Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 6 of 109
Found at i:890445 original size:21 final size:20
Alignment explanation
Indices: 890365--890446 Score: 65
Period size: 21 Copynumber: 4.0 Consensus size: 20
890355 CTACAAAGGA
890365 AAAACTAATCGATCCATTTTG
1 AAAA-TAATCGATCCATTTTG
* * * *
890386 AAAATCGATTGATTCATTTTT
1 AAAAT-AATCGATCCATTTTG
* *
890407 AAAATGATCAATCCATTTTG
1 AAAATAATCGATCCATTTTG
* *
890427 AAAACTAATTGATCTATTTT
1 AAAA-TAATCGATCCATTTT
890447 TAGAGGGGAT
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.34
21 31 0.66
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (20 bp):
AAAATAATCGATCCATTTTG
Found at i:905906 original size:55 final size:55
Alignment explanation
Indices: 905817--905924 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
905807 CAAACATATG
*
905817 AGGTGCTGCCCCATTTTGCTATTTGCTTAAAACAATCATAGCTATCTTT-TTTGCA
1 AGGTGCTGCCCCATTTTGCTACTTGCTTAAAACAATCATAGCTAT-TTTCTTTGCA
* *
905872 AGGTGCTGCCCCATTTTGTTACTTGCTTAGAACAATCATAGCTATTTTCTTTG
1 AGGTGCTGCCCCATTTTGCTACTTGCTTAAAACAATCATAGCTATTTTCTTTG
905925 TGATTCATCC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
54 3 0.06
55 46 0.94
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (55 bp):
AGGTGCTGCCCCATTTTGCTACTTGCTTAAAACAATCATAGCTATTTTCTTTGCA
Found at i:910665 original size:18 final size:18
Alignment explanation
Indices: 910643--910678 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
910633 TAAAATCCTA
910643 AAAAATTAAAAAGAAAATC
1 AAAAA-TAAAAAGAAAATC
*
910662 AAAAATAAAAATAAAAT
1 AAAAATAAAAAGAAAAT
910679 GACAAAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAAATAAAAAGAAAATC
Found at i:911823 original size:17 final size:17
Alignment explanation
Indices: 911795--911829 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
911785 TAAATAATTC
911795 TAAATTAAAATTT-TTT
1 TAAATTAAAATTTATTT
911811 TAAATTAAAAATTTATTT
1 TAAATT-AAAATTTATTT
911829 T
1 T
911830 TAAAAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 7 0.41
18 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAATTAAAATTTATTT
Found at i:911868 original size:23 final size:22
Alignment explanation
Indices: 911812--911870 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 22
911802 AAATTTTTTT
*
911812 AAATTAAAA-ATTTATTTTTAAA
1 AAATTAAAATA-TAATTTTTAAA
*
911834 AAATCAAGAAATATAATTTTTGAAA
1 AAAT-TA-AAATATAATTTTT-AAA
911859 AAATTAAAATAT
1 AAATTAAAATAT
911871 TAGAGAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
22 4 0.13
23 7 0.23
24 11 0.37
25 8 0.27
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (22 bp):
AAATTAAAATATAATTTTTAAA
Found at i:911998 original size:19 final size:19
Alignment explanation
Indices: 911957--912006 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
911947 TTTTTAGATT
**
911957 TTTTTTGAAAATTTTCAAGA
1 TTTTTT-AAAATTTAAAAGA
*
911977 TTTTTTAAAATTTAAAATA
1 TTTTTTAAAATTTAAAAGA
911996 TTTTTCTAAAA
1 TTTTT-TAAAA
912007 AATCAACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (19 bp):
TTTTTTAAAATTTAAAAGA
Found at i:912933 original size:13 final size:13
Alignment explanation
Indices: 912915--912954 Score: 66
Period size: 12 Copynumber: 3.2 Consensus size: 13
912905 GGATAATTTT
912915 AAATATAATATAA
1 AAATATAATATAA
912928 AAATATAATA-AA
1 AAATATAATATAA
912940 AAA-ATAATATAA
1 AAATATAATATAA
912952 AAA
1 AAA
912955 AATAGAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 6 0.23
12 10 0.38
13 10 0.38
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:912955 original size:13 final size:13
Alignment explanation
Indices: 912919--912958 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
912909 AATTTTAAAT
*
912919 ATAATATAAAAAT
1 ATAATATAAAAAA
912932 AT-A-ATAAAAAA
1 ATAATATAAAAAA
912943 ATAATATAAAAAA
1 ATAATATAAAAAA
912956 ATA
1 ATA
912959 GAAAAGATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 9 0.38
12 2 0.08
13 13 0.54
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
ATAATATAAAAAA
Found at i:913637 original size:16 final size:16
Alignment explanation
Indices: 913618--913658 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
913608 TTATTTAAAC
913618 TTAAATTAATTCAAAT
1 TTAAATTAATTCAAAT
* *
913634 TTAATTTGATTCAAAT
1 TTAAATTAATTCAAAT
913650 TTAAATTAA
1 TTAAATTAA
913659 CTCGAATATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (16 bp):
TTAAATTAATTCAAAT
Found at i:913767 original size:18 final size:19
Alignment explanation
Indices: 913744--913780 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
913734 ATTTTACTTT
*
913744 TTAAAAAT-ATTAATATAA
1 TTAAAAATAATAAATATAA
913762 TTAAAAATAATAAATATAA
1 TTAAAAATAATAAATATAA
913781 AATAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAAAAATAATAAATATAA
Found at i:913926 original size:11 final size:11
Alignment explanation
Indices: 913898--913937 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
913888 CTCTAACTAT
*
913898 ATAATAAAAAA
1 ATAATAAACAA
913909 ATAAATAAACAA
1 AT-AATAAACAA
913921 ATAATAAACAA
1 ATAATAAACAA
*
913932 TTAATA
1 ATAATA
913938 TTAAATCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (11 bp):
ATAATAAACAA
Found at i:914618 original size:42 final size:42
Alignment explanation
Indices: 914571--914655 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
914561 TCCGTGGTTA
*
914571 ATTGCTGCCATGTGTTCGATTTATATTTTGGGAACAAAAGCC
1 ATTGCTGCCATGTGTTCGATTTATATTTTGGCAACAAAAGCC
914613 ATTGCTGCCATGTGTTCGATTTATATTTTGGCAACAAAAGCC
1 ATTGCTGCCATGTGTTCGATTTATATTTTGGCAACAAAAGCC
914655 A
1 A
914656 ATATAATTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (42 bp):
ATTGCTGCCATGTGTTCGATTTATATTTTGGCAACAAAAGCC
Found at i:914916 original size:15 final size:14
Alignment explanation
Indices: 914894--914938 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 14
914884 ATTTTTTTAA
914894 AAAATAAATTTATT
1 AAAATAAATTTATT
* *
914908 ATTAATAAATTAATT
1 A-AAATAAATTTATT
914923 AAAATAAA-TTATT
1 AAAATAAATTTATT
914936 AAA
1 AAA
914939 TTTAATAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 7 0.27
14 7 0.27
15 12 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATAAATTTATT
Found at i:918794 original size:2 final size:2
Alignment explanation
Indices: 918787--918814 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
918777 AGTTCAAATG
918787 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
918815 GATTCACGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:929567 original size:21 final size:21
Alignment explanation
Indices: 929543--929593 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
929533 TATATTTTAA
*
929543 ATTAAATAAGA-AAATTTAATT
1 ATTAAATAA-ATAAAATTAATT
929564 ATT-AATAAATAAAATTAATT
1 ATTAAATAAATAAAATTAATT
*
929584 TTTATAATAA
1 ATTA-AATAA
929594 TTAATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 16 0.64
21 3 0.12
22 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTAAATAAATAAAATTAATT
Found at i:929603 original size:15 final size:15
Alignment explanation
Indices: 929572--929601 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
929562 TTATTAATAA
929572 ATAAAATTAATTTTT
1 ATAAAATTAATTTTT
929587 ATAATAATTAATTTT
1 ATAA-AATTAATTTT
929602 ATTCATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATAAAATTAATTTTT
Found at i:931843 original size:21 final size:20
Alignment explanation
Indices: 931795--931835 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
931785 TTATTTGACG
931795 TTTTTAAAATTAAAATTTAGA
1 TTTTT-AAATTAAAATTTAGA
931816 TTATTTAAATTAAAAGTTTA
1 TT-TTTAAATTAAAA-TTTA
931836 ATATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTTAAATTAAAATTTAGA
Found at i:933015 original size:3 final size:3
Alignment explanation
Indices: 933007--933041 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
932997 TTTCAACTTA
933007 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
933042 GTTGTTGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:933047 original size:3 final size:3
Alignment explanation
Indices: 933041--933066 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
933031 ATTATTATTA
933041 TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TG
933067 CTTTTGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
TGT
Found at i:937570 original size:39 final size:39
Alignment explanation
Indices: 937479--937670 Score: 113
Period size: 39 Copynumber: 4.9 Consensus size: 39
937469 ATGTAATTTC
* ** * *
937479 TCAGGGCTAAAGAGAAAATTGGAAGATTCCTGT-A-ACTT
1 TCAGGGCCAAAGAGAAAATCAGAAGACTCTTGTGATA-TT
* *
937517 CTCAGTGCCAAAGAGAAAATCAGAAGCCTCTTGTGATATT
1 -TCAGGGCCAAAGAGAAAATCAGAAGACTCTTGTGATATT
* * * **
937557 TCAGGGCCTAAGAGAAAATCAGAGGATTCTTGTGATAAA
1 TCAGGGCCAAAGAGAAAATCAGAAGACTCTTGTGATATT
* * * * * * * **
937596 TCAGGTCCAATGACAAAAACAAAAGACTCCTGTGTTAAC
1 TCAGGGCCAAAGAGAAAATCAGAAGACTCTTGTGATATT
* *
937635 TC-GGAGCCAAATAGAAAAT-TGAAAGACTCTTGTGAT
1 TCAGG-GCCAAAGAGAAAATCAG-AAGACTCTTGTGAT
937671 TTCTCCATGC
Statistics
Matches: 115, Mismatches: 34, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
38 2 0.02
39 109 0.95
40 3 0.03
41 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (39 bp):
TCAGGGCCAAAGAGAAAATCAGAAGACTCTTGTGATATT
Found at i:938790 original size:25 final size:25
Alignment explanation
Indices: 938761--938811 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
938751 CTGTTTTGGA
938761 CCACAAATACAATGCTGATTGGATT
1 CCACAAATACAATGCTGATTGGATT
938786 CCACAAATACAATGCTGATTGGATT
1 CCACAAATACAATGCTGATTGGATT
938811 C
1 C
938812 AGAGTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (25 bp):
CCACAAATACAATGCTGATTGGATT
Found at i:941505 original size:2 final size:2
Alignment explanation
Indices: 941498--941538 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
941488 GTTTTGAGGG
