Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009625.1 Hibiscus syriacus cultivar Beakdansim tig00117017_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: 6938204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 25
Found at i:2663356 original size:24 final size:24
Alignment explanation
Indices: 2663326--2663417 Score: 107
Period size: 24 Copynumber: 3.8 Consensus size: 24
2663316 GCTTTGCCTG
*
2663326 AAGAAAAAAAAAAGAAAAAAAGAG
1 AAGAAAAAAAAAAGAAAAAAAGAA
2663350 AAGAAAAAGAAAAAG-AAAAAAGAA
1 AAGAAAAA-AAAAAGAAAAAAAGAA
*
2663374 AAGAAAAAAGAAAA-AAAGAAAATAA
1 AAGAAAAAA-AAAAGAAA-AAAAGAA
*
2663399 AAGAAAAAAATAAATAAAA
1 AAGAAAAAAA-AAAGAAAA
2663418 TGAGGGTTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.02
24 31 0.52
25 25 0.42
26 3 0.05
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (24 bp):
AAGAAAAAAAAAAGAAAAAAAGAA
Found at i:2663363 original size:25 final size:25
Alignment explanation
Indices: 2663326--2663406 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 25
2663316 GCTTTGCCTG
*
2663326 AAGAAAAA-AAAAAGAAAAAAAGAG
1 AAGAAAAAGAAAAAGAAAAAAAGAA
2663350 AAGAAAAAGAAAAAG-AAAAAAGAA
1 AAGAAAAAGAAAAAGAAAAAAAGAA
* *
2663374 AAGAAAAAAGAAAAA-AAGAAAATAA
1 AAG-AAAAAGAAAAAGAAAAAAAGAA
2663399 AAGAAAAA
1 AAGAAAAA
2663407 AATAAATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
24 24 0.47
25 27 0.53
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (25 bp):
AAGAAAAAGAAAAAGAAAAAAAGAA
Found at i:2664853 original size:2 final size:2
Alignment explanation
Indices: 2664848--2664872 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2664838 TATATAAATA
2664848 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2664873 CGATTAGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2666746 original size:17 final size:17
Alignment explanation
Indices: 2666724--2666767 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
2666714 CAAGTGAAAC
2666724 CCTAAAATTTTACCGCA
1 CCTAAAATTTTACCGCA
2666741 CCTAAAATTTTACCGCA
1 CCTAAAATTTTACCGCA
2666758 CCTAAAATTT
1 CCTAAAATTT
2666768 GGGAACACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (17 bp):
CCTAAAATTTTACCGCA
Found at i:2669243 original size:31 final size:31
Alignment explanation
Indices: 2669208--2669306 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
2669198 CTTAAGGTGG
*
2669208 CCCTTGGGTAGGCTCTTAGGCCCAAGGTATT
1 CCCTTGGGTAGGCTCTAAGGCCCAAGGTATT
* *
2669239 CCCTTGGGTAGGCTGTAAGGCCCCGAGGTATT
1 CCCTTGGGTAGGCTCTAAGG-CCCAAGGTATT
** * *
2669271 -CCTTAAGTAGGCTCTAAGGCCTTAAGGTATC
1 CCCTTGGGTAGGCTCTAAGGCC-CAAGGTATT
2669302 CCCTT
1 CCCTT
2669307 AGGTTGACTC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
30 2 0.04
31 40 0.71
32 14 0.25
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.28
Consensus pattern (31 bp):
CCCTTGGGTAGGCTCTAAGGCCCAAGGTATT
Found at i:2676763 original size:32 final size:32
Alignment explanation
Indices: 2676695--2676788 Score: 91
Period size: 32 Copynumber: 3.0 Consensus size: 32
2676685 GGCCGTTAGG
* ** * * *
2676695 TAGGATCTTAGGCCCCAAGATGCTCCTTTAGA
1 TAGGCTCTTAGGCCCCAAGATATTCCCTTGGT
*
2676727 TAGGCTCTTAGGCCCCAAGGTATTCCCTTGGT
1 TAGGCTCTTAGGCCCCAAGATATTCCCTTGGT
* * *
2676759 TAGGCTCTAAGGCCCCGAGACATT-CCTTGG
1 TAGGCTCTTAGGCCCCAAGATATTCCCTTGG
2676789 GTATTCTATA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 6 0.12
32 45 0.88
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (32 bp):
TAGGCTCTTAGGCCCCAAGATATTCCCTTGGT
Found at i:2679744 original size:36 final size:36
Alignment explanation
Indices: 2679704--2679796 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 36
2679694 CTCCATGAGG
*
2679704 CAATCACAGGGCACTGAATGTGCCGTATCTAGGGTA
1 CAATCACAGGGCACTGAATGTGCCGTACCTAGGGTA
* * * *
2679740 CAATCATAGGGTACTGAATGTGTCGTACCTATGGTA
1 CAATCACAGGGCACTGAATGTGCCGTACCTAGGGTA
* *
2679776 CAATCACAGGACACTAAATGT
1 CAATCACAGGGCACTGAATGT
2679797 CCAATACAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (36 bp):
CAATCACAGGGCACTGAATGTGCCGTACCTAGGGTA
Found at i:2680068 original size:17 final size:17
Alignment explanation
Indices: 2680027--2680071 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2680017 ATATAACAAT
*
2680027 ATAGTAAAAGATATAGT
1 ATAGTAAAAGATATAGA
* *
2680044 ACAATAAAAGATATAGA
1 ATAGTAAAAGATATAGA
2680061 ATAGTAAAAGA
1 ATAGTAAAAGA
2680072 ATTAGTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.60, C:0.02, G:0.16, T:0.22
Consensus pattern (17 bp):
ATAGTAAAAGATATAGA
Found at i:2681653 original size:17 final size:17
Alignment explanation
Indices: 2681608--2681710 Score: 86
Period size: 18 Copynumber: 5.9 Consensus size: 17
2681598 AAGTATGATA
* *
2681608 TTTACAGTTATCATATG
1 TTTATAGTTATCAAATG
2681625 ATTT-TCAGTTAT-AAGATG
1 -TTTAT-AGTTATCAA-ATG
2681643 TTTATAGTTATCAAATG
1 TTTATAGTTATCAAATG
* *
2681660 ATTT-TCAGTTATGAGATG
1 -TTTAT-AGTTATCAAATG
*
2681678 TTTATAGTTATCAAATA
1 TTTATAGTTATCAAATG
2681695 TTCTATAGTTATCAAA
1 TT-TATAGTTATCAAA
2681711 CTTTGATTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
17 28 0.40
18 42 0.60
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.46
Consensus pattern (17 bp):
TTTATAGTTATCAAATG
Found at i:2681670 original size:53 final size:55
Alignment explanation
Indices: 2681602--2681710 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 55
2681592 CTGCCCAAGT
* *
2681602 ATGATATTTACAGTTATCATATGATTT-TCAGTTAT-AAGATGTT-TATAGTTATCAA
1 ATGATATTTACAGTTATCAGATG-TTTAT-AGTTATCAA-ATATTCTATAGTTATCAA
*
2681657 ATGAT-TTT-CAGTTATGAGATGTTTATAGTTATCAAATATTCTATAGTTATCAA
1 ATGATATTTACAGTTATCAGATGTTTATAGTTATCAAATATTCTATAGTTATCAA
2681710 A
1 A
2681711 CTTTGATTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
52 13 0.27
53 27 0.56
54 3 0.06
55 5 0.10
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (55 bp):
ATGATATTTACAGTTATCAGATGTTTATAGTTATCAAATATTCTATAGTTATCAA
Found at i:2681706 original size:35 final size:35
Alignment explanation
Indices: 2681608--2681693 Score: 145
Period size: 35 Copynumber: 2.5 Consensus size: 35
2681598 AAGTATGATA
* *
2681608 TTTACAGTTATCATATGATTTTCAGTTATAAGATG
1 TTTATAGTTATCAAATGATTTTCAGTTATAAGATG
*
2681643 TTTATAGTTATCAAATGATTTTCAGTTATGAGATG
1 TTTATAGTTATCAAATGATTTTCAGTTATAAGATG
2681678 TTTATAGTTATCAAAT
1 TTTATAGTTATCAAAT
2681694 ATTCTATAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (35 bp):
TTTATAGTTATCAAATGATTTTCAGTTATAAGATG
Found at i:2683330 original size:15 final size:15
Alignment explanation
Indices: 2683310--2683346 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
2683300 GTTTTGTATT
2683310 AAAAGTTATAAAGCG
1 AAAAGTTATAAAGCG
2683325 AAAAGTTATAAAGCG
1 AAAAGTTATAAAGCG
2683340 AAAAGTT
1 AAAAGTT
2683347 TGAGAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.22
Consensus pattern (15 bp):
AAAAGTTATAAAGCG
Found at i:2687774 original size:30 final size:31
Alignment explanation
Indices: 2687740--2687798 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2687730 GAAAATTTTG
* * *
2687740 GGGACC-ATTTTGTAATTTTTGAAAAGTTAC
1 GGGACCAATTTGGTAACTTTGGAAAAGTTAC
2687770 GGGACCAATTTGGTAACTTTGGAAAAGTT
1 GGGACCAATTTGGTAACTTTGGAAAAGTT
2687799 GTTAATGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.36
Consensus pattern (31 bp):
GGGACCAATTTGGTAACTTTGGAAAAGTTAC
Found at i:2688978 original size:45 final size:45
Alignment explanation
Indices: 2688889--2689159 Score: 472
Period size: 45 Copynumber: 6.0 Consensus size: 45
2688879 GTAAGTATGC
*
2688889 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
2688933 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
2688978 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
2689023 AAATAAGCTTAGGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
2689068 AAATAAGCTTACGGGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
2689113 AAATAAGCTTACGATCTTATGGGATTAAATGGTTAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
2689159 A
1 A
2689160 GAAATGTTAT
Statistics
Matches: 217, Mismatches: 8, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
44 25 0.12
45 168 0.77
46 24 0.11
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:2691981 original size:16 final size:16
Alignment explanation
Indices: 2691962--2692015 Score: 83
Period size: 17 Copynumber: 3.4 Consensus size: 16
2691952 TCTAAAAAAT
2691962 AGAAAACAAAAAAAGA
1 AGAAAACAAAAAAAGA
2691978 AGAAAACAAAAAAAAGA
1 AGAAAAC-AAAAAAAGA
*
2691995 AGAAAA-ATAAAAAGA
1 AGAAAACAAAAAAAGA
2692010 AGAAAA
1 AGAAAA
2692016 GGAAGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
15 14 0.39
16 7 0.19
17 15 0.42
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (16 bp):
AGAAAACAAAAAAAGA
Found at i:2691989 original size:17 final size:17
Alignment explanation
Indices: 2691962--2692015 Score: 78
Period size: 16 Copynumber: 3.4 Consensus size: 17
2691952 TCTAAAAAAT
2691962 AGAAAAC-AAAAAAAGA
1 AGAAAACAAAAAAAAGA
2691978 AGAAAACAAAAAAAAGA
1 AGAAAACAAAAAAAAGA
*
2691995 AG-AAA-AATAAAAAGA
1 AGAAAACAAAAAAAAGA
2692010 AGAAAA
1 AGAAAA
2692016 GGAAGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
15 11 0.31
16 13 0.37
17 11 0.31
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (17 bp):
AGAAAACAAAAAAAAGA
Found at i:2691992 original size:18 final size:17
Alignment explanation
Indices: 2691969--2692079 Score: 64
Period size: 17 Copynumber: 5.9 Consensus size: 17
2691959 AATAGAAAAC
*
2691969 AAAAAAAGAAGAAAACA
1 AAAAAAAGAAGAAAATA
2691986 AAAAAAAGAAGAAAAATAAAA
1 AAAAAAAGAAG-AAAAT---A
2692007 AGAAGAAAAGGAAGAAAA-A
1 A-AA-AAAA-GAAGAAAATA
2692026 AAATAGAAAGAAGAAAAATA
1 AAA-A-AAAGAAG-AAAATA
* *
2692046 CAAAGAAA-AAGAAGATAA
1 -AAAAAAAGAAGAAAAT-A
*
2692064 AAAAAAAGAAAAAAAT
1 AAAAAAAGAAGAAAAT
2692080 GAGAGATGCT
Statistics
Matches: 74, Mismatches: 7, Indels: 25
0.70 0.07 0.24
Matches are distributed among these distances:
17 21 0.28
18 21 0.28
19 12 0.16
20 1 0.01
21 5 0.07
22 2 0.03
23 8 0.11
24 4 0.05
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAAAAGAAGAAAATA
Found at i:2692006 original size:15 final size:15
