Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003373.1 Hibiscus syriacus cultivar Beakdansim tig00007087_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: 98699
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1007 original size:35 final size:35
Alignment explanation
Indices: 922--1013 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 35
912 TATGATGATG
* * * *
922 AATTAT-AAATGTTTATAATTATCAGATGATTTTC
1 AATTATCAAATATTTACAGTTATCAGATGATTTAC
956 AATTATCAAATATTTACAGTTATCAGATG-TTTAC
1 AATTATCAAATATTTACAGTTATCAGATGATTTAC
* * *
990 AGTTATCATATGTTTTACAGTTAT
1 AATTATCAAAT-ATTTACAGTTAT
1014 TACACGTAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
34 19 0.39
35 30 0.61
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
AATTATCAAATATTTACAGTTATCAGATGATTTAC
Found at i:1008 original size:18 final size:17
Alignment explanation
Indices: 930--1013 Score: 87
Period size: 17 Copynumber: 4.8 Consensus size: 17
920 TGAATTATAA
* *
930 ATGTTTATAATTATCAG
1 ATGTTTACAGTTATCAG
* * *
947 ATGATTTTCAATTATCAA
1 ATG-TTTACAGTTATCAG
*
965 ATATTTACAGTTATCAG
1 ATGTTTACAGTTATCAG
*
982 ATGTTTACAGTTATCAT
1 ATGTTTACAGTTATCAG
999 ATGTTTTACAGTTAT
1 ATG-TTTACAGTTAT
1014 TACACGTAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
17 32 0.57
18 24 0.43
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (17 bp):
ATGTTTACAGTTATCAG
Found at i:6180 original size:2 final size:2
Alignment explanation
Indices: 6173--6204 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
6163 TTTAATAAGT
6173 TC TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6205 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:6193 original size:15 final size:15
Alignment explanation
Indices: 6173--6201 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6163 TTTAATAAGT
6173 TCTCTCTCTCTCTCC
1 TCTCTCTCTCTCTCC
6188 TCTCTCTCTCTCTC
1 TCTCTCTCTCTCTC
6202 TCTATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (15 bp):
TCTCTCTCTCTCTCC
Found at i:9015 original size:24 final size:23
Alignment explanation
Indices: 8972--9027 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
8962 AGCAACTAAT
* *
8972 GAAATTTGAAGATTAGAATTTTA
1 GAAATTTTAAGATTAAAATTTTA
8995 GAAATTTTAAGAATTAAAATTTTA
1 GAAATTTTAAG-ATTAAAATTTTA
**
9019 TTAATTTTA
1 GAAATTTTA
9028 GAGTGACTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (23 bp):
GAAATTTTAAGATTAAAATTTTA
Found at i:13131 original size:66 final size:66
Alignment explanation
Indices: 13020--13152 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
13010 ACAACAACCT
* *
13020 AGCAGACCTCTCTACCAATGCATTCACAAACACTAAATCATCCCACATGCCAACATTCACACAGG
1 AGCAAACCTCTCTACCAATGCATTCACAAACACTAAATCATCCCACATGCCAAAATTCACACAGG
13085 A
66 A
*
13086 AGCAAACCTCTCTACCAATGCATTCATAAACACTAAATCATCCCACATGCCAAAATTCACACAGG
1 AGCAAACCTCTCTACCAATGCATTCACAAACACTAAATCATCCCACATGCCAAAATTCACACAGG
13151 A
66 A
13152 A
1 A
13153 TTTCAGGGGG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.40, C:0.33, G:0.08, T:0.19
Consensus pattern (66 bp):
AGCAAACCTCTCTACCAATGCATTCACAAACACTAAATCATCCCACATGCCAAAATTCACACAGG
A
Found at i:25771 original size:28 final size:27
Alignment explanation
Indices: 25741--25807 Score: 86
Period size: 24 Copynumber: 2.6 Consensus size: 27
25731 AAAATAGTAA
*
25741 AAAATATATTTTTGTTGATTAATTATG
1 AAAATATATTTTTGTTGATTAACTATG
*
25768 AAAAT-TA--TTAGTTGATTAACTATG
1 AAAATATATTTTTGTTGATTAACTATG
*
25792 AACATATATTTTTGTT
1 AAAATATATTTTTGTT
25808 TTATTGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
24 19 0.58
25 2 0.06
26 2 0.06
27 10 0.30
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.49
Consensus pattern (27 bp):
AAAATATATTTTTGTTGATTAACTATG
Found at i:35708 original size:61 final size:60
Alignment explanation
Indices: 35624--35745 Score: 199
Period size: 61 Copynumber: 2.0 Consensus size: 60
35614 GTCCAAGCTG
* * * *
35624 GACGTTAACCCGCTGATTGAAATATAATAAATCTGATCCCAAAAATTATTTGAATTATATA
