Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 38
Found at i:1087732 original size:53 final size:54
Alignment explanation
Indices: 1087668--1087774 Score: 137
Period size: 53 Copynumber: 2.0 Consensus size: 54
1087658 TTAACTAGAA
* ** *
1087668 ATCTGTGCAGAATTCACAGGAAAGGATGA-A-TGTTTGTCAAATGCTTTACGAAC
1 ATCTGGGCAGAAGCCACAGGAAAAGATGATAGTG-TTGTCAAATGCTTTACGAAC
* *
1087721 ATCTGGGCAGAAGCCATAGGAAAAGATGATAGTGTTGTCAAATGTTTTACGAAC
1 ATCTGGGCAGAAGCCACAGGAAAAGATGATAGTGTTGTCAAATGCTTTACGAAC
1087775 CAGTTATTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 24 0.52
54 20 0.43
55 2 0.04
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (54 bp):
ATCTGGGCAGAAGCCACAGGAAAAGATGATAGTGTTGTCAAATGCTTTACGAAC
Found at i:1088172 original size:22 final size:22
Alignment explanation
Indices: 1088141--1088198 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
1088131 ACATCTACAT
1088141 TCTTCCAAAGATGATAGATTCTC
1 TCTT-CAAAGATGATAGATTCTC
1088164 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1088186 TTTTCAAAGATGA
1 TCTTCAAAGATGA
1088199 AAGCTTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 30 0.88
23 4 0.12
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1088999 original size:76 final size:74
Alignment explanation
Indices: 1088871--1089040 Score: 214
Period size: 76 Copynumber: 2.3 Consensus size: 74
1088861 CTATTCCCCA
* * * * *
1088871 CATCTGTAAGACCTGCAGTGTAGGATGTTTTCAAAAAACCTCCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAACCTCCGGGAACTTTTTGA--TATCTAA
* * *
1088936 AGTCTCTGGGT
64 AGCCCCAGGGT
* * *
1088947 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAATCCTTCGGGAACTTTTTGATATCTAAAG
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAACCTCCGGGAACTTTTTGATATCTAAAG
1089012 CCCCAGGGT
66 CCCCAGGGT
*
1089021 CATCTGTAAGACTTACAGTG
1 CATCTGTAAGACCTACAGTG
1089041 AAAAATGATA
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
74 32 0.39
76 50 0.61
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (74 bp):
CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAACCTCCGGGAACTTTTTGATATCTAAAG
CCCCAGGGT
Found at i:1089672 original size:3 final size:3
Alignment explanation
Indices: 1089666--1089737 Score: 53
Period size: 3 Copynumber: 25.0 Consensus size: 3
1089656 ATTTGTTTTT
* * *
1089666 TTA TTA TTA -TA TTA TTA TTA ATA TTA TT- TTAA TTA -TA CTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
* * *
1089709 TTT TTA TTT TTA -TA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1089738 ATACTATTAC
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
2 8 0.15
3 43 0.81
4 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1089692 original size:17 final size:18
Alignment explanation
Indices: 1089670--1089746 Score: 63
Period size: 17 Copynumber: 4.4 Consensus size: 18
1089660 GTTTTTTTAT
1089670 TATTA-TATTATTATTAA
1 TATTATTATTATTATTAA
*
1089687 TATTATT-TTAATTA-TAC
1 TATTATTATT-ATTATTAA
* * *
1089704 TGTTATTTTTATT-TTTA
1 TATTATTATTATTATTAA
*
1089721 TATTATTAATATTATTAA
1 TATTATTATTATTATTAA
*
1089739 TACTATTA
1 TATTATTA
1089747 CAAGCCCAGA
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
17 29 0.63
18 17 0.37
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (18 bp):
TATTATTATTATTATTAA
Found at i:1091103 original size:20 final size:19
Alignment explanation
Indices: 1091072--1091127 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 19
1091062 ATTACAATAT
1091072 TATTTTATTATTACTTTTA
1 TATTTTATTATTACTTTTA
1091091 TATTTTAATTATTACTTTAATTA
1 TATTTT-ATTATTAC-TT--TTA
1091114 TTATTTTATTATTA
1 -TATTTTATTATTA
1091128 TTATCTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.19
20 8 0.25
21 2 0.06
23 10 0.31
24 6 0.19
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (19 bp):
TATTTTATTATTACTTTTA
Found at i:1092173 original size:24 final size:24
Alignment explanation
Indices: 1092141--1092192 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1092131 AAGACGCACC
1092141 AGGCGCAAAAGGTCTCTGGAGCCT
1 AGGCGCAAAAGGTCTCTGGAGCCT
*
1092165 AGGCGCAAAAGGTCTCTGGATCCT
1 AGGCGCAAAAGGTCTCTGGAGCCT
1092189 AGGC
1 AGGC
1092193 ACAAGGCGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.33, T:0.17
Consensus pattern (24 bp):
AGGCGCAAAAGGTCTCTGGAGCCT
Found at i:1095673 original size:13 final size:14
Alignment explanation
Indices: 1095657--1095685 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1095647 TTTATTTTTA
1095657 AAATTTAATA-ATT
1 AAATTTAATACATT
1095670 AAATTTAATACATT
1 AAATTTAATACATT
1095684 AA
1 AA
1095686 TTTCTATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTTAATACATT
Found at i:1098441 original size:31 final size:31
Alignment explanation
Indices: 1098398--1098461 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
1098388 AAAAACTTGT
*
1098398 TGAAAATAAAAGGTTGGCACCGAATGGTGCA
1 TGAAAATAAAAGGTTGGCACAGAATGGTGCA
*
1098429 TGAAAATCAAAGGTTGGCACAGAATGGTGCA
1 TGAAAATAAAAGGTTGGCACAGAATGGTGCA
1098460 TG
1 TG
1098462 GTCAAAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (31 bp):
TGAAAATAAAAGGTTGGCACAGAATGGTGCA
