Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009075.1 Hibiscus syriacus cultivar Beakdansim tig00112508_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: 1223780
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:967780 original size:26 final size:25
Alignment explanation
Indices: 967743--967859 Score: 76
Period size: 26 Copynumber: 5.0 Consensus size: 25
967733 ATGCCCTAAC
*
967743 GCATCCTTTCATGCATTTTAGTTAT
1 GCATCTTTTCATGCATTTTAGTTAT
*
967768 GACATCTTTTCATGC--CTTA---AT
1 G-CATCTTTTCATGCATTTTAGTTAT
967789 GCATCCTTTT-ATGCATTTTAGTTAT
1 GCAT-CTTTTCATGCATTTTAGTTAT
* * *
967814 GAAATCCTTTCATGC--CTTA---AT
1 G-CATCTTTTCATGCATTTTAGTTAT
*
967835 GCATCTTTTCATGTATTTTAGTTAT
1 GCATCTTTTCATGCATTTTAGTTAT
967860 AGATTCAGTT
Statistics
Matches: 68, Mismatches: 10, Indels: 28
0.64 0.09 0.26
Matches are distributed among these distances:
20 17 0.25
21 11 0.16
22 6 0.09
24 6 0.09
25 10 0.15
26 18 0.26
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (25 bp):
GCATCTTTTCATGCATTTTAGTTAT
Found at i:967846 original size:20 final size:20
Alignment explanation
Indices: 967770--967847 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 20
967760 TTAGTTATGA
967770 CATCTTTTCATGCCTTAATG
1 CATCTTTTCATGCCTTAATG
*
967790 CATCCTTTT-ATGCATTTTAGTTATG
1 CAT-CTTTTCATGC--CTTA---ATG
* *
967815 AAATCCTTTCATGCCTTAATG
1 -CATCTTTTCATGCCTTAATG
967836 CATCTTTTCATG
1 CATCTTTTCATG
967848 TATTTTAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
20 17 0.39
21 8 0.18
22 3 0.07
24 3 0.07
25 7 0.16
26 6 0.14
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (20 bp):
CATCTTTTCATGCCTTAATG
Found at i:971311 original size:16 final size:17
Alignment explanation
Indices: 971278--971311 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
971268 CATTCTATTT
*
971278 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
971295 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
971311 T
1 T
971312 AATAAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:971317 original size:23 final size:23
Alignment explanation
Indices: 971273--971317 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
971263 GATCACATTC
* * **
971273 TATTTTTATTTTATATTTTAAAT
1 TATTTTTATATTAAATAATAAAT
971296 TATTTTTATATTAAATAATAAA
1 TATTTTTATATTAAATAATAAA
971318 AATGTCACAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTTTTATATTAAATAATAAAT
Found at i:979093 original size:18 final size:17
Alignment explanation
Indices: 979062--979098 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
979052 TATGAATTTA
*
979062 TCTTCTATGTCACCTCT
1 TCTTCTATGCCACCTCT
979079 TCTTCCTATGCCACCTCT
1 TCTT-CTATGCCACCTCT
979097 TC
1 TC
979099 AACCTGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.41, G:0.05, T:0.43
Consensus pattern (17 bp):
TCTTCTATGCCACCTCT
Found at i:983949 original size:30 final size:31
Alignment explanation
Indices: 983893--983967 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 31
983883 TCGAAAAACA
* *
983893 TAAGATATGATCACTTTTATTTTTATTTAAT
1 TAAGATATGGTCACTTTCATTTTTATTTAAT
983924 TAAGATATGGTCACTTTCA-TTTTATTTAAT
1 TAAGATATGGTCACTTTCATTTTTATTTAAT
*
983954 TAAGATGTGGTCAC
1 TAAGATATGGTCAC
983968 CCGAAGTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 24 0.59
31 17 0.41
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCATTTTTATTTAAT
Found at i:984448 original size:39 final size:39
Alignment explanation
Indices: 984344--984449 Score: 96
Period size: 39 Copynumber: 2.7 Consensus size: 39
984334 CATAATCCTC
* *
984344 AAATTATTTCAC-TCTAACATTCTAAAATCCTAATTTCTT
1 AAATTATTTCACAT-TAACTTTCTAAATTCCTAATTTCTT
* *
984383 AAATT-TTGACACCA-TAA-TGTTTTAAATTCAC-AATTTCTT
1 AAATTATT-TCA-CATTAACT-TTCTAAATTC-CTAATTTCTT
984422 AAATTATTTCACATTAACTTTCTAAATT
1 AAATTATTTCACATTAACTTTCTAAATT
984450 ATTTTTAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
38 4 0.08
39 44 0.83
40 5 0.09
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (39 bp):
AAATTATTTCACATTAACTTTCTAAATTCCTAATTTCTT
Found at i:984737 original size:21 final size:22
Alignment explanation
Indices: 984713--984771 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
984703 TAATTATATA
984713 TATATTAACTTAAAATAT-TTT
1 TATATTAACTTAAAATATATTT
984734 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA--AAATATATTT
*
984758 TACGATTAACTTAA
1 TA-TATTAACTTAA
984772 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 12 0.36
23 7 0.21
24 5 0.15
25 9 0.27
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (22 bp):
TATATTAACTTAAAATATATTT
Found at i:984737 original size:23 final size:24
Alignment explanation
Indices: 984697--984759 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 24
984687 CGAATTATAA
984697 ATAATATAATTATATATATATTAACTT
1 ATAA-ATAATT-T-TATATATTAACTT
984724 A-AAAT-ATTTT-TATATTAACTT
1 ATAAATAATTTTATATATTAACTT
984745 ATTAAATATATTTTA
1 A-TAAATA-ATTTTA
984760 CGATTAACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
21 12 0.39
22 1 0.03
23 5 0.16
24 3 0.10
25 7 0.23
26 2 0.06
27 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (24 bp):
ATAAATAATTTTATATATTAACTT
Found at i:984755 original size:25 final size:27
Alignment explanation
Indices: 984717--984785 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 27
984707 TATATATATA
* *
984717 TTAACTTAAAATATTTTTA-TATTAAC
1 TTAATTTAAAATATTTTTACGATTAAC
984743 TT-A-TT-AAATATATTTTACGATTAAC
1 TTAATTTAAAATAT-TTTTACGATTAAC
984768 TTAATTTAAAAATATTTT
1 TTAATTT-AAAATATTTT
984786 ATTTTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
23 6 0.17
24 7 0.19
25 9 0.25
26 3 0.08
27 2 0.06
28 3 0.08
29 6 0.17
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (27 bp):
TTAATTTAAAATATTTTTACGATTAAC
Found at i:984826 original size:25 final size:27
Alignment explanation
Indices: 984768--984827 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
984758 TACGATTAAC
* *
984768 TTAATTTAAAAATATTTTATTTTTATT
1 TTAATTTAAAAATATTGTATATTTATT
*
984795 TTCATTTAAAAATA-TGTA-ATTTATT
1 TTAATTTAAAAATATTGTATATTTATT
984820 TTAATTTA
1 TTAATTTA
984828 TTAAAAGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 13 0.45
26 3 0.10
27 13 0.45
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TTAATTTAAAAATATTGTATATTTATT
Found at i:985298 original size:94 final size:94
Alignment explanation
Indices: 985133--985306 Score: 213
Period size: 94 Copynumber: 1.9 Consensus size: 94
985123 ATATAAATTA
* * * * *
985133 TTATTGTTTTTTGAATCTGAAAATTGTTTTAAAAGCATGTGACATCTCTAACTCATGTTTGGGAA
1 TTATTATTTTTCGAATCCGAAAACTGTTTTAAAAGCAAGTGACATCTCTAACTCATGTTTGGGAA
* *
985198 TATATACGGGAAAGACATGTTACATTTTT
66 CATATACGAGAAAGACATGTTACATTTTT
* * * * ** *
985227 TTATTATTTTTCGCATCCGAAAACTGTTTTAAAATCAAGTGACATCTCTGATTTGTGTTTTGGAA
1 TTATTATTTTTCGAATCCGAAAACTGTTTTAAAAGCAAGTGACATCTCTAACTCATGTTTGGGAA
*
985292 CGTATACGAGAAAGA
66 CATATACGAGAAAGA
985307 GGTTTTACAG
Statistics
Matches: 65, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
94 65 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (94 bp):
TTATTATTTTTCGAATCCGAAAACTGTTTTAAAAGCAAGTGACATCTCTAACTCATGTTTGGGAA
CATATACGAGAAAGACATGTTACATTTTT
Found at i:987862 original size:29 final size:28
Alignment explanation
Indices: 987820--987904 Score: 143
Period size: 29 Copynumber: 3.0 Consensus size: 28
987810 CAGTGACATC
987820 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCC-T
987849 ATAGGTCGCCATGCACGCCCGGCGTCCT
1 ATAGGTCGCCATGCACGCCCGGCGTCCT
*
987877 ATAAGGTCGACATGCACGCCCGGCGTCC
1 AT-AGGTCGCCATGCACGCCCGGCGTCC
987905 AACATTCTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
28 3 0.06
29 51 0.94
ACGTcount: A:0.16, C:0.38, G:0.28, T:0.18
Consensus pattern (28 bp):
ATAGGTCGCCATGCACGCCCGGCGTCCT
Found at i:988185 original size:37 final size:37
Alignment explanation
Indices: 988144--988216 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
988134 GGCCGGCGAC
988144 ATGGTAGGTCGCCATGGAGTCCCAGCGACATGGTAGA
1 ATGGTAGGTCGCCATGGAGTCCCAGCGACATGGTAGA
*
988181 ATGGTAGGTCGCCATGGAGTCCCGGCGACATGGTAG
1 ATGGTAGGTCGCCATGGAGTCCCAGCGACATGGTAG
988217 GTCGACATGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.37, T:0.19
Consensus pattern (37 bp):
ATGGTAGGTCGCCATGGAGTCCCAGCGACATGGTAGA
Found at i:988224 original size:13 final size:13
Alignment explanation
Indices: 988206--988232 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
988196 GGAGTCCCGG
988206 CGACATGGTAGGT
1 CGACATGGTAGGT
988219 CGACATGGTAGGT
1 CGACATGGTAGGT
988232 C
1 C
988233 TGCATCATCA
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:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (13 bp):
CGACATGGTAGGT
Found at i:988768 original size:21 final size:21
Alignment explanation
Indices: 988743--988786 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
988733 AATCTAGTTA
988743 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
988764 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
988785 AT
1 AT
988787 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:989310 original size:18 final size:18
Alignment explanation
Indices: 989287--989347 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
989277 AGATAATTTT
989287 TGTTTAAAAAAATTATTG
1 TGTTTAAAAAAATTATTG
* *
989305 TGTTTAAAAATATTTAGTG
1 TGTTTAAAAA-AATTATTG
*
989324 TTGTTTTAAAAAAA-TATTT
1 -TG-TTTAAAAAAATTATTG
989343 TGTTT
1 TGTTT
989348 TATTTATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 3 0.09
18 12 0.34
19 9 0.26
20 3 0.09
21 8 0.23
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (18 bp):
TGTTTAAAAAAATTATTG
Found at i:989609 original size:26 final size:25
Alignment explanation
Indices: 989580--989644 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
989570 AAATCATATT
*
