Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014233.1 Corchorus olitorius cultivar O-4 contig14266, 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: 80056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:25347 original size:2 final size:2
Alignment explanation
Indices: 25340--25378 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
25330 TCTTCGCTTT
*
25340 TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
25379 TATGTTAGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:31141 original size:51 final size:51
Alignment explanation
Indices: 31068--31341 Score: 451
Period size: 51 Copynumber: 5.3 Consensus size: 51
31058 AAAAAGTTTA
31068 AAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTT
1 AAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTT
* *
31119 AAAAACTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTAA
1 AAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTT-T
*
31171 AAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTA
1 AAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTT
31222 AAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTT
1 AAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTT
* * *
31273 AAAAAATTTAGTAATTA-GGAGACGGATGAGAGCTGTCTCTCCAAACATTTT
1 -AAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTT
*
31324 GAAAAAATTAGTAATTAG
1 -AAAAATTTAGTAATTAG
31342 CATAGTGACA
Statistics
Matches: 211, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
51 146 0.69
52 65 0.31
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (51 bp):
AAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTT
Found at i:31183 original size:103 final size:103
Alignment explanation
Indices: 31067--31341 Score: 473
Period size: 103 Copynumber: 2.7 Consensus size: 103
31057 TAAAAAGTTT
*
31067 AAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTTAAAAACTTAGTAA
1 AAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTTAAAAAATTAGTAA
31132 TTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTA
66 TTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTA
31170 AAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACA-TTTAAAAAATTTAGTA
1 AAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTTAAAAAA-TTAGTA
*
31234 ATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTT
65 ATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTA
* * *
31273 AAAAAATTTAGTAATTA-GGAGACGGATGAGAGCTGTCTCTCCAAACATTTTGAAAAAATTAGTA
1 AAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTT-AAAAAATTAGTA
31337 ATTAG
65 ATTAG
31342 CATAGTGACA
Statistics
Matches: 164, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
102 35 0.21
103 123 0.75
104 6 0.04
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.27
Consensus pattern (103 bp):
AAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTTAAAAAATTAGTAA
TTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTA
Found at i:31257 original size:154 final size:154
Alignment explanation
Indices: 31064--31341 Score: 479
Period size: 154 Copynumber: 1.8 Consensus size: 154
31054 ATTTAAAAAG
31064 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTT-AAAAACTTA
1 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTTAAAAAACTTA
*
