Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007860.1 Hibiscus syriacus cultivar Beakdansim tig00110223_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: 2941097
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 16
Found at i:2194380 original size:20 final size:19
Alignment explanation
Indices: 2194355--2194404 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2194345 TGAAAAGATT
2194355 TAATAAAATAAAATA-GATAA
1 TAATAAAATAAAA-AGGA-AA
2194375 TAAT-AAATAAAAAGGGAAA
1 TAATAAAATAAAAA-GGAAA
2194394 TAATAAAATAA
1 TAATAAAATAA
2194405 TAAATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 14 0.52
20 12 0.44
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (19 bp):
TAATAAAATAAAAAGGAAA
Found at i:2195151 original size:71 final size:74
Alignment explanation
Indices: 2195065--2195257 Score: 250
Period size: 76 Copynumber: 2.6 Consensus size: 74
2195055 AGCTAAAACA
* *
2195065 TCTTAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCT-AA-AAA-ATAATAT-T
1 TCTT-AATCCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAAACAAAGATAAAATAT
*
2195126 TAAAATAATAT
64 AAAAATAATAT
2195137 TCTTAATCCTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAACAAAGATAAAATAT
1 TCTTAATCCTAATTAAAATACTAAAAC-TATTTAAACTAAAATACCT-AAACAAAGATAAAATAT
2195202 AAAAATAATAT
64 AAAAATAATAT
* * * *
2195213 CCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 TCTTAATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATAC
2195258 AAAGATAAAA
Statistics
Matches: 107, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
70 6 0.06
71 35 0.33
72 4 0.04
73 2 0.02
74 3 0.03
75 6 0.06
76 50 0.47
77 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (74 bp):
TCTTAATCCTAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAACAAAGATAAAATATAA
AAATAATAT
Found at i:2195197 original size:25 final size:24
Alignment explanation
Indices: 2195150--2195197 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
2195140 TAATCCTAAT
* **
2195150 TAAAATACTAAAACATATTTAAAC
1 TAAAATACTAAAACAAAGATAAAC
2195174 TAAAATACCTAAAACAAAGATAAA
1 TAAAATA-CTAAAACAAAGATAAA
2195198 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.23
Consensus pattern (24 bp):
TAAAATACTAAAACAAAGATAAAC
Found at i:2195281 original size:76 final size:75
Alignment explanation
Indices: 2195068--2195281 Score: 226
Period size: 76 Copynumber: 2.9 Consensus size: 75
2195058 TAAAACATCT
* * * *
2195068 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC---CTAAAAAATAATATTT-A
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAA
*
2195128 AAATAATATTC
65 AAATAATATCC
* * * * *
2195139 TTAATCCTAATTAAAATACTAAAACATATTTAAACTAAAATACCTAAAACAAAGATA-AA-ATAT
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAAATAAA-ATATAATATTT
2195202 AAAAATAATATCC
63 AAAAATAATATCC
* *
2195215 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAA-ATAAAATATAATATTTAA
2195280 AA
65 AA
2195282 TATTATCGTA
Statistics
Matches: 117, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
70 5 0.04
71 33 0.28
72 1 0.01
74 6 0.05
75 10 0.09
76 60 0.51
77 2 0.02
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (75 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAAA
AATAATATCC
Found at i:2200042 original size:20 final size:20
Alignment explanation
Indices: 2200017--2200066 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
2200007 TGAAAAGATT
**
2200017 TAATAAAATAAAATA-GTTAA
1 TAATAAAATAAAA-AGGGAAA
2200037 TAAT-AAATAAAAAGGGAAA
1 TAATAAAATAAAAAGGGAAA
2200056 TAATAAAATAA
1 TAATAAAATAA
2200067 TAAATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 15 0.58
20 10 0.38
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
TAATAAAATAAAAAGGGAAA
Found at i:2200817 original size:72 final size:73
Alignment explanation
Indices: 2200740--2200966 Score: 244
Period size: 76 Copynumber: 3.1 Consensus size: 73
2200730 TAAAACATCT
* *
2200740 TAAATCCTAATTATAACACATAAAATTATTTAAACTAAAATACATAAAAAA-ATAATATTTAAAA
1 TAAATCCTAATTAAAACAC-TAAAACTATTTAAACTAAAATACATAAAAAATATAATATTTAAAA
*
2200804 A-AATATTC
65 ATAATATCC
* * * **
2200812 TAAATCCTAATTAAAACACTAAAAACTATTTAAACAAAAATACCTAAAACAAATATAAAAAATAA
1 TAAATCCTAATTAAAACACT-AAAACTATTTAAACTAAAATACAT-AAA-AAATATAATATTTAA
2200877 AAATAATATCC
63 AAATAATATCC
* * * * *
2200888 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTT-A
1 TAAATCCTAATTAAAACACTAAAA-CTATTTAAACTAAAATACATA-A-AAAATATAATATTTAA
*
2200952 AAATATTATCC
63 AAATAATATCC
2200963 TAAA
1 TAAA
2200967 CTTGAGTTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
71 1 0.01
72 39 0.30
73 3 0.02
74 3 0.02
75 31 0.24
76 50 0.39
77 1 0.01
ACGTcount: A:0.59, C:0.11, G:0.01, T:0.29
Consensus pattern (73 bp):
TAAATCCTAATTAAAACACTAAAACTATTTAAACTAAAATACATAAAAAATATAATATTTAAAAA
TAATATCC
Found at i:2200909 original size:76 final size:72
Alignment explanation
Indices: 2200731--2200931 Score: 215
Period size: 72 Copynumber: 2.7 Consensus size: 72
2200721 AAAACTAGCT
* * * * *
2200731 AAAACATCTTAAATCCTAATTATAACAC-ATAAAATTATTTAAACTAAAATACATAAAAAAATAA
1 AAAATATCCTAAAACCTAATTAAAACACTA-AAAACTATTTAAACTAAAATACATAAAAAAATAA
* **
2200795 TATTTAAA
65 AAAATAAA
* * * *
2200803 AAAATATTCTAAATCCTAATTAAAACACTAAAAACTATTTAAACAAAAATACCTAAAACAAATAT
1 AAAATATCCTAAAACCTAATTAAAACACTAAAAACTATTTAAACTAAAATACAT-AAA-AAA-AT
2200868 AAAAAATAAA
63 AAAAAATAAA
* * *
2200878 AATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACA
1 AA-AATATCCTAAAACCTAATTAAAACACTAAAAACTATTTAAACTAAAATACA
2200932 AAGATAAAAT
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
72 45 0.42
73 4 0.04
74 3 0.03
75 11 0.10
76 44 0.41
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (72 bp):
AAAATATCCTAAAACCTAATTAAAACACTAAAAACTATTTAAACTAAAATACATAAAAAAATAAA
AAATAAA
Found at i:2201456 original size:20 final size:20
Alignment explanation
Indices: 2201431--2201480 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
2201421 ATTAAAAATG
2201431 GTATCGATACCATCCTTCTT
1 GTATCGATACCATCCTTCTT
2201451 GTATCGATACCATCCTTCTT
1 GTATCGATACCATCCTTCTT
2201471 GTATCGATAC
1 GTATCGATAC
2201481 TACCCATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (20 bp):
GTATCGATACCATCCTTCTT
Found at i:2202349 original size:3 final size:3
Alignment explanation
Indices: 2202329--2202386 Score: 62
Period size: 3 Copynumber: 18.3 Consensus size: 3
2202319 AGAAACTTGA
* * *
2202329 AAT AAT AGT AAT ATT AAT AAT AAT AAT AAT AAAT AAT AAAT ATT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT -AAT
2202377 AAT AAT AAT A
1 AAT AAT AAT A
2202387 TAAATAGCCT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
3 38 0.83
4 8 0.17
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2202377 original size:27 final size:30
Alignment explanation
Indices: 2202328--2202392 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
2202318 CAGAAACTTG
2202328 AAATAATAGTAATATTAATAATAATAATAAT
1 AAATAATAG-AATATTAATAATAATAATAAT
2202359 AAATAATA-AATATTAAATAATAATAAT-AT
1 AAATAATAGAATATT-AATAATAATAATAAT
2202388 AAATA
1 AAATA
2202393 GCCTAGACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 13 0.39
30 12 0.36
31 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (30 bp):
AAATAATAGAATATTAATAATAATAATAAT
Found at i:2203488 original size:168 final size:168
Alignment explanation
Indices: 2203210--2203545 Score: 672
Period size: 168 Copynumber: 2.0 Consensus size: 168
2203200 GTAGAAACAC
2203210 TTAACTATTCAACAATAACAACCAGGAAAAGAAAACCCCAGAGACACAAACGAATGTAGTAACAC
1 TTAACTATTCAACAATAACAACCAGGAAAAGAAAACCCCAGAGACACAAACGAATGTAGTAACAC
2203275 CACGAGCAACATAAACCACGGGCCAAACCATAAAAAAGAACAGACTAGTTCCAAAGCTTAGTACC
66 CACGAGCAACATAAACCACGGGCCAAACCATAAAAAAGAACAGACTAGTTCCAAAGCTTAGTACC
2203340 AAAGCCAATCCACCAAAGCTCCTAAGCTGCTAATAAAA
131 AAAGCCAATCCACCAAAGCTCCTAAGCTGCTAATAAAA
2203378 TTAACTATTCAACAATAACAACCAGGAAAAGAAAACCCCAGAGACACAAACGAATGTAGTAACAC
1 TTAACTATTCAACAATAACAACCAGGAAAAGAAAACCCCAGAGACACAAACGAATGTAGTAACAC
2203443 CACGAGCAACATAAACCACGGGCCAAACCATAAAAAAGAACAGACTAGTTCCAAAGCTTAGTACC
66 CACGAGCAACATAAACCACGGGCCAAACCATAAAAAAGAACAGACTAGTTCCAAAGCTTAGTACC
2203508 AAAGCCAATCCACCAAAGCTCCTAAGCTGCTAATAAAA
131 AAAGCCAATCCACCAAAGCTCCTAAGCTGCTAATAAAA
2203546 AAGGCATACA
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 168 1.00
ACGTcount: A:0.47, C:0.26, G:0.13, T:0.14
Consensus pattern (168 bp):
TTAACTATTCAACAATAACAACCAGGAAAAGAAAACCCCAGAGACACAAACGAATGTAGTAACAC
CACGAGCAACATAAACCACGGGCCAAACCATAAAAAAGAACAGACTAGTTCCAAAGCTTAGTACC
AAAGCCAATCCACCAAAGCTCCTAAGCTGCTAATAAAA
Found at i:2203938 original size:20 final size:20
Alignment explanation
Indices: 2203915--2203965 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
2203905 TATTTTGAAA
2203915 ATAAAAATTTAATTTCATAG
1 ATAAAAATTTAATTTCATAG
*
2203935 ATAAAAACTTAATTTCATAG
1 ATAAAAATTTAATTTCATAG
2203955 ATAAAAATTTA
1 ATAAAAATTTA
2203966 TTAAAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (20 bp):
ATAAAAATTTAATTTCATAG
Found at i:2203996 original size:26 final size:26
Alignment explanation
Indices: 2203966--2204018 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2203956 TAAAAATTTA
2203966 TTAAAAACAAATATAAACCATAGAAG
1 TTAAAAACAAATATAAACCATAGAAG
2203992 TTAAAAACAAATATAAACCATAGAAG
1 TTAAAAACAAATATAAACCATAGAAG
2204018 T
1 T
2204019 GCTATCATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.60, C:0.11, G:0.08, T:0.21
Consensus pattern (26 bp):
TTAAAAACAAATATAAACCATAGAAG
Found at i:2204658 original size:2 final size:2
Alignment explanation
Indices: 2204651--2204685 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2204641 TTTATTAATG
* *
2204651 AT AT AT AT GT AT GT 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 AT AT AT A
2204686 ATACAGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2205566 original size:22 final size:20
Alignment explanation
Indices: 2205517--2205578 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
2205507 TCAGCCACCA
*
2205517 TGAATAGTGACTGATGGTGG
1 TGAATAGTGACTGACGGTGG
2205537 TGAATAGTGA-TCGACGGTGG
1 TGAATAGTGACT-GACGGTGG
2205557 TCGAAATAGTGACTGACGGTGG
1 T-G-AATAGTGACTGACGGTGG
2205579 CGGTGCACGG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 1 0.03
20 18 0.49
21 1 0.03
22 16 0.43
23 1 0.03
ACGTcount: A:0.26, C:0.10, G:0.39, T:0.26
Consensus pattern (20 bp):
TGAATAGTGACTGACGGTGG
Found at i:2206072 original size:28 final size:25
Alignment explanation
Indices: 2206014--2206085 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
2206004 TTGAAATTAT
* **
2206014 TATTATTATTATTTCCTA-AATTTA
1 TATTTTTATTATTTTTTATAATTTA
2206038 TATTTTTATATTTATTTTTTATAATTTA
1 TA-TTTT-TA-TTATTTTTTATAATTTA
2206066 -ATATTTTATTATTTTTTATA
