Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008528.1 Hibiscus syriacus cultivar Beakdansim tig00111403_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: 1199389
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:943279 original size:61 final size:62
Alignment explanation
Indices: 943214--943341 Score: 206
Period size: 61 Copynumber: 2.1 Consensus size: 62
943204 TGTAATTTAT
* *
943214 TCCAAATTTC-TTGCGATAGTCCTAGTTCGCGTTGCGATTTATTAAAAATTCGTTGCGATAG
1 TCCAAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTAAAAATTCGTTGCGATAG
**
943275 TCC-AAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTAAAAATTCGTTGCGATAG
943336 TCCAAA
1 TCCAAA
943342 AATCATGCAC
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
60 5 0.08
61 54 0.89
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (62 bp):
TCCAAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTAAAAATTCGTTGCGATAG
Found at i:943328 original size:21 final size:20
Alignment explanation
Indices: 943161--943341 Score: 97
Period size: 19 Copynumber: 8.9 Consensus size: 20
943151 TCGAAGTTCG
*
943161 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTAGTCCAAATT
* *
943180 CATTGCGA-TAGTCCAAGTT
1 CGTTGCGATTAGTCCAAATT
** *
943199 CGCGTTGTAATTTATTCCAAATTT
1 --CGTTGCGA-TTAGTCCAAA-TT
* *
943223 C-TTGCGA-TAGTCCTAGTT
1 CGTTGCGATTAGTCCAAATT
* **
943241 CGCGTTGCGATTTATTAAAAATT
1 --CGTTGCGA-TTAGTCCAAATT
*
943264 CGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTAGTCCAAATT
*
943283 CGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTAGTCCAAATT
*
943302 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTAGTCCAAATT
943325 CGTTGCGA-TAGTCCAAA
1 CGTTGCGATTAGTCCAAA
943342 AATCATGCAC
Statistics
Matches: 122, Mismatches: 25, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
18 3 0.02
19 54 0.44
20 1 0.01
21 39 0.32
22 1 0.01
23 22 0.18
24 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTAGTCCAAATT
Found at i:943661 original size:15 final size:15
Alignment explanation
Indices: 943638--943673 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
943628 AATAAAAAAA
*
943638 ATTGTTATCGTGACG
1 ATTGATATCGTGACG
*
943653 ATTGATATCTTGACG
1 ATTGATATCGTGACG
943668 ATTGAT
1 ATTGAT
943674 TTGAGGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (15 bp):
ATTGATATCGTGACG
Found at i:945518 original size:34 final size:34
Alignment explanation
Indices: 945473--945542 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
945463 TATTAAGTCA
*
945473 TATTCAAATATTGGCCTCTTTTATAACAATCAAG
1 TATTCAAATATTGGCCTATTTTATAACAATCAAG
*
945507 TATTTAAATATTGGCCTATTTTATAACAATCAAG
1 TATTCAAATATTGGCCTATTTTATAACAATCAAG
945541 TA
1 TA
945543 GGCCAAGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (34 bp):
TATTCAAATATTGGCCTATTTTATAACAATCAAG
Found at i:961534 original size:31 final size:31
Alignment explanation
Indices: 961499--961562 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
961489 CATATTGTTT
961499 AGCTCAACTTGACTCGAAAAGTTTAAAATTG
1 AGCTCAACTTGACTCGAAAAGTTTAAAATTG
*
961530 AGCTCGACTTGACTCGAAAAGTTTAAAATTG
1 AGCTCAACTTGACTCGAAAAGTTTAAAATTG
961561 AG
1 AG
961563 TTTGACTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (31 bp):
AGCTCAACTTGACTCGAAAAGTTTAAAATTG
Found at i:961567 original size:26 final size:28
Alignment explanation
Indices: 961506--961572 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 28
961496 TTTAGCTCAA
961506 CTTGACTCGAAAAGTTTAAAATTGAGCT
1 CTTGACTCGAAAAGTTTAAAATTGAGCT
961534 CGACTTGACTCGAAAAGTTTAAAATTGAG-T
1 ---CTTGACTCGAAAAGTTTAAAATTGAGCT
961564 -TTGACTCGA
1 CTTGACTCGA
961573 CTTTAAAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 9 0.25
30 1 0.03
31 26 0.72
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (28 bp):
CTTGACTCGAAAAGTTTAAAATTGAGCT
Found at i:962674 original size:26 final size:27
Alignment explanation
Indices: 962629--962690 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
962619 ATTTTATGTT
* * *
962629 AATAGTAAATTTTTATAATTTT-GAAAC
1 AATA-TAAATTTATAAAATTTTAGAAAA
962656 AATATAAATTTATAAAATTTTAGAAAA
1 AATATAAATTTATAAAATTTTAGAAAA
962683 AATA-AAAT
1 AATATAAAT
962691 AAATTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.61
27 12 0.39
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (27 bp):
AATATAAATTTATAAAATTTTAGAAAA
Found at i:971842 original size:22 final size:22
Alignment explanation
Indices: 971802--971843 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
971792 TCTATTTTCA
**
971802 TCTCCCAAAATTTTTAAGTTCG
1 TCTCCCAAAATTTAGAAGTTCG
*
971824 TCTCCTAAAATTTAGAAGTT
1 TCTCCCAAAATTTAGAAGTT
971844 TGCCCTCTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (22 bp):
TCTCCCAAAATTTAGAAGTTCG
Found at i:974200 original size:18 final size:20
Alignment explanation
Indices: 974155--974200 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
974145 ATTTTCAATT
974155 TTATAATAAAATATCTAACTA
1 TTATAATAAAATA-CTAACTA
974176 TAGTATAATAAAATA-TAA-TA
1 T--TATAATAAAATACTAACTA
974196 TTATA
1 TTATA
974201 TTCTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 4 0.17
20 3 0.13
21 4 0.17
23 12 0.52
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (20 bp):
TTATAATAAAATACTAACTA
Found at i:977470 original size:20 final size:20
Alignment explanation
Indices: 977433--977471 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
977423 GATTCGAATG
* *
977433 TTTAATAATTAAATTAAAAT
1 TTTAATAATGAAAATAAAAT
*
977453 TTTAATGATGAAAATAAAA
1 TTTAATAATGAAAATAAAA
977472 GTGAGAATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TTTAATAATGAAAATAAAAT
Found at i:978857 original size:29 final size:30
Alignment explanation
Indices: 978824--978998 Score: 120
Period size: 29 Copynumber: 5.9 Consensus size: 30
978814 TAAATTCATA
978824 ATATTTTA-TATATCTTAACTTTTAAAAAT
1 ATATTTTATTATATCTTAACTTTTAAAAAT
* *
978853 ATATTTTATTTTTATTTTAACTTATT--AAAT
1 ATATTTTA-TTATATCTTAACTT-TTAAAAAT
* * *
978883 ATATTTTATTCTTATTTTAA-TTTAAAAAAT
1 ATATTTTATT-ATATCTTAACTTTTAAAAAT
*
978913 AT-TTTTATTCTTATCTTCAA---TTAAAAAT
1 ATATTTTATT-ATATCTT-AACTTTTAAAAAT
* *
978941 ATATTTTATTTTTATTTTAAC--TTAAAAAT
1 ATATTTTA-TTATATCTTAACTTTTAAAAAT
978970 ATAATTTT-TTATTATCTTTAACTTTTAAA
1 AT-ATTTTATTA-TATC-TTAACTTTTAAA
978999 TTTTAAAAAT
Statistics
Matches: 123, Mismatches: 8, Indels: 27
0.78 0.05 0.17
Matches are distributed among these distances:
28 14 0.11
29 50 0.41
30 41 0.33
31 11 0.09
32 7 0.06
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (30 bp):
ATATTTTATTATATCTTAACTTTTAAAAAT
Found at i:978885 original size:30 final size:29
Alignment explanation
Indices: 978845--978993 Score: 178
Period size: 29 Copynumber: 5.1 Consensus size: 29
978835 ATCTTAACTT
*
978845 TTAAAAATATATTTTATTTTTATTTTAAC
1 TTAAAAATATATTTTATTCTTATTTTAAC
* *
978874 TTATTAAATATATTTTATTCTTATTTTAAT
1 TTA-AAAATATATTTTATTCTTATTTTAAC
*
978904 TTAAAAA-ATATTTTTATTCTTATCTTCAA-
1 TTAAAAATATA-TTTTATTCTTAT-TTTAAC
*
978933 TTAAAAATATATTTTATTTTTATTTTAAC
1 TTAAAAATATATTTTATTCTTATTTTAAC
*
978962 TTAAAAATATAATTTT-TTATTATCTTTAAC
1 TTAAAAATAT-ATTTTATTCTTAT-TTTAAC
978992 TT
1 TT
978994 TTAAATTTTA
Statistics
Matches: 105, Mismatches: 8, Indels: 13
0.83 0.06 0.10
Matches are distributed among these distances:
28 7 0.07
29 52 0.50
30 46 0.44
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (29 bp):
TTAAAAATATATTTTATTCTTATTTTAAC
Found at i:979191 original size:2 final size:2
Alignment explanation
Indices: 979152--979178 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
979142 TATAAGAATA
979152 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 A
979179 AATTAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:985715 original size:67 final size:69