31128 GTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACA-TTTAAAAAAATTTAGTAATTAGGGAG
66 GTAATTA-GGAGACCGATGAGAGCTGTCCCTCCAAACATTTTAAAAAAA-TTAGTAATTAGGGAG
31192 ACCGATGAGGGCTGTCCCTCCAAACA
129 ACCGATGAGGGCTGTCCCTCCAAACA
*
31218 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTTAAAAAATTTA
1 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTTAAAAAACTTA
* * *
31283 GTAATTAGGAGACGGATGAGAGCTGTCTCTCCAAACATTTTGAAAAAATTAGTAATTAG
66 GTAATTAGGAGACCGATGAGAGCTGTCCCTCCAAACATTTTAAAAAAATTAGTAATTAG
31342 CATAGTGACA
Statistics
Matches: 117, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
154 93 0.79
155 24 0.21
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (154 bp):
TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACATTTTAAAAAACTTA
GTAATTAGGAGACCGATGAGAGCTGTCCCTCCAAACATTTTAAAAAAATTAGTAATTAGGGAGAC
CGATGAGGGCTGTCCCTCCAAACA
Found at i:31753 original size:225 final size:218
Alignment explanation
Indices: 31360--31778 Score: 651
Period size: 225 Copynumber: 1.9 Consensus size: 218
31350 CAGATGCGAA
* *
31360 GATATAAGGCAGACATGGAGGGTACTTTGACAACATAGACAACAATCGTAGTGACAGACGCGGAA
1 GATACAAGGCAGACATGGAGGGTACTTTGACAACATAGAAAACAATCGTAGTGACAGACGCGGAA
*
31425 GATACAGTATATGGCCAGCAGCTGCAAATGAAGTAAGTTCATCATATTCTTAAATTTCCATTCTT
66 GATACAATATATGGCCAGCAGCTGCAAATGAAGTAAGTTCATCATATTCTTAAATTTCCATTCTT
* *
31490 TACGATAAATTGTTTTATTTGTGAATATTCCATTGCATGTGGCTGACAAAATCTTTTCTTTTTTC
131 TACAATAAAATGTTTTATTTGTGAATATTCCATTGCATGTGGCTGACAAAATCTTTTCTTTTTTC
31555 TGTCCCAGGTAGTTTTTGTGGCT
196 TGTCCCAGGTAGTTTTTGTGGCT
* *
31578 GATACAAGTCAGACATGGAGGGTACTTTGACAACATAGAAAACGATCGTAGTGACAGACGCAGAA
1 GATACAAGGCAGACATGGAGGGTACTTTGACAACATAGAAAACAATCGTAGTGACAGACGC-G--
* * *
31643 GCAGGATGATACAAT-TAGTGGCCAGTAGCTGCAAATGAAGTAAGTTTATCATATTTTTAAATTT
63 G-A--A-GATACAATATA-TGGCCAGCAGCTGCAAATGAAGTAAGTTCATCATATTCTTAAATTT
*
31707 CCATTCTTTACAATAAAATGTTTTATTTGTGAATATTCCATTGCATGTGGCTGATAAAATCTTTT
123 CCATTCTTTACAATAAAATGTTTTATTTGTGAATATTCCATTGCATGTGGCTGACAAAATCTTTT
*
31772 TTTTTTT
188 CTTTTTT
31779 TTTTTTTTTT
Statistics
Matches: 181, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
218 57 0.31
219 1 0.01
221 1 0.01
222 1 0.01
224 3 0.02
225 118 0.65
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (218 bp):
GATACAAGGCAGACATGGAGGGTACTTTGACAACATAGAAAACAATCGTAGTGACAGACGCGGAA
GATACAATATATGGCCAGCAGCTGCAAATGAAGTAAGTTCATCATATTCTTAAATTTCCATTCTT
TACAATAAAATGTTTTATTTGTGAATATTCCATTGCATGTGGCTGACAAAATCTTTTCTTTTTTC
TGTCCCAGGTAGTTTTTGTGGCT
Found at i:32052 original size:52 final size:52
Alignment explanation
Indices: 31971--32250 Score: 485
Period size: 52 Copynumber: 5.4 Consensus size: 52
31961 ATTTAAAGAG
*
31971 TTTAAAAATTTTAGTAATTA-GGAGACCGATGAGGGCTGTCCCTCCAAACAT
1 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
32022 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
1 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
*
32074 TTTAAAACATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
1 TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
32126 TTT-AAAAATCTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
1 TTTAAAAAAT-TTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
32178 TTT-AAAAATCTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
