Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007956.1 Hibiscus syriacus cultivar Beakdansim tig00110383_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: 3102597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 14
Found at i:937601 original size:3 final size:3
Alignment explanation
Indices: 937593--937631 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
937583 ATAACCATTA
937593 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
937632 CATCTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:939622 original size:43 final size:45
Alignment explanation
Indices: 939554--939649 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 45
939544 CCACAGCTCG
*
939554 TAATTTG-CACCGAAGTGCCAGATAA-TTATCCCAAATGACCACA
1 TAATTTGTCACCGAAGTGCCACATAATTTATCCCAAATGACCACA
* *
939597 TAATTTGTC-CCGAA-TGACCACATAATTTGTCCCGAATGACCACA
1 TAATTTGTCACCGAAGTG-CCACATAATTTATCCCAAATGACCACA
939641 TAATTTGTC
1 TAATTTGTC
939650 TCAAAGAACC
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
42 2 0.04
43 19 0.40
44 26 0.55
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (45 bp):
TAATTTGTCACCGAAGTGCCACATAATTTATCCCAAATGACCACA
Found at i:939664 original size:22 final size:22
Alignment explanation
Indices: 939582--939649 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
939572 CAGATAATTA
*
939582 TCCCAAATGACCACATAATTTG
1 TCCCGAATGACCACATAATTTG
939604 TCCCGAATGACCACATAATTTG
1 TCCCGAATGACCACATAATTTG
939626 TCCCGAATGACCACATAATTTG
1 TCCCGAATGACCACATAATTTG
939648 TC
1 TC
939650 TCAAAGAACC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (22 bp):
TCCCGAATGACCACATAATTTG
Found at i:941892 original size:21 final size:21
Alignment explanation
Indices: 941868--941917 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
941858 AAACTTAAGA
*
941868 CAAATTCCCAGTTCAAATTTG
1 CAAATGCCCAGTTCAAATTTG
941889 CAAATGCCCAGTTCAAA-TTG
1 CAAATGCCCAGTTCAAATTTG
941909 TCAAATGCC
1 -CAAATGCC
941918 TTCTGCAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (21 bp):
CAAATGCCCAGTTCAAATTTG
Found at i:942267 original size:16 final size:18
Alignment explanation
Indices: 942246--942281 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
942236 AGTAAATAAC
942246 ATAAATTAAA-AG-AATA
1 ATAAATTAAATAGTAATA
942262 ATAAATTAAATAGTAATA
1 ATAAATTAAATAGTAATA
942280 AT
1 AT
942282 TATATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
ATAAATTAAATAGTAATA
Found at i:942424 original size:30 final size:30
Alignment explanation
Indices: 942389--942536 Score: 242
Period size: 30 Copynumber: 4.9 Consensus size: 30
942379 ATAAAAAAAT
* *
942389 TTATTAAAAAGAAGAGAGCTGAGTTGTGAA
1 TTATTAAAAAGAAGAGAGTTCAGTTGTGAA
*
942419 TTATTAAAAAGAAGAGAGTTGAGTTGTGAA
1 TTATTAAAAAGAAGAGAGTTCAGTTGTGAA
*
942449 TTATTAAAAAAGAATAGAGTTCAGTTGTGAA
1 TTATT-AAAAAGAAGAGAGTTCAGTTGTGAA
942480 TTATTAAAAAGAAGAGAGTTCAGTTGTGAA
1 TTATTAAAAAGAAGAGAGTTCAGTTGTGAA
*
942510 TTATTAAAAAGAAGAGAGTTCATTTGT
1 TTATTAAAAAGAAGAGAGTTCAGTTGT
942537 CGACCAATCC
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
30 84 0.75
31 28 0.25
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (30 bp):
TTATTAAAAAGAAGAGAGTTCAGTTGTGAA
Found at i:942483 original size:61 final size:60
Alignment explanation
Indices: 942389--942536 Score: 242
Period size: 61 Copynumber: 2.5 Consensus size: 60
942379 ATAAAAAAAT
* * *
942389 TTATTAAAAAGAAGAGAGCTGAGTTGTGAATTATTAAAAAGAAGAGAGTTGAGTTGTGAA
1 TTATTAAAAAGAAGAGAGTTCAGTTGTGAATTATTAAAAAGAAGAGAGTTCAGTTGTGAA
*
942449 TTATTAAAAAAGAATAGAGTTCAGTTGTGAATTATTAAAAAGAAGAGAGTTCAGTTGTGAA
1 TTATT-AAAAAGAAGAGAGTTCAGTTGTGAATTATTAAAAAGAAGAGAGTTCAGTTGTGAA
*
942510 TTATTAAAAAGAAGAGAGTTCATTTGT
1 TTATTAAAAAGAAGAGAGTTCAGTTGT
942537 CGACCAATCC
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 25 0.31
61 56 0.69
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (60 bp):
TTATTAAAAAGAAGAGAGTTCAGTTGTGAATTATTAAAAAGAAGAGAGTTCAGTTGTGAA
Found at i:943796 original size:17 final size:17
Alignment explanation
Indices: 943774--943806 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
943764 CTTTTGTAAT
*
943774 TATTGTTTCTATTTTTG
1 TATTGTCTCTATTTTTG
943791 TATTGTCTCTATTTTT
1 TATTGTCTCTATTTTT
943807 TTCTTTATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.70
Consensus pattern (17 bp):
TATTGTCTCTATTTTTG
Found at i:949176 original size:26 final size:26
Alignment explanation
Indices: 949147--949205 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
949137 CTTGTGCGTC
949147 GATGCATCAAATGCACTAAGTGCATA
1 GATGCATCAAATGCACTAAGTGCATA
*
949173 GATGCATCAAATGCACTAAGTGCATC
1 GATGCATCAAATGCACTAAGTGCATA
949199 GATGCAT
1 GATGCAT
949206 GGTATGTACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (26 bp):
GATGCATCAAATGCACTAAGTGCATA
Found at i:956104 original size:117 final size:116
Alignment explanation
Indices: 955886--956105 Score: 248
Period size: 117 Copynumber: 1.9 Consensus size: 116
955876 TTCAAATTAA
* * * *
955886 AAATTTTTTTTTCAATATTTTCAAATTTCATTTTTGAAAGTTCTAAATTCTTCTTCAAGAGTTCA
1 AAATTTTTTTTTCAATATTTTCAAATTTCAGTTTTGAAAGCTCTAAACTCTTCTTCAACAGTTCA
* *
955951 TTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTG
66 TTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
* * * *
956002 AAATTTTCTTTTTCAA-AGTTTTCAGATTTTAGTTTTGAAAGCTCT-AACTCATTTTTCAACATT
1 AAATTTT-TTTTTCAATA-TTTTCAAATTTCAGTTTTGAAAGCTCTAAACTC-TTCTTCAACAGT
* * * **
956065 TCATTTTGTTTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
63 TCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
956106 ATCATTTTTA
Statistics
Matches: 85, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
116 12 0.14
117 69 0.81
118 4 0.05
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.50
Consensus pattern (116 bp):
AAATTTTTTTTTCAATATTTTCAAATTTCAGTTTTGAAAGCTCTAAACTCTTCTTCAACAGTTCA
TTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:958833 original size:23 final size:23
Alignment explanation
Indices: 958807--958890 Score: 66
Period size: 23 Copynumber: 3.6 Consensus size: 23
958797 ATTTTATATA
958807 GCACTACGGTGCAATTCTATGTG
1 GCACTACGGTGCAATTCTATGTG
* * * *
958830 GCACTTCGGTGCATTTCTACGCG
1 GCACTACGGTGCAATTCTATGTG
*
958853 GTC-CTTCGG-GACAAATTCT-TCGTG
1 G-CACTACGGTG-C-AATTCTAT-GTG
958877 GCACTACGGTGCAA
1 GCACTACGGTGCAA
958891 ATTTATACGA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
22 1 0.02
23 30 0.64
24 15 0.32
25 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTATGTG
Found at i:960956 original size:29 final size:30
Alignment explanation
Indices: 960887--960957 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
960877 AGTTACTTAA
*
960887 TAATAACATAATTGAACGTAAAATTAAAATT
1 TAATAATATAATTGAAC-TAAAATTAAAATT
* **
960918 TAGTGTTATAATTG-A-TAAAATTAAAAATT
1 TAATAATATAATTGAACTAAAATT-AAAATT
960947 TAATAATATAA
1 TAATAATATAA
960958 ATGAGTAGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
28 7 0.22
29 14 0.44
30 1 0.03
31 10 0.31
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.37
Consensus pattern (30 bp):
TAATAATATAATTGAACTAAAATTAAAATT
Found at i:963455 original size:16 final size:16
Alignment explanation
Indices: 963431--963462 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
963421 ATAAAAGTTA
963431 GATAAACTATTTATTT
1 GATAAACTATTTATTT
*
963447 GATACACTATTTATTT
1 GATAAACTATTTATTT
963463 CGCATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.50
Consensus pattern (16 bp):
GATAAACTATTTATTT
Found at i:966802 original size:3 final size:3
Alignment explanation
Indices: 966776--966818 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
966766 CTGTAAAAAC
* * *
966776 AAT AAA AAT ATT ATT AAT AA- AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
966819 ACAATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:966805 original size:20 final size:20
Alignment explanation
Indices: 966776--966815 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
966766 CTGTAAAAAC
* *
966776 AATAAAAATATTATTAATAA
1 AATAAAAATAATAATAATAA
*
966796 AATAATAATAATAATAATAA
1 AATAAAAATAATAATAATAA
966816 TAAACAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAAAATAATAATAATAA
Found at i:970641 original size:19 final size:19
Alignment explanation
Indices: 970579--970641 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
970569 AAAATACAAA
*
970579 ATATAATAATCCA-TA-AT
1 ATATAATAATTCATTATAT
970596 ATA-AATAATTCATTATAT
1 ATATAATAATTCATTATAT
*
970614 -TTTATATAATT-ATATATAT
1 ATATA-ATAATTCAT-TATAT
970633 ATATAATAA
1 ATATAATAA
970642 AAATAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
16 8 0.22
17 6 0.16
18 5 0.14
19 15 0.41
20 3 0.08
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATAATAATTCATTATAT
Found at i:972718 original size:27 final size:24
Alignment explanation
Indices: 972666--972723 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 24
972656 AATTATCGAT
*
972666 ATAATATATATTATATTAATACAA
1 ATAATATATATTATATTAATAAAA
*
972690 ATAATGATATGATATATATTACTAAAA
1 ATAAT-ATAT-AT-TATATTAATAAAA
972717 ATTAATA
1 A-TAATA
972724 ATTTCTAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 5 0.18
25 4 0.14
26 2 0.07
27 13 0.46
28 4 0.14
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (24 bp):
ATAATATATATTATATTAATAAAA
Found at i:974090 original size:19 final size:18
Alignment explanation
Indices: 974066--974103 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
974056 TTAAATAAAA
974066 AAGTTTAAAAATTAGATTT