989580 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AATAAATATCAAATC
* *
989606 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATCAAATC
989632 ATTATT-AATAATA
1 ATTATTAAATAATA
989645 TTAGTAATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.29
26 18 0.53
27 3 0.09
28 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAATAAATATCAAATC
Found at i:992562 original size:60 final size:60
Alignment explanation
Indices: 992491--993396 Score: 1025
Period size: 60 Copynumber: 15.7 Consensus size: 60
992481 GTATTTATAA
* *
992491 GATTTAGTAATGATTAGTAATGATGAAATTTTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
992551 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
992611 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
992671 GA-TTAGT-A--A-T-G-----ATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
992720 GA-TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * * * * *
992779 GA-TTAGTAAT-AAT-GAAATTAT--TATTAATGT-TTAATGATTTGATAATAATGAT--T--T
1 GATTTAGTAATGATTAGTAATAATGAAATT-AT-TATTAAT-ATTTAATGAT-TTGATAGTAAT
* * * * *
992833 -A-GTAATGAT---TAGTAATAATGAAATTATTATTATTTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
992888 GATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * *
992948 GATTTAGTAATGATTAGTAATAATAAAATTGTTTTTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
993008 GATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * * * * * * *
993068 GATTTAGTAAT-AAT-GAAATTAT--TATTAATATTTAATGATTTGAT-A-GTAAT-G-ATT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTA-TTAAT-ATTTAATGATTTGATAGTAAT
* * * * *
993122 TA-GTAATGAT---TAGTAATAAT-AAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * *
993177 GATTTAATAATGATTACGTAATAATGAAATTGTTATTAATATTTAATGACTTGATAGTAAT
1 GATTTAGTAATGATTA-GTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
993238 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
993298 GATTTAGTAATGATTAGTAATAAT-AAATTATTATTAAT-TTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * *
993356 GATTTAGTAATGATTTGATAGTAATG-ATTTATTATAAATAT
1 GATTTAGTAATGATTAG-TAATAATGAAATTATTATTAATAT
993397 GTCGAATTTG
Statistics
Matches: 733, Mismatches: 69, Indels: 88
0.82 0.08 0.10
Matches are distributed among these distances:
49 45 0.06
50 1 0.00
51 11 0.02
52 27 0.04
53 28 0.04
54 10 0.01
55 9 0.01
56 25 0.03
57 26 0.04
58 55 0.08
59 87 0.12
60 362 0.49
61 47 0.06
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
Found at i:992568 original size:21 final size:20
Alignment explanation
Indices: 992544--992632 Score: 58
Period size: 21 Copynumber: 4.4 Consensus size: 20
992534 AATGATTTGA
992544 TAGTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
* * *
992565 TAGTAATA-AT-GAAATTAT
1 TAGTAATATTTAGTAATGAT
* * *
992583 TATTAATATTTAATGATTTGA-
1 TAGTAATATTTAGT-A-ATGAT
*
992604 TATTAATGATTTAGTAATGAT
1 TAGTAAT-ATTTAGTAATGAT
992625 TAGTAATA
1 TAGTAATA
992633 ATGAAATTAT
Statistics
Matches: 50, Mismatches: 12, Indels: 13
0.67 0.16 0.17
Matches are distributed among these distances:
18 13 0.26
19 2 0.04
20 5 0.10
21 22 0.44
22 8 0.16
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (20 bp):
TAGTAATATTTAGTAATGAT
Found at i:992668 original size:39 final size:41
Alignment explanation
Indices: 992625--992719 Score: 104
Period size: 49 Copynumber: 2.2 Consensus size: 41
992615 TAGTAATGAT
992625 TAGTAAT-A-ATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATAAGATGAAATTATTATTAATTTTTAATGATTTGA
992664 TAGTAATGATTAGTAATGATGAAATTATTATTAATTTTTAATGATTTGA
1 TAG---T-A--A-TAA-GATGAAATTATTATTAATTTTTAATGATTTGA
992713 TAGTAAT
1 TAGTAAT
992720 GATTAGTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
39 3 0.07
42 2 0.04
43 2 0.04
45 2 0.04
46 2 0.04
47 1 0.02
49 34 0.74
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (41 bp):
TAGTAATAAGATGAAATTATTATTAATTTTTAATGATTTGA
Found at i:992680 original size:24 final size:24
Alignment explanation
Indices: 992653--992733 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
992643 TATTAATTTT
992653 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
*** * * * **
992677 TAATGATGAAATTATTATTAATTTT
1 TAATGATTTGA-TAGTAATGATTAG
992702 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
992726 TAATGATT
1 TAATGATT
992734 AGTAATAATG
Statistics
Matches: 40, Mismatches: 16, Indels: 2
0.69 0.28 0.03
Matches are distributed among these distances:
24 24 0.60
25 16 0.40
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (24 bp):
TAATGATTTGATAGTAATGATTAG
Found at i:992726 original size:10 final size:10
Alignment explanation
Indices: 992713--992739 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
992703 AATGATTTGA
992713 TAGTAATGAT
1 TAGTAATGAT
992723 TAGTAATGAT
1 TAGTAATGAT
992733 TAGTAAT
1 TAGTAAT
992740 AATGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:992816 original size:35 final size:35
Alignment explanation
Indices: 992775--992937 Score: 105
Period size: 35 Copynumber: 5.2 Consensus size: 35
992765 GATTTGATAG
992775 TAATGATTAGTAATAATGAAATTATTATTAATGTT
1 TAATGATTAGTAATAATGAAATTATTATTAATGTT
* *
992810 TAATGATT--TGATAAT--AATGA-T-TT-A-G--
1 TAATGATTAGTAATAATGAAATTATTATTAATGTT
* *
992835 TAATGATTAGTAATAATGAAATTATTATTATTTTT
1 TAATGATTAGTAATAATGAAATTATTATTAATGTT
* * *
992870 TAATGATT--TGAT-A-GTAATGA-T-TTAA----
1 TAATGATTAGTAATAATGAAATTATTATTAATGTT
* *
992895 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAATGTT
992930 TAATGATT
1 TAATGATT
992938 TGATAGTAAT
Statistics
Matches: 94, Mismatches: 14, Indels: 40
0.64 0.09 0.27
Matches are distributed among these distances:
25 16 0.17
27 10 0.11
28 2 0.02
29 13 0.14
30 4 0.04
31 15 0.16
32 1 0.01
33 9 0.10
35 24 0.26
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (35 bp):
TAATGATTAGTAATAATGAAATTATTATTAATGTT
Found at i:992900 original size:11 final size:11
Alignment explanation
Indices: 992821--992913 Score: 53
Period size: 11 Copynumber: 7.8 Consensus size: 11
992811 AATGATTTGA
992821 TAATAATGATT
1 TAATAATGATT
*
992832 TAGTAATGATT
1 TAATAATGATT
*
992843 AGTAATAATGAAAT
1 --TAATAATG-ATT
* *
992857 T-ATTATTATT
1 TAATAATGATT
**
992867 TTTTAATGATT
1 TAATAATGATT
992878 TGATAGTAATGATT
1 T-A-A-TAATGATT
992892 TAATAATGATT
1 TAATAATGATT
992903 AGTAATAATGA
1 --TAATAATGA
992914 AATTGTTATT
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
10 3 0.05
11 29 0.47
12 2 0.03
13 17 0.27
14 11 0.18
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (11 bp):
TAATAATGATT
Found at i:993316 original size:10 final size:11
Alignment explanation
Indices: 993291--993386 Score: 54
Period size: 14 Copynumber: 8.2 Consensus size: 11
993281 AATGATTTGA
993291 TAGTAATGATT
1 TAGTAATGATT
993302 TAGTAATGA-T
1 TAGTAATGATT
*
993312 TAGTAATAATAAAT
1 TAGTAATGAT---T
* * *
993326 TATTATTAATT
1 TAGTAATGATT
993337 T--TAATGATTT
1 TAGTAATGA-TT
993347 GATAGTAATGATT
1 --TAGTAATGATT
993360 TAGTAATGATTT
1 TAGTAATGA-TT
993372 GATAGTAATGATT
1 --TAGTAATGATT
993385 TA
1 TA
993387 TTATAAATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 24
0.70 0.05 0.25
Matches are distributed among these distances:
9 4 0.06
10 11 0.16
11 22 0.32
12 3 0.04
13 4 0.06
14 24 0.35
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:993357 original size:14 final size:14
Alignment explanation
Indices: 993338--993385 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
993328 TTATTAATTT
993338 TAATGATTTGATAG
1 TAATGATTTGATAG
993352 TAATGA-TT--TAG
1 TAATGATTTGATAG
993363 TAATGATTTGATAG
1 TAATGATTTGATAG
993377 TAATGATTT
1 TAATGATTT
993386 ATTATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 2 0.06
14 18 0.58
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:993366 original size:25 final size:25
Alignment explanation
Indices: 993338--993386 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
993328 TTATTAATTT
993338 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
993363 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
993387 TTATAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:995251 original size:15 final size:16
Alignment explanation
Indices: 995231--995264 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
995221 CAAAATAATT
995231 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
995246 TAATATAATAAACTTA
1 TAATATAATAAACTTA
995262 TAA
1 TAA
995265 AGTAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:995351 original size:30 final size:30
Alignment explanation
Indices: 995317--995422 Score: 142
Period size: 30 Copynumber: 3.5 Consensus size: 30
995307 TTTCTTTAAA
995317 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
995347 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* * *
995377 AAACTAATAAAATATTTTTTAATTATAA-TT
1 CAACTAATAAACTATTCTTTAA-TATAACTT
*
995407 CACTACTAAAAAACTA
1 CA--ACTAATAAACTA
995423 ATTAACTAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
30 52 0.78
31 5 0.07
32 10 0.15
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:995369 original size:15 final size:16
Alignment explanation
Indices: 995321--995375 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
995311 TTTAAACAAC
995321 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
**
995336 TAATATAAC--TTCAAC
1 TAATATAACTATTC-TT
995351 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
995366 TAATATAACT
1 TAATATAACT
995376 TAAACTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 6 0.19
15 15 0.48
16 10 0.32
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAACTATTCTT
Found at i:995582 original size:17 final size:17
Alignment explanation
Indices: 995560--995595 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
995550 TAAATTTTTT
995560 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
995577 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