941498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
941539 AAACACCTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:948789 original size:21 final size:21
Alignment explanation
Indices: 948760--948806 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
948750 TTTCATTAGT
*
948760 TTTATTTATTTT-TATTTTTTA
1 TTTACTTATTTTCT-TTTTTTA
948781 TTTACTTATTTTCTTTTTTTA
1 TTTACTTATTTTCTTTTTTTA
948802 TTTAC
1 TTTAC
948807 ATATATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTACTTATTTTCTTTTTTTA
Found at i:950461 original size:6 final size:6
Alignment explanation
Indices: 950451--950487 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
950441 TGATTTTGGG
*
950451 TTTTTA GTTTTA --TTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
950488 ACTTATTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
4 4 0.14
6 24 0.86
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:950472 original size:16 final size:16
Alignment explanation
Indices: 950451--950481 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
950441 TGATTTTGGG
950451 TTTTTAGTTTTATTTA
1 TTTTTAGTTTTATTTA
*
950467 TTTTTATTTTTATTT
1 TTTTTAGTTTTATTT
950482 TTATTTACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTAGTTTTATTTA
Found at i:950488 original size:16 final size:16
Alignment explanation
Indices: 950451--950520 Score: 61
Period size: 20 Copynumber: 4.1 Consensus size: 16
950441 TGATTTTGGG
*
950451 TTTTTAGTTTTATTTA
1 TTTTTATTTTTATTTA
950467 TTTTTATTTTTATTTTTA
1 TTTTTATTTTTA--TTTA
950485 TTTACTTATTTGCTTATTTA
1 TTT--TTATTT--TTATTTA
*
950505 TTTGT-TTTTTATTTA
1 TTTTTATTTTTATTTA
950520 T
1 T
950521 ATACATATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
15 8 0.17
16 11 0.24
17 3 0.07
18 8 0.17
20 13 0.28
22 3 0.07
ACGTcount: A:0.17, C:0.03, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTTTATTTTTATTTA
Found at i:951673 original size:27 final size:26
Alignment explanation
Indices: 951643--951699 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
951633 ATATGAAATA
951643 TTATATATAATTT-TTAATTTTAATATT
1 TTATA-ATAATTTGTTAATTTT-ATATT
* * *
951670 TTATAATATTTTGTTTATTTTATTTT
1 TTATAATAATTTGTTAATTTTATATT
951696 TTAT
1 TTAT
951700 TATTTTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TTATAATAATTTGTTAATTTTATATT
Found at i:951994 original size:31 final size:31
Alignment explanation
Indices: 951920--952004 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 31
951910 ATATAAATGT
* *
951920 TTTATATAAAAGTA-A-AATTATATATTTTTA
1 TTTATATAAAAATATATAATT-TTTATTTTTA
*
951950 TTTATATATAAATAT-TAATTTTTATTTCTTA
1 TTTATATAAAAATATATAATTTTTATTT-TTA
*
951981 TTTAT-TCAAAAATATATATTTTTT
1 TTTATAT-AAAAATATATAATTTTT
952005 GCTCTTATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
30 19 0.42
31 19 0.42
32 7 0.16
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (31 bp):
TTTATATAAAAATATATAATTTTTATTTTTA
Found at i:952118 original size:17 final size:18
Alignment explanation
Indices: 952098--952131 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
952088 TTTAAAGATG
*
952098 ATTATATCATA-AATATA
1 ATTATATAATATAATATA
952115 ATTATATAATATAATAT
1 ATTATATAATATAATAT
952132 TCATTGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTATATAATATAATATA
Found at i:959735 original size:22 final size:23
Alignment explanation
Indices: 959693--959751 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
959683 TGTTATTAAG
* *
959693 ATTATCATATAGT-TTT-TTATC
1 ATTATAATATATTATTTATTATC
*
959714 ATTATAA-ATTTTATTTATTATC
1 ATTATAATATATTATTTATTATC
959736 ATTATAATATATTATT
1 ATTATAATATATTATT
959752 GTATATTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 3 0.10
21 9 0.29
22 12 0.39
23 7 0.23
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (23 bp):
ATTATAATATATTATTTATTATC
Found at i:960601 original size:19 final size:20
Alignment explanation
Indices: 960565--960606 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
960555 CATCATGTTC
960565 TTTTTAGGTCAACAATA-TG
1 TTTTTAGGTCAACAATATTG
*
960584 TTTTTGGGTCAATC-ATATTG
1 TTTTTAGGTCAA-CAATATTG
960604 TTT
1 TTT
960607 GATATATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.50
Consensus pattern (20 bp):
TTTTTAGGTCAACAATATTG
Found at i:961368 original size:34 final size:34
Alignment explanation
Indices: 961330--961405 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
961320 TTCTTATCCA
*
961330 ATAATGCAATATGACTTT-TAGATATACATATCAT-
1 ATAATACAATATGA-TTTCTAGATATACATAT-ATG
* *
961364 ATAATACAATTTGATTTCTAGATATGCATATATG
1 ATAATACAATATGATTTCTAGATATACATATATG
961398 ATAATACA
1 ATAATACA
961406 TAAATATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 5 0.14
34 32 0.86
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (34 bp):
ATAATACAATATGATTTCTAGATATACATATATG
Found at i:963698 original size:23 final size:25
Alignment explanation
Indices: 963671--963727 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 25
963661 AAACATATGT
963671 TAATCAAATATAT-CACAT-AAGCA
1 TAATCAAATATATGCACATCAAGCA
*
963694 TAATCAAATATATGCATATCAAGCA
1 TAATCAAATATATGCACATCAAGCA
*
963719 TAAGCAAAT
1 TAATCAAAT
963728 TTGTGCATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 13 0.43
24 4 0.13
25 13 0.43
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (25 bp):
TAATCAAATATATGCACATCAAGCA
Found at i:963717 original size:25 final size:24
Alignment explanation
Indices: 963671--963737 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
963661 AAACATATGT
*
963671 TAATCAAATATAT-CACATAAGCA
1 TAATCAAATATATGCATATAAGCA
963694 TAATCAAATATATGCATATCAAGCA
1 TAATCAAATATATGCATAT-AAGCA
* * *
963719 TAAGCAAATTTGTGCATAT
1 TAATCAAATATATGCATAT
963738 GATATTTCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.34
24 4 0.11
25 21 0.55
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (24 bp):
TAATCAAATATATGCATATAAGCA
Found at i:967306 original size:292 final size:292
Alignment explanation
Indices: 966778--967364 Score: 1048
Period size: 292 Copynumber: 2.0 Consensus size: 292
966768 TTTTAGAAAA
966778 ATTTTACATCACACTTTGAAAAAGTCCAAATGGTTTTTATGCTTATAAATGTTCAAAAACAAGAT
1 ATTTTACATCACACTTTGAAAAAGTCCAAATGGTTTTTATGCTTATAAATGTTCAAAAACAAGAT
966843 TTGATATTTTAAGCCCAAAAATCCTTTAAAACTTGCATATAACACTTATGAAAAATTGAAACTAT
66 TTGATATTTTAAGCCCAAAAATCCTTTAAAACTTGCATATAACACTTATGAAAAATTGAAACTAT
* *
966908 TGCAAGTTATCAAGTTTTATTTATTTGAGCAAGTTTAAATCATTGAATTCAAGATATTCAAATTT
131 TGCAAGTTATCAAGTTTTATTTATTTGAACAAGTTTAAATCATTGAATTCAAGATATTCAAATTC
* *
966973 ATTTTATAATTAAAAGCTTGCTAAAATAAAATTTTATATTTTAATACTTGACTATAGCAAAAATC
196 ATTTTATAATTAAAAGCTTGCTAAAATAAAATTTCATATTTTAATACTTGACTATAACAAAAATC
967038 ACTTTCAAAACAAAATATAAAATTTCAAAATC
261 ACTTTCAAAACAAAATATAAAATTTCAAAATC
*
967070 ATTTTACATCACACTTTGAAAAAGTCCAAATGGTTTTTATGCTTATAAATGTTCAAAAACAATAT
1 ATTTTACATCACACTTTGAAAAAGTCCAAATGGTTTTTATGCTTATAAATGTTCAAAAACAAGAT
* * * * *
967135 TTGATATTTTAAGCTCAAAAATCTTTTAAAACTTGTATGTAGCACTTATGAAAAATTGAAACTAT
66 TTGATATTTTAAGCCCAAAAATCCTTTAAAACTTGCATATAACACTTATGAAAAATTGAAACTAT
* *
967200 TGCAAGTTATCAAGTTTTCTTTGTTTGAACAAGTTTAAATCATTGAATTCAAGATATTCAAATTC
131 TGCAAGTTATCAAGTTTTATTTATTTGAACAAGTTTAAATCATTGAATTCAAGATATTCAAATTC
* *
967265 ATTTTATAATTAAAAGCTTGCTAAAATAAAATTTCATATTTTAATGCTTGACTCTAACAAAAATC
196 ATTTTATAATTAAAAGCTTGCTAAAATAAAATTTCATATTTTAATACTTGACTATAACAAAAATC
967330 ACTTTCAAAACAAAATATAAAATTTCAAAATC
261 ACTTTCAAAACAAAATATAAAATTTCAAAATC
967362 ATT
1 ATT
967365 AAGCTTTTAA
Statistics
Matches: 281, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
292 281 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (292 bp):
ATTTTACATCACACTTTGAAAAAGTCCAAATGGTTTTTATGCTTATAAATGTTCAAAAACAAGAT
TTGATATTTTAAGCCCAAAAATCCTTTAAAACTTGCATATAACACTTATGAAAAATTGAAACTAT
TGCAAGTTATCAAGTTTTATTTATTTGAACAAGTTTAAATCATTGAATTCAAGATATTCAAATTC
ATTTTATAATTAAAAGCTTGCTAAAATAAAATTTCATATTTTAATACTTGACTATAACAAAAATC
ACTTTCAAAACAAAATATAAAATTTCAAAATC
Found at i:970979 original size:25 final size:25
Alignment explanation
Indices: 970950--971001 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
970940 ACATAGTTTT
970950 TATATGTTGCTGTATAAACATAAAG
1 TATATGTTGCTGTATAAACATAAAG
*
970975 TATATGTTGCTTTATAAACATAAAG
1 TATATGTTGCTGTATAAACATAAAG
971000 TA
1 TA
971002 AGCCTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (25 bp):
TATATGTTGCTGTATAAACATAAAG
Found at i:971647 original size:21 final size:21
Alignment explanation
Indices: 971605--971646 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
971595 TCAATTCGAA
971605 AATTAAATTAACTAAAATTTT
1 AATTAAATTAACTAAAATTTT
971626 AATTGAAATATAA-TAAAATTT
1 AATT-AAAT-TAACTAAAATTT
971647 ATATATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 12 0.63
23 3 0.16
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AATTAAATTAACTAAAATTTT
Found at i:971867 original size:23 final size:22
Alignment explanation
Indices: 971841--971929 Score: 74
Period size: 23 Copynumber: 4.0 Consensus size: 22
971831 AAATTAATCG
*
971841 AATTAACTTAATTAATTTTAATA
1 AATTAA-TTAATTAATATTAATA
* * *
971864 AATTAATT-TTTAAAATTAAAA
1 AATTAATTAATTAATATTAATA
*
971885 AATTTAATTCAATTAATATAAATA
1 AA-TTAATT-AATTAATATTAATA
*
971909 ATTTAATTTAATTAAT-TTAAT
1 AATTAA-TTAATTAATATTAAT
971930 TTTAAGTAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
21 11 0.21
22 12 0.23
23 17 0.33
24 12 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATTAATTAATTAATATTAATA
Found at i:971881 original size:13 final size:14
Alignment explanation
Indices: 971850--971882 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
971840 GAATTAACTT
971850 AATTAATTTTAATA
1 AATTAATTTTAATA
*
971864 AATTAATTTTTA-A
1 AATTAATTTTAATA
971877 AATTAA
1 AATTAA
971883 AAAATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTAATTTTAATA
Found at i:971899 original size:54 final size:54