1 AAGTTTAAAAATTA-ATTT
*
974085 AAGTTTAAATATTAATTT
1 AAGTTTAAAAATTAATTT
974103 A
1 A
974104 TATTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (18 bp):
AAGTTTAAAAATTAATTT
Found at i:986801 original size:28 final size:29
Alignment explanation
Indices: 986756--986820 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 29
986746 ATTGGAAAAA
** **
986756 TTGATTTTTTATCGAGTTTGAGGGCCAAT
1 TTGATTTTTTATAAAGTTAAAGGGCCAAT
**
986785 TTGATTTTTTA-AAAGTTAAAGGGCTTAT
1 TTGATTTTTTATAAAGTTAAAGGGCCAAT
986813 TTGATTTT
1 TTGATTTT
986821 CTTAGAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 19 0.63
29 11 0.37
ACGTcount: A:0.25, C:0.06, G:0.20, T:0.49
Consensus pattern (29 bp):
TTGATTTTTTATAAAGTTAAAGGGCCAAT
Found at i:986896 original size:15 final size:15
Alignment explanation
Indices: 986876--986905 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
986866 TAGAAAGAAA
*
986876 ATTAAATATAAAAAT
1 ATTAAAAATAAAAAT
986891 ATTAAAAATAAAAAT
1 ATTAAAAATAAAAAT
986906 TAGATTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAAAAATAAAAAT
Found at i:987585 original size:18 final size:18
Alignment explanation
Indices: 987558--987603 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
987548 CGCATATACC
*
987558 ATCATGATCAACATCTCT
1 ATCATTATCAACATCTCT
**
987576 ATCATTATCATGATCTCT
1 ATCATTATCAACATCTCT
987594 ATCATTATCA
1 ATCATTATCA
987604 TTAACCCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (18 bp):
ATCATTATCAACATCTCT
Found at i:987604 original size:18 final size:18
Alignment explanation
Indices: 987570--987604 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
987560 CATGATCAAC
987570 ATCTCTATCATTATCATG
1 ATCTCTATCATTATCATG
987588 ATCTCTATCATTATCAT
1 ATCTCTATCATTATCAT
987605 TAACCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.23, G:0.03, T:0.46
Consensus pattern (18 bp):
ATCTCTATCATTATCATG
Found at i:988748 original size:13 final size:13
Alignment explanation
Indices: 988730--988758 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
988720 CATATTGTCC
988730 TATAGGTCAATGT
1 TATAGGTCAATGT
988743 TATAGGTCAATGT
1 TATAGGTCAATGT
988756 TAT
1 TAT
988759 TTAACTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (13 bp):
TATAGGTCAATGT
Found at i:990890 original size:38 final size:39
Alignment explanation
Indices: 990846--990922 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
990836 TAATTTATAC
*
990846 ATAAA-TTTAATTTTGTAA-CTTCTA-ATTTTTATTTTTTA
1 ATAAATTTTAATTTTATAACCTT-TATA-TTTTATTTTTTA
990884 ATAAATTTTAATTTTATAACCTTTATATTTTATTTTTTA
1 ATAAATTTTAATTTTATAACCTTTATATTTTATTTTTTA
990923 CAAGACTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
38 5 0.14
39 26 0.74
40 4 0.11
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.61
Consensus pattern (39 bp):
ATAAATTTTAATTTTATAACCTTTATATTTTATTTTTTA
Found at i:997112 original size:3 final size:3
Alignment explanation
Indices: 997104--997128 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
997094 GATTTAAATC
997104 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
997129 TAATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:1009755 original size:20 final size:19
Alignment explanation
Indices: 1009730--1009769 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1009720 ACAGACTTTA
*
1009730 TAACTAATCATTAACAACCT
1 TAACTAAT-ACTAACAACCT
*
1009750 TAACTACTACTAACAACCT
1 TAACTAATACTAACAACCT
1009769 T
1 T
1009770 CTAGAATCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (19 bp):
TAACTAATACTAACAACCT
Found at i:1018458 original size:23 final size:23
Alignment explanation
Indices: 1018432--1018509 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
1018422 CACCACAGCT
*
1018432 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
1018455 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGGAGTGCCA
* *
1018478 CGTAGAATTGCACCGGAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
1018501 TATAATAAT
1 CAT-ATAAT
1018510 GTCCATAAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
23 42 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (23 bp):
CATATAATTGCACCGGAGTGCCA
Found at i:1018687 original size:103 final size:103
Alignment explanation
Indices: 1018516--1018733 Score: 364
Period size: 103 Copynumber: 2.1 Consensus size: 103
1018506 TAATGTCCAT
* *
1018516 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1018581 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACAAATGTTCCAAAGAATACATATATGTCCCG
* * *
1018619 AAGGACCACATATCATTCGTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1018684 GACTTCACAAATGTTTCAAAGAATACATATATGTCCCG
66 GACTTCACAAATGTTCCAAAGAATACATATATGTCCCG
*
1018722 AAAGACCACATA
1 AAGGACCACATA
1018734 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACAAATGTTCCAAAGAATACATATATGTCCCG
Found at i:1023972 original size:23 final size:23
Alignment explanation
Indices: 1023946--1024023 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
1023936 TACCACATCT
1023946 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
1023969 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
1023992 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
1024015 TATAATAAT
1 CAT-ATAAT
1024024 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:1024201 original size:103 final size:103
Alignment explanation
Indices: 1024030--1024247 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
1024020 TAATGTCCAT
* * *
1024030 AAGGACCACATATCATTCATTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCATCA
1 AAGGACCACATATCATTCATTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1024095 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1024133 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCATTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1024198 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1024236 AAGGACCACATA
1 AAGGACCACATA
1024248 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCATTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1026775 original size:84 final size:83
Alignment explanation
Indices: 1026681--1026914 Score: 235
Period size: 83 Copynumber: 2.8 Consensus size: 83
1026671 TTTTCTACAC
* * * *
1026681 AAACGCCACTATATATATGGCTATTGCGGCATTGTTTTTACATAAACGTCACTAAAGTATGTGTT
1 AAACGCCACTATATATATGGCTATAGCGG-ATTTTTTTTACATAAACGCCACTAAAGTACGTGTT
*
1026746 TGTAGTCG-CGTTTGCACTA
65 TGTAG-CGACGTTTGCACAA
* * * * *
1026765 AAACGGCACTATATATCT-GCTATAGCGGTGTTTTTTTTTAC-TAAACACCACTAAAGTACGAGT
1 AAACGCCACTATATATATGGCTATAGC-G-GATTTTTTTTACATAAACGCCACTAAAGTACGTGT
* * *
1026828 TTTTTGCGACGTTTTCACAA
64 TTGTAGCGACGTTTGCACAA
* * *
1026848 AAACACCACTGTATATTTGGCTATCA-C-GATTTTTTTTTACATAAACGCCACTAAAGTACGTGT
1 AAACGCCACTATATATATGGCTAT-AGCGGA-TTTTTTTTACATAAACGCCACTAAAGTACGTGT
1026911 TTGT
64 TTGT
1026915 GGTGGCATTT
Statistics
Matches: 122, Mismatches: 21, Indels: 15
0.77 0.13 0.09
Matches are distributed among these distances:
81 1 0.01
82 12 0.10
83 75 0.61
84 32 0.26
85 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (83 bp):
AAACGCCACTATATATATGGCTATAGCGGATTTTTTTTACATAAACGCCACTAAAGTACGTGTTT
GTAGCGACGTTTGCACAA
Found at i:1026926 original size:83 final size:84
Alignment explanation
Indices: 1026671--1026933 Score: 230
Period size: 83 Copynumber: 3.1 Consensus size: 84
1026661 TTATAGCTAA
* * * * * * *
1026671 TTTTCTACACAAACGCCACTATATATATGGCTATTGCGGCA-TTGTTTTTACATAAACGTCACTA
1 TTTTC-ACAAAAACACCACTATATATCT-GCTATAGCGGTATTTTTTTTTACATAAACGCCACTA
* *
1026735 AAGTATGTGTTTGTAGTCGCG
64 AAGTACGTGTTTGTAGTGGCG
* * ** * *
1026756 TTTGCACTAAAACGGCACTATATATCTGCTATAGCGGTGTTTTTTTTTAC-TAAACACCACTAAA
1 TTTTCACAAAAACACCACTATATATCTGCTATAGCGGTATTTTTTTTTACATAAACGCCACTAAA
* * * * *
1026820 GTACGAGTTTTTTGCGACG
66 GTACGTGTTTGTAGTGGCG
* *
1026839 TTTTCACAAAAACACCACTGTATATTTGGCTATCA-C-G-ATTTTTTTTTACATAAACGCCACTA
1 TTTTCACAAAAACACCACTATATATCT-GCTAT-AGCGGTATTTTTTTTTACATAAACGCCACTA
* *
1026901 AAGTACGTGTTTGTGGTGGCA
64 AAGTACGTGTTTGTAGTGGCG
*
1026922 TTTTCCCAAAAA
1 TTTTCACAAAAA
1026934 AAAAAACCAC
Statistics
Matches: 141, Mismatches: 33, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
82 11 0.08
83 92 0.65
84 33 0.23
85 5 0.04
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (84 bp):
TTTTCACAAAAACACCACTATATATCTGCTATAGCGGTATTTTTTTTTACATAAACGCCACTAAA
GTACGTGTTTGTAGTGGCG
Found at i:1027611 original size:12 final size:12
Alignment explanation
Indices: 1027594--1027619 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1027584 AAGGGTTAAT
1027594 ATATTGTCAAAC
1 ATATTGTCAAAC
1027606 ATATTGTCAAAC
1 ATATTGTCAAAC
1027618 AT
1 AT
1027620 TTTTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATATTGTCAAAC
Found at i:1027795 original size:31 final size:28
Alignment explanation
Indices: 1027760--1027816 Score: 69
Period size: 31 Copynumber: 1.9 Consensus size: 28
1027750 ATCATAGAAA
*
1027760 ATTTTAATTAAATAATAATAATAATTAATAT
1 ATTTTAATAAAAT-A-AATAA-AATTAATAT
*
1027791 ATTTTCATAAAATAAATAAAATTAAT
1 ATTTTAATAAAATAAATAAAATTAAT
1027817 TCCAGTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.29
29 5 0.21
30 1 0.04
31 11 0.46
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
ATTTTAATAAAATAAATAAAATTAATAT
Found at i:1030193 original size:28 final size:31
Alignment explanation
Indices: 1030142--1030212 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
1030132 AAGCAGTAAA
1030142 AAAATAGAAAC-TTAAGGGTCT-AAATA-AC
1 AAAATAGAAACTTTAAGGGTCTAAAATAGAC