Alignment explanation
Indices: 985629--985781 Score: 197
Period size: 68 Copynumber: 2.2 Consensus size: 69
985619 ACCCATTCAA
* * *
985629 GGGGAACCGATACCTCCTCAAT-G-AAATGAATTTCCAGAATGCTAT-AGGGGAATCGGTACCCC
1 GGGGAACCGATACCCCCTC-ATCGTAAATGAAATTCCAGAATGCT-TGAGGGGAATCGATACCCC
*
985691 -CAGGG
64 TAAGGG
* *
985696 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCTA
985761 AGGG
66 AGGG
*
985765 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
985782 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
66 2 0.03
67 20 0.27
68 33 0.44
69 20 0.27
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCTA
AGGG
Found at i:986121 original size:29 final size:29
Alignment explanation
Indices: 986087--986156 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
986077 CATATTATGA
**
986087 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
**
986116 TACATGACATGAATTCATATTGTATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
986145 TACATGACATGA
1 TACATGACATGA
986157 TTATGCAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:986214 original size:30 final size:31
Alignment explanation
Indices: 986172--986231 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
986162 CAGAAAAGTT
*
986172 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
986203 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
986232 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:986525 original size:22 final size:22
Alignment explanation
Indices: 986451--986517 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
986441 TTATGGACAT
*
986451 AATTCTACGGGTACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
986473 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
986495 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
986517 A
1 A
986518 TTTATACGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.28
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:992662 original size:68 final size:69
Alignment explanation
Indices: 992575--992728 Score: 197
Period size: 69 Copynumber: 2.2 Consensus size: 69
992565 ACCCATTCAA
* * *
992575 GGGGAACCGATACCTCCTCAAT-G-AAATGAATTTCCAGAATGCTAT-AGGGGAATCGGTACCCC
1 GGGGAACCGATACCCCCTC-ATCGTAAATGAAATTCCAGAATGCT-TGAGGGGAATCGATACCCC
*
992637 CAGGGG
64 CAAGGG
* * *
992643 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
992708 AGGG
66 AGGG
*
992712 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
992729 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
67 2 0.03
68 20 0.27
69 53 0.71
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.19
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
AGGG
Found at i:993069 original size:29 final size:29
Alignment explanation
Indices: 993035--993104 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
993025 CATATTATGA
**
993035 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
**
993064 TACATGACATGAATTCATATTGTATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
993093 TACATGACATGA
1 TACATGACATGA
993105 TTATGCAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:993162 original size:30 final size:31
Alignment explanation
Indices: 993120--993179 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
993110 CAGAAAAGTT
*
993120 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
993151 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
993180 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:993473 original size:22 final size:22
Alignment explanation
Indices: 993399--993465 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
993389 TTATGGACAT
993399 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
993421 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
993443 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
993465 A
1 A
993466 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:998121 original size:25 final size:26
Alignment explanation
Indices: 998072--998123 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
998062 AATTATATTT
* **
998072 TAAAAAAACCTAAAATATTTTAAATC
1 TAAAAAAACCTAAAACATTAAAAATC
998098 TAAAAAAACC-AAAACATTAAAAATC
1 TAAAAAAACCTAAAACATTAAAAATC
998123 T
1 T
998124 TAATTCCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.25
Consensus pattern (26 bp):
TAAAAAAACCTAAAACATTAAAAATC
Found at i:998284 original size:12 final size:12
Alignment explanation
Indices: 998267--998291 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
998257 AATCACAAAT
998267 ATTCACATCTTA
1 ATTCACATCTTA
998279 ATTCACATCTTA
1 ATTCACATCTTA
998291 A
1 A
998292 AAAATCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTCACATCTTA
Found at i:999313 original size:51 final size:52
Alignment explanation
Indices: 999248--999347 Score: 123
Period size: 51 Copynumber: 1.9 Consensus size: 52
999238 TACATTTCAA
* * * *
999248 TAGTTTAGATGAAAATGTCTTA-TTTATGCGATTAATTTATTGTTATTTTAAT
1 TAGTTTAGAGGAAAATGT-TTAGCTTATACGATTAATTTATTATTATTTTAAT
* *
999300 TAGTTTA-AGGAAAATGTTTAGCTTATATGATTAGTTTATTATTATTTT
1 TAGTTTAGAGGAAAATGTTTAGCTTATACGATTAATTTATTATTATTTT
999348 TGTGAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 3 0.07
51 31 0.76
52 7 0.17
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (52 bp):
TAGTTTAGAGGAAAATGTTTAGCTTATACGATTAATTTATTATTATTTTAAT
Found at i:1004239 original size:41 final size:41
Alignment explanation
Indices: 1004178--1004332 Score: 179
Period size: 41 Copynumber: 3.8 Consensus size: 41
1004168 TAAGAGATTC
* * * *
1004178 ATACAAACGTCGCTAAAGACTCATACTTTAGTGGCGTTTTT
1 ATACAAATGTTGCTATAGACTCGTACTTTAGTGGCGTTTTT
* * * *
1004219 ATACAAATGTTGTTATAGACTCTTAC-TTAGTGGCATTTCT
1 ATACAAATGTTGCTATAGACTCGTACTTTAGTGGCGTTTTT
* *
1004259 ATACAAATGTCT-CTATAGACTCGTATTTTAGTGACGTTTTT
1 ATACAAATGT-TGCTATAGACTCGTACTTTAGTGGCGTTTTT
* *
1004300 ATACAAACGTTGCTATAGACTTGTACTTTAGTG
1 ATACAAATGTTGCTATAGACTCGTACTTTAGTG
1004333 TTTACAATTT
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
40 34 0.36
41 61 0.64
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (41 bp):
ATACAAATGTTGCTATAGACTCGTACTTTAGTGGCGTTTTT
Found at i:1004327 original size:81 final size:82
Alignment explanation
Indices: 1004178--1004332 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 82
1004168 TAAGAGATTC
* * *
1004178 ATACAAACGTCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAATGTTGTTATAGACTCTT
1 ATACAAACGTCGCTAAAGACTCATACTTTAGTGACGTTTTTATACAAACGTTGCTATAGACTCTT
1004243 AC-TTAGTGGCATTTCT
66 ACTTTAGTGGCATTTCT
* * * * *
1004259 ATACAAATGTCTCTATAGACTCGTATTTTAGTGACGTTTTTATACAAACGTTGCTATAGACT-TG
1 ATACAAACGTCGCTAAAGACTCATACTTTAGTGACGTTTTTATACAAACGTTGCTATAGACTCT-
1004323 TACTTTAGTG
65 TACTTTAGTG
1004333 TTTACAATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
80 1 0.02
81 57 0.89
82 6 0.09
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (82 bp):
ATACAAACGTCGCTAAAGACTCATACTTTAGTGACGTTTTTATACAAACGTTGCTATAGACTCTT
ACTTTAGTGGCATTTCT
Found at i:1005237 original size:4 final size:4
Alignment explanation
Indices: 1005228--1005254 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1005218 TAAGCTGTGA
1005228 ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG
1005255 AATGAGAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:1008980 original size:24 final size:24
Alignment explanation
Indices: 1008948--1008993 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1008938 GAGTTTTCCA
1008948 TGAAGGATTTAGGGGAATTGTCCT
1 TGAAGGATTTAGGGGAATTGTCCT
1008972 TGAAGGATTTAGGGGAATTGTC
1 TGAAGGATTTAGGGGAATTGTC
1008994 TTACTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.07, G:0.35, T:0.33
Consensus pattern (24 bp):
TGAAGGATTTAGGGGAATTGTCCT