1 TTTAAAAAAT-TTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
* *
32230 TTTAAAAAGTTTAGCAATTAG
1 TTTAAAAAATTTAGTAATTAG
32251 CATAGTGACA
Statistics
Matches: 221, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
51 24 0.11
52 192 0.87
53 5 0.02
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (52 bp):
TTTAAAAAATTTAGTAATTAGGGAGACCGATGAGGGCTGTCCCTCCAAACAT
Found at i:32693 original size:7 final size:7
Alignment explanation
Indices: 32681--32709 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
32671 TTACCCCAAA
32681 TTGTTTG
1 TTGTTTG
32688 TTGTTTG
1 TTGTTTG
32695 TTGTTTG
1 TTGTTTG
32702 TTGTTTG
1 TTGTTTG
32709 T
1 T
32710 GAATGAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.28, T:0.72
Consensus pattern (7 bp):
TTGTTTG
Found at i:36682 original size:331 final size:331
Alignment explanation
Indices: 34719--39832 Score: 5403
Period size: 332 Copynumber: 15.4 Consensus size: 331
34709 ATTAGTTTCT
* * *
34719 GATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATAT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
** ** * * *
34784 TTCAATAAGTCT-TGGCGTAAAAAAATCATGCAAAACTGAGCTGGGACTCCGGAACGCGTTTTTA
66 TTCAAGGAGTCTCT-GCG-CCAAAAATCATGCAAAACTGAGCCGGG-CCCCGGAACGCGTTTTCA
* * * * * *
34848 CCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTTCAAAAATTGACCCA-AAATT
128 GCCAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGA-CCAGAAATA
* * * ** * *
34912 TTTTTCCTCAAATTCTTTTGCCAAAATACTCAT-AAAAATACATAATTCAATACCAACAAGATTG
192 TTTTTCCTC-AATT-TTTGGCCAAAATACTCATAAAAAATATATAATTGAACGCCAAAAATATTG
* * * * * *
34976 AAGGGATTTTCACACTTTTAATATTGTTTTT-CTAATTTTTT-CAAGATTAATTTCTAATTAAAT
255 GAGGGCTTTTCACGCTTCTAATATCGTTTTTCCT-ATTTTTTCCAA-ATTAATTTCTGATTAAAT
*
35039 CGACACAAGATTCA
318 CGAAACAAGATTCA
* * * * * * *
35053 TATACTCGTTAAAACAAATCCATAAATCCAATGTTGCTAAGATTTGATTAGATGAATAT--ATAT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
** * * * * * * *
35116 TTTGAGAAGTCTCGGCGCCAAAAATCATGCAAAACTGAGTCGGGGCCTCGAAACGCATTTTTAGC
66 TTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAG-CCGGGCCCCGGAACGCGTTTTCAGC
* ** * * * ** *
35181 CAAAAACC-ACAT-GAT-G-AC--GGTTTCAGCTAAAATTTTGCAAAAGCTGACCCA-AAACATT
130 CAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGA-CCAGAAATATT
* * * * * * * *
35239 TTTCCTTAATTTTTTTGTCACAATACTCGTAAAAAATATATAATTTAATGCCAAACAA-ATTGAA
194 TTTCCTCAA-TTTTTGGCCAAAATACTCATAAAAAATATATAATTGAACGCCAAA-AATATTGGA
* * * * * * * * * *
35303 GGCCTCTTCACGCTTATAATATTGTTTTTCTTTTTTTTTTTTCCGAATTAATTTCTAATAAAACC
257 GGGCTTTTCACGCTTCTAATATCGTTTTTC---CTATTTTTTCCAAATTAATTTCTGATTAAATC
* *
35368 AAAACAAGATTCT
319 GAAACAAGATTCA
* * * * *
35381 GATACTCTTAAAAATAAATCCTTAAAT-CATATGTGGCTGAGATTTGGA-TAGAT-AGATATAGT
1 GATGCTCGTAAAAACATATCCTTAAATCCA-ATGTGGCTGAGATTT-GATTAGATGA-ATATAGA
* * * * * **
35443 TATTTCAAGG-GTGT-TGAAGCTAAAAATCATGCAAAATTGAACCAGGGCCCCGGAATACGTTTT
63 TATTTCAAGGAGTCTCTG-CGCCAAAAATCATGCAAAACTGAGCC-GGGCCCCGGAACGCGTTTT
* * * * **
35506 TAGCCA-AAATCGTGATGGATAGTACATTATTTCAACTAAAATTTTGCAAAAATTGACCA-AAAC
126 CAGCCAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAA-
* * * * * ** * * ** *
35569 AATTTTTCTTCAAATTTTGGGCACAATACTCCGAAAATATATATAATTCAGTGCC-AAAGTGATT