995594 AC
1 AC
995596 AAGCTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (17 bp):
ACCCTAACCCTAAACTA
Found at i:995823 original size:27 final size:27
Alignment explanation
Indices: 995785--995837 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
995775 AGGGTCGGCT
995785 GCCATGCACCAATAATTGAAGAATCAC
1 GCCATGCACCAATAATTGAAGAATCAC
995812 GCCATGCACCAATAATTGAAGAATCA
1 GCCATGCACCAATAATTGAAGAATCA
995838 TGAGCCGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (27 bp):
GCCATGCACCAATAATTGAAGAATCAC
Found at i:995914 original size:25 final size:23
Alignment explanation
Indices: 995860--995914 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 23
995850 TCTCGTGGAT
*
995860 TGCAGCAATAATTGCTGCATGAA
1 TGCAGCAAAAATTGCTGCATGAA
995883 -GCAGCAAAAATTATGCTGCAAT-AA
1 TGCAGCAAAAA-T-TGCTGC-ATGAA
995907 TGCAGCAA
1 TGCAGCAA
995915 GCAGCGGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 9 0.33
23 1 0.04
24 8 0.30
25 9 0.33
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (23 bp):
TGCAGCAAAAATTGCTGCATGAA
Found at i:996122 original size:12 final size:12
Alignment explanation
Indices: 996105--996133 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
996095 ACACGACCCT
996105 CGTCGGAAGCCA
1 CGTCGGAAGCCA
996117 CGTCGGAAGCCA
1 CGTCGGAAGCCA
996129 CGTCG
1 CGTCG
996134 TAGGTCGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.34, G:0.34, T:0.10
Consensus pattern (12 bp):
CGTCGGAAGCCA
Found at i:999164 original size:20 final size:21
Alignment explanation
Indices: 999110--999174 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
999100 AGGGCAGTCA
*
999110 CCCCTTAGAATTTTAGTTCG-T
1 CCCCTTA-AATTTTAGTTCGCC
* *
999131 ACCCTGAAATTTTAGTTCGCC
1 CCCCTTAAATTTTAGTTCGCC
* *
999152 CCCCTTAAATTTAAGTTCACC
1 CCCCTTAAATTTTAGTTCGCC
999173 CC
1 CC
999175 ATAATATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 12 0.33
21 24 0.67
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.35
Consensus pattern (21 bp):
CCCCTTAAATTTTAGTTCGCC
Found at i:999807 original size:24 final size:24
Alignment explanation
Indices: 999775--999837 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
999765 TTTAGCTTAC
999775 AAACGAACATGTTCGCGAACATAT
1 AAACGAACATGTTCGCGAACATAT
* *
999799 AAACGAACAAGTTCACGAACATAT
1 AAACGAACATGTTCGCGAACATAT
* *
999823 AAATGAATATGTTCG
1 AAACGAACATGTTCG
999838 TGAATACTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.22
Consensus pattern (24 bp):
AAACGAACATGTTCGCGAACATAT
Found at i:1006438 original size:2 final size:2
Alignment explanation
Indices: 1006431--1006470 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1006421 AAACGATAAG
1006431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1006471 CATTAGCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1006586 original size:2 final size:2
Alignment explanation
Indices: 1006574--1006607 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1006564 ATAAAGTAAA
*
1006574 AT AT GT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1006608 AGTAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1006615 original size:49 final size:47
Alignment explanation
Indices: 1006523--1006621 Score: 112
Period size: 48 Copynumber: 2.1 Consensus size: 47
1006513 AAATATTAAG
1006523 AAAATGATGTATATATAACATATAAAAAAAAGTATTAAGAAATAAAGT
1 AAAATGATGTATATATAACATATAAAAAAAAGTATTAAGAAATAAA-T
* * * *
1006571 AAAAT-ATGTATATATATATATATATATAATA-TATATAAGTAAATAAAT
1 AAAATGATGTATATATA-ACATATAAAAAAAAGTAT-TAAG-AAATAAAT
1006619 AAA
1 AAA
1006622 TAATGAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
47 14 0.32
48 23 0.52
49 7 0.16
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (47 bp):
AAAATGATGTATATATAACATATAAAAAAAAGTATTAAGAAATAAAT
Found at i:1006620 original size:21 final size:21
Alignment explanation
Indices: 1006579--1006620 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1006569 GTAAAATATG
* *
1006579 TATATATATATATATATATAA
1 TATATATATATAAATAAATAA
1006600 TATATATA-AGTAAATAAATAA
1 TATATATATA-TAAATAAATAA
1006621 ATAATGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TATATATATATAAATAAATAA
Found at i:1008461 original size:107 final size:103
Alignment explanation
Indices: 1008129--1008882 Score: 1093
Period size: 98 Copynumber: 7.4 Consensus size: 103
1008119 GTATTGTTCC
* * *
1008129 GAGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA-TGAG-AATTGTTTATTGACAA
1008194 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
63 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1008235 GAGTCCAATATCCTTCGTTTTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGAC-A
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AA-TGAGAA-TTGTTTATTGACAA
1008299 CCAGCGGTCCCTTCGTCG-GAAGTTGAACTTGCGTTGTCTG
63 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1008339 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTGAAATTGAGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TG-AA-TGAGAA-TTGTTTATTGACA
* *
1008404 ACCAGCGGTCCCTTTGTCGTGAATTTGAACTTGCGTTGTCTG
62 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1008446 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAAATTGAGAAGTTTGTTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AA-TGAGAA--TTGTTTATTGACA
*
1008511 ACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
62 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1008553 GAGTCCAATATCCTTCGTTTTGAAGTTGAAATTGGCTC----TGA-AATTGTTTATTGACAACCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAGAATTGTTTATTGACAACCA
*
1008613 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1008651 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC----TGA-AATTGTTTATGGACAACCA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAGAATTGTTTATTGACAACCA
*
1008711 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1008749 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC----T-A-AATTGTTTATCGACCAA-C
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAGAATTGTTTATTGA-CAACC
*
1008807 --CGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1008844 GAGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1008883 GGTAAACTGA
Statistics
Matches: 619, Mismatches: 20, Indels: 28
0.93 0.03 0.04
Matches are distributed among these distances:
94 31 0.05
95 43 0.07
97 14 0.02
98 191 0.31
100 2 0.00
101 3 0.00
104 59 0.10
105 47 0.08
106 83 0.13
107 146 0.24
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (103 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAGAATTGTTTATTGACAACCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1009652 original size:9 final size:9
Alignment explanation
Indices: 1009629--1009675 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
1009619 CACCTTATTT
1009629 TCTTTTCT-
1 TCTTTTCTC
1009637 T-TTTTCTC
1 TCTTTTCTC
1009645 TCTTTTCTC
1 TCTTTTCTC
1009654 -CTTTT-TC
1 TCTTTTCTC
*
1009661 TCTTTTTTC
1 TCTTTTCTC
1009670 TCTTTT
1 TCTTTT
1009676 TTCCAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 8 0.23
8 12 0.34
9 15 0.43
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (9 bp):
TCTTTTCTC
Found at i:1009660 original size:18 final size:17
Alignment explanation
Indices: 1009629--1009676 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
1009619 CACCTTATTT
1009629 TCTTTTCT-TTTTTCTC
1 TCTTTTCTCTTTTTCTC
1009645 TCTTTTCTCCTTTTTCTC
1 TCTTTTCT-CTTTTTCTC
*
1009663 TTTTTTCTCTTTTT
1 TCTTTTCTCTTTTT
1009677 TCCAATTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 15 0.52
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TCTTTTCTCTTTTTCTC
Found at i:1009676 original size:9 final size:9
Alignment explanation
Indices: 1009634--1009678 Score: 72
Period size: 9 Copynumber: 5.0 Consensus size: 9
1009624 TATTTTCTTT
1009634 TCTTTTTTC
1 TCTTTTTTC
*
1009643 TCTCTTTTC
1 TCTTTTTTC
*
1009652 TCCTTTTTC
1 TCTTTTTTC
1009661 TCTTTTTTC
1 TCTTTTTTC
1009670 TCTTTTTTC
1 TCTTTTTTC
1009679 CAATTTAGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (9 bp):
TCTTTTTTC
Found at i:1016843 original size:23 final size:23
Alignment explanation
Indices: 1016817--1016860 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1016807 AATACGAATG
1016817 TAAAAACATGGAAA-ATAAAAAAA
1 TAAAAAC-TGGAAATATAAAAAAA
*
1016840 TAAAAACTTGAAATATAAAAA
1 TAAAAACTGGAAATATAAAAA
1016861 TGCAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (23 bp):
TAAAAACTGGAAATATAAAAAAA
Found at i:1021650 original size:2 final size:2
Alignment explanation
Indices: 1021645--1021697 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1021635 ATGTGACGTG
1021645 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
*
1021687 TA TA AA TA TA T
1 TA TA TA TA TA T
1021698 GTTTATAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1025350 original size:17 final size:17
Alignment explanation
Indices: 1025328--1025361 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1025318 GGAAAATCAT
1025328 TTTGGGTAGATAGCATG
1 TTTGGGTAGATAGCATG
*
1025345 TTTGGGTAGATATCATG
1 TTTGGGTAGATAGCATG
1025362 ATGGTGTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.32, T:0.38
Consensus pattern (17 bp):
TTTGGGTAGATAGCATG
Found at i:1032475 original size:136 final size:136
Alignment explanation
Indices: 1032222--1032612 Score: 502
Period size: 136 Copynumber: 2.9 Consensus size: 136
1032212 CAAAGCTCAA
* * * * * **
1032222 CCTCATCACGAAGGAGTCGCGTCATCCTTAGATAACCAGATGTCTTCATCATGAAGGAACTGTGT
1 CCTCATCACGTAGGAGCCGAGTCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCATGT
* * *
1032287 TATCTCAAATATTTTTAAAGATGGCCAGATGTCCTCATCACAAAGGAA-AATGTCATCCACTGAT
66 TATCTCAAATA-TCTTAAAGATGGCCAGACGTCCTCATCACAAAGGAACAATGTCATCCACTGAC
*
1032351 CAGAACT
130 CAAAACT
* *
1032358 CCTCATCAC-TAAGGAGCATC-A-TCATCCTTAGATAGCCAGATGACCTCATCACGAAGGAACCA