Found at i:1014527 original size:43 final size:44
Alignment explanation
Indices: 1014477--1014567 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 44
1014467 TTCACAAATG
*
1014477 CCACTATATGACATAACATTTAGCGACGTTTTTGGGA-AAAACA
1 CCACTATATGACAAAACATTTAGCGACGTTTTTGGGACAAAACA
* **
1014520 CCACTATATGTCAAAACATTTAGCGGTGTTTTTGGGACAAAACA
1 CCACTATATGACAAAACATTTAGCGACGTTTTTGGGACAAAACA
1014564 CCAC
1 CCAC
1014568 AAAAGAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 33 0.77
44 10 0.23
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (44 bp):
CCACTATATGACAAAACATTTAGCGACGTTTTTGGGACAAAACA
Found at i:1026115 original size:34 final size:30
Alignment explanation
Indices: 1026077--1026145 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1026067 TTGATATAAC
1026077 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1026111 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1026140 AATTTA
1 AATTTA
1026146 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1026156 original size:29 final size:30
Alignment explanation
Indices: 1026086--1026145 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1026076 CAATTTAAGG
1026086 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1026117 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1026146 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1026349 original size:20 final size:20
Alignment explanation
Indices: 1026324--1026397 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
1026314 AATGCAATTA
1026324 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
***
1026344 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTTCT
1026365 GTGCATCGATGCATCCTGT-T
1 GTGCATCGATGCATCCT-TCT
*
1026385 GTGCATCCATGCA
1 GTGCATCGATGCA
1026398 AGAAGGCCGC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:1026368 original size:21 final size:20
Alignment explanation
Indices: 1026324--1026379 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
1026314 AATGCAATTA
***
1026324 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCAGGCT
1026344 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-AGGCT
1026365 GTGCATCGATGCATC
1 GTGCATCGATGCATC
1026380 CTGTTGTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCAGGCT
Found at i:1026404 original size:41 final size:41
Alignment explanation
Indices: 1026324--1026404 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
1026314 AATGCAATTA
* *
1026324 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCCTTCTGTGCATCCATGCAACAAGGCT
*
1026365 GTGCATCGATGCATCCTGT-TGTGCATCCATGCAAGAAGGC
1 GTGCATCGATGCATCCT-TCTGTGCATCCATGCAACAAGGC
1026405 CGCAACGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 35 0.97
42 1 0.03
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (41 bp):
GTGCATCGATGCATCCTTCTGTGCATCCATGCAACAAGGCT
Found at i:1029666 original size:34 final size:30
Alignment explanation
Indices: 1029628--1029696 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1029618 TTGATATAAC
1029628 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1029662 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1029691 AATTTA
1 AATTTA
1029697 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1029707 original size:29 final size:30
Alignment explanation
Indices: 1029637--1029696 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1029627 CAATTTAAGG
1029637 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1029668 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1029697 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1029924 original size:41 final size:41
Alignment explanation
Indices: 1029878--1029957 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
1029868 GCAATTAGTG
*
1029878 CATCGATGCATCCT-TCTGTGCATCGATGCATC-AAGGCTGTA
1 CATCGATGCATCCTGT-TGTGCATCCATGCA-CGAAGGCTGTA
*
1029919 CATCGATGTATCCTGTTGTGCATCCATGCACGAAGGCTG
1 CATCGATGCATCCTGTTGTGCATCCATGCACGAAGGCTG
1029958 CAACGGCTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 1 0.03
41 33 0.94
42 1 0.03
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (41 bp):
CATCGATGCATCCTGTTGTGCATCCATGCACGAAGGCTGTA
Found at i:1032472 original size:56 final size:57
Alignment explanation
Indices: 1032375--1032481 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 57
1032365 GAATATATGA
** * *
1032375 ATAGTTGGGTGACTATTTTATAACTTTTAATAGTCGGGGGACTCAAGAAAACATCTT
1 ATAGTTGGGTGACTATTTTATAACTTTTAATAGTCAAGGGACACAACAAAACATCTT
*
1032432 ATAGTTGGG-GA-TCATTTTGTAACTTTTAATAGTCAAGGGACACAACAAAA
1 ATAGTTGGGTGACT-ATTTTATAACTTTTAATAGTCAAGGGACACAACAAAA
1032482 TAATATTCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
55 1 0.02
56 34 0.77
57 9 0.20
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (57 bp):
ATAGTTGGGTGACTATTTTATAACTTTTAATAGTCAAGGGACACAACAAAACATCTT
Found at i:1040473 original size:45 final size:45
Alignment explanation
Indices: 1040405--1040491 Score: 149
Period size: 45 Copynumber: 1.9 Consensus size: 45
1040395 ATTTTGAGTC
1040405 TATAATTATATAATTTTTTAAATTTTATAATACATATATTGTGTA
1 TATAATTATATAATTTTTTAAATTTTATAATACATATATTGTGTA
*
1040450 TATATATT-TATACTTTTTTAAATTTTATAATACATATATTGT
1 TATA-ATTATATAATTTTTTAAATTTTATAATACATATATTGT
1040492 AATTATATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 37 0.93
46 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (45 bp):
TATAATTATATAATTTTTTAAATTTTATAATACATATATTGTGTA
Found at i:1044022 original size:30 final size:31
Alignment explanation
Indices: 1043988--1044051 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
1043978 TATTATAAAT
1043988 ATAAAAT-ATAATTAATAACATTAA-TTA-TTA
1 ATAAAATAATAA-TAATAA-ATTAATTTATTTA
*
1044018 ATAAAATAATAATATTAAATTAATTTATTTA
1 ATAAAATAATAATAATAAATTAATTTATTTA
1044049 ATA
1 ATA
1044052 TTATTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.17
30 15 0.50
31 10 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (31 bp):
ATAAAATAATAATAATAAATTAATTTATTTA
Found at i:1044154 original size:30 final size:31
Alignment explanation
Indices: 1044093--1044155 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
1044083 ATTTCTGTAA
*
1044093 TTTTATAAATAAAAATACGTTAAATATTATAT
1 TTTTAAAAATAAAAATAC-TTAAATATTATAT
1044125 TTTTAAAAATAAAAATA-TTATAA-ATTATAT
1 TTTTAAAAATAAAAATACTTA-AATATTATAT
1044155 T
1 T
1044156 AAACATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 11 0.38
31 2 0.07
32 16 0.55
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (31 bp):
TTTTAAAAATAAAAATACTTAAATATTATAT
Found at i:1044182 original size:30 final size:30
Alignment explanation
Indices: 1044148--1044208 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1044138 AATATTATAA
1044148 ATTATATTAAACATTTATTAAAATAAGAAT
1 ATTATATTAAACATTTATTAAAATAAGAAT
** * *
1044178 ATTATATTAATTATTTGTTAAAATAATAAT
1 ATTATATTAAACATTTATTAAAATAAGAAT
1044208 A
1 A
1044209 ATATTATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (30 bp):
ATTATATTAAACATTTATTAAAATAAGAAT
Found at i:1044231 original size:22 final size:22
Alignment explanation
Indices: 1044206--1044252 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1044196 TAAAATAATA
* **
1044206 ATAATATTATAATATTAAAATT
1 ATAATATTAAAATAAGAAAATT
*
1044228 ATAATGTTAAAATAAGAAAATT
1 ATAATATTAAAATAAGAAAATT
1044250 ATA
1 ATA
1044253 TTATACTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAATATTAAAATAAGAAAATT
Found at i:1044237 original size:14 final size:14
Alignment explanation
Indices: 1044200--1044240 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1044190 ATTTGTTAAA
* *
1044200 ATAATAATAATATT
1 ATAATATTAAAATT
1044214 ATAATATTAAAATT
1 ATAATATTAAAATT
*
1044228 ATAATGTTAAAAT
1 ATAATATTAAAAT