1 GACGGTAACCCGCTGACTAAAATATAATAAATCTAATCCC-AAAATTATTTGAATTATATA
35685 GACGGTAACCCGCTGACTAAAATATAATAAATCTAATCCCAAAATTATTTGAATTATATA
1 GACGGTAACCCGCTGACTAAAATATAATAAATCTAATCCCAAAATTATTTGAATTATATA
35745 G
1 G
35746 TCGTTTGAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
60 21 0.37
61 36 0.63
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (60 bp):
GACGGTAACCCGCTGACTAAAATATAATAAATCTAATCCCAAAATTATTTGAATTATATA
Found at i:36140 original size:61 final size:60
Alignment explanation
Indices: 36058--36179 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 60
36048 GTCCAAGCTG
* * *
36058 GACGTTAACCCGCTGATTGAAATATAATAAATCTGATCCCAAAAATTATTTGAATTATATA
1 GACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCC-AAAATTATTTGAATTATATA
36119 GACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAATTATATA
1 GACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAATTATATA
36179 G
1 G
36180 TCGTTTGAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
60 21 0.36
61 37 0.64
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (60 bp):
GACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAATTATATA
Found at i:36573 original size:61 final size:60
Alignment explanation
Indices: 36491--36612 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 60
36481 GTCCAAGCTG
* * *
36491 GACGTTAACCCGCTGATTGAAATATAATAAATCTGATCCCAAAAATTATTTGAATTATATA
1 GACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCC-AAAATTATTTGAATTATATA
36552 GACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAATTATATA
1 GACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAATTATATA
36612 G
1 G
36613 TCGTTTGAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
60 21 0.36
61 37 0.64
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (60 bp):
GACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAATTATATA
Found at i:36643 original size:433 final size:434
Alignment explanation
Indices: 35521--37246 Score: 3382
Period size: 434 Copynumber: 4.0 Consensus size: 434
35511 GGTGTTACTT
35521 GTTTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTA
1 GTTTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTA
35586 ATCCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAA
66 ATCCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAA
*
35651 TAAATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTAAAATATAATAAA
131 TAAATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAA
35716 TCTAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATC
196 TCTAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATC
*
35781 TCAGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTTTTAACGAAAAAGGACAAGTTTG
261 TCAGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTG
*
35846 AAACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTCGGGAGACTCTACAAAGTAGT
326 AAACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGT
35911 ATCCTATAGTTAAAGGACTATTTTATAATTTTTAAAGGACTATA
391 ATCCTATAGTTAAAGGACTATTTTATAATTTTTAAAGGACTATA
35955 GTTTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTA
1 GTTTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTA
36020 ATCCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAA
66 ATCCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAA
36085 TAAATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAA
131 TAAATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAA
36150 TCTAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATC
196 TCTAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATC
*
36215 TCAGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTTTTAACGAAAAAGGACAAGTTTG
261 TCAGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTG
36280 AAACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGT
326 AAACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGT
36345 ATCCTATAGTTAAAGGACTATTTTATAATTTTTAAAGGACTATA
