Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009267.1 Hibiscus syriacus cultivar Beakdansim tig00112925_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: 1725308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1071906 original size:22 final size:21
Alignment explanation
Indices: 1071872--1071952 Score: 94
Period size: 22 Copynumber: 3.9 Consensus size: 21
1071862 AAATGAATAA
*
1071872 ATATTTTACTTTTATAAATTAT
1 ATATATTACTTTT-TAAATTAT
*
1071894 ATATATTA-TTTTTAAA-TAA
1 ATATATTACTTTTTAAATTAT
*
1071913 ATATTTTACTTTTATAAATTAT
1 ATATATTACTTTT-TAAATTAT
*
1071935 ATATATTATTTTTTAAAT
1 ATATATTACTTTTTAAAT
1071953 GTTATATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
19 9 0.18
20 8 0.16
21 13 0.26
22 20 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATATTACTTTTTAAATTAT
Found at i:1071918 original size:41 final size:42
Alignment explanation
Indices: 1071867--1071952 Score: 165
Period size: 41 Copynumber: 2.1 Consensus size: 42
1071857 TTTTTAAATG
1071867 AATAAATATTTTACTTTTATAAATTATATATATTA-TTTTTA
1 AATAAATATTTTACTTTTATAAATTATATATATTATTTTTTA
1071908 AATAAATATTTTACTTTTATAAATTATATATATTATTTTTTA
1 AATAAATATTTTACTTTTATAAATTATATATATTATTTTTTA
1071950 AAT
1 AAT
1071953 GTTATATTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 35 0.80
42 9 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (42 bp):
AATAAATATTTTACTTTTATAAATTATATATATTATTTTTTA
Found at i:1071958 original size:21 final size:20
Alignment explanation
Indices: 1071881--1071959 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 20
1071871 AATATTTTAC
*
1071881 TTTTATAAATTATATATATTA
1 TTTTTTAAATT-TATATATTA
** *
1071902 -TTTTTAAATAAATATTTTA
1 TTTTTTAAATTTATATATTA
*
1071921 CTTTTATAAATTATATATATTA
1 -TTTTTTAAATT-TATATATTA
1071943 TTTTTTAAATGTTATAT
1 TTTTTTAAAT-TTATAT
1071960 TAATATTAAG
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
19 7 0.16
20 8 0.18
21 22 0.49
22 8 0.18
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (20 bp):
TTTTTTAAATTTATATATTA
Found at i:1074038 original size:17 final size:17
Alignment explanation
Indices: 1074016--1074079 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
1074006 AAATAAATAA
1074016 ATAAATATTTTACTTTT
1 ATAAATATTTTACTTTT
*
1074033 ATAAATTATATATATTATTTTT
1 AT-AA--ATAT-T-TTACTTTT
1074055 AAATAAATATTTTACTTTT
1 --ATAAATATTTTACTTTT
1074074 ATAAAT
1 ATAAAT
1074080 TATATATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 8 0.21
18 2 0.05
19 7 0.18
20 5 0.13
21 5 0.13
22 7 0.18
23 2 0.05
24 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAAATATTTTACTTTT
Found at i:1074070 original size:41 final size:42
Alignment explanation
Indices: 1074013--1074100 Score: 169
Period size: 41 Copynumber: 2.1 Consensus size: 42
1074003 TTTAAATAAA
1074013 TAAATAAATATTTTACTTTTATAAATTATATATATTA-TTTT
1 TAAATAAATATTTTACTTTTATAAATTATATATATTATTTTT
1074054 TAAATAAATATTTTACTTTTATAAATTATATATATTATTTTT
1 TAAATAAATATTTTACTTTTATAAATTATATATATTATTTTT
1074096 TAAAT
1 TAAAT
1074101 GTTTTATTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 37 0.80
42 9 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (42 bp):
TAAATAAATATTTTACTTTTATAAATTATATATATTATTTTT
Found at i:1074094 original size:21 final size:22
Alignment explanation
Indices: 1074012--1074100 Score: 98
Period size: 21 Copynumber: 4.3 Consensus size: 22
1074002 TTTTAAATAA
*
1074012 ATAAA-TAAATATTTTACTTTT
1 ATAAATTAAATATATTACTTTT
*
1074033 ATAAATTATATATATTA-TTTT
1 ATAAATTAAATATATTACTTTT
*
1074054 -TAAA-TAAATATTTTACTTTT
1 ATAAATTAAATATATTACTTTT
*
1074074 ATAAATTATATATATTA-TTTT
1 ATAAATTAAATATATTACTTTT
*
1074095 TTAAAT
1 ATAAAT
1074101 GTTTTATTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
19 9 0.16
20 8 0.14
21 22 0.39
22 18 0.32
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATAAATTAAATATATTACTTTT
Found at i:1081220 original size:21 final size:21
Alignment explanation
Indices: 1081178--1081220 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1081168 TTTCTGGGCT
* *
1081178 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1081199 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1081220 A
1 A
1081221 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1081923 original size:23 final size:24
Alignment explanation
Indices: 1081871--1081939 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 24
1081861 CATTATTATA
1081871 TGGCACTACGGTGCAATTCTACGC
1 TGGCACTACGGTGCAATTCTACGC
* * *
1081895 T-ACACTCCGGTGCAATTCTATG-
1 TGGCACTACGGTGCAATTCTACGC
* *
1081917 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
1081940 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (24 bp):
TGGCACTACGGTGCAATTCTACGC
Found at i:1082693 original size:26 final size:26
Alignment explanation
Indices: 1082650--1082782 Score: 101
Period size: 26 Copynumber: 5.0 Consensus size: 26
1082640 TTAATAATTT
1082650 TCAAATAAATTT-GAGTTCGATTAATGG
1 TCAAAT-AATTTCG-GTTCGATTAATGG
*
1082677 TCAAATAATTTCGGTTCAATTAATGG
1 TCAAATAATTTCGGTTCGATTAATGG
* * * * * **
1082703 TTAAAGAAAAAAATTCTGTT--AATAATTT
1 -T---CAAATAATTTCGGTTCGATTAATGG
*
1082731 TCAAATAAATTTCGGTTCGATTAACGG
1 TCAAAT-AATTTCGGTTCGATTAATGG
1082758 TCAAATAATTTCGGTTCGATTAATG
1 TCAAATAATTTCGGTTCGATTAATG
1082783 TTAAAGAAAA
Statistics
Matches: 81, Mismatches: 17, Indels: 17
0.70 0.15 0.15
Matches are distributed among these distances:
24 3 0.04
25 8 0.10
26 35 0.43
27 19 0.23
28 5 0.06
30 11 0.14
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (26 bp):
TCAAATAATTTCGGTTCGATTAATGG
Found at i:1082768 original size:81 final size:80
Alignment explanation
Indices: 1082633--1082794 Score: 272
Period size: 81 Copynumber: 2.0 Consensus size: 80
1082623 TTATTCATTT
*
1082633 AATTCAGTTAATAATTTTCAAATAAATTTGAGTTCGATTAATGGTCAAATAATTTCGGTTCAATT
1 AATTCAGTTAATAATTTTCAAATAAATTTGAGTTCGATTAACGGTCAAATAATTTCGGTTCAATT
1082698 AATGGTTAAAGAAAAA
66 AAT-GTTAAAGAAAAA
* *
1082714 AATTCTGTTAATAATTTTCAAATAAATTTCG-GTTCGATTAACGGTCAAATAATTTCGGTTCGAT
1 AATTCAGTTAATAATTTTCAAATAAATTT-GAGTTCGATTAACGGTCAAATAATTTCGGTTCAAT
1082778 TAATGTTAAAGAAAAA
65 TAATGTTAAAGAAAAA
1082794 A
1 A
1082795 TTTTGGTTAA
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
80 13 0.17
81 63 0.82
82 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.37
Consensus pattern (80 bp):
AATTCAGTTAATAATTTTCAAATAAATTTGAGTTCGATTAACGGTCAAATAATTTCGGTTCAATT
AATGTTAAAGAAAAA
Found at i:1082865 original size:94 final size:94
Alignment explanation
Indices: 1082720--1082946 Score: 357
Period size: 94 Copynumber: 2.4 Consensus size: 94
1082710 AAAAAATTCT
* *
1082720 GTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAATGTT
1 GTTAATAATTTTCAAATAAATTTCGGTCCCATTAACGGTCAAATAATTTCGGTTCGATTAATGTT
* *
1082785 AAAGAAAAAATTTTGGTTAATTTGGTTCG
66 AAAGAAAAAAATTCGGTTAATTTGGTTCG
* *
1082814 GTTAATAATTTTCAAATAAATATT-TGTCCCATTAACGGTCAAATAATTTCGGTTTGATTAATGT
1 GTTAATAATTTTCAAATAAAT-TTCGGTCCCATTAACGGTCAAATAATTTCGGTTCGATTAATGT
1082878 TAAAGAAAAAAATTCGGTTAATTTGGTTCG
65 TAAAGAAAAAAATTCGGTTAATTTGGTTCG
* * *
1082908 ATTAATAATTTTCAAATAAATTTCGGTTCAATTAACGGT
1 GTTAATAATTTTCAAATAAATTTCGGTCCCATTAACGGT
1082947 TAAAGAAAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
93 2 0.02
94 117 0.97
95 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (94 bp):
GTTAATAATTTTCAAATAAATTTCGGTCCCATTAACGGTCAAATAATTTCGGTTCGATTAATGTT
AAAGAAAAAAATTCGGTTAATTTGGTTCG
Found at i:1083060 original size:144 final size:142
Alignment explanation
Indices: 1082853--1083111 Score: 437
Period size: 144 Copynumber: 1.8 Consensus size: 142
1082843 CATTAACGGT
* ** *
1082853 CAAATAATTTCGGTTTGATTAATGTTAAAGAAAAAAATTCGGTTAATTTGGTTCGATTAATAATT
1 CAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAATTCAATTAATTCGGTTCGATTAATAATT
1082918 TTCAAATAAATTTCGGTTCAATTAACGGTTAAAGAAAAAATAATTTATTTTATTCGGTTAATTCG
66 TTCAAATAAATTTCGGTTCAATTAACGGTTAAAGAAAAAATAATTTATTTTATTCGGTTAATTCG
1082983 GTAAATAATTTC
131 GTAAATAATTTC
*
1082995 CAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTCAATTAATTCGGTTCGGTTAATAA
1 CAAAT-AATTTCGGTTCGATTAAT-GTTAAAGAAAAAAATTCAATTAATTCGGTTCGATTAATAA
* *
1083060 TTTTCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAATTATTTATTT
64 TTTTCAAATAAATTTCGGTTCAATTAACGGTTAAAGAAAAAATAATTTATTT
1083112 AAACAAATAA
Statistics
Matches: 108, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
142 5 0.05
143 17 0.16
144 86 0.80
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (142 bp):
CAAATAATTTCGGTTCGATTAATGTTAAAGAAAAAAATTCAATTAATTCGGTTCGATTAATAATT
TTCAAATAAATTTCGGTTCAATTAACGGTTAAAGAAAAAATAATTTATTTTATTCGGTTAATTCG
GTAAATAATTTC
Found at i:1083085 original size:69 final size:69
Alignment explanation
Indices: 1082852--1083101 Score: 315
Period size: 69 Copynumber: 3.6 Consensus size: 69
1082842 CCATTAACGG
* * ** * *
1082852 TCAAAT-AATTTCGGTTTGATTAA-TGTTAAAGAAAAAAATTCGGTTAATTTGGTTCGATTAATA
1 TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAATTCAATTAATTCGGTTCGGTTAATA
1082915 ATTT
66 ATTT
* * * *
1082919 TCAAATAAATTTCGGTTCAATTAACGGTTAAAGAAAAAATAATTTATTTTATTCGGTTAATTCGG
1 TCAAATAAATTTCGGTTCGATTAACGGTTAAAG-AAAAA-AATTCAATTAATTCGG----TTCGG
*
1082984 TAAATAATTT
60 TTAATAATTT
* *
1082994 CCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTCAATTAATTCGGTTCGGTTAATA
1 TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAATTCAATTAATTCGGTTCGGTTAATA
1083059 ATTT
66 ATTT
1083063 TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAA
1 TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAA
1083102 TTATTTATTT
Statistics
Matches: 156, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
67 6 0.04
68 15 0.10
69 58 0.37
70 5 0.03
71 11 0.07
73 13 0.08
74 5 0.03
75 43 0.28
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (69 bp):
TCAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAATTCAATTAATTCGGTTCGGTTAATA
ATTT
Found at i:1086263 original size:22 final size:22
Alignment explanation
Indices: 1086237--1086278 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1086227 CTAAAAAATA
1086237 TTTTTAAAATAAT-ATTTTAACT
1 TTTTTAAAA-AATAATTTTAACT
*
1086259 TTTTTTAAAAATAATTTTAA
1 TTTTTAAAAAATAATTTTAA
1086279 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTTAAAAAATAATTTTAACT
Found at i:1086286 original size:2 final size:2
Alignment explanation
Indices: 1086279--1086303 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1086269 ATAATTTTAA
1086279 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 A
1086304 AATGAGAAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1086725 original size:3 final size:3
Alignment explanation
Indices: 1086717--1086794 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
1086707 TTTAGAACTC
1086717 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1086765 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1086795 TTGTTAATTT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1089808 original size:28 final size:28