Alignment explanation
Indices: 2691971--2692076 Score: 74
Period size: 15 Copynumber: 6.9 Consensus size: 15
2691961 TAGAAAACAA
*
2691971 AAAAAGAAGAAAACAAA
1 AAAAAGAAG-AAA-AAT
2691988 AAAAAGAAGAAAAAT
1 AAAAAGAAGAAAAAT
2692003 AAAAAGAAG--AAA-
1 AAAAAGAAGAAAAAT
** *
2692015 AGGAAGAAAAAAAAT
1 AAAAAGAAGAAAAAT
*
2692030 AGAAAGAAGAAAAAT
1 AAAAAGAAGAAAAAT
* *
2692045 ACAAAGAAAAAGAAGAT
1 AAAAAGAAGAA-AA-AT
*
2692062 AAAAAAAAAGAAAAA
1 -AAAAAGAAGAAAAA
2692077 AATGAGAGAT
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
12 6 0.08
13 3 0.04
14 3 0.04
15 33 0.46
16 6 0.08
17 13 0.18
18 8 0.11
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (15 bp):
AAAAAGAAGAAAAAT
Found at i:2692007 original size:24 final size:24
Alignment explanation
Indices: 2691980--2692025 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2691970 AAAAAAGAAG
2691980 AAAACAAAAAAAAGAAGAAAAATA
1 AAAACAAAAAAAAGAAGAAAAATA
* * *
2692004 AAAAGAAGAAAAGGAAGAAAAA
1 AAAACAAAAAAAAGAAGAAAAA
2692026 AAATAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (24 bp):
AAAACAAAAAAAAGAAGAAAAATA
Found at i:2692015 original size:27 final size:27
Alignment explanation
Indices: 2691985--2692078 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 27
2691975 AGAAGAAAAC
*
2691985 AAAAAAAAGAAGAAAAATAAAAAGAAG
1 AAAAAAAAGAAAAAAAATAAAAAGAAG
** *
2692012 AAAAGGAAGAAAAAAAATAGAAAGAAG
1 AAAAAAAAGAAAAAAAATAAAAAGAAG
*
2692039 AAAAATACAAAGAAAAAGAAGATAAAAAAAAAG
1 -AAAA-A-AAAGAAAAA-AA-AT-AAAAAGAAG
2692072 AAAAAAA
1 AAAAAAA
2692079 TGAGAGATGC
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
27 23 0.43
28 4 0.08
30 10 0.19
31 3 0.06
32 6 0.11
33 7 0.13
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.04
Consensus pattern (27 bp):
AAAAAAAAGAAAAAAAATAAAAAGAAG
Found at i:2692024 original size:17 final size:14
Alignment explanation
Indices: 2691955--2692015 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
2691945 CATAAGATCT
*
2691955 AAAAAATAGAA-AA
1 AAAAAAAAGAAGAA
*
2691968 CAAAAAAAGAAGAAAA
1 AAAAAAAAGAAG--AA
2691984 CAAAAAAAAGAAGAA
1 -AAAAAAAAGAAGAA
2691999 AAATAAAAAGAAGAA
1 AAA-AAAAAGAAGAA
2692014 AA
1 AA
2692016 GGAAGAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 9 0.22
14 3 0.08
15 15 0.38
16 2 0.05
17 11 0.28
ACGTcount: A:0.82, C:0.03, G:0.11, T:0.03
Consensus pattern (14 bp):
AAAAAAAAGAAGAA
Found at i:2692036 original size:24 final size:24
Alignment explanation
Indices: 2691988--2692065 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
2691978 AGAAAACAAA
2691988 AAAAAGAAGAAAAATAAAAAGAAG
1 AAAAAGAAGAAAAATAAAAAGAAG
* *
2692012 AAAAGGAAGAAAAA-AAATAGAAAG
1 AAAAAGAAGAAAAATAAAAAG-AAG
* * *
2692036 AAGAAA-AATACAAAGAAAAAGAAG
1 AA-AAAGAAGAAAAATAAAAAGAAG
2692060 ATAAAA
1 A-AAAA
2692066 AAAAAGAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 5 0.11
24 31 0.70
25 8 0.18
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.05
Consensus pattern (24 bp):
AAAAAGAAGAAAAATAAAAAGAAG
Found at i:2692037 original size:42 final size:39
Alignment explanation
Indices: 2691956--2692074 Score: 134
Period size: 41 Copynumber: 2.9 Consensus size: 39
2691946 ATAAGATCTA
*
2691956 AAAAATAGAAAACAAAAAAAGAAGAAAACAAAAA-AAAGAAG
1 AAAAATA-AAAA-GAAAAAAGAAGAAAA-AAAAAGAAAGAAG
2691997 AAAAATAAAAAGAAGAAAAGGAAGAAAAAAAATAGAAAGAAG
1 AAAAATAAAAAGAA-AAAA-GAAGAAAAAAAA-AGAAAGAAG
*
2692039 AAAAATACAAAG-AAAAAGAAGATAAAAAAAAAGAAA
1 AAAAATAAAAAGAAAAAAGAAG--AAAAAAAAAGAAA
2692075 AAAATGAGAG
Statistics
Matches: 70, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
39 6 0.09
40 21 0.30
41 25 0.36
42 18 0.26
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.04
Consensus pattern (39 bp):
AAAAATAAAAAGAAAAAAGAAGAAAAAAAAAGAAAGAAG
Found at i:2695947 original size:61 final size:61
Alignment explanation
Indices: 2695859--2695973 Score: 176
Period size: 61 Copynumber: 1.9 Consensus size: 61
2695849 AAAGGTGGAT
* *
2695859 ACGACCTTATGTATCATGTCCAGATTAGCACTATAGCATCAGCTTAGTGTAGGTGGTGGGC
1 ACGACCTTATGTATCATATCCAGATTAGCACTATAGCATAAGCTTAGTGTAGGTGGTGGGC
* * * *
2695920 ACGACCTTATGTGTCATATCTAGATTAGCACTATGGCGTAAGCTTAGTGTAGGT
1 ACGACCTTATGTATCATATCCAGATTAGCACTATAGCATAAGCTTAGTGTAGGT
2695974 TTAGCACTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (61 bp):
ACGACCTTATGTATCATATCCAGATTAGCACTATAGCATAAGCTTAGTGTAGGTGGTGGGC
Found at i:2696172 original size:45 final size:45
Alignment explanation
Indices: 2696083--2696488 Score: 636
Period size: 45 Copynumber: 9.0 Consensus size: 45
2696073 GTAAGTATGC
* *
2696083 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATAATGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
2696127 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
**
2696172 AAATAAGCTTACGAGCTTATAAAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * * *
2696217 AAATAAGCTTATGGGCTTATGGAATAAATGATTAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
2696262 AAATAAGCTTACCAACTTATGGAATAAATGGTTAGTAT-TATGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT-TGGTA
*
2696307 AAATAAGCTTACGAGCTTATGGAATAAATGGTTAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
2696352 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
2696397 AAATAAGCTTACGGGCTTATGGAATAAATGGTAAGTGTATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
2696442 AAATAAGCTTACGAGCTTATAGGATTAAATGGTTAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
2696488 A
1 A
2696489 GAAATGTTAT
Statistics
Matches: 334, Mismatches: 24, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
44 26 0.08
45 284 0.85
46 24 0.07
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:2696176 original size:24 final size:24
Alignment explanation
Indices: 2696149--2696222 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
2696139 GAGCTTATGG
2696149 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
* * ** *
2696173 AAT-AA-GCTTACG-AGCTT-ATAA
1 AATAAATG-GTAAGTATATTGGTAA
2696194 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
2696218 AATAA
1 AATAA
2696223 GCTTATGGGC
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
21 6 0.17
22 9 0.26
23 9 0.26
24 11 0.31
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (24 bp):
AATAAATGGTAAGTATATTGGTAA
Found at i:2696302 original size:21 final size:21
Alignment explanation
Indices: 2696278--2696344 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 21
2696268 GCTTACCAAC
2696278 TTATGGAATAAATGGTTAGTA
1 TTATGGAATAAATGGTTAGTA
* *
2696299 TTATGGTAA-AATAAGCTTACG-A
1 TTATGG-AATAA-ATGGTTA-GTA
2696321 GCTTATGGAATAAATGGTTAGTA
1 --TTATGGAATAAATGGTTAGTA
2696344 T
1 T
2696345 ATTGGTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
21 9 0.26
22 9 0.26
23 9 0.26
24 8 0.23
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.36
Consensus pattern (21 bp):
TTATGGAATAAATGGTTAGTA
Found at i:2696326 original size:24 final size:24
Alignment explanation
Indices: 2696299--2696373 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
2696289 ATGGTTAGTA
2696299 TTATGGTAAAATAAGCTTACGAGC
1 TTATGGTAAAATAAGCTTACGAGC
* *
2696323 TTATGG-AATAA-ATGGTT---AG-
1 TTATGGTAA-AATAAGCTTACGAGC
2696342 TATATTGGTAAAATAAGCTTACGAGC
1 T-TA-TGGTAAAATAAGCTTACGAGC
2696368 TTATGG
1 TTATGG
2696374 AATAAATGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 18
0.63 0.07 0.30
Matches are distributed among these distances:
19 1 0.03
20 4 0.11
21 5 0.13
22 6 0.16
23 6 0.16
24 11 0.29
25 4 0.11
26 1 0.03
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (24 bp):
TTATGGTAAAATAAGCTTACGAGC
Found at i:2700885 original size:17 final size:18
Alignment explanation
Indices: 2700840--2700886 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
2700830 CAAGTATGAT
* *
2700840 ATTTATAATTATAAGATG
1 ATTTACAATTATAAAATG
*
2700858 ATTTTCAATTATAAAATG
1 ATTTACAATTATAAAATG
2700876 -TTTACAATTAT
1 ATTTACAATTAT
2700887 CAGATATAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (18 bp):
ATTTACAATTATAAAATG
Found at i:2702853 original size:14 final size:14
Alignment explanation
Indices: 2702817--2702855 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2702807 CAATGCATGC
2702817 AAACATAAACAAAA
1 AAACATAAACAAAA
*
2702831 AAA-ATTAAAGAAAA
1 AAACA-TAAACAAAA
2702845 AAACATAAACA
1 AAACATAAACA
2702856 TGAGATGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 1 0.05
14 19 0.90
15 1 0.05
ACGTcount: A:0.77, C:0.10, G:0.03, T:0.10
Consensus pattern (14 bp):
AAACATAAACAAAA
Found at i:2709072 original size:31 final size:31
Alignment explanation
Indices: 2708988--2709101 Score: 106
Period size: 31 Copynumber: 3.7 Consensus size: 31
2708978 TCCGAGGCCC
* * *
2708988 CAAGATCATTCTTGGGTAGGCCATGCGACCCT
1 CAAGATCATTATTGGGTAGGCCCTGC-AGCCT
* * *
2709020 -GAGACCATTCTTGGGTAGGCCCTGCAGCCT
1 CAAGATCATTATTGGGTAGGCCCTGCAGCCT
* *
2709050 CAAGATCATTATTGGGTAGGCCC-GTAGCCC
1 CAAGATCATTATTGGGTAGGCCCTGCAGCCT
* *
2709080 CAAGTAACTTTATTGGGTAGGC
1 CAAG-ATCATTATTGGGTAGGC
2709102 TCTCAGGCCC
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
30 13 0.19
31 56 0.81
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (31 bp):
CAAGATCATTATTGGGTAGGCCCTGCAGCCT
Found at i:2715293 original size:45 final size:45
Alignment explanation
Indices: 2715184--2715457 Score: 394
Period size: 44 Copynumber: 6.2 Consensus size: 45
2715174 ATCAATAAAT
* * *
2715184 TTACCATTTATCCCATAAGCTCGTAAACTTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* * *
2715229 TT-CCATTTATTCCATAAGCTCATAAGCCTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
2715273 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
2715318 TTACCATTTATTCCATAAGCTCGTAAGCGTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
2715363 TTACCA-TTATTCCATAAGCTCGCAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
** * ** *
2715407 TTGTCA-TTATTCTATAAGCTAATCAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
2715451 TT-CCATT
1 TTACCATT
2715458 AACCTCATTT
Statistics
Matches: 209, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
43 2 0.01
44 116 0.56
45 91 0.44