190 TATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAATTGAACGCCAAAAAT-ATT
* * * ** *
35633 GGAAGGCTTTTTACGCTTCTAATATCGTTTTTCATATTTTTTTTCTGAATTAATTTCCGATTAAA
254 GGAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTA--TTTTTTCCAAATTAATTTCTGATTAAA
35698 TCGAAACAAGATTCA
317 TCGAAACAAGATTCA
* *
35713 GGTGCTCGTAAAAACATATCCTTAAATCGAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
* ** *
35778 TTCAAGGAGTCT-TGGCGCCAAAAATCATGCAAAACTGAACCGGGACCCAAGAAAGCGTTTTCAG
66 TTCAAGGAGTCTCT-GCGCCAAAAATCATGCAAAACTGAGCCGGG-CCCCGGAACGCGTTTTCAG
* * * * * *
35842 CTAGAAACCGTGATTGTTAGTACACGATTTCAGCTAAAATTTTGATAAAAATTGTAAC-GAAA-A
129 CCAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTG-CAAAAATTG-ACCAGAAATA
* * * * * * * **
35905 GTTTTTCCTTAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAACACCGAAACTATTTA
192 -TTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAATTGAACGCCAAAAATATTGG
* * *
35970 AGGGCTTTTCATGCTTCAAATATGGTTTTTCCTATTTTTTTCCAAATTAAATTT-TGATTAAATC
256 AGGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTCCAAATT-AATTTCTGATTAAATC
*
36034 GAAATAAGATTCA
319 GAAACAAGATTCA
* *
36047 GATGCTCGTAAAAAACATTTCCTTAAATACAATGTGGCTGAGATTTGATTAGATGAATATAGATA
1 GATGCTCGT-AAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATA
* * * * *
36112 TTTCAATGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCCGGAGCCTCGAAACGCTTTTTGAG
65 TTTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCCGG-GCCCCGGAACGCGTTTTCAG
* *
36177 CCAGAAACCGTGATAGTCATGATGGTTAGTACATGATTTCGGCTAAAATTTTACAAAAATTAACC
129 CCAGAAACC------G---TGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGA-C
* *
36242 CA-AAATATTTTTCCTCAATTTTTGCCCAAATTA-TGCATAAAAAATATATAATTGAACGCCAAA
184 CAGAAATATTTTTCCTCAATTTTTGGCCAAAATACT-CATAAAAAATATATAATTGAACGCCAAA
* * *
36305 AATATTGGTGGGCTTTTCACGCTTTTAATATCGTTTTTCCTA-TTTTTCCAAATTAATTTCCGAT
248 AATATTGGAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTGAT
36369 TAAATCGAAACAAGATTCA
313 TAAATCGAAACAAGATTCA
* * * *
36388 GATGCTCGTAAAAACATATCCCTAAATCCAATTTGACTGAGATTTGATTATATGAATATAGATAT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
** *
36453 TTCAAGGAGTCTCTATGCCAAAAATCATGCAAAACTGAGCCGGAGCCCCGGAACACGTTTTCAGC
66 TTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCCGG-GCCCCGGAACGCGTTTTCAGC
* *
36518 TAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAACATTTTGACCAGAAATAT
130 CAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAA-A-ATTGACCAGAAATAT
* * ** *
36583 TTTTCCTCAATTTTT-CCCAAAATACGCAT-AAAAATATATAATTGAATTCCAAAAATATTGGCG
193 TTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAATTGAACGCCAAAAATATTGGAG
* * * *
36646 GGCTTTTCACGCCTCTAATAACGTTTTTCCTATTTTTTCCAAATTAATTTCCGATTAAATAGAAA
258 GGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTGATTAAATCGAAA
36711 CAAGATTCA
323 CAAGATTCA
* * * * *
36720 GGTGCTCGTAAAAACATTTCCTTAAATCCAATGTGGCTGTGATTTGATTACATGAATATAGAAAT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
* ** * * * *
36785 TTCAAGGAGTCTCGGCAACAAAAATCAAGCAAAACTGAGCCGGGAACCAGGAACGCTTTTTCAGC
66 TTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCCGGG-CCCCGGAACGCGTTTTCAGC
** * * * * *
36850 TGGAAACCGTGATTGTTAGTACACGATTTCAGCTAAAATTTTG-ATAAAAATGA-AACGAAA-AG
130 CAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCA-AAAATTGACCA-GAAATA-