1 TAT-TTTTATTATTTTTTATA
2206086 TTAACATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
24 2 0.05
25 15 0.38
26 5 0.12
27 12 0.30
28 6 0.15
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (25 bp):
TATTTTTATTATTTTTTATAATTTA
Found at i:2206079 original size:29 final size:27
Alignment explanation
Indices: 2206011--2206079 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
2206001 ATTTTGAAAT
2206011 TATTATTATTA-TTATTTCCTAAATTTA
1 TATT-TTATTATTTATTTCCTAAATTTA
**
2206038 TATTTT-TATATTTATTTTTTATAATTTAA
1 TATTTTAT-TATTTATTTCCTA-AATTT-A
2206067 TATTTTATTATTT
1 TATTTTATTATTT
2206080 TTTATATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 12 0.34
28 5 0.14
29 12 0.34
30 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (27 bp):
TATTTTATTATTTATTTCCTAAATTTA
Found at i:2206089 original size:23 final size:25
Alignment explanation
Indices: 2206049--2206106 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
2206039 ATTTTTATAT
*
2206049 TTATTTTTTATAATTTAATATTTTA
1 TTATTTTTTATAATTTAACATTTTA
*
2206074 TTATTTTTTAT-A-TTAACATTTTC
1 TTATTTTTTATAATTTAACATTTTA
2206097 TTAATTTTTT
1 TT-ATTTTTT
2206107 GTGATGTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 11 0.37
24 8 0.27
25 11 0.37
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (25 bp):
TTATTTTTTATAATTTAACATTTTA
Found at i:2206202 original size:20 final size:20
Alignment explanation
Indices: 2206179--2206216 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2206169 TTTCTTTTTG
2206179 TTTAGCAT-TCAATATTTTAT
1 TTTAGCATCT-AATATTTTAT
*
2206199 TTTATCATCTAATATTTT
1 TTTAGCATCTAATATTTT
2206217 GATTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTAGCATCTAATATTTTAT
Found at i:2211739 original size:83 final size:83
Alignment explanation
Indices: 2211281--2212545 Score: 1362
Period size: 83 Copynumber: 15.3 Consensus size: 83
2211271 AAAAGCACCC
* * * * ** **
2211281 TCAACAAAGACCTTCGAGTTCAATTATACTCAGCTCAAAGGCACTTCATTTGCAATATAGTTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
*
2211346 GCCAAGAAGGGTTATCT-
66 GGCAAGAAGGGTTATCTG
* * * * *
2211363 TCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATTATTTGCAGTATAGCTT
1 T-CAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTC
*
2211428 AAGGCAAGAAGGGTAATCTG
64 AAGGCAAGAAGGGTTATCTG
* * * * * * * ** *
2211448 CCAAATAAAGACCTTCGAGTTTGATTACACTCAACTTAAAGGCACATCAATTGCAATATAGCTCA
1 TC-AACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCA
*
2211513 AGGCAAAAAGGGTTATCT-
65 AGGCAAGAAGGGTTATCTG
* * *
2211531 TC--CAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
**
2211594 GGCAAGAAGGGCCATCT-
66 GGCAAGAAGGGTTATCTG
* * *
2211611 TC--CAAAGACCTTTGAGTTTGATTACACTTAGCTCAAAGGCACATCATTTACAGCATAACTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
* * *
2211674 GGCTAGAAGGATTATTTG
66 GGCAAGAAGGGTTATCTG
* * * **
2211692 TCAACAAAGACCATCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGTTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
* *
2211757 GGCAAGAAAGGCTATCTG
66 GGCAAGAAGGGTTATCTG
* * * **
2211775 -C--CAAATACCTTCGAGTTCGATTACACTTAGCTCAAAGGCATATCA-TTACAATATAACTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
* *
2211836 GGCTATAAGGGTTATCTG
66 GGCAAGAAGGGTTATCTG
* * * *
2211854 TCAACAGAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTATAGTATAACTTAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
*
2211919 GGCTAGAAGGGTTATCTG
66 GGCAAGAAGGGTTATCTG
* * * *
2211937 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATTATTTGCAACATAACTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
2212002 GGCAAGAAGGGTTATCT-
66 GGCAAGAAGGGTTATCTG
* *
2212019 TC--CAAAGACCTTCGAGATCGATTACACTCAGCTCAAAGGCATATCATTTACAGCATAACTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
*
2212082 GGCTAGAAGGGTTATCTG
66 GGCAAGAAGGGTTATCTG
* * * *
2212100 TCAACAAAGACCTTCGAGTTCAATTACACTCAGCTCAAAGACACATCATTTACAGTATAAGTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
*
2212165 GGCTAA-AAGGGTTATATG
66 GGC-AAGAAGGGTTATCTG
* * * * *
2212183 TCAACAAAGCCCTTCGAGTTCAATTACACTCAGCTCAAAGGCACGTCATTTGCAGCATAGCTCAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
2212248 GGCAAGAAGGGTTATCTG
66 GGCAAGAAGGGTTATCTG
* * * *
2212266 -C--CAAAGACCTTCGAGTTCGATTACAATCAGCTCAAAGGTACATCATTTACAGTATAACTTAA
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
* * *
2212328 GGCGAGAAGAGTTATATG
66 GGCAAGAAGGGTTATCTG
* * * * * * * * *
2212346 TCATCAAAGTCATTTGAGTTTGATTATATTAAGCTCAAAGGCATATCAAATTTACAGCATAACTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTACAGCATAACTC
2212411 AAGGCGAA-AAGGGTTATCTG
64 AAGGC-AAGAAGGGTTATCTG
* * * * * * * * *
2212431 TCATCAAAGACTTTTGAGTTCGATTACATTCAGCTTAGAGGCATATCAAATTTACATCATAGCTC
1 TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTACAGCATAACTC
** **
2212496 AAGGTGAGAAGGACTATCTG
64 AAGGCAAGAAGGGTTATCTG
* *
2212516 TCAACAATGAAACCTTCGAGTTCAATTACA
1 TCAACAA--AGACCTTCGAGTTCGATTACA
2212546 TTCGGGTCAA
Statistics
Matches: 1008, Mismatches: 150, Indels: 45
0.84 0.12 0.04
Matches are distributed among these distances:
79 25 0.02
80 316 0.31
81 5 0.00
82 47 0.05
83 351 0.35
84 139 0.14
85 107 0.11
86 1 0.00
87 17 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (83 bp):
TCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAA
GGCAAGAAGGGTTATCTG
Found at i:2211748 original size:163 final size:163
Alignment explanation
Indices: 2211285--2212545 Score: 1356
Period size: 163 Copynumber: 7.7 Consensus size: 163
2211275 GCACCCTCAA
* * * * ** * *
2211285 CAAAGACCTTCGAGTTCAATTATACTCAGCTCAAAGGCACTTCATTTGCAATATAGTTCAAGCCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAATATAACTCAAGGCT
*
2211350 AGAAGGGTTATCT-TCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATTAT
66 AGAAGGGTTATCTGT-CAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAT
* * * *
2211414 TTGCAGTATAGCTTAAGGCAAGAAGGGTAATCTGC
129 TTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTTC
* * * * * *
2211449 CAAATAAAGACCTTCGAGTTTGATTACACTCAACTTAAAGGCACATCAATTGCAATATAGCTCAA
1 C----AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAATATAACTCAA
* * *
2211514 GGCAAAAAGGGTTATCT-TC--CAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATC
62 GGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC
**
2211576 ATTTGCAGCATAGCTCAAGGCAAGAAGGGCCATCTTC
127 ATTTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTTC
* * * **
2211613 CAAAGACCTTTGAGTTTGATTACACTTAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAATATAACTCAAGGCT
* * * *
2211678 AGAAGGATTATTTGTCAACAAAGACCATCGAGTTTGATTACACTCAGCTCAAAGGCACATCATTT
66 AGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
* * * *
2211743 GCAGCATAGTTCAAGGCAAGAAAGGCTATCTGC
131 GCAGCATAGCTCAAGGCAAGAAGGGTTATCTTC
* * *
2211776 CAAATACCTTCGAGTTCGATTACACTTAGCTCAAAGGCATATCA-TTACAATATAACTCAAGGCT
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAATATAACTCAAGGCT
* *
2211840 ATAAGGGTTATCTGTCAACAGAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
66 AGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
** * * * *
2211905 ATAGTATAACTTAAGGCTAGAAGGGTTATCTGTC
131 GCAGCATAGCTCAAGGCAAGAAGGGTTATCT-TC
* * * *
2211939 AACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATTATTTGCAACATAACTCAAGG
1 --CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAATATAACTCAAGG
* * *
2212004 CAAGAAGGGTTATCT-TC--CAAAGACCTTCGAGATCGATTACACTCAGCTCAAAGGCATATCAT
64 CTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAT
* * *
2212066 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC
129 TTGCAGCATAGCTCAAGGCAAGAAGGGTTATCT-TC
* * * *
2212102 AACAAAGACCTTCGAGTTCAATTACACTCAGCTCAAAGACACATCATTTACAGTATAAGTCAAGG
1 --CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAATATAACTCAAGG
* * * * *
2212167 CTAAAAGGGTTATATGTCAACAAAGCCCTTCGAGTTCAATTACACTCAGCTCAAAGGCACGTCAT
64 CTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAT
*
2212232 TTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTGC
129 TTGCAGCATAGCTCAAGGCAAGAAGGGTTATCTTC
* * * * *
2212267 CAAAGACCTTCGAGTTCGATTACAATCAGCTCAAAGGTACATCATTTACAGTATAACTTAAGGCG
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAATATAACTCAAGGCT
* * * * * * * * * * *
2212332 AGAAGAGTTATATGTCATCAAAGTCATTTGAGTTTGATTATATTAAGCTCAAAGGCATATCAAAT
66 AGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--AT
* *
2212397 TTACAGCATAACTCAAGGCGAA-AAGGGTTATCTGTC
129 TTGCAGCATAGCTCAAGGC-AAGAAGGGTTATCT-TC
* * * * * * *
2212433 ATCAAAGACTTTTGAGTTCGATTACATTCAGCTTAGAGGCATATCAAATTTAC-ATCATAGCTCA
1 --CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTACAAT-ATAACTCA
** * *
2212497 AGG-TGAGAAGGACTATCTGTCAACAATGAAACCTTCGAGTTCAATTACA
61 AGGCT-AGAAGGGTTATCTGTCAACAA--AGACCTTCGAGTTCGATTACA
2212546 TTCGGGTCAA
Statistics
Matches: 933, Mismatches: 138, Indels: 44
0.84 0.12 0.04
Matches are distributed among these distances:
160 64 0.07
161 2 0.00
162 99 0.11
163 364 0.39
164 76 0.08
165 75 0.08
166 102 0.11
167 1 0.00
168 104 0.11
169 1 0.00
170 31 0.03
172 14 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (163 bp):
CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAATATAACTCAAGGCT
AGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
GCAGCATAGCTCAAGGCAAGAAGGGTTATCTTC
Found at i:2212571 original size:87 final size:85
Alignment explanation
Indices: 2211533--2212692 Score: 409
Period size: 83 Copynumber: 14.0 Consensus size: 85
2211523 GGTTATCTTC
* * * * * *
2211533 CAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGG-CACATC--ATTTGCAGCATAGCTCAAG
1 CAAAAACCTTCAAGTTCGAATACATTCAGCTC-AAGGACATATCAAATTTACAACATAGCTCAAG
* * *
2211595 GCAAGAAGGGCCATCT-TC--
65 GCGAGAAGGACTATCTGTCAA
* ** * * * * *
2211613 CAAAGACCTTTGAGTTTGATTACACTT-AGCTCAAAGG-CACATC--ATTTACAGCATAACTCAA
1 CAAAAACCTTCAAGTTCGAATACA-TTCAGCTC-AAGGACATATCAAATTTACAACATAGCTCAA
* * *
2211674 GGCTAGAAGGATTATTTGTCAA
64 GGCGAGAAGGACTATCTGTCAA
* * * * * * * * * *
2211696 CAAAGACCATCGAGTTTGATTACACTCAGCTCAAAGG-CACATC--ATTTGCAGCATAGTTCAAG
1 CAAAAACCTTCAAGTTCGAATACATTCAGCTC-AAGGACATATCAAATTTACAACATAGCTCAAG
*
2211758 GCAAGAAAGG-CTATCTG-C--
65 GCGAG-AAGGACTATCTGTCAA
* * * * *
2211776 CAAATACCTTCGAGTTCGATTACACTT-AGCTCAAAGG-CATATC--A-TTACAATATAACTCAA
1 CAAAAACCTTCAAGTTCGAATACA-TTCAGCTC-AAGGACATATCAAATTTACAACATAGCTCAA
* * **
2211836 GGCTATAAGGGTTATCTGTCAA
64 GGCGAGAAGGACTATCTGTCAA
* * * * * * * ** * *
2211858 CAGAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG-CACATC--ATTTATAGTATAACTTAAG
1 CAAAAACCTTCAAGTTCGAATACATTCAGCTC-AAGGACATATCAAATTTACAACATAGCTCAAG
* **
2211920 GCTAGAAGGGTTATCTGTCAA
65 GCGAGAAGGACTATCTGTCAA
* * * * * * *
2211941 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGG-CATAT--TATTTGCAACATAACTCAAG