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:2715373 original size:89 final size:89
Alignment explanation
Indices: 2715184--2715457 Score: 401
Period size: 89 Copynumber: 3.1 Consensus size: 89
2715174 ATCAATAAAT
* * *
2715184 TTACCATTTATCCCATAAGCTCGTAAACTTATTTTACCAACATACTTCCATTTATTCCATAAGCT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTCCATTTATTCCATAAGCT
*
2715249 CATAAGCCTATTTTACCAACATAC
66 CATAAGCCTATTTTACCAATATAC
2715273 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAAGC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTT-CCATTTATTCCATAAGC
* *
2715338 TCGTAAGCGTATTTTACCAATATAC
65 TCATAAGCCTATTTTACCAATATAC
* * *
2715363 TTACCA-TTATTCCATAAGCTCGCAAGCTTATTTTACCAATATACTTGTCA-TTATTCTATAAGC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTT-CCATTTATTCCATAAGC
* * *
2715426 TAATCAGCTTATTTTACCAATATAC
65 TCATAAGCCTATTTTACCAATATAC
2715451 TT-CCATT
1 TTACCATT
2715458 AACCTCATTT
Statistics
Matches: 169, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
87 3 0.02
88 36 0.21
89 85 0.50
90 45 0.27
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (89 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTCCATTTATTCCATAAGCT
CATAAGCCTATTTTACCAATATAC
Found at i:2715475 original size:44 final size:44
Alignment explanation
Indices: 2715211--2715462 Score: 167
Period size: 45 Copynumber: 5.7 Consensus size: 44
2715201 AGCTCGTAAA
* * * *
2715211 CTTATTTTACCAACATACTT-CCATTTATTCC-ATAAGCTCATAAG
1 CTTATTTTACCAATATACTTGCCA-TTA-ACCTATAAGCTAATCAG
* * * * ** *
2715255 CCTATTTTACCAACATACTTACCATTTATTCC-ATAAGCTCGTAAG
1 CTTATTTTACCAATATACTTGCCA-TTA-ACCTATAAGCTAATCAG
* * ** *
2715300 CTTATTTTACCAATATACTTACCATTTATTCC-ATAAGCTCGTAAG
1 CTTATTTTACCAATATACTTGCCA-TTA-ACCTATAAGCTAATCAG
* * * **
2715345 CGTATTTTACCAATATACTTACCATTATTCC-ATAAGCT-CGCAAG
1 CTTATTTTACCAATATACTTGCCATTA-ACCTATAAGCTAATC-AG
* **
2715389 CTTATTTTACCAATATACTTGTCATTATTCTATAAGCTAATCAG
1 CTTATTTTACCAATATACTTGCCATTAACCTATAAGCTAATCAG
2715433 CTTATTTTACCAATATACTT-CCATTAACCT
1 CTTATTTTACCAATATACTTGCCATTAACCT
2715463 CATTTATCAA
Statistics
Matches: 187, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
43 9 0.05
44 88 0.47
45 90 0.48
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (44 bp):
CTTATTTTACCAATATACTTGCCATTAACCTATAAGCTAATCAG
Found at i:2715654 original size:59 final size:59
Alignment explanation
Indices: 2715591--2715702 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
2715581 CTTCCCCTTT
*
2715591 CATTTTAGCACACGAAGTGCCCTAT-TCAAAAATACATACCATTAGTATAATTTTGTTAC
1 CATTTTAGCACACGAAATGCCCTATGT-AAAAATACATACCATTAGTATAATTTTGTTAC
** * * *
2715650 CATTTTAGCACTTGAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTT
1 CATTTTAGCACACGAAATGCCCTATGTAAAAATACATACCATTAGTATAATTT
2715703 CCTTATCTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.35
Consensus pattern (59 bp):
CATTTTAGCACACGAAATGCCCTATGTAAAAATACATACCATTAGTATAATTTTGTTAC
Found at i:2715777 original size:59 final size:59
Alignment explanation
Indices: 2715646--2716361 Score: 525
Period size: 59 Copynumber: 12.3 Consensus size: 59
2715636 TATAATTTTG
* * * * * *
2715646 TTACCATTTTAGCAC-TTGAAATGCCCTATGTGAAAATCCATAC-CATTAGTATGATTTCC
1 TTACCATTTTAGCACACT-AAGTGCTCTATCTGGAAATCCATACAC-TCAGTATGATTTCC
* * * * * *
2715705 TTATC-TTTGTAGCACCCTTAGTACTTTATCTGGAAATCCATACACTCAGTATGATTCCC
1 TTACCATTT-TAGCACACTAAGTGCTCTATCTGGAAATCCATACACTCAGTATGATTTCC
* * *** *
2715764 TTACCATTTTAGCA-AATAAAATGC-CTTATCTGGAAATCCATATTTTCAATATGATTTCC
1 TTACCATTTTAGCACACT-AAGTGCTC-TATCTGGAAATCCATACACTCAGTATGATTTCC
* * * * * *
2715823 TTATCA-TTTAGCACACTCAGTGCTCCATATGGAAATCAATACACTCAGTATGATTTCT
1 TTACCATTTTAGCACACTAAGTGCTCTATCTGGAAATCCATACACTCAGTATGATTTCC
* * * *** *
2715881 TTACCATTTTAGCACA-TAAAATGCCCTATCTAGAAATCCATATTTTCAATATGATTTCC
1 TTACCATTTTAGCACACT-AAGTGCTCTATCTGGAAATCCATACACTCAGTATGATTTCC
* * * * * * *
2715940 TTATCA-TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCACTATGTTTTCC
1 TTACCATTTTAGCACACTAAGTGCTCTATCTGGAAATCCATACACTCAGTATGATTTCC
* * * * * *** *
2715998 TTACCATTTTTGTACA-TAAAATGCCCTATCTGGAAATCTATATTTTCAATATGATTTCC
1 TTACCATTTTAGCACACT-AAGTGCTCTATCTGGAAATCCATACACTCAGTATGATTTCC
* * * *
2716057 TTATCA-TTTAGCACACTAAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
1 TTACCATTTTAGCACACTAAGTGCTCTATCTGGAAATCCATACACTCAGTATGATTTCC
* * * * *** *
2716115 TTACCATTTTTGCACA-TAAAATGCCCTATCTAGAAATCCATATTTTCAATATGATTTCC
1 TTACCATTTTAGCACACT-AAGTGCTCTATCTGGAAATCCATACACTCAGTATGATTTCC
* ** * * *
2716174 TTATCA-TTTAGCACACGCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
1 TTACCATTTTAGCACACTAAGTGCTCTATCTGGAAATCCATACACTCAGTATGATTTCC
* * *** *
2716232 TTACCAATTTAGCACA-TAAAATG-TCATATCTGGAAATCCATATTTTCAATATGATTTCC
1 TTACCATTTTAGCACACT-AAGTGCTC-TATCTGGAAATCCATACACTCAGTATGATTTCC
* * * * *
2716291 TTATCA-TTTAG--CAC--AGTGCTCCATATGGAAATCTATACACTAAGTATGATTTCC
1 TTACCATTTTAGCACACTAAGTGCTCTATCTGGAAATCCATACACTCAGTATGATTTCC
2716345 TTACCATTTTAGCACAC
1 TTACCATTTTAGCACAC
2716362 AAGGTGCCAT
Statistics
Matches: 499, Mismatches: 133, Indels: 52
0.73 0.19 0.08
Matches are distributed among these distances:
54 33 0.07
55 7 0.01
56 2 0.00
57 3 0.01
58 186 0.37
59 263 0.53
60 5 0.01
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (59 bp):
TTACCATTTTAGCACACTAAGTGCTCTATCTGGAAATCCATACACTCAGTATGATTTCC
Found at i:2715894 original size:117 final size:117
Alignment explanation
Indices: 2715646--2716360 Score: 1071
Period size: 117 Copynumber: 6.1 Consensus size: 117
2715636 TATAATTTTG
* * * * ** *
2715646 TTACCATTTTAGCACTTGAAATGCCCTATGTGAAAATCCATACCATT-AGTATGATTTCCTTATC
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATA-TTTTCAATATGATTTCCTTATC
* * * * ** * * *
2715710 TTTGTAGCACCCTTAGTACTTTATCTGGAAATCCATACACTCAGTATGATTCCC
65 ATT-TAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
* *
2715764 TTACCATTTTAGCAAATAAAATGCCTTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
* *
2715829 TTTAGCACACTCAGTGCTCCATATGGAAATCAATACACTCAGTATGATTTCT
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
*
2715881 TTACCATTTTAGCACATAAAATGCCCTATCTAGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
* *
2715946 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCACTATGTTTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
* * *
2715998 TTACCATTTTTGTACATAAAATGCCCTATCTGGAAATCTATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
*
2716063 TTTAGCACACTAAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
* *
2716115 TTACCATTTTTGCACATAAAATGCCCTATCTAGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
*
2716180 TTTAGCACACGCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
* * *
2716232 TTACCAATTTAGCACATAAAATGTCATATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
*
2716297 TTTAG--CA--CAGTGCTCCATATGGAAATCTATACACTAAGTATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
2716345 TTACCATTTTAGCACA
1 TTACCATTTTAGCACA
2716361 CAAGGTGCCA
Statistics
Matches: 551, Mismatches: 45, Indels: 7
0.91 0.07 0.01
Matches are distributed among these distances:
113 55 0.10
115 2 0.00
117 440 0.80
118 54 0.10
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (117 bp):
TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
Found at i:2719156 original size:12 final size:13
Alignment explanation
Indices: 2719139--2719185 Score: 62
Period size: 12 Copynumber: 3.8 Consensus size: 13
2719129 TATCTTAGTA
2719139 TATAATATAT-TT
1 TATAATATATATT
*
2719151 TATAATATATACT
1 TATAATATATATT
*
2719164 T-TAATATATATA
1 TATAATATATATT
2719176 TATAATATAT
1 TATAATATAT
2719186 TTTCAAAGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
TATAATATATATT
Found at i:2720123 original size:25 final size:25
Alignment explanation
Indices: 2720095--2720147 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
2720085 ATTGGGACAA
* *
2720095 TATTTT-ATATAAAAGTATTTTATTT
1 TATTTTCATATAAAAATA-TATATTT
*
2720120 TATTTTCATTTAAAAATATATATTT
1 TATTTTCATATAAAAATATATATTT
2720145 TAT
1 TAT
2720148 GTTAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
TATTTTCATATAAAAATATATATTT
Found at i:2720390 original size:5 final size:5
Alignment explanation
Indices: 2720382--2720543 Score: 97
Period size: 5 Copynumber: 32.4 Consensus size: 5
2720372 TATATTTCTA
* *
2720382 AATAT AATAT -ATAT AATAT ATTAT AGTATAT AATAT -ATA- AATAC AATAAT
1 AATAT AATAT AATAT AATAT AATAT A--ATAT AATAT AATAT AATAT AAT-AT
* * * * *
2720432 ATACAT AATAT ATTAT AGTATAT AATAT ATAAAT ACTAT AATAT -ACAT
1 A-ATAT AATAT AATAT A--ATAT AATAT A-ATAT AATAT AATAT AATAT
* * *
2720480 AATAT AATAGT -ATAT AATAT -ATAT AAT-T ATTAT ATTAT ACTAT AATAT
1 AATAT AATA-T AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
*
2720528 TATAT -ATAT AATAT AA
1 AATAT AATAT AATAT AA
2720544 CTATGTATTA
Statistics
Matches: 124, Mismatches: 17, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
4 25 0.20
5 80 0.65
6 10 0.08
7 9 0.07
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:2720396 original size:26 final size:26
Alignment explanation
Indices: 2720367--2720574 Score: 84
Period size: 26 Copynumber: 8.0 Consensus size: 26
2720357 TTTTCAAAAC
*
2720367 TATAATATATTTCTA-AATATAATATA
1 TATAATATA-TTATAGAATATAATATA
*
2720393 TATAATATATTATAGTATATAATATA
1 TATAATATATTATAGAATATAATATA
*
2720419 TA-AATACA--AT--AATATACATA-A
1 TATAATATATTATAGAATATA-ATATA
* * * *
2720440 TATATTATAGTATATAATATATAAATA
1 TATAATATATTATAGAATATA-ATATA
*
2720467 CTATAATATA-CAT--AATATAATAGTA
1 -TATAATATATTATAGAATATAATA-TA
*
2720492 TATAATATA-TATA-ATTATTATATTATA
1 TATAATATATTATAGA--A-TATAATATA
* *
2720519 CTATAATATTATATATATAATATAACTATG
1 -TATAATA-TAT-TATAGAATATAA-TATA
* *
2720549 TAT--TATATGAAAGATATATAATATA
1 TATAATATATTATAGA-ATATAATATA
2720574 T
1 T
2720575 TATACCATAT
Statistics
Matches: 142, Mismatches: 19, Indels: 43
0.70 0.09 0.21
Matches are distributed among these distances:
21 8 0.06
22 7 0.05
23 2 0.01
24 15 0.11
25 25 0.18
26 38 0.27
27 8 0.06
28 21 0.15
29 9 0.06
30 4 0.03
31 4 0.03
32 1 0.01