* *
1030170 AAAATAGAAACTTTAGGGGT-TAAAATAGAT
1 AAAATAGAAACTTTAAGGGTCTAAAATAGAC
*
1030200 AAAATAAAAACTT
1 AAAATAGAAACTT
1030213 CATGGACCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 12 0.32
29 12 0.32
30 13 0.35
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (31 bp):
AAAATAGAAACTTTAAGGGTCTAAAATAGAC
Found at i:1030255 original size:61 final size:60
Alignment explanation
Indices: 1030163--1030315 Score: 150
Period size: 61 Copynumber: 2.5 Consensus size: 60
1030153 TTAAGGGTCT
* ** * * *
1030163 AAATAAC--AAAATAGAAACTTTAGGGGTTAAAATAG-ATAAAATAAAAACTTCATGGACCA
1 AAATAACAAAAAATAGAAAC-CTAGGGACTAAAATAGCA-AAAATAAAAACCTAAAGGACCA
* * * *
1030222 AAATAATAAAAAGTAGAAACCTAGAGGACTAAAATAGCAAAAATATAAACCTAAAGGACTA
1 AAATAACAAAAAATAGAAACCTAG-GGACTAAAATAGCAAAAATAAAAACCTAAAGGACCA
* *
1030283 AAATAGCAAAAAATAGAAACTTAGGGACTAAAA
1 AAATAACAAAAAATAGAAACCTAGGGACTAAAA
1030316 CAGTAATAGT
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
59 6 0.08
60 12 0.16
61 57 0.75
62 1 0.01
ACGTcount: A:0.58, C:0.10, G:0.14, T:0.18
Consensus pattern (60 bp):
AAATAACAAAAAATAGAAACCTAGGGACTAAAATAGCAAAAATAAAAACCTAAAGGACCA
Found at i:1030274 original size:30 final size:31
Alignment explanation
Indices: 1030229--1030315 Score: 124
Period size: 30 Copynumber: 2.9 Consensus size: 31
1030219 CCAAAATAAT
*
1030229 AAAAAGTAGAAACCTAGAGGACTAAAATAGC
1 AAAAAATAGAAACCTAGAGGACTAAAATAGC
* *
1030260 -AAAAATATAAACCTAAAGGACTAAAATAGC
1 AAAAAATAGAAACCTAGAGGACTAAAATAGC
*
1030290 AAAAAATAGAAACTTAG-GGACTAAAA
1 AAAAAATAGAAACCTAGAGGACTAAAA
1030316 CAGTAATAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
30 36 0.73
31 13 0.27
ACGTcount: A:0.59, C:0.11, G:0.15, T:0.15
Consensus pattern (31 bp):
AAAAAATAGAAACCTAGAGGACTAAAATAGC
Found at i:1032119 original size:35 final size:35
Alignment explanation
Indices: 1032073--1032148 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1032063 AAAACAGTCC
* *
1032073 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
1032108 TCAATTTCATTCTAAACCCTAAATTCTAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1032143 TCAATT
1 TCAATT
1032149 AATTCAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1032999 original size:13 final size:14
Alignment explanation
Indices: 1032976--1033004 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1032966 AAATTTATTT
1032976 TTCATATTTTATAA
1 TTCATATTTTATAA
1032990 TTCATA-TTTATAA
1 TTCATATTTTATAA
1033003 TT
1 TT
1033005 TAAGTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
TTCATATTTTATAA
Found at i:1033545 original size:3 final size:3
Alignment explanation
Indices: 1033537--1033570 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
1033527 ACCCTAAAAT
1033537 TAA TAA TAA TAA -AA GTAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA T
1033571 TAAATCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.86
4 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1033555 original size:15 final size:15
Alignment explanation
Indices: 1033531--1033563 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1033521 TACTTTACCC
*
1033531 TAAAATTAATAATAA
1 TAAAAGTAATAATAA
1033546 TAAAAGTAATAATAA
1 TAAAAGTAATAATAA
1033561 TAA
1 TAA
1033564 TAATAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
TAAAAGTAATAATAA
Found at i:1033993 original size:134 final size:133
Alignment explanation
Indices: 1033752--1034096 Score: 451
Period size: 134 Copynumber: 2.6 Consensus size: 133
1033742 ACACTACTCA
* * * *
1033752 TACGCAATGAAGA-GGTCTGGTTGTCTAAGGGTGACAAGACTCCTACGTGATGAGGAGATATGGT
1 TACGCGATGAAGACGG-CTGGTTATCT-AGGGTGACACGACTCCTACGTGATGAGGAGATCTGGT
* * *
1033816 TAGGGGATGACACGACTCATACGTGATGAAGAGTTCTGACCATCTTTAGGAAGGGTGATAACTCG
64 CAGGGGATAACACGAATCATACGTGATGAAGAGTTCTGACCATCTTTAGGAAGGGTGATAACTCG
* *
1033881 GTTCC
129 ATTAC
* *
1033886 TACGCGATGAAGACGGCTGGTTATCTAGGGTTGACACGGCTCCTACGTAATGAGGAGATCTGGTC
1 TACGCGATGAAGACGGCTGGTTATCTAGGG-TGACACGACTCCTACGTGATGAGGAGATCTGGTC
* * * *
1033951 GGGGGATAACATGAATCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGGTAACTCGA
65 AGGGGATAACACGAATCATACGTGATGAAGAGTTCTGACCATCTTTAGGAAGGGTGATAACTCGA
1034016 TTAC
130 TTAC
* * * * *
1034020 AACGTGATGAGGACGACTGGTTATCTAGGGGTGACACGACTTCTA-GTGATGAGGAGATCTGGTC
1 TACGCGATGAAGACGGCTGGTTATCTA-GGGTGACACGACTCCTACGTGATGAGGAGATCTGGTC
*
1034084 AGGGGATGACACG
65 AGGGGATAACACG
1034097 GTTCCTACAT
Statistics
Matches: 183, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
133 32 0.17
134 146 0.80
135 5 0.03
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.25
Consensus pattern (133 bp):
TACGCGATGAAGACGGCTGGTTATCTAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCA
GGGGATAACACGAATCATACGTGATGAAGAGTTCTGACCATCTTTAGGAAGGGTGATAACTCGAT
TAC
Found at i:1034845 original size:32 final size:32
Alignment explanation
Indices: 1034809--1034878 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
1034799 TTTGTTTCAA
* * * *
1034809 GATGTTGAATC-CCTAAATATGCTCCAATATTT
1 GATGTTGAATCTCC-AAAGATGCCCCAACATTC
1034841 GATGTTGAATCTCCAAAGATGCCCCAACATTC
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
1034873 GATGTT
1 GATGTT
1034879 TCTTGCTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 31 0.94
33 2 0.06
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTC
Found at i:1035949 original size:20 final size:20
Alignment explanation
Indices: 1035916--1035968 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
1035906 TCTTGTCTTC
**
1035916 TTTTTCTTCGCTTTATTATT
1 TTTTTCTTTTCTTTATTATT
* *
1035936 TTTTTCTTTTCTTTTTTCTT
1 TTTTTCTTTTCTTTATTATT
*
1035956 TGTTTTTTTTTCT
1 T-TTTTCTTTTCT
1035969 CTTTCTTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTTCTTTATTATT
Found at i:1035955 original size:32 final size:32
Alignment explanation
Indices: 1035916--1035987 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
1035906 TCTTGTCTTC
1035916 TTTTTCTTCGCTTTATTATTT-T-TTTCTTTTCT
1 TTTTTCTTCG-TTT-TTATTTCTCTTTCTTTTCT
* *
1035948 TTTTTCTTTGTTTTTTTTTCTCTTTCTTTTCT
1 TTTTTCTTCGTTTTTATTTCTCTTTCTTTTCT
1035980 TATTTTCT
1 T-TTTTCT
1035988 ATTGGTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 5 0.14
31 4 0.11
32 20 0.57
33 6 0.17
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.78
Consensus pattern (32 bp):
TTTTTCTTCGTTTTTATTTCTCTTTCTTTTCT
Found at i:1035961 original size:11 final size:12
Alignment explanation
Indices: 1035935--1035987 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 12
1035925 GCTTTATTAT
1035935 TTTTTTCTTTTC
1 TTTTTTCTTTTC
*
1035947 TTTTTTCTTTGTTT
1 TTTTTTC-TT-TTC
1035961 TTTTTTCTCTTTC
1 TTTTTTCT-TTTC
*
1035974 TTTTCTTATTTTC
1 TTTT-TTCTTTTC
1035987 T
1 T
1035988 ATTGGTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 7 0.21
13 14 0.41
14 13 0.38
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:1037880 original size:32 final size:32
Alignment explanation
Indices: 1037821--1037882 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1037811 GGTGAAAATA
1037821 ACACAAACAAAAGAAAATAAATAAGTTAGTGT
1 ACACAAACAAAAGAAAATAAATAAGTTAGTGT
* * *
1037853 ACACAAATAAAA-CAAATGAAATTAGTTAGT
1 ACACAAACAAAAGAAAAT-AAATAAGTTAGT
1037883 ACATGTAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.58, C:0.10, G:0.11, T:0.21
Consensus pattern (32 bp):
ACACAAACAAAAGAAAATAAATAAGTTAGTGT
Found at i:1039566 original size:21 final size:22
Alignment explanation
Indices: 1039542--1039582 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1039532 ACATATGATG
*
1039542 TAAAATAA-AATATTTACAACA
1 TAAAATAACAACATTTACAACA
1039563 TAAAATAACAACATTTACAA
1 TAAAATAACAACATTTACAA
1039583 TATGTACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAATAACAACATTTACAACA
Found at i:1039808 original size:60 final size:61
Alignment explanation
Indices: 1039733--1039943 Score: 225
Period size: 60 Copynumber: 3.5 Consensus size: 61
1039723 AGAATTCAAA
* *
1039733 GGACTAAAATGGCAAAAACATAAACTTAAATGG-CTAAAGTAGTAAAAAATAGAAACTTAAG
1 GGACTAAAATAGCAAAAACATAAACTTAAA-GGACTAAAATAGTAAAAAATAGAAACTTAAG
* * * * * * * *
1039794 GGTCT-AAATAGC-AAAACAAAAACTTTAGGGACCAAAACAGT-AAAAATAGAAACCTAAA
1 GGACTAAAATAGCAAAAACATAAACTTAAAGGACTAAAATAGTAAAAAATAGAAACTTAAG
* * *
1039852 GGACTAAAATAGCAAAAATATAAACCTAAAGGACTAAAATAGCAAAAAATAGAAACTT-AG
1 GGACTAAAATAGCAAAAACATAAACTTAAAGGACTAAAATAGTAAAAAATAGAAACTTAAG
* * * *
1039912 GGACTAAAATAGTAATAGCATAAACTTTAAGG
1 GGACTAAAATAGCAAAAACATAAACTTAAAGG
1039944 GTTAAAACAA
Statistics
Matches: 119, Mismatches: 27, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
58 21 0.18
59 27 0.23
60 54 0.45
61 17 0.14
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.18
Consensus pattern (61 bp):
GGACTAAAATAGCAAAAACATAAACTTAAAGGACTAAAATAGTAAAAAATAGAAACTTAAG
Found at i:1039818 original size:59 final size:59
Alignment explanation
Indices: 1039733--1039919 Score: 184
Period size: 59 Copynumber: 3.1 Consensus size: 59
1039723 AGAATTCAAA
* * *
1039733 GGACTAAAATGGCAAAAACATAAACTTAAATGG-CTAAAGTAGTAAAAAATAGAAACTTAAG
1 GGACT-AAATAGC-AAAACAAAAACTTAAA-GGACTAAAATAGTAAAAAATAGAAACTTAAG
* * * * * * *
1039794 GGTCTAAATAGCAAAACAAAAACTTTAGGGACCAAAACAGT-AAAAATAGAAACCTAAA
1 GGACTAAATAGCAAAACAAAAACTTAAAGGACTAAAATAGTAAAAAATAGAAACTTAAG
* *
1039852 GGACTAAAATAGCAAAA-ATATAAACCTAAAGGACTAAAATAGCAAAAAATAGAAACTT-AG
1 GGACT-AAATAGCAAAACA-A-AAACTTAAAGGACTAAAATAGTAAAAAATAGAAACTTAAG
1039912 GGACTAAA
1 GGACTAAA
1039920 ATAGTAATAG
Statistics
