 10 0.13
53 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (49 bp):
GAGAATGAGGCGTCCGCCGGTCTTACGGCCCTCATGGGGTCTTACGGCC
Found at i:17869 original size:180 final size:179
Alignment explanation
Indices: 17645--17994 Score: 594
Period size: 180 Copynumber: 1.9 Consensus size: 179
17635 GCCCATCATG
*
17645 CGGTCTTACGGCCGAGAAAGATGGCGTTCGGCCTGATAGCCCCCAAGTGGGGGAATTAGTGCAGA
1 CGGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATAGCCCCCAAGTGGGGGAATTAGTGCAGA
*
17710 GAATGAGGCGTCCGCCGGTCTTACGGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCG
66 GAATGAGGCGTCCGCCGGTCTTACAGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCG
* *
17775 GCCTGATTGCCCCCAAGT-GGGGGAATTACTGTAGAGAATGAGGCGTCTGC
131 GCCTGATTACCCCC-AGTAGGGGG-ATTACTGCAGAGAATGAGGCGTCTGC
* * *
17825 CGGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCAAGTGGGGGGATTATTGCAGA
1 CGGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATAGCCCCCAAGTGGGGGAATTAGTGCAGA
*
17890 GAATGAGGCGTCCGCCGGTCTTACAGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGTTCG
66 GAATGAGGCGTCCGCCGGTCTTACAGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCG
*
17955 GCCTGATTACCCCCAGTAGGGGGATTATTGCAGAGAATGA
131 GCCTGATTACCCCCAGTAGGGGGATTACTGCAGAGAATGA
17995 TCCAAGGGAA
Statistics
Matches: 160, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
179 18 0.11
180 142 0.89
ACGTcount: A:0.21, C:0.24, G:0.35, T:0.20
Consensus pattern (179 bp):
CGGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATAGCCCCCAAGTGGGGGAATTAGTGCAGA
GAATGAGGCGTCCGCCGGTCTTACAGCCCGTCATGGGGTCTTACGGCCGAGAAAGATGGCGCTCG
GCCTGATTACCCCCAGTAGGGGGATTACTGCAGAGAATGAGGCGTCTGC
Found at i:17891 original size:80 final size:80
Alignment explanation
Indices: 17746--17913 Score: 300
Period size: 80 Copynumber: 2.1 Consensus size: 80
17736 CCCGTCATGG
*
17746 GGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCAAGTGGGGGAATTACTGTAGAG
1 GGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCAAGTGGGGGAATTACTGCAGAG
*
17811 AATGAGGCGTCTGCC
66 AATGAGGCGTCCGCC
* *
17826 GGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCAAGTGGGGGGATTATTGCAGAG
1 GGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCAAGTGGGGGAATTACTGCAGAG
17891 AATGAGGCGTCCGCC
66 AATGAGGCGTCCGCC
17906 GGTCTTAC
1 GGTCTTAC
17914 AGCCCGTCAT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.20
Consensus pattern (80 bp):
GGTCTTACGGCCGAGAAAGATGGCGCTCGGCCTGATTGCCCCCAAGTGGGGGAATTACTGCAGAG
AATGAGGCGTCCGCC
Found at i:28895 original size:24 final size:26
Alignment explanation
Indices: 28848--28898 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 26
28838 CGGAGCGCGC
28848 TTAATGGTAACTGTGGTGGTCAGTGAT
1 TTAATGGTAAC-GTGGTGGTCAGTGAT
28875 TTAATGGTAAC-T-GTGGTCAGTGAT
1 TTAATGGTAACGTGGTGGTCAGTGAT
28899 CTATTAGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 12 0.50
25 1 0.04
27 11 0.46
ACGTcount: A:0.24, C:0.08, G:0.31, T:0.37
Consensus pattern (26 bp):
TTAATGGTAACGTGGTGGTCAGTGAT
Found at i:35142 original size:13 final size:13
Alignment explanation
Indices: 35124--35150 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35114 GTGAATTACG
35124 AAAACAAAACAAA
1 AAAACAAAACAAA
35137 AAAACAAAACAAA
1 AAAACAAAACAAA
35150 A
1 A
35151 CACCTTCAGG
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:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAACAAA
Found at i:46000 original size:21 final size:21
Alignment explanation