1 CAAAAACCTTCAAGTTCGAATACATTCAGCTC-AAGGACATATCAAATTTACAACATAGCTCAAG
* **
2212003 GCAAGAAGGGTTATCT-TC--
65 GCGAGAAGGACTATCTGTCAA
* * * * * * *
2212021 CAAAGACCTTCGAGATCGATTACACTCAGCTCAAAGG-CATATC--ATTTACAGCATAACTCAAG
1 CAAAAACCTTCAAGTTCGAATACATTCAGCTC-AAGGACATATCAAATTTACAACATAGCTCAAG
* **
2212083 GCTAGAAGGGTTATCTGTCAA
65 GCGAGAAGGACTATCTGTCAA
* * * * * **
2212104 CAAAGACCTTCGAGTTC-AATTACACTCAGCTCAAAGACACATC--ATTTACAGTATAAG-TCAA
1 CAAAAACCTTCAAGTTCGAA-TACATTCAGCTCAAGGACATATCAAATTTACAACAT-AGCTCAA
* * ** *
2212165 GGCTAAAAGGGTTATATGTCAA
64 GGCGAGAAGGACTATCTGTCAA
** * * ** * *
2212187 CAAAGCCCTTCGAGTTC-AATTACACTCAGCTCAAAGG-CACGTC--ATTTGCAGCATAGCTCAA
1 CAAAAACCTTCAAGTTCGAA-TACATTCAGCTC-AAGGACATATCAAATTTACAACATAGCTCAA
* **
2212248 GGCAAGAAGGGTTATCTG-C--
64 GGCGAGAAGGACTATCTGTCAA
* * * * ** * *
2212267 CAAAGACCTTCGAGTTCGATTACAATCAGCTCAAAGGTAC--ATC--ATTTACAGTATAACTTAA
1 CAAAAACCTTCAAGTTCGAATACATTCAGCTC-AAGG-ACATATCAAATTTACAACATAGCTCAA
* * *
2212328 GGCGAGAA-GAGTTATATGTCAT
64 GGCGAGAAGGA-CTATCTGTCAA
** * ** * * * * * *
2212350 CAAAGTCATTTGAGTTTGATTATATTAAGCTCAAAGG-CATATCAAATTTACAGCATAACTCAAG
1 CAAAAACCTTCAAGTTCGAATACATTCAGCTC-AAGGACATATCAAATTTACAACATAGCTCAAG
* ** *
2212414 GCGAAAAGGGTTATCTGTCAT
65 GCGAGAAGGACTATCTGTCAA
* * ** * * *
2212435 CAAAGACTTTTGAGTTCGATTACATTCAGCTTAGAGG-CATATCAAATTTACATCATAGCTCAAG
1 CAAAAACCTTCAAGTTCGAATACATTCAGCTCA-AGGACATATCAAATTTACAACATAGCTCAAG
*
2212499 GTGAGAAGGACTATCTGTCAA
65 GCGAGAAGGACTATCTGTCAA
* * * * * * *
2212520 CAATGAAACCTTCGAGTTC-AATTACATTCGGGTCAAGGACATGTTAAATTTACAACATAACTTA
1 CAA--AAACCTTCAAGTTCGAA-TACATTCAGCTCAAGGACATATCAAATTTACAACATAGCTCA
*
2212584 AGGCGAGAA-GAGCTATCTGTCAG
63 AGGCGAGAAGGA-CTATCTGTCAA
* * * *
2212607 C--AAATCTTTAAGTTCGAATACATTCAGCTCATGGACATATCAAATTTACAGCATAGCTCAAGG
1 CAAAAACCTTCAAGTTCGAATACATTCAGCTCAAGGACATATCAAATTTACAACATAGCTCAAGG
*
2212670 CGAGAAAGG-CTATCCGTCAA
66 CGAG-AAGGACTATCTGTCAA
2212690 CAA
1 CAA
2212693 GAATTTTTAA
Statistics
Matches: 902, Mismatches: 132, Indels: 87
0.80 0.12 0.08
Matches are distributed among these distances:
78 4 0.00
79 22 0.02
80 237 0.26
81 10 0.01
82 50 0.06
83 392 0.43
84 13 0.01
85 107 0.12
86 7 0.01
87 60 0.07
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (85 bp):
CAAAAACCTTCAAGTTCGAATACATTCAGCTCAAGGACATATCAAATTTACAACATAGCTCAAGG
CGAGAAGGACTATCTGTCAA
Found at i:2213220 original size:20 final size:20
Alignment explanation
Indices: 2213195--2213285 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
2213185 AAAAAAAAGA
*
2213195 GGTGAATAGTGACCGACAGT
1 GGTGAATAGTGACTGACAGT
*
2213215 GGTGAATAGTGATTGACAGT
1 GGTGAATAGTGACTGACAGT
* *
2213235 GGTAAATAATGACTGACAGT
1 GGTGAATAGTGACTGACAGT
** *
2213255 TATGAATAGTAACTGACAGT
1 GGTGAATAGTGACTGACAGT
*
2213275 GATGACATAGT
1 GGTGA-ATAGT
2213286 CGGAGAAGTC
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
20 54 0.92
21 5 0.08
ACGTcount: A:0.35, C:0.10, G:0.29, T:0.26
Consensus pattern (20 bp):
GGTGAATAGTGACTGACAGT
Found at i:2213475 original size:20 final size:20
Alignment explanation
Indices: 2213420--2213475 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2213410 TTCGTCCACC
** *
2213420 GTGAATAGTGAGTGACAGTG
1 GTGAATAGTGACCGATAGTG
2213440 GTGAATAGTGACCGATAGTG
1 GTGAATAGTGACCGATAGTG
2213460 GTGAATAGTGACCGAT
1 GTGAATAGTGACCGAT
2213476 GGTGACGGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.36, T:0.25
Consensus pattern (20 bp):
GTGAATAGTGACCGATAGTG
Found at i:2214012 original size:23 final size:25
Alignment explanation
Indices: 2213971--2214019 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
2213961 TATTTTTATA
*
2213971 TTTATTTTTTTATAAATTAATATTTT
1 TTTATTTTTTTAT-AATTAACATTTT
2213997 TTTA-TTTTTTAT-ATTAACATTTT
1 TTTATTTTTTTATAATTAACATTTT
2214020 CTTAACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
25 8 0.36
26 4 0.18
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTATTTTTTTATAATTAACATTTT
Found at i:2214029 original size:25 final size:24
Alignment explanation
Indices: 2213971--2214031 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
2213961 TATTTTTATA
* *
2213971 TTTATTTTTTTATAAATTAATATTT
1 TTTAATTTTTTAT-AATTAACATTT
*
2213996 TTTTATTTTTTAT-ATTAACATTT
1 TTTAATTTTTTATAATTAACATTT
2214019 TCTTAACTTTTTT
1 T-TTAA-TTTTTT
2214032 GACGTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 10 0.33
24 3 0.10
25 17 0.57
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTAATTTTTTATAATTAACATTT
Found at i:2214211 original size:19 final size:19
Alignment explanation
Indices: 2214183--2214221 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2214173 AAAGGTAAGT
* *
2214183 AATTTGAATTGAATTTTTA
1 AATTTAAATTGAAATTTTA
*
2214202 AATTTAAATTTAAATTTTA
1 AATTTAAATTGAAATTTTA
2214221 A
1 A
2214222 CTTTCACAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
AATTTAAATTGAAATTTTA
Found at i:2232268 original size:19 final size:19
Alignment explanation
Indices: 2232241--2232287 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
2232231 ATTATGTAAA
* *
2232241 TATTAAAAATATAATGGTT
1 TATTTAAAATATAATGATT
*
2232260 TATTTAAAAT-TAATTATT
1 TATTTAAAATATAATGATT
2232278 TA-TTAAAATA
1 TATTTAAAATA
2232288 CAATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.29
18 8 0.33
19 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TATTTAAAATATAATGATT
Found at i:2242776 original size:17 final size:17
Alignment explanation
Indices: 2242754--2242787 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2242744 GTATGAATAA
*
2242754 TTAAAAGATAATCTATT
1 TTAAAAAATAATCTATT
*
2242771 TTAAAAAATAATTTATT
1 TTAAAAAATAATCTATT
2242788 AATAATGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TTAAAAAATAATCTATT
Found at i:2253194 original size:22 final size:22
Alignment explanation
Indices: 2253161--2253216 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
2253151 GTTATGAGAT
*
2253161 TGTTA-ACTAAGTTGGTT-AAGGC
1 TGTTATAC-AAGTT-GTTAAAGAC
2253183 TGTTATACAAGTTGTTAAAGAC
1 TGTTATACAAGTTGTTAAAGAC
2253205 TGTTATACAAGT
1 TGTTATACAAGT
2253217 GCTCTTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 3 0.10
22 26 0.84
23 2 0.06
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (22 bp):
TGTTATACAAGTTGTTAAAGAC
Found at i:2256089 original size:14 final size:13
Alignment explanation
Indices: 2256070--2256128 Score: 61
Period size: 14 Copynumber: 4.6 Consensus size: 13
2256060 TAAAGCTCCA
2256070 AAGAAAGAAGAAAG
1 AAGAAAGAAG-AAG
2256084 AAGAAAGAATGAAG
1 AAGAAAGAA-GAAG
2256098 AA-AAAGAAG-AG
1 AAGAAAGAAGAAG
* *
2256109 AAG-AACAAGAAA
1 AAGAAAGAAGAAG
2256121 AAGAAAGA
1 AAGAAAGA
2256129 GGTGAGAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 9 0.24
12 5 0.13
13 9 0.24
14 14 0.37
15 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (13 bp):
AAGAAAGAAGAAG
Found at i:2256105 original size:20 final size:20
Alignment explanation
Indices: 2256074--2256125 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
2256064 GCTCCAAAGA
*
2256074 AAGAAGAAAGAAGA-AAGAATG
1 AAGAA-AAAGAAGAGAAGAA-C
2256095 AAGAAAAAGAAGAGAAGAAC
1 AAGAAAAAGAAGAGAAGAAC
2256115 AAGAAAAAGAA
1 AAGAAAAAGAA
2256126 AGAGGTGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (20 bp):
AAGAAAAAGAAGAGAAGAAC
Found at i:2257906 original size:20 final size:20
Alignment explanation
Indices: 2257881--2257931 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
2257871 AGTAAGGGAG
2257881 GTATCGATACTCCCATGGCA
1 GTATCGATACTCCCATGGCA
2257901 GTATCGATACTCCCATGGCA
1 GTATCGATACTCCCATGGCA
*
2257921 GTACCGATACT
1 GTATCGATACT
2257932 GCCTATTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (20 bp):
GTATCGATACTCCCATGGCA
Found at i:2261804 original size:30 final size:30
Alignment explanation
Indices: 2261770--2261832 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
2261760 AACACCTAAA
* *
2261770 TTTAAAAATTACATTGTTGGTCTCTAAACT
1 TTTAAAAATTACATTGTTGATCCCTAAACT
* * *
2261800 TTTAAAAATTGCCTTTTTGATCCCTAAACT
1 TTTAAAAATTACATTGTTGATCCCTAAACT
2261830 TTT
1 TTT
2261833 CCAAACTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (30 bp):
TTTAAAAATTACATTGTTGATCCCTAAACT
Found at i:2265878 original size:12 final size:12
Alignment explanation
Indices: 2265863--2265904 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
2265853 ATAGTCACTT
2265863 TTTCATATTTAC
1 TTTCATATTTAC
* *
2265875 TTTCATAATCAC
1 TTTCATATTTAC
2265887 TTTTCATATTTAC
1 -TTTCATATTTAC
2265900 TTTCA
1 TTTCA
2265905 AAGCACAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTCATATTTAC
Found at i:2265896 original size:25 final size:26
Alignment explanation
Indices: 2265848--2265904 Score: 98
Period size: 25 Copynumber: 2.2 Consensus size: 26
2265838 TTTTTCTTAT
*
2265848 CTTTCATAGTCACTTTTTCATATTTA
1 CTTTCATAATCACTTTTTCATATTTA
2265874 CTTTCATAATCAC-TTTTCATATTTA
1 CTTTCATAATCACTTTTTCATATTTA
2265899 CTTTCA
1 CTTTCA
2265905 AAGCACAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 18 0.60
26 12 0.40
ACGTcount: A:0.25, C:0.21, G:0.02, T:0.53
Consensus pattern (26 bp):
CTTTCATAATCACTTTTTCATATTTA
Found at i:2265901 original size:13 final size:13
Alignment explanation
Indices: 2265862--2265902 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2265852 CATAGTCACT
2265862 TTTTCATATTTAC
1 TTTTCATATTTAC
* *
2265875 -TTTCATAATCAC
1 TTTTCATATTTAC
2265887 TTTTCATATTTAC
1 TTTTCATATTTAC
2265900 TTT
1 TTT
2265903 CAAAGCACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTCATATTTAC
Found at i:2267650 original size:22 final size:23
Alignment explanation
Indices: 2267622--2267671 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
2267612 AGTCAACTCA
*
2267622 TTGACTTTGAC-GAGTTAACCCG
1 TTGACTTTGACTAAGTTAACCCG
2267644 TTGACTTTGACTAAGTTAACCCG
1 TTGACTTTGACTAAGTTAACCCG
2267667 TTGAC
1 TTGAC
2267672 CGTTGACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (23 bp):
TTGACTTTGACTAAGTTAACCCG
Found at i:2269749 original size:24 final size:24
Alignment explanation
Indices: 2269721--2269829 Score: 76
Period size: 24 Copynumber: 4.5 Consensus size: 24
2269711 GAATGTTTTA
*
2269721 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
** * * *
2269745 TCTGATACCTTATTTGAATTCTGC
1 TCTGATTTCTGATCTGAATTCTGT
* * *
2269769 TCTTATTTCTGACCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* * *
2269793 TATGATATT-TAATCTGAATTATGT
1 TCTGAT-TTCTGATCTGAATTCTGT
* *
2269817 TTTGATTTTTGAT
1 TCTGATTTCTGAT
2269830 ATCTCCGTTT
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 2 0.03
24 59 0.94
25 2 0.03
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.52
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:2272519 original size:29 final size:31