1 CCTCATCACGT-AGGAGC--CGAGTCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCA
** * *
1032420 TGCCATCTCAAATATCTTAAAGATGGCTAGACGTCCTCATCACGAAGGAACAATGTCATCCACTG
63 TGTTATCTCAAATATCTTAAAGATGGCCAGACGTCCTCATCACAAAGGAACAATGTCATCCACTG
1032485 ACCAAAACT
128 ACCAAAACT
* * *
1032494 CCTCATCACGTAGGAGCCGAGTCATCCTCAGATAACCAGACGTCCTTATCACGAAGGAACCATGT
1 CCTCATCACGTAGGAGCCGAGTCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCATGT
* * *
1032559 TATCTCAAATATCTTCAAAGATGGCCAGGCTTTCTCATCACAAAGGAACAATGT
66 TATCTCAAATATCTT-AAAGATGGCCAGACGTCCTCATCACAAAGGAACAATGT
1032613 TATACACCAG
Statistics
Matches: 218, Mismatches: 29, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
134 1 0.00
135 33 0.15
136 149 0.68
137 34 0.16
138 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (136 bp):
CCTCATCACGTAGGAGCCGAGTCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCATGT
TATCTCAAATATCTTAAAGATGGCCAGACGTCCTCATCACAAAGGAACAATGTCATCCACTGACC
AAAACT
Found at i:1036571 original size:2 final size:2
Alignment explanation
Indices: 1036564--1036613 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1036554 TTTTCTTTAA
1036564 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1036606 AT AT AT AT
1 AT AT AT AT
1036614 TTTTGATAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1049027 original size:26 final size:26
Alignment explanation
Indices: 1048976--1049027 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1048966 TATTTTAGCG
* * *
1048976 GACGAATTTCTAAAATTTTAAGAAAT
1 GACGAATTTATAAAATTTCAAAAAAT
*
1049002 GACGAATTTATAACATTTCAAAAAAT
1 GACGAATTTATAAAATTTCAAAAAAT
1049028 ATATATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (26 bp):
GACGAATTTATAAAATTTCAAAAAAT
Found at i:1050451 original size:13 final size:13
Alignment explanation
Indices: 1050433--1050458 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1050423 TTATGAACCC
1050433 GTGGATTTTATAT
1 GTGGATTTTATAT
1050446 GTGGATTTTATAT
1 GTGGATTTTATAT
1050459 TTTAAGTCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
GTGGATTTTATAT
Found at i:1064881 original size:19 final size:19
Alignment explanation
Indices: 1064857--1064894 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1064847 TCAAAAACAT
*
1064857 GGAAAGAATTTACCAAAAA
1 GGAAAGAATTAACCAAAAA
*
1064876 GGAAAGAGTTAACCAAAAA
1 GGAAAGAATTAACCAAAAA
1064895 AAATGTATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.18, T:0.13
Consensus pattern (19 bp):
GGAAAGAATTAACCAAAAA
Found at i:1068207 original size:18 final size:18
Alignment explanation
Indices: 1068184--1068231 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1068174 AATTTATCCT
*
1068184 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
1068202 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
1068219 TATTTATATATTT
1 TA-TTATATATTT
1068232 TCTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:1068829 original size:41 final size:42
Alignment explanation
Indices: 1068721--1068828 Score: 146
Period size: 41 Copynumber: 2.6 Consensus size: 42
1068711 CTGAATTTTC
* ** *
1068721 GTGTTTATTTCACGTAATTCGTTTTTCGGAAAATATTTTCCA
1 GTGTTTGTTTCACGTAATTCGTTTTTCAAAAAATATTTTACA
*
1068763 -TGTTTGTTTCACGTAATTCATTTTTCAAAAAATATTTTACA
1 GTGTTTGTTTCACGTAATTCGTTTTTCAAAAAATATTTTACA
* *
1068804 GTGTTTGTTTTACGTAATTGGTTTT
1 GTGTTTGTTTCACGTAATTCGTTTT
1068829 CCGAAACGTA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 36 0.63
42 21 0.37
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCGTTTTTCAAAAAATATTTTACA
Found at i:1069041 original size:16 final size:17
Alignment explanation
Indices: 1069017--1069049 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1069007 ATGTTATTTA
*
1069017 TTTATTAAT-TAATATT
1 TTTAATAATATAATATT
1069033 TTTAATAATATAATATT
1 TTTAATAATATAATATT
1069050 ATATTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAATAATATAATATT
Found at i:1069140 original size:52 final size:50
Alignment explanation
Indices: 1069026--1069140 Score: 128
Period size: 52 Copynumber: 2.2 Consensus size: 50
1069016 ATTTATTAAT
*
1069026 TAATATTTT-TAATAATATAATATTATATTTTTAATATTACATAAAATAA
1 TAATTTTTTATAATAATATAATATTATATTTTTAATATTACATAAAATAA
* *
1069075 TCAATTATATTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAA
1 T-AATT-TTTTATAATAATAT-A-ATATTATATTTTTAATATTACATAA-A-ATAA
1069129 TAATTTTTTATA
1 TAATTTTTTATA
1069141 TATTTAATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
49 1 0.02
50 3 0.05
51 3 0.05
52 19 0.35
53 11 0.20
54 18 0.33
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (50 bp):
TAATTTTTTATAATAATATAATATTATATTTTTAATATTACATAAAATAA
Found at i:1069146 original size:29 final size:28
Alignment explanation
Indices: 1069080--1069182 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 28
1069070 AATAATCAAT
*
1069080 TATATTATAATAATATA-AGATATTATATTTT
1 TATATT-TAATAATATATA-ATATT-T-TTTA
1069111 TAT-TTTAATAATATATAATAATTTTTTA
1 TATATTTAATAATATATAAT-ATTTTTTA
* *
1069139 TATATTTAATAATGA-ATCATATTATTTA
1 TATATTTAATAAT-ATATAATATTTTTTA
1069167 TATATTTTAATAATAT
1 TATA-TTTAATAATAT
1069183 TTTAATAAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
28 18 0.29
29 35 0.56
30 7 0.11
31 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
TATATTTAATAATATATAATATTTTTTA
Found at i:1069211 original size:23 final size:23
Alignment explanation
Indices: 1069185--1069229 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1069175 AATAATATTT
1069185 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1069208 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1069230 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1069598 original size:20 final size:20
Alignment explanation
Indices: 1069561--1069600 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1069551 TCCGGAAACG
**
1069561 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
1069581 TTTTCCAGAATTCAAATTCA
1 TTTTCCAGAAATCAAATTCA
1069601 ATAATTCATT
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:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:1069606 original size:28 final size:30
Alignment explanation
Indices: 1069574--1069644 Score: 119
Period size: 28 Copynumber: 2.4 Consensus size: 30
1069564 TCCAGAAATG
1069574 TAATTCATTTTCCAG-AATTCAAATT-CAA
1 TAATTCATTTTCCAGTAATTCAAATTCCAA
*
1069602 TAATTCATTTTCCAGTAATTCAAATTCCAG
1 TAATTCATTTTCCAGTAATTCAAATTCCAA
1069632 TAATTCATTTTCC
1 TAATTCATTTTCC
1069645 GAAAAACCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 15 0.38
29 10 0.25
30 15 0.38
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (30 bp):
TAATTCATTTTCCAGTAATTCAAATTCCAA
Found at i:1069622 original size:15 final size:15
Alignment explanation
Indices: 1069573--1069644 Score: 85
Period size: 15 Copynumber: 4.9 Consensus size: 15
1069563 TTCCAGAAAT
1069573 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
1069588 G-AATTCAAATT-CA
1 GTAATTCATTTTCCA
*
1069601 ATAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
1069616 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
1069631 GTAATTCATTTTCC
1 GTAATTCATTTTCC
1069645 GAAAAACCAA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
13 2 0.04
14 16 0.36
15 27 0.60
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:1070985 original size:3 final size:3
Alignment explanation
Indices: 1070979--1071047 Score: 79
Period size: 3 Copynumber: 23.0 Consensus size: 3
1070969 CTAATTTTTT
* * *
1070979 TTA TTA TTA CTA TAA TTA TTA TTA TTA -TA CTTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
1071024 TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
1071048 AAAAATAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
2 4 0.07
3 47 0.84
4 5 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1070995 original size:21 final size:21
Alignment explanation
Indices: 1070970--1071047 Score: 92
Period size: 21 Copynumber: 3.9 Consensus size: 21
1070960 CTGAAGATAC
* *
1070970 TAATTTTTTTTATTATTACTA
1 TAATTATTATTATTATTACTA
1070991 TAATTATTATTATTA-TACT-
1 TAATTATTATTATTATTACTA
*
1071010 T-ATTATTATAATTATTA-TA
1 TAATTATTATTATTATTACTA
1071029 TATATTATTATTATTATTA
1 TA-ATTATTATTATTATTA
1071048 AAAAATAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 13 0.27
19 4 0.08
20 4 0.08
21 28 0.57
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
TAATTATTATTATTATTACTA
Found at i:1072532 original size:26 final size:28
Alignment explanation
Indices: 1072487--1072538 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1072477 TATATATATA
*
1072487 ATAAATAATAATTTATATTT-TTTTTAC
1 ATAAATAATAATTAATATTTATTTTTAC
*
1072514 ATAAATTAT-ATTAATATTTATTTTT
1 ATAAATAATAATTAATATTTATTTTT
1072539 CAATATCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
ATAAATAATAATTAATATTTATTTTTAC
Found at i:1072659 original size:23 final size:22
Alignment explanation
Indices: 1072613--1072657 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1072603 ATATTATAAA
1072613 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
1072635 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
1072658 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:1072699 original size:118 final size:124
Alignment explanation
Indices: 1072478--1072716 Score: 292
Period size: 118 Copynumber: 2.0 Consensus size: 124
1072468 ATATAAATAT
* * *
1072478 ATATATATAATAAATAATAATTTATATTTTTTTTACATAAATTATATTAATATTTATTTTTCAAT
1 ATATATATAAAAAATAATAATTTATATTTTATTTAAATAAATTATATTAATATTTA--TTTCAAT
* * * * *
1072543 ATCGAAGAAAAGGGCAGTCTTAATACAACTGGATGTCCTATTCTGGTATTT-TAAAATTAA
64 ATCGAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTCTAAAATTAA
* *
1072603 ATAT-TATAAAAAATTATAATTTA-ATTTTATTTAAAT-TATTATATTAATATTTA-TT-AATAT
1 ATATATATAAAAAATAATAATTTATATTTTATTTAAATAAATTATATTAATATTTATTTCAATAT