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (26 bp):
TATAATATATTATAGAATATAATATA
Found at i:2720421 original size:33 final size:33
Alignment explanation
Indices: 2720383--2720578 Score: 138
Period size: 33 Copynumber: 5.7 Consensus size: 33
2720373 ATATTTCTAA
2720383 ATATAATATATATAATATATTATAGTATATAATAT
1 ATATAATATATATAATATATTATAGTATAT-A-AT
2720418 ATAAATACAATAATATACATAATATATTATAGTATATAAT
1 AT--AT--AAT-ATAT--ATAATATATTATAGTATATAAT
* * *
2720458 ATATAA-ATACTATAATATA-CATAATATAATAGT
1 ATATAATATA-TATAATATATTATAGTAT-ATAAT
*
2720491 ATATAATATATATAAT-TATTATATTATACT-AT
1 ATATAATATATATAATATATTATAGTATA-TAAT
* *
2720523 AATATTATATATATAATATAACTAT-GTAT-T-AT
1 -ATATAATATATATAATAT-ATTATAGTATATAAT
*
2720555 ATGA-AAGATATATAATATATTATA
1 AT-ATAATATATATAATATATTATA
2720579 CCATATATGC
Statistics
Matches: 132, Mismatches: 12, Indels: 38
0.73 0.07 0.21
Matches are distributed among these distances:
30 4 0.03
31 14 0.11
32 14 0.11
33 46 0.35
34 10 0.08
35 7 0.05
36 2 0.02
37 2 0.02
38 2 0.02
39 3 0.02
40 8 0.06
41 1 0.01
42 19 0.14
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (33 bp):
ATATAATATATATAATATATTATAGTATATAAT
Found at i:2720440 original size:42 final size:42
Alignment explanation
Indices: 2720384--2720542 Score: 220
Period size: 42 Copynumber: 3.8 Consensus size: 42
2720374 TATTTCTAAA
*
2720384 TATAATATATATAATATATTATAGTATATAATATATAAATAC
1 TATAATATACATAATATATTATAGTATATAATATATAAATAC
*
2720426 AATAATATACATAATATATTATAGTATATAATATATAAATAC
1 TATAATATACATAATATATTATAGTATATAATATATAAATAC
*
2720468 TATAATATACATAATATA--ATAGTATATAATATATATAATTAT
1 TATAATATACATAATATATTATAGTATATAATATATA-AA-TAC
*
2720510 TATATTATAC-T-ATAATATTATA-TATATAATATA
1 TATAATATACATAAT-ATATTATAGTATATAATATA
2720543 ACTATGTATT
Statistics
Matches: 107, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
40 19 0.18
41 6 0.06
42 79 0.74
43 3 0.03
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (42 bp):
TATAATATACATAATATATTATAGTATATAATATATAAATAC
Found at i:2721800 original size:76 final size:76
Alignment explanation
Indices: 2721720--2721935 Score: 224
Period size: 76 Copynumber: 2.8 Consensus size: 76
2721710 TATCTAAGAG
* ** *
2721720 ACAAGTCTC-AAGAAAATCAAGAATGAGGTTTATAAGGAAACAATCTTAAGGAATACTAAATTGA
1 ACAAGTC-CGAAGAAAATCAAGATTGATATTTCTAAGGAAACAATCTTAAGGAATACTAAATTGA
* *
2721784 GTTTTCTATAAT
65 GCTTTCTAGAAT
* * *
2721796 ACAAGTCCTAAGATAGA-CAAGATTGATATTTCTAGGGAAACAATCTTAAGG-ATGACTAAATTG
1 ACAAGTCCGAAGA-AAATCAAGATTGATATTTCTAAGGAAACAATCTTAAGGAAT-ACTAAATTG
*
2721859 AGCTTTCTAGGAT
64 AGCTTTCTAGAAT
* * * * * *
2721872 ACAAGTCCGAA-AAGAGTCAAGATTGATCTTTCTATGGAAACCATCTTAATGAAGACTAAATTGA
1 ACAAGTCCGAAGAA-AATCAAGATTGATATTTCTAAGGAAACAATCTTAAGGAATACTAAATTGA
2721936 TTTCTCGAAA
Statistics
Matches: 117, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
74 1 0.01
75 4 0.03
76 109 0.93
77 3 0.03
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (76 bp):
ACAAGTCCGAAGAAAATCAAGATTGATATTTCTAAGGAAACAATCTTAAGGAATACTAAATTGAG
CTTTCTAGAAT
Found at i:2721859 original size:38 final size:37
Alignment explanation
Indices: 2721755--2721938 Score: 96
Period size: 38 Copynumber: 4.9 Consensus size: 37
2721745 AGGTTTATAA
2721755 GGAAACAATCTTAAGGAAT-ACTAAATTGAGTTTTCTA-
1 GGAAACAATCTTAAGG-ATGACTAAATTGA-TTTTCTAG
* *
2721792 -TAATACAAGTCCTAA-GATAGAC-AAGATTGATATTTCTAG
1 GGAA-ACAA-TCTTAAGGAT-GACTAA-ATTGAT-TTTCTAG
*
2721831 GGAAACAATCTTAAGGATGACTAAATTGAGCTTTCTA-
1 GGAAACAATCTTAAGGATGACTAAATTGA-TTTTCTAG
* ** * * *
2721868 GGATACAAGTCCGAA--AAGAGTCAAGATTGATCTTTCTAT
1 GGAAACAA-TCTTAAGGATGACT-AA-ATTGAT-TTTCTAG
* * *
2721907 GGAAACCATCTTAATGAAGACTAAATTGATTT
1 GGAAACAATCTTAAGGATGACTAAATTGATTT
2721939 CTCGAAAGAG
Statistics
Matches: 113, Mismatches: 16, Indels: 36
0.68 0.10 0.22
Matches are distributed among these distances:
36 8 0.07
37 19 0.17
38 62 0.55
39 17 0.15
40 7 0.06
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (37 bp):
GGAAACAATCTTAAGGATGACTAAATTGATTTTCTAG
Found at i:2726042 original size:18 final size:19
Alignment explanation
Indices: 2726019--2726057 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2726009 TTTAAAATTC
2726019 ATTTTATAC-TAAAAGGCA
1 ATTTTATACTTAAAAGGCA
*
2726037 ATTTTATCCTTTAAAAGGCA
1 ATTTTATAC-TTAAAAGGCA
2726057 A
1 A
2726058 CATCATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (19 bp):
ATTTTATACTTAAAAGGCA
Found at i:2727898 original size:18 final size:18
Alignment explanation
Indices: 2727872--2727907 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2727862 AGAGAAGAAA
*
2727872 TTTTTCTTTTGTAATTGG
1 TTTTGCTTTTGTAATTGG
2727890 TTTTGCTTTTGTAATTGG
1 TTTTGCTTTTGTAATTGG
2727908 AGAGTACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.06, G:0.19, T:0.64
Consensus pattern (18 bp):
TTTTGCTTTTGTAATTGG
Found at i:2728396 original size:10 final size:10
Alignment explanation
Indices: 2728383--2728418 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
2728373 CCTTATATAT
2728383 TTTATTTTTA
1 TTTATTTTTA
*
2728393 TTTATTTTCA
1 TTTATTTTTA
2728403 TTTATCTTTTA
1 TTTAT-TTTTA
2728414 TTTAT
1 TTTAT
2728419 CATCACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:2728428 original size:21 final size:20
Alignment explanation
Indices: 2728384--2728429 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2728374 CTTATATATT
** *
2728384 TTATTTTTATTTATTTTCAT
1 TTATTTTTATTTATCATCAC
2728404 TTATCTTTTATTTATCATCAC
1 TTAT-TTTTATTTATCATCAC
2728425 TTATT
1 TTATT
2728430 GTTTTCCTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTTATTTATCATCAC
Found at i:2728663 original size:21 final size:21
Alignment explanation
Indices: 2728637--2728676 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2728627 TTTTTACTTA
2728637 TTTTATTTAT-CTCTATTTACT
1 TTTTATTTATCCT-TATTTACT
2728658 TTTTATTTATCCTTATTTA
1 TTTTATTTATCCTTATTTA
2728677 TTATTTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATTTATCCTTATTTACT
Found at i:2734409 original size:48 final size:49
Alignment explanation
Indices: 2734355--2734653 Score: 301
Period size: 48 Copynumber: 6.2 Consensus size: 49
2734345 ATTTTCTCAA
2734355 ATTTGATCTCCACGAAGAGATGGTGG-GACAAATCT-TCAAAGTTTCTAG
1 ATTTGATCTCCACGAAGAGATGGTGGAG-CAAATCTGTCAAAGTTTCTAG
* * * * * *
2734403 ATTTGATCTCCACGAAGTGATGGTGGAGCCAATC-ATCAAGGTTTTCCAC
1 ATTTGATCTCCACGAAGAGATGGTGGAGCAAATCTGTCAAAG-TTTCTAG
* * * * *
2734452 ATTTGATTTCCATGAAGAGATGATGGAGTAAAT-TATCAAAGTTT-TCAG
1 ATTTGATCTCCACGAAGAGATGGTGGAGCAAATCTGTCAAAGTTTCT-AG
* * * * *
2734500 ATTTGATATCCACTAAGAGATAGTAGG-GC-AATCTGTCAAAGTTTCCAA
1 ATTTGATCTCCACGAAGAGATGGT-GGAGCAAATCTGTCAAAGTTTCTAG
*
2734548 ATTTGATCTCCACGAAGAGATGATGGAGCAAAT-TGTCAAAGTTTCTAG
1 ATTTGATCTCCACGAAGAGATGGTGGAGCAAATCTGTCAAAGTTTCTAG
* * * * *
2734596 ATTTGGTCTCCATGAAGAGATGGTGGAGCGAATC-ATCAAAGTTTTTAG
1 ATTTGATCTCCACGAAGAGATGGTGGAGCAAATCTGTCAAAGTTTCTAG
2734644 ATTTGATCTC
1 ATTTGATCTC
2734654 TATAAAGAAA
Statistics
Matches: 204, Mismatches: 36, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
47 5 0.02
48 155 0.76
49 44 0.22
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (49 bp):
ATTTGATCTCCACGAAGAGATGGTGGAGCAAATCTGTCAAAGTTTCTAG
Found at i:2734674 original size:144 final size:144
Alignment explanation
Indices: 2734385--2734650 Score: 354
Period size: 144 Copynumber: 1.8 Consensus size: 144
2734375 TGGTGGGACA
* * * * * *
2734385 AATCTTCAAAGTTTCTAGATTTGATCTCCACGAAGTGATGGTGGAGCCAATCATCAAGGTTTTCC
1 AATCTTCAAAGTTTCCAAATTTGATCTCCACGAAGAGATGATGGAGCAAATCATCAAAGTTTTCC
* * *
2734450 ACATTTGATTTCCATGAAGAGATGATGGAGTAAATTATCAAAGTTTTCAGATTTGATATCCACTA
66 ACATTTGATCTCCATGAAGAGATGATGGAGCAAATCATCAAAGTTTTCAGATTTGATATCCACTA
*
2734515 AGAGATAGTAGGGC
131 AGAAATAGTAGGGC
**
2734529 AATCTGTCAAAGTTTCCAAATTTGATCTCCACGAAGAGATGATGGAGCAAATTGTCAAAG-TTTC
1 AATCT-TCAAAGTTTCCAAATTTGATCTCCACGAAGAGATGATGGAGCAAATCATCAAAGTTTTC
* * * * * *
2734593 TAGATTTGGTCTCCATGAAGAGATGGTGGAGCGAATCATCAAAGTTTTTAGATTTGAT
65 CACATTTGATCTCCATGAAGAGATGATGGAGCAAATCATCAAAGTTTTCAGATTTGAT
2734651 CTCTATAAAG
Statistics
Matches: 104, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
144 58 0.56
145 46 0.44
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (144 bp):
AATCTTCAAAGTTTCCAAATTTGATCTCCACGAAGAGATGATGGAGCAAATCATCAAAGTTTTCC
ACATTTGATCTCCATGAAGAGATGATGGAGCAAATCATCAAAGTTTTCAGATTTGATATCCACTA
AGAAATAGTAGGGC
Found at i:2734675 original size:96 final size:94
Alignment explanation
Indices: 2734351--2734653 Score: 344
Period size: 96 Copynumber: 3.1 Consensus size: 94
2734341 GATCATTTTC
*
2734351 TCAAATTTGATCTCCACGAAGAGATGGTGG-GACAAATCTTCAAAGTTTCTAGATTTGATCTCCA
1 TCAAATTTGATCTCCACGAAGAGATGATGGAG-CAAAT-TTCAAAGTTTCTAGATTTGATCTCCA
* * *
2734415 CGAAGTGATGGTGGAGCCAATCATCAAGGTTT
64 TGAAGAGATGGTGGAG-CAATCATCAAAGTTT
* * * * *
2734447 TCCACATTTGATTTCCATGAAGAGATGATGGAGTAAATTATCAAAGTTT-TCAGATTTGATATCC
1 T-CAAATTTGATCTCCACGAAGAGATGATGGAGCAAATT-TCAAAGTTTCT-AGATTTGATCTCC
* *
2734511 ACT-AAGAGATAGTAGG-GCAATCTGTCAAAGTTT
63 A-TGAAGAGATGGT-GGAGCAATC-ATCAAAGTTT
* *
2734544 CCAAATTTGATCTCCACGAAGAGATGATGGAGCAAATTGTCAAAGTTTCTAGATTTGGTCTCCAT
1 TCAAATTTGATCTCCACGAAGAGATGATGGAGCAAATT-TCAAAGTTTCTAGATTTGATCTCCAT
2734609 GAAGAGATGGTGGAGCGAATCATCAAAGTTT
65 GAAGAGATGGTGGAGC-AATCATCAAAGTTT
* *
2734640 TTAGATTTGATCTC
1 TCAAATTTGATCTC
2734654 TATAAAGAAA
Statistics
Matches: 172, Mismatches: 24, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
95 3 0.02
96 93 0.54
97 73 0.42
98 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (94 bp):
TCAAATTTGATCTCCACGAAGAGATGATGGAGCAAATTTCAAAGTTTCTAGATTTGATCTCCATG
AAGAGATGGTGGAGCAATCATCAAAGTTT
Found at i:2735904 original size:27 final size:25
Alignment explanation
Indices: 2735865--2735914 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
2735855 TAAATTGGAC
2735865 ACACATTATTTTTCAGGGAGAAAAGGA
1 ACACATTATTTTT--GGGAGAAAAGGA
2735892 ACACATT-TGTTTTGGGAGAAAAG
1 ACACATTAT-TTTTGGGAGAAAAG
2735915 AGAGGAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 10 0.45
26 1 0.05
27 11 0.50
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (25 bp):