391 ATCCTATAGTTAAAGGACTATTTTATAATTTTTAAAGGACTATA
36389 G-TTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTA
1 GTTTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTA
36453 ATCCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAA
66 ATCCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAA
36518 TAAATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAA
131 TAAATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAA
36583 TCTAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATC
196 TCTAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATC
36648 TCAGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTG
261 TCAGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTG
36713 AAACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGT
326 AAACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGT
36778 ATCCTATAGTTAAAGGACTATTTTATAATTTTTAAAGGACTATA
391 ATCCTATAGTTAAAGGACTATTTTATAATTTTTAAAGGACTATA
36822 GTTTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTA
1 GTTTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTA
* * *
36887 ATCCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAAACCGCCGACTGAAATATAA
66 ATCCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAA
36952 TAAATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAA
131 TAAATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAA
37017 TCTAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATC
196 TCTAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATC
37082 TCAGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTG
261 TCAGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTG
37147 AAACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGT
326 AAACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGT
37212 ATCCTATAGTTAAAGGACTATTTTATAATTTTTAA
391 ATCCTATAGTTAAAGGACTATTTTATAATTTTTAA
37247 TAATTAAGGG
Statistics
Matches: 1285, Mismatches: 6, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
433 432 0.34
434 853 0.66
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (434 bp):
GTTTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTA
ATCCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAA
TAAATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAA
TCTAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATC
TCAGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTG
AAACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGT
ATCCTATAGTTAAAGGACTATTTTATAATTTTTAAAGGACTATA
Found at i:37013 original size:61 final size:60
Alignment explanation
Indices: 36925--37046 Score: 199
Period size: 61 Copynumber: 2.0 Consensus size: 60
36915 GTCCAAGCTG
* *
36925 GACGTTAAACCGCCGACTGAAATATAATAAATCTGATCCCAAAAATTATTTGAATTATATA
1 GACGGTAAACCGCCGACTGAAATATAATAAATCTAATCCC-AAAATTATTTGAATTATATA
* *
36986 GACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAATTATATA
1 GACGGTAAACCGCCGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAATTATATA
37046 G
1 G
37047 TCGTTTGAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
60 21 0.37
61 36 0.63
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (60 bp):
GACGGTAAACCGCCGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAATTATATA
Found at i:37197 original size:867 final size:867
Alignment explanation
Indices: 35523--37246 Score: 3385
Period size: 867 Copynumber: 2.0 Consensus size: 867
35513 TGTTACTTGT
35523 TTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTAAT
1 TTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTAAT
35588 CCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAATA
66 CCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAATA
35653 AATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTAAAATATAATAAATC
131 AATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTAAAATATAATAAATC
35718 TAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATCTC
196 TAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATCTC
*
35783 AGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTTTTAACGAAAAAGGACAAGTTTGAA
261 AGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTGAA
35848 ACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTCGGGAGACTCTACAAAGTAGTAT
326 ACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTCGGGAGACTCTACAAAGTAGTAT
35913 CCTATAGTTAAAGGACTATTTTATAATTTTTAAAGGACTATAGTTTTAGTCTCTCGACTATTAAA
391 CCTATAGTTAAAGGACTATTTTATAATTTTTAAAGGACTATAGTTTTAGTCTCTCGACTATTAAA
35978 AGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTAATCCTTTTTTGTTGAAAATTTGA
456 AGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTAATCCTTTTTTGTTGAAAATTTGA
* * *
36043 CGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAATAAATCTGATCCCAAAAATTATT
521 CGGTCGTCCAAGCTGGACGTTAAACCGCCGACTGAAATATAATAAATCTGATCCCAAAAATTATT
36108 TGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAAT
586 TGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAAT
36173 TATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATCTCAGTCAGTACGTTAATATTCAA
651 TATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATCTCAGTCAGTACGTTAATATTCAA
*
36238 TTCAGACAATCACTAATTTTTTAACGAAAAAGGACAAGTTTGAAACATATGAGTTATCATATGAC
716 TTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTGAAACATATGAGTTATCATATGAC
36303 CATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGTATCCTATAGTTAAAGGACTATTT
781 CATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGTATCCTATAGTTAAAGGACTATTT
36368 TATAATTTTTAAAGGACTATAG
846 TATAATTTTTAAAGGACTATAG
36390 TTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTAAT
1 TTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTAAT
36455 CCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAATA
66 CCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAATA
*
36520 AATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAATC
131 AATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTAAAATATAATAAATC
36585 TAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATCTC
196 TAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATCTC
36650 AGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTGAA
261 AGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTGAA
*
36715 ACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGTAT
326 ACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTCGGGAGACTCTACAAAGTAGTAT
36780 CCTATAGTTAAAGGACTATTTTATAATTTTTAAAGGACTATAGTTTTAGTCTCTCGACTATTAAA
391 CCTATAGTTAAAGGACTATTTTATAATTTTTAAAGGACTATAGTTTTAGTCTCTCGACTATTAAA
36845 AGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTAATCCTTTTTTGTTGAAAATTTGA
456 AGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTAATCCTTTTTTGTTGAAAATTTGA
36910 CGGTCGTCCAAGCTGGACGTTAAACCGCCGACTGAAATATAATAAATCTGATCCCAAAAATTATT
521 CGGTCGTCCAAGCTGGACGTTAAACCGCCGACTGAAATATAATAAATCTGATCCCAAAAATTATT
36975 TGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAAT
586 TGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAAT
37040 TATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATCTCAGTCAGTACGTTAATATTCAA
651 TATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATCTCAGTCAGTACGTTAATATTCAA
37105 TTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTGAAACATATGAGTTATCATATGAC
716 TTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTGAAACATATGAGTTATCATATGAC
37170 CATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGTATCCTATAGTTAAAGGACTATTT
781 CATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGTATCCTATAGTTAAAGGACTATTT
37235 TATAATTTTTAA
846 TATAATTTTTAA
37247 TAATTAAGGG
Statistics
Matches: 850, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
867 850 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (867 bp):
TTTAGTCTCTCGACTATTAAAAGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTAAT
CCTTTTTTGTTGAAAATTTGACGGTCGTCCAAGCTGGACGTTAACCCGCTGATTGAAATATAATA