Alignment explanation
Indices: 1089769--1089985 Score: 185
Period size: 28 Copynumber: 7.6 Consensus size: 28
1089759 ATGACAAAAA
1089769 AAACTTAAAGGGCTAAAATAGTAAAAATC
1 AAACTTAAAGGGCT-AAATAGTAAAAATC
* * *
1089798 AAA-TTTAAGGGTCTAAATAGCAAAAATAG
1 AAACTTAAAGGG-CTAAATAGTAAAAAT-C
* *
1089827 AAACTTAAAGGACTAAATAGCAAAACAT-
1 AAACTTAAAGGGCTAAATAGTAAAA-ATC
*
1089855 AAACTTAAAGGACTAAAATAGTAAAAA-C
1 AAACTTAAAGGGCT-AAATAGTAAAAATC
** ** *
1089883 ATAACTTAAAGGGCTAACCAGTAATTATAG
1 A-AACTTAAAGGGCTAAATAGTAAAAAT-C
1089913 AAACTT-AAGGGCTAAATAGTAAAAATC
1 AAACTTAAAGGGCTAAATAGTAAAAATC
**
1089940 AAAACTT-AAGGGTCTAAATAGTAATTA-C
1 -AAACTTAAAGGG-CTAAATAGTAAAAATC
1089968 AAAACTTAAAGGGCTAAA
1 -AAACTTAAAGGGCTAAA
1089986 CAACAAATAA
Statistics
Matches: 157, Mismatches: 19, Indels: 25
0.78 0.09 0.12
Matches are distributed among these distances:
28 83 0.53
29 65 0.41
30 9 0.06
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.22
Consensus pattern (28 bp):
AAACTTAAAGGGCTAAATAGTAAAAATC
Found at i:1089872 original size:86 final size:85
Alignment explanation
Indices: 1089764--1089992 Score: 243
Period size: 86 Copynumber: 2.7 Consensus size: 85
1089754 CCAAAATGAC
* * *
1089764 AAAA-AAAACTTAAAGGGCTAAAATAGTAAAAATCA-AA-TTTAAGGGTCTAAATAGCAAAAATA
1 AAAATAAAACTTAAAGGACTAAAATAGTAAAAA-CATAACTTAAAGGG-CTAAACAGCAAAAATA
1089826 GAAACTTAAAGGACTAAATAGCA
64 GAAACTT-AAGGACTAAATAGCA
* * **
1089849 AAACAT-AAACTTAAAGGACTAAAATAGTAAAAACATAACTTAAAGGGCTAACCAGTAATTATAG
1 AAA-ATAAAACTTAAAGGACTAAAATAGTAAAAACATAACTTAAAGGGCTAAACAGCAAAAATAG
* *
1089913 AAACTTAAGGGCTAAATAGTA
65 AAACTTAAGGACTAAATAGCA
* * ** * *
1089934 AAAATCAAAACTTAAGGGTCT-AAATAGTAATTACAAAACTTAAAGGGCTAAACAACAAA
1 AAAAT-AAAACTTAAAGGACTAAAATAGTAAAAACATAACTTAAAGGGCTAAACAGCAAA
1089993 TAAAAATAGA
Statistics
Matches: 120, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
84 2 0.02
85 52 0.43
86 59 0.49
87 7 0.06
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.21
Consensus pattern (85 bp):
AAAATAAAACTTAAAGGACTAAAATAGTAAAAACATAACTTAAAGGGCTAAACAGCAAAAATAGA
AACTTAAGGACTAAATAGCA
Found at i:1089891 original size:57 final size:58
Alignment explanation
Indices: 1089692--1089985 Score: 204
Period size: 57 Copynumber: 5.2 Consensus size: 58
1089682 AAGTATTTAC
* * * *
1089692 AGGACTAAAATA--AAATTAACAGAAATTTAAAGGGTTGAATA-TAA-ATACATAAAGTTAA
1 AGGACTAAAATAGTAAA--AACA-AAACTTAAAGGGCTAAATAGTAATA-ACATAAACTTAA
* *
1089750 AGGACCAAAAT-G-ACAAAA-AAAACTTAAAGGGCTAAAATAGTAA-AA-ATCAAATTTAA
1 AGGACTAAAATAGTA-AAAACAAAACTTAAAGGGCT-AAATAGTAATAACAT-AAACTTAA
* * * * * *
1089806 GGGTCT-AAATAGCAAAAATAGAAACTTAAAGGACTAAATAGCAA-AACATAAACTTAA
1 AGGACTAAAATAGTAAAAACA-AAACTTAAAGGGCTAAATAGTAATAACATAAACTTAA
* ** * * *
1089863 AGGACTAAAATAGTAAAAACATAACTTAAAGGGCTAACCAGTAATTATAGAAACTT-A
1 AGGACTAAAATAGTAAAAACAAAACTTAAAGGGCTAAATAGTAATAACATAAACTTAA
* *
1089920 AGGGCT-AAATAGTAAAAATCAAAACTT-AAGGGTCTAAATAGTAATTACA-AAACTTAA
1 AGGACTAAAATAGTAAAAA-CAAAACTTAAAGGG-CTAAATAGTAATAACATAAACTTAA
*
1089977 AGGGCTAAA
1 AGGACTAAA
1089986 CAACAAATAA
Statistics
Matches: 192, Mismatches: 28, Indels: 32
0.76 0.11 0.13
Matches are distributed among these distances:
55 18 0.09
56 44 0.23
57 80 0.42
58 48 0.25
59 2 0.01
ACGTcount: A:0.54, C:0.10, G:0.14, T:0.22
Consensus pattern (58 bp):
AGGACTAAAATAGTAAAAACAAAACTTAAAGGGCTAAATAGTAATAACATAAACTTAA
Found at i:1091309 original size:17 final size:17
Alignment explanation
Indices: 1091287--1091323 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1091277 GGGCTTGTAA
*
1091287 TGGTCTTGAGCTCCGAT
1 TGGTCTTGAGCTCCAAT
*
1091304 TGGTCTTGGGCTCCAAT
1 TGGTCTTGAGCTCCAAT
1091321 TGG
1 TGG
1091324 GGCCTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.32, T:0.35
Consensus pattern (17 bp):
TGGTCTTGAGCTCCAAT
Found at i:1091791 original size:18 final size:18
Alignment explanation
Indices: 1091768--1091806 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1091758 GGGCTTGTAA
1091768 TGGTCTTGAGCTCCAGAT
1 TGGTCTTGAGCTCCAGAT
* *
1091786 TGGTCTTGGGCTCCATAT
1 TGGTCTTGAGCTCCAGAT
1091804 TGG
1 TGG
1091807 GGCCTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.21, G:0.31, T:0.36
Consensus pattern (18 bp):
TGGTCTTGAGCTCCAGAT
Found at i:1092202 original size:492 final size:482
Alignment explanation
Indices: 1091251--1092224 Score: 1623
Period size: 481 Copynumber: 2.0 Consensus size: 482
1091241 CTGAGTTGGG
1091251 TCACTTGTAACTTGGGCTTTAGTATTGGGCTTGTAATGGTCTTGAGCTCCGATTGGTCTTGGGCT
1 TCACTTGTAACTTGGGCTTTAGTATTGGGCTTGTAATGGTCTTGAGCTCCGATTGGTCTTGGGCT
1091316 CCAATTGGGGCCTAAAAAAATTGTAAAATGTAAATTAATAATAATAATTAATAATATTAATAATT
66 CCAATTGGGGCCTAAAAAAATTGTAAAATGTAAATTAATAATAATAATTAATAATATTAATAATT
1091381 TTTTGTAGATTCGGACAAAAACGTGTCTACGATAGCCTCTGTGCTTGAACTTAGACCTCTAGGAA
131 TTTTGTAGATTCGGACAAAAACGTGTCTACGATAGCCTCTGTGCTTGAACTTAGACCTCTAGGAA
1091446 TAACAATCATTCCTTTAACAACTGAATTAATTATTTCATGCAATTCTACTTCATTTTTATTGAGG
196 TAACAATCATTCCTTTAACAACTGAATTAATTATTTCATGCAATTCTACTTCATTTTTATTGAGG
* *
1091511 AGATAAACAAAATGGAACATTAATAAAAAAAACAACCAATTTATAAACGAACAAATACATATAGT
261 AGATAAACAAAATGGAACATTAAGAAAAAAAACAACAAATTTATAAACGAACAAATACATATAGT
1091576 TTGAAAGTTTAATAAAGAAAGCAAAACATTTGTGTTGAAGGTATTGTTCCTGTCCAAAAGGAGAG
326 TTGAAAGTTTAATAAAGAAAGCAAAACATTTGTGTTGAAGGTATTGTTCCTGTCCAAAAGGAGAG
1091641 TATTATTAACATAGAAGATTCTGCTGTTTCGATTGTGTTAACAAACGCAAAAGTAAATTAAATAA
391 TATTATTAACATAGAAGATTCTGCTGTTTCGATTGTGTTAACAAACGCAAAAGTAAATTAAATAA
1091706 AA-TTTCACTTTTTTTATATTAATATA
456 AATTTTCACTTTTTTTATATTAATATA
1091732 TCACTTGTAACTTGGGCTTTAGTATTGGGCTTGTAATGGTCTTGAGCTCCAGATTGGTCTTGGGC
1 TCACTTGTAACTTGGGCTTTAGTATTGGGCTTGTAATGGTCTTGAGCTCC-GATTGGTCTTGGGC
1091797 TCCATATTGGGGCCTAAAAAAATTGTAAAATGTAAATTAATAAT-A-AATTAAT-ATATTAATAA
65 TCCA-ATTGGGGCCTAAAAAAATTGTAAAATGTAAATTAATAATAATAATTAATAATATTAAT-A
1091859 TATTTTTTGTAGA-TCGGACAAAAAACGGGTGTCTACGATAGCCTCTGGTGCTTGAACTTAGACC
128 -ATTTTTTGTAGATTCGGAC-AAAAAC--GTGTCTACGATAGCCTCT-GTGCTTGAACTTAGACC
*
1091923 TCTAGGAATAACAATCATTCCTTTAAACCACTGAATTAATTTATTTCATGCAATTTCTACTTCAT
188 TCTAGGAATAACAATCATTCCTTT-AACAACTGAATTAA-TTATTTCATGCAA-TTCTACTTCAT
1091988 TTTTA-TGAGGAGATAAACAAAATGGAACATTAAGATAAAAAAAC-ACAATATTTATAAAATCGA
250 TTTTATTGAGGAGATAAACAAAATGGAACATTAAGA-AAAAAAACAACAA-ATTTAT-AAA-CGA
1092051 ACAAAATACAATATAGTTTGAAAGTTTAAT-AA-AAAGCAAAACA-TT-TG-TGAAGGTATTGTT
311 AC-AAATAC-ATATAGTTTGAAAGTTTAATAAAGAAAGCAAAACATTTGTGTTGAAGGTATTGTT
1092111 CCTATGTCCAAAA-GAGAGTGAATTATTAACATAGAAGATTCTGCGATGTTTCGATTGTGTTAAC
374 CC--TGTCCAAAAGGAGAGT--ATTATTAACATAGAAGATTCTGC--TGTTTCGATTGTGTTAAC
1092175 AAACGCAAAAGTAAATTAAATAAAATTTTCACTTTTTTTATATTAATATA
433 AAACGCAAAAGTAAATTAAATAAAATTTTCACTTTTTTTATATTAATATA
1092225 AGGTGCTTAG
Statistics
Matches: 466, Mismatches: 3, Indels: 36
0.92 0.01 0.07
Matches are distributed among these distances:
480 8 0.02
481 64 0.14
482 37 0.08
483 39 0.08
484 18 0.04
485 41 0.09
486 13 0.03
487 60 0.13
488 38 0.08
489 14 0.03
490 39 0.08
491 8 0.02
492 63 0.14
493 24 0.05
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (482 bp):
TCACTTGTAACTTGGGCTTTAGTATTGGGCTTGTAATGGTCTTGAGCTCCGATTGGTCTTGGGCT
CCAATTGGGGCCTAAAAAAATTGTAAAATGTAAATTAATAATAATAATTAATAATATTAATAATT
TTTTGTAGATTCGGACAAAAACGTGTCTACGATAGCCTCTGTGCTTGAACTTAGACCTCTAGGAA
TAACAATCATTCCTTTAACAACTGAATTAATTATTTCATGCAATTCTACTTCATTTTTATTGAGG
AGATAAACAAAATGGAACATTAAGAAAAAAAACAACAAATTTATAAACGAACAAATACATATAGT
TTGAAAGTTTAATAAAGAAAGCAAAACATTTGTGTTGAAGGTATTGTTCCTGTCCAAAAGGAGAG
TATTATTAACATAGAAGATTCTGCTGTTTCGATTGTGTTAACAAACGCAAAAGTAAATTAAATAA
AATTTTCACTTTTTTTATATTAATATA
Found at i:1094850 original size:12 final size:13
Alignment explanation
Indices: 1094828--1094856 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1094818 TTGAATCGGG
1094828 TTTTAAATTTTAA
1 TTTTAAATTTTAA
1094841 TTTT-AATTTTAA
1 TTTTAAATTTTAA
1094853 TTTT
1 TTTT
1094857 TGCAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:1097841 original size:27 final size:26
Alignment explanation
Indices: 1097802--1097853 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
1097792 AAGAAGAAGC
* *
1097802 AAAAAAGAAAAAAACAAAGAGAAAAT
1 AAAAAAAAAAAAAACAAAAAGAAAAT
*
1097828 AAAAAAAAACAAAAAGAAAAAGAAAA
1 AAAAAAAAA-AAAAACAAAAAGAAAA
1097854 GCAAAGAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.85, C:0.04, G:0.10, T:0.02
Consensus pattern (26 bp):
AAAAAAAAAAAAAACAAAAAGAAAAT
Found at i:1099736 original size:20 final size:22
Alignment explanation
Indices: 1099679--1099738 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
1099669 TTGGTACTAG
*
1099679 AAGGGAGTATCGATACCATAGT
1 AAGGTAGTATCGATACCATAGT
* * *
1099701 ATGGTAGTATCAATACCATGGT
1 AAGGTAGTATCGATACCATAGT
1099723 AAGG-A-TATCGATACCA
1 AAGGTAGTATCGATACCA
1099739 GGCAACATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 10 0.31
21 1 0.03
22 21 0.66
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (22 bp):
AAGGTAGTATCGATACCATAGT
Found at i:1099775 original size:18 final size:20
Alignment explanation
Indices: 1099745--1099789 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
1099735 ACCAGGCAAC
**
1099745 ATCGA-ACCTAAAATTGG-T
1 ATCGATACCTAAAAAGGGAT
1099763 ATCGATACC-AAAAAGGGAT
1 ATCGATACCTAAAAAGGGAT
1099782 ATCGATAC
1 ATCGATAC
1099790 AATAATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGATACCTAAAAAGGGAT
Found at i:1099813 original size:95 final size:94
Alignment explanation
Indices: 1099611--1099830 Score: 230
Period size: 95 Copynumber: 2.3 Consensus size: 94
1099601 CTACGAGGTG
* * * * *
1099611 GTATCGATACCATGATAAGTGGTATCGATACCAAGCAACATCGAATCTAATTTAGGTATTGGTAC
1 GTATCGATACCATGGTAA--GGTATCGATACCAAGCAACATCGAACCTAAATTAGGTATCGATAC
* * * * * *
1099676 TAGAAGGGAGTATCGATACCATAGTATGGTA
64 AAAAAGGGAGTATCGATACAATAATATAGAA
* *
1099707 GTATCAATACCATGGTAAGGATATCGATACCAGGCAACATCGAACCTAAAATT-GGTATCGATAC
1 GTATCGATACCATGGTAAGG-TATCGATACCAAGCAACATCGAACCT-AAATTAGGTATCGATA-
1099771 CAAAAAGGGA-TATCGATACAATAATATAGAA
63 CAAAAAGGGAGTATCGATACAATAATATAGAA
* *
1099802 GTATCGGTACCA-GGGAATGGTATCGATAC
1 GTATCGATACCATGGTAA-GGTATCGATAC
1099831 TATTGAGCTT
Statistics
Matches: 104, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
94 15 0.14
95 61 0.59
96 28 0.27
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (94 bp):
GTATCGATACCATGGTAAGGTATCGATACCAAGCAACATCGAACCTAAATTAGGTATCGATACAA
AAAGGGAGTATCGATACAATAATATAGAA
Found at i:1100284 original size:54 final size:54
Alignment explanation
Indices: 1100149--1100536 Score: 575
Period size: 54 Copynumber: 7.2 Consensus size: 54
1100139 TACCAAATGA
* *
1100149 CACTAAGTGTGCATTTCACGGAACTTATCCTATGTGGATGAATAACCATTT---
1 CACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAACCGTTTCGG
*
1100200 CACTAAGTGTGCATTTCACGGAATTTATCCTATGGGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAACCGTTTCGG
* * *
1100254 CACTAAGTGTGTATTTTACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAACCGTTTCGG
* *
1100308 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATAAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAACCGTTTCGG
* * * *
1100362 CAGTAAGTGTGTATTTCACGAAATTTATCATATGTGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAACCGTTTCGG
*
1100416 CACTAAGTGTGCATTTCACTGAATTTATCCTATGTGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAACCGTTTCGG
* * * * * *
1100470 CACTAAGTGTGTATTTTACGGAATTAATCCTATGAGAATGAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAACCGTTTCGG
*
1100524 CACTATGTGTGCA
1 CACTAAGTGTGCA
1100537 AAGCACGAAA
Statistics
Matches: 304, Mismatches: 30, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
51 48 0.16
54 256 0.84
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAACCGTTTCGG
Found at i:1100695 original size:58 final size:58
Alignment explanation
Indices: 1100560--1100746 Score: 277
Period size: 59 Copynumber: 3.2 Consensus size: 58
1100550 ATAATTTAAT
* *
1100560 TATGAATTTCCAGATAGGACACTTTGTGTGCTAAAATGATAATGAAATCATACTAAGTG
1 TATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAA-GAAATCATACTTAGTG
* * *
1100619 TATGAATTTCCAGATAGGGCAGTTTGTGTGTTAAAATGATAAGGAATCATACTTAGTG
1 TATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAAGAAATCATACTTAGTG
* *
1100677 TATGAATTTCCATATAGGGCACTTTGTGTGCTAAAATGATAAAGAAATCATAC-TACATG
1 TATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGAT-AAGAAATCATACTTA-GTG
1100736 TATGAATTTCC
1 TATGAATTTCC
1100747 GTATAGGAAA
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
58 53 0.46
59 63 0.54
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (58 bp):
TATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAATGATAAGAAATCATACTTAGTG
Found at i:1102493 original size:29 final size:28
Alignment explanation
Indices: 1102456--1102510 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 28
1102446 AAAACAGAGG
1102456 TAAAATCTCTCTTCTCTCATT-TTTTCCTC
1 TAAAATCTC-C-TCTCTCATTATTTTCCTC
* *
1102485 TAAACTCTCCTCTCTCGTTATTTTCC
1 TAAAATCTCCTCTCTCATTATTTTCC
1102511 AAAAGCCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.35
28 7 0.30
29 8 0.35
ACGTcount: A:0.16, C:0.33, G:0.02, T:0.49
Consensus pattern (28 bp):
TAAAATCTCCTCTCTCATTATTTTCCTC
Found at i:1103161 original size:3 final size:3
Alignment explanation
Indices: 1103147--1103186 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
1103137 CAAAATGAAT
1103147 TAA TAA -AA TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA T
1103187 TAAAATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1103175 original size:16 final size:16
Alignment explanation
Indices: 1103154--1103184 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1103144 AATTAATAAA
1103154 ATAATAATAATAATAT
1 ATAATAATAATAATAT
1103170 ATAATAATAATAATA
1 ATAATAATAATAATA
1103185 ATTAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATAATAATAATAT
Found at i:1104977 original size:85 final size:84
Alignment explanation
Indices: 1104818--1105060 Score: 324
Period size: 85 Copynumber: 2.9 Consensus size: 84
1104808 CATATAGAGG
* * * * *
1104818 AAATTTACAACATAGCTCAAGGTGAGAAGAGTTATCTGCCAACAAAACCTTCGAGTTCGATTACA
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATATGTCAACAAAACCTTCGAGTTCGATTACA
*
1104883 TTCAACTCAAGGGCATATC
66 TTCAGCTCAAGGGCATATC
1104902 AAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATATGTCAACCAAAACCTTCGAGTTCGATTAC
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATATGTCAA-CAAAACCTTCGAGTTCGATTAC
1104967 ATTCAGCTCAAGGGCATATC
65 ATTCAGCTCAAGGGCATATC
* * * * * * * * *
1104987 AAACTTACGGCATAACTCAAGGCGAGAAGGGCTATATGTCAATGAAGACTTTCAAGTTCGATTTC
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATATGTCAA-CAAAACCTTCGAGTTCGATTAC
*
1105052 ATTTAGCTC
65 ATTCAGCTC
1105061 GAAGATATAT
Statistics
Matches: 141, Mismatches: 17, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
84 37 0.26
85 104 0.74
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (84 bp):
AAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATATGTCAACAAAACCTTCGAGTTCGATTACA
TTCAGCTCAAGGGCATATC
Found at i:1108379 original size:19 final size:20
Alignment explanation
Indices: 1108355--1108411 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 20
1108345 TACACCGTAC
1108355 TATATATTATAT-TTATTAT
1 TATATATTATATATTATTAT
*
1108374 TATATAGTAGTATGATTATTAT
1 TATATATTA-TAT-ATTATTAT
1108396 TATATTATTAT-TATTA
1 TATA-TATTATATATTA
1108412 CTAATATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 8 0.25
20 7 0.22
21 1 0.03
22 12 0.38
23 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TATATATTATATATTATTAT
Found at i:1108407 original size:14 final size:14
Alignment explanation
Indices: 1108355--1108411 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
1108345 TACACCGTAC
1108355 TATA-TATTA-TAT
1 TATATTATTATTAT
*
1108367 T-TATTATTATATAG
1 TATATTATTAT-TAT
*
1108381 TAGTATGATTATTAT
1 TA-TATTATTATTAT
1108396 TATATTATTATTAT
1 TATATTATTATTAT
1108410 TA
1 TA
1108412 CTAATATCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
11 2 0.06
12 6 0.17
14 16 0.44
15 4 0.11
16 8 0.22
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
TATATTATTATTAT
Found at i:1108427 original size:34 final size:33
Alignment explanation
Indices: 1108359--1108427 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
1108349 CCGTACTATA
* * *
1108359 TATTATATTTATTATTATATAGTAGTATGATTAT
1 TATTATA-TTATTATTATATACTAATATCATTAT
1108393 TATTATATTATTATTAT-TACTAATATCATT-T
1 TATTATATTATTATTATATACTAATATCATTAT
1108424 TATT
1 TATT
1108428 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 5 0.16
32 10 0.31
33 10 0.31
34 7 0.22
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (33 bp):
TATTATATTATTATTATATACTAATATCATTAT
Found at i:1114943 original size:6 final size:6
Alignment explanation
Indices: 1114932--1114956 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1114922 ATCGATACCT
1114932 TTTGCA TTTGCA TTTGCA TTTGCA T
1 TTTGCA TTTGCA TTTGCA TTTGCA T
1114957 CTTTGCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TTTGCA
Found at i:1122325 original size:10 final size:10
Alignment explanation
Indices: 1122312--1122343 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1122302 TAAAAAGATG
*
1122312 AAAAAATTAA
1 AAAAAATGAA
1122322 AAAAAATGAA
1 AAAAAATGAA
1122332 AAAAAATGAA
1 AAAAAATGAA
1122342 AA
1 AA
1122344 TGAAAAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:1123462 original size:129 final size:133
Alignment explanation
Indices: 1123216--1123509 Score: 392
Period size: 129 Copynumber: 2.3 Consensus size: 133
1123206 GTGAGCCAAT
1123216 ATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATCA
1 ATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATCA
* * *
1123281 GAAAGCTTGTTTGACCTATCACTCGATTCAACGTATTTCAAATCAGTGACACCTCGCTTGAGGGA
66 GAAAGCTTGTTTGACCTATCACTCGATTCAACGCATTTCAAATCAGTCACACCTCGATTGAGGGA
1123346 TCA
131 TCA
* * *
1123349 ATTTCCAATGGAGAGTTCATAATGA-AAGAACTCATCCGACAGA-GG-G-AGAAGTTTATAATGA
1 ATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATCA
* *
1123410 -AATAGCTTGTTTGACCTATCACTCGATTC-ACGGCATTTCGAATCCGTCACACCTCGATTGAGG
66 GAA-AGCTTGTTTGACCTATCACTCGATTCAAC-GCATTTCAAATCAGTCACACCTCGATTGAGG
*
1123473 GATTGA
129 GA-TCA
*
1123479 CATTT-TAA-A-AGAGTTCATAATGAGAA-AACTC
1 -ATTTCCAATAGAGAGTTCATAATGAGAAGAACTC
1123510 GTCCTAAAGG
Statistics
Matches: 145, Mismatches: 11, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
128 23 0.16
129 69 0.48
130 5 0.03
131 6 0.04
132 18 0.12
133 24 0.17
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (133 bp):
ATTTCCAATAGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATCA
GAAAGCTTGTTTGACCTATCACTCGATTCAACGCATTTCAAATCAGTCACACCTCGATTGAGGGA
TCA
Found at i:1123902 original size:234 final size:236
Alignment explanation
Indices: 1123349--1124123 Score: 1182
Period size: 234 Copynumber: 3.3 Consensus size: 236
1123339 TGAGGGATCA
* *
1123349 ATTTCCAATGGAGAGTTCATAATGAAAGAACTCATCCGACAGAGG-G-AGAAGTTTATAATGA-A
1 ATTTCCAATGGAGAGTTCATAATGAAAGAACTCATCCAAC-GAGGAGAAGAAGTTCATAATGAGA
* * * * *
1123411 ATAGCTTGTTTGACCTATCACTCGATTCACGGCATTTCGAATCCGTCACACCTCGATTGAGGGAT
65 AGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGAT
*
1123476 TGACATTTT-AAAAGAGTTCATAATGAGAA-AACTCGTCCTAAAGGA-AAGTTCATAATGAGAAG
130 TGACATTTTCTAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAGTTCATAATGAGAAG
1123538 AACTTGTTCCTTTCAAGTCCATCACAGAA-AGATGGATCAAC
195 AACTTGTTCCTTTCAAGTCCATCACAGAATAGATGGATCAAC
*
1123579 ATTTCCAATGGAGAGTTCATAATGAGAAGAACCCATCCAACGAGGAGAAGAAGTTCATAATGAGA
1 ATTTCCAATGGAGAGTTCATAATGA-AAGAACTCATCCAACGAGGAGAAGAAGTTCATAATGAGA
* *
1123644 AGAGCTTGTTTGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGGGAT
65 AGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGAT
*
1123709 TGACATTTTCTAAAGAGTTCATAATGACAAGAACTCGTCCTAAAGGAGAAGTTCATAATGAGAAG
130 TGACATTTTCTAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAGTTCATAATGAGAAG
*
1123774 -ACTTGTTCCTTTCAAGTCCATCATAGAAATAGATGG-TCAAC
195 AACTTGTTCCTTTCAAGTCCATCACAG-AATAGATGGATCAAC
* * * *
1123815 ATTTCTAATGGAGAGTTCAT-ATGAGAA-AACTCATCCAACGAGGGGAAGAAGCTCAAAATGAGA
1 ATTTCCAATGGAGAGTTCATAATGA-AAGAACTCATCCAACGAGGAGAAGAAGTTCATAATGAGA
* *
1123878 AGAGCTTGTTCGACCTATCACTCGATTCACGGTATTTTGAATCAGTGACACCTCGCTTGAGGGAT
65 AGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGAT
1123943 TGACATTTTCT-AA-AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAA
130 TGACATTTTCTAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAG-AAGTTCATAATGAGAA
* *
1124006 GAACTTGTTCTTTTCAAGTCCATCACAGAATAGATGGATCAAT
194 GAACTTGTTCCTTTCAAGTCCATCACAGAATAGATGGATCAAC
* *
1124049 ATTTCCAATAGAGAGTTCATAATGAAAGAACTCATCCAACAAGGAAGAAG-AGTTCATAATGAGA
1 ATTTCCAATGGAGAGTTCATAATGAAAGAACTCATCCAACGAGG-AGAAGAAGTTCATAATGAGA
*
1124113 AGAACTTGTTC
65 AGAGCTTGTTC
1124124 AACTTCGCAT
Statistics
Matches: 499, Mismatches: 31, Indels: 25
0.90 0.06 0.05
Matches are distributed among these distances:
230 29 0.06
231 14 0.03
232 46 0.09
233 98 0.20
234 170 0.34
235 89 0.18
236 47 0.09
237 6 0.01
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (236 bp):
ATTTCCAATGGAGAGTTCATAATGAAAGAACTCATCCAACGAGGAGAAGAAGTTCATAATGAGAA
GAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGATT
GACATTTTCTAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAGTTCATAATGAGAAGA
ACTTGTTCCTTTCAAGTCCATCACAGAATAGATGGATCAAC
Found at i:1124210 original size:89 final size:88
Alignment explanation
Indices: 1124043--1124212 Score: 211
Period size: 89 Copynumber: 1.9 Consensus size: 88
1124033 GAATAGATGG
* *
1124043 ATCAATATTTCCAATAGAGAGTTCATAATGAAAGAACTCATCCAACAAGGAAGAAGAGTTCATAA
1 ATCAACATTTCCAATAGAGAGTTCATAATGAAAGAACTCATCCAACAAGGAAGAAAAGTTCATAA
*
1124108 TGAGAAGAACTTGTTCAACTTCGC
66 TAAGAAG-ACTTGTTCAACTTCGC
* * * *
1124132 ATCAACATTTTCAATGGAGAGTTCATAA-GAGAAGAACTCATCCGA-AAGAGAGATAATAAGTTC