Alignment explanation
Indices: 971823--971926 Score: 133
Period size: 54 Copynumber: 1.9 Consensus size: 54
971813 TTATTTGATT
*
971823 AATTAAAAAAATTAATCGAATTAACT-TAATTAATTTTAA-TAAATTAATTTTTAA
1 AATTAAAAAAATTAATCGAATTAA-TATAAATAA-TTTAATTAAATTAATTTTTAA
* *
971877 AATTAAAAAATTTAATTC-AATTAATATAAATAATTTAATTTAATTAATTT
1 AATTAAAAAAATTAA-TCGAATTAATATAAATAATTTAATTAAATTAATTT
971927 AATTTTAAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
53 6 0.14
54 36 0.82
55 2 0.05
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (54 bp):
AATTAAAAAAATTAATCGAATTAATATAAATAATTTAATTAAATTAATTTTTAA
Found at i:971924 original size:14 final size:14
Alignment explanation
Indices: 971885--971948 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
971875 AAAATTAAAA
971885 AATTTAATTCAA-TT
1 AATTTAATT-AATTT
* *
971899 AATATAAATAATTT
1 AATTTAATTAATTT
971913 AATTTAATTAATTT
1 AATTTAATTAATTT
* *
971927 AATTTTAAGTAATAT
1 AA-TTTAATTAATTT
971942 AATTTAA
1 AATTTAA
971949 AATTAATCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
13 2 0.05
14 28 0.67
15 12 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (14 bp):
AATTTAATTAATTT
Found at i:971939 original size:15 final size:15
Alignment explanation
Indices: 971907--971946 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
971897 TTAATATAAA
*
971907 TAATTTAA-TTTAAT
1 TAATTTAATTTTAAG
971921 TAATTTAATTTTAAG
1 TAATTTAATTTTAAG
*
971936 TAATATAATTT
1 TAATTTAATTT
971947 AAAATTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TAATTTAATTTTAAG
Found at i:972411 original size:23 final size:23
Alignment explanation
Indices: 972378--972425 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
972368 GAGTTTTGAA
*
972378 TTTTTTTTATACAAAT-TCTTTT
1 TTTTTTTTATACAAATATCATTT
*
972400 TTTTTTTATATATAAATATCATTT
1 TTTTTTT-TATACAAATATCATTT
972424 TT
1 TT
972426 ATAATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 8 0.36
24 7 0.32
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTTTTATACAAATATCATTT
Found at i:972886 original size:27 final size:27
Alignment explanation
Indices: 972856--972910 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
972846 CAGTTCGATC
*
972856 AATGGGTTCTTCTGCGTCTTCCCAGAG
1 AATGGATTCTTCTGCGTCTTCCCAGAG
*
972883 AATGGATTCTTCTGCTTCTTCCCAGAG
1 AATGGATTCTTCTGCGTCTTCCCAGAG
972910 A
1 A
972911 CCCGACAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (27 bp):
AATGGATTCTTCTGCGTCTTCCCAGAG
Found at i:975680 original size:35 final size:35
Alignment explanation
Indices: 975634--975704 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
975624 GTTAATAGCG
*
975634 ATTCATACTTTGAAAGAAATTGTGGAAGTCAGACT
1 ATTCATACTTTGAAAGAAATTGAGGAAGTCAGACT
*
975669 ATTCATACTTTGGAAGAAATTGAGGAAGTCAGACT
1 ATTCATACTTTGAAAGAAATTGAGGAAGTCAGACT
975704 A
1 A
975705 CATATAAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (35 bp):
ATTCATACTTTGAAAGAAATTGAGGAAGTCAGACT
Found at i:979495 original size:20 final size:20
Alignment explanation
Indices: 979467--979513 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
979457 AATTTAAATT
979467 TATTATTAAGATATTAAAAAA
1 TATT-TTAAGATATTAAAAAA
* * *
979488 TATTTTAATATTTTAAAATA
1 TATTTTAAGATATTAAAAAA
979508 TATTTT
1 TATTTT
979514 TTAATTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TATTTTAAGATATTAAAAAA
Found at i:980397 original size:21 final size:22
Alignment explanation
Indices: 980373--980413 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
980363 GGTAGATTCA
980373 TTCAA-TTCCCTTATTTCTCCT
1 TTCAAGTTCCCTTATTTCTCCT
*
980394 TTCAAGTTCCCTTTTTTCTC
1 TTCAAGTTCCCTTATTTCTC
980414 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.12, C:0.32, G:0.02, T:0.54
Consensus pattern (22 bp):
TTCAAGTTCCCTTATTTCTCCT
Found at i:986315 original size:18 final size:17
Alignment explanation
Indices: 986288--986335 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
986278 GATTTCATGT
**
986288 AAATTATTTTTATTTTTA
1 AAATT-TTTTTATTAATA
986306 AAATATTTTTTAATTAATA
1 AAAT-TTTTTT-ATTAATA
986325 AAATTTTTTTA
1 AAATTTTTTTA
986336 ATATATTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 15 0.58
19 10 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATTTTTTTATTAATA
Found at i:988316 original size:22 final size:22
Alignment explanation
Indices: 988291--988350 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
988281 ATTCAAAGTT
*
988291 TTGAAATTCAATGATTCCCAAC
1 TTGAAATTCAATGATTCACAAC
* * *
988313 TTGAAATTCAAAGGTTCACAAT
1 TTGAAATTCAATGATTCACAAC
988335 TTGAAATTCAATGATT
1 TTGAAATTCAATGATT
988351 AGAAATTACA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (22 bp):
TTGAAATTCAATGATTCACAAC
Found at i:988515 original size:18 final size:17
Alignment explanation
Indices: 988494--988539 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
988484 TTCACAAAGC
988494 TTTAAAGATTTGCAAGAA
1 TTTAAAGATTTGCAAG-A
* *
988512 TTTAAAGGTTTGTAAGA
1 TTTAAAGATTTGCAAGA
988529 TTTCAAAGATT
1 TTT-AAAGATT
988540 CACAAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.39
Consensus pattern (17 bp):
TTTAAAGATTTGCAAGA
Found at i:988666 original size:34 final size:34
Alignment explanation
Indices: 988566--988659 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 34
988556 TTCAAAAAAC
*
988566 TTTCAGATTTGCAAAAATTGATA-ATTTGCAAGAT
1 TTTCAGATTTGCAAAAATTGA-AGATTTGTAAGAT
* * * * *
988600 TTTTATATTTGTAAAAATTGGAGCTTTGTAAGAT
1 TTTCAGATTTGCAAAAATTGAAGATTTGTAAGAT
*
988634 TTTCAGATTTGCAAAACTTGAAGATT
1 TTTCAGATTTGCAAAAATTGAAGATT
988660 CATAAGAACT
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
33 1 0.02
34 46 0.98
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.41
Consensus pattern (34 bp):
TTTCAGATTTGCAAAAATTGAAGATTTGTAAGAT
Found at i:988793 original size:33 final size:32
Alignment explanation
Indices: 988642--988794 Score: 103
Period size: 33 Copynumber: 4.6 Consensus size: 32
988632 ATTTTCAGAT
*
988642 TTGCAA-AACTTGAAGATTCATAAGAACTCATA
1 TTGCAAGAA-TTGAAGATTCATAAGAACTCAAA
* * *
988674 TTGATAAGAATTGATGATTCATAAGAACTCATAT
1 TTG-CAAGAATTGAAGATTCATAAGAACTCA-AA
* * ** *
988708 TTGCAAGCATTGGAGATTTGTAA-AATTTTCAAA
1 TTGCAAGAATTGAAGATTCATAAGAA--CTCAAA
* *
988741 GTTGCAAGATTTTGAAAGATTCATAAGAACTTAAA
1 -TTGCAAGA-ATTG-AAGATTCATAAGAACTCAAA
*
988776 TTCGTAAGAATTGAAGATT
1 TT-GCAAGAATTGAAGATT
988795 TGAAAGAAAT
Statistics
Matches: 90, Mismatches: 21, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
32 5 0.06
33 43 0.48
34 20 0.22
35 12 0.13
36 8 0.09
37 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (32 bp):
TTGCAAGAATTGAAGATTCATAAGAACTCAAA
Found at i:989007 original size:22 final size:23
Alignment explanation
Indices: 988930--989085 Score: 130
Period size: 24 Copynumber: 6.9 Consensus size: 23
988920 AAAATTTTTG
988930 TTAAAGATTCACATT-AAAAA-T
1 TTAAAGATTCACATTCAAAAATT
* * *
988951 TCAAAGGTTCCCATTCGAAAAA--
1 TTAAAGATTCACATTC-AAAAATT
*
988973 TTCAAGAATTCACATCTC-AAAATT
1 TTAAAG-ATTCACAT-TCAAAAATT
* *
988997 TCAAAG-CTCACATTCATAAAATT
1 TTAAAGATTCACATTCA-AAAATT
*
989020 TTAAAGATTCACATTCGAGAAATT
1 TTAAAGATTCACATTC-AAAAATT
*
989044 TTAAAGATTCACA-TCCAAAATT
1 TTAAAGATTCACATTCAAAAATT
*
989066 TTAAAGA-TCACATTTAAAAA
1 TTAAAGATTCACATTCAAAAA
989086 ATCTTAGAGA
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
21 19 0.18
22 31 0.29
23 24 0.22
24 32 0.30
25 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAGATTCACATTCAAAAATT
Found at i:989031 original size:46 final size:44
Alignment explanation
Indices: 988930--989084 Score: 140
Period size: 46 Copynumber: 3.5 Consensus size: 44
988920 AAAATTTTTG
* *
988930 TTAAAGATTCACATT-AAAAATTCAAAGGTTCCCATTCGAAAAA--
1 TTAAAGATTCACATTCAAAATTTCAAA-GTTCACATTC-AAAAATT
* *
988973 TTCAAGAATTCACATCTCAAAATTTCAAAGCTCACATTCATAAAATT
1 TTAAAG-ATTCACAT-TCAAAATTTCAAAGTTCACATTCA-AAAATT
* *
989020 TTAAAGATTCACATTCGAGAAATTTTAAAGATTCACA-TCCAAAATT
1 TTAAAGATTCACATTC-A-AAATTTCAAAG-TTCACATTCAAAAATT
*
989066 TTAAAGA-TCACATTTAAAA
1 TTAAAGATTCACATTCAAAA
989085 AATCTTAGAG
Statistics
Matches: 94, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
43 8 0.09
44 10 0.11
45 22 0.23
46 32 0.34
47 17 0.18
48 5 0.05
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (44 bp):
TTAAAGATTCACATTCAAAATTTCAAAGTTCACATTCAAAAATT
Found at i:989037 original size:69 final size:69
Alignment explanation
Indices: 988944--989087 Score: 168
Period size: 69 Copynumber: 2.1 Consensus size: 69
988934 AGATTCACAT
* * *
988944 TAAAAATTCAAAGGTTCCCATTCGA-AAAATTC-AAGAATTCACATCTCAAAATTTCAAAGCTCA
1 TAAAAATTCAAAGATTCACATTCGAGAAAATTCAAAG-ATTCACATC-CAAAATTTCAAAGATCA
989007 CATTCA
64 CATTCA
* * * * *
989013 TAAAATTTTAAAGATTCACATTCGAGAAATTTTAAAGATTCACATCCAAAATTTTAAAGATCACA
1 TAAAAATTCAAAGATTCACATTCGAGAAAATTCAAAGATTCACATCCAAAATTTCAAAGATCACA
*
989078 TTTA
66 TTCA
989082 -AAAAAT
1 TAAAAAT
989088 CTTAGAGACT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
68 5 0.08
69 41 0.65
70 14 0.22
71 3 0.05
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.31
Consensus pattern (69 bp):
TAAAAATTCAAAGATTCACATTCGAGAAAATTCAAAGATTCACATCCAAAATTTCAAAGATCACA
TTCA
Found at i:989042 original size:24 final size:23
Alignment explanation
Indices: 988873--989079 Score: 119
Period size: 23 Copynumber: 9.0 Consensus size: 23
988863 GAAATCCATA
* *
988873 TCCAAAATTTTTAA-ATTTACA-
1 TCCAAAATTTTAAAGATTCACAT
* *
988894 TCCAAAATTCT-AAGATTCGCAT
1 TCCAAAATTTTAAAGATTCACAT
*
988916 TCGAAAAATTTTTGTTAAAGATTCACAT
1 TC-CAAAA---TT-TTAAAGATTCACAT
* * * *
988944 T--AAAAATTCAAAGGTTCCCAT
1 TCCAAAATTTTAAAGATTCACAT
* * *
988965 TCGAAAA-ATTCAAGAATTCACA-
1 TCCAAAATTTTAAAG-ATTCACAT
* *
988987 TCTCAAAATTTCAAAG-CTCACAT
1 TC-CAAAATTTTAAAGATTCACAT
*
989010 TCATAAAATTTTAAAGATTCACAT
1 TC-CAAAATTTTAAAGATTCACAT
*
989034 TCGAGAAATTTTAAAGATTCACA-