* * * * * * **
36912 TTTTCCCTCAATTTTTAGCCACAATAATCATAAAAAATATATAATTCAACGCCAAAACTATTTAA
192 TTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAATTGAACGCCAAAAATATTGGA
* * * * *
36977 GGGCTTTTCATGCTTCAAATATGGTTTTTCCTATTTTTTTCCAAATTAAATTCTAATTAAATCGA
257 GGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTCCAAATTAATTTCTGATTAAATCGA
37042 AACAAGATTCA
321 AACAAGATTCA
* * * * *
37053 GATGCTCGAAAAAACATTTCCTTAAATACAATGTGGCTGAGATTTGATTAGACGAATATATATAT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
* * * * *
37118 TTCAATGAGTCTCTGTGCTAAAAATCATACAAAACTGAGCCGGAGCCTCGGAACGCGTTTTCAGC
66 TTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCCGG-GCCCCGGAACGCGTTTTCAGC
* * * *
37183 CAGAAACCTTGATGGTTAGAACATGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAATATTT
130 CAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAATATTT
* * * *
37248 TTCCTCAATTTTTGCCCAAAATACGCATAAAAATATATATAATTGAACGCCAAAAAGATTGGCGG
195 TTCCTCAATTTTTGGCCAAAATACTCATAAAAA-ATATATAATTGAACGCCAAAAATATTGGAGG
* * *
37313 GCTTTTCACGCTTCTAATATGGTTTTTCCTATTTTTTCCAAATTAAGTTCTGATTAAATCGAAAT
259 GCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTGATTAAATCGAAAC
37378 AAGATTCA
324 AAGATTCA
* *
37386 GATGCTCGTAAAAACATTTCCTTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATAT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
** * * * * *
37451 TTCATTGAGTCTCGGC-CCAAAAATCATGCAAAACTGAGCAAGGGTCCCGGAACACGTTTTTAGC
66 TTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGC-CGGGCCCCGGAACGCGTTTTCAGC
* * *
37515 CAGAAAACGTGATGGTTAGTACATGATTTCGCCTAAAATTTTCCAAAAATTGACTC-GAAATATT
130 CAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGAC-CAGAAATATT
* * * ** * *
37579 TTTCCTCAATTTTTGGCCAAAACACGCATAAAAAATATATGATTGAACGCCAAAAGGATTGGCGT
194 TTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAATTGAACGCCAAAAATATTGGAGG
* * *
37644 ACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCTAAATTAATTTCTGA-TAAGATTGAAA
259 GCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTGATTAA-ATCGAAA
37708 CAAGATTCA
323 CAAGATTCA
* * *
37717 AATGCTCGTAAAAACATTTCCTTAAATCCAATGTGGTTGAGATTTGATTATATGAATGTAATATA
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGA-T-TA-G-ATG-AATATA
** * * * * *
37782 GATATTTCATTGAGTCTCTGCGCCAAAAATCATGCAACACTG-TCTGGAGCACCGGAACGTGTTT
61 GATATTTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCCGG-GCCCCGGAACGCGTTT
* * * * *
37846 TCAACCAGAAATCGTGATGGTTTGTACATGATTTCGGCTAAAATTTTGAAAAAATTTTGACCAAA
125 TCAGCCAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAA--TTGACCAGA
* * *
37911 AATATATTTCCTCAATTTTT--CTCAAAATACACAT-AAAAATATATAATTGAACGCCAAAAAGA
188 AATATTTTTCCTCAATTTTTGGC-CAAAATACTCATAAAAAATATATAATTGAACGCCAAAAATA
* * * *
37973 TT-GACGAGCTTTTCACGCTTTTAATATC-TTTATTCCAATTTTTTTCCAAATTAATTTCCGATT
252 TTGGA-GGGCTTTTCACGCTTCTAATATCGTTT-TTCCTA-TTTTTTCCAAATTAATTTCTGATT
*
38036 AGATCGAAACAAGATTCA
314 AAATCGAAACAAGATTCA
* * *
38054 GGTGCTCGTAAAAATATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATAAATATAGATAT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
* * * * * *
38119 TTCAAGGAGTCTCGGTGCCAAAAATCAAGCAAAACTGAGCCGGGACCCGGGAACCCG-TTTCGGC
66 TTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCCGGG-CCCCGGAACGCGTTTTCAGC