1 ATCAACATTTCCAATAGAGAGTTCATAATGA-AAGAACTCATCCAACAAG-GA-AGAA-AAGTTC
1124195 ATAATAAGAAG-CTTGTTC
62 ATAATAAGAAGACTTGTTC
1124213 GACCTATACT
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
88 5 0.07
89 47 0.67
90 3 0.04
91 15 0.21
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (88 bp):
ATCAACATTTCCAATAGAGAGTTCATAATGAAAGAACTCATCCAACAAGGAAGAAAAGTTCATAA
TAAGAAGACTTGTTCAACTTCGC
Found at i:1124296 original size:323 final size:324
Alignment explanation
Indices: 1123810--1124449 Score: 831
Period size: 323 Copynumber: 2.0 Consensus size: 324
1123800 AAATAGATGG
* * * *
1123810 TCAACATTTCTAATGGAGAGTTCATATGAGAAAACTCATCCAACGAGGGGAAGAAGCTCAAAATG
1 TCAACATTTCTAATGGAGAGTTCATAAGAGAAAACTCATCCAAAGAGGAGAAGAAGCTCAAAATA
** *
1123875 AGAAGAGCTTGTTCGACCTATCACTCGATTCACGGTATTTTGAATCAGTGACACCTCGCTTGAGG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGG
* * *
1123940 GATTGACATTTTCTAAAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGA
131 AATTGACATTTCCAAAAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGA-A
* *
1124005 AGAACTTGTTCTTTTCAAGTCCA-TCACAG-AATAGATGGA-TCAATATTTCCAAT-AGAGAGTT
195 AGAACTTGTTCCTTTCAAGTCCACT-ACAGAAATAGAT-GACTCAACATTTCCAATGA-AGAGTT
1124066 CATAATGA-AAGAACTCATCCAACAAG-GAAGAAG-AGTTCATAATGAGAAGAACTTGTTCAACT
257 CATAATGAGAAGAACTCATCC-ACAAGAG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT
1124128 TCGCA
320 TCGCA
* * * *
1124133 TCAACATTT-TCAATGGAGAGTTCATAAGAGAAGAACTCATCCGAAAGAGAGATAATAAGTTCAT
1 TCAACATTTCT-AATGGAGAGTTCATAAGAGAA-AACTCATCC-AAAGAG-GAGAAGAAGCTCAA
*
1124197 AATAAG-A-AGCTTGTTCGACCTAT-ACTCGATTCACGACA-TTCGAATCAGTGACGCCTCG-TT
62 AATAAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTT
* * *
1124257 AGAGGAATTGACATTTCCAAAAGAGTTCA-AATTAGAAGAACTCGTCTTAAATGAGAAAGTTCAT
127 -GAGGAATTGACATTTCC-AAA-AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCAT
* * *
1124321 AATGAAAGAACTTGTTCCTTTCAAGTCCACTACAGAAATAGGTGACTCAACATTTTCAGTGAAGA
189 AATGAAAGAACTTGTTCCTTTCAAGTCCACTACAGAAATAGATGACTCAACATTTCCAATGAAGA
* * *
1124386 TTTCATAATGAGAAGAACTCATCCACGAGAGAGAAGAAGTTCATAATGAGAATAACTTGTTCAA
254 GTTCATAATGAGAAGAACTCATCCACAAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1124450 TCCAACGACA
Statistics
Matches: 277, Mismatches: 26, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
321 2 0.01
322 63 0.23
323 121 0.44
324 71 0.26
325 6 0.02
326 14 0.05
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (324 bp):
TCAACATTTCTAATGGAGAGTTCATAAGAGAAAACTCATCCAAAGAGGAGAAGAAGCTCAAAATA
AGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGACACCTCGCTTGAGG
AATTGACATTTCCAAAAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAAA
GAACTTGTTCCTTTCAAGTCCACTACAGAAATAGATGACTCAACATTTCCAATGAAGAGTTCATA
ATGAGAAGAACTCATCCACAAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTCGCA
Found at i:1124626 original size:17 final size:18
Alignment explanation
Indices: 1124573--1124626 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 18
1124563 GGGATTAAAA
1124573 TATATATTATATTATT-T
1 TATATATTATATTATTAT
* * *
1124590 TATATACTATAGTATGAT
1 TATATATTATATTATTAT
1124608 TAT-TATTATATTATTAT
1 TATATATTATATTATTAT
1124625 TA
1 TA
1124627 CTAATATCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 26 0.87
18 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (18 bp):
TATATATTATATTATTAT
Found at i:1126146 original size:10 final size:10
Alignment explanation
Indices: 1126131--1126164 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1126121 AATGACGGTG
1126131 ATTTTATTCT
1 ATTTTATTCT
**
1126141 ATTTTATGAT
1 ATTTTATTCT
1126151 ATTTTATTCT
1 ATTTTATTCT
1126161 ATTT
1 ATTT
1126165 AAATTTAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.68
Consensus pattern (10 bp):
ATTTTATTCT
Found at i:1127870 original size:16 final size:16
Alignment explanation
Indices: 1127849--1127881 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1127839 TTAATAAATA
1127849 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1127865 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1127881 A
1 A
1127882 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1129607 original size:18 final size:18
Alignment explanation
Indices: 1129577--1129617 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1129567 CGACCAGTTT
1129577 ACCCGACCTGTTGA-CCTG
1 ACCCGACCTGTTGATCC-G
1129595 ACCCGACAC-GTTGATCCG
1 ACCCGAC-CTGTTGATCCG
1129613 ACCCG
1 ACCCG
1129618 TTGACCGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.20, C:0.41, G:0.22, T:0.17
Consensus pattern (18 bp):
ACCCGACCTGTTGATCCG
Found at i:1132112 original size:48 final size:48
Alignment explanation
Indices: 1132056--1132171 Score: 155
Period size: 48 Copynumber: 2.4 Consensus size: 48
1132046 TTCGATTTGA
*
1132056 ATTT-TGATCTGATACTTGACATGGATTCTGATCTGATATCTGACATGG
1 ATTTCTGATCTGATACTTGACATGGATTCTGATATGATATCTGACAT-G
* * * *
1132104 A-TTCTGATCTGATACTTGACTTGGATTCTGATATGTTATTTGACCTG
1 ATTTCTGATCTGATACTTGACATGGATTCTGATATGATATCTGACATG
*
1132151 ATTTCTGATATGATACTTGAC
1 ATTTCTGATCTGATACTTGAC
1132172 CTGATTTATG
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
47 4 0.07
48 56 0.93
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (48 bp):
ATTTCTGATCTGATACTTGACATGGATTCTGATATGATATCTGACATG
Found at i:1132178 original size:24 final size:24
Alignment explanation
Indices: 1132060--1132171 Score: 138
Period size: 24 Copynumber: 4.7 Consensus size: 24
1132050 ATTTGAATTT
1132060 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
1132084 TGATCTGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
*
1132108 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
* * * *
1132132 TGATATGTTATTTGACCT-GATTTC
1 TGATCTGATACTTGACATGGA-TTC
*
1132156 TGATATGATACTTGAC
1 TGATCTGATACTTGAC
1132172 CTGATTTATG
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
23 3 0.04
24 74 0.95
25 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:1132188 original size:24 final size:24
Alignment explanation
Indices: 1132108--1132181 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
1132098 ACATGGATTC
* * *
1132108 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
1132132 TGATATGTTATTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
1132156 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
1132180 TG
1 TG
1132182 TTTTGATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 2 0.05
24 40 0.95
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:1136552 original size:21 final size:21
Alignment explanation
Indices: 1136515--1136554 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1136505 TCTGCTGAAA
**
1136515 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGTTGCGGAGTATG
1136536 CTCCACCTGTTGCGGAGTA
1 CTCCACCTGTTGCGGAGTA
1136555 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGTTGCGGAGTATG
Found at i:1139246 original size:16 final size:16
Alignment explanation
Indices: 1139225--1139298 Score: 121
Period size: 16 Copynumber: 4.6 Consensus size: 16
1139215 CCAAAGATGT
1139225 CAACTTTCAATTTTGC
1 CAACTTTCAATTTTGC
* *
1139241 CAACTTTTAACTTTGC
1 CAACTTTCAATTTTGC
1139257 CAACTTTCAATTTTGC
1 CAACTTTCAATTTTGC
*
1139273 CAACTTTCAATTTTTC
1 CAACTTTCAATTTTGC
1139289 CAACTTTCAA
1 CAACTTTCAA
1139299 GCCAAACATA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 53 1.00
ACGTcount: A:0.27, C:0.26, G:0.04, T:0.43
Consensus pattern (16 bp):
CAACTTTCAATTTTGC
Found at i:1141242 original size:37 final size:37
Alignment explanation
Indices: 1141200--1141275 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
1141190 TCAGCCATGT
1141200 ATGGGAAATGATCAAAATGTTACAACGCTCAAGATTG
1 ATGGGAAATGATCAAAATGTTACAACGCTCAAGATTG
1141237 ATGGGAAATGATCAAAATGTTACAACGCTCAAGATTG
1 ATGGGAAATGATCAAAATGTTACAACGCTCAAGATTG
1141274 AT
1 AT
1141276 ACCTAATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (37 bp):
ATGGGAAATGATCAAAATGTTACAACGCTCAAGATTG
Found at i:1141714 original size:3 final size:3
Alignment explanation
Indices: 1141706--1141772 Score: 91
Period size: 3 Copynumber: 22.0 Consensus size: 3
1141696 TCTAATTTTA
* *
1141706 ATT ATT ATT ATT ATT GTT ATT ATT ATT GTT ATT ATT ATT ATGT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
1141751 ATT AATT ATT ATT ATT ATT ATT
1 ATT -ATT ATT ATT ATT ATT ATT
1141773 TTTGCAGGCC
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 1 0.02
3 52 0.91
4 4 0.07
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1142374 original size:13 final size:13
Alignment explanation
Indices: 1142356--1142386 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1142346 TTCAGGGAGA
*
1142356 AAAAAAAAACCAG
1 AAAAAAAAACAAG
1142369 AAAAAAAAACAAG
1 AAAAAAAAACAAG
1142382 AAAAA
1 AAAAA
1142387 GAGAACTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAAG
Found at i:1143027 original size:19 final size:19
Alignment explanation
Indices: 1142981--1143027 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1142971 CATTAATTTG
*
1142981 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
1143001 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
1143021 TATATTT
1 TATATTT
1143028 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:1144800 original size:23 final size:24
Alignment explanation
Indices: 1144770--1144817 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1144760 ATTAAAGTCA
*
1144770 TAATTGTTTT-TAAAAATAATATT
1 TAATTGTTTTAAAAAAATAATATT
1144793 TAATTGTTTTACAAAAAATAATATT
1 TAATTGTTTTA-AAAAAATAATATT
1144818 AAAAATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.45
25 12 0.55
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (24 bp):
TAATTGTTTTAAAAAAATAATATT
Found at i:1144809 original size:25 final size:27
Alignment explanation
Indices: 1144781--1144835 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
1144771 AATTGTTTTT
*
1144781 AAAAATAATATT-TAATTGTTTTA-CA
1 AAAAATAATATTAAAATTGTTTTAGCA
1144806 AAAAATAATATTAAAAATTGTTTTAGCA
1 AAAAATAATATT-AAAATTGTTTTAGCA
1144834 AA
1 AA
1144836 TAACCCATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 12 0.46
27 10 0.38
28 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (27 bp):
AAAAATAATATTAAAATTGTTTTAGCA
Found at i:1148494 original size:16 final size:16
Alignment explanation
Indices: 1148469--1148518 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
1148459 AGATCATATT
*
1148469 AAAGCGAAGAGAAAAG
1 AAAGCAAAGAGAAAAG
1148485 AAAGCAAAGAG-AAAG
1 AAAGCAAAGAGAAAAG
* *
1148500 AAA-CAAAGTGAAAAA
1 AAAGCAAAGAGAAAAG
1148515 AAAG
1 AAAG
1148519 AACAGAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 6 0.21
15 13 0.45
16 10 0.34
ACGTcount: A:0.68, C:0.06, G:0.24, T:0.02
Consensus pattern (16 bp):
AAAGCAAAGAGAAAAG
Found at i:1148512 original size:14 final size:15
Alignment explanation
Indices: 1148469--1148512 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1148459 AGATCATATT
*
1148469 AAAGCGAAGAGAAAAG
1 AAAGCAAAGAG-AAAG
1148485 AAAGCAAAGAGAAAG