AATCTGATCCCAAAAATTATTTGAATTATATAGACGGTAACCCGCTGACTAAAATATAATAAATC
TAATCCCAAAATTATTTGAATTATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATCTC
AGTCAGTACGTTAATATTCAATTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTGAA
ACATATGAGTTATCATATGACCATTTTGTAATTTTTAGTAGTCGGGAGACTCTACAAAGTAGTAT
CCTATAGTTAAAGGACTATTTTATAATTTTTAAAGGACTATAGTTTTAGTCTCTCGACTATTAAA
AGTTACAAAATTGTTACTTGACTATTCATATGTTCTAAACTAATCCTTTTTTGTTGAAAATTTGA
CGGTCGTCCAAGCTGGACGTTAAACCGCCGACTGAAATATAATAAATCTGATCCCAAAAATTATT
TGAATTATATAGACGGTAACCCGCTGACTGAAATATAATAAATCTAATCCCAAAATTATTTGAAT
TATATAGTCGTTTGAGATTTTGAGATCATATTTTATCATATCTCAGTCAGTACGTTAATATTCAA
TTCAGACAATCACTAATTTATTAACGAAAAAGGACAAGTTTGAAACATATGAGTTATCATATGAC
CATTTTGTAATTTTTAGTAGTTGGGAGACTCTACAAAGTAGTATCCTATAGTTAAAGGACTATTT
TATAATTTTTAAAGGACTATAG
Found at i:38018 original size:17 final size:17
Alignment explanation
Indices: 37989--38021 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
37979 TGAATCATTC
37989 TATATTTATATAATTTT
1 TATATTTATATAATTTT
38006 TATATGTTA-ATAATTT
1 TATAT-TTATATAATTT
38022 GTATTGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TATATTTATATAATTTT
Found at i:40527 original size:12 final size:12
Alignment explanation
Indices: 40512--40536 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40502 TAATCTCAAA
40512 GTTAATTTCTTT
1 GTTAATTTCTTT
40524 GTTAATTTCTTT
1 GTTAATTTCTTT
40536 G
1 G
40537 ATTTCACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.12, T:0.64
Consensus pattern (12 bp):
GTTAATTTCTTT
Found at i:40643 original size:41 final size:41
Alignment explanation
Indices: 40586--40707 Score: 226
Period size: 41 Copynumber: 3.0 Consensus size: 41
40576 GAGACAGCGG
40586 ATGTCAACGGAAATGATTGACAATGTCTCATTAACCTTCAT
1 ATGTCAACGGAAATGATTGACAATGTCTCATTAACCTTCAT
*
40627 ATGTCAACGGAAATGATTGACAATGTATCATTAACCTTCAT
1 ATGTCAACGGAAATGATTGACAATGTCTCATTAACCTTCAT
*
40668 ATGTCAACGGAAATGATTAACAATGTCTCATTAACCTTCA
1 ATGTCAACGGAAATGATTGACAATGTCTCATTAACCTTCA
40708 ACATATGATT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 78 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (41 bp):
ATGTCAACGGAAATGATTGACAATGTCTCATTAACCTTCAT
Found at i:41421 original size:59 final size:59
Alignment explanation
Indices: 41270--41407 Score: 206
Period size: 59 Copynumber: 2.3 Consensus size: 59
41260 GAATCTCCTA
* * **
41270 ACTATTAAAAGTTACAAAATGATCCATCAATTATAAGATGTTGTTTTATTGAGTTATTG
1 ACTATTAAAAGTTATAAAATGATCCATCAACTATAAGATGTTGTTTTATTGAGTTACCG
* *
41329 ACTATTAAAAGTTATAAAATGATCCTTCAACTATAGGATGTTGTTTTATTGAGTCT-CCG
1 ACTATTAAAAGTTATAAAATGATCCATCAACTATAAGATGTTGTTTTATTGAGT-TACCG
41388 ACTATTAAAAGTTATAAAAT
1 ACTATTAAAAGTTATAAAAT
41408 AATCACCTCA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
59 71 0.99
60 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (59 bp):
ACTATTAAAAGTTATAAAATGATCCATCAACTATAAGATGTTGTTTTATTGAGTTACCG
Found at i:51493 original size:17 final size:16
Alignment explanation
Indices: 51476--51524 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
51466 TGAATTTTTA
51476 AAATAAAATAATTATT
1 AAATAAAATAATTATT
* *
51492 AAATTAATTAAATTATT
1 AAATAAAAT-AATTATT
51509 --ATAAAAT-ATTATT
1 AAATAAAATAATTATT
51522 AAA
1 AAA
51525 ATATTATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 6 0.23
15 6 0.23
16 7 0.27
17 7 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATAAAATAATTATT
Found at i:51503 original size:21 final size:21
Alignment explanation
Indices: 51479--51537 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
51469 ATTTTTAAAA
*
51479 TAAAATAATTATTAAAT-TAAT
1 TAAAAT-ATTATAAAATATAAT
* *
51500 TAAATTATTATAAAATATTAT
1 TAAAATATTATAAAATATAAT
51521 TAAAATATTATAAAATA
1 TAAAATATTATAAAATA
51538 GCTATTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.27
21 24 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAAATATTATAAAATATAAT
Found at i:51547 original size:21 final size:20
Alignment explanation