Found at i:1100713 original size:31 final size:31
Alignment explanation
Indices: 1100665--1100728 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1100655 GAACAATTGT
*
1100665 TGAAAATCAAAGGTTGGCACCAAATGGTGCA
1 TGAAAATAAAAGGTTGGCACCAAATGGTGCA
* *
1100696 TGAAAATAAAAGTTTGGCACCGAATGGTGCA
1 TGAAAATAAAAGGTTGGCACCAAATGGTGCA
1100727 TG
1 TG
1100729 GTCAAAAGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.22
Consensus pattern (31 bp):
TGAAAATAAAAGGTTGGCACCAAATGGTGCA
Found at i:1102945 original size:22 final size:23
Alignment explanation
Indices: 1102903--1102952 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
1102893 GACTCAATGA
*
1102903 TTGA-GCTTATAATTTTATTCCT
1 TTGATGCTTATAATGTTATTCCT
*
1102925 TTGATGCTTTTAATGTT-TTCCT
1 TTGATGCTTATAATGTTATTCCT
1102947 TTGATG
1 TTGATG
1102953 TTGTTTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.18, C:0.12, G:0.14, T:0.56
Consensus pattern (23 bp):
TTGATGCTTATAATGTTATTCCT
Found at i:1106333 original size:14 final size:14
Alignment explanation
Indices: 1106298--1106325 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1106288 AAGTCAAAGG
1106298 GTTGACTCAAATGA
1 GTTGACTCAAATGA
1106312 GTTGACTCAAATGA
1 GTTGACTCAAATGA
1106326 TTTTACTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
GTTGACTCAAATGA
Found at i:1113018 original size:43 final size:43
Alignment explanation
Indices: 1112956--1113046 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 43
1112946 TAGATCAAGC
*
1112956 TCATGAAGGTAATCAAACCATCAA-GTTCACATGGGAGCCAAAT
1 TCATGAAGGTAACCAAACCAT-AATGTTCACATGGGAGCCAAAT
* *
1112999 TCATGAAGGTAACCCAACCATAATGTTCACATGGGAGCCTAAT
1 TCATGAAGGTAACCAAACCATAATGTTCACATGGGAGCCAAAT
1113042 TCATG
1 TCATG
1113047 CAAAGAAGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 2 0.05
43 42 0.95
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (43 bp):
TCATGAAGGTAACCAAACCATAATGTTCACATGGGAGCCAAAT
Found at i:1113976 original size:13 final size:15
Alignment explanation
Indices: 1113958--1113989 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1113948 ATGATCATTG
1113958 AAAAAAGT-AACAA-
1 AAAAAAGTCAACAAT
1113971 AAAAAAGTCAACAAT
1 AAAAAAGTCAACAAT
1113986 AAAA
1 AAAA
1113990 TTCAAAGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 5 0.29
15 4 0.24
ACGTcount: A:0.75, C:0.09, G:0.06, T:0.09
Consensus pattern (15 bp):
AAAAAAGTCAACAAT
Found at i:1116187 original size:3 final size:3
Alignment explanation
Indices: 1116181--1116206 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1116171 TAATAATAAT
1116181 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1116207 AATATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1117409 original size:2 final size:2
Alignment explanation
Indices: 1117402--1117426 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1117392 AGTCATATCC
1117402 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
1117427 ACCAGAATAT
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:1125733 original size:24 final size:24
Alignment explanation
Indices: 1125706--1125760 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
1125696 TTTTTTTTCT
*
1125706 TTTTCTTCTTTTTGAGTGCTTGAC
1 TTTTCTTCTTTTGGAGTGCTTGAC
1125730 TTTTCTTCTTTTGGAGTGCTTGAC
1 TTTTCTTCTTTTGGAGTGCTTGAC
1125754 TTTTCTT
1 TTTTCTT
1125761 TGCTAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.07, C:0.16, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGCTTGAC
Found at i:1127221 original size:28 final size:28
Alignment explanation
Indices: 1127168--1127221 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1127158 ATAAAATGAA
* **
1127168 TGATAATTATGCTTCCTTGATGTATATG
1 TGATAATCATGCTTAATTGATGTATATG
1127196 TGATAATCATGCTTAATATGAT-TATA
1 TGATAATCATGCTTAAT-TGATGTATA
1127222 AGACTATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 18 0.82
29 4 0.18
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.44
Consensus pattern (28 bp):
TGATAATCATGCTTAATTGATGTATATG
Found at i:1127894 original size:21 final size:20
Alignment explanation
Indices: 1127863--1127933 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
1127853 GATGTAAGGG
1127863 AGTATTAATACTCCA-CTAGGT
1 AGTA-TAATACTCCATC-AGGT
1127884 AGTATACATACTCCATCAGGT
1 AGTATA-ATACTCCATCAGGT
*
1127905 AGTATAAGTACTCCATCAAGT
1 AGTATAA-TACTCCATCAGGT
1127926 AGTA-AATA
1 AGTATAATA
1127934 TACTCAAAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
19 2 0.04
20 5 0.11
21 38 0.83
22 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (20 bp):
AGTATAATACTCCATCAGGT
Found at i:1134022 original size:43 final size:43
Alignment explanation
Indices: 1133957--1134254 Score: 515
Period size: 43 Copynumber: 6.9 Consensus size: 43
1133947 TTAATTATCG
* *
1133957 TTACAGTTCTCCCAGGTCCCTTTGCTGTGTACAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
1134000 TTATAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
1134043 TTACAGTTCCCCCAGGTCCTTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
1134086 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1134129 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