1 AAAGCAAAGAGAAAG
*
1148500 AAA-CAAAGTGAAA
1 AAAGCAAAGAGAAA
1148513 AAAAAGAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 9 0.35
15 7 0.27
16 10 0.38
ACGTcount: A:0.66, C:0.07, G:0.25, T:0.02
Consensus pattern (15 bp):
AAAGCAAAGAGAAAG
Found at i:1150124 original size:91 final size:90
Alignment explanation
Indices: 1150010--1150322 Score: 328
Period size: 91 Copynumber: 3.3 Consensus size: 90
1150000 TATTGAAGTA
*
1150010 AAATTCCGTCTC--TTGAGACATTTTTCCACAAACTTTGAGATTTTTCTAAAAACAAAATTTGTC
1 AAATTTCGTCTCATTTGAGACATTTTTCCACAAACTTTGAGATTTTTCTAAAAAC-AAATTTGTC
*
1150073 TTGCTTGAGACAATTTATTTCAAAAC
65 TCGCTTGAGACAATTTATTTCAAAAC
*
1150099 AAATTTCGTCTCATTTGAGACATTTTTCCTTTGAGATCCAAATTTTGA-ATTTGTT-TCACATTA
1 AAATTTCGTCTCATTTGAGACATTTTTCC------A--CAAACTTTGAGATTT-TTCT-A-A--A
** ** * *
1150162 AACAAGGTTGATCTCATTTGAGATCGTATCTATTTCAAAAC
53 AACAAATTTG-TCTCGCTTGAGA-C-AATTTATTTCAAAAC
** *
1150203 AAATTTCGTCTCGCTTGAGACATTTTTCCACAAACTTTGAGATTTTTCTAAAAACGAATTTTGTC
1 AAATTTCGTCTCATTTGAGACATTTTTCCACAAACTTTGAGATTTTTCTAAAAAC-AAATTTGTC
1150268 TCGCTTGAGACAATTTATTTCAAAAC
65 TCGCTTGAGACAATTTATTTCAAAAC
1150294 AAATTTCGTCTCATTTGAGACATTTTTCC
1 AAATTTCGTCTCATTTGAGACATTTTTCC
1150323 TTTGAGATCC
Statistics
Matches: 183, Mismatches: 20, Indels: 40
0.75 0.08 0.16
Matches are distributed among these distances:
89 11 0.06
91 55 0.30
92 1 0.01
93 14 0.08
94 5 0.03
95 1 0.01
96 12 0.07
97 6 0.03
98 6 0.03
99 12 0.07
100 1 0.01
101 5 0.03
102 13 0.07
103 1 0.01
104 40 0.22
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.40
Consensus pattern (90 bp):
AAATTTCGTCTCATTTGAGACATTTTTCCACAAACTTTGAGATTTTTCTAAAAACAAATTTGTCT
CGCTTGAGACAATTTATTTCAAAAC
Found at i:1150353 original size:195 final size:195
Alignment explanation
Indices: 1150021--1150470 Score: 791
Period size: 195 Copynumber: 2.3 Consensus size: 195
1150011 AATTCCGTCT
* *
1150021 CTTGAGACATTTTTCCACAAACTTTGAGATTTTTCTAAAAACAAAATTTGTCTTGCTTGAGACAA
1 CTTGAGACATTTTTCCACAAACTTTGAGATTTTTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
1150086 TTTATTTCAAAACAAATTTCGTCTCATTTGAGACATTTTTCCTTTGAGATCCAAATTTTGAATTT
66 TTTATTTCAAAACAAATTTCGTCTCATTTGAGACATTTTTCCTTTGAGATCCAAATTTTGAATTT
*
1150151 GTTTCACATTAAACAAGGTTGATCTCATTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCG
131 GTTTCACATTAAACAAAGTTGATCTCATTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCG
*
1150216 CTTGAGACATTTTTCCACAAACTTTGAGATTTTTCTAAAAACGAATTTTGTCTCGCTTGAGACAA
1 CTTGAGACATTTTTCCACAAACTTTGAGATTTTTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
1150281 TTTATTTCAAAACAAATTTCGTCTCATTTGAGACATTTTTCCTTTGAGATCCAAATTTTGAATTT
66 TTTATTTCAAAACAAATTTCGTCTCATTTGAGACATTTTTCCTTTGAGATCCAAATTTTGAATTT
1150346 GTTTCACATTAAACAAAGTTGATCTCATTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCG
131 GTTTCACATTAAACAAAGTTGATCTCATTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCG
* * * * *
1150411 CTTGAGACA-TTTTCCCCAAATTTTGAGA-ATTT-T-AAAACAAATTGTGTTTCGCTTGAGACA
1 CTTGAGACATTTTTCCACAAACTTTGAGATTTTTCTAAAAACAAATTTTGTCTCGCTTGAGACA
1150471 TTCTTTCCTT
Statistics
Matches: 245, Mismatches: 10, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
191 24 0.10
192 1 0.00
193 3 0.01
194 17 0.07
195 200 0.82
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (195 bp):
CTTGAGACATTTTTCCACAAACTTTGAGATTTTTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
TTTATTTCAAAACAAATTTCGTCTCATTTGAGACATTTTTCCTTTGAGATCCAAATTTTGAATTT
GTTTCACATTAAACAAAGTTGATCTCATTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCG
Found at i:1150623 original size:105 final size:103
Alignment explanation
Indices: 1150440--1150678 Score: 288
Period size: 105 Copynumber: 2.3 Consensus size: 103
1150430 ATTTTGAGAA
* *
1150440 TTTTAAAACAAATTGTGTTTCGCTTGAGACATTCTTTCCTTTGAGATACAAATTTTGAATTTGAT
1 TTTTAAAACAAATT-TGTCTCGCTTGAGACATTCTTCCCTTTGAGATACAAATTTTGAATTTGAT
*
1150505 TCACTAAAAACAAAATTAATCTCACCTT-AGATTCTTGTTTC
65 TCACTAAAAACAAAATTAATCTCA-CTTGAGA-TCGT-TTTC
* * *
1150546 TTTTAAAACAAATTTCGTCTCGCTTGAGACCTT-TTCCCTTTGAGATCCAAATTTTGAATTTGTT
1 TTTTAAAACAAATTT-GTCTCGCTTGAGACATTCTTCCCTTTGAGATACAAATTTTGAATTTGAT
* * *
1150610 TCAC-ATTAAACAAAGTTGATCTCACTTGAGATCGTTTTC
65 TCACTA-AAAACAAAATTAATCTCACTTGAGATCGTTTTC
**
1150649 -TCAAAAACAAACTTTGTCTCGCTTGAGACA
1 TTTTAAAACAAA-TTTGTCTCGCTTGAGACA
1150679 ATTTCTCTAA
Statistics
Matches: 117, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
102 23 0.20
103 7 0.06
104 7 0.06
105 51 0.44
106 29 0.25
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (103 bp):
TTTTAAAACAAATTTGTCTCGCTTGAGACATTCTTCCCTTTGAGATACAAATTTTGAATTTGATT
CACTAAAAACAAAATTAATCTCACTTGAGATCGTTTTC
Found at i:1150702 original size:37 final size:35
Alignment explanation
Indices: 1150651--1150749 Score: 110
Period size: 37 Copynumber: 2.8 Consensus size: 35
1150641 TCGTTTTCTC
* *
1150651 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAACAAATTTTGTCTCGCTTGAGACAATATCT-T
* ** *
1150687 AAAAAATAAATTTTGTCTCATTTGAGACTATATCTT
1 -AAAAACAAATTTTGTCTCGCTTGAGACAATATCTT
*
1150723 -AAAGCAAATTTTGTCTCGCTTGAGACA
1 AAAAACAAATTTTGTCTCGCTTGAGACA
1150750 TCATTTTCTC
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
34 22 0.43
36 1 0.02
37 28 0.55
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (35 bp):
AAAAACAAATTTTGTCTCGCTTGAGACAATATCTT
Found at i:1151039 original size:27 final size:27
Alignment explanation
Indices: 1151000--1151185 Score: 234
Period size: 29 Copynumber: 6.6 Consensus size: 27
1150990 TTTCTTTTGA
1151000 GAAAAAAATCTTTGAGTTTGTTCCTCTT
1 GAAAAAAATCTTTGAGTTTGTTCCT-TT
1151028 G-AAAAAATCTTTGAGTTTGTTCCTCTT
1 GAAAAAAATCTTTGAGTTTGTTCCT-TT
1151055 G-AAAAAATCTTTGAGTTTGTTCCTTTT
1 GAAAAAAATCTTTGAGTTTGTTCC-TTT
1151082 GAATAAAAATCTTTGAGTTTGTTCCTTTT
1 GAA-AAAAATCTTTGAGTTTGTTCC-TTT
*
1151111 GAATAAAAATCTTGGAGTTTGTTCCTTT
1 GAA-AAAAATCTTTGAGTTTGTTCCTTT
* *
1151139 GGAATAAAAATCTGTGAG-TTGTTTCGTTT
1 -GAA-AAAAATCTTTGAGTTTG-TTCCTTT
1151168 GAAAAAAAATCTTTGAGT
1 G-AAAAAAATCTTTGAGT
1151186 CTATTTACTT
Statistics
Matches: 146, Mismatches: 5, Indels: 13
0.89 0.03 0.08
Matches are distributed among these distances:
27 52 0.36
28 22 0.15
29 72 0.49
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (27 bp):
GAAAAAAATCTTTGAGTTTGTTCCTTT
Found at i:1151144 original size:58 final size:57
Alignment explanation
Indices: 1150993--1151185 Score: 261
Period size: 58 Copynumber: 3.4 Consensus size: 57
1150983 AAGACAATTT
1150993 CTTTTGAGAAAAAAATCTTTGAGTTTGTTCCTCTTG-A-AAAAATCTTTGAGTTTGTTC
1 CTTTTGA-AAAAAAATCTTTGAGTTTGTTCCT-TTGAATAAAAATCTTTGAGTTTGTTC
*
1151050 CTCTTG--AAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAAAATCTTTGAGTTTGTTCC-TTTGAATAAAAATCTTTGAGTTTGTTC
* * * *
1151106 CTTTTGAATAAAAATCTTGGAGTTTGTTCCTTTGGAATAAAAATCTGTGAG-TTGTTT
1 CTTTTGAAAAAAAATCTTTGAGTTTGTTCCTTT-GAATAAAAATCTTTGAGTTTGTTC
*
1151163 CGTTTGAAAAAAAATCTTTGAGT
1 CTTTTGAAAAAAAATCTTTGAGT
1151186 CTATTTACTT
Statistics
Matches: 121, Mismatches: 9, Indels: 12
0.85 0.06 0.08
Matches are distributed among these distances:
54 25 0.21
55 2 0.02
56 25 0.21
57 33 0.27
58 36 0.30
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.44
Consensus pattern (57 bp):
CTTTTGAAAAAAAATCTTTGAGTTTGTTCCTTTGAATAAAAATCTTTGAGTTTGTTC
Found at i:1151272 original size:30 final size:30
Alignment explanation
Indices: 1151232--1151429 Score: 153
Period size: 30 Copynumber: 6.1 Consensus size: 30
1151222 AATTTTGTGA
*
1151232 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* *
1151262 AAAAAACTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* * * *
1151292 AAAATTTTGTCTCTTTTAAGATAGTTTCTTTTGAAAC
1 AAAA------ATC-TTTGAGATTGTTTCTTTGGAAAC
*
1151329 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* * * *
1151359 AAAATTTTGTCTCTCTTAAGATAGTTTCTTTTGAAAC
1 AAAA------ATCT-TTGAGATTGTTTCTTTGGAAAC
*
1151396 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
1151426 AAAA
1 AAAA
1151430 TTTTGTCTCT
Statistics
Matches: 130, Mismatches: 24, Indels: 28
0.71 0.13 0.15
Matches are distributed among these distances:
30 76 0.58
31 5 0.04
36 4 0.03
37 45 0.35
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:1151292 original size:90 final size:88
Alignment explanation
Indices: 1151144--1151306 Score: 238
Period size: 90 Copynumber: 1.8 Consensus size: 88
1151134 CCTTTGGAAT
* *
1151144 AAAAATCTGTGAGTTGTTTCGTTTGAAAAAAAATCTTTGAGTCTATTTACTTTGAAACAAAGTTT
1 AAAAATCTGTGAGTTGTTTCGTTTGAAAAAAAAACTTTGAGTCTATTTACTTTGAAACAAAATTT
1151209 TGTCTCTTGAGACAATTTTGTGA
66 TGTCTCTTGAGACAATTTTGTGA
* * * *
1151232 AAAAATCTTTGAGATTGTTTCTTTTGAAACAAAAAACTTTGAGTTTGTTT-CTTTGGAAACAAAA
1 AAAAATCTGTGAG-TTGTTTCGTTTGAAA-AAAAAACTTTGAGTCTATTTACTTT-GAAACAAAA
1151296 TTTTGTCTCTT
63 TTTTGTCTCTT
1151307 TTAAGATAGT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
88 12 0.18
89 18 0.27
90 36 0.55
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (88 bp):
AAAAATCTGTGAGTTGTTTCGTTTGAAAAAAAAACTTTGAGTCTATTTACTTTGAAACAAAATTT
TGTCTCTTGAGACAATTTTGTGA
Found at i:1151322 original size:67 final size:67
Alignment explanation
Indices: 1151243--1151474 Score: 396
Period size: 67 Copynumber: 3.5 Consensus size: 67
1151233 AAAATCTTTG
* * *
1151243 AGATTGTTTCTTTTGAAACAAAAAACTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1151308 TA
66 TA
1151310 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1151375 TA
66 TA
1151377 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1151442 TA
66 TA
* * *
1151444 AGACAATTTCTTTTG-AA-AAAAATCTTCGAGT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGT
1151475 CTTTTCTCTT
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
65 13 0.08
66 2 0.01
67 144 0.91
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (67 bp):
AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
TA
Found at i:1151328 original size:37 final size:37
Alignment explanation
Indices: 1151278--1151466 Score: 138
Period size: 37 Copynumber: 5.5 Consensus size: 37
1151268 CTTTGAGTTT
1151278 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
* * * * *
1151315 GTTTCTTTTGAAACAAAA------ATC-TTTGAGTTT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
*
1151345 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
* * * * *
1151382 GTTTCTTTTGAAACAAAA------ATC-TTTGAGTTT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
* *
1151412 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGACA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
* *
1151449 ATTTCTTTTGAAA-AAAAT
1 GTTTCTTTGGAAACAAAAT
1151467 CTTCGAGTCT
Statistics
Matches: 112, Mismatches: 26, Indels: 29
0.67 0.16 0.17
Matches are distributed among these distances:
30 45 0.40
31 4 0.04
36 9 0.08
37 54 0.48
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (37 bp):
GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATA
Found at i:1152125 original size:31 final size:31
Alignment explanation