1 TCCA-AAATTTTAAAGATTCACAT
989057 TCCAAAATTTTAAAGA-TCACAT
1 TCCAAAATTTTAAAGATTCACAT
989079 T
1 T
989080 TAAAAAATCT
Statistics
Matches: 143, Mismatches: 26, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
20 2 0.01
21 32 0.22
22 27 0.19
23 34 0.24
24 30 0.21
25 4 0.03
26 2 0.01
27 1 0.01
28 11 0.08
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (23 bp):
TCCAAAATTTTAAAGATTCACAT
Found at i:989280 original size:44 final size:45
Alignment explanation
Indices: 989230--989342 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 45
989220 ATTTACATCT
*
989230 AAAATTCAAAGATTTTCATTTGAAAATT-TTAGATATTCACACCC
1 AAAATTCAAAGATTTTCATTTGAAAATTCTTAGAGATTCACACCC
* * * * * *
989274 AAAATTCAAAGATTTGCAATTG-AAATTCTTAGAGATTTATATCT
1 AAAATTCAAAGATTTTCATTTGAAAATTCTTAGAGATTCACACCC
* *
989318 AAGATTCAAATATTTTCATTTGAAA
1 AAAATTCAAAGATTTTCATTTGAAA
989343 CTCAAAGATT
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
43 5 0.09
44 49 0.88
45 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (45 bp):
AAAATTCAAAGATTTTCATTTGAAAATTCTTAGAGATTCACACCC
Found at i:989347 original size:21 final size:20
Alignment explanation
Indices: 989323--989374 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
989313 TATCTAAGAT
989323 TCAAATATTTTCATTTGAAAC
1 TCAAA-ATTTTCATTTGAAAC
**
989344 TCAAAGATTCGCATTTGAAAC
1 TCAAA-ATTTTCATTTGAAAC
*
989365 TTAAAATTTT
1 TCAAAATTTT
989375 GAAAATTCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (20 bp):
TCAAAATTTTCATTTGAAAC
Found at i:992141 original size:60 final size:59
Alignment explanation
Indices: 992029--992343 Score: 347
Period size: 60 Copynumber: 5.3 Consensus size: 59
992019 ATTTTTTTAA
* *
992029 TTTTAAAA--TTTATTTTCAAGAAAAAAATT-ATACTTTCAGCTTTTCCTTAAAAATATTT
1 TTTTAAAATTTTTATTTTCAAG--AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTT
* *
992087 TTTTAAAACTTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTT
1 TTTTAAAA-TTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTT
* * *
992147 TTTTGAAATTTTTATCTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAAATATTT
1 TTTTAAAATTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCC-TCAAAAATATTT
* * *
992207 TTCTTGATAATTTTTATTCTT-AAGAAAAATTGGTACTTCCAACTTTTCCTCAAAAATATATTTT
1 TT-TT-AAAATTTTTATT-TTCAAGAAAAATTGATACTTTCAACTTTTCCTC-AAAA-ATA-TTT
* * * * *
992271 TTTTGAAA-TTTTAATTT-AAAAAAAATTGATACTTTCAACTTTTTCTC-AAAATACTT
1 TTTTAAAATTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTT
*
992327 TTTGAAAATTTTTATTT
1 TTTTAAAATTTTTATTT
992344 CTAAAATTTT
Statistics
Matches: 219, Mismatches: 26, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
56 8 0.04
57 10 0.05
58 11 0.05
59 42 0.19
60 74 0.34
61 21 0.10
62 41 0.19
63 7 0.03
64 5 0.02
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (59 bp):
TTTTAAAATTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTT
Found at i:992414 original size:73 final size:71
Alignment explanation
Indices: 992276--992416 Score: 187
Period size: 72 Copynumber: 2.0 Consensus size: 71
992266 ATTTTTTTTG
*
992276 AAATTTTAATTTAAAAAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTTGAAAATTTTTA
1 AAATTTTAATTTAAAAAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTTGAAAATATTTA
992341 TTTCTA
66 TTTCTA
* * * *
992347 AAATTTTATTTTCAAGAAAAATTGATACTTTCAA-TTTTTTTCCAAAA-ACATTTTTTTAAAATA
1 AAATTTTAATTT-AAAAAAAATTGATACTTTCAACTTTTTCT-CAAAATAC--TTTTTGAAAATA
992410 TTTATTT
62 TTTATTT
992417 TTAAGAAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
71 19 0.31
72 25 0.41
73 17 0.28
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (71 bp):
AAATTTTAATTTAAAAAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTTGAAAATATTTA
TTTCTA
Found at i:992742 original size:44 final size:44
Alignment explanation
Indices: 992606--993192 Score: 518
Period size: 45 Copynumber: 13.0 Consensus size: 44
992596 CAAAACACCC
* * * * * *
992606 CTAAGCAGAGGTTC-ACAACTTTTTAGAGAATAAACAAAACTCTT
1 CTAAACAGAGGCTCAACAACTTTTGA-AAAATAAACAAAGCTCCT
* * ** *
992650 CTAAATAAAGGCTCAACAACTTTTTGAAAAATAAACAAAATTCTT
1 CTAAACAGAGGCTCAACAAC-TTTTGAAAAATAAACAAAGCTCCT
**
992695 CTAAACAGAGGCTCAATGACTTTTGAAAAATAAACAAAGCTCCT
1 CTAAACAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCCT
* * *
992739 CT-AACAAAGGCTTAACAACTTTGGAAAAATAAACAAAGC-CCAT
1 CTAAACAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCC-T
* * * *
992782 CTAAACAAAGGCTCAATCAAACGCTCAATGACTTTTGAAAAATGAATAAAACTCCT
1 CTAAACAGAGG--C--TC-AA----C-A--ACTTTTGAAAAATAAACAAAGCTCCT
*
992838 CTAATCAGAGGCTCAACAACTTTTGAAAAAATAAACAAAGCTCCT
1 CTAAACAGAGGCTCAACAACTTTTG-AAAAATAAACAAAGCTCCT
* * * *
992883 CTAAATAGAAGCTCAACAACTTTTAAAAAAATAAACAAAGCTCAT
1 CTAAACAGAGGCTCAACAACTTTT-GAAAAATAAACAAAGCTCCT
* * * *** *
992928 CTAATCAAAGGCTTAGTGACATTTTAAAAAATAAACAAAGCTCCT
1 CTAAACAGAGGCTCAACAAC-TTTTGAAAAATAAACAAAGCTCCT
* * ** *
992973 CTAATCAAAGGCTCAATGACTTTGTGAAAAATAAATAAAGCTCCT
1 CTAAACAGAGGCTCAACAACTTT-TGAAAAATAAACAAAGCTCCT
* *
993018 TTAAATAGAGGCTCAACAACTTTTGAAAAAATAAACAAAGCTCCT
1 CTAAACAGAGGCTCAACAACTTTTG-AAAAATAAACAAAGCTCCT
* * * *
993063 CTAATCAGAAGCTTAACAACTTTTGAAAAATAAACAAAGCTCTT
1 CTAAACAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCCT
* * ** *
993107 TTAATCAGAGGCTCAATGACTTTT-AAAAATAAATAAAGCTCCT
1 CTAAACAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCCT
*
993150 CTAATCAGAGGCTCAACAAC-TTTGAAAAATAAACAAAGCTCCT
1 CTAAACAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCCT
993193 TGACAATCAT
Statistics
Matches: 449, Mismatches: 71, Indels: 47
0.79 0.13 0.08
Matches are distributed among these distances:
42 5 0.01
43 87 0.19
44 90 0.20
45 215 0.48
46 11 0.02
47 1 0.00
48 1 0.00
49 2 0.00
51 2 0.00
52 2 0.00
53 1 0.00
54 2 0.00
56 28 0.06
57 2 0.00
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.25
Consensus pattern (44 bp):
CTAAACAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCCT
Found at i:994210 original size:17 final size:16
Alignment explanation
Indices: 994188--994236 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
994178 TGAGTCATCC
*
994188 TTTTTAATTTTTTTTA
1 TTTTTTATTTTTTTTA
*
994204 TTTTTTATTTTTTTCTC
1 TTTTTTATTTTTTT-TA
994221 TTTTTTATCTTTTTTT
1 TTTTTTAT-TTTTTTT
994237 TTCTTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 13 0.45
17 10 0.34
18 6 0.21
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTATTTTTTTTA
Found at i:997615 original size:12 final size:12
Alignment explanation
Indices: 997595--997624 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
997585 TATGACATAC
997595 TCTTCAGAATCA
1 TCTTCAGAATCA
*
997607 TCTTTAGAATCA
1 TCTTCAGAATCA
997619 TCTTCA
1 TCTTCA
997625 TTGTCAAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (12 bp):
TCTTCAGAATCA
Found at i:1000836 original size:15 final size:14
Alignment explanation
Indices: 1000814--1000843 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1000804 TGTATCATCA
1000814 TATTTTTTAAATTT
1 TATTTTTTAAATTT
1000828 TATTATTTTAAATTT
1 TATT-TTTTAAATTT
1000843 T
1 T
1000844 GGTAGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTTTTAAATTT
Found at i:1003265 original size:58 final size:58
Alignment explanation
Indices: 1003203--1003513 Score: 324
Period size: 58 Copynumber: 5.3 Consensus size: 58
1003193 ATTTTTTTAA
* * *
1003203 TTTTAAAATTTTATTTTCAAGAAAAATTAATGCTTTCGACTTTTTCTCAAAAATATTT
1 TTTTAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTT
* * *
1003261 TTTTAAACTTTTATTTTTAA-AGAAAATTGATACTTTTAACTTTTTCTCAAAAATATTT
1 TTTTAAAATTTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTTCTCAAAAATATTT
* * * *
1003319 TTTTGAAATTTTTATCTTCAAGAAAAATTGATACTCTCAACTTTTTCATAAAAAATATTT
1 TTTT-AAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTC-TCAAAAATATTT
* * * * * *
1003379 TTCTTGATAATTTTATTCTT-AAGAAAAATT-AGTACTTCCAACTTTTCCTTAAAAGTGTTT
1 TT-TT-AAAATTTTATT-TTCAAGAAAAATTGA-TACTTTCAACTTTTTCTCAAAAATATTT
*** * *
1003439 TTTTTTTATTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTTCTC-AAAATACTT
1 TTTTAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTT
*
1003496 TTTGAAAATTTTTATTTT
1 TTTTAAAA-TTTTATTTT
1003514 AGAAATTTTA
Statistics
Matches: 208, Mismatches: 35, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
57 13 0.06
58 95 0.46
59 38 0.18
60 26 0.12
61 34 0.16
62 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.50
Consensus pattern (58 bp):
TTTTAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTT
Found at i:1003270 original size:26 final size:26
Alignment explanation
Indices: 1003241--1003331 Score: 69
Period size: 29 Copynumber: 3.3 Consensus size: 26
1003231 AATGCTTTCG
1003241 ACTTTTTCTCAAAAATATTTTTTTAA
1 ACTTTTTCTCAAAAATATTTTTTTAA
* * *
1003267 ACTTTTATTTTTAAAGAAAATTGATACTTTT-A
1 AC-TTT-TTCTCAAA-AATATT--T--TTTTAA
1003299 ACTTTTTCTCAAAAATATTTTTTTGAA
1 ACTTTTTCTCAAAAATATTTTTTT-AA
1003326 A-TTTTT
1 ACTTTTT
1003332 ATCTTCAAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
25 4 0.08
26 7 0.14
27 6 0.12
28 6 0.12
29 10 0.20
30 6 0.12
31 4 0.08
32 3 0.06
33 4 0.08
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (26 bp):
ACTTTTTCTCAAAAATATTTTTTTAA
Found at i:1003521 original size:130 final size:130
Alignment explanation
Indices: 1003387--1003620 Score: 314
Period size: 130 Copynumber: 1.8 Consensus size: 130
1003377 TTTTCTTGAT
* * * **
1003387 AATTTTATTCTTAAGAAAAATT-AGTACTTCCAACTTTTC-CTTAAAAGTGTTTTTTTTTTAT-T
1 AATTTTATTCTTAAGAAAAATTGA-TACTTCCAACTTTTCTC-AAAAAAT-ATTTTTTTAAATCT
1003449 TTAATTTCAAGAAAAATTGATACTT-TCAACTTTTTCTCAAAATACTTTTTGAAAATTTTTATTT
63 TTAATTTCAAGAAAAATTGATACTTCT-AACTTTTTCTCAAAATACTTTTTGAAAATTTTTATTT
1003513 TAGA
127 TAGA
* *
1003517 AATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCTCAAAAAATATTTTTTTAAATCTTTA