* *
1134172 TTACAGTTCCCCTAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
1134215 TTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAA
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAA
1134255 TGTGTGCAAG
Statistics
Matches: 242, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 242 1.00
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.31
Consensus pattern (43 bp):
TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:1134260 original size:15 final size:15
Alignment explanation
Indices: 1134240--1134269 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1134230 GTCCCTTTGT
1134240 TGTGTGCAAGGGTAA
1 TGTGTGCAAGGGTAA
1134255 TGTGTGCAAGGGTAA
1 TGTGTGCAAGGGTAA
1134270 GCCTTACAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.40, T:0.27
Consensus pattern (15 bp):
TGTGTGCAAGGGTAA
Found at i:1134304 original size:58 final size:58
Alignment explanation
Indices: 1134197--1134307 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
1134187 GTTCCTTTGC
* *
1134197 TGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAA
1 TGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTTGCTATGTGCAAGGGTAA
* *
1134255 TGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGG-CTCTTTTGCTATGTGCAAG
1 TGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTC-CCTTTGCTATGTGCAAG
1134308 TATAAGACCT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 1 0.02
58 47 0.98
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.31
Consensus pattern (58 bp):
TGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTTGCTATGTGCAAGGGTAA
Found at i:1139488 original size:30 final size:29
Alignment explanation
Indices: 1139418--1139488 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
1139408 AAGGGAGACA
*
1139418 AAATTTTGT-TTTCAAGGAAACATACTCG
1 AAATTTTGTGTTTCAAGGAAACATACTCC
* * *
1139446 AAGTTTTATGTTTCAAGTGAAACA-ATTTCC
1 AAATTTTGTGTTTCAAG-GAAACATA-CTCC
1139476 AAATTTTGTGTTT
1 AAATTTTGTGTTT
1139489 TGAGGAAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 7 0.21
29 8 0.24
30 19 0.56
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.42
Consensus pattern (29 bp):
AAATTTTGTGTTTCAAGGAAACATACTCC
Found at i:1141129 original size:2 final size:2
Alignment explanation
Indices: 1141117--1141157 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1141107 AGCTTTATTT
*
1141117 TA TA CA 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 TA TA TA T
1141158 TGGGTATACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1153047 original size:60 final size:60
Alignment explanation
Indices: 1152946--1153064 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
1152936 AATAATAATG
** * * * ** *
1152946 CTCATTTTTAATTGGTCTTTAAACTTTTGAATATTTTAATTTCAT-CTTCAAATTATGATT
1 CTCATTTGAAATTGATCTTTAAACTTTTAAACATTCGAATTTCATCCTT-AAAATATGATT
*
1153006 CTCATTTGAAATTGATCTTTAAGCTTTTAAACATTCGAATTTCATCCTTAAAATATGAT
1 CTCATTTGAAATTGATCTTTAAACTTTTAAACATTCGAATTTCATCCTTAAAATATGAT
1153065 ATTTTTAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 46 0.94
61 3 0.06
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (60 bp):
CTCATTTGAAATTGATCTTTAAACTTTTAAACATTCGAATTTCATCCTTAAAATATGATT
Found at i:1156109 original size:21 final size:21
Alignment explanation
Indices: 1156083--1156125 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1156073 CATGGGGACT
1156083 AATTTATCCTTTACTAGGTGC
1 AATTTATCCTTTACTAGGTGC
1156104 AATTTATCCTTTACTAGGTGC
1 AATTTATCCTTTACTAGGTGC
1156125 A
1 A
1156126 CTATGGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (21 bp):
AATTTATCCTTTACTAGGTGC
Found at i:1157860 original size:28 final size:28
Alignment explanation
Indices: 1157827--1157962 Score: 200
Period size: 28 Copynumber: 4.9 Consensus size: 28
1157817 CCGACATTGC
* *
1157827 TTTCAAGCACTAGCTCAACGACATAATG
1 TTTCAAGCACTAGCTCGACGACATCATG
*
1157855 TTTCAAGCACTAGCTTGACGACATCATG
1 TTTCAAGCACTAGCTCGACGACATCATG
*
1157883 TTTCAAGCACTAGCTCGACGGCATCATG
1 TTTCAAGCACTAGCTCGACGACATCATG
*
1157911 TTTCAAGCACTAGCTCGATGACATCATG
1 TTTCAAGCACTAGCTCGACGACATCATG
* * *
1157939 CTTCAAACACTGGCTCGACGACAT
1 TTTCAAGCACTAGCTCGACGACAT
1157963 AATATAAATG
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 97 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (28 bp):
TTTCAAGCACTAGCTCGACGACATCATG
Found at i:1169652 original size:29 final size:29
Alignment explanation
Indices: 1169620--1169722 Score: 95
Period size: 29 Copynumber: 3.6 Consensus size: 29
1169610 AAAAAACAAG
1169620 TTAACCCTAAATTTTATAAGTAGTTTAAT
1 TTAACCCTAAATTTTATAAGTAGTTTAAT
* *
1169649 TTAACCCTAAATTTTAGAA--A-TTTATGAA
1 TTAACCCTAAATTTTATAAGTAGTTTA--AT
** * *
1169677 CAAACACTAAAATGTTATAAGTAGTTTAAT
1 TTAACCCT-AAATTTTATAAGTAGTTTAAT
*
1169707 TTAACCTTAAATTTTA
1 TTAACCCTAAATTTTA
1169723 GGGTGTGGTA
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
26 4 0.07
27 1 0.02
28 6 0.11
29 34 0.62
30 5 0.09
31 1 0.02
32 4 0.07
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.41
Consensus pattern (29 bp):