Indices: 1152090--1152201 Score: 88
Period size: 31 Copynumber: 3.6 Consensus size: 31
1152080 ACCCCGATCT
1152090 TTGAGAACA-TTTCCCTTAAAAACAAATTTTC
1 TTGAG-ACAGTTTCCCTTAAAAACAAATTTTC
** * ** ** *
1152121 TTGAGACAGTTTTCAATGAAACCCCGA-TCT-
1 TTGAGACAG-TTTCCCTTAAAAACAAATTTTC
1152151 TTGAGAACA-TTTCCCTTAAAAACAAATTTTC
1 TTGAG-ACAGTTTCCCTTAAAAACAAATTTTC
*
1152182 TTGAGACAGTTTCCTTTAAA
1 TTGAGACAGTTTCCCTTAAA
1152202 TCATCTTTGA
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
29 10 0.17
30 13 0.22
31 25 0.43
32 10 0.17
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (31 bp):
TTGAGACAGTTTCCCTTAAAAACAAATTTTC
Found at i:1152130 original size:62 final size:62
Alignment explanation
Indices: 1152059--1152193 Score: 263
Period size: 61 Copynumber: 2.2 Consensus size: 62
1152049 TTTGTCTCAT
1152059 TTGAGACAGTTTTTCAATGAAACCCCGATCTTTGAGAACATTTCCCTTAAAAACAAATTTTC
1 TTGAGACAGTTTTTCAATGAAACCCCGATCTTTGAGAACATTTCCCTTAAAAACAAATTTTC
1152121 TTGAGACAG-TTTTCAATGAAACCCCGATCTTTGAGAACATTTCCCTTAAAAACAAATTTTC
1 TTGAGACAGTTTTTCAATGAAACCCCGATCTTTGAGAACATTTCCCTTAAAAACAAATTTTC
1152182 TTGAGACAGTTT
1 TTGAGACAGTTT
1152194 CCTTTAAATC
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 61 0.85
62 11 0.15
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (62 bp):
TTGAGACAGTTTTTCAATGAAACCCCGATCTTTGAGAACATTTCCCTTAAAAACAAATTTTC
Found at i:1152302 original size:28 final size:28
Alignment explanation
Indices: 1152255--1152331 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
1152245 GAGACAGTTG
1152255 CTTTTGAAACACATCATCTTTGAGTTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTTTGTTT
* *
1152286 -TTCTTGAAACGAATCTTTGGGTTTGTTT
1 CTT-TTGAAACAAATCTTTGAGTTTGTTT
1152314 CTTTTGAAACAAATCTTT
1 CTTTTGAAACAAATCTTT
1152332 AATTTGGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 29 0.71
29 2 0.05
30 3 0.07
31 7 0.17
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.48
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTTTGTTT
Found at i:1152432 original size:40 final size:40
Alignment explanation
Indices: 1152377--1152704 Score: 151
Period size: 40 Copynumber: 7.5 Consensus size: 40
1152367 TGGCCAGCCG
* * *
1152377 TCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGACC
* * **
1152417 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGACC
* *
1152459 GTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCAT--CC--CC---AGA---CCAGACC
* * * * *
1152510 TCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGACC
*
1152550 TCCTCATCACGTAGGAGCCGTGTCA-CCCCTAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCC-AG---ACCAGACC
* *
1152592 GTCCTCATCACGTAGGAACCGTGTTATTGCCTTCCTAAAGATGGCCAAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCA-T-CC--CC---AGA---CC-AGACC
* * * * *
1152644 TCTTCATCACGTATGAGCCGTGTCATCCACC-GACCAAATC
1 TCCTCATCACGTAGGAACCGTGTCATCC-CCAGACCAGACC
1152684 TCCTCATCACGTAGGAACCGT
1 TCCTCATCACGTAGGAACCGT
1152705 TTCACCCTTA
Statistics
Matches: 219, Mismatches: 37, Indels: 64
0.68 0.12 0.20
Matches are distributed among these distances:
39 4 0.02
40 77 0.35
41 2 0.01
42 2 0.01
43 58 0.26
44 2 0.01
45 2 0.01
46 4 0.02
47 2 0.01
48 6 0.03
49 2 0.01
50 33 0.15
51 24 0.11
52 1 0.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGACC
Found at i:1152467 original size:43 final size:43
Alignment explanation
Indices: 1152409--1152615 Score: 154
Period size: 43 Copynumber: 4.7 Consensus size: 43
1152399 TCATCCCCAG
* *
1152409 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCATAGATA
* * *
1152452 ACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTG---TCA---TCC-ATAGATA
* * * * ***
1152502 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCG---
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCATAGATA
* * *
1152542 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCATAGATA
*
1152585 ACCAG-CCGTCCTCATCACGTAGGAACCGTGT
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTGT
1152616 TATTGCCTTC
Statistics
Matches: 129, Mismatches: 22, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
40 33 0.26
42 2 0.02
43 54 0.42
44 3 0.02
46 3 0.02
47 3 0.02
49 2 0.02
50 28 0.22
51 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.22
Consensus pattern (43 bp):
ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCCATAGATA
Found at i:1152596 original size:133 final size:133
Alignment explanation
Indices: 1152358--1152721 Score: 550
Period size: 133 Copynumber: 2.7 Consensus size: 133
1152348 AAACCATAAC
* * * * ** *
1152358 TCCTAAAGATGGCCAG-CCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTC
1 TCCTAAAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCCTC
*
1152422 ATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
65 ATCACGTAGGAGCCGTGTCACCCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
1152487 ACCT
130 ACCT
1152491 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCCTCA
1 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCCTCA
* **
1152556 TCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATTG
66 TCACGTAGGAGCCGTGTCACCCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
1152621 CCT
131 CCT
* *
1152624 TCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCCGTGTCATCCACCGACCAAATCTCCTC
1 TCCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCCTC
* * * *
1152689 ATCACGTAGGAACCGTTTCACCCTTAGACAACC
65 ATCACGTAGGAGCCGTGTCACCCATAGATAACC
1152722 CGAACTCTTC
Statistics
Matches: 212, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
133 134 0.63
134 78 0.37
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (133 bp):
TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGATCTCCTCA
TCACGTAGGAGCCGTGTCACCCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
CCT
Found at i:1152924 original size:3 final size:3
Alignment explanation
Indices: 1152916--1152970 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
1152906 TCTAATTTTA
*
1152916 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATGT -TT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT -ATT ATT ATT
1152962 ATT ATT ATT
1 ATT ATT ATT
1152971 TTTGCAGGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 42 0.89
4 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1153565 original size:14 final size:14
Alignment explanation
Indices: 1153546--1153577 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1153536 GTTCAGGGAG
*
1153546 AAAAAAAAACCAGA
1 AAAAAAAAACAAGA
1153560 AAAAAAAAACAAGA
1 AAAAAAAAACAAGA
1153574 AAAA
1 AAAA
1153578 GAACTACTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACAAGA
Found at i:1154191 original size:19 final size:19
Alignment explanation
Indices: 1154145--1154191 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1154135 CATTAATTTG
*
1154145 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
1154165 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
1154185 TATATTT
1 TATATTT
1154192 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:1157304 original size:138 final size:138
Alignment explanation
Indices: 1157056--1157374 Score: 521
Period size: 138 Copynumber: 2.3 Consensus size: 138
1157046 TTCTACAGTT
*
1157056 ATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTGCCAAGTCCCATCAGAAATAATA
1 ATAATGGAAGGCGCGCCCCCAGGAACGCGCTTTCACCACTTTGCCAAGTCCCATCAGAAATAATA
* * *
1157121 GGTACTGACATTAATAGTTCCCCAGTGGACATAAGTGACATAATAGGGCAATGATAACATATTGT
66 GGTACTGACATGAATAGTTCCCCAGGGGACATAAGTGACATAATAGGGCAATGATAACATATTCT
*
1157186 CTGAGAAA
131 CTGACAAA
* * * * *
1157194 ATAATGGAAGGTGCGCCCCCAAGAACGCGCTTTCACCACTTTGTCAAGTCCCCTCGGAAATAATA
1 ATAATGGAAGGCGCGCCCCCAGGAACGCGCTTTCACCACTTTGCCAAGTCCCATCAGAAATAATA
* *
1157259 GGTACTGACATGAATAGTTCTCCAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
66 GGTACTGACATGAATAGTTCCCCAGGGGACATAAGTGACATAATAGGGCAATGATAACATATTCT
1157324 CTGACAAA
131 CTGACAAA
*
1157332 ATAATGGAATGCGCGCCCCCAGGAACGCGCTTTCACCACTTTG
1 ATAATGGAAGGCGCGCCCCCAGGAACGCGCTTTCACCACTTTG
1157375 GGTACTGACA
Statistics
Matches: 166, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
138 166 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (138 bp):
ATAATGGAAGGCGCGCCCCCAGGAACGCGCTTTCACCACTTTGCCAAGTCCCATCAGAAATAATA
GGTACTGACATGAATAGTTCCCCAGGGGACATAAGTGACATAATAGGGCAATGATAACATATTCT
CTGACAAA
Found at i:1157484 original size:117 final size:116
Alignment explanation
Indices: 1157259--1157477 Score: 339
Period size: 117 Copynumber: 1.9 Consensus size: 116
1157249 GGAAATAATA
* * * * *
1157259 GGTACTGACATGAATAGTTCTCCAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 GGTACTGACATAAATAGTGCCCCAGAGGACATGAGTGACATAATAGGGCAATGATAACATATTAT
* *
1157324 CTGACAAAATAATGGAATGCGCGCCCCCAGGAACGCGCTTTCACCACTTTG
66 CTGACAAAATAATGGAAGGCACGCCCCCAGGAACGCGCTTTCACCACTTTG
* *
1157375 GGTACTGACATAAATAGTGCCCCCGAAGGACATGGGTGACATAATAGGGCAATGATAACATATTA
1 GGTACTGACATAAATAGTGCCCCAG-AGGACATGAGTGACATAATAGGGCAATGATAACATATTA
*
1157440 TCTGACAAAATAATGGAAGGCACGCCCCTAGGAACGCG
65 TCTGACAAAATAATGGAAGGCACGCCCCCAGGAACGCG
1157478 TCTTCACGTG
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
116 21 0.23
117 71 0.77
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (116 bp):
GGTACTGACATAAATAGTGCCCCAGAGGACATGAGTGACATAATAGGGCAATGATAACATATTAT
CTGACAAAATAATGGAAGGCACGCCCCCAGGAACGCGCTTTCACCACTTTG
Found at i:1160639 original size:22 final size:24
Alignment explanation
Indices: 1160611--1160665 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
1160601 TTTATGATAT
*
1160611 TTATTTAATAT-AATAATTAA-TA
1 TTATTTAATATAAAAAATTAATTA
*
1160633 TTATTTATTATAAAAAATTAATTA
1 TTATTTAATATAAAAAATTAATTA
1160657 TTAATTTAA
1 TT-ATTTAA
1160666 AATATTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.37
23 8 0.30
24 4 0.15
25 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTATTTAATATAAAAAATTAATTA
Found at i:1160658 original size:21 final size:20
Alignment explanation
Indices: 1160632--1160672 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1160622 AATAATTAAT
*
1160632 ATTATTTATTATAAAAAATTA
1 ATTATTAATT-TAAAAAATTA
*
1160653 ATTATTAATTTAAAATATTA
1 ATTATTAATTTAAAAAATTA
1160673 TAATAATTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTATTAATTTAAAAAATTA
Found at i:1161466 original size:37 final size:37
Alignment explanation
Indices: 1161412--1161516 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1161402 CCTTTTCGTC
*
1161412 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * * * *
1161449 TTGCTAGGATTTGAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
1161486 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
1161517 CCACAAGAAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:1162241 original size:17 final size:19
Alignment explanation
Indices: 1162199--1162250 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 19
1162189 TTCTCTTTAT
*
1162199 TTTATTATTCTTGTATTAC
1 TTTATTATTCTTATATTAC
1162218 TTGTATTATT-TTATATTA-