Indices: 51498--51556 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
51488 TATTAAATTA
*
51498 ATTAAATTATTATAAAATATT
1 ATTAAA-TATTATAAAATACT
51519 ATTAAAATATTATAAAATAGCT
1 ATT-AAATATTATAAAATA-CT
*
51541 ATTAAAT-TTATTAAAT
1 ATTAAATATTATAAAAT
51557 TGTTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 8 0.24
21 19 0.56
22 7 0.21
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTAAATATTATAAAATACT
Found at i:51554 original size:9 final size:10
Alignment explanation
Indices: 51481--51623 Score: 69
Period size: 11 Copynumber: 13.9 Consensus size: 10
51471 TTTTAAAATA
51481 AAATAATTATT
1 AAAT-ATTATT
*
51492 AAAT-TAATT
1 AAATATTATT
*
51501 AAATTATTATA
1 AAA-TATTATT
51512 AAATATTATT
1 AAATATTATT
*
51522 AAAATATTATA
1 -AAATATTATT
*
51533 AAATAGCTATT
1 AAATA-TTATT
51544 AAAT-TTATT
1 AAATATTATT
* *
51553 AAATTGTTATA
1 AAA-TATTATT
*
51564 AAATAGTCATT
1 AAATA-TTATT
* * * *
51575 CATTTTTATC
1 AAATATTATT
*
51585 AAATTACTA-T
1 AAA-TATTATT
51595 AAATAATTATT
1 AAAT-ATTATT
*
51606 AGAT-TTATT
1 AAATATTATT
51615 AAATATTAT
1 AAATATTAT
51624 AGCCATTACA
Statistics
Matches: 96, Mismatches: 25, Indels: 23
0.67 0.17 0.16
Matches are distributed among these distances:
9 23 0.24
10 28 0.29
11 45 0.47
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (10 bp):
AAATATTATT
Found at i:51567 original size:20 final size:21
Alignment explanation
Indices: 51500--51568 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
51490 TTAAATTAAT
* *
51500 TAAATTATTATAAAATA-TTA
1 TAAAATATTATAAAATAGCTA
51520 TTAAAATATTATAAAATAGCTA
1 -TAAAATATTATAAAATAGCTA
* * * *
51542 TTAAAT-TTATTAAATTGTTA
1 TAAAATATTATAAAATAGCTA
51562 TAAAATA
1 TAAAATA
51569 GTCATTCATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 16 0.41
21 21 0.54
22 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (21 bp):
TAAAATATTATAAAATAGCTA
Found at i:57582 original size:43 final size:41
Alignment explanation
Indices: 57533--57738 Score: 175
Period size: 43 Copynumber: 4.9 Consensus size: 41
57523 GAAAGTGTGG
57533 TTAAAAAATTAGGGGTTCAATTATAAAGGTAAAAAGTGAAA
1 TTAAAAAATTAGGGGTTCAATTATAAAGGTAAAAAGTGAAA
** * *
57574 TTGAAAAAATTAGGGACCTCAATTATAAAGG-AAAAA-TTAGGA
1 TT-AAAAAATTAGGG-GTTCAATTATAAAGGTAAAAAGTGA-AA
* **
57616 TTAAAAAAATTAGAGGTAT-AATTTATAAAGGTAAAAAGTGGGA
1 TT-AAAAAATTAGGGGT-TCAA-TTATAAAGGTAAAAAGTGAAA
** * *
57659 TTGAAAATTTTAAGGGTTTCAATTATAAAGGTAACAAGTGAAA
1 TT-AAAAAATT-AGGGGTTCAATTATAAAGGTAAAAAGTGAAA
* * *
57702 TTACAAAAATTAAGAGTCTCAATTATAAAAGTAAAAA
1 TTA-AAAAATTAGGGGT-TCAATTATAAAGGTAAAAA
57739 TTTAAAATTT
Statistics
Matches: 129, Mismatches: 25, Indels: 20
0.74 0.14 0.11
Matches are distributed among these distances:
41 6 0.05
42 45 0.35
43 71 0.55
44 7 0.05
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.28
Consensus pattern (41 bp):
TTAAAAAATTAGGGGTTCAATTATAAAGGTAAAAAGTGAAA
Found at i:57689 original size:85 final size:84
Alignment explanation
Indices: 57479--57665 Score: 213
Period size: 84 Copynumber: 2.2 Consensus size: 84
57469 ATTAAATGTA
* * * * *
57479 AAAAAGT-AAGATTAAAAAAATTAGGGACCTTAGTTCTAAAAGGAGAAAGTGT-GG-TT-AAAAA
1 AAAAAGTGAA-ATTGAAAAAATTAGGGACCTCAATTAT-AAAGGA-AAAAT-TAGGATTAAAAAA
*
57540 ATTAGGGGTTCAATTATAAAGGT
62 ATTAGAGGTTCAATTATAAAGGT
57563 AAAAAGTGAAATTGAAAAAATTAGGGACCTCAATTATAAAGGAAAAATTAGGATTAAAAAAATTA
1 AAAAAGTGAAATTGAAAAAATTAGGGACCTCAATTATAAAGGAAAAATTAGGATTAAAAAAATTA
57628 GAGGTAT-AATTTATAAAGGT
66 GAGGT-TCAA-TTATAAAGGT
**
57648 AAAAAGTGGGATTGAAAA
1 AAAAAGTGAAATTGAAAA
57666 TTTTAAGGGT
Statistics
Matches: 89, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
81 1 0.01
82 6 0.07
83 8 0.09
84 45 0.51
85 29 0.33
ACGTcount: A:0.50, C:0.04, G:0.21, T:0.25
Consensus pattern (84 bp):
AAAAAGTGAAATTGAAAAAATTAGGGACCTCAATTATAAAGGAAAAATTAGGATTAAAAAAATTA
GAGGTTCAATTATAAAGGT
Found at i:60401 original size:2 final size:2
Alignment explanation
Indices: 60394--60422 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60384 GAATAGTACA