Matches: 102, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
58 22 0.22
59 35 0.34
60 28 0.27
61 17 0.17
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (59 bp):
GGACTAAATAGCAAAACAAAAACTTAAAGGACTAAAATAGTAAAAAATAGAAACTTAAG
Found at i:1039871 original size:30 final size:30
Alignment explanation
Indices: 1039730--1039923 Score: 155
Period size: 30 Copynumber: 6.5 Consensus size: 30
1039720 ACAAGAATTC
* * * *
1039730 AAAGGACTAAAATGGCAAAAACATAAACTT
1 AAAGGACTAAAATAGCAAAAATAGAAACCT
* * *
1039760 AAATGG-CTAAAGTAGTAAAAAATAGAAACTT
1 AAA-GGACTAAAATAG-CAAAAATAGAAACCT
* * *
1039791 AAGGGTCT-AAATAGCAAAACA-A-AAACTT
1 AAAGGACTAAAATAGCAAAA-ATAGAAACCT
* * * * *
1039819 TAGGGACCAAAACAGTAAAAATAGAAACCT
1 AAAGGACTAAAATAGCAAAAATAGAAACCT
*
1039849 AAAGGACTAAAATAGCAAAAATATAAACCT
1 AAAGGACTAAAATAGCAAAAATAGAAACCT
1039879 AAAGGACTAAAATAGCAAAAAATAGAAA-CT
1 AAAGGACTAAAATAGC-AAAAATAGAAACCT
* *
1039909 TAGGGACTAAAATAG
1 AAAGGACTAAAATAG
1039924 TAATAGCATA
Statistics
Matches: 133, Mismatches: 23, Indels: 16
0.77 0.13 0.09
Matches are distributed among these distances:
28 12 0.09
29 15 0.11
30 78 0.59
31 28 0.21
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (30 bp):
AAAGGACTAAAATAGCAAAAATAGAAACCT
Found at i:1041353 original size:3 final size:3
Alignment explanation
Indices: 1041345--1041378 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
1041335 TAATTAAAAT
1041345 TAA TAA TAA TAA -AA GTAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA T
1041379 TAAATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.86
4 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1041363 original size:15 final size:15
Alignment explanation
Indices: 1041339--1041371 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1041329 AATTTCTAAT
*
1041339 TAAAATTAATAATAA
1 TAAAAGTAATAATAA
1041354 TAAAAGTAATAATAA
1 TAAAAGTAATAATAA
1041369 TAA
1 TAA
1041372 TAATAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
TAAAAGTAATAATAA
Found at i:1043498 original size:15 final size:15
Alignment explanation
Indices: 1043480--1043546 Score: 54
Period size: 15 Copynumber: 4.8 Consensus size: 15
1043470 ATATATTTAA
1043480 ATTAAATATATAAAT
1 ATTAAATATATAAAT
* *
1043495 ATTATATATATATAT
1 ATTAAATATATAAAT
1043510 ATT-AAT-T-T-AA-
1 ATTAAATATATAAAT
* *
1043520 ATTAAATTTATTAAT
1 ATTAAATATATAAAT
*
1043535 ATTATATATATA
1 ATTAAATATATA
1043547 TATAAAATGA
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
10 3 0.08
11 4 0.10
12 2 0.05
13 2 0.05
14 4 0.10
15 25 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTAAATATATAAAT
Found at i:1043518 original size:40 final size:38
Alignment explanation
Indices: 1043465--1043550 Score: 136
Period size: 40 Copynumber: 2.2 Consensus size: 38
1043455 TTGGGTCGGG
1043465 TATATATATATTTAAATTAAATATATAAATATTATATA
1 TATATATATATTTAAATTAAATATATAAATATTATATA
* *
1043503 TATATATATTAATTTAAATTAAATTTATTAATATTATATA
1 TATATATA-T-ATTTAAATTAAATATATAAATATTATATA
1043543 TATATATA
1 TATATATA
1043551 AAATGATTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 8 0.18
39 1 0.02
40 35 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (38 bp):
TATATATATATTTAAATTAAATATATAAATATTATATA
Found at i:1054527 original size:2 final size:2
Alignment explanation
Indices: 1054520--1054595 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
1054510 ATGAGAAATT
1054520 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1054562 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1054596 AATCGTTAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1056422 original size:13 final size:12
Alignment explanation
Indices: 1056408--1056492 Score: 55
Period size: 13 Copynumber: 6.5 Consensus size: 12
1056398 TTGAAGAAAG
1056408 AAAAAAGAAAAAGA
1 AAAAAAG-AAAA-A
1056422 AAAAAAGAAAAA
1 AAAAAAGAAAAA
*
1056434 AAATAAATAAATAA
1 AAA-AAAGAAA-AA
*
1056448 ATAAAATGAAAAA
1 A-AAAAAGAAAAA
**
1056461 ATGAAAAA-ATGAA
1 A--AAAAAGAAAAA
1056474 AAAAAAGAACAAA
1 AAAAAAGAA-AAA
1056487 AAAAAA
1 AAAAAA
1056493 ACTAAAGAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
11 5 0.09
12 5 0.09
13 25 0.45
14 19 0.34
15 2 0.04
ACGTcount: A:0.82, C:0.01, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:1056426 original size:8 final size:8
Alignment explanation
Indices: 1056401--1056493 Score: 66
Period size: 8 Copynumber: 11.0 Consensus size: 8
1056391 GCTTTGCTTG
1056401 AAGAAAGAA
1 AAGAAA-AA
1056410 AA-AAGAAA
1 AAGAA-AAA
1056418 AAGAAAAA
1 AAGAAAAA
1056426 AAGAAAAA
1 AAGAAAAA
1056434 AA-ATAAATA
1 AAGA-AAA-A
*
1056443 AATAAATAA
1 AAGAAA-AA
1056452 AATGAAAAA
1 AA-GAAAAA
*
1056461 ATGAAAAA
1 AAGAAAAA
*
1056469 ATGAAAAAA
1 AAG-AAAAA
1056478 AAGAACAAA
1 AAGAA-AAA
1056487 AA-AAAAA
1 AAGAAAAA
1056494 CTAAAGAGAG
Statistics
Matches: 72, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
7 4 0.06
8 35 0.49
9 28 0.39
10 5 0.07
ACGTcount: A:0.82, C:0.01, G:0.10, T:0.08
Consensus pattern (8 bp):
AAGAAAAA
Found at i:1056427 original size:14 final size:13
Alignment explanation
Indices: 1056404--1056493 Score: 53
Period size: 14 Copynumber: 6.7 Consensus size: 13
1056394 TTGCTTGAAG
1056404 AAAGAAAAAAGAA
1 AAAGAAAAAAGAA
1056417 AAAGAAAAAAAGAA
1 AAAG-AAAAAAGAA
*
1056431 AAA-AAATAAATAA
1 AAAGAAA-AAAGAA
*
1056444 ATAA-ATAAAATGAAA
1 A-AAGA-AAAAAG-AA
1056459 AAATGAAAAAATGAA
1 AAA-GAAAAAA-GAA
* *
1056474 AAA-AAAGAACAA
1 AAAGAAAAAAGAA
1056486 AAA-AAAAA
1 AAAGAAAAA
1056494 CTAAAGAGAG
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
12 12 0.19
13 15 0.24
14 19 0.31
15 14 0.23
16 2 0.03
ACGTcount: A:0.82, C:0.01, G:0.09, T:0.08
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:1056428 original size:21 final size:20
Alignment explanation
Indices: 1056404--1056490 Score: 75
Period size: 21 Copynumber: 4.2 Consensus size: 20
1056394 TTGCTTGAAG
1056404 AAAGAAAAAAGAAAAAGAAAA
1 AAAGAAAAAA-AAAAAGAAAA
* *
1056425 AAAGAAAAAAAATAAATAAAT
1 AAAGAAAAAAAA-AAAGAAAA
* *
1056446 AAATAAAATGAAAAAATGAAAA
1 AAAGAAAA--AAAAAAAGAAAA
* * *
1056468 AATGAAAAAAAAGAACAAAA
1 AAAGAAAAAAAAAAAGAAAA
1056488 AAA
1 AAA
1056491 AAACTAAAGA
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
20 13 0.25
21 23 0.45
22 11 0.22
23 4 0.08
ACGTcount: A:0.82, C:0.01, G:0.09, T:0.08
Consensus pattern (20 bp):
AAAGAAAAAAAAAAAGAAAA
Found at i:1056435 original size:17 final size:17
Alignment explanation
Indices: 1056401--1056493 Score: 66
Period size: 17 Copynumber: 5.4 Consensus size: 17
1056391 GCTTTGCTTG
*
1056401 AAGAAAGAAAA-AAGAAA
1 AAGAAA-AAAAGAAAAAA
1056418 AAGAAAAAAAGAAAAAA
1 AAGAAAAAAAGAAAAAA
* * *
1056435 AATAAATAAATAAATAAA
1 AAGAAAAAAAGAAA-AAA
* *
1056453 ATGAAAAAATG-AAAAA
1 AAGAAAAAAAGAAAAAA
*
1056469 ATGAAAAAAAAGAACAAAA
1 AAG-AAAAAAAGAA-AAAA
1056488 AA-AAAA
1 AAGAAAA
1056494 CTAAAGAGAG
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
16 10 0.17
17 35 0.58
18 10 0.17
19 5 0.08
ACGTcount: A:0.82, C:0.01, G:0.10, T:0.08
Consensus pattern (17 bp):
AAGAAAAAAAGAAAAAA
Found at i:1056459 original size:25 final size:25
Alignment explanation
Indices: 1056404--1056487 Score: 79
Period size: 25 Copynumber: 3.4 Consensus size: 25
1056394 TTGCTTGAAG
1056404 AAAGAAAAAA-G-AAAAA-GAAAAA
1 AAAGAAAAAATGAAAAAATGAAAAA
*
1056426 AAGAAAAAAAAT-AAATAAAT-AAATAA
1 AA-AGAAAAAATGAAA-AAATGAAA-AA
*
1056452 AATGAAAAAATGAAAAAATGAAAAA
1 AAAGAAAAAATGAAAAAATGAAAAA
1056477 AAAGAACAAAA
1 AAAGAA-AAAA
1056488 AAAAAACTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
22 2 0.04
23 7 0.14
24 2 0.04
25 24 0.49
26 14 0.29
ACGTcount: A:0.81, C:0.01, G:0.10, T:0.08
Consensus pattern (25 bp):
AAAGAAAAAATGAAAAAATGAAAAA
Found at i:1058074 original size:133 final size:133
Alignment explanation
Indices: 1057894--1058227 Score: 402
Period size: 132 Copynumber: 2.5 Consensus size: 133
1057884 CAATATTTTT
* ** * *
1057894 AGATCTGATTTTCCTTCAAGAAGTAGCAGAACATATCCCTATTTTTTCCATATTTGATTTTCCCT
1 AGATCTGATTTTCCCTCAAGAAGTAGTGGAACAAATCCCT-TTTTTTCCATATTTGATATTCCCT
* * * * * * * *
1057959 GAGGAACAATATAGCAAATCTACCTCGATTTAATCTTTCCTGAAGAACAGTGGAATGAAT-ACGT
65 GAGGAACAATAGAACAAATCTACCTCGATTCAATATTCCCTAAAGAAAAATGGAATGAATAACGT
1058023 TTCC
130 TTCC
* * * * * *
1058027 AGATCTGATTTTCCCTCAAGAAGTAGTGGAATAGATCTCTCTCTTTT-CAGATTTTATATTCCCT
1 AGATCTGATTTTCCCTCAAGAAGTAGTGGAACAAATCCCT-TTTTTTCCATATTTGATATTCCCT
* * * *
1058091 GAGGAACAGTGGAACAAATTTACCTCGATTCAATATTCCCTAAAGAAAAATGTAATGAATCAACG
65 GAGGAACAATAGAACAAATCTACCTCGATTCAATATTCCCTAAAGAAAAATGGAATGAAT-AACG
1058156 TTTCC
129 TTTCC
* *
1058161 ATATCTGATTTTCCCTCAAGAAGTAGTGGAACAAATCCCTTTTTTTCCATATTTGATCTTCCCTG
1 AGATCTGATTTTCCCTCAAGAAGTAGTGGAACAAATCCCTTTTTTTCCATATTTGATATTCCCTG
1058226 AG
66 AG
1058228 TAAAAGTGGA
Statistics
Matches: 167, Mismatches: 31, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
132 62 0.37
133 44 0.26
134 61 0.37
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (133 bp):
AGATCTGATTTTCCCTCAAGAAGTAGTGGAACAAATCCCTTTTTTTCCATATTTGATATTCCCTG
AGGAACAATAGAACAAATCTACCTCGATTCAATATTCCCTAAAGAAAAATGGAATGAATAACGTT
TCC
Found at i:1058223 original size:134 final size:134
Alignment explanation
Indices: 1057749--1058302 Score: 469
Period size: 134 Copynumber: 4.1 Consensus size: 134
1057739 TGAGTAAACA
* * *
1057749 TTTCTAGATCTGATTTTCCCTCAAGAAGTAGCGG-ACATATCCATATTTTTTTATAGATTT-ATT
1 TTTCCAGATCTGATTTTCCCTCAAGAAGTAGCGGAACATATCCCTATTTTTTCAT--ATTTGA-T
* * *
1057812 TTTCCCTGAGGAATAGTGGAAAAAAATATACCTCAATCGATTCAATCTTCCCTGAAA-ATCAAT-