1 TT-TATTATTCTTATATTAC
*
1162236 TTTATT-TTGTTATAT
1 TTTATTATTCTTATAT
1162251 ATATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.07
17 10 0.33
18 2 0.07
19 9 0.30
20 7 0.23
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTATTATTCTTATATTAC
Found at i:1162721 original size:4 final size:4
Alignment explanation
Indices: 1162682--1162814 Score: 64
Period size: 4 Copynumber: 33.0 Consensus size: 4
1162672 TTCTTTTGTC
* *
1162682 ATTT AATTT ATTA ATTT ATATAT ATTT ACTTT -TTT ATTT ATTT -TAT
1 ATTT -ATTT ATTT ATTT AT-T-T ATTT A-TTT ATTT ATTT ATTT ATTT
* * * *
1162728 ATAT ATAT ATATT ATTCGT ACTTT -GTT A-TT A-TT ATTT GTTT ATTT
1 ATTT ATTT AT-TT ATT--T A-TTT ATTT ATTT ATTT ATTT ATTT ATTT
* * *
1162773 ATTT ATTT ATTT ATTT -TTT TTTT TTTT ATAT ATTT A-TT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1162815 GTTTTTTTTA
Statistics
Matches: 105, Mismatches: 10, Indels: 27
0.74 0.07 0.19
Matches are distributed among these distances:
3 19 0.18
4 66 0.63
5 13 0.12
6 5 0.05
7 2 0.02
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:1162721 original size:12 final size:11
Alignment explanation
Indices: 1162704--1162821 Score: 62
Period size: 11 Copynumber: 10.1 Consensus size: 11
1162694 AATTTATATA
1162704 TATTTACTTTTT
1 TATTTA-TTTTT
1162716 TATTTATTTTAT
1 TATTTATTTT-T
* * *
1162728 ATATATATATAT
1 -TATTTATTTTT
*
1162740 TATTCGTACTTTGT
1 TATT--TA-TTTTT
1162754 TATTATTATTTGTT
1 TA-T-TTATTT-TT
1162768 TATTTATTTATT
1 TATTTATTT-TT
1162780 TATTTA-TTTT
1 TATTTATTTTT
1162790 T-TTT-TTTTT
1 TATTTATTTTT
* *
1162799 TATATATTTAT
1 TATTTATTTTT
*
1162810 TATTTGTTTTT
1 TATTTATTTTT
1162821 T
1 T
1162822 TTACTTACTA
Statistics
Matches: 82, Mismatches: 13, Indels: 23
0.69 0.11 0.19
Matches are distributed among these distances:
9 8 0.10
10 5 0.06
11 22 0.27
12 22 0.27
13 13 0.16
14 10 0.12
15 1 0.01
16 1 0.01
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (11 bp):
TATTTATTTTT
Found at i:1162819 original size:23 final size:23
Alignment explanation
Indices: 1162756--1162822 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 23
1162746 TACTTTGTTA
*
1162756 TTATTATTTGTTTATTTATTTATTTAT
1 TTATTATTTG--T-TTT-TTTATATAT
* *
1162783 TTATTTTTTTTTTTTTTATATAT
1 TTATTATTTGTTTTTTTATATAT
1162806 TTATTATTTGTTTTTTT
1 TTATTATTTGTTTTTTT
1162823 TACTTACTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 23 0.66
24 3 0.09
25 1 0.03
27 8 0.23
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (23 bp):
TTATTATTTGTTTTTTTATATAT
Found at i:1162819 original size:27 final size:26
Alignment explanation
Indices: 1162753--1162823 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 26
1162743 TCGTACTTTG
* * * *
1162753 TTATTATTATTTGTTTATTTATTTAT
1 TTATTATTTTTTTTTTTTTTATATAT
1162779 TTATTTATTTTTTTTTTTTTTATATAT
1 TTA-TTATTTTTTTTTTTTTTATATAT
*
1162806 TTATTATTTGTTTTTTTT
1 TTATTATTTTTTTTTTTT
1162824 ACTTACTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 17 0.44
27 22 0.56
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (26 bp):
TTATTATTTTTTTTTTTTTTATATAT
Found at i:1162833 original size:27 final size:25
Alignment explanation
Indices: 1162756--1162836 Score: 87
Period size: 24 Copynumber: 3.2 Consensus size: 25
1162746 TACTTTGTTA
1162756 TTATTATTTGTTTATTTATTTATT-TAT
1 TTATTATTTG-TT-TTT-TTTATTATAT
*
1162783 TTATT-TTTTTTTTTTTTA-TATAT
1 TTATTATTTGTTTTTTTTATTATAT
1162806 TTATTATTTGTTTTTTTTACTTACTAT
1 TTATTATTTGTTTTTTTTA-TTA-TAT
1162833 TTAT
1 TTAT
1162837 CTTTGCTTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
22 1 0.02
23 12 0.26
24 15 0.32
25 2 0.04
26 5 0.11
27 12 0.26
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (25 bp):
TTATTATTTGTTTTTTTTATTATAT
Found at i:1163996 original size:19 final size:20
Alignment explanation
Indices: 1163960--1163997 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1163950 ACCTTACTAA
*
1163960 CTCTTTTCATTTTTTTTCCT
1 CTCTTTTCATTTTATTTCCT
1163980 CTCTTTT-ATTTTATTTCC
1 CTCTTTTCATTTTATTTCC
1163998 ATCATCTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (20 bp):
CTCTTTTCATTTTATTTCCT
Found at i:1167437 original size:17 final size:17
Alignment explanation
Indices: 1167417--1167453 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1167407 GAAATGAAGC
*
1167417 AAAAAGAAGAAAACAAA
1 AAAAAGAACAAAACAAA
*
1167434 AAAAAGAACAAAATAAA
1 AAAAAGAACAAAACAAA
1167451 AAA
1 AAA
1167454 GAAAAAGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.84, C:0.05, G:0.08, T:0.03
Consensus pattern (17 bp):
AAAAAGAACAAAACAAA
Found at i:1168076 original size:22 final size:22
Alignment explanation
Indices: 1168048--1168102 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1168038 GTTACCCCAT
1168048 CAAACCTTTGAGCATCAAATAC
1 CAAACCTTTGAGCATCAAATAC
*
1168070 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATAC
1168092 CAAACCTTTGA
1 CAAACCTTTGA
1168103 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATAC
Found at i:1169183 original size:106 final size:106
Alignment explanation
Indices: 1169054--1170011 Score: 1441
Period size: 106 Copynumber: 9.0 Consensus size: 106
1169044 ATATCGTGCC
* * * * *
1169054 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTTGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1169119 AATTTTAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1169160 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1169225 AATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1169266 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1169331 AATTTCAGAGCCAATTTTAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1169372 AATCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** * *
1169437 AATTTCAGAGCCAATTTCAACTTTTCAGCAAAGGATATTGT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1169478 ACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1169543 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1169584 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** *
1169649 AATTTCAGATTCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1169690 ACTCCAGACAATGCAAGTTCGACTTCACGACGAAGGGACCGCTGGTTGTTAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1169755 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1169796 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1169861 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1169902 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * * *
1169967 GATTCCAGAGCCAATTTTAACTACAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1170008 ACTC
1 ACTC
1170012 GGAACAATGC
Statistics
Matches: 776, Mismatches: 75, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
106 776 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1170793 original size:37 final size:37
Alignment explanation
Indices: 1170740--1170844 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1170730 CCTTTTCGTC
* *
1170740 CTACTAGGATTCAAACTTCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * * *
1170777 TTGCTAGGATTTAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
1170814 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
1170845 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:1171500 original size:17 final size:17
Alignment explanation
Indices: 1171470--1171562 Score: 55
Period size: 17 Copynumber: 5.0 Consensus size: 17
1171460 TATATATGTA
*
1171470 TATT-TTTATATTTTAT
1 TATTATTTATTTTTTAT
1171486 TATTATTTATTTTTTATTT
1 TATTATTTATTTTTTA--T
* *
1171505 CTCTTCTTTATTATATTGTAT
1 -TATTATTTATT-T-TT-TAT
1171526 TATTACTTGTATTATTTTA-
1 TATTA-TT-TATT-TTTTAT
1171545 TATTATTTATTTTGTTAT
1 TATTATTTATTTT-TTAT
1171563 ATATATATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
16 6 0.10
17 17 0.28
18 2 0.03
19 6 0.10
20 14 0.23
21 6 0.10
22 8 0.13
23 2 0.03
ACGTcount: A:0.23, C:0.04, G:0.03, T:0.70
Consensus pattern (17 bp):
TATTATTTATTTTTTAT
Found at i:1171501 original size:56 final size:57
Alignment explanation
Indices: 1171441--1171562 Score: 146
Period size: 56 Copynumber: 2.1 Consensus size: 57
1171431 TATATTTTCC
1171441 TTTTATTCTACTT-TTATATTATATATGTA-TATT-TT-TA-TATTTTATTATTATTTATT
1 TTTTATTCT-CTTCTT-TATTATAT-TGTATTATTATTGTATTATTTTA-TATTATTTATT
1171497 TTTTATTTCTCTTCTTTATTATATTGTATTATTACTTGTATTATTTTATATTATTTATT
1 TTTTA-TTCTCTTCTTTATTATATTGTATTATTA-TTGTATTATTTTATATTATTTATT
1171556 TTGTTAT
1 TT-TTAT
1171563 ATATATATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 13
0.82 0.00 0.18
Matches are distributed among these distances:
55 4 0.07
56 20 0.34
57 6 0.10
58 2 0.03
59 16 0.28
60 10 0.17
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (57 bp):
TTTTATTCTCTTCTTTATTATATTGTATTATTATTGTATTATTTTATATTATTTATT
Found at i:1171572 original size:52 final size:48
Alignment explanation
Indices: 1171459--1171572 Score: 106
Period size: 52 Copynumber: 2.3 Consensus size: 48
1171449 TACTTTTATA
* *
1171459 TTATATATGTATATTTTTATATTTTATTATTATTTATTTTTTATTTCTC
1 TTATATAT-TATATTTTTATATTGTATTATTATTTATTATTTATTTCTC
* * *
1171508 TTCTTTATTATATTGTATTATTACTTGTATTATT-TTATATTATTTATTT-TG
1 TTATATATTATATT-T-TTA-TA-TTGTATTATTATT-TATTATTTATTTCTC
1171559 TTATATATATATAT
1 TTATATAT-TATAT
1171573 ACGTATGTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
48 6 0.12
49 7 0.13
50 3 0.06
51 11 0.21
52 25 0.48
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (48 bp):
TTATATATTATATTTTTATATTGTATTATTATTTATTATTTATTTCTC
Found at i:1172135 original size:18 final size:21
Alignment explanation
Indices: 1172112--1172159 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 21
1172102 ATTTTATTTT
1172112 TTTACTTAC-T-ATTTTATC-
1 TTTACTTACTTCATTTTATCA
*
1172130 TTTACTTTCTTCATTTTATCA
1 TTTACTTACTTCATTTTATCA
1172151 TTTTACTTA
1 -TTTACTTA
1172160 ATTTGGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 8 0.33
19 1 0.04
20 8 0.33
22 7 0.29
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTACTTACTTCATTTTATCA
Found at i:1175047 original size:17 final size:17
Alignment explanation
Indices: 1175025--1175060 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1175015 TAATTTTAAC
*
1175025 AATAATCAATATTCATA
1 AATAATAAATATTCATA
*
1175042 AATAATAAATATTTATA
1 AATAATAAATATTCATA
1175059 AA
1 AA
1175061 ACTCCTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATAAATATTCATA
Found at i:1176851 original size:18 final size:17
Alignment explanation
Indices: 1176818--1176862 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
1176808 CCGTGGCTTC
*
1176818 TTCTCCTCTTCTTTCTT
1 TTCTCCTCTACTTTCTT
1176835 TTCTCCATCTACTTTCTT
1 TTCTCC-TCTACTTTCTT
*
1176853 CTGCTCCTCT
1 -TTCTCCTCT
1176863 TTCTTTTCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 13 0.54
19 5 0.21
ACGTcount: A:0.04, C:0.38, G:0.02, T:0.56
Consensus pattern (17 bp):
TTCTCCTCTACTTTCTT
Found at i:1176864 original size:33 final size:33
Alignment explanation
Indices: 1176814--1176900 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