TTAACCCTAAATTTTATAAGTAGTTTAAT
Found at i:1173831 original size:90 final size:90
Alignment explanation
Indices: 1173678--1173843 Score: 305
Period size: 90 Copynumber: 1.8 Consensus size: 90
1173668 CTAACACACT
*
1173678 CTTTTATAGCCAAGTTACCCTAATCATATTAAGGTTTTTATTATTTCAAATTAATTAAATCTATA
1 CTTTTATAGCCAAGTTACCCTAATCATATTAAGGATTTTATTATTTCAAATTAATTAAATCTATA
1173743 TTTAATTAATTGGAATTTAATAATC
66 TTTAATTAATTGGAATTTAATAATC
* *
1173768 CTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATA
1 CTTTTATAGCCAAGTTACCCTAATCATATTAAGGATTTTATTATTTCAAATTAATTAAATCTATA
1173833 TTTAATTAATT
66 TTTAATTAATT
1173844 AAAATTAAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 73 1.00
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.46
Consensus pattern (90 bp):
CTTTTATAGCCAAGTTACCCTAATCATATTAAGGATTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGGAATTTAATAATC
Found at i:1181452 original size:90 final size:90
Alignment explanation
Indices: 1181299--1181465 Score: 300
Period size: 90 Copynumber: 1.9 Consensus size: 90
1181289 CCTAACACAC
1181299 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTTATTATTTCAAATTAATTAAATCTAT
1181364 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGGAATTTAATAAT
**
1181389 CCTTTTATATTCAAGTTACCCTAATCATATTAGGGA-TTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTA-GGATTTTTATTATTTCAAATTAATTAAATCTA
1181453 TATTTAATTAATT
65 TATTTAATTAATT
1181466 AAAATTAAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
90 71 0.96
91 3 0.04
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGGAATTTAATAAT
Found at i:1185414 original size:26 final size:26
Alignment explanation
Indices: 1185385--1185469 Score: 84
Period size: 26 Copynumber: 3.2 Consensus size: 26
1185375 AATAGTATCC
1185385 AAATTAGAAATAAAAAATAATGACTA
1 AAATTAGAAATAAAAAATAATGACTA
* * *
1185411 AAATGCATA-AAATAAAATAATAGTAAC-C
1 AAAT---TAGAAATAAAA-AATAATGACTA
*
1185439 AAATCAGAAATAAAAAATAATGACTA
1 AAATTAGAAATAAAAAATAATGACTA
1185465 AAATT
1 AAATT
1185470 CATAAAATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
25 8 0.18
26 16 0.36
28 12 0.27
29 9 0.20
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.22
Consensus pattern (26 bp):
AAATTAGAAATAAAAAATAATGACTA
Found at i:1185414 original size:54 final size:55
Alignment explanation
Indices: 1185356--1185506 Score: 200
Period size: 54 Copynumber: 2.8 Consensus size: 55
1185346 ATAAGAGGCC
* * * *
1185356 AAAATGTAATAAAACAAAA-AATAGTATCCAAATTAGAAATAAAAAATAATGACT
1 AAAATGTCATAAAATAAAATAATAGTAACCAAATCAGAAATAAAAAATAATGACT
1185410 AAAATG-CATAAAATAAAATAATAGTAACCAAATCAGAAATAAAAAATAATGACT
1 AAAATGTCATAAAATAAAATAATAGTAACCAAATCAGAAATAAAAAATAATGACT
* ** **
1185464 AAAAT-TCATAAAATAAAAGAGCAGTAGTCAAATCAGAAATAAA
1 AAAATGTCATAAAATAAAATAATAGTAACCAAATCAGAAATAAA
1185507 TATGACTGAA
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
53 10 0.12
54 76 0.88
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (55 bp):
AAAATGTCATAAAATAAAATAATAGTAACCAAATCAGAAATAAAAAATAATGACT
Found at i:1185427 original size:28 final size:27
Alignment explanation
Indices: 1185392--1185481 Score: 103
Period size: 28 Copynumber: 3.3 Consensus size: 27
1185382 TCCAAATTAG
1185392 AAATAAAAAATAATGACTAAAATGCATA
1 AAATAAAAAATAATGACTAAAAT-CATA
* * * *
1185420 AAATAAAATAATAGTAAC-CAAATCA-G
1 AAATAAAA-AATAATGACTAAAATCATA
1185446 AAATAAAAAATAATGACTAAAATTCATA
1 AAATAAAAAATAATGACTAAAA-TCATA
1185474 AAATAAAA
1 AAATAAAA
1185482 GAGCAGTAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
25 7 0.14
26 11 0.22
27 5 0.10
28 20 0.40
29 7 0.14
ACGTcount: A:0.66, C:0.08, G:0.06, T:0.21
Consensus pattern (27 bp):
AAATAAAAAATAATGACTAAAATCATA
Found at i:1185481 original size:26 final size:26
Alignment explanation
Indices: 1185398--1185481 Score: 89
Period size: 27 Copynumber: 3.2 Consensus size: 26
1185388 TTAGAAATAA
*
1185398 AAAATAATGACTAAAATGCATAAAAT
1 AAAATAATGACTAAAATTCATAAAAT
* * * *
1185424 AAAATAAT-AGTAACCAAATCAGAAATAA
1 AAAATAATGACTAA--AATTCATAAA-AT
1185452 AAAATAATGACTAAAATTCATAAAAT
1 AAAATAATGACTAAAATTCATAAAAT
1185478 AAAA
1 AAAA
1185482 GAGCAGTAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
25 4 0.09
26 13 0.29
27 15 0.33
28 9 0.20
29 4 0.09
ACGTcount: A:0.64, C:0.08, G:0.06, T:0.21
Consensus pattern (26 bp):
AAAATAATGACTAAAATTCATAAAAT
Found at i:1186948 original size:39 final size:39
Alignment explanation
Indices: 1186903--1186984 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
1186893 CTAGCATGGC
* ** *
1186903 GTTGCTGATTCGAAATGTTCTGAATCGAGCAAAGAAAAT
1 GTTGCTGATTCGAAATATAATGAATCGAGAAAAGAAAAT
* *
1186942 GTTGCTGATTCGAAGTATAATGAATCGAGAAAAGGAAAT
1 GTTGCTGATTCGAAATATAATGAATCGAGAAAAGAAAAT
1186981 GTTG
1 GTTG
1186985 AAAACATCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.28
Consensus pattern (39 bp):
GTTGCTGATTCGAAATATAATGAATCGAGAAAAGAAAAT
Found at i:1187109 original size:20 final size:20
Alignment explanation
Indices: 1187081--1187131 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1187071 GCATCATGCT
*
1187081 CGAAAGACTTACTAATGGCC