* * * *
1072663 CGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATATTTCTAAA
66 CGAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTCTAAA
1072717 TAAATAAACA
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
118 45 0.45
119 6 0.06
122 16 0.16
123 11 0.11
124 17 0.17
125 4 0.04
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (124 bp):
ATATATATAAAAAATAATAATTTATATTTTATTTAAATAAATTATATTAATATTTATTTCAATAT
CGAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCCTATTCTGATATTTCTAAAATTAA
Found at i:1080542 original size:115 final size:115
Alignment explanation
Indices: 1080340--1080675 Score: 557
Period size: 115 Copynumber: 2.9 Consensus size: 115
1080330 TACGTTCTCG
*
1080340 TAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1080405 GGTATGAACCCCAAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCA
66 GGTATGAACCCCAAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCA
*
1080455 TAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
*
1080520 GGTATGAACCCCAAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTATGAACCCCAAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCA
* * * * *
1080570 TAGTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
* * * *
1080635 GGTAGGAACCCC-AGAACCAATCATTAGAATTAAAAGATGAA
66 GGTATGAACCCCAAAAACCAATCATTGGATTTAAAAGATGAA
1080676 CTGCATGATC
Statistics
Matches: 207, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
114 25 0.12
115 182 0.88
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (115 bp):
TAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
GGTATGAACCCCAAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCA
Found at i:1082718 original size:54 final size:54
Alignment explanation
Indices: 1082636--1082801 Score: 287
Period size: 54 Copynumber: 3.1 Consensus size: 54
1082626 CAATGATTGA
1082636 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
*
1082690 GAACATCTGAGCAGAAACTACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
* * **
1082744 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGCGCCGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1082798 GAAC
1 GAAC
1082802 CTGCTATTCT
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
Found at i:1083185 original size:22 final size:22
Alignment explanation
Indices: 1083159--1083237 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
1083149 ACATCTACAT
1083159 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1083181 TCTTCAAAGATGATAGATTCCC
1 TCTTCAAAGATGATAGATTCTC
* * *
1083203 TTTTTAAAGATGACAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1083225 TTTTCAAAGATGA
1 TCTTCAAAGATGA
1083238 AAGCTTTATC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1083840 original size:113 final size:112
Alignment explanation
Indices: 1083645--1084503 Score: 989
Period size: 113 Copynumber: 7.5 Consensus size: 112
1083635 GATTCAAATC
* * *
1083645 CATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATAAGAAGAACTTATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1083710 AGAAGAAGTTCATAATGAGAAG-ATCTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAAT-TTGTTCAACTTTT-GCTTGAATT
* *
1083758 CATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGAATAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* * *
1083823 AGAAGAAGTTCATAATGAGAAGAACTTGCTCAACTTTTCGCTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTT-GCTTGAATT
* *
1083871 CATCACTCGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* * * *
1083936 GGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGTTTAAATT
63 AGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTGCTTGAATT
* * * *
1083987 CATTATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCT-AA-AG
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
*
1084050 AGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATT
63 AGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC-TTTTGCTTGAATT
* * * * *
1084101 CATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAA-AAAG
1 CATCATTCGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAA-
* *
1084164 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTGAATT
64 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTGCTTGAATT
* * * *
1084214 CATCATTTGATGGATTAAAATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* * * ** *
1084279 GGAAGAAGAAATTCATAATGAGAAGAATTTGGTCAACCTTTTGCTCAAATC
63 AGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTGCTTGAATT
* * * *
1084330 CATCACTT-GATGGATCAGCTTTCCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG-AA
1 CATCA-TTCGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAA
* * *
1084392 GAAAGAAGGAA-TTCATAATGAGAAGAATTTGTTCAAATTTTTGCTCGATTT
64 G-AAGAA-GAAGTTCATAATGAGAAGAATTTGTTC-AACTTTTGCTTGAATT
* ** * ** * *
1084443 CATCATTCGATGGATTAGTATTGCTAGAAAGAGTTCATAATAAGAAGAACTCATCTAAAGA
1 CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1084504 GGATAAGAGC
Statistics
Matches: 652, Mismatches: 71, Indels: 45
0.85 0.09 0.06
Matches are distributed among these distances:
111 6 0.01
112 10 0.02
113 332 0.51
114 94 0.14
115 5 0.01
116 195 0.30
117 10 0.02
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
CATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTGCTTGAATT
Found at i:1084278 original size:343 final size:342
Alignment explanation
Indices: 1083638--1084506 Score: 1143
Period size: 343 Copynumber: 2.5 Consensus size: 342
1083628 TAGCAAGGAT
* *
1083638 TCAAATCCATCA-TTCGATGGATCAACATTGCCAGGTCGAGTTCATAATAAGAAGAACT-T-ATC
1 TCAAATCCATCACTT-GATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCTCATC
* * *
1083700 TGAAGAAAGAAGAAGAAGTTCATAATGAGAAG-ATCTTGTTCAACTTTTCGCTTGAATTCATCAT
65 T-AA-AGAGAAGAAGAAATTCATAATGAGAAGAAT-TTGTTCAACTTTTTGCTTGAATTCATCAT
* * ** *
1083764 TCGATGGATCAACATTGCCAG-GTCGAGTTCATAATGAGAATAACTCATCTGAAGAAA-GAAGAA
127 TCGATGGATCAGCTTTGCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAA-AAAGGAAGAA
*
1083827 GAAGTTCATAATGAGAAGAACTTGCTCAACTTTTCGCTCGAATTCATCACTCGATGGATTAACAT
190 GAAGTTCATAATGAGAAGAACTTGCTCAACTTTTCGCTCGAATTCATCACTCGATGGATTAAAAT
*
1083892 TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
255 TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAAATTCATAATGA
* *
1083957 GAAGAATTTATTCAACCTTTTGT
320 GAAGAATTTAGTCAACCTTTTGC
* * * * *
1083980 TTAAATTCATTATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATC
1 TCAAATCCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTC-TCATC
*
1084045 TAAAGAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATTCATCATTTG
65 TAAAGAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATTCATCATTCG
*
1084110 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGT
130 ATGGATCAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGT
* * * * * * * *
1084175 TCATAATGAGAAGAATTTGTTTAACCTTTT-GTTTGAATTCATCATTTGATGGATTAAAATTTCC
195 TCATAATGAGAAGAACTTGCTCAA-CTTTTCGCTCGAATTCATCACTCGATGGATTAAAATTGCC
1084239 AGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAG
259 AGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAG
*
1084304 AATTTGGTCAACCTTTTGC
324 AATTTAGTCAACCTTTTGC
* * * *
1084323 TCAAATCCATCACTTGATGGATCAGCTTTCCCAGAG-AAAGTTCATAATGAGAAGAA--CTCATC
1 TCAAATCCATCACTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCTCATC
* * * * *
1084385 TGAAGAAGAAAGAAGGAATTCATAATGAGAAGAATTTGTTCAAATTTTTGCTCGATTTCATCATT
65 TAAAG-AG-AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATTCATCATT
* * * *
1084450 CGATGGATTAG-TATTGCTAGA-AAGAGTTCATAATAAGAAGAACTCATCT-AAAGAGGA
128 CGATGGATCAGCT-TTGCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAAAAGGA
1084507 TAAGAGCTTA
Statistics
Matches: 465, Mismatches: 49, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
340 9 0.02
341 13 0.03
342 143 0.31
343 284 0.61
344 12 0.03
345 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (342 bp):
TCAAATCCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCTCATCT
AAAGAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATTCATCATTCGA
TGGATCAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTT
CATAATGAGAAGAACTTGCTCAACTTTTCGCTCGAATTCATCACTCGATGGATTAAAATTGCCAG
GTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
TTTAGTCAACCTTTTGC
Found at i:1084409 original size:229 final size:228
Alignment explanation
Indices: 1083676--1084497 Score: 1061
Period size: 229 Copynumber: 3.6 Consensus size: 228
1083666 TGCCAGGTCG
* *
1083676 AGTTCATAATAAGAAGAACTTATCTGAAGAA-AGAAGAAGAAGTTCATAATGAGAAG-ATCTTGT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGA-AAGAAGAAGTTCATAATGAGAAGAAT-TTGT
* *
1083739 TCAA-CTTTTCGCTTGAATTCATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGA
64 TCAACCTTTT-GCTTGAATTCATCATTCGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGA
* * *
1083803 ATAA--C-TCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGCTCAA-CTTTTCGC
128 AGAACTCATCATCTGAAG-AAGAAGAAGAAATTCATAATGAGAAGAATTTGCTCAACCTTTT-GC
* * * * * *
1083864 TCGAATTCATCACTCGATGGATTAACATTGCCAG-GTAG
191 TCGAATTCATCACTTGATGGATCAGCTTTCCCAGAG-AA
* *
1083902 AGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTA
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAATTTG
* * * *
1083967 TTCAACCTTTTGTTTAAATTCATTATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGA
63 TTCAACCTTTTGCTTGAATTCATCATTCGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGA
* * * * *
1084032 AGAACTCGTCATCTAAAG-AGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTT
128 AGAACTCATCATCTGAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGCTCAACCTTTTGCTC
* *
1084096 GAATTCATCATTTGATGGATCAGCTTTTCCAGAGAA
193 GAATTCATCACTTGATGGATCAGCTTTCCCAGAGAA
* * *
1084132 AGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * *
1084197 AACCTTTTGTTTGAATTCATCATTTGATGGATTAAAATTTCCAGGTAGAGTTCATAATGAGAAGA
66 AACCTTTTGCTTGAATTCATCATTCGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGA
* *
1084262 ACTCATCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGGTCAACCTTTTGCTCAA
131 ACTCATCATCTGAAGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGCTCAACCTTTTGCTCGA
*
1084327 ATCCATCACTTGATGGATCAGCTTTCCCAGAGAA
195 ATTCATCACTTGATGGATCAGCTTTCCCAGAGAA
1084361 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGGAA-TTCATAATGAGAAGAATTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAA-GAAGTTCATAATGAGAAGAATTTGTT
** * * ** * ** *
1084425 CAAATTTTTGCTCGATTTCATCATTCGATGGATTAGTATTGCTAGAAAGAGTTCATAATAAGAAG
65 CAACCTTTTGCTTGAATTCATCATTCGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAG
1084490 AACTCATC
130 AACTCATC
1084498 TAAAGAGGAT
Statistics
Matches: 526, Mismatches: 56, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
226 17 0.03
227 117 0.22
228 3 0.01
229 283 0.54
230 91 0.17
231 6 0.01
232 9 0.02
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (228 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTTGAATTCATCATTCGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGA
ACTCATCATCTGAAGAAGAAGAAGAAATTCATAATGAGAAGAATTTGCTCAACCTTTTGCTCGAA
TTCATCACTTGATGGATCAGCTTTCCCAGAGAA
Found at i:1084753 original size:3 final size:3
Alignment explanation
Indices: 1084747--1084815 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
1084737 CTAATTTTTT
* * * *
1084747 TTA TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1084795 -TA TATA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA
1084816 AAAAATAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1086418 original size:23 final size:22
Alignment explanation
Indices: 1086372--1086416 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1086362 ATATTATAAA
1086372 AAATTATAATTTAATTTTATTT
1 AAATTATAATTTAATTTTATTT
*
1086394 AAATTATTATATTAATATTTATT
1 AAATTATAAT-TTAAT-TTTATT
1086417 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTATAATTTAATTTTATTT
Found at i:1086464 original size:118 final size:125
Alignment explanation
Indices: 1086233--1086475 Score: 277
Period size: 118 Copynumber: 2.0 Consensus size: 125
1086223 TGTAGTCATA
*
1086233 TAAATATATATATAATAAATAAAAATTTATATTTTTTTACATAAATTATATTAATATTTATTTTT
1 TAAATATATATATAATAAATAAAAATTTATATTTTTTTAAATAAATTATATTAATATTTA--TTT
* * * * *
1086298 CAATATCGAAGAAAAGGGCAGTCTTAATACAACTGGATGTCATATTCTGGTATTT-TAAAAT
64 CAATATCGAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCATATTCTGATATTTCTAAAAT
* * *
1086359 TAAATAT-TATA-AA-AAATTATAATTTA-ATTTTATTTAAAT-TATTATATTAATATTTA-TT-
1 TAAATATATATATAATAAATAAAAATTTATATTTT-TTTAAATAAATTATATTAATATTTATTTC
* * * * *
1086417 AATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATATTTCTAAA
65 AATATCGAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCATATTCTGATATTTCTAAA
1086476 TAAATAAACA
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
118 44 0.44
119 6 0.06
122 21 0.21
123 17 0.17
124 2 0.02
125 4 0.04
126 7 0.07
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (125 bp):
TAAATATATATATAATAAATAAAAATTTATATTTTTTTAAATAAATTATATTAATATTTATTTCA
ATATCGAAGAAAAGAGCAGTCTTAAGACAACTAGAAGTCATATTCTGATATTTCTAAAAT
Found at i:1087331 original size:16 final size:17
Alignment explanation
Indices: 1087301--1087337 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1087291 ATATTTTATT
1087301 TATATTTTATATATAAA
1 TATATTTTATATATAAA
*
1087318 TATATTTT-TATATAAT
1 TATATTTTATATATAAA
1087334 TATA
1 TATA
1087338 ACTTTGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:1087336 original size:26 final size:26
Alignment explanation
Indices: 1087287--1087337 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1087277 TTCTAAATAA
* *
1087287 ATAAATATTTTATTTATATTTTATAT
1 ATAAATATATTATTTATATATTATAT
1087313 ATAAATATATT-TTTATATAATTATA
1 ATAAATATATTATTTATAT-ATTATA
1087338 ACTTTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATAAATATATTATTTATATATTATAT
Found at i:1095976 original size:24 final size:24
Alignment explanation
Indices: 1095949--1095995 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1095939 ACATGTTATA
*
1095949 TCATTAAAGTGATGATGTGACATG
1 TCATAAAAGTGATGATGTGACATG
1095973 TCATAAAAGTGATGATGTGACAT
1 TCATAAAAGTGATGATGTGACAT
1095996 CACATCATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (24 bp):
TCATAAAAGTGATGATGTGACATG
Found at i:1096277 original size:20 final size:20
Alignment explanation
Indices: 1096252--1096292 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1096242 ACACAGTAAG
1096252 TTTTATTAAAATAATATTTT
1 TTTTATTAAAATAATATTTT
* *
1096272 TTTTATTTAAATATTATTTT
1 TTTTATTAAAATAATATTTT
1096292 T
1 T
1096293 AAACTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATTAAAATAATATTTT
Found at i:1096295 original size:13 final size:15
Alignment explanation
Indices: 1096277--1096308 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1096267 ATTTTTTTTA
1096277 TTTAAA-TATT-ATT
1 TTTAAACTATTAATT
1096290 TTTAAACTATTAATT
1 TTTAAACTATTAATT
1096305 TTTA
1 TTTA
1096309 TTTTTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 4 0.24
15 7 0.41
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAAACTATTAATT
Found at i:1098647 original size:15 final size:15
Alignment explanation
Indices: 1098629--1098682 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1098619 TAACCGGTTT
*
1098629 CGGTTTTTGAAAAAC
1 CGGTTTTTAAAAAAC
1098644 CGGTTTTTTTAAAAAAC
1 CGG--TTTTTAAAAAAC
* *
1098661 CGGTTATAAAAAAAC
1 CGGTTTTTAAAAAAC
*
1098676 CGATTTT
1 CGGTTTT
1098683 AATATTCCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 18 0.56
17 14 0.44
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (15 bp):
CGGTTTTTAAAAAAC
Found at i:1098658 original size:17 final size:17
Alignment explanation
Indices: 1098632--1098665 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1098622 CCGGTTTCGG
*
1098632 TTTTTGAAAAACCGGTT
1 TTTTTAAAAAACCGGTT
1098649 TTTTTAAAAAACCGGTT
1 TTTTTAAAAAACCGGTT
1098666 ATAAAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (17 bp):
TTTTTAAAAAACCGGTT
Found at i:1098878 original size:21 final size:21
Alignment explanation
Indices: 1098854--1098903 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1098844 ACACTTAGGG
1098854 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
1098875 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
1098896 TACCGATT
1 AACCGATT
1098904 TCCCCACGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:1099123 original size:13 final size:13
Alignment explanation
Indices: 1099102--1099156 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1099092 AAGTTCGATA
*
1099102 AATTCAAATACTT
1 AATTGAAATACTT
1099115 AATTGAAATACTT
1 AATTGAAATACTT
* *
1099128 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
1099142 AATTGAAATACTT
1 AATTGAAATACTT
1099155 AA
1 AA
1099157 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:1099233 original size:32 final size:33
Alignment explanation
Indices: 1099142--1099240 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
1099132 AACTCAACAT
* * *
1099142 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
1099175 AATTCAAATACTTAAAAAATTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1099208 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1099240 A
1 A
1099241 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 12 0.20
33 49 0.80
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:1099261 original size:21 final size:22
Alignment explanation
Indices: 1099237--1099283 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
1099227 TTCAAGTTCG
*
1099237 ATAATTGAAACAAAGTT-TACA
1 ATAATTGAAACAAAGTTATAAA
*
1099258 ATAATTGAAATAAAGTTATAAA
1 ATAATTGAAACAAAGTTATAAA
1099280 ATAA
1 ATAA
1099284 ACTACATTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAATTGAAACAAAGTTATAAA
Found at i:1101579 original size:13 final size:14
Alignment explanation
Indices: 1101556--1101596 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
1101546 TTCCGGATAA
1101556 AAACCGGTTTTTTT
1 AAACCGGTTTTTTT
*
1101570 -AACCGATTTTTTT
1 AAACCGGTTTTTTT
1101583 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
1101597 ATTCGGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 12 0.52
15 11 0.48
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.49
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:1103389 original size:22 final size:22
Alignment explanation
Indices: 1103355--1103400 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1103345 GATCCTTTAT
*
1103355 TTATCTTTCTTTAATTTAATTA
1 TTATCTTTCTTTAAATTAATTA
*
1103377 TTAT-TTTCTTTTAAATTATTTA
1 TTATCTTTC-TTTAAATTAATTA
1103399 TT
1 TT
1103401 TTAATTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATCTTTCTTTAAATTAATTA
Found at i:1106661 original size:134 final size:133
Alignment explanation
Indices: 1106421--1107847 Score: 1512
Period size: 134 Copynumber: 10.7 Consensus size: 133
1106411 GAAATATGAT
* * * **
1106421 GAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCATATCTGGGGACGTTGATTAATTCCACTGT
1 GAGGGATATGTTCC-CTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATCCATTCCACTGT
1106486 CACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
65 CACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
1106551 AAGA
130 AAGA
* * *
1106555 GAGGGATATGTTCCCTTTTTTCTTGAGGGAAAATCATATATGGGGGA-GTTGATCCATTCCACTG
1 GAGGGATATGTTCCC-TTCTTCTTGAGGGAAAATCAGATCT-GGGGATGTTGATCCATTCCACTG
* * * *
1106619 TCACTCAGGGAAGATTGAATCGAGGAAGACTTGTTTCACTGTTACTCAGAGAATATTAAATCTTG
64 TCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTG
*
1106684 AAAAA
129 AAAGA
** * * * * *
1106689 GAGGGATCTAT-TTTACTTTTTCTTAAGGGAAAATCAAATCTGGGGATGTTGATACATTTCACTG