Indices: 45962--46001 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
45952 TATGAATTTC
*
45962 GAACAAGAGAGATTTATTAGT
1 GAACAAGAGAAATTTATTAGT
45983 GAACAAG-GAAATTATATTA
1 GAACAAGAGAAATT-TATTA
46002 TCCTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (21 bp):
GAACAAGAGAAATTTATTAGT
Found at i:60249 original size:8 final size:8
Alignment explanation
Indices: 60236--60265 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
60226 CTCCCGACCT
60236 ATATATAA
1 ATATATAA
60244 ATATATAA
1 ATATATAA
*
60252 ATATATAT
1 ATATATAA
60260 ATATAT
1 ATATAT
60266 CTTTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATATAA
Found at i:60439 original size:2 final size:2
Alignment explanation
Indices: 60428--60457 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
60418 ACTCCCGGCC
60428 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60458 CTTTTTCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60526 original size:194 final size:192
Alignment explanation
Indices: 60153--60532 Score: 604
Period size: 192 Copynumber: 2.0 Consensus size: 192
60143 TCTAAAAGCA
*
60153 TCAAATCACTTACATTTGACCCACTATGTATTAGTAGAGCGATACTTAAAAGTTAGTAATATATA
1 TCAAATCACTTACATTTGACCCACTATGTATTAGCAGAGCGATACTTAAAAGTTAGTAATATATA
*
60218 TACTTCAACTCCCGACCTATATATAAATATATAAATATATATATATATCTTTTTAATTAATTAAT
66 TACTTCAACTCCCGACCTATATATAAATATATAAATATATATATATATCTTTTTAACTAATTAAT
*
60283 TAAGGAATTTCCAAGTTTTTTGGCCTTGAGAATAATTTCTTTCGATCGAGTTCTAATTTCTT
131 TAAGGAATCTCCAAGTTTTTTGGCCTTGAGAATAATTTCTTTCGATCGAGTTCTAATTTCTT
* * *
60345 TCAAATCACTTGCATTTGACCCACTGTGTGTTA-CAGTAGCGATACTTAAAAGTTTAGTAATATA
1 TCAAATCACTTACATTTGACCCACTATGTATTAGCAG-AGCGATACTTAAAAG-TTAGTAATATA
* * *
60409 TATACTTCAACTCCCGGCCTATATA-ATATATATATATATATATATATATCTTTTTCTAACTAAT
64 TATACTTCAACTCCCGACCTATATATAAATATATAAATATATATATATATC-TTTT-TAACTAAT
*
60473 TAATTAAGGAATCTCCAAGTTTTTTGGCTTTGA-AACTAATTTCTTTCGATCGAGTTCTAA
127 TAATTAAGGAATCTCCAAGTTTTTTGGCCTTGAGAA-TAATTTCTTTCGATCGAGTTCTAA
60533 CTTTTAATTT
Statistics
Matches: 173, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
191 2 0.01
192 68 0.39
193 41 0.24
194 62 0.36
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.40
Consensus pattern (192 bp):
TCAAATCACTTACATTTGACCCACTATGTATTAGCAGAGCGATACTTAAAAGTTAGTAATATATA
TACTTCAACTCCCGACCTATATATAAATATATAAATATATATATATATCTTTTTAACTAATTAAT
TAAGGAATCTCCAAGTTTTTTGGCCTTGAGAATAATTTCTTTCGATCGAGTTCTAATTTCTT
Found at i:60626 original size:16 final size:16
Alignment explanation
Indices: 60605--60636 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
60595 AATCCTTTAG
60605 TCAAACAAATAATTAA
1 TCAAACAAATAATTAA
60621 TCAAACAAATAATTAA
1 TCAAACAAATAATTAA
60637 AGCGGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (16 bp):
TCAAACAAATAATTAA
Found at i:62199 original size:25 final size:25
Alignment explanation
Indices: 62165--62213 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
62155 TGTTAGTTTG
62165 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
*
62190 TAGAGACCGAGTGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
62214 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.33, T:0.14
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:62469 original size:2 final size:2
Alignment explanation
Indices: 62462--62487 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62452 GGGTTACAAC
62462 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
