Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002900.1 Hibiscus syriacus cultivar Beakdansim tig00005991_pilon, 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: 258366
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:208886 original size:20 final size:19
Alignment explanation
Indices: 208836--208888 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
208826 AATTTTGTTA
208836 TTATTTCTTTTTTTTTATT
1 TTATTTCTTTTTTTTTATT
*
208855 TTATTTCATTTTTTATTATTT
1 TTATTTC-TTTTTTTTTA-TT
208876 TTATTT-TTTTTTT
1 TTATTTCTTTTTTT
208889 CATTTTTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 13 0.43
20 9 0.30
21 8 0.27
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (19 bp):
TTATTTCTTTTTTTTTATT
Found at i:208895 original size:10 final size:10
Alignment explanation
Indices: 208839--208895 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
208829 TTTGTTATTA
208839 TTTC-TTTTT
1 TTTCATTTTT
* *
208848 TTTTATTTTA
1 TTTCATTTTT
208858 TTTCATTTTT
1 TTTCATTTTT
208868 TATT-ATTTTT
1 T-TTCATTTTT
*
208878 ATT--TTTTT
1 TTTCATTTTT
208886 TTTCATTTTT
1 TTTCATTTTT
208896 CATTTTTTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
8 7 0.18
9 5 0.13
10 24 0.63
11 2 0.05
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTCATTTTT
Found at i:208897 original size:35 final size:34
Alignment explanation
Indices: 208827--208903 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 34
208817 AAAATTTAAA
208827 ATTTTGTTATTATTTCTTTTTTTTTATTTTATTTC
1 ATTTT-TTATTATTTCTTTTTTTTTATTTTATTTC
*
208862 ATTTTTTATTATTT-TTATTTTTTT-TTTCATTTTTC
1 ATTTTTTATTATTTCTT-TTTTTTTATTT--TATTTC
208897 ATTTTTT
1 ATTTTTT
208904 CATTTTTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
33 5 0.13
34 16 0.42
35 17 0.45
ACGTcount: A:0.14, C:0.05, G:0.01, T:0.79
Consensus pattern (34 bp):
ATTTTTTATTATTTCTTTTTTTTTATTTTATTTC
Found at i:208942 original size:3 final size:3
Alignment explanation
Indices: 208934--208983 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
208924 TCTATGTTCT
208934 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
208981 TTA
1 TTA
208984 ACATTTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:211754 original size:96 final size:97
Alignment explanation
Indices: 211581--211778 Score: 294
Period size: 96 Copynumber: 2.1 Consensus size: 97
211571 TAATTATATA
* *
211581 TATATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCTCGGCTTTATGGA
1 TATATATACAATAAAGCTTGAGCTGTCCCTCTAAAGAAATTGGTTAAACGCCTCGGCTTTATAGA
* * *
211646 TAAGATTTAGCTAGCCTGATAAAGGTGATTAT
66 TAAAAGTCAGCTAGCCTGATAAAGGTGATTAT
211678 TATA-ATACAATAAAGCTTGAGCTGTCCCTCTAAAGAAATTGGTTAAATTC-CCT-GGCTTTATA
1 TATATATACAATAAAGCTTGAGCTGTCCCTCTAAAGAAATTGGTTAAA--CGCCTCGGCTTTATA
*
211740 GATAAAAGTCAGCTAGCCTTATAAAGGTGATTAT
64 GATAAAAGTCAGCTAGCCTGATAAAGGTGATTAT
*
211774 AATAT
1 TATAT
211779 TGAGTTGTCC
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
96 83 0.91
97 7 0.08
98 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (97 bp):
TATATATACAATAAAGCTTGAGCTGTCCCTCTAAAGAAATTGGTTAAACGCCTCGGCTTTATAGA
TAAAAGTCAGCTAGCCTGATAAAGGTGATTAT
Found at i:212939 original size:74 final size:75
Alignment explanation
Indices: 212834--212997 Score: 251
Period size: 74 Copynumber: 2.2 Consensus size: 75
212824 AAATGACTAA
* *
212834 GGGTATCGGTACCCATTGAGCATTATGTTTTTCTCGGAGCCAAAATTGGCATAGGGGTATCGGT-
1 GGGTATCGGTACCTATTGAGCATTATGTTTTTCTCGGAGCCAAAATTGGCATAGGAGTATCGGTA
212898 ACCCTATGAG
66 ACCCTATGAG
* * *
212908 GGGTATCGTTACCTATTTG-GCATTCTGTTTTTCTCGGAGCCAAAATTTGCATAGGAGTATCGGT
1 GGGTATCGGTACCTA-TTGAGCATTATGTTTTTCTCGGAGCCAAAATTGGCATAGGAGTATCGGT
212972 ACACCCTATGAG
65 A-ACCCTATGAG
212984 GGGTATCGGTACCT
1 GGGTATCGGTACCT
212998 CCCTATTTAA
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
74 55 0.68
75 3 0.04
76 23 0.28
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (75 bp):
GGGTATCGGTACCTATTGAGCATTATGTTTTTCTCGGAGCCAAAATTGGCATAGGAGTATCGGTA
ACCCTATGAG
Found at i:219802 original size:84 final size:84
Alignment explanation
Indices: 219661--220454 Score: 1237
Period size: 84 Copynumber: 9.5 Consensus size: 84
219651 GTTAACCAAA
* * * *
219661 ACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGAGATAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