60394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60423 GATTACATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61034 original size:17 final size:17
Alignment explanation
Indices: 61012--61061 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
61002 TGTTAAACAG
*
61012 GCTTTTAAACAGGTCAA
1 GCTTTTAAACAAGTCAA
*
61029 GCTTTTAAACATA-CCAA
1 GCTTTTAAACA-AGTCAA
61046 GCTTTTAAACAAGTCA
1 GCTTTTAAACAAGTCA
61062 GGTCATGCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 1 0.04
17 27 0.96
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (17 bp):
GCTTTTAAACAAGTCAA
Found at i:62599 original size:31 final size:32
Alignment explanation
Indices: 62518--62628 Score: 93
Period size: 32 Copynumber: 3.5 Consensus size: 32
62508 TGATTATTGA
* * *
62518 ATCGGTTGTTTTTC-GGTTTGGGTTAATACCAG
1 ATCGGTTGATTTTCGGGTCT-GATTAATACCAG
* *
62550 ATCGGTTGATTTTTGGGTCTGATTAATA-CAT
1 ATCGGTTGATTTTCGGGTCTGATTAATACCAG
* * * * *
62581 ATCGGTTAGA-TTTCGGGTCGGGTCAATATCGG
1 ATCGGTT-GATTTTCGGGTCTGATTAATACCAG
62613 ATCGGTTGATTTTCGG
1 ATCGGTTGATTTTCGG
62629 TTTAGGTCGA
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
31 25 0.39
32 35 0.55
33 4 0.06
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.41
Consensus pattern (32 bp):
ATCGGTTGATTTTCGGGTCTGATTAATACCAG
Found at i:63268 original size:18 final size:18
Alignment explanation
Indices: 63216--63271 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
63206 TTAAACTTTC
63216 TATT-ATTTTATTATAAAT
1 TATTAATTTTATT-TAAAT
* * *
63234 ATAATATTTTTA-ATAAAT
1 -TATTAATTTTATTTAAAT
63252 TATTAATTTTATTTAAAT
1 TATTAATTTTATTTAAAT
63270 TA
1 TA
63272 ATTTAATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 9 0.31
18 12 0.41
19 3 0.10
20 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTAATTTTATTTAAAT
Found at i:63442 original size:21 final size:21
Alignment explanation
Indices: 63418--63457 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
63408 TTCGAGTTGC
63418 TTTTGGTTCGGGTTAATTTAG
1 TTTTGGTTCGGGTTAATTTAG
*
63439 TTTTTGTTCGGGTTAATTT
1 TTTTGGTTCGGGTTAATTT
63458 CGGTTCTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.05, G:0.25, T:0.57
Consensus pattern (21 bp):
TTTTGGTTCGGGTTAATTTAG
Found at i:67047 original size:21 final size:20
Alignment explanation
Indices: 67023--67082 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
67013 ACTTTGAAAA
67023 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
67044 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
67058 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
67079 AAAT
1 AAAT
67083 ACTTCTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 3 0.10
21 10 0.33
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.43
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:67068 original size:35 final size:35
Alignment explanation
Indices: 67022--67136 Score: 142
Period size: 35 Copynumber: 3.2 Consensus size: 35
67012 AACTTTGAAA
67022 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
* **
67057 AAAATGGTTTTCAAAGTTTGGTAAATACTTCTTTG
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
67092 AAAAATAGCTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 -AAAAT-GATTTTCAAAGTTTGGTAAATGTTTCTTTG
67128 AAAAATGAT
1 -AAAATGAT
67137 AATGGGATAA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
35 34 0.49
36 14 0.20
37 21 0.30
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (35 bp):
AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:71239 original size:15 final size:15
Alignment explanation
Indices: 71216--71246 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
71206 TGTTACGGAA
*
71216 GCCATTAAGGAGATG
1 GCCAGTAAGGAGATG
71231 GCCAGTAAGGAGATG
1 GCCAGTAAGGAGATG
71246 G
1 G
71247 TTTGGCTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.39, T:0.16
Consensus pattern (15 bp):
GCCAGTAAGGAGATG
Found at i:71698 original size:35 final size:37