1044241 AAGAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
ATAATATTAAAATT
Found at i:1044290 original size:21 final size:22
Alignment explanation
Indices: 1044265--1044309 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1044255 ATACTCTAAA
1044265 AATTA-TTAATAA-ATATATTTT
1 AATTATTTAATAACAT-TATTTT
1044286 AATTATTTAATAACATTATTTT
1 AATTATTTAATAACATTATTTT
1044308 AA
1 AA
1044310 ATAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.23
22 15 0.68
23 2 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTATTTAATAACATTATTTT
Found at i:1045709 original size:43 final size:43
Alignment explanation
Indices: 1045648--1045735 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
1045638 AATAATAGTG
*
1045648 AAATTAAACTTGAGTGATGAACAACCCTAAAATTAGAAAGTAA
1 AAATTAAACTTGAGTGATGAACAACCCTAAAATAAGAAAGTAA
*
1045691 AAATTAAACTTGAGTGATGAATAACCCTAAAATAAGAAAGTAA
1 AAATTAAACTTGAGTGATGAACAACCCTAAAATAAGAAAGTAA
1045734 AA
1 AA
1045736 TGCGCTAAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.53, C:0.10, G:0.14, T:0.23
Consensus pattern (43 bp):
AAATTAAACTTGAGTGATGAACAACCCTAAAATAAGAAAGTAA
Found at i:1055221 original size:14 final size:14
Alignment explanation
Indices: 1055202--1055235 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1055192 GCAAAACAAG
1055202 TTCTTCTTTTATTT
1 TTCTTCTTTTATTT
*
1055216 TTCTTCTTTTCTTT
1 TTCTTCTTTTATTT
1055230 TTCTTC
1 TTCTTC
1055236 AAAACCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTTCTTTTATTT
Found at i:1063693 original size:36 final size:36
Alignment explanation
Indices: 1063646--1063720 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
1063636 CTTTTGAATT
1063646 CTCTAAGTATTGAAAATTAGAAGATGTTTTTTCATC
1 CTCTAAGTATTGAAAATTAGAAGATGTTTTTTCATC
*
1063682 CTCTAAGTATTGAAAATTAGAAGATGTTTTTTTATC
1 CTCTAAGTATTGAAAATTAGAAGATGTTTTTTCATC
1063718 CTC
1 CTC
1063721 CAAAGGATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (36 bp):
CTCTAAGTATTGAAAATTAGAAGATGTTTTTTCATC
Found at i:1064622 original size:35 final size:36
Alignment explanation
Indices: 1064576--1064677 Score: 127
Period size: 35 Copynumber: 2.8 Consensus size: 36
1064566 TGGCAACCAA
1064576 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTCT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTCT
* * *
1064613 CTTTG-AAAAT-AGTTTTCAAAGGTTAGTAAATGTTT
1 CTTTGAAAAATGA-TTTTCAAAGTTTGGTAAATGTCT
*
1064648 CTTTGAAAAATAGTTTTTCAAAGTTTGGTA
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTA
1064678 GATGGTTGTT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
34 1 0.02
35 30 0.55
36 5 0.09
37 19 0.35
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTCT
Found at i:1064690 original size:36 final size:36
Alignment explanation
Indices: 1064576--1064694 Score: 129
Period size: 37 Copynumber: 3.3 Consensus size: 36
1064566 TGGCAACCAA
1064576 CTTTGAAAAA-ATGATTTTCAAAGTTTGGTAAAT-GTCT
1 CTTTGAAAAATA-G-TTTTCAAAGTTTGGTAAATGGT-T
* * *
1064613 CTTTG-AAAATAGTTTTCAAAGGTTAGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGGTT
*
1064648 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGGTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGGTT
*
1064685 -GTTGAAAAAT
1 CTTTGAAAAAT
1064695 GATAATGGGA
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
35 23 0.33
36 22 0.31
37 25 0.36
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.41
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGGTT
Found at i:1065542 original size:21 final size:21
Alignment explanation
Indices: 1065498--1065542 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1065488 GATTTCTGGG
* * *
1065498 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
1065519 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
1065540 CAA
1 CAA
1065543 ACGAACATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:1066312 original size:31 final size:30
Alignment explanation
Indices: 1066273--1066338 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
1066263 GTCGAGGGTT
**
1066273 TTACCTATG-TCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTAACGA-ACATATGGACAG
*
1066303 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAACGAACATATGGACAG
1066334 TTACC
1 TTACC
1066339 GAGGATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 5 0.16
31 21 0.68
32 5 0.16
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (30 bp):
TTACCTATGTTCTAACGAACATATGGACAG
Found at i:1066382 original size:29 final size:30
Alignment explanation
Indices: 1066327--1066392 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
1066317 AAGGAACATA
*
1066327 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
* *
1066357 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
1066386 TGGATAG
1 TGGATAG
1066393 GTCCTTCGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 21 0.64
30 12 0.36
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.32
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:1070503 original size:21 final size:21
Alignment explanation
Indices: 1070459--1070503 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1070449 GATTTCTGGG
* * *
1070459 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
1070480 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
1070501 CAA
1 CAA
1070504 ACGAACATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:1071270 original size:31 final size:30
Alignment explanation
Indices: 1071231--1071296 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
1071221 GTCGAGGGTT
**
1071231 TTACCTATG-TCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTAACGA-ACATATGGACAG
*
1071261 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAACGAACATATGGACAG
1071292 TTACC
1 TTACC
1071297 GAGGATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 5 0.16
31 21 0.68
32 5 0.16
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (30 bp):
TTACCTATGTTCTAACGAACATATGGACAG
Found at i:1071380 original size:29 final size:30
Alignment explanation
Indices: 1071285--1071377 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
1071275 AAGGAACATA
1071285 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1071315 TGTACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
1071345 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1071374 TGGA
1 TGGA
1071378 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 18 0.31
30 40 0.69
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1072430 original size:17 final size:16
Alignment explanation
Indices: 1072410--1072443 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1072400 ATTCATTACT
1072410 ATTTACGTGAATAGTAA
1 ATTT-CGTGAATAGTAA
*
1072427 ATTTTGTGAATAGTAA
1 ATTTCGTGAATAGTAA
1072443 A
1 A
1072444 AAAAATTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (16 bp):
ATTTCGTGAATAGTAA
Found at i:1076787 original size:103 final size:103
Alignment explanation
Indices: 1076604--1077034 Score: 799
Period size: 103 Copynumber: 4.2 Consensus size: 103
1076594 GTAGAGGGTC
*
1076604 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
*
1076669 TTGATCTTTGTCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1076707 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1076772 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1076810 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1076875 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* *
1076913 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACAGGTGTGAGGTCTGTTGAGACACCTAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1076978 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1077016 TATGTGGTCCTTAGGGACA
1 TATGTGGTCCTTCGGGACA
1077035 ACTTTATATG
Statistics