1 GAGGGA--TATGTTCCCTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATCCATTCCACTG
* * * * *
1106753 TCACTTAGGGAAGATTAAATCGAGGCAAACTTATTCCACTGTTACTCAGGAAATATCAAATCTTG
64 TCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTG
1106818 AAAGA
129 AAAGA
* * * * * *
1106823 GATGGATATGTTCCTCTTCTTTTTGAGGGAAAATCAGATCTGTGAATGTTGATCTATTCTACTGT
1 GAGGGATATGTTCC-CTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATCCATTCCACTGT
* * * *
1106888 CACTCGGGGAAGATTGAATCGAGGTAGACTTATTCCATTGTTACTC-GGGAAATATCAAATCTTG
65 CACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGG-AATATCAAATCTTG
1106952 AAAGA
129 AAAGA
* * * * ** ** *
1106957 GATGGATATGTTCCGTTTCTTTTTTAGGGAAAATCAGATCTTTGGATGTTG-TTTATTCTACTGT
1 GAGGGATATGTTCC-CTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATCCATTCCACTGT
* *
1107021 CACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATATTGA
65 CACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
*
1107086 AATA
130 AAGA
* *
1107090 GAGAGATATGTTCCACTTCTTCTTGA-GGAAAATCAGATATGGGGGA-GTTGATCCATTCCACTG
1 GAGGGATATGTTCC-CTTCTTCTTGAGGGAAAATCAGATCT-GGGGATGTTGATCCATTCCACTG
*
1107153 TCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACT-TTCACTCAGGGAATATCAAATCTC
64 TCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTT-ACTCAGGGAATATCAAATCTT
1107217 GAAAGA
128 GAAAGA
** * * *
1107223 G-GGGTATCTAT-TTCGGTTCTTCTTGAGGGAAAATTAGATCTGGGG-TAGTTGACCCATTCCAA
1 GAGGG-A--TATGTTCCCTTCTTCTTGAGGGAAAATCAGATCTGGGGAT-GTTGATCCATTCCAC
* * * * * *
1107285 TATCACTCAAGGAAAACTGAATCGAGGTAGACTTGTTTCACT-TTCACTCAGGGAATATCAAATC
62 TGTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTT-ACTCAGGGAATATCAAATC
**
1107349 TCAAAAGA
126 TTGAAAGA
* * * *
1107357 GGGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGGA-ATTGACCCATTCCACTG
1 GAGGGATATGTTCC-CTTCTTCTTGAGGGAAAATCAGATCT-GGGGATGTTGATCCATTCCACTG
* * * * * * *
1107421 TCACTCAGGAAAGACTAAATCGAGGCAGACATGTTCCACTGTCACTCAGGCAATATCAAATATTG
64 TCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTG
1107486 AAAGA
129 AAAGA
** * * * * * *
1107491 GAGGGATCTAT-TTTGCTTCTACTTGAGGGAAAAATTAGATATAGGGATATTGATTCATTCCACT
1 GAGGGA--TATGTTCCCTTCTTCTTGAGGG-AAAATCAGATCTGGGGATGTTGATCCATTCCACT
* ** * * ** * *
1107555 ATTGCTCAAGGAAGATTGCATCGAGATAGATTTGTTCCACTGTTACTTAGGGAATATCAAATCTT
63 GTCACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTT
*
1107620 AAAAGA
128 GAAAGA
* * * * * * * *
1107626 GAGGGATTTGTTCCACTTCTTCTAGAGGAAAAATCAAATCTGGAGACGTTGATTCATTCCACTAT
1 GAGGGATATGTTCC-CTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATCCATTCCACTGT
* * ** * * *
1107691 CACTCAAGGAAGATTGAATCAAATCAGACTTGTTCTACTGTTACTTAGGGAATATCAAATCATGA
65 CACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
1107756 AAGA
130 AAGA
* * * * * * * *
1107760 GAGTGATTTGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGAGAGGTTGATTCATTCTACTAT
1 GAGGGATATG-TTCCCTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATCCATTCCACTGT
*
1107825 CACTTAGGGAAGATTGAATCGAG
65 CACTCAGGGAAGATTGAATCGAG
1107848 TTCAATTCGC
Statistics
Matches: 1093, Mismatches: 169, Indels: 62
0.83 0.13 0.05
Matches are distributed among these distances:
132 26 0.02
133 197 0.18
134 744 0.68
135 120 0.11
136 6 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (133 bp):
GAGGGATATGTTCCCTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATCCATTCCACTGTC
ACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAA
AGA
Found at i:1121588 original size:29 final size:30
Alignment explanation
Indices: 1121524--1121598 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
1121514 GAAAAAAAAT
* *
1121524 AAAAT-AAAGTAAAAATATAATATATATAA
1 AAAATAAAAATAAAAATAGAATATATATAA
1121553 ATAAATAAAAATAAAAATAGAATAT-TA-AGA
1 A-AAATAAAAATAAAAATAGAATATATATA-A
* *
1121583 AAAATATATATAAAAA
1 AAAATAAAAATAAAAA
1121599 CGTATAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 15 0.38
30 8 0.21
31 16 0.41
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (30 bp):
AAAATAAAAATAAAAATAGAATATATATAA
Found at i:1121702 original size:14 final size:15
Alignment explanation
Indices: 1121664--1121712 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 15
1121654 TAATATATCT
1121664 ATATATATAATGATATAA
1 ATATATATAA--ATA-AA
1121682 GATATATATAAA-AAA
1 -ATATATATAAATAAA
1121697 ATATATATAAATAAA
1 ATATATATAAATAAA
1121712 A
1 A
1121713 AAAGGAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.38
15 6 0.21
16 1 0.03
17 1 0.03
19 10 0.34
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (15 bp):
ATATATATAAATAAA
Found at i:1121710 original size:18 final size:18
Alignment explanation
Indices: 1121683--1121740 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
1121673 ATGATATAAG
*
1121683 ATATATATAAAAAAATAT
1 ATATAAATAAAAAAATAT
*
1121701 ATATAAATAAAAAAAGGAAT
1 ATATAAATAAAAAAA--TAT
1121721 ATAGTAAATAAAAAAATAT
1 ATA-TAAATAAAAAAATAT
1121740 A
1 A
1121741 ATTAAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 14 0.41
19 3 0.09
20 5 0.15
21 12 0.35
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
ATATAAATAAAAAAATAT
Found at i:1121746 original size:18 final size:18
Alignment explanation
Indices: 1121689--1121746 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
1121679 TAAGATATAT
1121689 ATAAAAAAATAT-ATATAA
1 ATAAAAAAATATAAT-TAA
* *
1121707 ATAAAAAAAGGAATATAGTAA
1 ATAAAAAAA--TATA-ATTAA
1121728 ATAAAAAAATATAATTAA
1 ATAAAAAAATATAATTAA
1121746 A
1 A
1121747 AATATGTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 14 0.44
19 3 0.09
20 2 0.06
21 12 0.38
22 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
ATAAAAAAATATAATTAA
Found at i:1124344 original size:20 final size:20
Alignment explanation
Indices: 1124319--1124356 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1124309 TTTGGTTCAC
*
1124319 GGAATGTAATATTACCAGTA
1 GGAATGTAAGATTACCAGTA
1124339 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1124357 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTA
Found at i:1127356 original size:2 final size:2
Alignment explanation
Indices: 1127347--1127541 Score: 52
Period size: 2 Copynumber: 96.0 Consensus size: 2
1127337 ATAAAACAAT
1127347 TA TA -A TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
1127385 TG TA TGA TGA -A TG T- TA TGA TA CTC TA TA TA TA -A TT TA TA TC
1 TA TA T-A T-A TA TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA
* *
1127426 TCA TA GT- TA TA TA GTT TA TA TA GT- TA TA TT TA TA TA CTA TA TA
1 T-A TA -TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* * * * *
1127469 TA AA CTA TA TA TA GTT TG TA TA CT- TA TA GTT TA TA TT TA TA TA
1 TA TA -TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* * *
1127512 -A TA TA TA AA TA TA AA TA TA AA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
1127542 GTTTGTATAC
Statistics
Matches: 141, Mismatches: 28, Indels: 48
0.65 0.13 0.22
Matches are distributed among these distances:
1 11 0.08
2 112 0.79
3 18 0.13
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1127453 original size:15 final size:14
Alignment explanation
Indices: 1127435--1127509 Score: 57
Period size: 15 Copynumber: 5.3 Consensus size: 14
1127425 CTCATAGTTA
1127435 TATAGTTTATATAGT
1 TATAGTTTATATA-T
*
1127450 TATA-TTTATATAC
1 TATAGTTTATATAT
* *
1127463 TATA-TATAAACTAT
1 TATAGTTTATA-TAT
*
1127477 ATATAGTTTGTATACT
1 -TATAGTTTATATA-T
1127493 TATAGTTTATAT-T
1 TATAGTTTATATAT
1127506 TATA
1 TATA
1127510 TAATATATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
13 13 0.27
14 10 0.21
15 21 0.44
16 4 0.08
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (14 bp):
TATAGTTTATATAT
Found at i:1127837 original size:17 final size:19
Alignment explanation
Indices: 1127815--1127859 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
1127805 TTTTTCTATC
1127815 TCTCTCTAAA-CTCTGA-T
1 TCTCTCTAAACCTCTGACT
*
1127832 TCTCTCAAAATCCTCTGACT
1 TCTCTCTAAA-CCTCTGACT
1127852 TCTCTCTA
1 TCTCTCTA
1127860 GAATTCTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.39
19 6 0.26
20 8 0.35
ACGTcount: A:0.22, C:0.33, G:0.04, T:0.40
Consensus pattern (19 bp):
TCTCTCTAAACCTCTGACT
Found at i:1128387 original size:46 final size:47
Alignment explanation
Indices: 1128327--1128427 Score: 136
Period size: 46 Copynumber: 2.2 Consensus size: 47
1128317 TATCTTCTTA
*
1128327 TTCTCTAA-TCCTAAATCTAACCAAGACTCTTCTTATTT-TGTTCATC
1 TTCTCTAACTCCTAAATCTAACCAAGACTCCTCTT-TTTCTGTTCATC
* *
1128373 TTCTCTAACT-CTAAATCTAACCGAGACTCCTCTTTTTCTGTTCGTC
1 TTCTCTAACTCCTAAATCTAACCAAGACTCCTCTTTTTCTGTTCATC
*
1128419 TTCCCTAAC
1 TTCTCTAAC
1128428 CGAGATTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
45 3 0.06
46 45 0.92
47 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.06, T:0.42
Consensus pattern (47 bp):
TTCTCTAACTCCTAAATCTAACCAAGACTCCTCTTTTTCTGTTCATC
Found at i:1128560 original size:46 final size:46
Alignment explanation
Indices: 1128488--1128589 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
1128478 CATCTTCTTC
* * *
1128488 TTCTCTAACCGTAAATCTAACTGAGACTCTTATTCTTATGTTCATA
1 TTCTCTAACCCTAAATCTAACCGAGACTCTTATTCTTATATTCATA
* *
1128534 TTCTCTAACCCTAAATCTAACCGAGACTCTTATTCTTCTATTCATT
1 TTCTCTAACCCTAAATCTAACCGAGACTCTTATTCTTATATTCATA
1128580 TTCTCTAACC
1 TTCTCTAACC
1128590 GAGACATTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.41
Consensus pattern (46 bp):
TTCTCTAACCCTAAATCTAACCGAGACTCTTATTCTTATATTCATA
Found at i:1128610 original size:161 final size:161
Alignment explanation
Indices: 1128318--1128610 Score: 390
Period size: 161 Copynumber: 1.8 Consensus size: 161
1128308 AGTATTATTT
* * * *
1128318 ATCTTCTTATTCTCTAATCCTAAATCTAACCAAGACTCTTCTTATTTTGTTCATCTTCTCTAACT
1 ATCTTCTTATTCTCTAATCCTAAATCTAACCAAGACTCTTATTATTATGTTCATATTCTCTAACC