219726 GGCTATCTGCCAACAAAAG
66 GGCTATCTGCCAACAAAAG
* *
219745 ACCTTCGAGTTCGATTACACTTAGCTCAAAGGCACATCATTTGTAGCATAGCTCAAGGCGAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
* *
219810 GGTTATCTGCCAATAAAAG
66 GGCTATCTGCCAACAAAAG
* *
219829 ACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
*
219894 GGCTATCTGCCAACAAAAA
66 GGCTATCTGCCAACAAAAG
* **
219913 ACCTTCGAGTTCGATTACACTCAGCTCAAAAGCACATCATTTATAGCATAGCTCAAGGCGAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
*
219978 GGCTATCTGCTAACAAAAG
66 GGCTATCTGCCAACAAAAG
* * * * ** * *
219997 ACCTTCGAGTTTGCTTACACTCAGCTCGAAGGCACATCATTTACAATATAGCTCAAGGGGAAAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
*
220062 GGCTATCTGCTAACAAAAG
66 GGCTATCTGCCAACAAAAG
* * *
220081 ACCTTCGAGTTTGATTACACTCAACTCAAAGGAACATCATTTGCAGCATAGCTCAAGGCGAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
*
220146 GGTTATCTGCCAACAAAAG
66 GGCTATCTGCCAACAAAAG
* * *
220165 ACATTCGAGTTCGATTACACTCAACTCAAAGACACATCATTTGCAGCATAGCTCAAGGCGAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
* *
220230 GGTTATCTGGCAACAAAAG
66 GGCTATCTGCCAACAAAAG
* *
220249 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAAGGTGAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
*
220314 GGTTATCTGCCAACAAAAG
66 GGCTATCTGCCAACAAAAG
* *
220333 ACCTTCGAGTTTGATTACACTCATCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
220398 GGCTATCTGCCAACAAAAG
66 GGCTATCTGCCAACAAAAG
*
220417 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGAACATC
1 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC
220455 CAATTTACAA
Statistics
Matches: 649, Mismatches: 61, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 649 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (84 bp):
ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAG
GGCTATCTGCCAACAAAAG
Found at i:224255 original size:16 final size:18
Alignment explanation
Indices: 224221--224259 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
224211 TATAACTAAA
224221 TTTAGTTTTTATATGTTT
1 TTTAGTTTTTATATGTTT
224239 TTTA-TTTTTATAT-TTT
1 TTTAGTTTTTATATGTTT
224255 TTTAG
1 TTTAG
224260 ATGACGACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (18 bp):
TTTAGTTTTTATATGTTT
Found at i:226118 original size:148 final size:147
Alignment explanation
Indices: 225821--226123 Score: 480
Period size: 148 Copynumber: 2.1 Consensus size: 147
225811 TTAATTTTAA
* * *
225821 TAAATAAATGACTCATATGGGGTCACTCATCCGGGTCCATTGAAATAATATATCGCATGAAACTT
1 TAAATAAATGACTCATATGGGGCCACTAATCCGGGTCCATTGAAATAATATATCGCATGAAACTC
* * *
225886 ATCACTTCGACATGACAAGTTCGTGAATAATTGTAATTTTTATTGTATTCTCCAAAATAAAAAAA
66 ATCACTTCGACATGACAAGTTCGTGAATAACTATAATTTTTATTGTATTCTACAAAATAAAAAAA
225951 TGGGTGCCCTATTGAGC
131 TGGGTGCCCTATTGAGC
* * *
225968 TAAATAAATGGCTCATATAGGGGCCACTAATCCGGGTCTATTGAAATAATATATCGCATGGAACT
1 TAAATAAATGACTCATAT-GGGGCCACTAATCCGGGTCCATTGAAATAATATATCGCATGAAACT
* *
226033 CATCACTTCGACATGACGAGTTCGTGAATAACTATAATTTTTATTGTATTCTACAAAATAGAAAA
65 CATCACTTCGACATGACAAGTTCGTGAATAACTATAATTTTTATTGTATTCTACAAAATAAAAAA
* *
226098 ATGGGTGTCCTATTGGGC
130 ATGGGTGCCCTATTGAGC
226116 TAAATAAA
1 TAAATAAA
226124 AAAAAACGAG
Statistics
Matches: 142, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
147 17 0.12
148 125 0.88
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (147 bp):
TAAATAAATGACTCATATGGGGCCACTAATCCGGGTCCATTGAAATAATATATCGCATGAAACTC
ATCACTTCGACATGACAAGTTCGTGAATAACTATAATTTTTATTGTATTCTACAAAATAAAAAAA
TGGGTGCCCTATTGAGC
Found at i:228817 original size:19 final size:18
Alignment explanation
Indices: 228793--228869 Score: 64
Period size: 19 Copynumber: 4.1 Consensus size: 18
228783 GAATAATAAT
*
228793 AATAAATAAATGATAAAAA
1 AATAAATAAA-AATAAAAA
* *
228812 AATAAAAAAATAATGAAAAT
1 AATAAATAAA-AAT-AAAAA
* **
228832 AATAAATCAAAGCAAAATA
1 AATAAATAAAAATAAAA-A
228851 AATAAATAAAAATAAAAA
1 AATAAATAAAAATAAAAA
228869 A
1 A
228870 GTCAAAGAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
18 6 0.13
19 27 0.60
20 12 0.27
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (18 bp):
AATAAATAAAAATAAAAA
Found at i:229046 original size:22 final size:19
Alignment explanation