Alignment explanation
Indices: 2272463--2272526 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
2272453 TTTTTGATCC
*
2272463 CTAAACTTTTCTAAACTTTATACTTTGGCTA
1 CTAAACTTTTCTAAACTTTACACTTTGGCTA
* * *
2272494 CTAAAC-TTTC-AAATTTTACATTTTGGTTA
1 CTAAACTTTTCTAAACTTTACACTTTGGCTA
2272523 CTAA
1 CTAA
2272527 CCAAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 19 0.66
30 4 0.14
31 6 0.21
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.45
Consensus pattern (31 bp):
CTAAACTTTTCTAAACTTTACACTTTGGCTA
Found at i:2272612 original size:3 final size:3
Alignment explanation
Indices: 2272604--2272638 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2272594 ACATATCTAC
2272604 AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2272639 TATTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2272643 original size:3 final size:3
Alignment explanation
Indices: 2272637--2272673 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2272627 AATAATAATA
2272637 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2272674 CAAATAATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2278382 original size:9 final size:9
Alignment explanation
Indices: 2278367--2278416 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
2278357 CATCTATTAG
2278367 GAAAAAAGAA
1 GAAAAAA-AA
2278377 -AAAAAAAGA
1 GAAAAAAA-A
2278386 TGAAAAAAAA
1 -GAAAAAAAA
2278396 G-AAAAAAA
1 GAAAAAAAA
2278404 GAAAAAAAA
1 GAAAAAAAA
2278413 GAAA
1 GAAA
2278417 TTGAATCAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 9 0.25
9 19 0.53
10 1 0.03
11 7 0.19
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:2278391 original size:12 final size:10
Alignment explanation
Indices: 2278368--2278416 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
2278358 ATCTATTAGG
2278368 AAAAAAGAAA
1 AAAAAAGAAA
2278378 AAAAAAGATGAA
1 AAAAAAGA--AA
2278390 AAAAAAG--A
1 AAAAAAGAAA
2278398 AAAAAAG-AA
1 AAAAAAGAAA
2278407 AAAAAAGAAA
1 AAAAAAGAAA
2278417 TTGAATCAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 8 0.23
9 8 0.23
10 10 0.29
12 9 0.26
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:2278400 original size:17 final size:17
Alignment explanation
Indices: 2278367--2278416 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
2278357 CATCTATTAG
*
2278367 GAAAAAAGAAAAAAAAAGA
1 GAAAAAA-AAGAAAAAA-A
2278386 TGAAAAAAAAGAAAAAAA
1 -GAAAAAAAAGAAAAAAA
2278404 GAAAAAAAAGAAA
1 GAAAAAAAAGAAA
2278417 TTGAATCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 13 0.45
18 1 0.03
19 8 0.28
20 7 0.24
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (17 bp):
GAAAAAAAAGAAAAAAA
Found at i:2281630 original size:23 final size:23
Alignment explanation
Indices: 2281604--2281672 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
2281594 CACCACAGCT
2281604 CGTATAATTGCACCGAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
* * *
2281627 CGTATAATTGCACTGGAGTGCCG
1 CGTATAATTGCACCGAAGTGCCA
* * * *
2281650 CATAGAATTACACCGTAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
2281673 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (23 bp):
CGTATAATTGCACCGAAGTGCCA
Found at i:2281859 original size:103 final size:103
Alignment explanation
Indices: 2281688--2281905 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
2281678 TAATGTCCAT
* * *
2281688 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
2281753 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTACAAAGAATACATATATGTCCCG
* *
2281791 AAGGACCACATATCATTTCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
2281856 GACTTCACACATGTTACAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTACAAAGAATACATATATGTCCCG
2281894 AAGGACCACATA
1 AAGGACCACATA
2281906 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTACAAAGAATACATATATGTCCCG
Found at i:2283310 original size:20 final size:20
Alignment explanation
Indices: 2283269--2283329 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 20
2283259 TTCGCTTGAG
*
2283269 GGGTATCGATTCTCCATTGAAT
1 GGGTACCGATTC-CC-TTGAAT
2283291 GGGTACCGATTCCCTTGAAT
1 GGGTACCGATTCCCTTGAAT
2283311 GGGTACCGATTCCCCTTGA
1 GGGTACCGATT-CCCTTGA
2283330 CCAAAAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 17 0.46
21 9 0.24
22 11 0.30
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.31
Consensus pattern (20 bp):
GGGTACCGATTCCCTTGAAT
Found at i:2285242 original size:331 final size:333
Alignment explanation
Indices: 2284797--2285455 Score: 1043
Period size: 331 Copynumber: 2.0 Consensus size: 333
2284787 AAATGATTTT
* * * * ** * *
2284797 CAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAAAGTAAGAAAATGATTTTCAAT
1 CAAAGTTTCTCATTTAA-CTGTGCAGAAAATGAAATTGTTAAAAAGTAAGAAAACAATTTCCAAA
* *
2284862 GTTTCTTACCCAGTAAACTATTTCCCAAAGATGATAAGTCCTCCGGGCCATCTGTAAAACCTCAG
65 GTTTCTTACCCAATAAACAATTTCCCAAAGATGATAAGTCCTCCGGGCCATCTGTAAAACCTCAG
* *
2284927 GGTATGATGTTTTCACATGAAAATGAGAAAGTGATTACCAAAGTTTCTCATTTAATGTTCAGAAA
130 GGTAGGATGTTTTCACATGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTCAGAAA
* * *
2284992 ATGAAATTGTTAATAAGTAAGAAAATAATTTCCAAAGTTTCTTACCCAGTAAAAAATTTCCCAAA
195 ATGAAATTGTTAAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACCCAGTAAAAAATGTCCCAAA
* ** *
2285057 GATGATAAGTCCTTCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCACATGAAAATGAGAA
260 GATGATAAGTCCTCCAAGCCATCTGTAAAACCTCAGGGTATGATGTTTTCACATGAAAATGAGAA
2285122 AGCGGTTAC
325 AGCGGTTAC
*
2285131 CAAAGTTTCTCATTTAA-TGTGCAGAAAATGAAATTGTTAAAAAGTAAGAAAGCAATTTCCAAAG
1 CAAAGTTTCTCATTTAACTGTGCAGAAAATGAAATTGTTAAAAAGTAAGAAAACAATTTCCAAAG
*
2285195 TTTCTTA-CCAATAAACAATTTCCCAAAGATGATAAGTCCTTCGGGCCATCTGTAAAACCTCAGG
66 TTTCTTACCCAATAAACAATTTCCCAAAGATGATAAGTCCTCCGGGCCATCTGTAAAACCTCAGG
* *
2285259 GTAGGATGTTTTCACATGTAATTGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTCAGAAAA
131 GTAGGATGTTTTCACATGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTCAGAAAA
* * * *
2285324 TGAAATTGTTAAAAAGTAAGAAAGCAATTTTCAAAGTTTCTTACCTAGTAAACAATGTCCCAAAG
196 TGAAATTGTTAAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACCCAGTAAAAAATGTCCCAAAG
*
2285389 ATGATAAGTCCTCCAAGCCATCTGTAAAACCTCAGGGTATGATGTTTTCACATGACAATGAGAAA
261 ATGATAAGTCCTCCAAGCCATCTGTAAAACCTCAGGGTATGATGTTTTCACATGAAAATGAGAAA
2285454 GC
326 GC
2285456 TGTCGTAACC
Statistics
Matches: 297, Mismatches: 28, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
331 235 0.79
332 45 0.15
334 17 0.06
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (333 bp):
CAAAGTTTCTCATTTAACTGTGCAGAAAATGAAATTGTTAAAAAGTAAGAAAACAATTTCCAAAG
TTTCTTACCCAATAAACAATTTCCCAAAGATGATAAGTCCTCCGGGCCATCTGTAAAACCTCAGG
GTAGGATGTTTTCACATGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTCAGAAAA
TGAAATTGTTAAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACCCAGTAAAAAATGTCCCAAAG
ATGATAAGTCCTCCAAGCCATCTGTAAAACCTCAGGGTATGATGTTTTCACATGAAAATGAGAAA
GCGGTTAC
Found at i:2285289 original size:165 final size:166
Alignment explanation
Indices: 2284778--2285455 Score: 1034
Period size: 166 Copynumber: 4.1 Consensus size: 166
2284768 AGTTGTTCAA
** ** * * *
2284778 AAAATGAGAAAATGATTTTCAAAGTTTCTCATTTAATCTTTTCTGAAAATGAAATTGTTGAAAAG
1 AAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAA--TGTTCAGAAAATGAAATTGTTAAAAAG
** * * *
2284843 TAAGAAAATGATTTTCAATGTTTCTTACCCAGTAAACTATTTCCCAAAGATGATAAGTCCTCCGG
64 TAAGAAAACAATTTCCAAAGTTTCTTACCCAGTAAACAATTTCCCAAAGATGATAAGTCCTCCGG
2284908 GCCATCTGTAAAACCTCAGGGTATGATGTTTTCACATG
129 GCCATCTGTAAAACCTCAGGGTATGATGTTTTCACATG
* *
2284946 AAAATGAGAAAGTGATTACCAAAGTTTCTCATTTAATGTTCAGAAAATGAAATTGTTAATAAGTA
1 AAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTCAGAAAATGAAATTGTTAAAAAGTA
* * * *
2285011 AGAAAATAATTTCCAAAGTTTCTTACCCAGTAAAAAATTTCCCAAAGATGATAAGTCCTTCGGGT
66 AGAAAACAATTTCCAAAGTTTCTTACCCAGTAAACAATTTCCCAAAGATGATAAGTCCTCCGGGC
2285076 CATCTGTAAAACCTCAGGGTATGATGTTTTCACATG
131 CATCTGTAAAACCTCAGGGTATGATGTTTTCACATG
* *
2285112 AAAATGAGAAAGCGGTTACCAAAGTTTCTCATTTAATGTGCAGAAAATGAAATTGTTAAAAAGTA
1 AAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTCAGAAAATGAAATTGTTAAAAAGTA
* * *
2285177 AGAAAGCAATTTCCAAAGTTTCTTA-CCAATAAACAATTTCCCAAAGATGATAAGTCCTTCGGGC
66 AGAAAACAATTTCCAAAGTTTCTTACCCAGTAAACAATTTCCCAAAGATGATAAGTCCTCCGGGC
*
2285241 CATCTGTAAAACCTCAGGGTAGGATGTTTTCACATG
131 CATCTGTAAAACCTCAGGGTATGATGTTTTCACATG
* *
2285277 TAATTGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTCAGAAAATGAAATTGTTAAAAAGTA
1 AAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTCAGAAAATGAAATTGTTAAAAAGTA
* * * * **
2285342 AGAAAGCAATTTTCAAAGTTTCTTACCTAGTAAACAATGTCCCAAAGATGATAAGTCCTCCAAGC
66 AGAAAACAATTTCCAAAGTTTCTTACCCAGTAAACAATTTCCCAAAGATGATAAGTCCTCCGGGC
2285407 CATCTGTAAAACCTCAGGGTATGATGTTTTCACATG
131 CATCTGTAAAACCTCAGGGTATGATGTTTTCACATG
*
2285443 ACAATGAGAAAGC
1 AAAATGAGAAAGC
2285456 TGTCGTAACC
Statistics
Matches: 470, Mismatches: 39, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
165 156 0.33
166 281 0.60
168 33 0.07
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (166 bp):
AAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTCAGAAAATGAAATTGTTAAAAAGTA
AGAAAACAATTTCCAAAGTTTCTTACCCAGTAAACAATTTCCCAAAGATGATAAGTCCTCCGGGC
CATCTGTAAAACCTCAGGGTATGATGTTTTCACATG
Found at i:2287486 original size:3 final size:3
Alignment explanation
Indices: 2287470--2287566 Score: 115
Period size: 3 Copynumber: 31.7 Consensus size: 3
2287460 TTTGGGCTTG
* * *
2287470 TAA TAA TATT TAA TAA TAA TAT TAA TAA TAAA TAA TAA TAT TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* *
2287517 TAA TAA TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
2287562 TAA TA
1 TAA TA
2287567 TTTAAATTAA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
2 2 0.03
3 71 0.89
4 7 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:2287924 original size:124 final size:121
Alignment explanation
Indices: 2287700--2287984 Score: 366
Period size: 124 Copynumber: 2.4 Consensus size: 121
2287690 ATGTTGAATA
* * *
2287700 AATTCTTCTCT-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGTTGAC
1 AATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTAAC
* * * *
2287764 CTATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTT-ATTATG
66 CTATCTCCTTCTGTGATAGAATCATACAAAAGGTTGAACAAGCTCTT-TTCATTATG
* *
2287820 AACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAGGTTGATGC
1 AA-TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG---GGATGATGC
* * * *
2287884 TAATCTATCTGCTTCTGTGATAGAATTATACAAAAGGTTGAACAAGCTCTTTTCATTGTG
62 TAACCTATCTCCTTCTGTGATAGAATCATACAAAAGGTTGAACAAGCTCTTTTCATTATG
2287944 AA--CTTC-TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 AATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