1 AATTTTATTCTTAAGAAAAATTGATACTTCCAACTTTTCTCAAAAAATATTTTTTTAAATCTTTA
* * *
1003582 TTTTTAAGAAAAATTGGTACTTCTAACTTTTTCTCAAAA
66 ATTTCAAGAAAAATTGATACTTCTAACTTTTTCTCAAAA
1003621 ATATATATAT
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
129 9 0.10
130 78 0.87
131 3 0.03
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (130 bp):
AATTTTATTCTTAAGAAAAATTGATACTTCCAACTTTTCTCAAAAAATATTTTTTTAAATCTTTA
ATTTCAAGAAAAATTGATACTTCTAACTTTTTCTCAAAATACTTTTTGAAAATTTTTATTTTAGA
Found at i:1003570 original size:72 final size:72
Alignment explanation
Indices: 1003446--1003585 Score: 203
Period size: 72 Copynumber: 1.9 Consensus size: 72
1003436 TTTTTTTTTT
*
1003446 ATTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTTGAAAATTTTTAT
1 ATTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTTGAAAATCTTTAT
1003511 TTTAGAA
66 TTTAGAA
* * **
1003518 ATTTTATTTTTAAGAAAAATTGATACTTTCAAC-TTTTCTCAAAAAATA-TTTTTTTAAATCTTT
1 ATTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTTCTC--AAAATACTTTTTGAAAATCTTT
1003581 ATTTT
64 ATTTT
1003586 TAAGAAAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
71 7 0.11
72 48 0.79
73 6 0.10
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.50
Consensus pattern (72 bp):
ATTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAATACTTTTTGAAAATCTTTAT
TTTAGAA
Found at i:1003708 original size:18 final size:18
Alignment explanation
Indices: 1003685--1003719 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1003675 TTCTCAAAAA
1003685 TATTTTTAAAAAAAATTT
1 TATTTTTAAAAAAAATTT
*
1003703 TATTTTTAAGAAAAATT
1 TATTTTTAAAAAAAATT
1003720 AATACTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
TATTTTTAAAAAAAATTT
Found at i:1003733 original size:123 final size:122
Alignment explanation
Indices: 1003519--1003747 Score: 331
Period size: 123 Copynumber: 1.9 Consensus size: 122
1003509 ATTTTAGAAA
* **
1003519 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCTCAAAAAATATTTTTTTAAATCTTTATT
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTCAAAAAATATTTTTAAAAATCTTTATT
**
1003584 TTTAAGAAAAATTGGTACTTCTAACTTTTTC-TCAAAAATATATATATTTTGCTAAAC
66 TTTAAGAAAAATTAATACTTCTAACTTTTTCGT-AAAAATATATATATTTTGCTAAAC
*
1003641 TTTTATTTTCAAGAAAAATTGATACTTTCAATTTTTCTC-AAAAATATTTTTAAAAAAAAT-TTT
1 TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTCAAAAAATATTTTT---AAAAATCTTT
1003704 ATTTTTAAGAAAAATTAATACTT-TCAACTTTTTCGTAAAAATAT
63 ATTTTTAAGAAAAATTAATACTTCT-AACTTTTTCGTAAAAATAT
1003748 TTTTTAAAAA
Statistics
Matches: 96, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
121 12 0.12
122 38 0.40
123 41 0.43
124 5 0.05
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (122 bp):
TTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCTCAAAAAATATTTTTAAAAATCTTTATT
TTTAAGAAAAATTAATACTTCTAACTTTTTCGTAAAAATATATATATTTTGCTAAAC
Found at i:1003827 original size:58 final size:59
Alignment explanation
Indices: 1003500--1003826 Score: 362
Period size: 59 Copynumber: 5.5 Consensus size: 59
1003490 ATACTTTTTG
* *
1003500 AAAATTTTTATTTTAGAAATTTTATTTTTAAGAAAAATTGATACTTTCAAC-TTTTCTCAA
1 AAAATATTT-TTTTAAAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTC-A
*
1003560 AAAATATTTTTTT--AAATCTTTATTTTTAAGAAAAATTGGTAC-TTCTAACTTTTTCTCA
1 AAAATATTTTTTTAAAAAT-TTTATTTTTAAGAAAAATTGATACTTTC-AACTTTTTCTCA
* * *
1003618 AAAATATATATATTTTGCTAAACTTTTATTTTCAAGAAAAATTGATACTTTCAA-TTTTTCTCA
1 AAAATAT-T-T-TTTT--AAAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCA
** *
1003681 AAAATATTTTTAAAAAAAATTTTATTTTTAAGAAAAATTAATACTTTCAACTTTTTCGT-A
1 AAAATATTTTT-TTAAAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTC-TCA
* ** * *
1003741 AAAATATTTTTTAAAAAAAATTATTTTTAAGGAAAATTGATA-TTTTAACTTTTTCTCA
1 AAAATATTTTTTTAAAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCA
*
1003799 AAAATATTGTTTTTGAAAATTTTATTTT
1 AAAATATT-TTTTTAAAAATTTTATTTT
1003827 AGGAAAATCA
Statistics
Matches: 230, Mismatches: 21, Indels: 33
0.81 0.07 0.12
Matches are distributed among these distances:
57 8 0.03
58 55 0.24
59 85 0.37
60 29 0.13
61 6 0.03
62 1 0.00
63 16 0.07
64 24 0.10
65 6 0.03
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (59 bp):
AAAATATTTTTTTAAAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCA
Found at i:1005823 original size:18 final size:18
Alignment explanation
Indices: 1005801--1005850 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1005791 ACTATTGATA
1005801 ATTATATTTATATTATAT
1 ATTATATTTATATTATAT
* ** *
1005819 TTTATATAAAAATTATAT
1 ATTATATTTATATTATAT
1005837 ATTATAATTTATAT
1 ATTAT-ATTTATAT
1005851 AAATATAAAA
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATATTTATATTATAT
Found at i:1005863 original size:25 final size:25
Alignment explanation
Indices: 1005810--1005867 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
1005800 AATTATATTT
* * *
1005810 ATATTATATTTTATATAAAAATTAT
1 ATATTATAATTTATATAAAAATAAA
*
1005835 ATATTATAATTTATATAAATATAAA
1 ATATTATAATTTATATAAAAATAAA
1005860 ATA-TATAA
1 ATATTATAA
1005868 AATTTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATTATAATTTATATAAAAATAAA
Found at i:1007462 original size:13 final size:13
Alignment explanation
Indices: 1007444--1007468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1007434 AAATAAAATG
1007444 AAATAAAATTAAA
1 AAATAAAATTAAA
1007457 AAATAAAATTAA
1 AAATAAAATTAA
1007469 TTGAAAAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAAATTAAA
Found at i:1007797 original size:16 final size:17
Alignment explanation
Indices: 1007776--1007807 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1007766 GACAAAATGA
1007776 TATAAAAAA-ATAAAAT
1 TATAAAAAATATAAAAT
1007792 TATAAAAAATATAAAA
1 TATAAAAAATATAAAA
1007808 ACAAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
TATAAAAAATATAAAAT
Found at i:1007941 original size:23 final size:23
Alignment explanation
Indices: 1007915--1007971 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
1007905 TTAAAAAAAA
*
1007915 TAAAATTATTTAGAATATTAAA-T
1 TAAAATTATTTAGAAT-TAAAATT
*
1007938 TAAAATT-TTTATAATTAAAATT
1 TAAAATTATTTAGAATTAAAATT
*
1007960 TTAAATTATTTA
1 TAAAATTATTTA
1007972 ATATTTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 4 0.14
22 14 0.48
23 11 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAATTATTTAGAATTAAAATT
Found at i:1010253 original size:16 final size:15
Alignment explanation
Indices: 1010232--1010264 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
1010222 ACTAATTTGA
1010232 TTTATAGCACTACTTT
1 TTTATAGCACTA-TTT
1010248 TTTATAGCACTATTT
1 TTTATAGCACTATTT
1010263 TT
1 TT
1010265 AAGAGCTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (15 bp):
TTTATAGCACTATTT
Found at i:1010958 original size:64 final size:64
Alignment explanation
Indices: 1010884--1011016 Score: 214
Period size: 64 Copynumber: 2.1 Consensus size: 64
1010874 GTTGTCTTGT
* *
1010884 ATTGTTGGGGTGAATGGTTTTTCCTTTTTTGTAAGATGG-TTAAAGCACTTAGCTGTGCTTGGG
1 ATTGTTGGGGTGAATGGTTTTTCCTTTTCTGTAAGAAGGTTTAAAGCACTTAGCTGTGCTTGGG
* *
1010947 AGTTGTTGGGGTGACTGGTTTTTCCTTTTCTGTAAGAAGGTTTGAAGCACTTAGCTGTGCTTGGG
1 A-TTGTTGGGGTGAATGGTTTTTCCTTTTCTGTAAGAAGGTTTAAAGCACTTAGCTGTGCTTGGG
1011012 ATTGT
1 ATTGT
1011017 GATATGAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
63 1 0.02
64 39 0.61
65 24 0.38
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.42
Consensus pattern (64 bp):
ATTGTTGGGGTGAATGGTTTTTCCTTTTCTGTAAGAAGGTTTAAAGCACTTAGCTGTGCTTGGG
Found at i:1013437 original size:73 final size:75
Alignment explanation
Indices: 1013350--1013490 Score: 198
Period size: 74 Copynumber: 1.9 Consensus size: 75
1013340 TATTTAAATA
* * * *
1013350 TATTATGAAAATAATTATTTTTT-AAAATTCTACAGTTTCAACATAAACTACT-TTTT-TAGATG
1 TATTATAAAAATAATTATTTTTTCAAAATTCCACAATTTCAACATAAACTA-TATTTTCAAGATG
1013412 AAAACATAATC
65 AAAACATAATC
* *
1013423 TATTATAAAAATAATTGTTTTTTCAAAATTCCACAATTTCAACATAGACTATATTTTCAAGATGA
1 TATTATAAAAATAATTATTTTTTCAAAATTCCACAATTTCAACATAAACTATATTTTCAAGATGA
1013488 AAA
66 AAA
1013491 ACGTAGTATT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
73 22 0.37
74 28 0.47
75 9 0.15
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (75 bp):
TATTATAAAAATAATTATTTTTTCAAAATTCCACAATTTCAACATAAACTATATTTTCAAGATGA
AAACATAATC
Found at i:1017110 original size:17 final size:17
Alignment explanation
Indices: 1017088--1017122 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1017078 ATAATGCATA
1017088 AACAAAAAAAAAAAAAC
1 AACAAAAAAAAAAAAAC
* *
1017105 AACAAATAAGAAAAAAC
1 AACAAAAAAAAAAAAAC
1017122 A
1 A
1017123 GAAACCTACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.83, C:0.11, G:0.03, T:0.03
Consensus pattern (17 bp):
AACAAAAAAAAAAAAAC
Found at i:1020024 original size:15 final size:15
Alignment explanation
Indices: 1020004--1020051 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1019994 CTTCATTCCC
*
1020004 AAATAA-AATAATTAA
1 AAATAATAATAA-CAA
1020019 AAATAATAATAACAA
1 AAATAATAATAACAA
1020034 AAATAAT--T-ACAA
1 AAATAATAATAACAA
1020046 AAATAA
1 AAATAA
1020052 ATAAAGGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 10 0.32
13 1 0.03
15 15 0.48
16 5 0.16
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAATAATAACAA
Found at i:1020040 original size:12 final size:12
Alignment explanation
Indices: 1020008--1020051 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
1019998 ATTCCCAAAT
1020008 AAAATAATTAA-A
1 AAAATAA-TAACA
1020020 AATAATAATAACA
1 AA-AATAATAACA
*
1020033 AAAATAATTACA
1 AAAATAATAACA
1020045 AAAATAA
1 AAAATAA
1020052 ATAAAGGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 21 0.72
13 8 0.28
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAATAACA
Found at i:1020508 original size:13 final size:13
Alignment explanation