Matches: 319, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 319 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1077070 original size:23 final size:23
Alignment explanation
Indices: 1077044--1077111 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1077034 AACTTTATAT
*
1077044 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
1077067 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
1077090 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1077112 AGCTGTGGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1083968 original size:103 final size:103
Alignment explanation
Indices: 1083789--1084320 Score: 992
Period size: 103 Copynumber: 5.2 Consensus size: 103
1083779 GTAGAGTGTC
*
1083789 TATGTGATCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1083854 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
1083892 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGTTGAGATACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1083957 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
* *
1083995 TATGTGGTTCTTCGGGATATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1084060 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
1084098 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1084163 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1084201 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACCTAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
1084266 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
1084304 TATGTGGTCCTTAGGGA
1 TATGTGGTCCTTCGGGA
1084321 AACTTTATAT
Statistics
Matches: 416, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 416 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1084357 original size:23 final size:23
Alignment explanation
Indices: 1084331--1084393 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1084321 AACTTTATAT
1084331 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTATGC
* * *
1084354 GGCACTACGGTGCAATTCTATGT
1 GGCACTTCGGTGCATTTCTATGC
1084377 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
1084394 ATACGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTATGC
Found at i:1086358 original size:35 final size:35
Alignment explanation
Indices: 1086250--1086343 Score: 161
Period size: 35 Copynumber: 2.7 Consensus size: 35
1086240 CAACTTTGAA
* *
1086250 AAAATGGTTTTCAAAGTTTGTTAAATGTTTCTTTG
1 AAAATAGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1086285 AAAATAGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATAGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1086320 AAAATAGTTTTTCAAAGTTTGGTA
1 AAAATAG-TTTTCAAAGTTTGGTA
1086344 GATGGTTGTA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 40 0.71
36 16 0.29
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (35 bp):
AAAATAGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:1086360 original size:36 final size:35
Alignment explanation
Indices: 1086250--1086358 Score: 121
Period size: 35 Copynumber: 3.1 Consensus size: 35
1086240 CAACTTTGAA
* * * * *
1086250 AAAATGGTTTTCAAAGTTTGTTAAATGTTTCTTTG
1 AAAATAGTTTTCAAAGTTTGGTAAATGGTTCGTAG
* * *
1086285 AAAATAGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATAGTTTTCAAAGTTTGGTAAATGGTTCGTAG
*
1086320 AAAATAGTTTTTCAAAGTTTGGTAGATGGTT-GTAG
1 AAAATAG-TTTTCAAAGTTTGGTAAATGGTTCGTAG
1086355 AAAA
1 AAAA
1086359 ATGATAATGG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 46 0.69
36 21 0.31
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (35 bp):
AAAATAGTTTTCAAAGTTTGGTAAATGGTTCGTAG
Found at i:1089861 original size:18 final size:18
Alignment explanation
Indices: 1089837--1089881 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1089827 TTTGTCTCGT
1089837 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
* *
1089855 AGTACCACTATGTTCCGA
1 AGGACCACTATGTCCCGA
1089873 AGGACCACT
1 AGGACCACT
1089882 GATAATCCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:1090943 original size:29 final size:29
Alignment explanation
Indices: 1090910--1090969 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1090900 ACACAACCCA
1090910 TAAATTCCATTTTGAGCACGAAAATGTCT
1 TAAATTCCATTTTGAGCACGAAAATGTCT
1090939 TAAATTCCATTTTGAGCACGAAAATGTCT
1 TAAATTCCATTTTGAGCACGAAAATGTCT
1090968 TA
1 TA
1090970 CTTTGTCCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (29 bp):
TAAATTCCATTTTGAGCACGAAAATGTCT
Found at i:1095028 original size:27 final size:28
Alignment explanation
Indices: 1094985--1095037 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1094975 AATTCTAGTC
* *
1094985 GATATATCATGTATATTTCTTCATATAT
1 GATATATCATATATATTGCTTCATATAT
*
1095013 GATATA-CATATATATTGCTTTATAT
1 GATATATCATATATATTGCTTCATAT
1095038 TTTTTCATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (28 bp):
GATATATCATATATATTGCTTCATATAT
Found at i:1095909 original size:39 final size:40
Alignment explanation
Indices: 1095832--1095942 Score: 109
Period size: 39 Copynumber: 2.8 Consensus size: 40
1095822 TCACCATTAC
* * * * * *
1095832 CACCT-CCACCACCATCATCGCCATTTGTTGATTCATCTA
1 CACCTACCACCACCACCACCACCATCTGTAGATTAATCTA
* * *
1095871 TACC-ACCACCATCAGCACCACCATCTGTAGATTAATCTA
1 CACCTACCACCACCACCACCACCATCTGTAGATTAATCTA
1095910 CACCATTACCACCACCACCACCACCATCTGTAG
1 CACC--TACCACCACCACCACCACCATCTGTAG
1095943 GTTCACCTAC
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
39 33 0.58
42 24 0.42
ACGTcount: A:0.29, C:0.41, G:0.07, T:0.23
Consensus pattern (40 bp):
CACCTACCACCACCACCACCACCATCTGTAGATTAATCTA
Found at i:1102892 original size:23 final size:25
Alignment explanation
Indices: 1102834--1102898 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 25
1102824 AAAAATTTCA
1102834 AAAGCTCG-A-TTGAAGCTCGAGACT
1 AAAGCTCGAATTTG-AGCTCGAGACT
* *
1102858 CAAGCTCAAATTTGAGCTCGA-A-T
1 AAAGCTCGAATTTGAGCTCGAGACT
*
1102881 AAAGCTCGAATTTAAGCT
1 AAAGCTCGAATTTGAGCT
1102899 TAATCTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
23 16 0.47
24 7 0.21
25 8 0.24
26 3 0.09
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (25 bp):
AAAGCTCGAATTTGAGCTCGAGACT
Found at i:1103027 original size:34 final size:30
Alignment explanation
Indices: 1102989--1103057 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1102979 TTGATATAAC
1102989 AATTTAAGGCAAAATAGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1103023 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1103052 AATTTA
1 AATTTA
1103058 TTTAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1103039 original size:30 final size:30
Alignment explanation
Indices: 1102998--1103057 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1102988 CAATTTAAGG
1102998 CAAAATAGTTTTTGGACTTGAATTGAATTTA
1 CAAAATAGTTTTTGGACTT-AATTGAATTTA
1103029 CAAAAT-GTTTTTGGACTTAATTGAATTTA
1 CAAAATAGTTTTTGGACTTAATTGAATTTA
1103058 TTTAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATAGTTTTTGGACTTAATTGAATTTA
Found at i:1103218 original size:20 final size:20
Alignment explanation
Indices: 1103193--1103245 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1103183 AATGCAATTA
*
1103193 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
1103213 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
1103233 GTGCATCCATGCA
1 GTGCATCGATGCA
1103246 CGAAGGCTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.30, G:0.23, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:1105754 original size:7 final size:7
Alignment explanation
Indices: 1105742--1105853 Score: 79
Period size: 7 Copynumber: 16.0 Consensus size: 7
1105732 ACCTTAAGCT
1105742 ATAAACC
1 ATAAACC
1105749 ATAAACC
1 ATAAACC
1105756 ATAAACC
1 ATAAACC
1105763 ATAAACC
1 ATAAACC
* *
1105770 TTACACTC
1 ATAAAC-C
1105778 -TAAACC