1 CGAAGGACTTACTAATGGCC
*
1187101 CGAAGGACTTACTGATGGCC
1 CGAAGGACTTACTAATGGCC
1187121 CGAAGGACTTA
1 CGAAGGACTTA
1187132 AGCTAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (20 bp):
CGAAGGACTTACTAATGGCC
Found at i:1187335 original size:42 final size:40
Alignment explanation
Indices: 1187251--1187359 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 40
1187241 ACCCGAAGGT
* * *
1187251 CTTATGGATGCCCGAAGGACTT-ATCATCTTGCTTGAAAGA
1 CTTAT-GATGCCCGAAGGACTTAAGCATCATGCTCGAAAGA
*
1187291 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTAT-GATG-CCCGAAGGACTTAAGCATCATGCTCGAAAGA
*
1187333 CTTACTGACGGCCCGAAGGACTTAAGC
1 CTTA-TGA-TGCCCGAAGGACTTAAGC
1187360 TGATTCAAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
40 9 0.16
41 11 0.19
42 36 0.62
43 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTATGATGCCCGAAGGACTTAAGCATCATGCTCGAAAGA
Found at i:1187499 original size:226 final size:225
Alignment explanation
Indices: 1187101--1187582 Score: 730
Period size: 226 Copynumber: 2.1 Consensus size: 225
1187091 ACTAATGGCC
* * * *
1187101 CGAAGGACTTACTGATGGCCCGAAGGACTTAAGCTAATTCAAAGTGTGTAAATTAAGCAATAGGA
1 CGAAAGACTTACTGATGGCCCGAAGGACTTAAGCTAATTCAAAGTGCGTAAATCAAGAAATAGGA
* * * *
1187166 TATGTTAACCCCTTTGGGGGGTGTTGCTGATTCAAAGTGTTATGAATCGAGCAAAGAAAATGTTG
66 AATGTTAACCCCTCTGGAGGGCGTTGCTGATTCAAAGTGTTATGAATCGAGCAAAGAAAATGTTG
* * * *
1187231 CAAACATCCTACCCGAAGGTCTTATGGATGCCCGAAGGACTTATCATCTTGCTTGAAAGACTTAT
131 AAAACATCCTACCCGAAGGTCATATGGATGCCCGAAGGACTTATCATCTTGCTCGAAACACTTAT
* *
1187296 AGATGACCCGAAGGATTTAAGCATCATGCT
196 AGATAACCCGAAGGATTTAAGCATCAAGCT
* * * *
1187326 CGAAAGACTTACTGACGGCCCGAAGGACTTAAGCTGATTCAAAGTGCGTGAATCGAGAAATAGGA
1 CGAAAGACTTACTGATGGCCCGAAGGACTTAAGCTAATTCAAAGTGCGTAAATCAAGAAATAGGA
* * *
1187391 AATGTTAACTCCTCTGGTAGGGCGTTGCTGATTCAAAGTGTTGTGAATCGAGCAAAGGAAATGTT
66 AATGTTAACCCCTCTGG-AGGGCGTTGCTGATTCAAAGTGTTATGAATCGAGCAAAGAAAATGTT
*
1187456 GAAAACATCCTGCCCGAAGGTCATATGGATGCCCGAAGGACTTATCATCTTGCTCGAAACACTTA
130 GAAAACATCCTACCCGAAGGTCATATGGATGCCCGAAGGACTTATCATCTTGCTCGAAACACTTA
*
1187521 TAGATAACCTGAAGGATTTAAGCATCAAGCT
195 TAGATAACCCGAAGGATTTAAGCATCAAGCT
* *
1187552 CGAAAGACTTACTGATTGCCCGAATGACTTA
1 CGAAAGACTTACTGATGGCCCGAAGGACTTA
1187583 CTCATCAAGA
Statistics
Matches: 230, Mismatches: 26, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
225 71 0.31
226 159 0.69
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (225 bp):
CGAAAGACTTACTGATGGCCCGAAGGACTTAAGCTAATTCAAAGTGCGTAAATCAAGAAATAGGA
AATGTTAACCCCTCTGGAGGGCGTTGCTGATTCAAAGTGTTATGAATCGAGCAAAGAAAATGTTG
AAAACATCCTACCCGAAGGTCATATGGATGCCCGAAGGACTTATCATCTTGCTCGAAACACTTAT
AGATAACCCGAAGGATTTAAGCATCAAGCT
Found at i:1187714 original size:21 final size:21
Alignment explanation
Indices: 1187690--1187752 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
1187680 AAATTGTCTC
1187690 AAGGGAGACAAAATTTGTTTT
1 AAGGGAGACAAAATTTGTTTT
* *
1187711 AA-GG-G--AAAA--TGTCTC
1 AAGGGAGACAAAATTTGTTTT
*
1187726 AAGAGAGACAAAATTTGTTTT
1 AAGGGAGACAAAATTTGTTTT
1187747 AAGGGA
1 AAGGGA
1187753 AACTGTCTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
15 6 0.20
16 1 0.03
17 5 0.17
19 5 0.17
20 2 0.07
21 11 0.37
ACGTcount: A:0.41, C:0.06, G:0.25, T:0.27
Consensus pattern (21 bp):
AAGGGAGACAAAATTTGTTTT
Found at i:1187724 original size:36 final size:36
Alignment explanation
Indices: 1187628--1187988 Score: 393
Period size: 36 Copynumber: 10.1 Consensus size: 36
1187618 CTTTAAATCT
* * * *
1187628 TTTGTTTCTAGTGAAACTATCTCAAGCA-AGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAG-AGAGACAAAA
* * *
1187664 TCTTCTGTTTCAAGGCAAATTGTCTCAAGGGAGACAAAA
1 --TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
1187703 TTTGTTTTAAGGGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1187739 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
1187775 TTTATTTTAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* ** *
1187811 ATCATTTCAAGGGAAACAT-TCTC-A-A-AG-----T
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
* *
1187839 TTATGTTTCAAGAGG-AACTGTCTCAAGGGAGTCAAAA
1 TT-TGTTTCAAG-GGAAACTGTCTCAAGAGAGACAAAA
1187876 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1187912 TTTGTTTCAAGGGAAGCTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
1187948 TTCGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1187984 TTTGT
1 TTTGT
1187989 GTTGAGTAAA
Statistics
Matches: 279, Mismatches: 29, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
28 2 0.01
29 14 0.05
30 3 0.01
32 2 0.01
33 2 0.01
34 1 0.00
35 3 0.01
36 219 0.78
37 5 0.02
38 2 0.01
39 26 0.09
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:1187956 original size:137 final size:137
Alignment explanation
Indices: 1187720--1187972 Score: 409
Period size: 137 Copynumber: 1.8 Consensus size: 137
1187710 TAAGGGAAAA
* *
1187720 TGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTTAA
1 TGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAA
*
1187785 GGGAAACTGTCTCAAGAGAGACAAAAATCATTTCAAGGGAAACAT-TCTCAAAGTTTATGTTTCA