ACACATTATTTTTGGGAGAAAAGGA
Found at i:2736204 original size:17 final size:17
Alignment explanation
Indices: 2736182--2736216 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2736172 ATGTCCATCT
* *
2736182 TATTTTATTTTTTTCTA
1 TATTTTATATGTTTCTA
2736199 TATTTTATATGTTTCTA
1 TATTTTATATGTTTCTA
2736216 T
1 T
2736217 GTCATCAATA
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:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (17 bp):
TATTTTATATGTTTCTA
Found at i:2736244 original size:2 final size:2
Alignment explanation
Indices: 2736237--2736270 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2736227 TTAATTATGT
2736237 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
2736271 GACACACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2736425 original size:15 final size:15
Alignment explanation
Indices: 2736401--2736445 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
2736391 TATTACGTAC
*
2736401 ATATTCTTATATATT
1 ATATTATTATATATT
2736416 ATATTATTATATATT
1 ATATTATTATATATT
* *
2736431 ATATTTTTATTTATT
1 ATATTATTATATATT
2736446 TTCATTTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
ATATTATTATATATT
Found at i:2736459 original size:21 final size:21
Alignment explanation
Indices: 2736435--2736475 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2736425 TATATTATAT
*
2736435 TTTTATTTATTTTCATTTATC
1 TTTTATTTATTATCATTTATC
2736456 TTTTATTTATTATCATTTAT
1 TTTTATTTATTATCATTTAT
2736476 TGTTTTCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTATTTATTATCATTTATC
Found at i:2736465 original size:11 final size:10
Alignment explanation
Indices: 2736427--2736476 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
2736417 TATTATTATA
2736427 TATTATATTTT
1 TATT-TATTTT
2736438 TATTTATTTT
1 TATTTATTTT
*
2736448 CATTTATCTTT
1 TATTTAT-TTT
*
2736459 TATTTATTAT
1 TATTTATTTT
*
2736469 CATTTATT
1 TATTTATT
2736477 GTTTTCCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 21 0.62
11 13 0.38
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTATTTT
Found at i:2736731 original size:22 final size:23
Alignment explanation
Indices: 2736676--2736731 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
2736666 TATACATATT
*
2736676 TTTATTTATTTTATTTATCTCTA
1 TTTACTTATTTTATTTATCTCTA
*
2736699 TTTACTT-TTTTATTTATCTTTA
1 TTTACTTATTTTATTTATCTCTA
*
2736721 TTT-GTTATTTT
1 TTTACTTATTTT
2736732 CCTTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 21 0.72
23 6 0.21
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTACTTATTTTATTTATCTCTA
Found at i:2776619 original size:21 final size:22
Alignment explanation
Indices: 2776589--2776662 Score: 87
Period size: 21 Copynumber: 3.3 Consensus size: 22
2776579 ATATGTGTTA
2776589 TATGTGGTCCTTCGGGACA-TC
1 TATGTGGTCCTTCGGGACATTC
* *
2776610 TATGTAGTCCTTCGGGACAATTT
1 TATGTGGTCCTTCGGGAC-ATTC
*
2776633 TACGTGGTCCTTCGGGACAAATTC
1 TATGTGGTCCTTCGGGAC--ATTC
2776657 TATGTG
1 TATGTG
2776663 ACCCTAGTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 17 0.39
22 1 0.02
23 17 0.39
24 9 0.20
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (22 bp):
TATGTGGTCCTTCGGGACATTC
Found at i:2779439 original size:81 final size:81
Alignment explanation
Indices: 2779299--2779839 Score: 681
Period size: 81 Copynumber: 6.7 Consensus size: 81
2779289 CAAAGGCATT
* * * * *
2779299 TAACTAGCATGATTGGCAACTTTATGCCAAATGCATATTTAGGCATTTAATCTTTTACTCAAATG
1 TAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGG
* *
2779364 TATTTAATCCTTT-TTC
66 CATTTAA-CCTTTCATC
* * * *
2779380 TAACTAGCTTGATTGACACCTTTCTGCCAAATGCTCAGTTAGGCATTTAATCTTCTACTCAAAGG
1 TAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGG
* * *
2779445 AATTAAACCTTTTATC
66 CATTTAACCTTTCATC
* * * * *
2779461 TAATTAGCATGATTGGCACCTTTCTGCTAAATGCACAGTTATGCACTTAATCCTTTACTCAAAGG
1 TAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGG
2779526 CATTTAACCTTTCATC
66 CATTTAACCTTTCATC
* * * ** * *
2779542 TAACTAG-ATGACTGGCACATTTCTACCAAAAACACAATTAGACATTTAATCTTTTACTCAAAGG
1 TAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGG
2779606 CATTTAACCTTTCATC
66 CATTTAACCTTTCATC
* * * * *
2779622 TAACTAGCATGATTGGCACATTTCTGCCAAATACACAGTTAGACATTTAATTTTTTACTCAAAGA
1 TAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGG
2779687 CATTTAACCTTTCATC
66 CATTTAACCTTTCATC
* * * ** *
2779703 TAACTAGCATGATTGGCACCTTTTTGTCAATTGCATTGTTAGACATTTAATCTTTTACTCAAAGG
1 TAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGG
2779768 CATTTAACCTTTCATC
66 CATTTAACCTTTCATC
* * * * *
2779784 TATCTAGCATGATTGGCACTTTTTTGCCAAATGCAGAGTTAGGCATTTAATTTTTT
1 TAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAATCTTTT
2779840 TTACTCATAA
Statistics
Matches: 399, Mismatches: 59, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
80 74 0.19
81 325 0.81
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (81 bp):
TAACTAGCATGATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTTAATCTTTTACTCAAAGG
CATTTAACCTTTCATC
Found at i:2779648 original size:242 final size:243
Alignment explanation
Indices: 2779337--2779802 Score: 654
Period size: 242 Copynumber: 1.9 Consensus size: 243
2779327 AAATGCATAT
* * * * * *
2779337 TTAGGCATTTAATCTTTTACTCAAATGTATTTAATCCTTTTTCTAACTAGCTTGATTGACACCTT
1 TTAGACATTTAATCTTTTACTCAAAGGCATTTAATCCTTTATCTAACTAGCATGATTGACACATT
* * * * *
2779402 TCTGCCAAATGCTCAGTTAGGCATTTAATCTTCTACTCAAAGGA-ATTAAACCTTTTATCTAATT
66 TCTGCCAAATACACAGTTAGACATTTAATCTTCTACTCAAA-GACATTAAACCTTTCATCTAACT
2779466 AGCATGATTGGCACCTTTCTG-CTAAATGCACAGTTATG-CACTTAATCCTTTACTCAAAGGCAT
130 AGCATGATTGGCACCTTTCTGTC-AAATGCACAGTTA-GACACTTAATCCTTTACTCAAAGGCAT
2779529 TTAACCTTTCATCTAACTAG-ATGACTGGCACATTTCTACCAAAAACACAA
193 TTAACCTTTCATCTAACTAGCATGACTGGCACATTTCTACCAAAAACACAA
*
2779579 TTAGACATTTAATCTTTTACTCAAAGGCATTTAA-CCTTTCATCTAACTAGCATGATTGGCACAT
1 TTAGACATTTAATCTTTTACTCAAAGGCATTTAATCCTTT-ATCTAACTAGCATGATTGACACAT
* * *
2779643 TTCTGCCAAATACACAGTTAGACATTTAATTTTTTACTCAAAGACATTTAACCTTTCATCTAACT
65 TTCTGCCAAATACACAGTTAGACATTTAATCTTCTACTCAAAGACATTAAACCTTTCATCTAACT
* * ** * *
2779708 AGCATGATTGGCACCTTTTTGTCAATTGCATTGTTAGACATTTAATCTTTTACTCAAAGGCATTT
130 AGCATGATTGGCACCTTTCTGTCAAATGCACAGTTAGACACTTAATCCTTTACTCAAAGGCATTT
* *
2779773 AACCTTTCATCTATCTAGCATGATTGGCAC
195 AACCTTTCATCTAACTAGCATGACTGGCAC
2779803 TTTTTTGCCA
Statistics
Matches: 196, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
241 8 0.04
242 177 0.90
243 11 0.06
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Consensus pattern (243 bp):
TTAGACATTTAATCTTTTACTCAAAGGCATTTAATCCTTTATCTAACTAGCATGATTGACACATT
TCTGCCAAATACACAGTTAGACATTTAATCTTCTACTCAAAGACATTAAACCTTTCATCTAACTA
GCATGATTGGCACCTTTCTGTCAAATGCACAGTTAGACACTTAATCCTTTACTCAAAGGCATTTA
ACCTTTCATCTAACTAGCATGACTGGCACATTTCTACCAAAAACACAA
Found at i:2790367 original size:9 final size:9
Alignment explanation
Indices: 2790353--2790388 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
2790343 AAAACCCACT
2790353 AAAAATGAA
1 AAAAATGAA
2790362 AAAAATTG-A
1 AAAAA-TGAA
2790371 AAAAATGAA
1 AAAAATGAA
2790380 AAAAATGAA
1 AAAAATGAA
2790389 GTTGTGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 2 0.08
9 21 0.84
10 2 0.08
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (9 bp):
AAAAATGAA
Found at i:2792338 original size:18 final size:18
Alignment explanation
Indices: 2792315--2792354 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2792305 CAGAGAAATA
2792315 GACTTATATTTTCCTAGT
1 GACTTATATTTTCCTAGT
2792333 GACTTATATTTTCCTAGT
1 GACTTATATTTTCCTAGT
2792351 GACT
1 GACT
2792355 CCTATCACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.47
Consensus pattern (18 bp):
GACTTATATTTTCCTAGT
Found at i:2795161 original size:23 final size:23
Alignment explanation
Indices: 2795135--2795196 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
2795125 TAAAGTTCGA
2795135 GGGCGATC-AGATGGAGTTTAAAT
1 GGGCGATCGA-ATGGAGTTTAAAT
2795158 GGGCGATCGAATGGAGTTTAAAT
1 GGGCGATCGAATGGAGTTTAAAT
* *
2795181 GGTCGAACGATATGGA
1 GGGCGATCGA-ATGGA
2795197 ACGAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 29 0.83
24 6 0.17
ACGTcount: A:0.31, C:0.10, G:0.35, T:0.24
Consensus pattern (23 bp):
GGGCGATCGAATGGAGTTTAAAT
Found at i:2797342 original size:32 final size:32
Alignment explanation
Indices: 2797272--2797344 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
2797262 CCTAAAGTGA
* * *
2797272 CCCTTGGGTGGGCTCTGAGGCCCCGAGAAACT
1 CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACT
** *
2797304 TTCTTGGGTAGGCTCTCAGGCCCCAAGACACT
1 CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACT
2797336 CCCTTGGGT
1 CCCTTGGGT
2797345 TAATCATAGG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.15, C:0.32, G:0.30, T:0.23
Consensus pattern (32 bp):
CCCTTGGGTAGGCTCTCAGGCCCCAAGAAACT
Found at i:2800987 original size:33 final size:32
Alignment explanation
Indices: 2800921--2801024 Score: 140
Period size: 31 Copynumber: 3.3 Consensus size: 32
2800911 AATGATGATG
2800921 GAGTGACCATTTCGTTACAAATT-GATAACGT
1 GAGTGACCATTTCGTTACAAATTAGATAACGT
*
2800952 GAGTGACCATTTCGTTACAAATTGAGATAATGT
1 GAGTGACCATTTCGTTACAAATT-AGATAACGT
* * * *
2800985 GAGTGACAATTTTGATACAAATCA-ATAACGT
1 GAGTGACCATTTCGTTACAAATTAGATAACGT
2801016 GAGTGACCA
1 GAGTGACCA
2801025 ATATGTTACT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
31 37 0.58
32 1 0.02
33 26 0.41
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (32 bp):
GAGTGACCATTTCGTTACAAATTAGATAACGT
Found at i:2803166 original size:19 final size:20
Alignment explanation
Indices: 2803123--2803172 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2803113 CACGAAATGT
2803123 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
*
2803143 AAGATTACCTGTGGGAAT-A
1 AAGATTACCAGTGGGAATAA
2803162 AAGATTACCAG
1 AAGATTACCAG
2803173 GGAATAGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:2803346 original size:15 final size:15
Alignment explanation
Indices: 2803328--2803358 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2803318 AAATTCTAAA