1 ATAAACC
1105784 ATAAACC
1 ATAAACC
1105791 ATAAA-C
1 ATAAACC
*
1105797 ATTTAA-C
1 A-TAAACC
1105804 ACTAAACTC
1 A-TAAAC-C
1105813 -TAAACC
1 ATAAACC
* **
1105819 TTAAATA
1 ATAAACC
*
1105826 ATATACC
1 ATAAACC
1105833 ATAAACC
1 ATAAACC
* *
1105840 CTAAATC
1 ATAAACC
1105847 ATAAACC
1 ATAAACC
1105854 CTATCACATA
Statistics
Matches: 82, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
6 4 0.05
7 76 0.93
8 1 0.01
9 1 0.01
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (7 bp):
ATAAACC
Found at i:1105808 original size:28 final size:28
Alignment explanation
Indices: 1105750--1105823 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
1105740 CTATAAACCA
*
1105750 TAAACCATAAACCATAAACCTTACACTC
1 TAAACCATAAACCATAAACCTTACACAC
*
1105778 TAAACCATAAACCATAAACATTTA-ACAC
1 TAAACCATAAACCATAAAC-CTTACACAC
*
1105806 TAAACTC-TAAACCTTAAA
1 TAAAC-CATAAACCATAAA
1105824 TAATATACCA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 37 0.90
29 4 0.10
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (28 bp):
TAAACCATAAACCATAAACCTTACACAC
Found at i:1105953 original size:14 final size:14
Alignment explanation
Indices: 1105934--1105963 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1105924 TATAATTATC
*
1105934 AATAATGTATTTTT
1 AATAATGTAATTTT
1105948 AATAATGTAATTTT
1 AATAATGTAATTTT
1105962 AA
1 AA
1105964 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:1106398 original size:38 final size:38
Alignment explanation
Indices: 1106342--1106419 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
1106332 TACCAACAAA
1106342 ATGAGACAAAAGAGGAGCACCAATCATAGACATAAGCC
1 ATGAGACAAAAGAGGAGCACCAATCATAGACATAAGCC
* * * *
1106380 ATGAGGCAAAAGATGAGCACTAATCGTAGACATAAGCC
1 ATGAGACAAAAGAGGAGCACCAATCATAGACATAAGCC
1106418 AT
1 AT
1106420 AAGGTAAGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (38 bp):
ATGAGACAAAAGAGGAGCACCAATCATAGACATAAGCC
Found at i:1107301 original size:6 final size:6
Alignment explanation
Indices: 1107290--1107315 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1107280 ATTTTTTGGG
1107290 TTATAA TTATAA TTATAA TTATAA TT
1 TTATAA TTATAA TTATAA TTATAA TT
1107316 TTCATTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:1108665 original size:13 final size:13
Alignment explanation
Indices: 1108647--1108677 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1108637 TTAATATTTA
*
1108647 TTTTATTTTATTC
1 TTTTATATTATTC
1108660 TTTTATATTATTC
1 TTTTATATTATTC
1108673 TTTTA
1 TTTTA
1108678 AAAAAATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTATATTATTC
Found at i:1112991 original size:24 final size:25
Alignment explanation
Indices: 1112930--1113010 Score: 76
Period size: 24 Copynumber: 3.2 Consensus size: 25
1112920 TAAACTTCAA
*
1112930 AAAAT-AATAAAATATATATATATTTT
1 AAAATAAAT-AAATA-ATATATATTAT
*
1112956 AAAATAAATAAA-AATATATATGAT
1 AAAATAAATAAATAATATATATTAT
* *
1112980 AAAATTATTAAATTTAATATATATTAT
1 AAAATAAATAAA--TAATATATATTAT
1113007 AAAA
1 AAAA
1113011 AACTATTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
24 19 0.41
25 1 0.02
26 8 0.17
27 18 0.39
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (25 bp):
AAAATAAATAAATAATATATATTAT
Found at i:1117140 original size:7 final size:7
Alignment explanation
Indices: 1117124--1117165 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
1117114 TTTTTTCAAA
*
1117124 GTCAATG
1 GTCAACG
1117131 GTCAACG
1 GTCAACG
*
1117138 GTCAATG
1 GTCAACG
1117145 GTCAACG
1 GTCAACG
1117152 GTCAACG
1 GTCAACG
*
1117159 ATCAACG
1 GTCAACG
1117166 TTGGATCGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:1117143 original size:14 final size:14
Alignment explanation
Indices: 1117124--1117156 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1117114 TTTTTTCAAA
1117124 GTCAATGGTCAACG
1 GTCAATGGTCAACG
1117138 GTCAATGGTCAACG
1 GTCAATGGTCAACG
1117152 GTCAA
1 GTCAA
1117157 CGATCAACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.21
Consensus pattern (14 bp):
GTCAATGGTCAACG
Found at i:1118867 original size:22 final size:22
Alignment explanation
Indices: 1118835--1118906 Score: 126
Period size: 22 Copynumber: 3.2 Consensus size: 22
1118825 CGAAATAAAA
*
1118835 ATAATGATTAGAATACTAAATGT
1 ATAAT-ATTAGAATACTGAATGT
1118858 ATAATATTAGAATACTGAATGT
1 ATAATATTAGAATACTGAATGT
1118880 ATAATATTAGAATACTGAATGT
1 ATAATATTAGAATACTGAATGT
1118902 ATAAT
1 ATAAT
1118907 TAGACTTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 43 0.90
23 5 0.10
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.36
Consensus pattern (22 bp):
ATAATATTAGAATACTGAATGT
Found at i:1126534 original size:17 final size:19
Alignment explanation
Indices: 1126508--1126549 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1126498 TCACTAATTT
1126508 TATTTAAAA-TA-AAAAAA
1 TATTTAAAATTACAAAAAA
* *
1126525 TATTTCAAATTACAATAAA
1 TATTTAAAATTACAAAAAA
1126544 TATTTA
1 TATTTA
1126550 TAATCATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 8 0.40
18 2 0.10
19 10 0.50
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TATTTAAAATTACAAAAAA
Found at i:1128107 original size:2 final size:2
Alignment explanation
Indices: 1128102--1128132 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1128092 TTAGAATGAG
1128102 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1128133 TAAATAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1128562 original size:44 final size:44
Alignment explanation
Indices: 1128506--1128607 Score: 113
Period size: 44 Copynumber: 2.3 Consensus size: 44
1128496 GAGATTCGAG
* * *
1128506 GCTCATAGTTTTTTTCCATTATACAT-TT-TATCTTTATAATT-GA
1 GCTCATAATTTTTTTCAATT-T-CATGTTCTACCTTTATAATTGGA
1128549 GGACTC-TAATTTTTTTCAATTTCATGTTCTACCTTTATAATTGGA
1 -G-CTCATAATTTTTTTCAATTTCATGTTCTACCTTTATAATTGGA
1128594 GCTCATAATTTTTT
1 GCTCATAATTTTTT
1128608 AAGCTCACTT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
42 3 0.06
43 6 0.12
44 36 0.72
45 5 0.10
ACGTcount: A:0.25, C:0.15, G:0.09, T:0.52
Consensus pattern (44 bp):
GCTCATAATTTTTTTCAATTTCATGTTCTACCTTTATAATTGGA
Found at i:1128625 original size:42 final size:41
Alignment explanation
Indices: 1128578--1128687 Score: 130
Period size: 41 Copynumber: 2.6 Consensus size: 41
1128568 TTTCATGTTC
* *
1128578 TACCTTTATAATTGGAGCTCATAATTTTTTAAGCTCACTTTT
1 TACCTTTATAATT-GAGCTCATAATTTTTCAAGCACACTTTT
* * *
1128620 TACCTTTATAATTGAGGTCCTAATTTTTCAATCACACTTTT
1 TACCTTTATAATTGAGCTCATAATTTTTCAAGCACACTTTT
* * *
1128661 TACTTTTATAATTTAGGCACATAATTT
1 TACCTTTATAATTGA-GCTCATAATTT
1128688 AATAATTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 36 0.63
42 21 0.37
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.47
Consensus pattern (41 bp):
TACCTTTATAATTGAGCTCATAATTTTTCAAGCACACTTTT
Found at i:1128658 original size:41 final size:41
Alignment explanation
Indices: 1128531--1128673 Score: 144
Period size: 41 Copynumber: 3.4 Consensus size: 41
1128521 CCATTATACA
* * *
1128531 TTTTATCTTTATAATTGAGGACTCTAATTTTTTTCAATTTCA-T
1 TTTTACCTTTATAATTGAGGTC-CTAA--TTTTTCAATCTCACT
* * * * *
1128574 GTTCTACCTTTATAATTGGAGCTCATAATTTTTTAAGCTCACT
1 -TTTTACCTTTATAATT-GAGGTCCTAATTTTTCAATCTCACT
*
1128617 TTTTACCTTTATAATTGAGGTCCTAATTTTTCAATCACACT
1 TTTTACCTTTATAATTGAGGTCCTAATTTTTCAATCTCACT
*
1128658 TTTTACTTTTATAATT
1 TTTTACCTTTATAATT
1128674 TAGGCACATA
Statistics
Matches: 82, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
41 35 0.43
42 25 0.30
43 1 0.01
44 17 0.21
45 4 0.05
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (41 bp):
TTTTACCTTTATAATTGAGGTCCTAATTTTTCAATCTCACT
Found at i:1128685 original size:83 final size:85
Alignment explanation
Indices: 1128531--1128687 Score: 187
Period size: 83 Copynumber: 1.9 Consensus size: 85