66 GGGAAACTGTCTCAAGAGAGACAAAAATCATTTCAAGAGAAAC-TGTCTCAAAGTTTATGTTTCA
1187849 AGAGGAAC
130 AGAGGAAC
* * *
1187857 TGTCTCAAGGGAGTCAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA
1 TGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAA
* * *
1187922 GGGAAGCTGTCTCAAGAGAGACAAAATTCGTTTCAAGAGAAACTGTCTCAA
66 GGGAAACTGTCTCAAGAGAGACAAAAATCATTTCAAGAGAAACTGTCTCAA
1187973 GAGAGACAAA
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
136 1 0.01
137 105 0.99
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.26
Consensus pattern (137 bp):
TGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAA
GGGAAACTGTCTCAAGAGAGACAAAAATCATTTCAAGAGAAACTGTCTCAAAGTTTATGTTTCAA
GAGGAAC
Found at i:1193552 original size:26 final size:25
Alignment explanation
Indices: 1193471--1193610 Score: 81
Period size: 26 Copynumber: 5.3 Consensus size: 25
1193461 AAAATGCAAT
* *
1193471 AAAACAAAAAATAGTAGCCAAATCA
1 AAAATAAAAAACAGTAGCCAAATCA
* *
1193496 GAAATAAAAATA-A-T-GACTAAAATGCA
1 AAAATAAAAA-ACAGTAG-C-CAAAT-CA
1193522 TAAAATAAAATAACAGTAGCCAAATCA
1 -AAAATAAAA-AACAGTAGCCAAATCA
* * *
1193549 AAAATAAAAAATAGT-GACTAAAATGCTT
1 AAAATAAAAAACAGTAG-C-CAAAT-C-A
*
1193577 AAAATAAAAGAGCAGTAGCCAAATCA
1 AAAATAAAA-AACAGTAGCCAAATCA
1193603 AAAATAAA
1 AAAATAAA
1193611 TAGTGACTGA
Statistics
Matches: 88, Mismatches: 12, Indels: 29
0.68 0.09 0.22
Matches are distributed among these distances:
23 1 0.01
24 3 0.03
25 19 0.22
26 24 0.27
27 13 0.15
28 19 0.22
29 7 0.08
30 2 0.02
ACGTcount: A:0.61, C:0.11, G:0.10, T:0.17
Consensus pattern (25 bp):
AAAATAAAAAACAGTAGCCAAATCA
Found at i:1193580 original size:28 final size:27
Alignment explanation
Indices: 1193497--1193585 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 27
1193487 GCCAAATCAG
*
1193497 AAAT-AAAAATAATGACTAAAATGCATA
1 AAATAAAAAATAGTGACTAAAATGC-TA
* * *
1193524 AAATAAAATAACAGT-AGC-CAAAT-CAA
1 AAATAAAA-AATAGTGA-CTAAAATGCTA
1193550 AAATAAAAAATAGTGACTAAAATGCTTA
1 AAATAAAAAATAGTGACTAAAATGC-TA
1193578 AAATAAAA
1 AAATAAAA
1193586 GAGCAGTAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
25 6 0.12
26 14 0.29
27 6 0.12
28 17 0.35
29 5 0.10
ACGTcount: A:0.63, C:0.09, G:0.08, T:0.20
Consensus pattern (27 bp):
AAATAAAAAATAGTGACTAAAATGCTA
Found at i:1193580 original size:54 final size:53
Alignment explanation
Indices: 1193446--1193610 Score: 215
Period size: 54 Copynumber: 3.1 Consensus size: 53
1193436 AAATTGCTAA
* * * * *
1193446 AAAAAATAAGAGACCAAAATGCAATAAAACAAAAAATAGTAGCCAAATCAGAAAT
1 AAAAAAT-AGTGACTAAAATGC-ATAAAATAAAAAACAGTAGCCAAATCAAAAAT
*
1193501 -AAAAATAATGACTAAAATGCATAAAATAAAATAACAGTAGCCAAATCAAAAAT
1 AAAAAATAGTGACTAAAATGCATAAAATAAAA-AACAGTAGCCAAATCAAAAAT
* *
1193554 AAAAAATAGTGACTAAAATGCTTAAAATAAAAGAGCAGTAGCCAAATCAAAAAT
1 AAAAAATAGTGACTAAAATGCATAAAATAAAA-AACAGTAGCCAAATCAAAAAT
1193608 AAA
1 AAA
1193611 TAGTGACTGA
Statistics
Matches: 98, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
52 10 0.10
53 30 0.31
54 58 0.59
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.16
Consensus pattern (53 bp):
AAAAAATAGTGACTAAAATGCATAAAATAAAAAACAGTAGCCAAATCAAAAAT
Found at i:1201046 original size:20 final size:20
Alignment explanation
Indices: 1201009--1201079 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1200999 TCGAGGCTGT
* *
1201009 AAGAACAATATTGGTACTTG
1 AAGAACAATATCGATACTTG
*
1201029 AAGAACAATATCGATACTAACG
1 AAGAACAATATCGATACT--TG
1201051 AAGAACAATATCGATA-TTGG
1 AAGAACAATATCGATACTT-G
*
1201071 ATGAACAAT
1 AAGAACAAT
1201080 GCCGGTACTG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 25 0.58
21 1 0.02
22 17 0.40
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (20 bp):
AAGAACAATATCGATACTTG
Found at i:1209147 original size:162 final size:162
Alignment explanation
Indices: 1208880--1209203 Score: 578
Period size: 162 Copynumber: 2.0 Consensus size: 162
1208870 CTTAGAAAGT
*
1208880 TCTCTAACTATATCTCTTTTGACCCTTTTCGAAGCTACTTCAGACGATATAGAAACGACGTAGTA
1 TCTCTAACTATATCTCTATTGACCCTTTTCGAAGCTACTTCAGACGATATAGAAACGACGTAGTA
*
1208945 ATGAACATCCATTGTAACATCCACTAAGAGTTATAAAACCTCGATATAGGCTTTTGACTCCTCTT
66 ATGAACATCCATTGTAACATCCACTAAGACTTATAAAACCTCGATATAGGCTTTTGACTCCTCTT
1209010 AGTTCACTGGCTTTGTGAGGTAGATTAAGGGG
131 AGTTCACTGGCTTTGTGAGGTAGATTAAGGGG
**
1209042 TCTCTAACTATATCTCTATTGACCCTTTTTTAAGCTACTTCAGACGATATA-ATAACGACGTAGT
1 TCTCTAACTATATCTCTATTGACCCTTTTCGAAGCTACTTCAGACGATATAGA-AACGACGTAGT
*
1209106 AATGAACATCCATTGTAACATCCACTAAGACTTATAAAACCTCGATATAGTCTTTTGACTCCTCT
65 AATGAACATCCATTGTAACATCCACTAAGACTTATAAAACCTCGATATAGGCTTTTGACTCCTCT
*
1209171 TAGTTCGCTGGCTTTGTGAGGTAGATTAAGGGG
130 TAGTTCACTGGCTTTGTGAGGTAGATTAAGGGG
1209204 AGTTGAACTT
Statistics
Matches: 155, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
161 1 0.01
162 154 0.99
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (162 bp):
TCTCTAACTATATCTCTATTGACCCTTTTCGAAGCTACTTCAGACGATATAGAAACGACGTAGTA
ATGAACATCCATTGTAACATCCACTAAGACTTATAAAACCTCGATATAGGCTTTTGACTCCTCTT
AGTTCACTGGCTTTGTGAGGTAGATTAAGGGG
Found at i:1212143 original size:2 final size:2
Alignment explanation