Indices: 229016--229060 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 19
229006 TAGAAGTAGT
229016 AAAATAATAAGAAATAAAAAA
1 AAAATAATAA-AAA-AAAAAA
229037 AAAATTAATAAAAAAACAAAA
1 AAAA-TAATAAAAAAA-AAAA
229058 AAA
1 AAA
229061 GATCAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 14 0.64
22 6 0.27
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.13
Consensus pattern (19 bp):
AAAATAATAAAAAAAAAAA
Found at i:230240 original size:4 final size:4
Alignment explanation
Indices: 230231--230324 Score: 69
Period size: 4 Copynumber: 24.5 Consensus size: 4
230221 AACAAAAAGG
*
230231 AAAT AAAT AAAT AAAT -AAG AAAT AAAT -AAT AAAT -AAT -AAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
230275 AACAAT AAAT AAAT -AAT -AAT AAACG ATAGT AAA- AAAT -AAT AAAT
1 -A-AAT AAAT AAAT AAAT AAAT AAA-T A-AAT AAAT AAAT AAAT AAAT
230319 AAAT AA
1 AAAT AA
230325 TATTTTTAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
3 23 0.31
4 43 0.58
5 4 0.05
6 4 0.05
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:230293 original size:34 final size:34
Alignment explanation
Indices: 230250--230326 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
230240 AATAAATAAG
* *
230250 AAATAAATAATAAATAATAATAAATAACAATAAAT
1 AAAT-AATAATAAACAATAATAAAAAACAATAAAT
* * *
230285 AAATAATAATAAACGATAGTAAAAAATAATAAAT
1 AAATAATAATAAACAATAATAAAAAACAATAAAT
230319 AAATAATA
1 AAATAATA
230327 TTTTTAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 33 0.89
35 4 0.11
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (34 bp):
AAATAATAATAAACAATAATAAAAAACAATAAAT
Found at i:230326 original size:7 final size:7
Alignment explanation
Indices: 230231--230320 Score: 55
Period size: 7 Copynumber: 12.9 Consensus size: 7
230221 AACAAAAAGG
230231 AAATAAAT
1 AAAT-AAT
230239 AAATAAAT
1 AAAT-AAT
230247 AAGA-AAT
1 AA-ATAAT
230254 AAATAAT
1 AAATAAT
230261 AAATAAT
1 AAATAAT
230268 -AATAA-
1 AAATAAT
*
230273 ATAACAAT
1 A-AATAAT
230281 AAATAA-
1 AAATAAT
230287 ATAATAAT
1 A-AATAAT
**
230295 AAACGAT
1 AAATAAT
* *
230302 -AGTAAA
1 AAATAAT
230308 AAATAAT
1 AAATAAT
230315 AAATAA
1 AAATAA
230321 ATAATATTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
6 9 0.14
7 42 0.66
8 12 0.19
9 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.23
Consensus pattern (7 bp):
AAATAAT
Found at i:230326 original size:14 final size:14
Alignment explanation
Indices: 230232--230297 Score: 78
Period size: 14 Copynumber: 4.4 Consensus size: 14
230222 ACAAAAAGGA
230232 AATAAATAAATAAAT
1 AATAAATAAAT-AAT
*
230247 AAGAAATAAATAAT
1 AATAAATAAATAAT
*
230261 AAATAATAATAAATAAC
1 -AAT-A-AATAAATAAT
230278 AATAAATAAATAAT
1 AATAAATAAATAAT
230292 AATAAA
1 AATAAA
230298 CGATAGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
14 18 0.41
15 13 0.30
16 4 0.09
17 9 0.20
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (14 bp):
AATAAATAAATAAT
Found at i:230453 original size:39 final size:38
Alignment explanation
Indices: 230368--230616 Score: 316
Period size: 37 Copynumber: 6.6 Consensus size: 38
230358 AAAATGCTCC
* *
230368 TTTAAAAACTATGTATTATATATTAGTTTTTAAAAATGT
1 TTTAAAAACTATATATTATATA-TAGTTTTCAAAAATGT
230407 TTTCAAAAACTATATATTATATA-AGTTTTCAAAAAATGT
1 TTT-AAAAACTATATATTATATATAGTTTTC-AAAAATGT
230446 TTTCAAAAACTATATATTATATA-AGTTTTC-AAAATGAT
1 TTT-AAAAACTATATATTATATATAGTTTTCAAAAATG-T
* * *
230484 TTTAAAAACCATATATTATACATA-TTTTCTAAAATGT
1 TTTAAAAACTATATATTATATATAGTTTTCAAAAATGT
*
230521 TTTAAAAACTATATA-T-TATATAGTTTTCAAAAGTGT
1 TTTAAAAACTATATATTATATATAGTTTTCAAAAATGT
*
230557 TTTAAAAACTATATATTATATACA-TTTTC-AAAATGTT
1 TTTAAAAACTATATATTATATATAGTTTTCAAAAATG-T
*
230594 TTTAGAAACTATATATTATATAT
1 TTTAAAAACTATATATTATATAT
230617 GTATTTTCAA
Statistics
Matches: 189, Mismatches: 12, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
35 5 0.03
36 32 0.17
37 71 0.38
38 22 0.12
39 41 0.22
40 18 0.10
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (38 bp):
TTTAAAAACTATATATTATATATAGTTTTCAAAAATGT
Found at i:230645 original size:110 final size:113
Alignment explanation
Indices: 230368--230613 Score: 331
Period size: 110 Copynumber: 2.2 Consensus size: 113
230358 AAAATGCTCC
* * * *
230368 TTTAAAAACTATGTATTATATATTAGTTTT-TAAAAATGTTTTCAAAAACTATATATTATATAAG