2803328 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
2803343 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
2803358 T
1 T
2803359 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:2808423 original size:20 final size:21
Alignment explanation
Indices: 2808377--2808437 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
2808367 TTCCCTGTGG
2808377 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
2808400 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
2808420 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2808438 TGCACTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:2819788 original size:6 final size:6
Alignment explanation
Indices: 2819769--2819803 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
2819759 GTTTTTAAAA
2819769 AATTAT ATATTAT AATTAT AATTAT AATTAT AATT
1 AATTAT A-ATTAT AATTAT AATTAT AATTAT AATT
2819804 TTATTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AATTAT
Found at i:2819830 original size:27 final size:27
Alignment explanation
Indices: 2819800--2819861 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
2819790 TTATAATTAT
*
2819800 AATTTTATTTTATATACAAAATTTTAA
1 AATTTTATTTTAAATACAAAATTTTAA
2819827 AATTTTATTTTAAATACAAAATTTTAA
1 AATTTTATTTTAAATACAAAATTTTAA
2819854 AATTTTAT
1 AATTTTAT
2819862 AAATGTGACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
AATTTTATTTTAAATACAAAATTTTAA
Found at i:2819936 original size:21 final size:21
Alignment explanation
Indices: 2819910--2819951 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2819900 CGTGACAATC
2819910 AAACACCTAAAATTGTAACAT
1 AAACACCTAAAATTGTAACAT
2819931 AAACACCTAAAATTGTAACAT
1 AAACACCTAAAATTGTAACAT
2819952 TGGTAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (21 bp):
AAACACCTAAAATTGTAACAT
Found at i:2824070 original size:24 final size:21
Alignment explanation
Indices: 2824018--2824073 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
2824008 ACATTCCCCT
*
2824018 AATTAAA-AAAACAATATACA
1 AATTAAATAAAACAATATAAA
2824038 AATTAAAATATAAACTAATACTAAA
1 AATT-AAATA-AAAC-AATA-TAAA
2824063 AATTAAATAAA
1 AATTAAATAAA
2824074 TAAAACATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 3 0.10
22 1 0.03
23 6 0.20
24 9 0.30
25 7 0.23
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (21 bp):
AATTAAATAAAACAATATAAA
Found at i:2827809 original size:26 final size:27
Alignment explanation
Indices: 2827747--2827817 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
2827737 TTGGTGTAAT
2827747 TGATTCTTTTAGTATATTTTATTTTTA
1 TGATTCTTTTAGTATATTTTATTTTTA
*
2827774 TGATTGTTTTAGTATATTTTA-TTTTA
1 TGATTCTTTTAGTATATTTTATTTTTA
2827800 TGATTCTTTTA-TAT-TTTT
1 TGATTCTTTTAGTATATTTT
2827818 GTAAATAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 4 0.10
25 3 0.07
26 15 0.36
27 20 0.48
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.68
Consensus pattern (27 bp):
TGATTCTTTTAGTATATTTTATTTTTA
Found at i:2829647 original size:17 final size:17
Alignment explanation
Indices: 2829625--2829688 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
2829615 ATTGAACAAG
2829625 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* * *
2829642 TTCTTCTCTCTTGTTGGATGAG
1 TTCTTCTC-ATT-AT-GA--AC
2829664 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
2829681 TTCTTCTC
1 TTCTTCTC
2829689 TCTTGTTGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
17 17 0.47
18 2 0.06
19 3 0.08
20 3 0.08
21 2 0.06
22 9 0.25
ACGTcount: A:0.16, C:0.23, G:0.11, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:2829670 original size:22 final size:22
Alignment explanation
Indices: 2829642--2829710 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
2829632 CATTATGAAC
2829642 TTCTTCTCTCTTGTTGGATGAG
1 TTCTTCTCTCTTGTTGGATGAG
* * *
2829664 TTCTTCTC-ATT-AT-GA--AC
1 TTCTTCTCTCTTGTTGGATGAG
2829681 TTCTTCTCTCTTGTTGGATGAG
1 TTCTTCTCTCTTGTTGGATGAG
2829703 TTCTTCTC
1 TTCTTCTC
2829711 ATTATGAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
17 9 0.25
18 2 0.06
19 3 0.08
20 3 0.08
21 2 0.06
22 17 0.47
ACGTcount: A:0.12, C:0.22, G:0.16, T:0.51
Consensus pattern (22 bp):
TTCTTCTCTCTTGTTGGATGAG
Found at i:2829677 original size:39 final size:39
Alignment explanation
Indices: 2829623--2829724 Score: 197
Period size: 39 Copynumber: 2.6 Consensus size: 39
2829613 GGATTGAACA
2829623 AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGATG
1 AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGATG
2829662 AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGATG
1 AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGATG
2829701 AGTTCTTCTCATTATGAAC-TCTTC
1 AGTTCTTCTCATTATGAACTTCTTC
2829725 ACTGAGAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 5 0.08
39 58 0.92
ACGTcount: A:0.17, C:0.22, G:0.14, T:0.48
Consensus pattern (39 bp):
AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGATG
Found at i:2829876 original size:117 final size:117
Alignment explanation
Indices: 2829662--2829876 Score: 326
Period size: 117 Copynumber: 1.8 Consensus size: 117
2829652 TTGTTGGATG
** * *
2829662 AGTTCTTCTCATTATGAACTTCTTCTCTCTTGTTGGATGAGTTCTTCTCATTATGAACTCTTCAC
1 AGTTCTTCTCATTATGAACTTCTTCTCTCTCATTGGATGAGTTATTCTCATTATGAACTCTCCAC
*
2829727 TGAGAATGTTGATCCACATCATTCTGTGATGGAATCGAACCAAGGTTGAACA
66 TGAAAATGTTGATCCACATCATTCTGTGATGGAATCGAACCAAGGTTGAACA
*
2829779 AGTTTTTCTCATTATGAACTTCTTCT-TCCTCATTGGATGAGTTATTCTCATTATGAACTCTCCA
1 AGTTCTTCTCATTATGAACTTCTTCTCT-CTCATTGGATGAGTTATTCTCATTATGAACTCTCCA
* *
2829843 CTGAAAATGTTGATCCATC-TCTTTCTGTTATGGA
65 CTGAAAATGTTGATCCA-CATCATTCTGTGATGGA
2829877 TTTGAAAGGA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
116 1 0.01
117 86 0.98
118 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.40
Consensus pattern (117 bp):
AGTTCTTCTCATTATGAACTTCTTCTCTCTCATTGGATGAGTTATTCTCATTATGAACTCTCCAC
TGAAAATGTTGATCCACATCATTCTGTGATGGAATCGAACCAAGGTTGAACA
Found at i:2830992 original size:17 final size:17
Alignment explanation
Indices: 2830970--2831007 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2830960 TCATTTTCTC
2830970 TTTTCATTTTTTCATTT
1 TTTTCATTTTTTCATTT
2830987 TTTTCATTTTTTCATTT
1 TTTTCATTTTTTCATTT
2831004 TTTT
1 TTTT
2831008 TCTTCAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTCATTTTTTCATTT
Found at i:2831007 original size:9 final size:8
Alignment explanation
Indices: 2830970--2831006 Score: 65
Period size: 8 Copynumber: 4.5 Consensus size: 8
2830960 TCATTTTCTC
2830970 TTTTCATT
1 TTTTCATT
2830978 TTTTCATTT
1 TTTTCA-TT
2830987 TTTTCATT
1 TTTTCATT
2830995 TTTTCATT
1 TTTTCATT
2831003 TTTT
1 TTTT
2831007 TTCTTCAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCATT
Found at i:2838976 original size:9 final size:9
Alignment explanation
Indices: 2838944--2838968 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2838934 TAAAAGGGAA
2838944 AAATAAAAT
1 AAATAAAAT
2838953 AAATAAAAT
1 AAATAAAAT
2838962 AAATAAA
1 AAATAAA
2838969 TAAGATAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2839627 original size:17 final size:18
Alignment explanation
Indices: 2839591--2839633 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2839581 ATATATACGT
* *
2839591 ATAATAATAATAACATGA
1 ATAATAATAAAAAAATGA
2839609 ATAATAA-AAAAAAATGA
1 ATAATAATAAAAAAATGA
2839626 ATAA-AATA
1 ATAATAATA
2839634 TCCATATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 13 0.59
18 7 0.32
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (18 bp):
ATAATAATAAAAAAATGA
Found at i:2841106 original size:106 final size:106
Alignment explanation
Indices: 2840916--2841431 Score: 700
Period size: 106 Copynumber: 5.0 Consensus size: 106
2840906 TATTGTTCCT
* * ** *
2840916 AGTCCAATATCCTCCG-TCGTGAAGTTGGAATTGGCT-TCGGGACTGGGAAATTGTTTGTTGACA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCT-GAAATTGGGAAATTGTTTGTTGACA
* * * * * *
2840979 GCCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTGTGTTGTCTCG
64 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
* * *
2841022 AGTTCAATATACTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGCTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
2841087 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
*
2841128 AGTCCAATATCCTTCGCTGTGAAGTTGAAA-----T-T---A---GGAGATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
2841181 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
* * * *
2841222 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTATAAAATTGGGAAATTGTTTGTTGATAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
2841287 CAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
* * *
2841328 AGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
2841393 CAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
2841432 CGGGTGGCAC
Statistics
Matches: 368, Mismatches: 28, Indels: 28
0.87 0.07 0.07
Matches are distributed among these distances:
94 89 0.24
97 1 0.00
99 1 0.00
100 2 0.01
101 1 0.00
103 1 0.00
106 271 0.74
107 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.36
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
Found at i:2841156 original size:43 final size:43
Alignment explanation
Indices: 2841095--2841250 Score: 150
Period size: 43 Copynumber: 3.4 Consensus size: 43
2841085 ACCAGCCGTC
*
2841095 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATAT
1 CCTTCGCTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATAT
* * * ** ***
2841138 CCTTCGCTGTGAAGTTGAAATTAGGAGATTGTTTGTTGACAACCAGCCGT
1 CCTTCGCTGTGAAGTTGAACTT--GTG-TTG--TCTTGA-GTCCA-ATAT
*
2841188 CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATAT
1 -CCTTCGCTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATAT
2841232 CCTTCGCTGTGAAGTTGAA
1 CCTTCGCTGTGAAGTTGAA
2841251 ATTGACTATA
Statistics
Matches: 86, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
43 38 0.44
44 1 0.01
45 5 0.06
46 8 0.09
48 8 0.09
49 5 0.06
50 1 0.01
51 20 0.23
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (43 bp):
CCTTCGCTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATAT
Found at i:2841308 original size:200 final size:204
Alignment explanation
Indices: 2840964--2841433 Score: 678
Period size: 200 Copynumber: 2.3 Consensus size: 204
2840954 GGGACTGGGA
* * * * * *
2840964 AATTGTTTGTTGACAGCCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTTCAA
1 AATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAA
* * *
2841029 TATACTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGCTGACAACCAGCCGT
66 TATACTTCGCTGTGAAGTTGAAATTGACTATAAAATTGGGAAATTGTTTGCTGACAACCAGCCGT
2841094 CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
131 CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
2841159 TAG-G-A-G
196 TAGCGAAGG
*
2841165 -ATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAA
1 AATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAA
* * * *
2841229 TATCCTTCGCTGTGAAGTTGAAATTGACTATAAAATTGGGAAATTGTTTGTTGATAACCAGTCGT
66 TATACTTCGCTGTGAAGTTGAAATTGACTATAAAATTGGGAAATTGTTTGCTGACAACCAGCCGT
*
2841294 CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTTGCTGTGAAGTTGAAAT
131 CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
*
2841359 TGGCTCTGAAATTGGG
196 TAG--C-G-AA---GG
* *
2841375 AAGTTATTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
1 AA-TTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
2841434 GGTGGCACGA
Statistics
Matches: 238, Mismatches: 19, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
200 181 0.76
204 1 0.00
206 1 0.00
210 1 0.00
211 1 0.00
212 53 0.22
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.37
Consensus pattern (204 bp):
AATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAA
TATACTTCGCTGTGAAGTTGAAATTGACTATAAAATTGGGAAATTGTTTGCTGACAACCAGCCGT
CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
TAGCGAAGG
Found at i:2842327 original size:36 final size:38
Alignment explanation
Indices: 2842269--2842345 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 38
2842259 GAAACAATTT
* *
2842269 CAAAGGTTTTTTTCCAATGGAAACAGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGGAAACAGTCTCAAGAGAGA
*
2842307 CAAA-GTTTGTTT-CAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGGAAACAGTCTCAAGAGAGA
2842343 CAA
1 CAA
2842346 TGGTGAGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 25 0.69
37 7 0.19
38 4 0.11
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (38 bp):
CAAAGGTTTGTTTCCAAGGGAAACAGTCTCAAGAGAGA
Found at i:2842927 original size:161 final size:160
Alignment explanation
Indices: 2842651--2842972 Score: 571
Period size: 156 Copynumber: 2.0 Consensus size: 160
2842641 TATGTATGCT
2842651 AAAAATGATAAATGTGATGCTCTCAAGTATGTCTAGATGCATGCAACATGAATAATGTCATTTAT
1 AAAAATGATAAATGTGATGCTCTCAAGTATGTCTAGATGCATGCAACATGAATAATGTCATTTAT
2842716 CTCTTGGATAGAGCCATTTTTCCTGCTTGTTCCTGCATGTAGAGGAAATG-C-TCAGAAGGT-TG
66 CTCTTGGATAGAGCCATTTTTCCTGCTTGTTCCTGCATGTAGAGGAAATGCCTTCAGAAGGTCTG
2842778 ATAATTCGCATTAGGATG-TGAATCCCCAA
131 ATAATTCGCATTAGGATGTTGAATCCCCAA
2842807 AAAAATGATAAATGTGATGCTCTCAAGTATGTCTAAGATGCATGCAACATGAATTAATGTCATTT
1 AAAAATGATAAATGTGATGCTCTCAAGTATGTCT-AGATGCATGCAACATGAA-TAATGTCATTT
2842872 ATCTCTTGGATAGAGCCTCATTTTTTCCTGCTTGTTCCTGCATGTAGAGGAAATGCCTTCAGAAG
64 ATCTCTTGGATAGAG-C-CA-TTTTTCCTGCTTGTTCCTGCATGTAGAGGAAATGCCTTCAGAAG
2842937 GTCTGATAATTCGCATTAGGATGTTGAATCCCCAA
126 GTCTGATAATTCGCATTAGGATGTTGAATCCCCAA
2842972 A
1 A
2842973 GATGCCCCAA
Statistics
Matches: 157, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
156 34 0.22
157 18 0.11
158 26 0.17
159 1 0.01
160 2 0.01
161 34 0.22
162 1 0.01
163 9 0.06
164 20 0.13
165 12 0.08
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (160 bp):
AAAAATGATAAATGTGATGCTCTCAAGTATGTCTAGATGCATGCAACATGAATAATGTCATTTAT
CTCTTGGATAGAGCCATTTTTCCTGCTTGTTCCTGCATGTAGAGGAAATGCCTTCAGAAGGTCTG
ATAATTCGCATTAGGATGTTGAATCCCCAA
Found at i:2842995 original size:18 final size:18
Alignment explanation
Indices: 2842968--2843003 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2842958 TGTTGAATCC
*
2842968 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
2842986 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
2843004 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:2844053 original size:16 final size:16
Alignment explanation
Indices: 2844029--2844077 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
2844019 TTTTTGTCCC
*
2844029 TCTTCCTTTTGATTTTT
1 TCTT-CTTTTCATTTTT
2844046 TCTTCTTTTCATTTTT
1 TCTTCTTTTCATTTTT
*
2844062 ACTTCTTTTCATTTTT
1 TCTTCTTTTCATTTTT
2844078 GTTCTTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 26 0.87
17 4 0.13
ACGTcount: A:0.08, C:0.18, G:0.02, T:0.71
Consensus pattern (16 bp):
TCTTCTTTTCATTTTT
Found at i:2844082 original size:15 final size:15
Alignment explanation
Indices: 2844042--2844083 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
2844032 TCCTTTTGAT
2844042 TTTTTCTTCTTTTCA
1 TTTTTCTTCTTTTCA
2844057 TTTTTACTTCTTTTCA
1 TTTTT-CTTCTTTTCA
*
2844073 TTTTTGTTCTT
1 TTTTTCTTCTT
2844084 GATTGAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTTCTTCTTTTCA
Found at i:2848546 original size:9 final size:9
Alignment explanation
Indices: 2848516--2848567 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
2848506 AGATAAAGAG
2848516 AATAAAATAA
1 AATAAAAT-A
*
2848526 AATGGAAA-A
1 AAT-AAAATA
2848535 AATAAAATA
1 AATAAAATA
*
2848544 AATTAAATA
1 AATAAAATA
*
2848553 AATTAAATA
1 AATAAAATA
2848562 AATAAA
1 AATAAA
2848568 TAAGATAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 3 0.08
9 27 0.75
10 3 0.08
11 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (9 bp):
AATAAAATA
Found at i:2848711 original size:38 final size:38
Alignment explanation
Indices: 2848611--2848711 Score: 98
Period size: 39 Copynumber: 2.6 Consensus size: 38
2848601 TTTATATAGT
*** *
2848611 AATATTTGAAAAAT-GAAAAAAAATATATATATACATCA
1 AATATTT-AAAAATAGAAAAGCTATATATATATACAACA
* *
2848649 AATTATTAATAAAATA-AATCAGCTATATATATATACAACA
1 AA-TATTTA-AAAATAGAA-AAGCTATATATATATACAACA
2848689 AATATTTAAAAATAGAAAAGCTA
1 AATATTTAAAAATAGAAAAGCTA
2848712 CCCTCTCACT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
38 14 0.28
39 18 0.36
40 18 0.36
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (38 bp):
AATATTTAAAAATAGAAAAGCTATATATATATACAACA
Found at i:2849108 original size:2 final size:2
Alignment explanation
Indices: 2849101--2849137 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2849091 TTAAAGAAAC
2849101 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 A
2849138 ATAAAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2849214 original size:18 final size:17
Alignment explanation
Indices: 2849193--2849235 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2849183 AAATATACGT
2849193 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
2849211 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
2849228 ATAA-AATA
1 ATAATAATA
2849236 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:2855404 original size:2 final size:2
Alignment explanation
Indices: 2855397--2855427 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2855387 CTATGTTGTT
2855397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2855428 TACTATACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2857942 original size:2 final size:2
Alignment explanation
Indices: 2857931--2857984 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
2857921 TGATTATGGT
2857931 TA TA -A 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
*
2857972 TA T- TA TA TG TA TA
1 TA TA TA TA TA TA TA
2857985 CTTTTATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2862205 original size:16 final size:18
Alignment explanation
Indices: 2862175--2862207 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2862165 CCACAACAAT
2862175 TTTAGTTAAATATAATTG
1 TTTAGTTAAATATAATTG
2862193 TTTA-TTAAA-ATAATT
1 TTTAGTTAAATATAATT
2862208 TTCTTGAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
TTTAGTTAAATATAATTG
Found at i:2864011 original size:242 final size:244
Alignment explanation
Indices: 2863586--2864072 Score: 960
Period size: 242 Copynumber: 2.0 Consensus size: 244
2863576 AAGTTTGAAA
2863586 GTGTCCTTATTTTAGATGTTATTTGGATTTGATCATAACGTGTTTAATGAAATGTTTCTATTTAG
1 GTGTCCTTATTTTAGATGTTATTTGGATTTGATCATAACGTGTTTAATGAAATGTTTCTATTTAG
2863651 TGTTTTTGCTTCAACAATGCCTTTATGTATTGTAGATTTATTGAGATAATTTTAGAAATGAAGTT
66 TGTTTTTGCTTCAACAATGCCTTTATGTATTGTAGATTTATTGAGATAATTTTAGAAATGAAGTT
2863716 ATCTTTAATGTATATGATTTTGATATTTTTAGAGATTTAAAATTGCATGTTACTTTCTTGCTGCA
131 ATCTTTAATGTATATGATTTTGATATTTTTAGAGATTTAAAATTGCATGTTACTTTCTTGCTGCA
2863781 TTGGTA-TTGC-AAAGTATATTTAGCATTTGTTAAATATTGGTCTGGTT
196 TTGGTATTTGCAAAAGTATATTTAGCATTTGTTAAATATTGGTCTGGTT
2863828 GTGTCCTTATTTTAGATGTTATTTGGATTTGATCATAACGTGTTTAATGAAATGTTTCTATTTAG
1 GTGTCCTTATTTTAGATGTTATTTGGATTTGATCATAACGTGTTTAATGAAATGTTTCTATTTAG
2863893 TGTTTTTGCTTCAACAATGCCTTTATGTATTGTAGATTTATTGAGATAATTTTAGAAATGAAGTT
66 TGTTTTTGCTTCAACAATGCCTTTATGTATTGTAGATTTATTGAGATAATTTTAGAAATGAAGTT
2863958 ATCTTTAATGTATATGATTTTGATATTTTTAGAGATTTAAAATTGCATGTTACTTTCTTGCTGCA
131 ATCTTTAATGTATATGATTTTGATATTTTTAGAGATTTAAAATTGCATGTTACTTTCTTGCTGCA
2864023 TTGGTATTTGCAAAAGTATATTTAGCATTTGTTAAATATTGGTCTGGTT
196 TTGGTATTTGCAAAAGTATATTTAGCATTTGTTAAATATTGGTCTGGTT
2864072 G
1 G
2864073 CTCTCATGAA
Statistics
Matches: 243, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
242 201 0.83
243 4 0.02
244 38 0.16
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (244 bp):
GTGTCCTTATTTTAGATGTTATTTGGATTTGATCATAACGTGTTTAATGAAATGTTTCTATTTAG
TGTTTTTGCTTCAACAATGCCTTTATGTATTGTAGATTTATTGAGATAATTTTAGAAATGAAGTT
ATCTTTAATGTATATGATTTTGATATTTTTAGAGATTTAAAATTGCATGTTACTTTCTTGCTGCA
TTGGTATTTGCAAAAGTATATTTAGCATTTGTTAAATATTGGTCTGGTT
Found at i:2867551 original size:22 final size:22
Alignment explanation
Indices: 2867517--2867559 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2867507 AAATCCATCA
2867517 AAGAAAATCAAAGCACTCAAAG