1128521 CCATTATACA
* ** *
1128531 TTTTATCTTTATAATTGAGGACTCTAATTTTTTTCAATTTCATGTTCTACCTTTATAATTGGAGC
1 TTTTACCTTTATAATTGAGGACTCTAA-TTTTTTCAATCACATGTTCTACCTTTATAATTAGAGC
*
1128596 TCATAATTTTTTAAGCTCACT
65 ACATAATTTTTTAAGCTCACT
* * *
1128617 TTTTACCTTTATAATTGAGGTC-CTAA-TTTTTCAATCACACT-TTTTACTTTTATAATTTAG-G
1 TTTTACCTTTATAATTGAGGACTCTAATTTTTTCAATCACA-TGTTCTACCTTTATAA-TTAGAG
1128678 CACATAATTT
64 CACATAATTT
1128688 AATAATTTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
83 33 0.54
84 4 0.07
85 4 0.07
86 20 0.33
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (85 bp):
TTTTACCTTTATAATTGAGGACTCTAATTTTTTCAATCACATGTTCTACCTTTATAATTAGAGCA
CATAATTTTTTAAGCTCACT
Found at i:1131177 original size:171 final size:171
Alignment explanation
Indices: 1130892--1131327 Score: 698
Period size: 171 Copynumber: 2.5 Consensus size: 171
1130882 CTAGGCTCTT
* * * * *
1130892 TGTAGAAGGTATTCATTTTAAACCTGAGGAGCCAGTTTCTGACAAAATGGAAAAGAAAGGTTCAT
1 TGTAGAAGGTATTCATTCTAAACCTGAAGAGCCAGCTTCTGAAAAAATGGAAAAGCAAGGTTCAT
*
1130957 ATGAAGCCTATTCCTGCAACGATATGGAGGAGGATGCCGGAAATATGAGTAAAAACAGCATCAA-
66 ATGAAGCTTATTCCTGCAACGATATGGAGGAGGATGCCGGAAATATGAGTAAAAACAGCAT-AAC
* *
1131021 GCCTTCCTGTGAAGCTTTTCCAAATGAATTTGATTGGAACTC
130 ACCTTCCTGTGAAGCTTTTCCAAATGAATTTGATCGGAACTC
*
1131063 TGTAGAAGGTATTCGA-TCTAAACCTGAAGAGCCAGCGTCTGAAAAAATGGAAAAGCAAGGTTCA
1 TGTAGAAGGTATTC-ATTCTAAACCTGAAGAGCCAGCTTCTGAAAAAATGGAAAAGCAAGGTTCA
1131127 TATGAAGCTTATTCCTGCAACGATATGGAGGAGGAT-CCTGGAAATATGAGTAAAAACAGCATAA
65 TATGAAGCTTATTCCTGCAACGATATGGAGGAGGATGCC-GGAAATATGAGTAAAAACAGCATAA
* *
1131191 CACCTTCTTGTGAAGCTTTTCCTAATGAATTTGATCGGAACTC
129 CACCTTCCTGTGAAGCTTTTCCAAATGAATTTGATCGGAACTC
* *
1131234 TGTTGAAGGTATTCATTCTAAACCTGAAGAGCCAGCTTCTGAAAAAATGGAAAAGCAAGGTGCAT
1 TGTAGAAGGTATTCATTCTAAACCTGAAGAGCCAGCTTCTGAAAAAATGGAAAAGCAAGGTTCAT
*
1131299 ATGAAGCTTATTCCTGCAACAATATGGAG
66 ATGAAGCTTATTCCTGCAACGATATGGAG
1131328 AGTAAGAACA
Statistics
Matches: 246, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
170 5 0.02
171 240 0.98
172 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (171 bp):
TGTAGAAGGTATTCATTCTAAACCTGAAGAGCCAGCTTCTGAAAAAATGGAAAAGCAAGGTTCAT
ATGAAGCTTATTCCTGCAACGATATGGAGGAGGATGCCGGAAATATGAGTAAAAACAGCATAACA
CCTTCCTGTGAAGCTTTTCCAAATGAATTTGATCGGAACTC
Found at i:1134588 original size:59 final size:57
Alignment explanation
Indices: 1134479--1134590 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 57
1134469 ACTATAATTA
* * *
1134479 TTATTTTAAATGACCTTAAACTTTTCAACATTTCAATTTTATCCTCAAACTATGAGT
1 TTATTCTAAATGACCCTAAACTTTTCAACATTTCAATTTCATCCTCAAACTATGAGT
* *
1134536 TTATTCTAAATTGATCCCTAAACTTTTTGAATATTTCAATTTCATCC-CAAACTAT
1 TTATTCTAAA-TGA-CCCTAAAC-TTTTCAACATTTCAATTTCATCCTCAAACTAT
1134591 TCGTATATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 9 0.19
58 3 0.06
59 15 0.32
60 20 0.43
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (57 bp):
TTATTCTAAATGACCCTAAACTTTTCAACATTTCAATTTCATCCTCAAACTATGAGT
Found at i:1134598 original size:29 final size:29
Alignment explanation
Indices: 1134508--1134598 Score: 67
Period size: 30 Copynumber: 3.1 Consensus size: 29
1134498 ACTTTTCAAC
* * *
1134508 ATTTCAATTTTATCCTCAAACTATGAGTTT
1 ATTTCAATTTCATCC-CAAACTATTAGTAT
* * * * *
1134538 A-TTCTAAATTGATCCCTAAACTTTTTGAAT
1 ATTTC-AATTTCATCCC-AAACTATTAGTAT
*
1134568 ATTTCAATTTCATCCCAAACTATTCGTAT
1 ATTTCAATTTCATCCCAAACTATTAGTAT
1134597 AT
1 AT
1134599 ACTAATTACA
Statistics
Matches: 46, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
29 16 0.35
30 27 0.59
31 3 0.07
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (29 bp):
ATTTCAATTTCATCCCAAACTATTAGTAT
Found at i:1134846 original size:24 final size:25
Alignment explanation
Indices: 1134819--1134879 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
1134809 TTGACACGAT
1134819 AATTAATTTATTGAATT-AAATTAA
1 AATTAATTTATTGAATTAAAATTAA
*
1134843 AATT-ATTGAATTGAATTAAAATTAA
1 AATTAATT-TATTGAATTAAAATTAA
*
1134868 GATTAAATTTAT
1 AATT-AATTTAT
1134880 AAAATATGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 3 0.10
24 12 0.40
25 10 0.33
26 2 0.07
27 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (25 bp):
AATTAATTTATTGAATTAAAATTAA
Found at i:1134850 original size:19 final size:19
Alignment explanation
Indices: 1134826--1134866 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1134816 GATAATTAAT
1134826 TTATTGAATTAAATTAAAA
1 TTATTGAATTAAATTAAAA
*
1134845 TTATTGAATTGAATTAAAA
1 TTATTGAATTAAATTAAAA
1134864 TTA
1 TTA
1134867 AGATTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (19 bp):
TTATTGAATTAAATTAAAA
Found at i:1134914 original size:2 final size:2
Alignment explanation
Indices: 1134907--1134941 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1134897 AATGATTTTG
1134907 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 A
1134942 ATTTTTCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1142202 original size:28 final size:28
Alignment explanation
Indices: 1142157--1142213 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1142147 TTGTCGTTGC
* *
1142157 TTTCAAGCACTGATTCGACGTCATAATG
1 TTTCAAGCACTGACTCGACGACATAATG
*
1142185 TTTCAAGCACTGGCTCGACGACATAATG
1 TTTCAAGCACTGACTCGACGACATAATG
1142213 T
1 T
1142214 AAACAGAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (28 bp):
TTTCAAGCACTGACTCGACGACATAATG
Found at i:1144618 original size:631 final size:630
Alignment explanation
Indices: 1143416--1144676 Score: 2513
Period size: 631 Copynumber: 2.0 Consensus size: 630
1143406 TACAGCCGTG
1143416 TTGTTTTGCTGAAATGGGGATGTGGTACAAAGAACATAAATGCTACTATTGTTGTAGATTTCCTC
1 TTGTTTTGCTGAAATGGGGATGTGGTACAAAGAACATAAATGCTACTATTGTTGTAGATTTCCTC
1143481 AATAATTGCCTGTTCACATATGCATTAAGTCAAGTGGTTGAGTATTGATTCAAAACAGATTGGCC
66 AATAATTGCCTGTTCACATATGCATTAAGTCAAGTGGTTGAGTATTGATTCAAAACAGATTGGCC
1143546 TTAAAGGCTGTATAGTCTTAAAGTTCTGAAGGGTTAGATATGCATGTTCTTTTGTAGTTAGGTGG
131 TTAAAGGCTGTATAGTCTTAAAGTTCTGAAGGGTTAGATATGCATGTTCTTTTGTAGTTAGGTGG
1143611 TATGGGTTGTATTCATTGCAAGTTCTACTTCCCCATTTGAAACCGAATTAATGAAAAAAATATTA
196 TATGGGTTGTATTCATTGCAAGTTCTACTTCCCCATTTGAAACCGAATTAATGAAAAAAATATTA
1143676 TTTCGACAAACCCTTTGTCGAAATAGACAAGTGTCTGTGGGCCTGTGCTCCTGCAACATCTAAAT
261 TTTCGACAAACCCTTTGTCGAAATAGACAAGTGTCTGTGGGCCTGTGCTCCTGCAACATCTAAAT
1143741 AGAGAAGGATATTCATCAAAAGAACCCCCTACTTGGAGACCACCAACATGAAATGAAATAGATAT
326 AGAGAAGGATATTCATCAAAAGAACCCCCTACTTGGAGACCACCAACATGAAATGAAATAGATAT
1143806 TGGTTTGTGACTACGCCTGAAGGAATCCTTTTGTGATTAGATGTTAAGCCCAGACAGGTGTTTTG
391 TGGTTTGTGACTACGCCTGAAGGAATCCTTTTGTGATTAGATGTTAAGCCCAGACAGGTGTTTTG
1143871 TTAGTGTAACTGCCTCATGTTTCTTATGCCCTTGCAGTGTTAAACTAAGTGAGTTCCCATGAAAA
456 TTAGTGTAACTGCCTCATGTTTCTTATGCCCTTGCAGTGTTAAACTAAGTGAGTTCCCATGAAAA
1143936 ATATGCTCTTCACTGAATTCATATATTAGCTGGGGAGAAAACAGTTATAGGATGTTAGTGTCTCC
521 ATATGCTCTTCACTGAATTCATATATTAGCTGGGGAGAAAACAGTTATAGGATGTTAGTGTCTCC
1144001 AGCGTTTTACTAAACAATATGCTTGTTTGCATATATTATCTTCAC
586 AGCGTTTTACTAAACAATATGCTTGTTTGCATATATTATCTTCAC
1144046 TTGTTTTGCTGAAATGGGGATGTGGTACAAAGAACATAAATGCTACTATTGTTGTAGATTTCCTC
1 TTGTTTTGCTGAAATGGGGATGTGGTACAAAGAACATAAATGCTACTATTGTTGTAGATTTCCTC
1144111 AATAATTGCCTGTTCACATATGCATTAAGTTCAAGTGGTTGAGTATTGATTCAAAACAGATTGGC
66 AATAATTGCCTGTTCACATATGCATTAAG-TCAAGTGGTTGAGTATTGATTCAAAACAGATTGGC
1144176 CTTAAAGGCTGTATAGTCTTAAAGTTCTGAAGGGTTAGATATGCATGTTCTTTTGTAGTTAGGTG
130 CTTAAAGGCTGTATAGTCTTAAAGTTCTGAAGGGTTAGATATGCATGTTCTTTTGTAGTTAGGTG
1144241 GTATGGGTTGTATTCATTGCAAGTTCTACTTCCCCATTTGAAACCGAATTAATGAAAAAAATATT
195 GTATGGGTTGTATTCATTGCAAGTTCTACTTCCCCATTTGAAACCGAATTAATGAAAAAAATATT
1144306 ATTTCGACAAACCCTTTGTCGAAATAGACAAGTGTCTGTGGGCCTGTGCTCCTGCAACATCTAAA