63 TTTCCCTGAGGAACAGTGG-AACAAATATA-C-C--TCGATTCAATCTTCCCT-AAAGAACAATG
**
1057875 TGAATGAATCAATA
122 T-AATGAATCAACG
** * *
1057889 TTTTTAGATCTGATTTTCCTTCAAGAAGTAGCAGAACATATCCCTATTTTTTCCATATTTGATTT
1 TTTCCAGATCTGATTTTCCCTCAAGAAGTAGCGGAACATATCCCTATTTTTT-CATATTTGATTT
* ** * * * * * * *
1057954 TCCCTGAGGAACAATATAGCAAATCTACCTCGATTTAATCTTTCCTGAAGAACAGTGGAATGAAT
65 TCCCTGAGGAACAGTGGAACAAATATACCTCGATTCAATCTTCCCTAAAGAACAATGTAATGAAT
1058019 --ACG
130 CAACG
* * * * * * * * *
1058022 TTTCCAGATCTGATTTTCCCTCAAGAAGTAGTGGAATAGATCTCTCTCTTTTCAGATTTTATATT
1 TTTCCAGATCTGATTTTCCCTCAAGAAGTAGCGGAACATATCCCTATTTTTTCATATTTGATTTT
* * *
1058087 CCCTGAGGAACAGTGGAACAAATTTACCTCGATTCAATATTCCCTAAAGAAAAATGTAATGAATC
66 CCCTGAGGAACAGTGGAACAAATATACCTCGATTCAATCTTCCCTAAAGAACAATGTAATGAATC
1058152 AACG
131 AACG
* * * *
1058156 TTTCCATATCTGATTTTCCCTCAAGAAGTAGTGGAACAAATCCCT-TTTTTTCCATATTTGATCT
1 TTTCCAGATCTGATTTTCCCTCAAGAAGTAGCGGAACATATCCCTATTTTTT-CATATTTGATTT
* * * * * ** * * * * *
1058220 TCCCTGAGTAAAAGTGGAATAAGTCTGTCTCGATTCAATCTT-TCTAAAGAATAGTGGAATGAGT
65 TCCCTGAGGAACAGTGGAACAAATATACCTCGATTCAATCTTCCCTAAAGAACAATGTAATGAAT
*
1058284 CAACC
130 CAACG
1058289 TTTCTCA-ATCTGAT
1 TTTC-CAGATCTGAT
1058303 CTACCTTGAA
Statistics
Matches: 338, Mismatches: 67, Indels: 25
0.79 0.16 0.06
Matches are distributed among these distances:
132 62 0.18
133 80 0.24
134 91 0.27
135 26 0.08
137 1 0.00
138 1 0.00
139 7 0.02
140 51 0.15
141 17 0.05
142 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (134 bp):
TTTCCAGATCTGATTTTCCCTCAAGAAGTAGCGGAACATATCCCTATTTTTTCATATTTGATTTT
CCCTGAGGAACAGTGGAACAAATATACCTCGATTCAATCTTCCCTAAAGAACAATGTAATGAATC
AACG
Found at i:1059455 original size:11 final size:11
Alignment explanation
Indices: 1059414--1059458 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1059404 CCGGTCTGAG
1059414 CCGAGCCGTTGA
1 CCGA-CCGTTGA
* *
1059426 CCGGCCATTGA
1 CCGACCGTTGA
1059437 CCGA-CGTTGA
1 CCGACCGTTGA
1059447 CCGACCGTTGA
1 CCGACCGTTGA
1059458 C
1 C
1059459 TTTATTCGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
10 9 0.32
11 16 0.57
12 3 0.11
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.18
Consensus pattern (11 bp):
CCGACCGTTGA
Found at i:1060899 original size:12 final size:12
Alignment explanation
Indices: 1060881--1060937 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
1060871 TGAATGCTTT
1060881 CTCTGATTTCTG
1 CTCTGATTTCTG
*
1060893 TTCTGATTTCTG
1 CTCTGATTTCTG
* *
1060905 CTCTAATTTCTA
1 CTCTGATTTCTG
* *
1060917 TTTTGATTTCTG
1 CTCTGATTTCTG
1060929 CTCTGATTT
1 CTCTGATTT
1060938 TTGATATCTC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (12 bp):
CTCTGATTTCTG
Found at i:1060913 original size:24 final size:24
Alignment explanation
Indices: 1060881--1060937 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
1060871 TGAATGCTTT
*
1060881 CTCTGATTTCTGTTCTGATTTCTG
1 CTCTGATTTCTATTCTGATTTCTG
* *
1060905 CTCTAATTTCTATTTTGATTTCTG
1 CTCTGATTTCTATTCTGATTTCTG
1060929 CTCTGATTT
1 CTCTGATTT
1060938 TTGATATCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (24 bp):
CTCTGATTTCTATTCTGATTTCTG
Found at i:1061119 original size:31 final size:31
Alignment explanation
Indices: 1061081--1061156 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
1061071 TAAGACGACC
* * *
1061081 CTTGGGTAGGCTCTGCGGCCCTGAGATTTTT
1 CTTGGGTAGGCTCTGCGGCCCCGAGAATTGT
* * *
1061112 CTTGGGTAAGCCTATGTGGCCCCGAGAATTGT
1 CTTGGGT-AGGCTCTGCGGCCCCGAGAATTGT
1061144 CTTGGGTAGGCTC
1 CTTGGGTAGGCTC
1061157 GCAGGTCCCA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
31 11 0.31
32 25 0.69
ACGTcount: A:0.13, C:0.22, G:0.33, T:0.32
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGCGGCCCCGAGAATTGT
Found at i:1065522 original size:18 final size:18
Alignment explanation
Indices: 1065499--1065553 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
1065489 TTGAGGGATT
1065499 ATAGTGGTCATTCGGGAC
1 ATAGTGGTCATTCGGGAC
* *
1065517 ATAGTGGTCCTTCGGGAT
1 ATAGTGGTCATTCGGGAC
*
1065535 AAAGTGGTCATTCGGGAC
1 ATAGTGGTCATTCGGGAC
1065553 A
1 A
1065554 AATTTTTAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (18 bp):
ATAGTGGTCATTCGGGAC
Found at i:1077822 original size:14 final size:14
Alignment explanation
Indices: 1077788--1077824 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1077778 TTATGCATAA
*
1077788 GGACAGCTGGCACT
1 GGACAGTTGGCACT
1077802 GGACAGTTGGCACT
1 GGACAGTTGGCACT
1077816 GGACAGTTG
1 GGACAGTTG
1077825 TCTCTGCACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.38, T:0.19
Consensus pattern (14 bp):
GGACAGTTGGCACT
Found at i:1081574 original size:3 final size:3
Alignment explanation
Indices: 1081566--1081590 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1081556 TTAGTGAGGC
1081566 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1081591 CAAGGAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1081838 original size:23 final size:24
Alignment explanation
Indices: 1081812--1081870 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 24
1081802 CTCGTATAAA
1081812 TGCACT-GAAGTGCAACGTAGAAT
1 TGCACTCGAAGTGCAACGTAGAAT
**
1081835 TGCA-TCGAAGTGCCGCGTAGAAT
1 TGCACTCGAAGTGCAACGTAGAAT
*
1081858 TGCAC-CGTAGTGC
1 TGCACTCGAAGTGC
1081871 TATATAAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 1 0.03
23 30 0.97
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (24 bp):
TGCACTCGAAGTGCAACGTAGAAT
Found at i:1088772 original size:23 final size:23
Alignment explanation
Indices: 1088714--1088765 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1088704 CTTGTATAAA
*
1088714 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1088737 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1088760 TGCACC
1 TGCACC
1088766 TTAGTGCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1089045 original size:32 final size:31
Alignment explanation
Indices: 1088985--1089045 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
1088975 TACATAGTAT
** *
1088985 ATCACATAGATATATCCCTTTGCTTACATTC
1 ATCACATAGATATATAACTTTGCATACATTC
*
1089016 ATCACATAGTTCATATAACTTTGCATACAT
1 ATCACATAGAT-ATATAACTTTGCATACAT
1089046 ATTCATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (31 bp):
ATCACATAGATATATAACTTTGCATACATTC
Found at i:1090443 original size:26 final size:26
Alignment explanation
Indices: 1090403--1090464 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
1090393 CGGGACATAG
* *
1090403 TGGTCTTTCGGGACATATATGATATA
1 TGGTCCTTCGAGACATATATGATATA
* *
1090429 TGGTCCTTCGAGACATATGTGATATG
1 TGGTCCTTCGAGACATATATGATATA
1090455 TGGTCCTTCG
1 TGGTCCTTCG
1090465 GGATATAGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (26 bp):
TGGTCCTTCGAGACATATATGATATA
Found at i:1090470 original size:24 final size:24
Alignment explanation
Indices: 1090402--1090471 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 24
1090392 TCGGGACATA
*
1090402 GTGGTCTTTCGGGACATATATGATAT
1 GTGGTCCTTCGGG--ATATATGATAT
* * *
1090428 ATGGTCCTTCGAGACATATGTGATAT
1 GTGGTCCTTCG-G-GATATATGATAT
1090454 GTGGTCCTTCGGGATATA
1 GTGGTCCTTCGGGATATA
1090472 GTGGTCCTTC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
24 4 0.11
25 1 0.03
26 29 0.83
27 1 0.03
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (24 bp):
GTGGTCCTTCGGGATATATGATAT
Found at i:1090477 original size:18 final size:17
Alignment explanation
Indices: 1090449--1090487 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
1090439 AGACATATGT
1090449 GATATGTGGTCCTTCGG
1 GATATGTGGTCCTTCGG
1090466 GATATAGTGGTCCTTCGG
1 GATAT-GTGGTCCTTCGG
1090484 GATA
1 GATA
1090488 AATTATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.33
Consensus pattern (17 bp):
GATATGTGGTCCTTCGG
Found at i:1093307 original size:7 final size:7
Alignment explanation
Indices: 1093263--1093305 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
1093253 CCAGAACCTT
1093263 TTCTTCC
1 TTCTTCC
1093270 TTCTTCC
1 TTCTTCC
1093277 TTCTTCC
1 TTCTTCC
1093284 TTCTTCC
1 TTCTTCC
1093291 TTCTTCC
1 TTCTTCC
*
1093298 TCCTTCC
1 TTCTTCC
1093305 T
1 T
1093306 CCCATTGCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
TTCTTCC
Found at i:1093414 original size:21 final size:21
Alignment explanation
Indices: 1093388--1093443 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1093378 TATTTGGTTG
*
1093388 TTATATAAGGTTAAGGAAAGC
1 TTATATAAGCTTAAGGAAAGC
1093409 TTATATAAGCTTAAGGAAAGC
1 TTATATAAGCTTAAGGAAAGC
1093430 TTATATAAGCTTAA
1 TTATATAAGCTTAA
1093444 AGCATTAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (21 bp):
TTATATAAGCTTAAGGAAAGC
Found at i:1094754 original size:18 final size:18
Alignment explanation
Indices: 1094723--1094758 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1094713 AGGGTTCTAT
*
1094723 GTGGTTCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
1094741 GTGGTCCTTTGGGACATA
1 GTGGTCCTTCGGGACATA
1094759 TGTGATATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:1094780 original size:26 final size:26
Alignment explanation
Indices: 1094741--1094808 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
1094731 TCGGGACATA
*
1094741 GTGGTCCTTTGGGACATATGTGATAT
1 GTGGTCCTTCGGGACATATGTGATAT
1094767 GTGGTCCTTCGGGACATATGTGATAT
1 GTGGTCCTTCGGGACATATGTGATAT
1094793 GTGGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
1094809 AATTCTACGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (26 bp):
GTGGTCCTTCGGGACATATGTGATAT