Indices: 1020490--1020514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1020480 AAATAAAATG
1020490 AAATAAAATTAAA
1 AAATAAAATTAAA
1020503 AAATAAAATTAA
1 AAATAAAATTAA
1020515 TTGAAAAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAAATTAAA
Found at i:1020850 original size:16 final size:17
Alignment explanation
Indices: 1020829--1020860 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1020819 GACAAAATGA
1020829 TATAAAAAA-ATAAAAT
1 TATAAAAAATATAAAAT
1020845 TATAAAAAATATAAAA
1 TATAAAAAATATAAAA
1020861 ACAAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
TATAAAAAATATAAAAT
Found at i:1023052 original size:2 final size:2
Alignment explanation
Indices: 1023045--1023076 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1023035 GGTGATTCTT
*
1023045 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1023077 CACACACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1023979 original size:64 final size:64
Alignment explanation
Indices: 1023897--1024029 Score: 205
Period size: 64 Copynumber: 2.1 Consensus size: 64
1023887 GTTGTCTTGT
* * *
1023897 ATTGCTGGGGTGAATGGTTTTTCCTTTTTTGTAAGATGG-TTAAAGCACTTAGCTGTGCTTGGG
1 ATTGTTGGGGTGAATGGTTTTTCCTTTTCTGTAAGAAGGTTTAAAGCACTTAGCTGTGCTTGGG
* *
1023960 AGTTGTTGGGGTGACTGGTTTTTCCTTTTCTGTAAGAAGGTTTGAAGCACTTAGCTGTGCTTGGG
1 A-TTGTTGGGGTGAATGGTTTTTCCTTTTCTGTAAGAAGGTTTAAAGCACTTAGCTGTGCTTGGG
1024025 ATTGT
1 ATTGT
1024030 GATATGAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
63 1 0.02
64 38 0.60
65 24 0.38
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.41
Consensus pattern (64 bp):
ATTGTTGGGGTGAATGGTTTTTCCTTTTCTGTAAGAAGGTTTAAAGCACTTAGCTGTGCTTGGG
Found at i:1026338 original size:74 final size:73
Alignment explanation
Indices: 1026179--1026319 Score: 178
Period size: 74 Copynumber: 1.9 Consensus size: 73
1026169 TATTTAAATA
* * * *
1026179 TATTATGAAAATAATTCTTTTTTAAAATTCTACAGTTTCAACATAAACTACTTTTTTAGATGAAA
1 TATTATGAAAATAATTATTTTTTAAAATTCCACAATTTCAACATAAACTACTTTTTAAGATGAAA
1026244 ACATAATC
66 ACATAATC
* *
1026252 TATTATAAAAATAATTATTTTTTCAAAATTCCATAATTTCAACA-AAGACTA-TGTTTTCAAGAT
1 TATTATGAAAATAATTATTTTTT-AAAATTCCACAATTTCAACATAA-ACTACT-TTTT-AAGAT
1026315 GAAAA
62 GAAAA
1026320 ACGTAGTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
73 24 0.41
74 25 0.43
75 9 0.16
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (73 bp):
TATTATGAAAATAATTATTTTTTAAAATTCCACAATTTCAACATAAACTACTTTTTAAGATGAAA
ACATAATC
Found at i:1028560 original size:57 final size:57
Alignment explanation
Indices: 1028353--1028714 Score: 469
Period size: 57 Copynumber: 6.1 Consensus size: 57
1028343 ACCCCCCTTT
1028353 TTTTTTGAAAATTTATTTCTAAGGAAAATTGATAC-TTCAACTTTTCCCCAAAAATA
1 TTTTTTGAAAATTTATTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA
* * *
1028409 TTTTTTTTGGAAATTTCGATTT-TCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAACCCT-
1 --TTTTTTGAAAATTT--ATTTCT-AAGGAAAATTGATACTTTCAACTTTTCCCCAAAAA---TA
*
1028472 TTTTTTGAAAATTTATTTCAAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA
1 TTTTTTGAAAATTTATTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA
* *
1028529 TTTTTTGAAAATTTATTTCTAAGGAAAATTGATACTCTCAACTTTTCCCTAAAAATA
1 TTTTTTGAAAATTTATTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA
*
1028586 TTTTATTTTGGAAATTTATTTTTCTTGTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA
1 --TT-TTTTGAAAATTTA--TTTC---TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA
* *
1028651 TTTTTTGGAAATTTATTTCTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA
1 TTTTTTGAAAATTTATTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA
1028708 TATTTTT
1 T-TTTTT
1028715 TTAGAATTTT
Statistics
Matches: 272, Mismatches: 14, Indels: 36
0.84 0.04 0.11
Matches are distributed among these distances:
56 1 0.00
57 92 0.34
58 18 0.07
59 40 0.15
60 34 0.12
61 31 0.11
62 17 0.06
63 2 0.01
64 1 0.00
65 36 0.13
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.44
Consensus pattern (57 bp):
TTTTTTGAAAATTTATTTCTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA
Found at i:1028636 original size:122 final size:118
Alignment explanation
Indices: 1028311--1028728 Score: 507
Period size: 122 Copynumber: 3.5 Consensus size: 118
1028301 TTTTTTGTAG
*
1028311 GGAAAATTGATACTTTCAACTTTT-CCTCAAAAACCCCCCT-TTTTTTTTGAAAATTTA--TTTC
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAA------TATTTTTTTTGGAAATTTATTTTTC
1028372 TAAGGAAAATTGATAC-TTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTCGATTT-TCAA
59 TAAGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAATTT--ATTTCT-AA
* *** * *
1028435 GAAAAATTGATACTTTCAACTTTT-CCTCAAAAACCCTTTTTTTGAAAATTTA--TTTCAAAGGA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTTGGAAATTTATTTTTCTAAGGA
*
1028497 AAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTCTAA
65 AAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
*
1028551 GGAAAATTGATACTCTCAACTTTTCCCTAAAAATATTTTATTTTGGAAATTTATTTTTCTTGTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTT-TTTTGGAAATTTATTTTTC---TAA
1028616 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
62 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
*
1028673 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTAG-AATTT-TTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTTGGAAATTTATTTTT
1028729 ATTTTTATTT
Statistics
Matches: 268, Mismatches: 15, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
116 36 0.13
117 16 0.06
118 13 0.05
119 39 0.15
120 26 0.10
121 5 0.02
122 98 0.37
123 3 0.01
124 32 0.12
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.44
Consensus pattern (118 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTTTCTAAGGAA
AATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
Found at i:1028828 original size:24 final size:24
Alignment explanation
Indices: 1028794--1028840 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1028784 AACCTAATCT
* * *
1028794 AATAAATAAAAAATAAAATAAACA
1 AATAAACAAAAAAAAAAAAAAACA
1028818 AATAAACAAAAAAAAAAAAAAAC
1 AATAAACAAAAAAAAAAAAAAAC
1028841 CTAGAGCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (24 bp):
AATAAACAAAAAAAAAAAAAAACA
Found at i:1029186 original size:20 final size:20
Alignment explanation
Indices: 1029161--1029198 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1029151 GAACACCGGT
*
1029161 GCCGGATTCTGGAAATTTTC
1 GCCGGAATCTGGAAATTTTC
1029181 GCCGGAATCTGGAAATTT
1 GCCGGAATCTGGAAATTT
1029199 CACCGGAAGT
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:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GCCGGAATCTGGAAATTTTC
Found at i:1029204 original size:19 final size:20
Alignment explanation
Indices: 1029162--1029206 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1029152 AACACCGGTG
* *
1029162 CCGGATTCTGGAAATTTTCG
1 CCGGAATCTGGAAATTTTCA
1029182 CCGGAATCTGGAAA-TTTCA
1 CCGGAATCTGGAAATTTTCA
1029201 CCGGAA
1 CCGGAA
1029207 GTTGGCCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (20 bp):
CCGGAATCTGGAAATTTTCA
Found at i:1029305 original size:31 final size:31
Alignment explanation
Indices: 1029262--1029329 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1029252 GGACAGGTCG
* ** *
1029262 CCGGAAACTTCAATGTTGGCCGGAATTTTCA
1 CCGGAAAATTCAAACTTCGCCGGAATTTTCA
*
1029293 CCGGAAAATTCAAACTTCGCCGGAATTTTCG
1 CCGGAAAATTCAAACTTCGCCGGAATTTTCA
1029324 CCGGAA
1 CCGGAA
1029330 TCTGGAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (31 bp):
CCGGAAAATTCAAACTTCGCCGGAATTTTCA
Found at i:1029392 original size:26 final size:25
Alignment explanation
Indices: 1029338--1029390 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
1029328 AATCTGGAAA
*
1029338 TTTCCCAGAAATTTCCAGAAAAAAT
1 TTTCCCAAAAATTTCCAGAAAAAAT
*
1029363 TTTCGCCAAAAATTTCTA-AAAAAAT
1 TTTC-CCAAAAATTTCCAGAAAAAAT
1029388 TTT
1 TTT
1029391 TCTCACTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (25 bp):
TTTCCCAAAAATTTCCAGAAAAAAT
Found at i:1030074 original size:6 final size:6
Alignment explanation
Indices: 1030063--1030108 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
1030053 AAATATTTTG
1030063 TTTATT TTTATT TTTACTCAT TTTA-- TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTA-T--T TTTATT TTTATT TTTATT TTTATT TTT
1030109 GGTGTTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
4 4 0.11
6 25 0.71
7 1 0.03
9 5 0.14
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:1032329 original size:64 final size:56
Alignment explanation
Indices: 1032245--1032656 Score: 499
Period size: 57 Copynumber: 7.0 Consensus size: 56
1032235 TCTTGTGTGG
1032245 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTGGAAATTTATTTTTAA
*
1032302 GGAAAATTGATACTTTCAACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAATTTATTTTTAA
1 GGAAAATTG--A---T--ACTTTCAAC-TTTTCCCAAAAATATTTTTTGGAAATTTATTTTTAA
* *
1032366 GGAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTTGAAAATTTA-TTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATA--TTTTTTGGAAATTTATTTTTAA
* *
1032423 GGAAAATTGATACTTT-AACTTTTCCTCAAAAATATTTTTTTGAAATTT-TGATTTCAA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTGGAAATTTAT--TTTTAA
*
1032480 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATA---TTTTTTGGAAA-TTT-ATTTTTAA
**
1032542 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTT-GAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTGGAAATTTATTTTTAA
1032598 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTCGATTTTTA
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATA-TTTTTTGGAAATTT--ATTTTTA
1032657 TTTAAAGAAA
Statistics
Matches: 316, Mismatches: 12, Indels: 51
0.83 0.03 0.13
Matches are distributed among these distances:
55 13 0.04
56 60 0.19
57 78 0.25
58 42 0.13
59 8 0.03
60 7 0.02
61 10 0.03
62 42 0.13
63 1 0.00