1 TTTAAAAACCATATATTATACA-TA-TTTTCT-AAAACGTTTT-AAAAACTATATATTATATAAG
230432 TTTTCAAAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGAT
62 TTTTCAAAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGAT
*
230484 TTTAAAAACCATATATTATACATATTTTCTAAAATGTTTTAAAAACTATATATTATAT-AGTTTT
1 TTTAAAAACCATATATTATACATATTTTCTAAAACGTTTTAAAAACTATATATTATATAAGTTTT
* *
230548 C-AAAAGTGTTTT-AAAAACTATATATTATATACA-TTTTCAAAATGTT
66 CAAAAAATGTTTTCAAAAACTATATATTATATA-AGTTTTCAAAATGAT
* *
230594 TTTAGAAACTATATATTATA
1 TTTAAAAACCATATATTATA
230614 TATGTATTTT
Statistics
Matches: 121, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
110 49 0.40
111 11 0.09
112 7 0.06
113 18 0.15
114 14 0.12
115 3 0.02
116 19 0.16
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.44
Consensus pattern (113 bp):
TTTAAAAACCATATATTATACATATTTTCTAAAACGTTTTAAAAACTATATATTATATAAGTTTT
CAAAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGAT
Found at i:231713 original size:84 final size:82
Alignment explanation
Indices: 231225--232394 Score: 1029
Period size: 84 Copynumber: 14.1 Consensus size: 82
231215 CTTGCTTTGG
* * *
231225 GCTATGCTGTAAATGATGTGCCTTGTAGCTGAGCGTAGTCGAACTCAAAGGTCTTTG--GCAGAT
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGCAGAT
*
231288 AACCCTTCTAGCCTTGA
66 AACCCTTCTAGACTTGA
* * * * ** * *
231305 GCTATACCGCAAATGATGTGTCGTT-GAACTGAGTATAATCGAACTCAAAGGTCTTTGTTGGCAG
1 GCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTT-GCAG
*
231369 ATAACCCTTCTAGCCTTGA
64 ATAACCCTTCTAGACTTGA
* * * *
231388 GTTATGCTGCAAATGATATGCCTTGGAGCTAAGCGTTGTCGAACTCGAAGGTCTTTG--GCAGAT
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGCAGAT
* *
231451 AGCCCTTCTAGCCTTGA
66 AACCCTTCTAGACTTGA
* * * * * * *
231468 GCTATACCGCAAATGATGTATCGTT-GAGCTGAGTGTAATCGAACTCAAAGGTCTTTGTTGGCAG
1 GCTATGCTGCAAATGATGT-GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTT-GCAG
231532 ATAACCCTTCTAG-CTTTGA
64 ATAACCCTTCTAGAC-TTGA
* * * * * * * *
231551 GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTATTTAG-T--AG
1 GCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGCAG
* * *
231613 ATAGCCCTTCTCGACTTAA
64 ATAACCCTTCTAGACTTGA
* * * * *
231632 GCTATGTTGCAAATGATGTGCCTTGTAGTTGAGTGTAGTCAAACTCGAAGGTCTTTGATTGACAG
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG-TTG-CAG
*
231697 ATAACCCTTCTAGACTTAA
64 ATAACCCTTCTAGACTTGA
* * *
231716 GTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAG
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTG-CAG
* *
231781 ATAACCCTTTTAGCCTTGA
64 ATAACCCTTCTAGACTTGA
* ** * * * * *
231800 GTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG--GCAGA
1 GCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGCAGA
* * * *
231863 TAGCTCTTCTCGACTTAA
65 TAACCCTTCTAGACTTGA
* * * *
231881 GCTATGTTGTAAATGATGTGCCTTGTAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTAGCAG
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTT-GCAG
* * *
231946 ATAACCATTCTCGACTTAA
64 ATAACCCTTCTAGACTTGA
* * * * *
231965 GTTATGCTACAAATGATATGCCTTGGAGATGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAG
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTG-CAG
*
232030 ATAACCCTTCTAGCCTTGA
64 ATAACCCTTCTAGACTTGA
* * ** *** * * *
232049 GTTATGCTGTAAATGATGCACACTCAAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG--GCAGA
1 GCTATGCTGCAAATGATGTGC-CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGCAGA
* * * *
232112 TAGCCCTTCTTGATTTAA
65 TAACCCTTCTAGACTTGA
* *
232130 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTTGGCA
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-GTT-GCA
* * *
232195 GATAACCCTTCTCGACCTAA
63 GATAACCCTTCTAGACTTGA
* ** * * * *
232215 GTTATATTGCAAATGATATGCCTTGGAGCTGAACGTATTCGAACTCGAAGGTCTTTTGGTGGCAG
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-GTTGCAG
* * *
232280 ATAGCCCTTTTTGACTTGA
64 ATAACCCTTCTAGACTTGA
* * * *
232299 GCTATGTTGCAAATGATGTGCCTTCGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTGTTGGCAA
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT-CTTTGTT-GCAG
* *
232364 ATAGA-CCTTCTTGCCTTGA
64 ATA-ACCCTTCTAGACTTGA
*
232383 GCTATGTTGCAA
1 GCTATGCTGCAA
232395 CTAATTTCTT
Statistics
Matches: 885, Mismatches: 169, Indels: 68