** ** * * * *
38183 TGGAAACCGTGATTATTAGTACACGATTTCAGCTAAAATTTTG-ATAAA-TGAAACA-AAA-AGT
130 CAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTG-ACCAGAAATA-T
* * * * **
38244 TTTTCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATTCAACGCCAAAACTATTTAAG
193 TTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAATTGAACGCCAAAAATATTGGAG
* * * * *
38309 GGCTTTTCATGCTTCAAATATGGTTTTTCCAAATTTTTTCCAAATTAAATTCTGATTAAATCGAA
258 GGCTTTTCACGCTTCTAATATCGTTTTTCC-TATTTTTTCCAAATTAATTTCTGATTAAATCGAA
*
38374 ACAAGATTCG
322 ACAAGATTCA
* * * * * * *
38384 GATGCGCGAAAAAACATTTCCTTATATACAATGTGGCTGAGATTTGATTAGACGAATATAGATGT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
* * * *
38449 TTCAATGAGTCTCTGCGCTAAAAATCATACAAAACTGAGCCGGAGCCTCGGAACGCGTTTTCAGC
66 TTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCCGG-GCCCCGGAACGCGTTTTCAGC
* * * * *
38514 CAGAAACCCTGAT-GTTAGTACATGATTTCTGCTAAATTTTTACAAAAATTGACCCGAAAT-TTT
130 CAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAATATTT
* * *
38577 TTCCTCAATTTTT-GCCTAAAATACGCATAGAAAATATATTAA-TGAACGCCAAAAATATTGGCG
195 TTCCTCAATTTTTGGCC-AAAATACTCATAAAAAATATA-TAATTGAACGCCAAAAATATTGGAG
* *
38640 GGCTTTTCACGCTTCTAATATGGTTTTTCCTATTTTTGTCCAAATTAAATTCTGATTAAATCGAA
258 GGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTT-TCCAAATTAATTTCTGATTAAATCGAA
38705 ACAAGATTCA
322 ACAAGATTCA
* * * *
38715 AATGCTCGTAAAAACATTTCCTTAAATACAATGTGACTGAGATTTGATTAGATGAATATAGATAT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
* * * * * *
38780 TTCAACGACTCTCTGCGCCAAAAATCATACAAAACTGAGCCGGAGCCTCAGAACGCGTATTCAGC
66 TTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCCGG-GCCCCGGAACGCGTTTTCAGC
* *
38845 CAGAAACCGTGATGGTTAGTACATGATTTTGGCTAAAATTTTCCAAAAATTGA-CACGAAATATT
130 CAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCA-GAAATATT
* ** * * * * * *
38909 TCTCCTCAATTTTTGGGAAAAATACACATAAAAAATAGATAATTAAACACCAAAAAGATTGGCGG
194 TTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAATTGAACGCCAAAAATATTGGAGG
*
38974 GCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCCGATTAAATCGAAAC
259 GCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTGATTAAATCGAAAC
*
39039 AAGATTTA
324 AAGATTCA
* * * * * *
39047 GGTGCTCATAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGGTTAGATAAATATAGATAT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
* * * **
39112 TTCAAGGAGTATCGGCGCC--AAATCATGCAAAACTAAGCCAGGGCCCAAGAACGCGTTTTCAGC
66 TTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCC-GGGCCCCGGAACGCGTTTTCAGC
* * * * * *
39175 C-GATAACCGTTATCGTTAGTACACGATTTCAGCTAAAATTTTG-ATAAAACTGA-AACGAAA-A
130 CAGA-AACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCA-AAAATTGACCA-GAAATA
* * * * * * * *
39236 GTTTTTCCTTAATATTTAGCCACAATGCTCATAAAAAATATATTATTCAACG-CAAAAACTATTT
192 -TTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAATTGAACGCCAAAAA-TATTG
* * * * * *
39300 AAGGGCTTTTCATGCTTCAAATATGGTTTTTCCTATTTTTTTCCAAATTAAGTTATGATTAAATC
255 GAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTCCAAATTAATTTCTGATTAAATC
39365 GAAACAAGATTCA
319 GAAACAAGATTCA
* * * *
39378 GATGCTCGTAAAAACATTTCCTTAAATCTAATGTCGATGAGATTTGATTAGATGAATATAGATAT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