64 55 0.17
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.46
Consensus pattern (56 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGGAAATTTATTTTTAA
Found at i:1032681 original size:14 final size:13
Alignment explanation
Indices: 1032659--1032730 Score: 51
Period size: 13 Copynumber: 5.4 Consensus size: 13
1032649 GATTTTTATT
*
1032659 TAAAGAAAATAGAA
1 TAAAAAAAATA-AA
1032673 TAAAAAAAATAAA
1 TAAAAAAAATAAA
1032686 TAAAAATAGAA-AAA
1 TAAAAA-A-AATAAA
* *
1032700 TAAAGAAAGTAAA
1 TAAAAAAAATAAA
1032713 -ACAAAAATAA-AAA
1 TA-AAAAA-AATAAA
1032726 TAAAA
1 TAAAA
1032731 TTAAGATAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
12 2 0.04
13 22 0.47
14 21 0.45
15 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.14
Consensus pattern (13 bp):
TAAAAAAAATAAA
Found at i:1032701 original size:27 final size:26
Alignment explanation
Indices: 1032671--1032730 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
1032661 AAGAAAATAG
1032671 AATAAAAAAAATAAATA-AAAATAGAAA
1 AATAAAAAAAATAAA-ACAAAA-AGAAA
* * *
1032698 AATAAAGAAAGTAAAACAAAAATAAA
1 AATAAAAAAAATAAAACAAAAAGAAA
1032724 AATAAAA
1 AATAAAA
1032731 TTAAGATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.13
Consensus pattern (26 bp):
AATAAAAAAAATAAAACAAAAAGAAA
Found at i:1032739 original size:17 final size:16
Alignment explanation
Indices: 1032717--1032756 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1032707 AGTAAAACAA
*
1032717 AAATAAAAATAAAATT
1 AAATAAAAAGAAAATT
*
1032733 AAGATAAAAAGAATATT
1 AA-ATAAAAAGAAAATT
1032750 AAATAAA
1 AAATAAA
1032757 CCTAATCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATAAAAAGAAAATT
Found at i:1033698 original size:4 final size:4
Alignment explanation
Indices: 1033691--1033915 Score: 69
Period size: 4 Copynumber: 55.2 Consensus size: 4
1033681 ATATTATAGG
* * *
1033691 ATAA ATAA ATAA AAATA AT-A ATAA CATATA TATAA TTAG ATAA ATACAA
1 ATAA ATAA ATAA ATA-A ATAA ATAA -ATA-A -ATAA ATAA ATAA AT--AA
* *
1033740 ATAA AAAA ATAA ATAA A-AT ATAA A-ATA AT-A AT-A AT-A AT-A AT-A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA
* * * * *
1033782 ATAA ATAA ATTATA ATATA AT-A ATAA ATAT ATAA CTAT ACAT ATAA ATATTA
1 ATAA ATAA A-TA-A ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A
* * * * *
1033834 ATAGA A-AGA A-AA ATAA ATAA ATAG ATAA ATAA ATAA AGAT ATAC ATAT
1 ATA-A ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* *
1033882 ATTA ATAC ATAGTA ATAA ATAA ATAA AT-A ATAA A
1 ATAA ATAA ATA--A ATAA ATAA ATAA ATAA ATAA A
1033916 ATACATAAAA
Statistics
Matches: 170, Mismatches: 32, Indels: 38
0.71 0.13 0.16
Matches are distributed among these distances:
3 29 0.17
4 108 0.64
5 16 0.09
6 17 0.10
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (4 bp):
ATAA
Found at i:1033712 original size:3 final size:3
Alignment explanation
Indices: 1033698--1033807 Score: 61
Period size: 3 Copynumber: 35.7 Consensus size: 3
1033688 AGGATAAATA
* *
1033698 AAT AAA AAT AAT AAT AAC ATAT ATAT AATT AGAT AAAT ACA- AAT AA-
1 AAT AAT AAT AAT AAT AAT A-AT A-AT AA-T A-AT -AAT A-AT AAT AAT
*
1033744 AAA AAT AAAT AA- AAT -AT AA- AAT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
1033788 AAAT TAT AAT -AT AAT AAT AA
1 -AAT AAT AAT AAT AAT AAT AA
1033808 ATATATAACT
Statistics
Matches: 87, Mismatches: 7, Indels: 26
0.73 0.06 0.22
Matches are distributed among these distances:
2 11 0.13
3 52 0.60
4 22 0.25
5 2 0.02
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1033790 original size:34 final size:33
Alignment explanation
Indices: 1033739--1033807 Score: 102
Period size: 34 Copynumber: 2.1 Consensus size: 33
1033729 GATAAATACA
1033739 AATAAAAAAATAAATAAAATATAAAATAATAAT
1 AATAAAAAAATAAATAAAATATAAAATAATAAT
* * *
1033772 AATAATAATAATAAATAAATTATAATATAATAAT
1 AATAA-AAAAATAAATAAAATATAAAATAATAAT
1033806 AA
1 AA
1033808 ATATATAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 5 0.16
34 27 0.84
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (33 bp):
AATAAAAAAATAAATAAAATATAAAATAATAAT
Found at i:1033826 original size:6 final size:6
Alignment explanation
Indices: 1033730--1033836 Score: 50
Period size: 6 Copynumber: 18.2 Consensus size: 6
1033720 ATATAATTAG
* * *
1033730 ATAAAT ACAAAT AAAAAA ATAAAT A-AAAT ATAAA- AT-AAT A-ATAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATA-AAT
* *
1033775 A-ATAAT AATAAAT A-AATT AT-AAT AT-AAT AATAAAT ATATAACT ATACAT
1 ATA-AAT -ATAAAT ATAAAT ATAAAT ATAAAT -ATAAAT ATA-AA-T ATAAAT
*
1033824 ATAAAT ATTAAT A
1 ATAAAT ATAAAT A
1033837 GAAAGAAAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
4 2 0.03
5 19 0.24
6 44 0.55
7 10 0.12
8 5 0.06
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (6 bp):
ATAAAT
Found at i:1034136 original size:21 final size:20
Alignment explanation
Indices: 1034110--1034166 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 20
1034100 AACATTTTCA
1034110 TTTTTTTGATTTTTTTTATA-
1 TTTTTTTG-TTTTTTTTATAT
1034130 TTTTTTTGTTTTTTTTATATT
1 TTTTTTTGTTTTTTTTATA-T
1034151 TTTTTTTGTTTTTTTT
1 TTTTTTTGTTTTTTTT
1034167 TTTAACTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.31
20 8 0.23
21 16 0.46
ACGTcount: A:0.09, C:0.00, G:0.05, T:0.86
Consensus pattern (20 bp):
TTTTTTTGTTTTTTTTATAT
Found at i:1034396 original size:42 final size:42
Alignment explanation
Indices: 1034177--1034459 Score: 376
Period size: 41 Copynumber: 6.8 Consensus size: 42
1034167 TTTAACTAAA
* * * *
1034177 GCTCATCTAAACAGAGGCTCAACAACTTTGAGAAACA-TAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAA-AGTAAATT
*
1034220 ACTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
** * *
1034261 GCTCCTCTAAACAGAGGCACCATAACTTTTG-AAGGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
* * *
1034302 GCTCCTCTAAACAGAGGTACCACAACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
* * * *
1034343 GCTCTTTTAAACAGAGGCATCATGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1034385 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1034427 GCTCCTCTAAACAGAGGCACCACGACTTTGGAA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAA
1034460 GAGGCACCAC
Statistics
Matches: 214, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
40 1 0.00
41 107 0.50
42 82 0.38
43 24 0.11
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.24
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
Found at i:1034464 original size:20 final size:20
Alignment explanation
Indices: 1034439--1034479 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1034429 TCCTCTAAAC
1034439 AGAGGCACCACGACTTTGGA
1 AGAGGCACCACGACTTTGGA
1034459 AGAGGCACCACGACTTTGGA
1 AGAGGCACCACGACTTTGGA
1034479 A
1 A
1034480 AAATAAATTG
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:0.32, C:0.24, G:0.29, T:0.15
Consensus pattern (20 bp):
AGAGGCACCACGACTTTGGA
Found at i:1034494 original size:62 final size:62
Alignment explanation
Indices: 1034397--1034521 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
1034387 TCCTCTAAAC
*
1034397 AGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
1 AGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
*
1034459 AGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGATTTTGGA
1 AGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
1034521 A
1 A
1034522 AGTAAATTGC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (62 bp):
AGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
Found at i:1034519 original size:42 final size:42
Alignment explanation
Indices: 1034459--1034577 Score: 188
Period size: 41 Copynumber: 2.9 Consensus size: 42
1034449 CGACTTTGGA
1034459 AGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAAC
1 AGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAAC
* *
1034501 AGAGGCACCACGATTTTGG-AAAGTAAATTGCTCCTCTAAAC
1 AGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAAC
*
1034542 AGAGGCACCACTACTTT-GAAAAAGTAAATTGCTCCT
1 AGAGGCACCACGACTTTGGAAAAA-TAAATTGCTCCT
1034578 TGACAATCAT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
40 1 0.01
41 39 0.56
42 30 0.43
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (42 bp):
AGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAAC
Found at i:1034577 original size:145 final size:145
Alignment explanation
Indices: 1034314--1034577 Score: 413
Period size: 145 Copynumber: 1.8 Consensus size: 145
1034304 TCCTCTAAAC
* * * * * * *
1034314 AGAGGTACCACAACTTTTGAAAGTAAATTGCTCTTTTAAACAGAGGCATCATGACTTTGGAAAAG
1 AGAGGCACCACAACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAG
*
1034379 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGG
66 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGG
1034444 CACCACGACTTTGGA
131 CACCACGACTTTGGA
* *
1034459 AGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGATTTTGG-AAA
1 AGAGGCACCACAACTTTGG-AAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAA
*
1034523 GTAAATTGCTCCTCTAAACAGAGGCACCACTACTTTGAAAAAGTAAATTGCTCCT
65 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCT
1034578 TGACAATCAT
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
145 72 0.67
146 35 0.33
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (145 bp):
AGAGGCACCACAACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAG
TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGG
CACCACGACTTTGGA
Found at i:1035797 original size:18 final size:18
Alignment explanation
Indices: 1035776--1035812 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1035766 CCAAAATCTC
1035776 TTTTTTTTCATTTTTTCA
1 TTTTTTTTCATTTTTTCA
**
1035794 TTTTTTTTTTTTTTTTCA
1 TTTTTTTTCATTTTTTCA
1035812 T
1 T
1035813 CATTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTTCATTTTTTCA
Found at i:1035798 original size:19 final size:18
Alignment explanation