Found at i:1097602 original size:22 final size:22
Alignment explanation
Indices: 1097569--1097611 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1097559 TTTAGTCCTA
*
1097569 TTTTCATTTTATTT-ATTTTAT
1 TTTTCATGTTATTTCATTTTAT
1097590 TTTTGCATGTTATTTCATTTTA
1 TTTT-CATGTTATTTCATTTTA
1097612 GTCATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTTCATGTTATTTCATTTTAT
Found at i:1098237 original size:131 final size:131
Alignment explanation
Indices: 1098053--1098414 Score: 494
Period size: 131 Copynumber: 2.8 Consensus size: 131
1098043 TATTGAGAAC
** * *
1098053 AATAATAGATTTTCATTTCGGTTTGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTAT
1 AATAATATCTTTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTAT
* *
1098118 TCTCGATTGGAAATAATTCGATATTATCGTTTTCTCTCGAATCAATATTGATTTTTAAAATGGAA
66 TCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAAAT-GAA
*
1098183 TG
130 AG
* * * *
1098185 -GTTATATCTTTTCATTTCGATTGGAGTAATAAATTATTGCTTTATA-GTATGAGAGGTCATTTA
1 AATAATATCTTTTCATTTCGATTGGAGTAATAAATGATTGCTTTA-AGGCATGAGAGGTCATTTA
* * * * *
1098248 TTCTCGATTGGAAATCATTAGATATTATTGTTTTCACTCGAATCGATATTGAATTTTAAGATGAA
65 TTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAAATGAA
1098313 AG
130 AG
* * * * *
1098315 AATAATATCTCTTCATTTCGATTGTAGTAATAAATGATTGTTTTAAGGCATAAAAGGTCATTTAT
1 AATAATATCTTTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTAT
*
1098380 TCTCGATTGGAAATAATTAGATATTATCATTTTCT
66 TCTCGATTGGAAATAATTAGATATTATCGTTTTCT
1098415 ATCTTAAAAT
Statistics
Matches: 198, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
130 5 0.03
131 192 0.97
132 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (131 bp):
AATAATATCTTTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTAT
TCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAAATGAAA
G
Found at i:1103583 original size:133 final size:133
Alignment explanation
Indices: 1103419--1103874 Score: 700
Period size: 133 Copynumber: 3.4 Consensus size: 133
1103409 AGCAAATCTC
* *
1103419 AAGCCATCCAGTAAGAAAACATATAGGAAAGCATGATAAGTAGCTTTCAGTGTGACTATAAATGC
1 AAGCCATCCGGAAAGAAAACATATAGGAAAGCATGATAAGTAGCTTTCAGTGTGACTATAAATGC
1103484 AAACATTCACAGAAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCCTTCCAATGAA
66 AAACATTCACAGAAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCCTTCCAATGAA
1103549 AGA
131 AGA
*
1103552 AAGCCATCCGGAAAGAAAACATATAGGAAAGCATGATAAGTAGCTTTCGGTGTGACTATAAATGC
1 AAGCCATCCGGAAAGAAAACATATAGGAAAGCATGATAAGTAGCTTTCAGTGTGACTATAAATGC
*
1103617 AAACATTCACAGAAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCCTTCCAATAAA
66 AAACATTCACAGAAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCCTTCCAATGAA
1103682 AGA
131 AGA
* * * * *
1103685 AAGCCATCCGGAAAGAAAACATATAGGAAAACATGATAAGTAGCTTTCAGTGTGATTGTGAATGT
1 AAGCCATCCGGAAAGAAAACATATAGGAAAGCATGATAAGTAGCTTTCAGTGTGACTATAAATGC
* * * * * *
1103750 AAACATTCGCAGGAAATAGAAAATAATTTCAGAAACAAATAGAAATGAAGATTTACATCCAAAGA
66 AAACATTCACAGAAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGA-TTCCTTCCAATGA
1103815 AAG-
130 AAGA
* * * * * *
1103818 AA-CCATTCGGTAAGAGAACATATACGAAAGCATGATAAGTAGTTTTCAGTGTAACTA
1 AAGCCATCCGGAAAGAAAACATATAGGAAAGCATGATAAGTAGCTTTCAGTGTGACTA
1103875 CAAACTACAT
Statistics
Matches: 296, Mismatches: 26, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
132 46 0.16
133 238 0.80
134 12 0.04
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.22
Consensus pattern (133 bp):
AAGCCATCCGGAAAGAAAACATATAGGAAAGCATGATAAGTAGCTTTCAGTGTGACTATAAATGC
AAACATTCACAGAAAATAGAACATAATTTCAGAAACAAATAGAAATGAAGATTCCTTCCAATGAA
AGA
Found at i:1106356 original size:199 final size:198
Alignment explanation
Indices: 1105956--1106657 Score: 851
Period size: 199 Copynumber: 3.5 Consensus size: 198
1105946 TTTTATAAGT
* * * *
1105956 AAACCGGTATATTTATACCGGTAACATTGTAAATTTACTTATTACATTATAATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGTTATATTATAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * * * * *
1106021 TGTTTTTTGGATCGATACTTTTTATAAATGTATCGACACTATATGCGTTCACCCTTTTGGGCATT
66 TGTTTTTGGGATCGATAC-TTTTAAAAATGTATCGACACTTTATGAGTGCACCCGTTTGGGCATT
* * * *
1106086 CATTTTAGA-AAAAAGTATCGACACAACA-TTAAAAAGTGTCGACACATTATGTTGACATATTCT
130 CATTATGGACAAAAA-TATCGACACAA-ATTTAAAAAGTGTCGATACATTATGTTGACATATTTT
*
1106149 CACATA
193 CTCATA
* ** * * * *
1106155 AAACCGATATAAATATACTGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTATACCGGTTATATTATAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
1106220 TGTTTTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATAAGTGCACCCGTCT-GGCATT
66 TGTTTTTGGGATCGATAC-TTTTAAAAATGTATCGACACTTTATGAGTGCACCCGTTTGGGCATT
* * * * *
1106284 CATTATGGACAAAATATATCGACACAAATTTAATAAGTATCGATACTTTATGATGACCTATTTTC
130 CATTATGGACAAAA-ATATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACATATTTTC
1106349 TCATA
194 TCATA
* * *
1106354 AAATCGGTATATTTATACCGGTTATATTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGTTATATTATAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
1106419 T-TTTATTGGGATCGATACTTTTAATAATTGTATCGACACTTTATGTGTGCACCCCGTTTGGGCA
66 TGTTT-TTGGGATCGATACTTTTAA-AAATGTATCGACACTTTATGAGTGCA-CCCGTTTGGGCA
* * * * *
1106483 TTCATTCTGGACAATAAGTATCAACACAAA-TTAAACAAGTGTCGATACATTATGTTTACATGTT
128 TTCATTATGGACAA-AAATATCGACACAAATTTAAA-AAGTGTCGATACATTATGTTGACATATT
*
1106547 TTCTAAT-
191 TTCTCATA
* * * *
1106554 TAACCGGTATATTTATACCGGTTACATTATTAATTTACCTATTACATTATAATTATTGGTTTCGA
1 AAACCGGTATATTTATACCGGTTATATTATAAATTTACCTATTACATTATAATTATCGGTTTCGA
1106619 TGTTTTTTGGG-TCGATACTTTTAGAAAATGTATCGACAC
66 TG-TTTTTGGGATCGATACTTTTA-AAAATGTATCGACAC
1106658 ATATTTAGGT
Statistics
Matches: 429, Mismatches: 62, Indels: 23
0.83 0.12 0.04
Matches are distributed among these distances:
198 23 0.05
199 244 0.57
200 95 0.22
201 62 0.14
202 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (198 bp):
AAACCGGTATATTTATACCGGTTATATTATAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTTTTGGGATCGATACTTTTAAAAATGTATCGACACTTTATGAGTGCACCCGTTTGGGCATTC
ATTATGGACAAAAATATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACATATTTTCTC
ATA
Found at i:1110897 original size:18 final size:18
Alignment explanation
Indices: 1110874--1110957 Score: 150
Period size: 18 Copynumber: 4.7 Consensus size: 18
1110864 ATTTTCTTCA
*
1110874 TCTTTTCTTTTTCCTCCC
1 TCTTTTCTTCTTCCTCCC
1110892 TCTTTTCTTCTTCCTCCC
1 TCTTTTCTTCTTCCTCCC
*
1110910 TCTTTTTTTCTTCCTCCC
1 TCTTTTCTTCTTCCTCCC
1110928 TCTTTTCTTCTTCCTCCC
1 TCTTTTCTTCTTCCTCCC
1110946 TCTTTTCTTCTT
1 TCTTTTCTTCTT
1110958 TATATTTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTTTTCTTCTTCCTCCC
Found at i:1111170 original size:25 final size:25
Alignment explanation
Indices: 1111142--1111230 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
1111132 CCATCTTAAG
1111142 TTCACCCCTCAACACCTCAACTTCTT
1 TTCACCCCTCAACACCTCAACTTC-T
1111168 TCATCACTTTACCCCTCAACACCTCAACTTCT
1 T--TCA-----CCCCTCAACACCTCAACTTCT
* *
1111200 TTCACCACTTC-ACCCCTCAACTTCT
1 TTCACC-CCTCAACACCTCAACTTCT
1111225 TTCACC
1 TTCACC
1111231 ACTCCATCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
25 21 0.40
26 4 0.08
28 3 0.06
30 3 0.06
32 2 0.04
33 20 0.38
ACGTcount: A:0.22, C:0.46, G:0.00, T:0.31
Consensus pattern (25 bp):
TTCACCCCTCAACACCTCAACTTCT
Found at i:1111186 original size:33 final size:33
Alignment explanation
Indices: 1111142--1111220 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
1111132 CCATCTTAAG
*
1111142 TTCACCCCTCAACACCTCAACTTCTTTCATCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
*
1111175 TTTACCCCTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1111208 TTCACCCCTCAAC
1 TTCACCCCTCAAC
1111221 TTCTTTCACC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAACTTCTTTCACCAC
Found at i:1111292 original size:21 final size:20
Alignment explanation
Indices: 1111267--1111329 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 20
1111257 CCCATTATGC
*
1111267 CTCTCAAGTGTCTCTTAGACT
1 CTCTCAAGT-TCTCTTCGACT
1111288 CTCTCAAGCTTCTCTTCGACT
1 CTCTCAAG-TTCTCTTCGACT
1111309 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAG-TTCTCTTCGACT
1111330 TTTGATTATC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 38 0.97
22 1 0.03
ACGTcount: A:0.16, C:0.33, G:0.11, T:0.40
Consensus pattern (20 bp):
CTCTCAAGTTCTCTTCGACT
Found at i:1113743 original size:20 final size:20
Alignment explanation
Indices: 1113718--1113758 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1113708 GTAGCGCTTT
1113718 ACCGGTTTTGTCATTTAGAG
1 ACCGGTTTTGTCATTTAGAG
1113738 ACCGGTTTTGTCATTTAGAG
1 ACCGGTTTTGTCATTTAGAG
1113758 A
1 A
1113759 TCGATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (20 bp):
ACCGGTTTTGTCATTTAGAG
Found at i:1113766 original size:20 final size:20
Alignment explanation
Indices: 1113718--1113771 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1113708 GTAGCGCTTT
*
1113718 ACCGGTTTTGTCATTTAGAG
1 ACCGATTTTGTCATTTAGAG
*
1113738 ACCGGTTTTGTCATTTAGAG
1 ACCGATTTTGTCATTTAGAG
* *
1113758 ATCGATTTTATCAT
1 ACCGATTTTGTCAT
1113772 ATTTTTACCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (20 bp):
ACCGATTTTGTCATTTAGAG
Found at i:1114087 original size:182 final size:182
Alignment explanation
Indices: 1113763--1114550 Score: 1134
Period size: 182 Copynumber: 4.3 Consensus size: 182
1113753 TAGAGATCGA
* * * * * *
1113763 TTTTATCATATTTTTACCTGTTATATCGTTATGGGTCAATACATTTTTATAAAGTATCGACACTT