Indices: 1212136--1212164 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1212126 TTTATCTTTG
1212136 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1212165 ATAACTAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1230947 original size:15 final size:15
Alignment explanation
Indices: 1230929--1230965 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1230919 AATAAAATAT
1230929 AAATTAATATTTTTA
1 AAATTAATATTTTTA
*
1230944 AAATTAGTATTTTTA
1 AAATTAATATTTTTA
*
1230959 GAATTAA
1 AAATTAA
1230966 ACTTTATAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
AAATTAATATTTTTA
Found at i:1232504 original size:25 final size:25
Alignment explanation
Indices: 1232471--1232559 Score: 133
Period size: 25 Copynumber: 3.6 Consensus size: 25
1232461 TTTTTGTCAA
1232471 CAGTCAACGATCAACGTTTAACGGT
1 CAGTCAACGATCAACGTTTAACGGT
* *
1232496 CAGTTAACGATCAACGTTTAACAGT
1 CAGTCAACGATCAACGTTTAACGGT
**
1232521 CAGTCAACGATCAACGTTTAACGAC
1 CAGTCAACGATCAACGTTTAACGGT
*
1232546 CAGTCAACGCTCAA
1 CAGTCAACGATCAA
1232560 TGATCAACGG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (25 bp):
CAGTCAACGATCAACGTTTAACGGT
Found at i:1238273 original size:19 final size:19
Alignment explanation
Indices: 1238249--1238290 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1238239 AAAAATATTC
1238249 ATACGATAAACATATACGT
1 ATACGATAAACATATACGT
*
1238268 ATACGATAAACATATATGT
1 ATACGATAAACATATACGT
1238287 ATAC
1 ATAC
1238291 ATATCTCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (19 bp):
ATACGATAAACATATACGT
Found at i:1241247 original size:35 final size:35
Alignment explanation
Indices: 1241144--1241535 Score: 197
Period size: 36 Copynumber: 10.9 Consensus size: 35
1241134 TTTTTATTAT
*
1241144 ATATATATATATTATAG--TTTGAAATCATTTTGAAA
1 ATATATA-ATA-TATAGTTTTTGAAAACATTTTGAAA
*
1241179 ACTATATAATATATGGTTTTCTAAAAAGAAAACATTTTGAAA
1 A-TATATAATATATAGTTTT-T-----GAAAACATTTTGAAA
*
1241221 ATATATAATATATGGTTTTTGAAAACATTTTTTGAAAA
1 ATATATAATATATAGTTTTTGAAAACA--TTTTG-AAA
* * *
1241259 CAAATATATTATATAGTTTTTGAAAATATTTTTGAAA
1 -ATATATAATATATAGTTTTTGAAAACA-TTTTGAAA
* *
1241296 CCATATATATTATATAGTTTTT-AAAACCATTTTCAAA
1 --ATATATAATATATAGTTTTTGAAAA-CATTTTGAAA
1241333 ACTTATATAATATATAG-TTTT-AAAATCATTTT-AAA
1 A--TATATAATATATAGTTTTTGAAAA-CATTTTGAAA
***
1241368 ATTTATATAATATATAGTTTAAAAAAACATTTTTG-AA
1 A--TATATAATATATAGTTTTTGAAAACA-TTTTGAAA
* *
1241405 ACATAT-A-ATATAG-TTTT-AAAACGTTTTTGAAA
1 ATATATAATATATAGTTTTTGAAAAC-ATTTTGAAA
* * * * *
1241437 A-CTATAACATAT--TGTTTGAAAACGTTTTTTAAA
1 ATATATAATATATAGTTTTTGAAAAC-ATTTTGAAA
* * * *
1241470 ATTATGTAATATAT-GGTTTTGAAAATATCTTCGAAA
1 A-TATATAATATATAGTTTTTGAAAACAT-TTTGAAA
* *
1241506 TATATATTATATAAAG-TTTT-AAAACATTTT
1 -ATATATAATATATAGTTTTTGAAAACATTTT
1241536 TTTTATCATA
Statistics
Matches: 289, Mismatches: 35, Indels: 67
0.74 0.09 0.17
Matches are distributed among these distances:
31 13 0.04
32 9 0.03
33 25 0.09
34 7 0.02
35 50 0.17
36 52 0.18
37 46 0.16
38 30 0.10
39 23 0.08
40 1 0.00
41 18 0.06
42 15 0.05
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (35 bp):
ATATATAATATATAGTTTTTGAAAACATTTTGAAA
Found at i:1241254 original size:13 final size:13
Alignment explanation
Indices: 1241236--1241260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1241226 TAATATATGG
1241236 TTTTTGAAAACAT
1 TTTTTGAAAACAT
1241249 TTTTTGAAAACA
1 TTTTTGAAAACA
1241261 AATATATTAT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTTGAAAACAT
Found at i:1241304 original size:38 final size:37
Alignment explanation
Indices: 1241207--1241536 Score: 216
Period size: 35 Copynumber: 9.3 Consensus size: 37
1241197 TTCTAAAAAG
*
1241207 AAAACA-TTTTG-AAA-ATATATAATATATGGTTTTT
1 AAAACATTTTTGAAAACATATATAATATATAGTTTTT
* *
1241241 GAAAACATTTTTTGAAAACAAATATATTATATAGTTTTT
1 -AAAACA-TTTTTGAAAACATATATAATATATAGTTTTT
* * *
1241280 GAAAATATTTTTGAAACCATATATATTATATAGTTTTT
1 -AAAACATTTTTGAAAACATATATAATATATAGTTTTT
* *
1241318 AAAACCA-TTTTCAAAACTTATATAATATATAG-TTTT
1 AAAA-CATTTTTGAAAACATATATAATATATAGTTTTT
** **
1241354 AAAATCA-TTTT-AAAATTTATATAATATATAGTTTAAA
1 AAAA-CATTTTTGAAAACATATATAATATATAGTTT-TT
1241391 AAAACATTTTTG-AAAC--ATAT-A-ATATAG-TTTT
1 AAAACATTTTTGAAAACATATATAATATATAGTTTTT
* *
1241422 AAAACGTTTTTGAAAAC-TATA-ACATAT-T-G-TTTG
1 AAAACATTTTTGAAAACATATATA-ATATATAGTTTTT
* * * * * *
1241455 AAAACGTTTTTTAAAA-TTATGTAATATATGGTTTTG
1 AAAACATTTTTGAAAACATATATAATATATAGTTTTT
* * * * * *
1241491 AAAATATCTTCG-AAATATATATTATATAAAG-TTTT
1 AAAACATTTTTGAAAACATATATAATATATAGTTTTT
1241526 AAAACATTTTT
1 AAAACATTTTT
1241537 TTTATCATAT
Statistics
Matches: 239, Mismatches: 36, Indels: 40
0.76 0.11 0.13
Matches are distributed among these distances:
31 11 0.05
32 6 0.03
33 35 0.15
34 5 0.02
35 46 0.19
36 39 0.16
37 41 0.17
38 33 0.14
39 23 0.10
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (37 bp):
AAAACATTTTTGAAAACATATATAATATATAGTTTTT
Found at i:1241349 original size:37 final size:37
Alignment explanation
Indices: 1241144--1241411 Score: 205
Period size: 37 Copynumber: 7.1 Consensus size: 37
1241134 TTTTTATTAT
*