2287985 CTTCTTCTTC
Statistics
Matches: 146, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
120 37 0.25
121 17 0.12
122 33 0.23
123 2 0.01
124 57 0.39
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.42
Consensus pattern (121 bp):
AATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTAAC
CTATCTCCTTCTGTGATAGAATCATACAAAAGGTTGAACAAGCTCTTTTCATTATG
Found at i:2287983 original size:36 final size:36
Alignment explanation
Indices: 2287931--2288056 Score: 234
Period size: 36 Copynumber: 3.5 Consensus size: 36
2287921 TTGAACAAGC
* *
2287931 TCTTTTCATTGTGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
2287967 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
2288003 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
2288039 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
2288057 TCTCTGGAAA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 88 1.00
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.48
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
Found at i:2287991 original size:20 final size:20
Alignment explanation
Indices: 2287966--2288028 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
2287956 TTCAGATGAG
2287966 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTTC
* *
2287986 TTCTTCTTCA-GATG-A---G
1 TTCTTC-TCATTATGAACTTC
2288002 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTTC
2288022 TTCTTCT
1 TTCTTCT
2288029 TCAGATGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
15 3 0.09
16 9 0.27
17 1 0.03
19 1 0.03
20 16 0.48
21 3 0.09
ACGTcount: A:0.17, C:0.24, G:0.08, T:0.51
Consensus pattern (20 bp):
TTCTTCTCATTATGAACTTC
Found at i:2288133 original size:17 final size:17
Alignment explanation
Indices: 2288111--2288199 Score: 60
Period size: 17 Copynumber: 5.1 Consensus size: 17
2288101 GTTGAACAAA
*
2288111 TTCTTCTCATTATGAAT
1 TTCTTCTCATTATGAAC
* *
2288128 TTCTTCTTTCA-GATG-AG
1 TTCTTC--TCATTATGAAC
2288145 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
2288162 TTCTTCTTC-TTCA-GATGAG
1 TTCTTC-TCATT-ATGA--AC
2288181 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
2288198 TT
1 TT
2288200 TCTCTGGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
15 3 0.05
16 3 0.05
17 27 0.48
18 9 0.16
19 14 0.25
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:2288154 original size:34 final size:36
Alignment explanation
Indices: 2288111--2288202 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
2288101 GTTGAACAAA
2288111 TTCTTCTCATTATGAATTTCTTC-T-TTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
*
2288145 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
2288181 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
2288203 CTGGAAAAGC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
34 22 0.42
35 1 0.02
36 26 0.49
37 4 0.08
ACGTcount: A:0.20, C:0.21, G:0.10, T:0.50
Consensus pattern (36 bp):
TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
Found at i:2288163 original size:143 final size:143
Alignment explanation
Indices: 2287966--2288278 Score: 563
Period size: 143 Copynumber: 2.2 Consensus size: 143
2287956 TTCAGATGAG
2287966 TTCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCTTC
1 TTCTTCTCATTATGAACTTCTTC-T-TTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCTTC
*
2288031 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCTATCAAGTGATGGATTTGAAC
64 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAAC
*
2288096 AAAAGGTTGAACAAA
129 AAAAAGTTGAACAAA
*
2288111 TTCTTCTCATTATGAATTTCTTCTTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCTTCAG
1 TTCTTCTCATTATGAACTTCTTCTTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCTTCAG
*
2288176 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGTTTTGAACAA
66 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAA
*
2288241 AAAGTTGAACAAG
131 AAAGTTGAACAAA
2288254 TTCTTCTCATTATGAACTTCTTCTT
1 TTCTTCTCATTATGAACTTCTTCTT
2288279 CCTTCTTCAG
Statistics
Matches: 162, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
143 139 0.86
144 1 0.01
145 22 0.14
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (143 bp):
TTCTTCTCATTATGAACTTCTTCTTTCAGATGAGTTCTTCTCATTATGAACTTCTTCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAA
AAAGTTGAACAAA
Found at i:2288471 original size:113 final size:113
Alignment explanation
Indices: 2288143--2289064 Score: 1232
Period size: 113 Copynumber: 8.2 Consensus size: 113
2288133 CTTTCAGATG
2288143 AGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
2288204 TGGAAAAGCTGATCCATCAAGTGATGGTTTTGAACAAAAAGTTGAACA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
*
2288252 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTATTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-T
* * * * * * ** *
2288317 AC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACA
62 TCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
*
2288368 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
2288433 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT--A-A
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
* *
2288478 A-TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-T
* * * * * * **
2288542 AC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACA
62 TCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
*
2288593 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCTGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * *
2288658 TGGAAAAACCGATCTATCAAGTGATGGTTTTGAACAAAAAGTTGAACA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
* ****
2288706 AATTCTTCTCATTATGAA--T-TTCTT-C-T-TTCAGATGAGTTCTTCTCATTATGAACTCGAAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * * *
2288765 TGGAAATGTTGATCCATTGAA-TGAT-GAATTCAAGCAAAAAGTTGAACA
66 TGGAAAAGCTGATCCA-TCAAGTGATGGATTTGAA-CAAAAAGTTGAACA
*
2288813 AGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
2288878 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAAGCTGAACA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
2288926 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
2288991 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
*
2289039 AGTTCTTCTCATTATGAACTTTTTCT
1 AGTTCTTCTCATTATGAACTTCTTCT
2289065 GGAAAAGCTG
Statistics
Matches: 705, Mismatches: 80, Indels: 52
0.84 0.10 0.06
Matches are distributed among these distances:
106 5 0.01
107 73 0.10
108 4 0.01
109 55 0.08
110 12 0.02
111 3 0.00
112 70 0.10
113 340 0.48
114 6 0.01
115 2 0.00
116 133 0.19
117 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACA
Found at i:2288730 original size:17 final size:17
Alignment explanation
Indices: 2288708--2288757 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
2288698 GTTGAACAAA
*
2288708 TTCTTCTCATTATGAAT
1 TTCTTCTCATTATGAAG
*
2288725 TTCTTCTTTCA-GATG-AG
1 TTCTTC--TCATTATGAAG
2288742 TTCTTCTCATTATGAA
1 TTCTTCTCATTATGAA
2288758 CTCGAACTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
15 3 0.12
16 3 0.12
17 14 0.54
18 3 0.12
19 3 0.12
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTATGAAG
Found at i:2288835 original size:220 final size:226
Alignment explanation
Indices: 2288143--2289064 Score: 1363
Period size: 225 Copynumber: 4.1 Consensus size: 226
2288133 CTTTCAGATG
2288143 AGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
2288204 TGGAAAAGCTGATCCATCAAGTGATGGTTTTGAACAAAAAGTTGAACAAGTTCTTCTCATTATGA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGA
* *
2288269 ACTTCTTCTTCCTTCTTCAGATGACGAGTTATTCTCATTATGAACTCTACCTGGCAATGTTGATC
131 A-TTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATC
*
2288334 CATCAAATGATGAATTCAAACAAAAGGTTGAACA
193 CATCAAATGATGAATTCAAACAAAAAGTTGAACA
*
2288368 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
2288433 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT----AAATTCTTCTCATTATGA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGA
* *
2288494 ATTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATC
131 A-TTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATC
2288559 CATCAAATGATGAATTCAAACAAAAAGTTGAACA
193 CATCAAATGATGAATTCAAACAAAAAGTTGAACA
*
2288593 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCTGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * *
2288658 TGGAAAAACCGATCTATCAAGTGATGGTTTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGA
* *
2288723 A-T-TTCTT-C-T-TTCAGAT-GAGTTCTTCTCATTATGAACTCGAACTGGAAATGTTGATCCAT
131 ATTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCAT
** *
2288782 TGAATGATGAATTCAAGCAAAAAGTTGAACA
196 CAAATGATGAATTCAAACAAAAAGTTGAACA
*
2288813 AGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * *
2288878 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAAGCTGAACAAGTTCTTCTCATTATGA
66 TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGA
* * *
2288943 ACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCC
131 A-TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTAC-CTGGAAATGTTGATCC
* * ** *
2289006 ATCAAGTGATGGATTTGAGCAAAAAGTTGAACA
194 ATCAAATGATGAATTCAAACAAAAAGTTGAACA
*
2289039 AGTTCTTCTCATTATGAACTTTTTCT
1 AGTTCTTCTCATTATGAACTTCTTCT
2289065 GGAAAAGCTG
Statistics
Matches: 637, Mismatches: 45, Indels: 29
0.90 0.06 0.04
Matches are distributed among these distances:
220 190 0.30
222 1 0.00
223 12 0.02
224 2 0.00
225 231 0.36
226 98 0.15
227 1 0.00
228 6 0.01
229 96 0.15
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (226 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGA
ATTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCAT
CAAATGATGAATTCAAACAAAAAGTTGAACA
Found at i:2289576 original size:22 final size:22
Alignment explanation
Indices: 2289497--2289573 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
2289487 CATAAAGCTT
2289497 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* * *
2289519 TCATATTTAAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
*
2289541 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2289563 TCATCTTTGAA
1 TCATCTTTGAA
2289574 GAGTGTAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2290052 original size:54 final size:53
Alignment explanation
Indices: 2289922--2290128 Score: 239
Period size: 54 Copynumber: 3.9 Consensus size: 53
2289912 ATCAGAATAG
*
2289922 CAGA-TTCGTAAAACATTTGACAATACATTCAT-CTTTTCCTGT-GTTATCTG-T
1 CAGAGTTCGTAAAACATTTGACAACACATTCATCCTTTT-CTGTGGTT-TCTGCT
* * ** *
2289973 C-GAGAT-GTAAAACACTTGACAACACATTCATATTTTTCTGTGGCTTCTGCT
1 CAGAGTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCT
2290024 CAGATGTTCGTAAAACATTTGACAACACATTCATCC-TTTCTTGTGGTTTCTGCT
1 CAGA-GTTCGTAAAACATTTGACAACACATTCATCCTTTTC-TGTGGTTTCTGCT