1 TTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTT
* * * *
1113828 TGA-AGGCGCTAAAACAACTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAATTATCG
66 T-ATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATCG
* * * * * **
1113892 ACACTTTCAATATATCCAGTAGCTCTTTACCGATTTTGCCTTTTCGAGACCGG
130 ACACTTGCAATATATCCGGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCGG
* * *
1113945 TTTTATCATATTTTTACCTATTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACGT
1 TTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTT
*
1114010 TATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTATCGATACTTATATTAAAGTATCGA
66 TATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATCGA
* *
1114075 TACTTGCAATATATTCGGTATCTCTTTACCGG--TTGTCTTTTCCTGACCGG
131 CACTTGCAATATATCCGGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCGG
1114125 TTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTT
1 TTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTT
*
1114190 TCTAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATCGA
66 TATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATCGA
* *
1114255 CACTTGCAATGTATCTGGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCGG
131 CACTTGCAATATATCCGGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCGG
1114307 TTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTT
1 TTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTT
* * * **
1114372 TATAGGCGCTAAAATTGCTTCACCTTTAAATTCATTATGTGTCGATACTTATATTAAAGTATCGA
66 TATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATCGA
* * * * ** *
1114437 CACGTGCAATATATCCGGTAAT-GCTTTATCGGTTTTATCTTTTTGTGACCGA
131 CACTTGCAATATATCCGGT-ATCTCTTTACCGGTTTTGTCTTTTCCTGACCGG
* * * * * *
1114489 TTTTGTCATATTTTTTCCTGTTATATTGATATGGATCGATACATTTTTATAAAGTATCGACA
1 TTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACA
1114551 TAAACCGACA
Statistics
Matches: 551, Mismatches: 51, Indels: 8
0.90 0.08 0.01
Matches are distributed among these distances:
180 168 0.30
181 1 0.00
182 380 0.69
183 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (182 bp):
TTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTT
TATAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTATCGA
CACTTGCAATATATCCGGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCGG
Found at i:1114433 original size:362 final size:363
Alignment explanation
Indices: 1113760--1114550 Score: 1172
Period size: 362 Copynumber: 2.2 Consensus size: 363
1113750 ATTTAGAGAT
* * *
1113760 CGATTTTATCATATTTTTACCTGTTATATCGTTATGGGTCAATACATTTTTATAAAGTATCGACA
1 CGATTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACA
* * *
1113825 CTTTGAAGGCGCTAAAACAACTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAATTAT
66 CTTTCAAGGCGCTAAAACAACTTCTCCTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTAT
* *
1113890 CGACACTTTCAATATATCCAGTAGCTCTTTACCGATTTTGCCTTTTCGAGACCGGTTTTATCATA
131 CGACACTTGCAATATATCCAGTAGCTCTTTACCGATTTTGCCTTTTCCAGACCGGTTTTATCATA
1113955 TTTTTACCTATTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACGTTATAGGCGCT
196 TTTTTACCTATTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACGTTATAGGCGCT
* * *
1114020 AAAACTACTTCTCCTTTAAATTCACAATGTATCGATACTTATATTAAAGTATCGATACTTGCAAT
261 AAAACTACTTCACCTTTAAATTCACAATGTATCGATACTTATATTAAAGTATCGACACGTGCAAT
* * *
1114085 ATATTCGGT-ATCTCTTTACCGG-TTGTCTTTTCCTGAC
326 ATATCCGGTAAT-GCTTTACCGGTTTATCTTTTCCTGAC
* * * *
1114122 CGGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACA
1 CGATTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACA
* * *
1114187 CTTTCTAGGCGCTAAAACTACTTCTCCTTTAAATTCACAATGTGTCGATACTTATATTAAAGTAT
66 CTTTCAAGGCGCTAAAACAACTTCTCCTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTAT
* ** * * * * *
1114252 CGACACTTGCAATGTATCTGGTATCTCTTTACCGGTTTTGTCTTTTCCTGACCGGTTTTGTCATA
131 CGACACTTGCAATATATCCAGTAGCTCTTTACCGATTTTGCCTTTTCCAGACCGGTTTTATCATA
* *
1114317 TTTTTACCTGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACTTTATAGGCGCT
196 TTTTTACCTATTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACGTTATAGGCGCT
* * ** *
1114382 AAAATTGCTTCACCTTTAAATTCATTATGTGTCGATACTTATATTAAAGTATCGACACGTGCAAT
261 AAAACTACTTCACCTTTAAATTCACAATGTATCGATACTTATATTAAAGTATCGACACGTGCAAT
* **
1114447 ATATCCGGTAATGCTTTATCGGTTTTATCTTTTTGTGAC
326 ATATCCGGTAATGCTTTACCGG-TTTATCTTTTCCTGAC
* * *
1114486 CGATTTTGTCATATTTTTTCCTGTTATATTGATATGGATCGATACATTTTTATAAAGTATCGACA
1 CGATTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACA
1114551 TAAACCGACA
Statistics
Matches: 380, Mismatches: 46, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
362 308 0.81
363 2 0.01
364 70 0.18
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (363 bp):
CGATTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACA
CTTTCAAGGCGCTAAAACAACTTCTCCTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTAT
CGACACTTGCAATATATCCAGTAGCTCTTTACCGATTTTGCCTTTTCCAGACCGGTTTTATCATA
TTTTTACCTATTATATCGTTGTGGATCGATACATATTTATAAAGAATCGACACGTTATAGGCGCT
AAAACTACTTCACCTTTAAATTCACAATGTATCGATACTTATATTAAAGTATCGACACGTGCAAT
ATATCCGGTAATGCTTTACCGGTTTATCTTTTCCTGAC
Found at i:1116926 original size:30 final size:30
Alignment explanation
Indices: 1116890--1116947 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1116880 AGTGAACCGG
*
1116890 TGGTTCAAACCGGTTTTATCGATTTTCAGC
1 TGGTTCAAACCGGTTCTATCGATTTTCAGC
** *
1116920 TGGTTCACCCCGGTTCTATCGGTTTTCA
1 TGGTTCAAACCGGTTCTATCGATTTTCA
1116948 ATCGGTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.40
Consensus pattern (30 bp):
TGGTTCAAACCGGTTCTATCGATTTTCAGC
Found at i:1117534 original size:47 final size:48
Alignment explanation
Indices: 1117475--1117574 Score: 175
Period size: 47 Copynumber: 2.1 Consensus size: 48
1117465 TTACATTTGA
1117475 AATTTAACTTTTAAAAATATTTTTAAAAAATGTAGTTTAAAATTTAAC
1 AATTTAACTTTTAAAAATATTTTTAAAAAATGTAGTTTAAAATTTAAC
* *
1117523 AATTT-ACTTTTAAAAGTGTTTTTAAAAAATGTAGTTTAAAATTTAAC
1 AATTTAACTTTTAAAAATATTTTTAAAAAATGTAGTTTAAAATTTAAC
1117570 AATTT
1 AATTT
1117575 GAAATTGCTG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 45 0.90
48 5 0.10
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (48 bp):
AATTTAACTTTTAAAAATATTTTTAAAAAATGTAGTTTAAAATTTAAC
Found at i:1118032 original size:21 final size:22
Alignment explanation
Indices: 1117989--1118057 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 22
1117979 ATATGAAATA
* *
1117989 CAAAAATATATATATAATTATAAT
1 CAAAAATATAT-T-TTATAATAAT
1118013 -AAAAATATATTTTATAATAACT
1 CAAAAATATATTTTATAATAA-T
* *
1118035 CAATATTAATATTTTATAATAAT
1 CAAAAAT-ATATTTTATAATAAT
1118058 TTTTTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 7 0.18
22 2 0.05
23 15 0.39
24 14 0.37
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
CAAAAATATATTTTATAATAAT
Found at i:1123393 original size:13 final size:12
Alignment explanation
Indices: 1123368--1123398 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
1123358 AGTGAGGCAT
1123368 AATGATAATAAC
1 AATGATAATAAC
1123380 AATGATATATAAC
1 AATGATA-ATAAC
1123393 AATGAT
1 AATGAT
1123399 GCTATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (12 bp):
AATGATAATAAC
Found at i:1123687 original size:23 final size:22
Alignment explanation
Indices: 1123620--1123704 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 22
1123610 CATATAAATT
1123620 TGCACCGAAGTGCCACGTAGAA
1 TGCACCGAAGTGCCACGTAGAA
** * *
1123642 TTTATCCCAAAG-GACCGCGTAGAGA
1 TGCA--CCGAAGTG-CCACGTAGA-A
1123667 TGCACCGAAGTGCCACGTAGAA
1 TGCACCGAAGTGCCACGTAGAA
*
1123689 TTGCACCGTAGTGCCA
1 -TGCACCGAAGTGCCA
1123705 TATAATATGT
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
22 3 0.06
23 28 0.58
24 14 0.29
25 3 0.06
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (22 bp):
TGCACCGAAGTGCCACGTAGAA
Found at i:1128473 original size:21 final size:22
Alignment explanation
Indices: 1128447--1128491 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1128437 AAATGCAAAT
1128447 AGGGAATCG-GTACCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
* *
1128468 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
1128490 AG
1 AG
1128492 TACTGCTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (22 bp):
AGGGAATCGAGTACCCTGCTAC
Found at i:1128822 original size:13 final size:12
Alignment explanation
Indices: 1128797--1128827 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
1128787 AGTGAGGCAT
1128797 AATGATAATAAC
1 AATGATAATAAC
1128809 AATGATATATAAC
1 AATGATA-ATAAC
1128822 AATGAT
1 AATGAT
1128828 GCTATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (12 bp):
AATGATAATAAC
Found at i:1129116 original size:23 final size:22
Alignment explanation
Indices: 1129049--1129133 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 22
1129039 CATATAAATT
1129049 TGCACCGAAGTGCCACGTAGAA
1 TGCACCGAAGTGCCACGTAGAA
** * *
1129071 TTTATCCCAAAG-GACCGCGTAGAGA
1 TGCA--CCGAAGTG-CCACGTAGA-A
1129096 TGCACCGAAGTGCCACGTAGAA
1 TGCACCGAAGTGCCACGTAGAA
*
1129118 TTGCACCGTAGTGCCA
1 -TGCACCGAAGTGCCA
1129134 TATAATATGT
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
22 3 0.06
23 28 0.58
24 14 0.29
25 3 0.06
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (22 bp):
TGCACCGAAGTGCCACGTAGAA
Found at i:1140970 original size:32 final size:34
Alignment explanation
Indices: 1140888--1140975 Score: 80
Period size: 33 Copynumber: 2.6 Consensus size: 34
1140878 ACTGAAGTTA