0.79 0.15 0.06
Matches are distributed among these distances:
79 1 0.00
80 191 0.22
81 111 0.13
82 8 0.01
83 104 0.12
84 338 0.38
85 132 0.15
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (82 bp):
GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGCAGAT
AACCCTTCTAGACTTGA
Found at i:231827 original size:249 final size:249
Alignment explanation
Indices: 231227--232346 Score: 1368
Period size: 249 Copynumber: 4.5 Consensus size: 249
231217 TGCTTTGGGC
* * * *
231227 TATGCTGTAAATGATGTGCCTTGTAGCTGAGCGTAGTCGAACTCAAAGGTC-TTT-G-G-CAGAT
1 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGAT
* * * * * * * * *
231288 AACCCTTCTAGCCTTGAGCTATACCGCAAATGATGTGTCGTTGAA-CTGAGTATAATCGAACTCA
66 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
* * * * * * *
231352 AAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGC
131 AGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
* * * * * * *
231417 TAAGCGTTGTCGAACTCGAAGGTCTTT-G--G-CAGATAGCCCTTCTAGCCTTGAGC
193 TGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGT
* * * * * * * *
231470 TATACCGCAAATGATGTAT-CGTT-GAGCTGAGTGTAATCGAACTCAAAGGTC-TTTGTTGGCAG
1 TATGCTGCAAATGA--TATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAG
*
231532 ATAACCCTTCTAGCTTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
64 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
* * * * * *
231597 CGAGGGTATTTAGTAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTGCCTTGTAGTT
129 CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
* *
231662 GAGTGTAGTCAAACTCGAAGGTCTTTGATTGACAGATAACCCTTCTAGACTTAAGT
194 GAGCGTAGTCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGT
231718 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGAT
1 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGAT
* *
231783 AACCCTTTTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
66 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
* * * *
231848 AGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATGTTGTAAATGATGTGCCTTGTAGCTGA
131 AGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGA
* *
231913 GCGTAGTCAAACTCGAAGGTCTTTGGTT-AGCAGATAACCATTCTCGACTTAAGT
196 GCGTAGTCAAACTCGAAGGTCTTTGGTTGA-CAGATAACCCTTCTAGACTTAAGT
* *
231967 TATGCTACAAATGATATGCCTTGGAGATGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGAT
1 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGAT
** * *
232032 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGCACACTCAAAGCTGAGTGTAATCGAACTCG
66 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
* *
232097 AGGGTCTTTGGCAGATAGCCCTTCTTGATTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGA
131 AGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGA
* * * *
232162 GCGTAGTCAAACTCAAAGGTCTTTTGGTTGGCAGATAACCCTTCTCGACCTAAGT
196 GCGTAGTCAAACTCGAAGGTC-TTTGGTTGACAGATAACCCTTCTAGACTTAAGT
** * * *
232217 TATATTGCAAATGATATGCCTTGGAGCTGAACGTATTCGAACTCGAAGGTCTTTTGGTGGCAGAT
1 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGAT
* * * * * * * * * *
232282 AGCCCTTTTTGACTTGAGCTATGTTGCAAATGATGTGCCTTCG-AGCTGAGCGTAGTCGAACTCG
66 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
232346 A
131 A
232347 AGGTATTTTG
Statistics
Matches: 760, Mismatches: 101, Indels: 26
0.86 0.11 0.03
Matches are distributed among these distances:
243 39 0.05
244 70 0.09
245 4 0.01
246 45 0.06
247 25 0.03
248 58 0.08
249 401 0.53
250 118 0.16
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (249 bp):
TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGAT
AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
AGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGA
GCGTAGTCAAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTAGACTTAAGT
Found at i:231880 original size:165 final size:162
Alignment explanation
Indices: 231227--232350 Score: 1078
Period size: 165 Copynumber: 6.8 Consensus size: 162
231217 TGCTTTGGGC
* * *
231227 TATGCTGTAAATGATGTGCCTTGTAGCTGAGCGTAGTCGAACTCAAAGGTCTTTG-GCAGATAAC
1 TATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTGCAGATAGC
* * * * * * * *
231291 CCTTCTAGCCTTGAGCTATACCGCAAATGATGTGTCGTTGAACTGAGTATAATCGAACTCAAAGG
66 CCTTCTAGACTTGAGCTATGCTGCAAATGATGTG-CCTTGAGCTGAGTGTAGTCGAACTCGAAGG