Alignment explanation
Indices: 71639--71755 Score: 134
Period size: 35 Copynumber: 3.3 Consensus size: 37
71629 GGCAACCAAC
* *
71639 TTTGAAAAA-ATGATTTTAAAGTTTGGTAAATGTTTA
1 TTTGAAAAATAGGTTTTTAAAGTTTGGTAAATGTTTA
*
71675 TTTG-AAAAT-GGTTTTTAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATAGGTTTTTAAAGTTTGGTAAATGTTTA
* ** *
71710 TTTGAAAAATAGTTTTTTAAAGTTAAGTAGATGTTT-
1 TTTGAAAAATAGGTTTTTAAAGTTTGGTAAATGTTTA
*
71746 GTTGAAAAAT
1 TTTGAAAAAT
71756 GATAATGTGA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
35 31 0.44
36 18 0.26
37 21 0.30
ACGTcount: A:0.36, C:0.01, G:0.18, T:0.45
Consensus pattern (37 bp):
TTTGAAAAATAGGTTTTTAAAGTTTGGTAAATGTTTA
Found at i:73507 original size:2 final size:2
Alignment explanation
Indices: 73500--73529 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
73490 AAAAGTCTAA
73500 AT AT 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 AT AT
73530 CAAAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76261 original size:169 final size:169
Alignment explanation
Indices: 75982--76324 Score: 686
Period size: 169 Copynumber: 2.0 Consensus size: 169
75972 CAATTCAATC
75982 ATAACATGTGCACTAACGGTGTTGATCATAAGGTACACGAATGTACTATCGTTGAACTGATAACT
1 ATAACATGTGCACTAACGGTGTTGATCATAAGGTACACGAATGTACTATCGTTGAACTGATAACT
76047 GAAAAGTACTCAACTTAATAGCATGTCAAATATACCTACGACTCTCAATGCAACATAAAATGGAC
66 GAAAAGTACTCAACTTAATAGCATGTCAAATATACCTACGACTCTCAATGCAACATAAAATGGAC
76112 TTATATACCACAATAAATTCATTTATAAATCAACATTTG
131 TTATATACCACAATAAATTCATTTATAAATCAACATTTG
76151 ATAACATGTGCACTAACGGTGTTGATCATAAGGTACACGAATGTACTATCGTTGAACTGATAACT
1 ATAACATGTGCACTAACGGTGTTGATCATAAGGTACACGAATGTACTATCGTTGAACTGATAACT
76216 GAAAAGTACTCAACTTAATAGCATGTCAAATATACCTACGACTCTCAATGCAACATAAAATGGAC
66 GAAAAGTACTCAACTTAATAGCATGTCAAATATACCTACGACTCTCAATGCAACATAAAATGGAC
76281 TTATATACCACAATAAATTCATTTATAAATCAACATTTG
131 TTATATACCACAATAAATTCATTTATAAATCAACATTTG
76320 ATAAC
1 ATAAC
76325 TATAAACGTT
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 174 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (169 bp):
ATAACATGTGCACTAACGGTGTTGATCATAAGGTACACGAATGTACTATCGTTGAACTGATAACT
GAAAAGTACTCAACTTAATAGCATGTCAAATATACCTACGACTCTCAATGCAACATAAAATGGAC
TTATATACCACAATAAATTCATTTATAAATCAACATTTG
Found at i:78715 original size:18 final size:18
Alignment explanation
Indices: 78692--78749 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
78682 TCTTTAAAAA
78692 AATTATATATAATTTAAT
1 AATTATATATAATTTAAT
*
78710 AATTATATAT-ATAT-AT
1 AATTATATATAATTTAAT
78726 -A-TATATAATAATTTAAAT
1 AATTATAT-ATAATTT-AAT
78744 AATTAT
1 AATTAT
78750 TAATAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 5 0.16
15 3 0.09
16 5 0.16
17 3 0.09
18 12 0.38
19 1 0.03
20 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTATATATAATTTAAT
Found at i:79590 original size:22 final size:23
Alignment explanation
Indices: 79560--79605 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
79550 TGATTTAGTG
*
79560 CTGATTGATTCAGTA-AAAAGTA
1 CTGAATGATTCAGTACAAAAGTA
*
79582 CTGAATGATTCAGTACAGAAGTA
1 CTGAATGATTCAGTACAAAAGTA
79605 C
1 C
79606 ATTATGAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (23 bp):
CTGAATGATTCAGTACAAAAGTA
Found at i:80357 original size:22 final size:21
Alignment explanation
Indices: 80324--80365 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
80314 TTAGTTCGGA
*
80324 TTTAAATCAAACTTATAAAAC
1 TTTAAATAAAACTTATAAAAC
80345 TTTATAATAAAACTTATAAAA
1 TTTA-AATAAAACTTATAAAA
80366 AATATATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (21 bp):
TTTAAATAAAACTTATAAAAC
Found at i:92628 original size:12 final size:13
Alignment explanation
Indices: 92611--92640 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
92601 ACATTTACTT
92611 TTAATTG-AAAAA
1 TTAATTGAAAAAA
92623 TTAATTGAAAAAA
1 TTAATTGAAAAAA
92636 TTAAT
1 TTAAT
92641 GTATCTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
TTAATTGAAAAAA
Done.