1176804 GTGACCGTGG
* * *
1176814 CTTCTTCTCCTCTTCTTTCTTTTCTCCATCTAC
1 CTTCTTCTGCTCCTCTTTCTTTTCCCCATCTAC
* * *
1176847 TTTCTTCTGCTCCTCTTTCTTTTCCCCTTCTTC
1 CTTCTTCTGCTCCTCTTTCTTTTCCCCATCTAC
1176880 CTTCTT-TGGCTCCTCTTTCTT
1 CTTCTTCT-GCTCCTCTTTCTT
1176901 CTCCGGTTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
32 1 0.02
33 45 0.98
ACGTcount: A:0.02, C:0.38, G:0.03, T:0.56
Consensus pattern (33 bp):
CTTCTTCTGCTCCTCTTTCTTTTCCCCATCTAC
Found at i:1177797 original size:21 final size:21
Alignment explanation
Indices: 1177760--1177803 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1177750 AGAAGAAATT
*
1177760 ATACATTAATTTAAAGATCAA
1 ATACATTAATTTAAAGAACAA
*
1177781 ATACA-TAATTATGAAGAACAA
1 ATACATTAATT-TAAAGAACAA
1177802 AT
1 AT
1177804 GAGGAAACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.30
Consensus pattern (21 bp):
ATACATTAATTTAAAGAACAA
Found at i:1178058 original size:13 final size:13
Alignment explanation
Indices: 1178004--1178052 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
1177994 TGCGTCATAA
1178004 ATTTATGACGCGC
1 ATTTATGACGCGC
* *
1178017 ATTTATGACACAC
1 ATTTATGACGCGC
1178030 ATTTATGACGCGC
1 ATTTATGACGCGC
1178043 ATTTATGACG
1 ATTTATGACG
1178053 TTCATTGAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:1178134 original size:84 final size:84
Alignment explanation
Indices: 1178030--1178193 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
1178020 TATGACACAC
* * * *
1178030 ATTTATGACGCGCATTTATGACGTT-CATTGA-GCGTCATTGAAGC-CCCGTCA-TAAATTAAGA
1 ATTTATGACACGCATGTATGAC-TTACATT-ACGCGTCATTGAAGCACACGCCATTAAA--AAGA
*
1178091 TGACACACATTTGTGTGTCATAA
62 TGACACACATTCGTGTGTCATAA
*
1178114 ATTTATGACACGCATGTATGACTTACATTACGTGTCATTGAAGCACACGCCATTAAAAAGATGAC
1 ATTTATGACACGCATGTATGACTTACATTACGCGTCATTGAAGCACACGCCATTAAAAAGATGAC
*
1178179 AGACATTCGTGTGTC
66 ACACATTCGTGTGTC
1178194 GTGATTGTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
83 3 0.04
84 57 0.83
85 5 0.07
86 4 0.06
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (84 bp):
ATTTATGACACGCATGTATGACTTACATTACGCGTCATTGAAGCACACGCCATTAAAAAGATGAC
ACACATTCGTGTGTCATAA
Found at i:1178226 original size:2 final size:2
Alignment explanation
Indices: 1178219--1178253 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1178209 AAATTATTGT
1178219 TA TA 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 TA TA T
1178254 TGTAGATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1182976 original size:31 final size:31
Alignment explanation
Indices: 1182938--1183142 Score: 365
Period size: 31 Copynumber: 6.6 Consensus size: 31
1182928 TTCATAGATT
* *
1182938 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
1182969 CCGAAGAACATATGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
1183000 CCGAAAAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
1183031 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
1183062 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
1183093 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
1183124 CCGAAGAATATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
1183143 CCTCGACCCT
Statistics
Matches: 167, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 167 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:1184115 original size:18 final size:17
Alignment explanation
Indices: 1184092--1184160 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 17
1184082 TTTATTTAGG
1184092 GGGGAATCGATACCCCCA
1 GGGGAATCG-TACCCCCA
**
1184110 GGGGAATC-TATTCCCA
1 GGGGAATCGTACCCCCA
1184126 -GGGAATCGATACCCCCCA
1 GGGGAATCG-TA-CCCCCA
1184144 GGGGAATCTGTACCCCC
1 GGGGAATC-GTACCCCC
1184161 TGGACATTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 7 0.17
16 6 0.14
17 2 0.05
18 17 0.40
19 9 0.21
20 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (17 bp):
GGGGAATCGTACCCCCA
Found at i:1194981 original size:18 final size:17
Alignment explanation
Indices: 1194948--1194981 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1194938 GAATAATTAA
1194948 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
1194965 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
1194982 AAACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:1198011 original size:28 final size:28
Alignment explanation
Indices: 1197910--1198018 Score: 94
Period size: 28 Copynumber: 3.9 Consensus size: 28
1197900 AATAATACTT
* * *
1197910 AAGCGGTATAGCCCACCATATATCATTC
1 AAGCGGCATAGCCGACCATATATAATTC
* **
1197938 AAGCGGCAGAGGTGACCATATATCAATT-
1 AAGCGGCATAGCCGACCATATAT-AATTC
* * * * *
1197966 AGGCGGTATAACCAACCATATATTATTC
1 AAGCGGCATAGCCGACCATATATAATTC
*
1197994 AAGTGGCATAGCCGACCATATATAA
1 AAGCGGCATAGCCGACCATATATAA
1198019 ACACAAGTGC
Statistics
Matches: 59, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
27 3 0.05
28 53 0.90
29 3 0.05
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (28 bp):
AAGCGGCATAGCCGACCATATATAATTC
Found at i:1200443 original size:25 final size:27
Alignment explanation
Indices: 1200415--1200478 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
1200405 ATCTATTAAT
*
1200415 AATATAATTAT-G-TATTGATAAAA-AA
1 AATATAATTATAGAAATT-ATAAAATAA
*
1200440 AATATAAATATAGAAATTATAAAATAA
1 AATATAATTATAGAAATTATAAAATAA
*
1200467 ACTATAATTATA
1 AATATAATTATA
1200479 TTTTAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 10 0.31
26 7 0.22
27 15 0.47
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (27 bp):
AATATAATTATAGAAATTATAAAATAA
Found at i:1200502 original size:27 final size:26
Alignment explanation
Indices: 1200472--1200522 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
1200462 AATAAACTAT
1200472 AATTATAT-TTTAAAAATTAAAAATTTC
1 AATTATATATTT--AAATTAAAAATTTC
*
1200499 AATTTTATATTTAAATTAAAAATT
1 AATTATATATTTAAATTAAAAATT
1200523 ATTTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 7 0.32
28 3 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AATTATATATTTAAATTAAAAATTTC
Found at i:1200560 original size:23 final size:24
Alignment explanation
Indices: 1200516--1200561 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1200506 TATTTAAATT
**
1200516 AAAAATTATTTAATTTTTTATTAA
1 AAAAATTATTTAATTTAATATTAA
*
1200540 AAAAATTA-TTGATTTAATATTA
1 AAAAATTATTTAATTTAATATTA
1200562 CTTAGTTCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
AAAAATTATTTAATTTAATATTAA
Found at i:1202388 original size:13 final size:13
Alignment explanation
Indices: 1202370--1202394 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1202360 CTCAAAGCTT
1202370 ATATATAATTATC
1 ATATATAATTATC
1202383 ATATATAATTAT
1 ATATATAATTAT
1202395 GTACGTGCGT
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:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATAATTATC
Found at i:1210754 original size:24 final size:24
Alignment explanation
Indices: 1210716--1210765 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1210706 AAACAAGTTT
*
1210716 GATGATGGAGAAAGCAAAACAAAA
1 GATGATGAAGAAAGCAAAACAAAA
* *
1210740 GATGATGAAGGAAGCAAAATAAAA
1 GATGATGAAGAAAGCAAAACAAAA
1210764 GA
1 GA
1210766 GCATAGTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.58, C:0.06, G:0.26, T:0.10
Consensus pattern (24 bp):
GATGATGAAGAAAGCAAAACAAAA
Found at i:1212250 original size:21 final size:21
Alignment explanation
Indices: 1212226--1212299 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
1212216 ACGTTGCATT
*
1212226 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
** ** **
1212247 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
1212267 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
1212288 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1212300 TTTCTATTTT
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:1212276 original size:41 final size:41
Alignment explanation
Indices: 1212222--1212331 Score: 177
Period size: 41 Copynumber: 2.7 Consensus size: 41
1212212 ATTCACGTTG
* *
1212222 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1212263 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
1212304 TATTTTGCGTTGCGATAGTTG-AAATCGC
1 CATTTCGCGTTGCGATAGTTGAAAATCGC
1212332 AACGCGATCT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 7 0.11
41 58 0.89
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:1212383 original size:21 final size:21
Alignment explanation
Indices: 1212359--1212458 Score: 77
Period size: 21 Copynumber: 5.0 Consensus size: 21
1212349 CGCAAATTCG
1212359 AGTTGCATTTCGCGTTGCGAT
1 AGTTGCATTTCGCGTTGCGAT
* **
1212380 AGTTGAAAATCGCGTTGCGAT
1 AGTTGCATTTCGCGTTGCGAT
* *
1212401 -TTTCCATTTCGC---GCGAT
1 AGTTGCATTTCGCGTTGCGAT
*
1212418 --TTTCTATTTCGCGTTGCGAT
1 AGTTGC-ATTTCGCGTTGCGAT
* *
1212438 AGTTGAAATTCGCGTTGCGAT
1 AGTTGCATTTCGCGTTGCGAT
1212459 TTTCCAAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
16 3 0.05
17 12 0.20
20 12 0.20
21 32 0.52
22 2 0.03
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (21 bp):
AGTTGCATTTCGCGTTGCGAT
Found at i:1212418 original size:17 final size:17
Alignment explanation
Indices: 1212396--1212430 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1212386 AAATCGCGTT
1212396 GCGATTTTCCATTTCGC
1 GCGATTTTCCATTTCGC
*
1212413 GCGATTTTCTATTTCGC
1 GCGATTTTCCATTTCGC
1212430 G
1 G
1212431 TTGCGATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.26, G:0.20, T:0.43
Consensus pattern (17 bp):
GCGATTTTCCATTTCGC
Found at i:1212467 original size:21 final size:21
Alignment explanation
Indices: 1212367--1212511 Score: 67
Period size: 21 Copynumber: 7.2 Consensus size: 21
1212357 CGAGTTGCAT
* *
1212367 TTCGCGTTGCGATAGTT-GAAA
1 TTCGCGTTGCGAT-TTTCCAAA
* *
1212388 ATCGCGTTGCGATTTTCC-AT
1 TTCGCGTTGCGATTTTCCAAA
* *
1212408 TTCGC---GCGATTTT-CTAT
1 TTCGCGTTGCGATTTTCCAAA
* *
1212425 TTCGCGTTGCGATAGTT-GAAA
1 TTCGCGTTGCGAT-TTTCCAAA
1212446 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATTTTCCAAA
* ** *
1212467 TT--TGTTGCGATAGTCTACAA
1 TTCGCGTTGCGATTTTCCA-AA
*
1212487 TT-GTCGTTGTGATTTTCCAAA
1 TTCG-CGTTGCGATTTTCCAAA
1212508 TTCG
1 TTCG
1212512 TTGAAAAAAA
Statistics
Matches: 93, Mismatches: 20, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
16 1 0.01
17 15 0.16
19 11 0.12
20 18 0.19
21 37 0.40
22 11 0.12
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (21 bp):
TTCGCGTTGCGATTTTCCAAA
Found at i:1212475 original size:19 final size:19
Alignment explanation
Indices: 1212451--1212514 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
1212441 TGAAATTCGC
1212451 GTTGCGATTTTCCAAATTT
1 GTTGCGATTTTCCAAATTT
** *
1212470 GTTGCGATAGTCTACAATTGT
1 GTTGCGATTTTCCA-AATT-T
* *
1212491 CGTTGTGATTTTCCAAATTC
1 -GTTGCGATTTTCCAAATTT
1212511 GTTG
1 GTTG
1212515 AAAAAAAAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 15 0.44
20 4 0.12
21 5 0.15
22 10 0.29
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.44
Consensus pattern (19 bp):
GTTGCGATTTTCCAAATTT
Done.