* *
231356 TCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
130 TC-TTGTTGGCAGATAACCCTTCTAGACTTAAGT
* * * *
231390 TATGCTGCAAATGATATGCCTTGGAGCTAAGCGTTGTCGAACTCGAAGGTCTTTG-GCAGATAGC
1 TATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTGCAGATAGC
* * * * * * *
231454 CCTTCTAGCCTTGAGCTATACCGCAAATGATGTATCGTTGAGCTGAGTGTAATCGAACTCAAAGG
66 CCTTCTAGACTTGAGCTATGCTGCAAATGATGT-GCCTTGAGCTGAGTGTAGTCGAACTCGAAGG
*
231519 TCTTTGTTGGCAGATAACCCTTCTAG-CTTTGAGT
130 TC-TTGTTGGCAGATAACCCTTCTAGAC-TTAAGT
* * * * * *
231553 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTATTTAGT--AGATA
1 TATGCTGTAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTGCAGATA
* * * * *
231616 GCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTGCCTTGTAGTTGAGTGTAGTCAAACTCGAA
64 GCCCTTCTAGACTTGAGCTATGCTGCAAATGATGTGCCTTG-AGCTGAGTGTAGTCGAACTCGAA
*
231681 GGTCTTTGATTGACAGATAACCCTTCTAGACTTAAGT
128 GGTC-TTG-TTGGCAGATAACCCTTCTAGACTTAAGT
* *
231718 TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGAT
1 TATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-GTG-CAGAT
* * * * ** * *
231783 AACCCTTTTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
63 AGCCCTTCTAGACTTGAGCTATGCTGCAAATGATGTG-CCTTG-AGCTGAGTGTAGTCGAACTCG
* * * * *
231848 AGGGTC-T-TTGGCAGATAGCTCTTCTCGACTTAAGC
126 AAGGTCTTGTTGGCAGATAACCCTTCTAGACTTAAGT
* * *
231883 TATGTTGTAAATGATGTGCCTTGTAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTAGCAGAT
1 TATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-G-T-GCAGAT
* * * * * * * * *
231948 AACCATTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGGAGATGAGCGTAGTCGAACTCGA
63 AGCCCTTCTAGACTTGAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGTGTAGTCGAACTCGA
* *
232013 AGGTCTT-TTGGTGACAGATAACCCTTCTAGCCTTGAGT
127 AGGTCTTGTT-G-G-CAGATAACCCTTCTAGACTTAAGT
** *** * * *
232051 TATGCTGTAAATGATGCACACTCAAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG-GCAGATAG
1 TATGCTGTAAATGATGTGC-CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTGCAGATAG
* * * * * *
232115 CCCTTCTTGATTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCAAAG
65 CCCTTCTAGACTTGAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGTGTAGTCGAACTCGAAG
* *
232180 GTCTTTTGGTTGGCAGATAACCCTTCTCGACCTAAGT
129 GTC--TT-GTTGGCAGATAACCCTTCTAGACTTAAGT
** * * * *
232217 TATATTGCAAATGATATGCCTTGGAGCTGAACGTATTCGAACTCGAAGGTCTTTTGGTGGCAGAT
1 TATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-GT-GCAGAT
* * * *
232282 AGCCCTTTTTGACTTGAGCTATGTTGCAAATGATGTGCCTTCGAGCTGAGCGTAGTCGAACTCGA
63 AGCCCTTCTAGACTTGAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGTGTAGTCGAACTCGA
232347 AGGT
127 AGGT
232351 ATTTTGTTGG
Statistics
Matches: 802, Mismatches: 130, Indels: 52
0.82 0.13 0.05
Matches are distributed among these distances:
162 1 0.00
163 170 0.21
164 147 0.18
165 246 0.31
166 39 0.05
167 6 0.01
168 68 0.08
169 125 0.16
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (162 bp):
TATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTGCAGATAGC
CCTTCTAGACTTGAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGTGTAGTCGAACTCGAAGGT
CTTGTTGGCAGATAACCCTTCTAGACTTAAGT
Found at i:233629 original size:83 final size:87
Alignment explanation
Indices: 233525--233748 Score: 269
Period size: 95 Copynumber: 2.5 Consensus size: 87
233515 GGCTAGCTGG
*
233525 ATCCATAAAGCCGGGGAGTTTAACCAATTGCTCTAGAGGGACAACTTA-ATATA-TA-AA-CACC
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTATATATAGTATAATCACC
* *
233586 TTTATCAGGTTAGCTGAATCTT
66 TTTATCAGGCTAGCTGAATATT
*
233608 ATCCATAAAGTCGGGGCGTTTAACCAATTGC-CTTAGAGGGACAGCTCAAGCTTTATTATATAGT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTC-TAGAGGG--A---CAA-C-TTA-TATATAGT
*
233672 ATAATTACCTTTATCAGGCTAGCTGAATATT
57 ATAATCACCTTTATCAGGCTAGCTGAATATT
* *
233703 ATCCATAAAGCCGAGGCGTTTAACCAATTTCTCTAGAGGGACAACT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACT
233749 CAAGCTTTAT
Statistics
Matches: 119, Mismatches: 8, Indels: 23
0.79 0.05 0.15
Matches are distributed among these distances:
82 1 0.01
83 36 0.30
85 1 0.01
88 4 0.03
89 2 0.02
90 6 0.05
92 5 0.04
93 3 0.03
94 2 0.02
95 58 0.49