260 ATTTCGACAAACCCTTTGTCGAAATAGACAAGTGTCTGTGGGCCTGTGCTCCTGCAACATCTAAA
1144371 TAGAGAAGGATATTCATCAAAAGAACCCCCTACTTGGAGACCACCAACATGAAATGAAATAGATA
325 TAGAGAAGGATATTCATCAAAAGAACCCCCTACTTGGAGACCACCAACATGAAATGAAATAGATA
1144436 TTGGTTTGTGACTACGCCTGAAGGAATCCTTTTGTGATTAGATGTTAAGCCCAGACAGGTGTTTT
390 TTGGTTTGTGACTACGCCTGAAGGAATCCTTTTGTGATTAGATGTTAAGCCCAGACAGGTGTTTT
1144501 GTTAGTGTAACTGCCTCATGTTTCTTATGCCCTTGCAGTGTTAAACTAAGTGAGTTCCCATGAAA
455 GTTAGTGTAACTGCCTCATGTTTCTTATGCCCTTGCAGTGTTAAACTAAGTGAGTTCCCATGAAA
1144566 AATATGCTCTTCACTGAATTCATATATTAGCTGGGGAGAAAACAGTTATAGGATGTTAGTGTCTC
520 AATATGCTCTTCACTGAATTCATATATTAGCTGGGGAGAAAACAGTTATAGGATGTTAGTGTCTC
1144631 CAGCGTTTTACTAAACAATATGCTTGTTTGCATATATTATCTTCAC
585 CAGCGTTTTACTAAACAATATGCTTGTTTGCATATATTATCTTCAC
1144677 CAATGAAAGT
Statistics
Matches: 630, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
630 94 0.15
631 536 0.85
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (630 bp):
TTGTTTTGCTGAAATGGGGATGTGGTACAAAGAACATAAATGCTACTATTGTTGTAGATTTCCTC
AATAATTGCCTGTTCACATATGCATTAAGTCAAGTGGTTGAGTATTGATTCAAAACAGATTGGCC
TTAAAGGCTGTATAGTCTTAAAGTTCTGAAGGGTTAGATATGCATGTTCTTTTGTAGTTAGGTGG
TATGGGTTGTATTCATTGCAAGTTCTACTTCCCCATTTGAAACCGAATTAATGAAAAAAATATTA
TTTCGACAAACCCTTTGTCGAAATAGACAAGTGTCTGTGGGCCTGTGCTCCTGCAACATCTAAAT
AGAGAAGGATATTCATCAAAAGAACCCCCTACTTGGAGACCACCAACATGAAATGAAATAGATAT
TGGTTTGTGACTACGCCTGAAGGAATCCTTTTGTGATTAGATGTTAAGCCCAGACAGGTGTTTTG
TTAGTGTAACTGCCTCATGTTTCTTATGCCCTTGCAGTGTTAAACTAAGTGAGTTCCCATGAAAA
ATATGCTCTTCACTGAATTCATATATTAGCTGGGGAGAAAACAGTTATAGGATGTTAGTGTCTCC
AGCGTTTTACTAAACAATATGCTTGTTTGCATATATTATCTTCAC
Found at i:1148538 original size:59 final size:59
Alignment explanation
Indices: 1148437--1148555 Score: 134
Period size: 59 Copynumber: 2.0 Consensus size: 59
1148427 AAACACTTTG
* * * *
1148437 AGGACCAATTTAGAATGAAGGTCGTAGTTTAGGGATAAAATTG-AAATGTTCAAAGTTTA
1 AGGACCAATATAGAATGAAGGTCATAGTTTAGGAATAAAATTGAAAAT-TTAAAAGTTTA
* **
1148496 AGGACTAATATAGAATGATA-GTCATAGTTTAGGAATGGAATTGTAAAATTTAAAAGTTTA
1 AGGACCAATATAGAATGA-AGGTCATAGTTTAGGAATAAAATTG-AAAATTTAAAAGTTTA
1148556 TGGTCAAGAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
59 35 0.70
60 11 0.22
61 4 0.08
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (59 bp):
AGGACCAATATAGAATGAAGGTCATAGTTTAGGAATAAAATTGAAAATTTAAAAGTTTA
Found at i:1164545 original size:15 final size:16
Alignment explanation
Indices: 1164516--1164545 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1164506 ATATAAATAT
1164516 TTTAAAACAATAATTG
1 TTTAAAACAATAATTG
1164532 TTTAAAAC-ATAATT
1 TTTAAAACAATAATT
1164546 TCAAAACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (16 bp):
TTTAAAACAATAATTG
Found at i:1164728 original size:31 final size:32
Alignment explanation
Indices: 1164673--1164745 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 32
1164663 GGCTCGAGAA
* **
1164673 CCTACCCAAGAAAGTTACTCGGGGCCACGTGG
1 CCTACCCAAGAAAGATACTCGGGGCCACGAAG
*
1164705 CCTACCCAAGAAAGAT-CTCGGGGCCTCGAAG
1 CCTACCCAAGAAAGATACTCGGGGCCACGAAG
1164736 CCTACCCAAG
1 CCTACCCAAG
1164746 GGTCACCTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 22 0.59
32 15 0.41
ACGTcount: A:0.27, C:0.34, G:0.25, T:0.14
Consensus pattern (32 bp):
CCTACCCAAGAAAGATACTCGGGGCCACGAAG
Found at i:1167241 original size:23 final size:24
Alignment explanation
Indices: 1167199--1167243 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1167189 ACTCGGTCAA
* *
1167199 AGTCAAAGCTTAACGGGTTGACTC
1 AGTCAAAGCTCAACGAGTTGACTC
1167223 AGTCAAAG-TCAACGAGTTGAC
1 AGTCAAAGCTCAACGAGTTGAC
1167244 CTGGTGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (24 bp):
AGTCAAAGCTCAACGAGTTGACTC
Found at i:1169041 original size:23 final size:23
Alignment explanation
Indices: 1169015--1169087 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 23
1169005 AAACAAACGA
**
1169015 TAAACGAACATGTTCGTGAATGC
1 TAAACGAACATGTTCGTGAACAC
* * * *
1169038 TAAATGAACACGTTTGTGAACAT
1 TAAACGAACATGTTCGTGAACAC
* *
1169061 TAAACGAACATGTTCGCGAACAA
1 TAAACGAACATGTTCGTGAACAC
1169084 TAAA
1 TAAA
1169088 TAAACGAACA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (23 bp):
TAAACGAACATGTTCGTGAACAC
Found at i:1169130 original size:26 final size:30
Alignment explanation
Indices: 1169082--1169139 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
1169072 GTTCGCGAAC
*
1169082 AATAAATAAACGAACACGGACAA-CTTAAAA
1 AATAAATAAACGAACAC-GACAATATTAAAA
1169112 AATAAATAAACG-A-AC-ACAATATTAAAA
1 AATAAATAAACGAACACGACAATATTAAAA
1169139 A
1 A
1169140 TTTAAACGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.15
27 7 0.27
28 2 0.08
29 1 0.04
30 12 0.46
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.16
Consensus pattern (30 bp):
AATAAATAAACGAACACGACAATATTAAAA
Found at i:1173654 original size:16 final size:18
Alignment explanation
Indices: 1173614--1173656 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
1173604 AATTTTTTTC
1173614 TCTTTTCTTCTCTCTTTA
1 TCTTTTCTTCTCTCTTTA
1173632 TC--TTCTTCTC-CTTT-
1 TCTTTTCTTCTCTCTTTA
1173646 TCTTTTCTTCT
1 TCTTTTCTTCT
1173657 GTCTGAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.09
15 4 0.17
16 15 0.65
18 2 0.09
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTTTTCTTCTCTCTTTA
Found at i:1175391 original size:2 final size:2
Alignment explanation
Indices: 1175384--1175410 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1175374 TATAAATTAA
1175384 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 A
1175411 AACTTAACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1175772 original size:2 final size:2
Alignment explanation
Indices: 1175767--1175816 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1175757 TATCGTTATG
1175767 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1175809 CT CT CT CT
1 CT CT CT CT
1175817 GTTAAATGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1180196 original size:26 final size:21
Alignment explanation
Indices: 1180146--1180202 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1180136 ATAAAATTCG
1180146 ATTTGATTTGATTAATTTTAT
1 ATTTGATTTGATTAATTTTAT
1180167 ATTTGATTTGATTAATTTTAT
1 ATTTGATTTGATTAATTTTAT
*
1180188 ATTTAATTTGATTAA
1 ATTTGATTTGATTAA
1180203 AAATACTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (21 bp):
ATTTGATTTGATTAATTTTAT
Found at i:1180318 original size:2 final size:2
Alignment explanation
Indices: 1180311--1180341 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1180301 CTCTCGACTT
1180311 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1180342 GAAAAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1183768 original size:2 final size:2
Alignment explanation
Indices: 1183761--1183865 Score: 187
Period size: 2 Copynumber: 53.5 Consensus size: 2
1183751 TTTTTAAAAC
*
1183761 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1183802 AT AT AT AT AT AT AT A- 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
1183843 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1183866 CACCCCCATC
Statistics
Matches: 99, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
1 2 0.02
2 97 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1194823 original size:19 final size:19
Alignment explanation
Indices: 1194799--1194859 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 19
1194789 TTTTGGTGCA
*
1194799 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
1194818 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCC-CT
1194839 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGA-TCCCCCC
1194860 ACAGGGGATC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 10 0.29
20 6 0.17
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Done.