62488 CTTTTTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63309 original size:92 final size:95
Alignment explanation
Indices: 63171--63351 Score: 255
Period size: 92 Copynumber: 1.9 Consensus size: 95
63161 CTGTCCAAAT
*
63171 TTTCATTTATCCTATCAAAATATGGCACGCAAGTAGATTATTGAAAAAAAAAAAAAA-CTGGCTA
1 TTTCATTTATCCTATCAAAATATGGCACGCAAGTAGATTATCGAAAAAAAAAAAAAATCTGGCTA
*
63235 TATATTGGGAC-ATGAATGAACCGTCCCACA
66 TATA-TCGGACAATGAATGAACCGTCCCACA
* *
63265 TTTCA-TTA-CCTATCAAAATGTGGCACGACAAGTAGCTTA-CGAAAAAAAAAAAAAATTCTGGC
1 TTTCATTTATCCTATCAAAATATGGCACG-CAAGTAGATTATCGAAAAAAAAAAAAAA-TCTGGC
63327 TATATATCGGACATATGAATGAACC
64 TATATATCGGACA-ATGAATGAACC
63352 CTAGTCAGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
92 33 0.42
93 18 0.23
94 16 0.21
95 11 0.14
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (95 bp):
TTTCATTTATCCTATCAAAATATGGCACGCAAGTAGATTATCGAAAAAAAAAAAAAATCTGGCTA
TATATCGGACAATGAATGAACCGTCCCACA
Found at i:69175 original size:2 final size:2
Alignment explanation
Indices: 69137--69162 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
69127 GGTATATCAA
69137 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
69163 GCGTTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69307 original size:209 final size:209
Alignment explanation
Indices: 68943--69368 Score: 613
Period size: 209 Copynumber: 2.0 Consensus size: 209
68933 CTAGTGTGTG
* * **
68943 TATATATATATGGTAAATTATACAATACACCGACGGTGGAGTTTAGCAGACTACATAAGTGGGTC
1 TATATATATATGGTAAATTATACAATACACCGACAGTGGAGTTTAGCAGACTACACAAGCAGGTC
* *
69008 CTGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTAAAAAA
66 CTGAAGGGTGACATGTGTCCCCTAGGGACTAAATTGAAATATTTAAAACTTAATTAATTAAAAAA
* * * * *
69073 ATGGACATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACTGCCGGTATATCAAA
131 ATGGACATGTGTCAACTCCACAACCCACTTCTGAAGTCCAAAATTTACACCGCCGATATATCAAA
69138 TATATATATATATA
196 TATATATATATATA
** * * * * *
69152 TATATATATATGCGTTTA-TATATAATACACTGTCAGTGGAGTTTAGCAGATTGCACAAGCAGG-
1 TATATATATATG-GTAAATTATACAATACACCGACAGTGGAGTTTAGCAGACTACACAAGCAGGT
* * *
69215 CCTTGAAGGGTGACATGTGTCCCCTAGGGACTAAATTGAAATATTTAAAATTTAATTAATTCAGA
65 CC-TGAAGGGTGACATGTGTCCCCTAGGGACTAAATTGAAATATTTAAAACTTAATTAATTAAAA
* *
69280 AAATGGACATGTGTCAACTCTACAACCCACTTCTGAAGTCCAAAATTTACACCGCCGATGTATCA
129 AAATGGACATGTGTCAACTCCACAACCCACTTCTGAAGTCCAAAATTTACACCGCCGATATATCA
69345 AATATATATATATATA
194 AATATATATATATATA
69361 TATATATA
1 TATATATA
69369 GCCTATTTAT
Statistics
Matches: 192, Mismatches: 23, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
208 2 0.01
209 187 0.97
210 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (209 bp):
TATATATATATGGTAAATTATACAATACACCGACAGTGGAGTTTAGCAGACTACACAAGCAGGTC
CTGAAGGGTGACATGTGTCCCCTAGGGACTAAATTGAAATATTTAAAACTTAATTAATTAAAAAA
ATGGACATGTGTCAACTCCACAACCCACTTCTGAAGTCCAAAATTTACACCGCCGATATATCAAA
TATATATATATATA
Found at i:85357 original size:49 final size:49
Alignment explanation
Indices: 85302--85404 Score: 188
Period size: 49 Copynumber: 2.1 Consensus size: 49
85292 TCAAGGCCGA
* *
85302 GCACAGTGTATGACAAAAGTCAAGGGTATACTTTCTCATCGATTAGAAT
1 GCACAGTGTATGACAAAAGTCAAGAGTATACTCTCTCATCGATTAGAAT
85351 GCACAGTGTATGACAAAAGTCAAGAGTATACTCTCTCATCGATTAGAAT
1 GCACAGTGTATGACAAAAGTCAAGAGTATACTCTCTCATCGATTAGAAT
85400 GCACA
1 GCACA
85405 TACATTCAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (49 bp):
GCACAGTGTATGACAAAAGTCAAGAGTATACTCTCTCATCGATTAGAAT
Done.