96 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (87 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTATATATAGTATAATCACC
TTTATCAGGCTAGCTGAATATT
Found at i:233740 original size:95 final size:94
Alignment explanation
Indices: 233573--233768 Score: 295
Period size: 95 Copynumber: 2.1 Consensus size: 94
233563 GGACAACTTA
** * * * *
233573 ATATATAAACACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTG
1 ATATATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATTG
*
233638 CCTTAGAGGGACAGCTCAAGCTTTATTAT
66 CCTTAGAGGGACAACTCAAGCTTTATTAT
233667 ATAGTATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATT
1 ATA-TATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATT
*
233732 -TCTCTAGAGGGACAACTCAAGCTTTATTAT
65 GCCT-TAGAGGGACAACTCAAGCTTTATTAT
233762 ATATATA
1 ATATATA
233769 TAATATTATA
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 9 0.10
95 83 0.90
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (94 bp):
ATATATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATTG
CCTTAGAGGGACAACTCAAGCTTTATTAT
Found at i:237407 original size:15 final size:15
Alignment explanation
Indices: 237344--237413 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
237334 AATTAATGTT
*
237344 AAATAAATAAAT-AA
1 AAATAAAAAAATAAA
*
237358 AAATGAAAAAAATAAT
1 AAAT-AAAAAAATAAA
** *
237374 AAATCAAAGCAA-AAG
1 AAAT-AAAAAAATAAA
237389 AAATAAAAAAATAAA
1 AAATAAAAAAATAAA
237404 AAATAAAAAA
1 AAATAAAAAA
237414 GTCAAAGAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
14 9 0.20
15 25 0.57
16 10 0.23
ACGTcount: A:0.79, C:0.03, G:0.04, T:0.14
Consensus pattern (15 bp):
AAATAAAAAAATAAA
Found at i:238963 original size:39 final size:38
Alignment explanation
Indices: 238866--239202 Score: 411
Period size: 39 Copynumber: 8.8 Consensus size: 38
238856 AAAAATCTTT
*
238866 AAAAATGTTCCTTTAAAAACTATATATTATATATTAGTTTTT
1 AAAAATGTT--TTTAAAAACTATATATTATATA--AGTTTTC
*
238908 AAAAATGTTTTCAAAAACTATATATTATATAAGTTTTC
1 AAAAATGTTTTTAAAAACTATATATTATATAAGTTTTC
238946 AAAAAATGTTTTTAAAAACTATATATTATATAAGTTTTC
1 -AAAAATGTTTTTAAAAACTATATATTATATAAGTTTTC
* * *
238985 AAAAAATGTTTTCAAAAAATATATATCATATAAGTTTTC
1 -AAAAATGTTTTTAAAAACTATATATTATATAAGTTTTC
* *
239024 AAAAATTTTTTTCAAAAATTATATATTATATAAGTTTTC
1 AAAAATGTTTTT-AAAAACTATATATTATATAAGTTTTC
* *
239063 -AAAATGATTTTT-AAAACCATATATTATACATA-TTTTC
1 AAAAATG-TTTTTAAAAACTATATATTATATA-AGTTTTC
*
239100 TAAAATG-TTTTAAAAACTATATATTATAT-AGTTTTC
1 AAAAATGTTTTTAAAAACTATATATTATATAAGTTTTC
*
239136 AAAAGTG-TTTTAAAAACTATATATTATATACA-TTTT-
1 AAAAATGTTTTTAAAAACTATATATTATATA-AGTTTTC
* *
239172 TAAAATGTTTTTAGAAACTATATATTATATA
1 AAAAATGTTTTTAAAAACTATATATTATATA
239203 CATATTTTCG
Statistics
Matches: 264, Mismatches: 21, Indels: 25
0.85 0.07 0.08
Matches are distributed among these distances:
35 1 0.00
36 41 0.16
37 61 0.23
38 29 0.11
39 102 0.39
40 21 0.08
42 9 0.03
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (38 bp):
AAAAATGTTTTTAAAAACTATATATTATATAAGTTTTC
Found at i:239037 original size:13 final size:13
Alignment explanation
Indices: 239019--239043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
239009 ATCATATAAG
239019 TTTTCAAAAATTT
1 TTTTCAAAAATTT
239032 TTTTCAAAAATT
1 TTTTCAAAAATT
239044 ATATATTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTCAAAAATTT
Found at i:247538 original size:3 final size:3
Alignment explanation
Indices: 247530--247604 Score: 68
Period size: 3 Copynumber: 26.0 Consensus size: 3
247520 GGCCTATTTT
*
247530 TAA TAA TAA T-T TAA TAA TAA T-A TAA T-A TAA TAA T-A TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
** **
247572 TTT TAA TAA TAA TTT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
247605 CAAAATGGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
2 7 0.12
3 47 0.82
4 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:247583 original size:12 final size:12
Alignment explanation
Indices: 247527--247596 Score: 76
Period size: 12 Copynumber: 6.1 Consensus size: 12
247517 TTTGGCCTAT
247527 TTTTAATAATAA
1 TTTTAATAATAA
247539 -TTTAATAATAA
1 TTTTAATAATAA
*
247550 -TATAAT-ATAA
1 TTTTAATAATAA
**
247560 TAAT-ATATATAA
1 TTTTAATA-ATAA
247572 TTTTAATAATAA
1 TTTTAATAATAA
247584 TTTTAATAATAA
1 TTTTAATAATAA
247596 T
1 T