* * *
2290078 TAGACGTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGTTTCT
1 CAGA-GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCT
2290129 ACCAAGATTT
Statistics
Matches: 133, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
50 33 0.25
51 10 0.08
52 2 0.02
53 6 0.05
54 78 0.59
55 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (53 bp):
CAGAGTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCT
Found at i:2292306 original size:114 final size:114
Alignment explanation
Indices: 2292106--2292325 Score: 343
Period size: 114 Copynumber: 1.9 Consensus size: 114
2292096 GATCATGCAG
* * *
2292106 TTCATCTTTCAATTTCAATGATTGGTTATGGGATTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAATCTCAATGATTGGTTATGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
2292171 ATACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAACAAA
66 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAACAAA
* * *
2292220 TTCATCTTTCAAATCT-AATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAT
1 TTCATCTTTC-AATCTCAATGATTGGTTATGGGATTCATACCAAACCAGATCAGATAACTCAAAG
2292284 AACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
65 AACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
2292326 CGAGAATGTG
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
114 92 0.96
115 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAATCTCAATGATTGGTTATGGGATTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAACAAA
Found at i:2294584 original size:6 final size:6
Alignment explanation
Indices: 2294573--2294629 Score: 80
Period size: 6 Copynumber: 9.5 Consensus size: 6
2294563 TGATTCAATT
* *
2294573 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTG GTTTT- TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
2294620 TTCTTTC TTT
1 TT-TTTC TTT
2294630 GCTAGATGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
5 4 0.09
6 36 0.78
7 6 0.13
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:2294930 original size:2 final size:2
Alignment explanation
Indices: 2294923--2294962 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2294913 ACAACAAAGG
2294923 AT AT AT AT AT 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 AT AT AT AT AT
2294963 TAAAAGGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2300887 original size:3 final size:3
Alignment explanation
Indices: 2300871--2300955 Score: 118
Period size: 3 Copynumber: 27.7 Consensus size: 3
2300861 TTTGGGCTTG
* *
2300871 TAA TAA TATT TAA TAA TAA TAT TAA TAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
2300918 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
2300956 TTTAAATGAA
Statistics
Matches: 74, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.03
3 65 0.88
4 7 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2303672 original size:44 final size:44
Alignment explanation
Indices: 2303609--2303700 Score: 166
Period size: 44 Copynumber: 2.1 Consensus size: 44
2303599 GAAAGATTGA
*
2303609 ATATGTTTATCTTGTCTGATGATCGAAATGGTATAACTATGACT
1 ATATGTTTATCTTGTCTGATGACCGAAATGGTATAACTATGACT
*
2303653 ATATGTTTATCTTGTCTGATGACCTAAATGGTATAACTATGACT
1 ATATGTTTATCTTGTCTGATGACCGAAATGGTATAACTATGACT
2303697 ATAT
1 ATAT
2303701 TACAAATTAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.41
Consensus pattern (44 bp):
ATATGTTTATCTTGTCTGATGACCGAAATGGTATAACTATGACT
Found at i:2305523 original size:2 final size:2
Alignment explanation
Indices: 2305516--2305552 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2305506 GACTTTTAGT
2305516 TC TC TC TC TC TC TC TC TC TC 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 TC TC T
2305553 TGTCCCCTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2307476 original size:2 final size:2
Alignment explanation
Indices: 2307469--2307507 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2307459 GATTTAGTTA
2307469 AT AT AT AT AT 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 AT AT AT AT AT A
2307508 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2312802 original size:2 final size:2
Alignment explanation
Indices: 2312797--2312836 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2312787 GTGTGTGTGT
2312797 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2312837 CAAGGAATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2313955 original size:75 final size:75
Alignment explanation
Indices: 2313876--2314017 Score: 189
Period size: 75 Copynumber: 1.9 Consensus size: 75
2313866 TTTAAGGATG
* ** *
2313876 TATATTCAATTAAAATATAAAA-ATATTA-TTATGAATTTATATTCTATTGAAATAAGAATATAT
1 TATATTCAATT-AAATA-AAAATATATCATTTATGAATTTATATTAAATTAAAATAAGAATATAT
2313939 TATTTATAAATT
64 TATTTATAAATT
* * *
2313951 TATATTTAATTAAATAAAAATATATCATTTATGAATTTATATTAAATTAAAATATGAATCTATTA
1 TATATTCAATTAAATAAAAATATATCATTTATGAATTTATATTAAATTAAAATAAGAATATATTA
2314016 TT
66 TT
2314018 ACGTATTTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
73 4 0.07
74 10 0.17
75 44 0.76
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.46
Consensus pattern (75 bp):
TATATTCAATTAAATAAAAATATATCATTTATGAATTTATATTAAATTAAAATAAGAATATATTA
TTTATAAATT
Found at i:2314028 original size:37 final size:38
Alignment explanation
Indices: 2313861--2314004 Score: 168
Period size: 37 Copynumber: 3.8 Consensus size: 38
2313851 GATAATGTTC
* * *
2313861 TATTATTTAAGGATGTATATTCAATTAAAATATAAAA-A
1 TATTATTTATGAATTTATATTCAATTAAAATA-AAAATA
* * *
2313899 TATTA-TTATGAATTTATATTCTATTGAAATAAGAATA
1 TATTATTTATGAATTTATATTCAATTAAAATAAAAATA
* *
2313936 TATTATTTATAAATTTATATTTAATT-AAATAAAAATA
1 TATTATTTATGAATTTATATTCAATTAAAATAAAAATA
* *
2313973 TATCATTTATGAATTTATATTAAATTAAAATA
1 TATTATTTATGAATTTATATTCAATTAAAATA
2314005 TGAATCTATT
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
36 3 0.03
37 60 0.67
38 27 0.30
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (38 bp):
TATTATTTATGAATTTATATTCAATTAAAATAAAAATA
Found at i:2317314 original size:8 final size:9
Alignment explanation
Indices: 2317289--2317313 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2317279 TTTTTAAATT
2317289 TTATTTTTA
1 TTATTTTTA
2317298 TTATTTTTA
1 TTATTTTTA
2317307 TTATTTT
1 TTATTTT
2317314 ACTAACTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTATTTTTA
Found at i:2318144 original size:18 final size:18
Alignment explanation
Indices: 2318121--2318165 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
2318111 ACTATATGAC
*
2318121 GACATTGCTTATCTTTTG
1 GACATTCCTTATCTTTTG
2318139 GACATTCCTTATCTTTTG
1 GACATTCCTTATCTTTTG
2318157 GACATTCCT
1 GACATTCCT
2318166 ATTGACCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.47
Consensus pattern (18 bp):
GACATTCCTTATCTTTTG
Found at i:2328220 original size:35 final size:36
Alignment explanation
Indices: 2328173--2328245 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 36
2328163 GGAAACAAGT
*
2328173 AATGCAAATCAAGCCTTCACAAAAGAGAAGTGAAGC
1 AATGCAAATCAAGCCTTCACAAAAGACAAGTGAAGC
*
2328209 AATGC-AATCAAGCCTTCACAAAAGACTAGTGAAGC
1 AATGCAAATCAAGCCTTCACAAAAGACAAGTGAAGC
2328244 AA
1 AA
2328246 GATCAGATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 30 0.86
36 5 0.14
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.15
Consensus pattern (36 bp):
AATGCAAATCAAGCCTTCACAAAAGACAAGTGAAGC
Found at i:2335393 original size:27 final size:27
Alignment explanation
Indices: 2335363--2335463 Score: 202
Period size: 27 Copynumber: 3.7 Consensus size: 27
2335353 TCATCTTTCT
2335363 AATGAATTAGAAATTAAGGAACTAAGG
1 AATGAATTAGAAATTAAGGAACTAAGG
2335390 AATGAATTAGAAATTAAGGAACTAAGG
1 AATGAATTAGAAATTAAGGAACTAAGG
2335417 AATGAATTAGAAATTAAGGAACTAAGG
1 AATGAATTAGAAATTAAGGAACTAAGG
2335444 AATGAATTAGAAATTAAGGA
1 AATGAATTAGAAATTAAGGA
2335464 GGAATTTCCT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.52, C:0.03, G:0.22, T:0.23
Consensus pattern (27 bp):
AATGAATTAGAAATTAAGGAACTAAGG
Found at i:2336011 original size:14 final size:15
Alignment explanation
Indices: 2335985--2336013 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2335975 TTTATTTGCT
2335985 TTAGTTCTTTTAATA
1 TTAGTTCTTTTAATA
2336000 TTAGTT-TTTTAATA
1 TTAGTTCTTTTAATA
2336014 GAATAGACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (15 bp):
TTAGTTCTTTTAATA
Found at i:2337376 original size:21 final size:21
Alignment explanation
Indices: 2337350--2337400 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2337340 AAAGGTTTAC
*
2337350 TATCGATACTCATTCATAG-AT
1 TATCGATACTCAAT-ATAGAAT
*
2337371 TATCGATAC-CAATGTAGAAT
1 TATCGATACTCAATATAGAAT
2337391 TATCGATACT
1 TATCGATACT
2337401 GAGGTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 3 0.12
20 14 0.54
21 9 0.35
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (21 bp):
TATCGATACTCAATATAGAAT
Found at i:2337579 original size:20 final size:20
Alignment explanation
Indices: 2337536--2337605 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
2337526 CAGTCTAGGG
* **
2337536 GTATCGATACCAACAGGTGG
1 GTATCGATACCAAAAGGTCA
* *
2337556 GTATCGATACCAAAAGTTTA
1 GTATCGATACCAAAAGGTCA
* *
2337576 GTATCGATACTAAAGGGTCA
1 GTATCGATACCAAAAGGTCA
2337596 GTATCGATAC
1 GTATCGATAC
2337606 TTATGAAGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (20 bp):
GTATCGATACCAAAAGGTCA
Found at i:2367707 original size:40 final size:40
Alignment explanation
Indices: 2367663--2367744 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 40
2367653 ACCCTAGCCG
* * *
2367663 AAGCATAGGGGCCA-CCTGAGGGGAGTGCCCATA-GGTCCAT
1 AAGCAAAGGAGCCACCCT-AGGAGAGTGCCC-TAGGGTCCAT
*
2367703 AAGCAAAGGAGCCACCCTATGAGAGTGCCCTAGGGTCCAT
1 AAGCAAAGGAGCCACCCTAGGAGAGTGCCCTAGGGTCCAT
2367743 AA
1 AA
2367745 AGTCTTACCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
39 2 0.06
40 31 0.86
41 3 0.08
ACGTcount: A:0.29, C:0.26, G:0.30, T:0.15
Consensus pattern (40 bp):
AAGCAAAGGAGCCACCCTAGGAGAGTGCCCTAGGGTCCAT
Found at i:2368660 original size:24 final size:24
Alignment explanation
Indices: 2368633--2368680 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2368623 GTTCAGTATG
* * *
2368633 AGTTGACTCGATTTGAGTTGACTC
1 AGTTAACTCGATCTAAGTTGACTC
2368657 AGTTAACTCGATCTAAGTTGACTC
1 AGTTAACTCGATCTAAGTTGACTC
2368681 GGTTCTAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (24 bp):
AGTTAACTCGATCTAAGTTGACTC
Found at i:2369715 original size:24 final size:25
Alignment explanation
Indices: 2369688--2369736 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
2369678 ATTTTATATA
2369688 TATATTAACTT-TAAAAAATATTTT
1 TATATTAACTTATAAAAAATATTTT
* *
2369712 TATATTAACTTATTAAATATATTTT
1 TATATTAACTTATAAAAAATATTTT
2369737 ATGTTAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