* * * * ** ** *
1128383 CTAAATCTAACCGAGACTCCTCTTTTTCTGTTCGTCTTCCCTAACCGAGATTTTTCTTATTCTTT
66 CTAAATCTAACCGAGACTCCTATTCTTCTATTCATCTTCCCTAACCGAGACATTTCCCACTCTTT
1128448 TTCTTCTATTCATATTCTTCAAGTAATGTTC
131 TTCTTCTATTCATATTCTTCAAGTAATGTTC
* ** *
1128479 ATCTTCTTCTTCTCTAA-CCGTAAATCTAACTGAGACTCTTATTCTTATGTTCATATTCTCTAAC
1 ATCTTCTTATTCTCTAATCC-TAAATCTAACCAAGACTCTTATTATTATGTTCATATTCTCTAAC
* * *
1128543 CCTAAATCTAACCGAGACTCTTATTCTTCTATTCATTTTCTCTAACCGAGACATTTCCCACTCTT
65 CCTAAATCTAACCGAGACTCCTATTCTTCTATTCATCTTCCCTAACCGAGACATTTCCCACTCTT
1128608 TTT
130 TTT
1128611 TCTGTTCATT
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
160 2 0.02
161 109 0.98
ACGTcount: A:0.23, C:0.26, G:0.06, T:0.45
Consensus pattern (161 bp):
ATCTTCTTATTCTCTAATCCTAAATCTAACCAAGACTCTTATTATTATGTTCATATTCTCTAACC
CTAAATCTAACCGAGACTCCTATTCTTCTATTCATCTTCCCTAACCGAGACATTTCCCACTCTTT
TTCTTCTATTCATATTCTTCAAGTAATGTTC
Found at i:1135895 original size:20 final size:20
Alignment explanation
Indices: 1135872--1135914 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1135862 AATCCACCAC
*
1135872 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
1135892 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
1135912 ATG
1 ATG
1135915 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:1138567 original size:13 final size:14
Alignment explanation
Indices: 1138549--1138578 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1138539 ATGTTCAATA
1138549 AATAAAATT-ATTT
1 AATAAAATTAATTT
1138562 AATAAAATTAATTT
1 AATAAAATTAATTT
1138576 AAT
1 AAT
1138579 GATTATAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAAAATTAATTT
Found at i:1138740 original size:19 final size:19
Alignment explanation
Indices: 1138716--1138752 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1138706 TTATAAACTT
1138716 AAAATCTCACAACTTCATC
1 AAAATCTCACAACTTCATC
*
1138735 AAAATCTCACAATTTCAT
1 AAAATCTCACAACTTCAT
1138753 TAGTGATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATCTCACAACTTCATC
Found at i:1139136 original size:48 final size:48
Alignment explanation
Indices: 1139029--1139123 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
1139019 TTCGGAATCG
* * *
1139029 AATCGGTTTCGGATCACCACCGCTCAGGTCACAAACAATTTTGACTCA
1 AATCGGTTTCAGATCACCACCACTCAGATCACAAACAATTTTGACTCA
** * * *
1139077 AATCAATTTCAGATCACCCCCATTCAGATCACAAACAGTTTTGACTC
1 AATCGGTTTCAGATCACCACCACTCAGATCACAAACAATTTTGACTC
1139124 GAGTTGGTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (48 bp):
AATCGGTTTCAGATCACCACCACTCAGATCACAAACAATTTTGACTCA
Found at i:1140091 original size:92 final size:89
Alignment explanation
Indices: 1139964--1140141 Score: 284
Period size: 92 Copynumber: 2.0 Consensus size: 89
1139954 TTGCGTAAGT
*
1139964 GAGGTACTATTACTTGTATACATATCCTAAATAAATTTAGATGAGTGATTATAATATAAATGAAG
1 GAGGGACTATTACTTGTATACATATCCTAAATAAATTTAGATGAGTGATTATAATATAAATGAAG
*
1140029 TTAGGTAAAATTTGAAATTTAAAGC
66 TTAGATAAAATTTG-AATTTAAAGC
* *
1140054 GAGGGACTATTACTTGTATATATATATCCTAAATAAATTTAGATGAGTGATTATAATATAACTGA
1 GAGGGACTATTACTTG--TATACATATCCTAAATAAATTTAGATGAGTGATTATAATATAAATGA
*
1140119 AGTTAGATAAATTTTGAATTTAA
64 AGTTAGATAAAATTTGAATTTAA
1140142 TATTTTAGAG
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
90 15 0.19
91 7 0.09
92 59 0.73
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (89 bp):
GAGGGACTATTACTTGTATACATATCCTAAATAAATTTAGATGAGTGATTATAATATAAATGAAG
TTAGATAAAATTTGAATTTAAAGC
Found at i:1141616 original size:17 final size:17
Alignment explanation
Indices: 1141594--1141639 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
1141584 TTATCGATAC
*
1141594 TAGTATCGATACTTGCA
1 TAGTATCGATACTTGAA
1141611 TAGTATCGATACTTGAA
1 TAGTATCGATACTTGAA
*
1141628 TAATATCGATAC
1 TAGTATCGATAC
1141640 CAATTTTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (17 bp):
TAGTATCGATACTTGAA
Found at i:1147055 original size:22 final size:22
Alignment explanation
Indices: 1147018--1147076 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
1147008 CAACAATTAC
*
1147018 ATAATTATATTATATAAAAAATA
1 ATAATAATA-TATATAAAAAATA
1147041 ATAAGTAATAATATATATAAAAATTA
1 ATAA-TAAT-ATATATA-AAAAA-TA
1147067 ATAATAATAT
1 ATAATAATAT
1147077 TTTATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 4 0.13
24 11 0.35
25 10 0.32
26 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
ATAATAATATATATAAAAAATA
Found at i:1147083 original size:29 final size:28
Alignment explanation
Indices: 1147021--1147095 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 28
1147011 CAATTACATA
1147021 ATTATATTATATAAAAAATAATAAGTAAT
1 ATTATA-TATATAAAAAATAATAAGTAAT
*
1147050 A--ATATATATAAAAATTAATAA-TAAT
1 ATTATATATATAAAAAATAATAAGTAAT
* * *
1147075 ATTTTATATATATACAATAAT
1 ATTATATATATAAAAAATAAT
1147096 CTATAAACAC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 5 0.13
26 16 0.41
27 17 0.44
29 1 0.03
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (28 bp):
ATTATATATATAAAAAATAATAAGTAAT
Found at i:1150075 original size:2 final size:2
Alignment explanation
Indices: 1150029--1150060 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1150019 AGTACTCAAA
1150029 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1150061 TTTATGGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1153320 original size:21 final size:20
Alignment explanation
Indices: 1153294--1153350 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
1153284 TGAATATAAT
1153294 AAATAATATTATTTATTAGAA
1 AAATAATATTATTTATTA-AA
* *
1153315 AAATAATAATAATTTTTTAAA
1 AAATAAT-ATTATTTATTAAA
1153336 AGAATAAT-TTATTTA
1 A-AATAATATTATTTA
1153351 ACATTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.17
21 10 0.33
22 15 0.50
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
AAATAATATTATTTATTAAA
Found at i:1153458 original size:26 final size:27
Alignment explanation
Indices: 1153406--1153460 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
1153396 TTTATAAATA
* *
1153406 AAAATAAAAATATTACTATATTTTATT
1 AAAATAAAAATATTACTAAATTATATT
1153433 AAAAT-AAAATGATTA-TAAATTATATT
1 AAAATAAAAAT-ATTACTAAATTATATT
1153459 AA
1 AA
1153461 TTTATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (27 bp):
AAAATAAAAATATTACTAAATTATATT
Found at i:1153702 original size:23 final size:21
Alignment explanation
Indices: 1153665--1153755 Score: 91
Period size: 21 Copynumber: 4.4 Consensus size: 21
1153655 TTAAAAATAA
1153665 AATATAATAAAATATTATTAT
1 AATATAATAAAATATTATTAT
1153686 AATATAATTAAATATATTATTAT
1 AATATAA-TAAA-ATATTATTAT
* * *
1153709 AATATTAGAAAATAATATTAT
1 AATATAATAAAATATTATTAT
*
1153730 -AT-TATTAAAATATCTA-TA-
1 AATATAATAAAATAT-TATTAT
1153748 AATATAAT
1 AATATAAT
1153756 TCAATAATTA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
19 11 0.19
20 7 0.12
21 16 0.28
22 7 0.12
23 16 0.28
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (21 bp):
AATATAATAAAATATTATTAT
Found at i:1153725 original size:26 final size:24
Alignment explanation
Indices: 1153647--1153734 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 24
1153637 ATTAATGATT
*
1153647 ATATATTATTA-AAAATAAAATATA
1 ATATATTATTATAATATAAAA-ATA
**
1153671 ATAAAATATTATTATAATATAATTA-A
1 AT---ATATTATTATAATATAAAAATA
1153697 ATATATTATTATAATATTAGAAAATA
1 ATATATTATTATAATA-TA-AAAATA
1153723 ATAT-TATATTAT
1 ATATAT-TATTAT
1153735 TAAAATATCT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
23 14 0.27
24 4 0.08
25 3 0.06
26 14 0.27
27 10 0.20
28 6 0.12
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (24 bp):
ATATATTATTATAATATAAAAATA
Found at i:1159523 original size:12 final size:12
Alignment explanation
Indices: 1159496--1159536 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1159486 TCAAGCTGTA
* *
1159496 TAGGAATATGAA
1 TAGGAATAGGAG
1159508 TAGGAATAGGAG
1 TAGGAATAGGAG
*
1159520 TAGGAGTAGGAG
1 TAGGAATAGGAG
1159532 TAGGA
1 TAGGA
1159537 GCAGGAGAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (12 bp):
TAGGAATAGGAG
Found at i:1159537 original size:6 final size:6
Alignment explanation
Indices: 1159508--1159543 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1159498 GGAATATGAA
* *
1159508 TAGGAA TAGGAG TAGGAG TAGGAG TAGGAG CAGGAG
1 TAGGAG TAGGAG TAGGAG TAGGAG TAGGAG TAGGAG
1159544 AAGGGAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.36, C:0.03, G:0.47, T:0.14
Consensus pattern (6 bp):
TAGGAG
Found at i:1160833 original size:3 final size:3
Alignment explanation
Indices: 1160827--1160856 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1160817 TTTTTTTATC
1160827 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1160857 AATAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1162117 original size:15 final size:13
Alignment explanation
Indices: 1162096--1162129 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
1162086 TATATTATCT
1162096 TTTTAATTTCAATA
1 TTTTAATTT-AATA
1162110 TGTTTAATTTAATA
1 T-TTTAATTTAATA
1162124 TTTTAA
1 TTTTAA
1162130 ATATTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 6 0.32
15 8 0.42
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTAATTTAATA
Found at i:1162151 original size:2 final size:2
Alignment explanation
Indices: 1162144--1162181 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1162134 TATTTATTCG
1162144 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
1162182 GATGATTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1162373 original size:2 final size:2
Alignment explanation
Indices: 1162366--1162418 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1162356 ATTTATTATG
*
1162366 TA TA TA TA TA TA TA TC 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
1162408 TA TA TA TA TA T
1 TA TA TA TA TA T
1162419 GAAAGATTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.