247597 AATAATAACA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
10 6 0.12
11 18 0.36
12 23 0.46
13 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTTAATAATAA
Found at i:248077 original size:73 final size:73
Alignment explanation
Indices: 247957--248305 Score: 610
Period size: 73 Copynumber: 4.8 Consensus size: 73
247947 AACTCGAAAT
* * *
247957 AACTGTCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAA-ATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
*
248022 TTCAAGTGA
65 TTCGAGTGA
*
248031 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
248096 TCGAGTGA
66 TCGAGTGA
*
248104 AACTGTCTCAAGCGAGACAAAATTTGCTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
248169 TCGAGTGA
66 TCGAGTGA
*
248177 AACTGTATCAAGCGAGAC-AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
248241 TCGAGTGA
66 TCGAGTGA
*
248249 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
248306 TTGCTATTTG
Statistics
Matches: 264, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
72 70 0.27
73 173 0.66
74 21 0.08
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (73 bp):
AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
TCGAGTGA
Found at i:248256 original size:145 final size:146
Alignment explanation
Indices: 247957--248305 Score: 610
Period size: 145 Copynumber: 2.4 Consensus size: 146
247947 AACTCGAAAT
* * *
247957 AACTGTCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAA-ATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
*
248022 TTCAAGTGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
65 TTCAAGTGAAACTGTATCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
248087 AATTCTGTTTCGAGTGA
130 AATTCTGTTTCGAGTGA
*
248104 AACTGTCTCAAGCGAGACAAAATTTGCTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
*
248169 TCGAGTGAAACTGTATCAAGCGAGAC-AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
66 TCAAGTGAAACTGTATCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
*
248233 GTTCTGTTTCGAGTGA
131 ATTCTGTTTCGAGTGA
*
248249 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
1 AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
248306 TTGCTATTTG
Statistics
Matches: 193, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
145 108 0.56
146 64 0.33
147 21 0.11
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (146 bp):
AACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
TCAAGTGAAACTGTATCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
ATTCTGTTTCGAGTGA
Found at i:250531 original size:76 final size:76
Alignment explanation
Indices: 250395--250569 Score: 226
Period size: 76 Copynumber: 2.3 Consensus size: 76
250385 ATGATGATAT
* * * *
250395 GGGCCTTCAGCATGCCCCAACA-TTAGCTAATATAAGTGTTCAAAATGCATCAACAGTCCTGATT
1 GGGCTTTCAGCATGCCCCAACATTTAGCTAATATAAATATTCAAAATACATCAACAGTCCTGATT
250459 CTGATTGAAAG
66 CTGATTGAAAG
* * * * * *
250470 GGGCTTTCAGCATGCCCCAACATTTTGTTGATATAAATATTCAAAATACTTCAATATTCCTGATT
1 GGGCTTTCAGCATGCCCCAACATTTAGCTAATATAAATATTCAAAATACATCAACAGTCCTGATT
250535 CTGATTGAAAG
66 CTGATTGAAAG
* * *
250546 GGGTTTTCATCATGCCACAACATT
1 GGGCTTTCAGCATGCCCCAACATT
250570 CGCTTCTTGT
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
75 21 0.24
76 65 0.76
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (76 bp):
GGGCTTTCAGCATGCCCCAACATTTAGCTAATATAAATATTCAAAATACATCAACAGTCCTGATT
CTGATTGAAAG
Found at i:251550 original size:31 final size:31
Alignment explanation
Indices: 251507--251569 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
251497 AGATGTGGTC
*
251507 TGAATTCATCAATTGCAGAGTTGACAGATTT
1 TGAAATCATCAATTGCAGAGTTGACAGATTT
251538 TGAAATCATCAATTGCAGAGTTGACAGATTT
1 TGAAATCATCAATTGCAGAGTTGACAGATTT
251569 T
1 T
251570 ATATGTGCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (31 bp):
TGAAATCATCAATTGCAGAGTTGACAGATTT
Found at i:258287 original size:29 final size:29
Alignment explanation
Indices: 258255--258311 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
258245 ATTTTAAAAT
*
258255 TATAATTATGAAA-AATATATTAATTTATA
1 TATAATTAT-AAATAAAATATTAATTTATA
* *
258284 TATATTTATAAATAAAATATTTATTTAT
1 TATAATTATAAATAAAATATTAATTTAT
258312 TAGAATATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TATAATTATAAATAAAATATTAATTTATA
Done.