TATATTAACTTATAAAAAATATTTT
Found at i:2369880 original size:2 final size:2
Alignment explanation
Indices: 2369873--2369918 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2369863 AGAATAAATA
2369873 AT AT AT AT AT AT 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 AT AT AT AT AT AT
2369915 AT AT
1 AT AT
2369919 TAAATTGAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2375850 original size:20 final size:22
Alignment explanation
Indices: 2375825--2375882 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
2375815 TTCCCCTTGA
2375825 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
2375845 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
2375868 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2375883 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:2379464 original size:20 final size:20
Alignment explanation
Indices: 2379439--2379476 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2379429 TTCCCCTTGA
2379439 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
2379459 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
2379477 TTAAAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:2382403 original size:19 final size:18
Alignment explanation
Indices: 2382357--2382405 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
2382347 TTTTCTTCTG
2382357 TATAAAAATATTAAAATA
1 TATAAAAATATTAAAATA
* * *
2382375 TATATTAAATATTAAAGTCT
1 TATA-AAAATATTAAAAT-A
2382395 TATAAAAATAT
1 TATAAAAATAT
2382406 AATTAAAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 4 0.16
19 17 0.68
20 4 0.16
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
TATAAAAATATTAAAATA
Found at i:2391744 original size:22 final size:22
Alignment explanation
Indices: 2391718--2391777 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
2391708 TTGGTGCAAA
2391718 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * * *
2391740 GGGAACCGATTCCCTC-TGTAG
1 GGGAATCGATACCCCCTTGAAG
2391761 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
2391778 GGGGTTCTGT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:2393384 original size:18 final size:18
Alignment explanation
Indices: 2393349--2393387 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2393339 AGAGCAGCAC
*
2393349 GAGGAACAAGCACCTCCA
1 GAGGAACAACCACCTCCA
* *
2393367 GAGGAACAACCTCGTCCA
1 GAGGAACAACCACCTCCA
2393385 GAG
1 GAG
2393388 TATCAAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.31, G:0.26, T:0.08
Consensus pattern (18 bp):
GAGGAACAACCACCTCCA
Found at i:2393681 original size:17 final size:17
Alignment explanation
Indices: 2393652--2393689 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2393642 CATTTTGGAT
2393652 ATTT-TGGAATGTTTGA
1 ATTTGTGGAATGTTTGA
*
2393668 ATTTGTGGATTGTTTGA
1 ATTTGTGGAATGTTTGA
*
2393685 CTTTG
1 ATTTG
2393690 AATTTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (17 bp):
ATTTGTGGAATGTTTGA
Found at i:2398073 original size:35 final size:34
Alignment explanation
Indices: 2398034--2398282 Score: 118
Period size: 35 Copynumber: 7.1 Consensus size: 34
2398024 ATTTACTTAA
*
2398034 AATAAATATCTTTTAATATTCAAATTTAAATATAT
1 AATAAATATCTTTTAATATTCAAATTTAAA-AGAT
*
2398069 AATAAAATATCTTTTAAT-TTAAAATATTTAAAAGAT
1 AAT-AAATATCTTTTAATATT-CAA-ATTTAAAAGAT
** * * *
2398105 -ATGGATACCTTTGAATATTCAAACTTAAAGAGAT
1 AATAAATATCTTTTAATATTCAAATTTAAA-AGAT
* * *
2398139 AATAGATATCTTTTAAT-TTGAAGTATTCAAAACGAT
1 AATAAATATCTTTTAATATTCAA--ATTTAAAA-GAT
* * * * *
2398175 -ATAATTATATTTTAATGTTCAAAGTTAAATAAAT
1 AATAAATATCTTTTAATATTCAAATTTAAA-AGAT
* * *
2398209 AACAAAAAAATCTTTTAAT-TTTAAATATTCAAAAGA-
1 -A-ATAAATATCTTTTAATATTCAAAT-TT-AAAAGAT
*
2398245 ATATAATTATCTTATTAATATAT-AAA-TTAAAGAGAT
1 A-ATAAATATCTT-TTAATAT-TCAAATTTAAA-AGAT
2398281 AA
1 AA
2398283 ATATTTTTTT
Statistics
Matches: 161, Mismatches: 32, Indels: 42
0.69 0.14 0.18
Matches are distributed among these distances:
33 6 0.04
34 30 0.19
35 52 0.32
36 42 0.26
37 27 0.17
38 4 0.02
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (34 bp):
AATAAATATCTTTTAATATTCAAATTTAAAAGAT
Found at i:2398141 original size:70 final size:70
Alignment explanation
Indices: 2398043--2398265 Score: 225
Period size: 70 Copynumber: 3.1 Consensus size: 70
2398033 AAATAAATAT
* * *
2398043 CTTTTAATATTCAAATTTAAATATATAATAAAATATCTTTTAATTTAAAATATTTAAAAGATATG
1 CTTTTAATATTCAAACTTAAATAAATAATAAAATATCTTTTAATTTAAAATATTCAAAAGATAT-
*
2398108 GA-TAC
65 AATTAC
* * * * * *
2398113 CTTTGAATATTCAAACTTAAAGAGATAAT-AGATATCTTTTAATTTGAAGTATTCAAAACGATAT
1 CTTTTAATATTCAAACTTAAATAAATAATAAAATATCTTTTAATTTAAAATATTCAAAA-GATAT
*
2398177 AATTAT
65 AATTAC
* * * * * *
2398183 ATTTTAATGTTCAAAGTTAAATAAATAACAAAAAAATCTTTTAATTTTAAATATTCAAAAGAATA
1 CTTTTAATATTCAAACTTAAATAAATAA-TAAAATATCTTTTAATTTAAAATATTCAAAAG-ATA
*
2398248 TAATTAT
64 TAATTAC
2398255 CTTATTAATAT
1 CTT-TTAATAT
2398266 ATAAATTAAA
Statistics
Matches: 124, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
69 26 0.21
70 54 0.44
71 1 0.01
72 37 0.30
73 6 0.05
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.41
Consensus pattern (70 bp):
CTTTTAATATTCAAACTTAAATAAATAATAAAATATCTTTTAATTTAAAATATTCAAAAGATATA
ATTAC
Found at i:2398293 original size:140 final size:139
Alignment explanation
Indices: 2398035--2398329 Score: 332
Period size: 140 Copynumber: 2.1 Consensus size: 139
2398025 TTTACTTAAA
* * * * * *
2398035 ATAAATATCTTTTAATATTCAAATTTAAATATATAATAAAATATCTTTTAATTTAAAATATTTAA
1 ATAAATATATTTTAATATTCAAAGTTAAATAAATAAAAAAAAATCTTTTAATTTAAAATATTCAA
*
2398100 AAGATATGGATACCTTTGAATATTCAAACTTAAAGAGATAATAGATATCTTTTAATTT-GAAGTA
66 AAGATATGAATACCTTTGAATATTCAAACTTAAAGAGATAATAGATATCTTTTAATTTGGAA-TA
*
2398164 TTCAAAACGAT
130 TT-AAAAAGAT
* * *
2398175 ATAATTATATTTTAATGTTCAAAGTTAAATAAATAACAAAAAAATCTTTTAATTTTAAATATTCA
1 ATAAATATATTTTAATATTCAAAGTTAAATAAATAA-AAAAAAATCTTTTAATTTAAAATATTCA
* * * *
2398240 AAAGAATAT-AATTATCTTATTAATATAT-AAA-TTAAAGAGATAA-ATAT-TTTTTTAATTTGG
65 AAAG-ATATGAA-TACCTT-TGAATAT-TCAAACTTAAAGAGATAATAGATATCTTTTAATTTGG
2398300 AATATTAAAAAGAT
126 AATATTAAAAAGAT
* *
2398314 ATAAATTTAATTTAAT
1 ATAAATATATTTTAAT
2398330 TATTAAACTC
Statistics
Matches: 131, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
139 20 0.15
140 45 0.34
141 35 0.27
142 21 0.16
143 9 0.07
144 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (139 bp):
ATAAATATATTTTAATATTCAAAGTTAAATAAATAAAAAAAAATCTTTTAATTTAAAATATTCAA
AAGATATGAATACCTTTGAATATTCAAACTTAAAGAGATAATAGATATCTTTTAATTTGGAATAT
TAAAAAGAT
Found at i:2402254 original size:6 final size:6
Alignment explanation
Indices: 2402243--2402274 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2402233 CAACGACAAT
2402243 GGGTTA GGGTTA GGGTTA GGGTTA GGGTTA GG
1 GGGTTA GGGTTA GGGTTA GGGTTA GGGTTA GG
2402275 ATTTAGGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.31
Consensus pattern (6 bp):
GGGTTA
Found at i:2403650 original size:15 final size:16
Alignment explanation
Indices: 2403630--2403663 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2403620 TTTAATATAA
*
2403630 TTATTTAT-ATTTAAT
1 TTATTTATCAGTTAAT
2403645 TTATTTATCAGTTAAT
1 TTATTTATCAGTTAAT
2403661 TTA
1 TTA
2403664 AACAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (16 bp):
TTATTTATCAGTTAAT
Found at i:2416959 original size:35 final size:35
Alignment explanation
Indices: 2416914--2416980 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
2416904 TAAATTAAAG
*
2416914 ATTTTAGAATTTAAGGTTTAAAATGTAATTGAATT
1 ATTTTAGAATTTAAGGTTTAAAATGAAATTGAATT
* ** *
2416949 ATTTTGGAATTTGGGGTTTAGAATGAAATTGA
1 ATTTTAGAATTTAAGGTTTAAAATGAAATTGA
2416981 GGAATGTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (35 bp):
ATTTTAGAATTTAAGGTTTAAAATGAAATTGAATT
Found at i:2417343 original size:12 final size:11
Alignment explanation
Indices: 2417321--2417355 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2417311 TAAATTTATT
2417321 AAATTAAATTA
1 AAATTAAATTA
2417332 AAATTAAAATTA
1 AAATT-AAATTA
*
2417344 AAATCAAATTA
1 AAATTAAATTA
2417355 A
1 A
2417356 TAGAATGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATTAAATTA
Found at i:2417343 original size:17 final size:17
Alignment explanation
Indices: 2417321--2417355 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2417311 TAAATTTATT
*
2417321 AAATTAAATTAAAATTA
1 AAATTAAAATAAAATTA
*
2417338 AAATTAAAATCAAATTA
1 AAATTAAAATAAAATTA
2417355 A
1 A
2417356 TAGAATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATTAAAATAAAATTA
Found at i:2417478 original size:24 final size:24
Alignment explanation
Indices: 2417446--2417497 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
2417436 TTATAATAAT
* *
2417446 TAAATAGTTAAGTGATCTGATTTA
1 TAAATAGTTAAGTGATCTAATTGA
2417470 TAAATAGTTAAGTGATCTAATTGA
1 TAAATAGTTAAGTGATCTAATTGA
2417494 TAAA
1 TAAA
2417498 ATTGAAAGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.38
Consensus pattern (24 bp):
TAAATAGTTAAGTGATCTAATTGA
Found at i:2417905 original size:20 final size:21
Alignment explanation
Indices: 2417864--2417911 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
2417854 TAAATAATTT
*
2417864 AAAAA-TAACGTTTTTCATAA
1 AAAAATTAACGTTTTTCAAAA
*
2417884 AAAAATTAATGTTTTT-AAAA
1 AAAAATTAACGTTTTTCAAAA
*
2417904 AATAATTA
1 AAAAATTA
2417912 TTGAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (21 bp):
AAAAATTAACGTTTTTCAAAA
Found at i:2421851 original size:43 final size:43
Alignment explanation
Indices: 2421794--2421885 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 43
2421784 ATTTCAAAAC
* * * * *
2421794 CACCTAAGGGGGTTTTGAAACCATGCCCAAAATTTCCTAATTT
1 CACCTTAGGGGGTTTCGAAACCATACACAAAATTGCCTAATTT
* * * *
2421837 CACCTTAGGTGGTTTCGAAACCCTATAGAAAATTGCCTAATTT
1 CACCTTAGGGGGTTTCGAAACCATACACAAAATTGCCTAATTT
2421880 CACCTT
1 CACCTT
2421886 TTAAAATCTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (43 bp):
CACCTTAGGGGGTTTCGAAACCATACACAAAATTGCCTAATTT
Found at i:2422282 original size:2 final size:2
Alignment explanation
Indices: 2422275--2422338 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
2422265 TAAGCCGAGA
2422275 AT AT AT AT AT AT 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 AT AT AT AT AT AT
2422317 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
2422339 GATTATTATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2423130 original size:17 final size:17
Alignment explanation
Indices: 2423108--2423140 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2423098 TAAAAAGGGT
2423108 AAATTA-CACGTTTTATA
1 AAATTATCAC-TTTTATA
2423125 AAATTATCACTTTTAT
1 AAATTATCACTTTTAT
2423141 TTTATTTTAG
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:0.39, C:0.12, G:0.03, T:0.45