Indices: 1035776--1035838 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 18
1035766 CCAAAATCTC
1035776 TTTTTTTTCATTTTTTCAT
1 TTTTTTTTC-TTTTTTCAT
*
1035795 TTTTTTTTTTTTTTTCAT
1 TTTTTTTTCTTTTTTCAT
1035813 CATTTTTTTTCTTTTTGCTCAT
1 --TTTTTTTTCTTTTT--TCAT
1035835 TTTT
1 TTTT
1035839 CATCCATTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.24
19 8 0.21
20 17 0.45
22 4 0.11
ACGTcount: A:0.08, C:0.11, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTCAT
Found at i:1035818 original size:18 final size:18
Alignment explanation
Indices: 1035786--1035838 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1035776 TTTTTTTTCA
**
1035786 TTTTTTCATTTTTTTTTT
1 TTTTTTCATCATTTTTTT
1035804 TTTTTTCATCATTTTTTT
1 TTTTTTCATCATTTTTTT
1035822 TCTTTTTGC-TCATTTTT
1 T-TTTTT-CATCATTTTT
1035839 CATCCATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 17 0.55
19 13 0.42
20 1 0.03
ACGTcount: A:0.08, C:0.11, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTCATCATTTTTTT
Found at i:1035834 original size:22 final size:21
Alignment explanation
Indices: 1035791--1035834 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1035781 TTTCATTTTT
**
1035791 TCATTTTTTTTTTTTTTTTCA
1 TCATTTTTTTTTTTTTGCTCA
1035812 TCATTTTTTTTCTTTTTGCTCA
1 TCATTTTTTTT-TTTTTGCTCA
1035834 T
1 T
1035835 TTTTCATCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.75
Consensus pattern (21 bp):
TCATTTTTTTTTTTTTGCTCA
Found at i:1039862 original size:59 final size:58
Alignment explanation
Indices: 1039680--1040193 Score: 724
Period size: 59 Copynumber: 8.8 Consensus size: 58
1039670 TTGTGTGGGA
*
1039680 AAAATTGATACTTTCAACTTTTTCCCTAAAAATATTTTTTGGAAATTT-ATTTT-AAGG
1 AAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTTGAAATTTGATTTTCAAGG
* * *
1039737 AAAATTGATACTTTCAACTTTTTCCC-AAAAATATTTTTTGGAAA-TTCATTTTTAAGG
1 AAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTTGAAATTTGATTTTCAAGG
1039794 AAAATTGATACTTTCAACTTTT-CCTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTGAAA-TTTGATTTTCAAGG
1039853 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTG-AAATTTGATTTTCAAGG
* *
1039912 AAAATTGATACTTTCAACTTTT-CCTCAAAAATATTTTTTTGAAACTTTGATTATCAAGA
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTGAAA-TTTGATTTTCAAGG
* *
1039971 AAAATTGATACTTTCAACTTTTCCCTAAAATTATTTTTTAGAAATTT-ATTCTT-AAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTGATT-TTCAAGG
* *
1040028 AAAATTGATACTTTCAACTTTTCTCTAAAAATATTTTTTAGAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAA-TTTGATTTTCAAGG
** *
1040087 AAAATTGATACTTTCAACTTTT-CCTCAAAAACCTCTTTTTTGAAATTT-ATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAATAT-TTTTTTGAAATTTGATTTTCAAGG
1040145 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTT-GAAATTT
1040194 TCGATTTTTA
Statistics
Matches: 419, Mismatches: 18, Indels: 38
0.88 0.04 0.08
Matches are distributed among these distances:
55 4 0.01
56 27 0.06
57 113 0.27
58 59 0.14
59 198 0.47
60 18 0.04
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTGATTTTCAAGG
Found at i:1040030 original size:175 final size:175
Alignment explanation
Indices: 1039680--1040183 Score: 772
Period size: 175 Copynumber: 2.9 Consensus size: 175
1039670 TTGTGTGGGA
*
1039680 AAAATTGATACTTTCAACTTTTTCCCTAAAAATA-TTTTTTGGAAATTT-ATTTT-AAGGAAAAT
1 AAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTTGAAAATTTGATTTTCAAGGAAAAT
* *
1039742 TGATACTTTCAACTTTTTCC-CAAAAATATTTTTTGGAAATTCATTTTTAAGGAAAATTGATACT
65 TGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTGAAATTTATTTTTAAGGAAAATTGATACT
*
1039806 TTCAACTTTT-CCTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGG
129 TTCAACTTTTCCCT-AAAAATATTTTTTAGAAACTTTGATTTTCAAGG
1039853 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTGATTTTCAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTGATTTTCAAGGAAAATT
* * *
1039918 GATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAACTTTGATTATCAAGAAAAATTGATACT
66 GATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAA-TTT-ATTTTTAAGGAAAATTGATACT
*
1039983 TTCAACTTTTCCCTAAAATTATTTTTTAGAAA-TTT-ATTCTT-AAGG
129 TTCAACTTTTCCCTAAAAATATTTTTTAGAAACTTTGATT-TTCAAGG
* * *
1040028 AAAATTGATACTTTCAACTTTTCTCTAAAAATATTTTTTAGAAATTTTGATTTTCAAGGAAAATT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTGATTTTCAAGGAAAATT
**
1040093 GATACTTTCAACTTTTCCTCAAAAACCTCTTTTTTGAAATTTATTTTTAAGGAAAATTGATACTT
66 GATACTTTCAACTTTTCCTCAAAAATAT-TTTTTTGAAATTTATTTTTAAGGAAAATTGATACTT
1040158 TCAACTTTTCCCTAAAAATATTTTTT
130 TCAACTTTTCCCTAAAAATATTTTTT
1040184 TTGGAAATTT
Statistics
Matches: 305, Mismatches: 17, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
172 15 0.05
173 31 0.10
174 56 0.18
175 138 0.45
176 17 0.06
177 45 0.15
178 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.45
Consensus pattern (175 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTGATTTTCAAGGAAAATT
GATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAATTTATTTTTAAGGAAAATTGATACTTT
CAACTTTTCCCTAAAAATATTTTTTAGAAACTTTGATTTTCAAGG
Found at i:1040087 original size:234 final size:230
Alignment explanation
Indices: 1039680--1040193 Score: 777
Period size: 234 Copynumber: 2.2 Consensus size: 230
1039670 TTGTGTGGGA
* * *
1039680 AAAATTGATACTTTCAACTTTTTCCCTAAAAATATTTTTTGGAAATTTATTTTAAGGAAAATTGA
1 AAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTTGAAATTTATTTCAAGAAAAATTGA
* *
1039745 TACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAATTCATTTTTAAGGAAAATTGATACTTTCA
65 TACTTTCAACTTTTTCCCAAAAATATTTTTTAGAAATTCATTCTTAAGGAAAATTGATACTTTCA
*
1039810 ACTTTTCCTCAAAAATATTTTTTTGAAACTTTGATTTTCAAGGAAAATTGATACTTTCAACTTTT
130 ACTTTTCCTCAAAAATATTTTTTAGAAACTTTGATTTTCAAGGAAAATTGATACTTTCAACTTTT
*
1039875 CC-CTAAAAATAT-TTTTTTGAAAATTTGATTTTCAAGG
195 CCTC-AAAAACATCTTTTTTG-AAATTT-ATTTTCAAGG
1039912 AAAATTGATACTTTCAACTTTT-CCTCAAAAATATTTTTTTGAAACTTTGATTATCAAGAAAAAT
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTGAAA-TTT-ATT-TCAAGAAAAAT
* *
1039976 TGATACTTTCAAC-TTTTCCCTAAAATTATTTTTTAGAAATTTATTCTTAAGGAAAATTGATACT
62 TGATACTTTCAACTTTTTCCC-AAAAATATTTTTTAGAAATTCATTCTTAAGGAAAATTGATACT
*
1040040 TTCAACTTTT-CTCTAAAAATATTTTTTAGAAATTTTGATTTTCAAGGAAAATTGATACTTTCAA
126 TTCAACTTTTCCTC-AAAAATATTTTTTAGAAACTTTGATTTTCAAGGAAAATTGATACTTTCAA
* *
1040104 CTTTTCCTCAAAAACCTCTTTTTTGAAATTTATTTTTAAGG
190 CTTTTCCTCAAAAACATCTTTTTTGAAATTTATTTTCAAGG
1040145 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTT-GAAATTT
1040194 TCGATTTTTA
Statistics
Matches: 259, Mismatches: 12, Indels: 20
0.89 0.04 0.07
Matches are distributed among these distances:
230 3 0.01
231 21 0.08
232 21 0.08
233 51 0.20
234 151 0.58
235 12 0.05
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (230 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTATTTCAAGAAAAATTGAT
ACTTTCAACTTTTTCCCAAAAATATTTTTTAGAAATTCATTCTTAAGGAAAATTGATACTTTCAA
CTTTTCCTCAAAAATATTTTTTAGAAACTTTGATTTTCAAGGAAAATTGATACTTTCAACTTTTC
CTCAAAAACATCTTTTTTGAAATTTATTTTCAAGG
Found at i:1040245 original size:27 final size:27
Alignment explanation
Indices: 1040211--1040281 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
1040201 TTATTTAAAG
*
1040211 AAAATAGAATAATAAAAAAAAT-AAATA
1 AAAATAGAA-AATAAAAAAAATAAAACA
*
1040238 AAAATAGAAAAATAAAGAAAAGTAAAACA
1 AAAATAG-AAAATAAA-AAAAATAAAACA
1040267 AAAATA-AAAATAAAA
1 AAAATAGAAAATAAAA
1040282 TTAAGATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 1 0.03
27 21 0.54
28 7 0.18
29 10 0.26
ACGTcount: A:0.79, C:0.01, G:0.06, T:0.14
Consensus pattern (27 bp):
AAAATAGAAAATAAAAAAAATAAAACA
Found at i:1040250 original size:18 final size:17
Alignment explanation
Indices: 1040211--1040281 Score: 74
Period size: 17 Copynumber: 4.1 Consensus size: 17
1040201 TTATTTAAAG
*
1040211 AAAATAGAATAATAA-AA
1 AAAATA-AATAAAAATAA
1040228 AAAATAAATAAAAATAGA
1 AAAATAAATAAAAATA-A
* *
1040246 AAAATAAAGAAAAGTAA
1 AAAATAAATAAAAATAA
1040263 AACAA-AAATAAAAATAA
1 AA-AATAAATAAAAATAA
1040280 AA
1 AA
1040282 TTAAGATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
16 7 0.15
17 22 0.48
18 17 0.37
ACGTcount: A:0.79, C:0.01, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAATAAATAAAAATAA
Found at i:1040290 original size:17 final size:16
Alignment explanation
Indices: 1040207--1040307 Score: 55
Period size: 17 Copynumber: 6.1 Consensus size: 16
1040197 ATTTTTATTT
1040207 AAAGAAAA-TAGAATAA
1 AAAGAAAATTA-AATAA
*
1040223 TAAA-AAAAATAAATAAA
1 -AAAGAAAATTAAAT-AA
* *
1040240 AATAGAAAAATAAA-GA
1 AA-AGAAAATTAAATAA
**
1040256 AAAGTAAAACAAAAATAA
1 AAAG-AAAA-TTAAATAA
*
1040274 AAATAAAATTAAGATAA
1 AAAGAAAATTAA-ATAA
*
1040291 AAAGAATATTAAATAA
1 AAAGAAAATTAAATAA
1040307 A
1 A
1040308 CCTAATCTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
15 2 0.03
16 23 0.34
17 30 0.44
18 13 0.19
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (16 bp):
AAAGAAAATTAAATAA
Found at i:1041332 original size:11 final size:12
Alignment explanation
Indices: 1041234--1041348 Score: 61
Period size: 10 Copynumber: 9.8 Consensus size: 12
1041224 ATATTATAGG
1041234 ATAAATA-AATA
1 ATAAATATAATA
1041245 A-AAATAATAATAA
1 ATAAAT-ATAAT-A
*
1041258 CATATATATAATTA
1 -ATAAATATAA-TA
*
1041272 GATAAATACAAATA
1 -ATAAATA-TAATA
1041286 CA-AAA-ATAA-A
1 -ATAAATATAATA
1041296 A-AAATATAA-A
1 ATAAATATAATA
1041306 AT-AATAATAATA
1 ATAAAT-ATAATA
*
1041318 ATAAATA-AATT
1 ATAAATATAATA
1041329 AT-AATATAATA
1 ATAAATATAATA
1041340 ATAAATATA
1 ATAAATATA
1041349 TAACTATACA
Statistics
Matches: 82, Mismatches: 8, Indels: 27
0.70 0.07 0.23
Matches are distributed among these distances:
9 4 0.05
10 18 0.22
11 18 0.22
12 14 0.17
13 7 0.09
14 15 0.18
15 6 0.07
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.29
Consensus pattern (12 bp):
ATAAATATAATA
Done.