** * *
39443 TTCATTGAGTCTCTGCGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGGAACGCGTTTTGTAG
66 TTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCCGG-GCCCCGGAACGCGTTTT-CAG
* *
39508 CCAGAAACCGTGA-----CGTACTTGATTTCGGCTAAAATTTTGCAAAAATTTTGACCAGAAATA
129 CCAGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAA--TTGACCAGAAATA
* * * * *
39568 TATTTCCTCAA-TTTTGCCCAAAATACGCATAAAAAATATATAATTGGACGCCAAAAATATTGGC
192 TTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAATTGAACGCCAAAAATATTGGA
*
39632 GGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCCGATTAAATCGAA
257 GGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTGATTAAATCGAA
39697 ACAAGATTCA
322 ACAAGATTCA
* * *
39707 GGTGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAAATTTGATTAGATAAATATAGATAT
1 GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
* * * *
39772 TTCAAGGAGTCTCGGCGCCAAAAATCAGGCAAAACTGAGCCGGGGCCCCAGAACTCGTTTT
66 TTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCC-GGGCCCCGGAACGCGTTTT
39833 TAGCTAAAAA
Statistics
Matches: 4030, Mismatches: 615, Indels: 275
0.82 0.12 0.06
Matches are distributed among these distances:
324 17 0.00
325 91 0.02
326 2 0.00
327 6 0.00
328 104 0.03
329 251 0.06
330 481 0.12
331 701 0.17
332 750 0.19
333 610 0.15
334 234 0.06
335 211 0.05
336 152 0.04
337 107 0.03
338 27 0.01
340 119 0.03
341 43 0.01
342 2 0.00
343 91 0.02
344 31 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (331 bp):
GATGCTCGTAAAAACATATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT
TTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAACGCGTTTTCAGCC
AGAAACCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCAGAAATATTTT
TCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAATTGAACGCCAAAAATATTGGAGGGC
TTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTGATTAAATCGAAACAA
GATTCA
Found at i:42040 original size:86 final size:85
Alignment explanation
Indices: 41896--42061 Score: 296
Period size: 86 Copynumber: 1.9 Consensus size: 85
41886 ATGGAAATGG
* *
41896 AGGTACACGAGAAGACAGCGGCTCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGGCT
1 AGGTACACGAGAAGACAACGGCTCTCAACAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGGCT
*
41961 CGCGGACGCGACACACACGA
66 CGCGGACACGACACACACGA
41981 AGGTACACGAGAAGGACAACGGCTCTCAACAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGGC
1 AGGTACACGAGAA-GACAACGGCTCTCAACAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGGC
42046 TCGCGGACACGACACA
65 TCGCGGACACGACACA
42062 GGTGCTCCAT
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
85 13 0.17
86 64 0.83
ACGTcount: A:0.28, C:0.31, G:0.31, T:0.10
Consensus pattern (85 bp):
AGGTACACGAGAAGACAACGGCTCTCAACAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGGCT
CGCGGACACGACACACACGA
Found at i:42218 original size:41 final size:35
Alignment explanation
Indices: 42127--42194 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
42117 TTGTTGCCAC
*
42127 AAGAATATCCTGAGGAAAGAAACAGAAACAGAGCG
1 AAGAATATCCTGGGGAAAGAAACAGAAACAGAGCG
42162 AAGAATATCCTGGGGAAAGAAACAGAAACAGAG
1 AAGAATATCCTGGGGAAAGAAACAGAAACAGAG
42195 AGAGAGCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.51, C:0.13, G:0.26, T:0.09