Consensus pattern (17 bp):
AAATTATCACTTTTATA
Found at i:2425034 original size:20 final size:19
Alignment explanation
Indices: 2424997--2425044 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2424987 TCTAAATCCC
*
2424997 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATTCCATTTTG
2425016 ATTTTCAAAA-TCCATTTTTG
1 -TTTTCAAAATTCCA-TTTTG
*
2425036 CTTTCAAAA
1 TTTTCAAAA
2425045 GAAAATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (19 bp):
TTTTCAAAATTCCATTTTG
Found at i:2427039 original size:5 final size:5
Alignment explanation
Indices: 2427031--2427105 Score: 150
Period size: 5 Copynumber: 15.0 Consensus size: 5
2427021 ATAAAATAAA
2427031 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
2427081 GATAT GATAT GATAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT
2427106 AGAGAATAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 70 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
GATAT
Found at i:2427755 original size:23 final size:20
Alignment explanation
Indices: 2427722--2427764 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
2427712 TAGAAAAAGT
2427722 ATATTTATAATATTATAAAAA
1 ATATTTATAAT-TTATAAAAA
*
2427743 ATATTTATTTAATTTTTAAAAA
1 ATATTTA--TAATTTATAAAAA
2427765 TCCAAAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 8 0.42
23 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTTATAATTTATAAAAA
Found at i:2427961 original size:31 final size:31
Alignment explanation
Indices: 2427923--2428002 Score: 116
Period size: 26 Copynumber: 2.7 Consensus size: 31
2427913 AGTATTGCTG
*
2427923 AGCTCGACTCGACTCGAAAACTTTGAAATGA
1 AGCTCGACTCGACTCGAAAACTTTGAAATAA
2427954 A----G-CTCGACTCGAAAACTTTGAAATAA
1 AGCTCGACTCGACTCGAAAACTTTGAAATAA
2427980 AGCTCGACTCGACTCGAAAACTT
1 AGCTCGACTCGACTCGAAAACTT
2428003 GTGAGCTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
26 24 0.56
27 1 0.02
30 1 0.02
31 17 0.40
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (31 bp):
AGCTCGACTCGACTCGAAAACTTTGAAATAA
Found at i:2428009 original size:26 final size:26
Alignment explanation
Indices: 2427921--2428009 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 26
2427911 TGAGTATTGC
2427921 TGAGCTCGACTCGACTCGAAAACTT-
1 TGAGCTCGACTCGACTCGAAAACTTG
**
2427946 TGAAAT-GAAGCTCGACTCGAAAACTTTG
1 TGAGCTCG-A-CTCGACTCGAAAAC-TTG
*
2427974 AAATAAAGCTCGACTCGACTCGAAAACTTG
1 ---T-GAGCTCGACTCGACTCGAAAACTTG
2428004 TGAGCT
1 TGAGCT
2428010 TAAAATTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
24 1 0.02
25 5 0.10
26 18 0.37
27 3 0.06
30 3 0.06
31 15 0.31
32 3 0.06
33 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (26 bp):
TGAGCTCGACTCGACTCGAAAACTTG
Found at i:2429734 original size:24 final size:24
Alignment explanation
Indices: 2429707--2429753 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2429697 TTATCATTTC
*
2429707 TTGTCATCCTTCTTTTCATCTTTT
1 TTGTCATCCTCCTTTTCATCTTTT
* *
2429731 TTGTCGTCCTCCTTTTCTTCTTT
1 TTGTCATCCTCCTTTTCATCTTT
2429754 AGCAGGTCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.04, C:0.28, G:0.06, T:0.62
Consensus pattern (24 bp):
TTGTCATCCTCCTTTTCATCTTTT
Found at i:2431980 original size:29 final size:30
Alignment explanation
Indices: 2431914--2431981 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
2431904 AATTATGATT
*
2431914 TAAATTTTAAAATTTAAAAAATATAATAAC
1 TAAATTTTAAAATGTAAAAAATATAATAAC
*** * *
2431944 TTCTTTTTAATA-GTAAAAGATATAATAAC
1 TAAATTTTAAAATGTAAAAAATATAATAAC
2431973 TAAATTTTA
1 TAAATTTTA
2431982 TCAAATTAGA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.41
Consensus pattern (30 bp):
TAAATTTTAAAATGTAAAAAATATAATAAC
Found at i:2432613 original size:14 final size:14
Alignment explanation
Indices: 2432594--2432621 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2432584 ATTTCAACTA
2432594 AAAATTAAAATATT
1 AAAATTAAAATATT
2432608 AAAATTAAAATATT
1 AAAATTAAAATATT
2432622 CTAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATTAAAATATT
Found at i:2438827 original size:2 final size:2
Alignment explanation
Indices: 2438814--2438848 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2438804 AAATTTGCTT
*
2438814 TA TA TG 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 TA T
2438849 TGCAGCCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2441499 original size:104 final size:105
Alignment explanation
Indices: 2441302--2441509 Score: 346
Period size: 104 Copynumber: 2.0 Consensus size: 105
2441292 TAATGTCTGC
* **
2441302 ACCATTAATAGCTTAAACGTCCATCGGGAGATTAGATTGCTTTACAAGATCAAACAGTGCTGTTA
1 ACCATTAATAGCTTAAACGTCCATCGGGAGACTAGAAAGCTTTACAAGATCAAACAGTGCTGTTA
* *
2441367 TTAGGGATTAAAAAGTTGGCCGACATGCAAAATTGACTTT
66 TTAGGGATTAAAAAGTTGACCGACATGCAAAAATGACTTT
*
2441407 ACCATTAATAGCTTAAACGTCCATCGGGAGACTAGAAAGCTTTAC-AGATCAAACAGTGTTGTTA
1 ACCATTAATAGCTTAAACGTCCATCGGGAGACTAGAAAGCTTTACAAGATCAAACAGTGCTGTTA
*
2441471 TTAGGGATTAAAAAGTTGACCGATATGCAAAAATGACTT
66 TTAGGGATTAAAAAGTTGACCGACATGCAAAAATGACTT
2441510 AAAACGATTT
Statistics
Matches: 96, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
104 54 0.56
105 42 0.44
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (105 bp):
ACCATTAATAGCTTAAACGTCCATCGGGAGACTAGAAAGCTTTACAAGATCAAACAGTGCTGTTA
TTAGGGATTAAAAAGTTGACCGACATGCAAAAATGACTTT
Found at i:2446640 original size:21 final size:23
Alignment explanation
Indices: 2446616--2446674 Score: 104
Period size: 21 Copynumber: 2.7 Consensus size: 23
2446606 AAAGGCTTCT
2446616 CCTTTTATCTTCTTCTTC-A-CC
1 CCTTTTATCTTCTTCTTCAACCC
2446637 CCTTTTATCTTCTTCTTCAACCC
1 CCTTTTATCTTCTTCTTCAACCC
2446660 CCTTTTATCTTCTTC
1 CCTTTTATCTTCTTC
2446675 ACCCATCCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 18 0.50
22 1 0.03
23 17 0.47
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.53
Consensus pattern (23 bp):
CCTTTTATCTTCTTCTTCAACCC
Found at i:2447059 original size:16 final size:15
Alignment explanation
Indices: 2447020--2447062 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
2447010 TTACTACTTG
2447020 TATGTAATCTACTCA
1 TATGTAATCTACTCA
2447035 TATGTAATCTACTCA
1 TATGTAATCTACTCA
2447050 -AGTAGTAATCTAC
1 TA-T-GTAATCTAC
2447063 ATGAGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.04
15 16 0.62
16 9 0.35
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (15 bp):
TATGTAATCTACTCA
Found at i:2447221 original size:80 final size:80
Alignment explanation
Indices: 2447066--2447214 Score: 262
Period size: 80 Copynumber: 1.9 Consensus size: 80
2447056 AATCTACATG
* * *
2447066 AGTTTTTTGTTTGTATGGGGTGGAATAGCATGTGTGGGACTTAGGTGTTTGATTTGTTATAATGG
1 AGTTGTTTGTTTGTATGGGGTGGAATAGCATGCGTGGGACTTAGGTGCTTGATTTGTTATAATGG
*
2447131 ACGTTCTAAGTGTTA
66 AAGTTCTAAGTGTTA
2447146 AGTTGTTTGTTTGTATGGGGTGGAATAGCATGCGTGGGACTTAGGTGCTTGATTTGTTATAATGG
1 AGTTGTTTGTTTGTATGGGGTGGAATAGCATGCGTGGGACTTAGGTGCTTGATTTGTTATAATGG
2447211 AAGT
66 AAGT
2447215 GTTAAGTTGG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.20, C:0.05, G:0.33, T:0.42
Consensus pattern (80 bp):
AGTTGTTTGTTTGTATGGGGTGGAATAGCATGCGTGGGACTTAGGTGCTTGATTTGTTATAATGG
AAGTTCTAAGTGTTA
Found at i:2447554 original size:21 final size:21
Alignment explanation
Indices: 2447530--2447596 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 21
2447520 GATACCACTA
*
2447530 GTATCTATACTAGATAAATTG
1 GTATCCATACTAGATAAATTG
* *
2447551 GTATCCATAC-CGCT--A---
1 GTATCCATACTAGATAAATTG
*
2447566 GTATCTATACTAGATAAATTG
1 GTATCCATACTAGATAAATTG
2447587 GTATCCATAC
1 GTATCCATAC
2447597 CGAAAGATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 12
0.63 0.13 0.23
Matches are distributed among these distances:
15 9 0.27
16 2 0.06
18 2 0.06
20 2 0.06
21 18 0.55
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (21 bp):
GTATCCATACTAGATAAATTG
Found at i:2447598 original size:36 final size:36
Alignment explanation
Indices: 2447512--2447598 Score: 156
Period size: 36 Copynumber: 2.4 Consensus size: 36
2447502 TACCTGATGG
* *
2447512 TTGGTATCGATACCACTAGTATCTATACTAGATAAA
1 TTGGTATCCATACCGCTAGTATCTATACTAGATAAA
2447548 TTGGTATCCATACCGCTAGTATCTATACTAGATAAA
1 TTGGTATCCATACCGCTAGTATCTATACTAGATAAA
2447584 TTGGTATCCATACCG
1 TTGGTATCCATACCG
2447599 AAAGATTAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (36 bp):
TTGGTATCCATACCGCTAGTATCTATACTAGATAAA
Found at i:2448577 original size:86 final size:86
Alignment explanation
Indices: 2448479--2448651 Score: 321
Period size: 86 Copynumber: 2.0 Consensus size: 86
2448469 GACTAAAGTT
*
2448479 TCCTTCCGTGCAATTTGGTAAG-CTAATATATATAAAAGACTAATAAGCGCATCATAACGTTCTA
1 TCCTTCAGTGCAATTTGGT-AGTCTAATATATATAAAAGACTAATAAGCGCATCATAACGTTCTA
2448543 GAGGATAAAATGAGTGAGATAG
65 GAGGATAAAATGAGTGAGATAG
2448565 TCCTTCAGTGCAATTTGGTAGTCTAATATATATAAAAGACTAATAAGCGCATCATAACGTTCTAG
1 TCCTTCAGTGCAATTTGGTAGTCTAATATATATAAAAGACTAATAAGCGCATCATAACGTTCTAG
2448630 AGGATAAAATGAGTGAGATAG
66 AGGATAAAATGAGTGAGATAG
2448651 T
1 T
2448652 AGTGGGTGAG
Statistics
Matches: 85, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
85 2 0.02
86 83 0.98
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (86 bp):
TCCTTCAGTGCAATTTGGTAGTCTAATATATATAAAAGACTAATAAGCGCATCATAACGTTCTAG
AGGATAAAATGAGTGAGATAG
Found at i:2451073 original size:21 final size:21
Alignment explanation
Indices: 2451048--2451097 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2451038 AGTTGTGGGG
*
2451048 ATGTTTTTAGTTTTTTATTAA
1 ATGTTTTTAGTATTTTATTAA
* *
2451069 ATGTTTTTGGTATTTTATTTA
1 ATGTTTTTAGTATTTTATTAA
2451090 AT-TTTTTA
1 ATGTTTTTA
2451098 AATAATTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.68
Consensus pattern (21 bp):
ATGTTTTTAGTATTTTATTAA
Found at i:2451807 original size:20 final size:20
Alignment explanation
Indices: 2451631--2451818 Score: 122
Period size: 19 Copynumber: 9.6 Consensus size: 20
2451621 AAATGACCAA
*
2451631 CAAATTCGCAACGCG-ATCT
1 CAAATTCGCAACGCGAATTT
* *
2451650 CAAATTCGCAAC-CCAGTTT
1 CAAATTCGCAACGCGAATTT
*
2451669 CCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCGAAT-T-T
* ** *
2451692 -AAA-TCACATTGCGATTTT
1 CAAATTCGCAACGCGAATTT
**
2451710 CCAAATTCGCAACGCGAAAGT
1 -CAAATTCGCAACGCGAATTT
* * *
2451731 CAAATTCGTAAC-TGAATTC
1 CAAATTCGCAACGCGAATTT
* *
2451750 CAAATTCGTAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
*
2451769 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
*
2451788 CAAATTCACAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
2451808 -AATTTCGCAAC
1 CAAATTCGCAAC
2451819 AGGTTTTAGT
Statistics
Matches: 132, Mismatches: 28, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
18 2 0.02
19 74 0.56
20 40 0.30
21 14 0.11
22 1 0.01
23 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Done.