1140888 AAAAATT-AAATTCA-AGTATTTA-ATTTTAAATTTT
1 AAAAATTAAAATT-ATA-TATTTAGA-TTTAAATTTT
*
1140922 AAAAATTTAAATTATAT-TTTAGATTTAAA-TTT
1 AAAAATTAAAATTATATATTTAGATTTAAATTTT
*
1140954 AAATA-TAAAATATATATATTTA
1 AAAAATTAAAAT-TATATATTTA
1140976 ATATAACAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
31 5 0.11
32 12 0.26
33 14 0.30
34 10 0.21
35 6 0.13
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (34 bp):
AAAAATTAAAATTATATATTTAGATTTAAATTTT
Found at i:1142979 original size:12 final size:12
Alignment explanation
Indices: 1142964--1142996 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1142954 ATCGAATGAT
1142964 TTAAAATTTAAC
1 TTAAAATTTAAC
1142976 TTAAAATTTAAC
1 TTAAAATTTAAC
1142988 TTAAAATTT
1 TTAAAATTT
1142997 TAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (12 bp):
TTAAAATTTAAC
Found at i:1143017 original size:24 final size:25
Alignment explanation
Indices: 1142980--1143029 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1142970 TTTAACTTAA
* * *
1142980 AATTTAACTTAAAATTTTAAATATT
1 AATTTAACTAAAAAATATAAATATT
1143005 AATTTAA-TAAAAAATATAAATATT
1 AATTTAACTAAAAAATATAAATATT
1143029 A
1 A
1143030 CAAAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
AATTTAACTAAAAAATATAAATATT
Found at i:1144376 original size:13 final size:13
Alignment explanation
Indices: 1144358--1144384 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1144348 ATTTTGCCAC
1144358 TTCCTTCATTTTA
1 TTCCTTCATTTTA
1144371 TTCCTTCATTTTA
1 TTCCTTCATTTTA
1144384 T
1 T
1144385 GTAACTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (13 bp):
TTCCTTCATTTTA
Found at i:1144543 original size:15 final size:15
Alignment explanation
Indices: 1144523--1144561 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1144513 AAATGTCCAT
*
1144523 TTCAAAATTGTTTCA
1 TTCAAAATTATTTCA
1144538 TTCAAAA-TATTTCA
1 TTCAAAATTATTTCA
1144552 TTACAAAATT
1 TT-CAAAATT
1144562 CAATAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 8 0.38
15 12 0.57
16 1 0.05
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.44
Consensus pattern (15 bp):
TTCAAAATTATTTCA
Found at i:1146453 original size:14 final size:15
Alignment explanation
Indices: 1146427--1146460 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
1146417 ATCTTATTAG
1146427 TATTTTTTAAAATAA
1 TATTTTTTAAAATAA
1146442 TATTTTTT-AAATAA
1 TATTTTTTAAAATAA
1146456 TATTT
1 TATTT
1146461 AAAAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTTTTAAAATAA
Found at i:1174224 original size:17 final size:17
Alignment explanation
Indices: 1174198--1174231 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1174188 TCTTTCACTA
* *
1174198 CTTTACCATGATTTATT
1 CTTTAACATGAATTATT
1174215 CTTTAACATGAATTATT
1 CTTTAACATGAATTATT
1174232 ATATATCTAT
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:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (17 bp):
CTTTAACATGAATTATT
Found at i:1182752 original size:19 final size:19
Alignment explanation
Indices: 1182725--1182769 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
1182715 AGCATTGAGC
*
1182725 AGAAGAAA-GAAATGGAGA
1 AGAAGAAAGGAAATGAAGA
1182743 AGAGAGAAAGGAAATGAAGA
1 AGA-AGAAAGGAAATGAAGA
1182763 AGAAGAA
1 AGAAGAA
1182770 GAAGAACATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 3 0.12
19 9 0.38
20 12 0.50
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.04
Consensus pattern (19 bp):
AGAAGAAAGGAAATGAAGA
Found at i:1184000 original size:23 final size:23
Alignment explanation
Indices: 1183960--1184003 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1183950 ATTAATTATT
*
1183960 ATTTAAATTAACTATATTATTTG
1 ATTTAAATCAACTATATTATTTG
* *
1183983 ATTTAAATCAATTTTATTATT
1 ATTTAAATCAACTATATTATT
1184004 ATTTTAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTAAATCAACTATATTATTTG
Found at i:1185107 original size:21 final size:22
Alignment explanation
Indices: 1185066--1185110 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1185056 TAATCATTAC
*
1185066 TAAATCATTAATATCATATCAT
1 TAAATCATTAATATCAAATCAT
1185088 TAAAT-ATTAATAAT-AAATCAT
1 TAAATCATTAAT-ATCAAATCAT
1185109 TA
1 TA
1185111 TTAATAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:1185165 original size:15 final size:15
Alignment explanation
Indices: 1185126--1185173 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1185116 AATCATTACT
* *
1185126 AAATCATATAATTATT
1 AAATCAT-TAAATATC
*
1185142 AAATTATTAAATATC
1 AAATCATTAAATATC
1185157 AAATCATTAAATATC
1 AAATCATTAAATATC
1185172 AA
1 AA
1185174 TAATAAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 22 0.79
16 6 0.21
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:1185167 original size:76 final size:74
Alignment explanation
Indices: 1185061--1185212 Score: 207
Period size: 76 Copynumber: 2.0 Consensus size: 74
1185051 ATTACTAATC
* * *
1185061 ATTACTAAATCATTAATATCATATCATTAAATATTAATAATAAATCATTATTAAT-AATCATTAC
1 ATTACTAAATCATTAATATCAAATCATTAAATATCAATAATAAATCATTAGTAATAAATCA-TAC
*
1185125 TAAATCATATA
65 CAAATCAT-TA
* * *
1185136 ATTATTAAATTATTAAATATCAAATCATTAAATATCAATAATAAATCATTAGTAGTAAATCATAC
1 ATTACTAAATCATT-AATATCAAATCATTAAATATCAATAATAAATCATTAGTAATAAATCATAC
1185201 CAAATCATTA
65 CAAATCATTA
1185211 AT
1 AT
1185213 ATAAAACCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
75 16 0.24
76 47 0.69
77 5 0.07
ACGTcount: A:0.50, C:0.11, G:0.01, T:0.38
Consensus pattern (74 bp):
ATTACTAAATCATTAATATCAAATCATTAAATATCAATAATAAATCATTAGTAATAAATCATACC
AAATCATTA
Found at i:1185176 original size:59 final size:58
Alignment explanation
Indices: 1185056--1185177 Score: 131
Period size: 59 Copynumber: 2.1 Consensus size: 58
1185046 TTATTATTAC
* * *
1185056 TAATCATTACTAAATCATTAATATCATATCATTAAATATTAATAATAAATCATTATTAA
1 TAATCATTACTAAATCATTAATATCAAATCATTAAATATAAATAATAAA-CATTATCAA
* * * *
1185115 TAATCATTACTAAATCATATAATTATTAAATTATTAAATATCAAATCATTAA-A-TATCAA
1 TAATCATTACTAAATCAT-TAA-TATCAAATCATTAAATAT-AAATAATAAACATTATCAA
1185174 TAAT
1 TAAT
1185178 AAATCATTAG
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
59 27 0.51
60 4 0.08
61 15 0.28
62 7 0.13
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (58 bp):
TAATCATTACTAAATCATTAATATCAAATCATTAAATATAAATAATAAACATTATCAA
Found at i:1185207 original size:24 final size:21
Alignment explanation
Indices: 1185156--1185239 Score: 75
Period size: 19 Copynumber: 4.0 Consensus size: 21
1185146 TATTAAATAT
* *
1185156 CAAATCATTAAATATCAATAA-
1 CAAATCATT-AGTATAAATAAC
*
1185177 TAAATCATTAGTAGTAAATCATAC
1 CAAATCATTAGTA-TAAAT-A-AC
*
1185201 CAAATCATTAATAT-AA-AAC
1 CAAATCATTAGTATAAATAAC
1185220 CAAATCATTAGTATAAATAA
1 CAAATCATTAGTATAAATAA
1185240 TAATAAGATT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
19 15 0.29
20 6 0.12
21 14 0.27
22 3 0.06
23 2 0.04
24 11 0.22
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.30
Consensus pattern (21 bp):
CAAATCATTAGTATAAATAAC
Found at i:1188417 original size:28 final size:30
Alignment explanation
Indices: 1188377--1188437 Score: 99
Period size: 28 Copynumber: 2.1 Consensus size: 30
1188367 ATTTTTCATA
1188377 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
*
1188407 TAATAT-A-ATATAATTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1188435 TAA
1 TAA
1188438 CAAACTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 23 0.77
29 1 0.03
30 6 0.20
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1188474 original size:14 final size:14
Alignment explanation
Indices: 1188455--1188516 Score: 90
Period size: 14 Copynumber: 4.4 Consensus size: 14
1188445 TTACCTGATC
1188455 TCTTCTTCTCCCTT
1 TCTTCTTCTCCCTT
*
1188469 TCTTCTTCTTCCTT
1 TCTTCTTCTCCCTT
1188483 TCATTCTTCTCCCTT
1 TC-TTCTTCTCCCTT
*
1188498 TCTTCTTCTTCC-T
1 TCTTCTTCTCCCTT
1188511 TCTTCT
1 TCTTCT
1188517 CCCTTTCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
13 7 0.16
14 24 0.55
15 13 0.30
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.60
Consensus pattern (14 bp):
TCTTCTTCTCCCTT
Found at i:1189871 original size:16 final size:18
Alignment explanation
Indices: 1189836--1189877 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
1189826 ATAATAAAAA
*
1189836 TATATTAAATATTTAATT
1 TATATTAAATATTAAATT
1189854 TATA-TAAAT-TTAAATT
1 TATATTAAATATTAAATT
*
1189870 TAAATTAA
1 TATATTAA
1189878 TAAAAATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 9 0.43
17 8 0.38
18 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATATTAAATATTAAATT
Found at i:1189884 original size:22 final size:22
Alignment explanation
Indices: 1189819--1189889 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
1189809 CGAGTAAATT
*
1189819 ATTTAAAATAATAAAAATATATTAA
1 ATTTAAATTAAT-AAAA-AT-TTAA
* * *
1189844 ATATTTAATTTATATAAATTTAA
1 AT-TTAAATTAATAAAAATTTAA
*
1189867 ATTTAAATTAATAAAAATCTAA
1 ATTTAAATTAATAAAAATTTAA
1189889 A
1 A
1189890 ATGATATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
22 17 0.46
23 6 0.16
24 2 0.05
25 5 0.14
26 7 0.19
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTTAAATTAATAAAAATTTAA
Found at i:1190276 original size:25 final size:25
Alignment explanation
Indices: 1190248--1190295 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
1190238 AGAGGTGATC
1190248 AAATT-ATTTAAATTTTATAAATTTA
1 AAATTAATTT-AATTTTATAAATTTA
1190273 AAATTAATTTAATTTTATAAATT
1 AAATTAATTTAATTTTATAAATT
1190296 AATTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AAATTAATTTAATTTTATAAATTTA
Done.