1 AAGAAAATCAAAGCACTCAAAG
* *
2867539 AAGAAATTGAAAGCACTCAAA
1 AAGAAAATCAAAGCACTCAAA
2867560 AATGAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.16, G:0.14, T:0.12
Consensus pattern (22 bp):
AAGAAAATCAAAGCACTCAAAG
Found at i:2869087 original size:20 final size:18
Alignment explanation
Indices: 2869049--2869088 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
2869039 TTATTAGTTT
*
2869049 TTCATTTTATAACTTTGA
1 TTCATTTTATAAATTTGA
2869067 TTCATTTTATAGCAATTTGA
1 TTCATTTTATA--AATTTGA
2869087 TT
1 TT
2869089 AGTATAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
20 8 0.42
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (18 bp):
TTCATTTTATAAATTTGA
Found at i:2879808 original size:20 final size:20
Alignment explanation
Indices: 2879765--2879808 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2879755 AAATATTTCA
* *
2879765 TCACTTTTATAGATGATTAT
1 TCACTTTTATAGATGACTAC
2879785 TCACTTTTATAGATGACTAC
1 TCACTTTTATAGATGACTAC
2879805 TCAC
1 TCAC
2879809 GATACATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (20 bp):
TCACTTTTATAGATGACTAC
Found at i:2881544 original size:26 final size:26
Alignment explanation
Indices: 2881484--2881549 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
2881474 AATGTTATCT
*
2881484 AAAATTAAATAGAA-AATTTAATATTA
1 AAAATTAAATA-AATAATATAATATTA
* * * *
2881510 TAAAGTAAATAAATAATATGATTTTA
1 AAAATTAAATAAATAATATAATATTA
2881536 AAAATTAAATAAAT
1 AAAATTAAATAAAT
2881550 GTTTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.35
Consensus pattern (26 bp):
AAAATTAAATAAATAATATAATATTA
Found at i:2881559 original size:19 final size:22
Alignment explanation
Indices: 2881519--2881558 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2881509 ATAAAGTAAA
2881519 TAAATAATATGATTTTAAAAAT
1 TAAATAATATGATTTTAAAAAT
2881541 TAAATAA-ATG-TTTTAAAA
1 TAAATAATATGATTTTAAAA
2881559 TGATTGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 3 0.17
22 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
TAAATAATATGATTTTAAAAAT
Found at i:2885770 original size:19 final size:20
Alignment explanation
Indices: 2885733--2885776 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2885723 ATGTTGTCAA
2885733 TAAACTAAGAAAGAAAAATC
1 TAAACTAAGAAAGAAAAATC
*
2885753 TAAACTAAGAAA-AAAAATG
1 TAAACTAAGAAAGAAAAATC
2885772 TAAAC
1 TAAAC
2885777 AAAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAACTAAGAAAGAAAAATC
Found at i:2892788 original size:10 final size:10
Alignment explanation
Indices: 2892773--2892813 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
2892763 TTCATCACAC
2892773 CAAATTCTCT
1 CAAATTCTCT
*
2892783 CAAATTTTCT
1 CAAATTCTCT
*
2892793 CAATTTCTCT
1 CAAATTCTCT
*
2892803 CAAATACTCT
1 CAAATTCTCT
2892813 C
1 C
2892814 TCTGTTTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:2892892 original size:17 final size:18
Alignment explanation
Indices: 2892855--2892895 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2892845 ATATTATGTA
*
2892855 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
2892873 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
2892890 TTTACT
1 TTTACT
2892896 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:2894461 original size:18 final size:18
Alignment explanation
Indices: 2894438--2894472 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2894428 CAGCAGCCCC
*
2894438 CGCAACCATTTATGATGT
1 CGCAACCATATATGATGT
2894456 CGCAACCATATATGATG
1 CGCAACCATATATGATG
2894473 CCGCCAGTGC
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:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (18 bp):
CGCAACCATATATGATGT
Found at i:2895040 original size:26 final size:24
Alignment explanation
Indices: 2894969--2895040 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
2894959 TTATATTTGT
2894969 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
2894994 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
2895016 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
2895041 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:2898912 original size:30 final size:29
Alignment explanation
Indices: 2898850--2898912 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
2898840 TACTGCTACG
* *
2898850 GGTGTTAGATCGGGAAATATAATATGACC
1 GGTGTTAGATCGGGAAATATAAGATCACC
* *
2898879 GGTGTTAGATCGGTAAATATACCGATCACC
1 GGTGTTAGATCGGGAAATATA-AGATCACC
2898909 GGTG
1 GGTG
2898913 ATTTTTCGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (29 bp):
GGTGTTAGATCGGGAAATATAAGATCACC
Found at i:2900707 original size:50 final size:50
Alignment explanation
Indices: 2900639--2900752 Score: 176
Period size: 50 Copynumber: 2.3 Consensus size: 50
2900629 AGTAACTAAT
* *
2900639 TAATAAAATAATAATAAACTAAAAATAATATTTT-ATTTTATCATAATTCC
1 TAATAAAATAATAATAAACT-AAAATAATATTTTAACTATATCATAATTCC
* *
2900689 TAATAAAATAATAATAAACTAAAATAATATTTTAACTATATCTTAATTCT
1 TAATAAAATAATAATAAACTAAAATAATATTTTAACTATATCATAATTCC
2900739 TAATAAAATAATAA
1 TAATAAAATAATAA
2900753 ATATAATCCT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
49 13 0.22
50 46 0.78
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (50 bp):
TAATAAAATAATAATAAACTAAAATAATATTTTAACTATATCATAATTCC
Found at i:2901885 original size:19 final size:19
Alignment explanation
Indices: 2901842--2901885 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2901832 GAATGCAAAA
*
2901842 ATGGCATCGATACCATAAT
1 ATGGTATCGATACCATAAT
* * *
2901861 AGGGTATCGGTACCATAGT
1 ATGGTATCGATACCATAAT
2901880 ATGGTA
1 ATGGTA
2901886 GGATAGATAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (19 bp):
ATGGTATCGATACCATAAT
Found at i:2902338 original size:55 final size:55
Alignment explanation
Indices: 2902254--2902509 Score: 345
Period size: 55 Copynumber: 4.7 Consensus size: 55
2902244 GTGCAAAAAT
*
2902254 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGAGCACTATATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
* * * *
2902309 TTAAGATATTCATAATAAGTGGATGAATTTACGTTTGGGCACTATATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
*
2902364 TTAAGAAATTCATACTAAGTGGATGAATTCCCGTATGGGCACT-TAATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTAT-ATGTGTAAAC
** **
2902419 TTAAGAAATTCATACTAAGTGGATGAATTTCTTTATGGGCACTATATGTACAAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGT-GTAAAC
* * * * *
2902475 -TAGGAAATTAATACTAAGTGTATAAATTTTCGTAT
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTAT
2902510 TGGTAGCAGG
Statistics
Matches: 176, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
54 1 0.01
55 170 0.97
56 5 0.03
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (55 bp):
TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAAAC
Found at i:2909035 original size:55 final size:55
Alignment explanation
Indices: 2908967--2909279 Score: 459
Period size: 55 Copynumber: 5.7 Consensus size: 55
2908957 GTGTGCAAAC
2908967 ACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAA
1 ACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAA
**
2909022 ACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGTCCACTATATGTGTAA
1 ACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAA
* * *
2909077 ACTTAATAAATTCATACTAAGTGGTTGAATTTCCGTATGGGCACCATATGTGTAA
1 ACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAA
* *
2909132 ACTTAAGAAATTCATACTAACTGGATAAATTTCCGTATGGGCAC-ATTATGTGTAA
1 ACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTA-TATGTGTAA
* * ** *
2909187 ACTTAAGAAATTCACACTAAGTTGATGAATTTTTGTATGGGCACTATATGTGCAAA
1 ACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTG-TAA
* * *
2909243 AC-TAGGAAATTCATACTAAGTGTATAAATTTCCGTAT
1 ACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTAT
2909280 TGGTAGCAAG
Statistics
Matches: 230, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
54 1 0.00
55 224 0.97
56 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (55 bp):
ACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGTAA
Found at i:2910463 original size:18 final size:17
Alignment explanation
Indices: 2910413--2910463 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
2910403 AGTTGCATTC
*
2910413 AACATTTTAATTAACTG
1 AACATTTTAATTAACTA
*
2910430 AAC-TATTAA-T-ACTA
1 AACATTTTAATTAACTA
2910444 AACAATTTTAATTAACTA
1 AAC-ATTTTAATTAACTA
2910462 AA
1 AA
2910464 TCACTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
14 6 0.22
15 1 0.04
16 10 0.37
17 4 0.15
18 6 0.22
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (17 bp):
AACATTTTAATTAACTA
Found at i:2910651 original size:2 final size:2
Alignment explanation
Indices: 2910646--2910671 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2910636 TTTGTATTAA
2910646 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
2910672 CATTTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2912621 original size:22 final size:22
Alignment explanation
Indices: 2912591--2912650 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
2912581 TGAACCAGTT
*
2912591 GAGCCGACCGAGCCGATCGACC
1 GAGCTGACCGAGCCGATCGACC
* *
2912613 GAGCTGACCGAGCTGATCGATC
1 GAGCTGACCGAGCCGATCGACC
*
2912635 GAGCTGAACGAGCCGA
1 GAGCTGACCGAGCCGA
2912651 CCAAGCTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.25, C:0.32, G:0.33, T:0.10
Consensus pattern (22 bp):
GAGCTGACCGAGCCGATCGACC
Found at i:2914060 original size:18 final size:18
Alignment explanation
Indices: 2914034--2914068 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2914024 TCGAAAGGAC
*
2914034 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2914052 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
2914069 CCGGATATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2919184 original size:18 final size:18
Alignment explanation
Indices: 2919158--2919192 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2919148 TCGAAAGGAC
*
2919158 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2919176 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
2919193 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Done.