Consensus pattern (35 bp):
AAGAATATCCTGGGGAAAGAAACAGAAACAGAGCG
Found at i:42236 original size:4 final size:4
Alignment explanation
Indices: 42215--42345 Score: 219
Period size: 4 Copynumber: 32.5 Consensus size: 4
42205 GAATATCCTG
* *
42215 GGGA GAGA GAGA GAGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA
1 GGGA GGGA GGGA G-GGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA
42264 GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA
1 GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA
42312 GGGA GGGGA GGGA -GGA GGGA GGGA GGGA GGGA GG
1 GGGA -GGGA GGGA GGGA GGGA GGGA GGGA GGGA GG
42346 AGGAGAGAGA
Statistics
Matches: 122, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
3 3 0.02
4 112 0.92
5 7 0.06
ACGTcount: A:0.27, C:0.00, G:0.73, T:0.00
Consensus pattern (4 bp):
GGGA
Found at i:42355 original size:2 final size:2
Alignment explanation
Indices: 42348--42393 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
42338 GAGGGAGGAG
*
42348 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GC GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
42389 GA GA G
1 GA GA G
42394 TGAGCGACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.46, C:0.02, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:66549 original size:13 final size:13
Alignment explanation
Indices: 66528--66564 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
66518 GATAATTCTT
66528 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
66541 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
66554 CTTGACCCTCC
1 TTTGACCCTCC
66565 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:66625 original size:40 final size:40
Alignment explanation
Indices: 66563--66642 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
66553 ACTTGACCCT
* * *
66563 CCTAATAATTAAGGAAATAAATTAAATGCGGGTTTAGCCC
1 CCTAATAATCAAGGAAAGAAATTAAATGCAGGTTTAGCCC
* *
66603 CCTAATAATCAAGGTAAGAAATTAAATTCAGGTTTAGCCC
1 CCTAATAATCAAGGAAAGAAATTAAATGCAGGTTTAGCCC
66643 ATAGTTATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (40 bp):
CCTAATAATCAAGGAAAGAAATTAAATGCAGGTTTAGCCC
Found at i:66754 original size:14 final size:13
Alignment explanation
Indices: 66735--66773 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
66725 TTTTTTTATA
66735 ACAAATCAGGAGGG
1 ACAAAT-AGGAGGG
*
66749 ACAAATTGGAGGG
1 ACAAATAGGAGGG
*
66762 ACAAATTGGAGG
1 ACAAATAGGAGG
66774 ATCATGTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.41, C:0.10, G:0.36, T:0.13
Consensus pattern (13 bp):
ACAAATAGGAGGG
Found at i:66761 original size:13 final size:13
Alignment explanation
Indices: 66743--66773 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
66733 TAACAAATCA
66743 GGAGGGACAAATT
1 GGAGGGACAAATT
66756 GGAGGGACAAATT
1 GGAGGGACAAATT
66769 GGAGG
1 GGAGG
66774 ATCATGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.45, T:0.13
Consensus pattern (13 bp):
GGAGGGACAAATT
Found at i:79664 original size:2 final size:2
Alignment explanation
Indices: 79657--79689 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
79647 AGAATCCCTG
79657 TA TA TA TA TA 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 TA T
79690 TCAATGTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.