1241144 ATATATATATATTATAG--TTTGAAATCATTTTGAAAAC
1 ATATATA-ATA-TATAGTTTTTGAAAACATTTTGAAAAC
*
1241181 -TATATAATATATGGTTTTCTAAAAAGAAAACATTTTG-AAA-
1 ATATATAATATATAGTTTT-T-----GAAAACATTTTGAAAAC
*
1241221 ATATATAATATATGGTTTTTGAAAACATTTTTTGAAAAC
1 ATATATAATATATAGTTTTTGAAAACA--TTTTGAAAAC
* * * *
1241260 AAATATATTATATAGTTTTTGAAAATATTTTTGAAACC
1 ATATATAATATATAGTTTTTGAAAACA-TTTTGAAAAC
* *
1241298 ATATATATTATATAGTTTTT-AAAACCATTTTCAAAAC
1 ATATATAATATATAGTTTTTGAAAA-CATTTTGAAAAC
* *
1241335 TTATATAATATATAG-TTTT-AAAATCATTTT-AAAAT
1 ATATATAATATATAGTTTTTGAAAA-CATTTTGAAAAC
* ***
1241370 TTATATAATATATAGTTTAAAAAAACATTTTTG-AAAC
1 ATATATAATATATAGTTTTTGAAAACA-TTTTGAAAAC
1241407 ATATA
1 ATATA
1241412 ATATAGTTTT
Statistics
Matches: 194, Mismatches: 19, Indels: 36
0.78 0.08 0.14
Matches are distributed among these distances:
34 4 0.02
35 29 0.15
36 26 0.13
37 46 0.24
38 33 0.17
39 23 0.12
40 1 0.01
41 21 0.11
42 11 0.06
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.43
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTGAAAACATTTTGAAAAC
Found at i:1241432 original size:31 final size:33
Alignment explanation
Indices: 1241373--1241470 Score: 94
Period size: 33 Copynumber: 3.0 Consensus size: 33
1241363 TTAAAATTTA
* * *
1241373 TATAATATATAGTTTAAAAAAACATTTTTG-AAAC
1 TATAACATATAGTTT--GAAAACGTTTTTGAAAAC
*
1241407 -ATATA-ATATAGTTTTAAAACGTTTTTGAAAAC
1 TATA-ACATATAGTTTGAAAACGTTTTTGAAAAC
* *
1241439 TATAACATATTGTTTGAAAACGTTTTTTAAAA
1 TATAACATATAGTTTGAAAACGTTTTTGAAAA
1241471 TTATGTAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
31 11 0.20
32 5 0.09
33 38 0.69
34 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (33 bp):
TATAACATATAGTTTGAAAACGTTTTTGAAAAC
Found at i:1242238 original size:20 final size:17
Alignment explanation
Indices: 1242199--1242241 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 17
1242189 GGAGCGCACA
1242199 CGCCGGAAACGAAGGGT
1 CGCCGGAAACGAAGGGT
*
1242216 CGCCTGGAAAGCGAAAGGTT
1 CGCC-GGAAA-CG-AAGGGT
1242236 CGCCGG
1 CGCCGG
1242242 GGAGGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.18
18 5 0.23
19 4 0.18
20 9 0.41
ACGTcount: A:0.26, C:0.26, G:0.40, T:0.09
Consensus pattern (17 bp):
CGCCGGAAACGAAGGGT
Found at i:1243543 original size:30 final size:31
Alignment explanation
Indices: 1243481--1243552 Score: 94
Period size: 30 Copynumber: 2.3 Consensus size: 31
1243471 AAGTATAAAG
1243481 TTTAACAAGTTTAGGGGACTAAAAGGGTAATT
1 TTTAA-AAGTTTAGGGGACTAAAAGGGTAATT
* *
1243513 TTTAAAAGTTTA-GGGA-TCATAAGTGTAATT
1 TTTAAAAGTTTAGGGGACT-AAAAGGGTAATT
1243543 TTTAAAAGTT
1 TTTAAAAGTT
1243553 ATGTATTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 1 0.03
30 24 0.65
31 7 0.19
32 5 0.14
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.38
Consensus pattern (31 bp):
TTTAAAAGTTTAGGGGACTAAAAGGGTAATT
Found at i:1247353 original size:2 final size:2
Alignment explanation
Indices: 1247342--1247386 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1247332 TGCATGTGTC
1247342 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1247383 TA TA
1 TA TA
1247387 AAATATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1249727 original size:13 final size:13
Alignment explanation
Indices: 1249709--1249742 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1249699 TAAGATTTTC
*
1249709 TTTGAAAATCATT
1 TTTGAAAATCAAT
1249722 TTTG-AAATCAAT
1 TTTGAAAATCAAT
1249734 TTTGAAAAT
1 TTTGAAAAT
1249743 TACCCCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:1251943 original size:20 final size:20
Alignment explanation
Indices: 1251918--1251973 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1251908 AAAACCTGAC
1251918 GAGTGTATCGATGCACTACA
1 GAGTGTATCGATGCACTACA
*
1251938 GAGTGTATCGATGCACTGCA
1 GAGTGTATCGATGCACTACA
*
1251958 GAGTGTATTGATGCAC
1 GAGTGTATCGATGCAC
1251974 ATTCAAGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (20 bp):
GAGTGTATCGATGCACTACA
Found at i:1255852 original size:21 final size:20
Alignment explanation
Indices: 1255828--1255866 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1255818 TCATTTTTCA
*
1255828 ATTTTTAAATATCATTTCTGT
1 ATTTTTAAA-ATAATTTCTGT
1255849 ATTTTTAAAATAATTTCT
1 ATTTTTAAAATAATTTCT
1255867 CATAATCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTTAAAATAATTTCTGT
Found at i:1257870 original size:65 final size:64
Alignment explanation
Indices: 1257779--1257928 Score: 160
Period size: 65 Copynumber: 2.3 Consensus size: 64
1257769 CTTGGGGTGT
* * * * * * *
1257779 ATCAGTACACTAATTACATTCGATGTTTCAA-AAGATCCAGGAGTGAATCGATGCATGG-TGTTT
1 ATCAGTACACAAAATGCATTCAATGTTTCAATAAAAT-CAAGAGTGAATCAATGCATGGCTG--T
*
1257842 GC
63 CC
* * *
1257844 ATCGGTACATAAAATGCATTCAATGTTTCAATAAAATCAAGAGTGCATCAATGCATGGCTGTCC
1 ATCAGTACACAAAATGCATTCAATGTTTCAATAAAATCAAGAGTGAATCAATGCATGGCTGTCC
1257908 ATCAGTACACAAAATGCATTC
1 ATCAGTACACAAAATGCATTC
1257929 GAAGTAGGGT
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
64 21 0.30
65 43 0.61
66 6 0.09
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCAGTACACAAAATGCATTCAATGTTTCAATAAAATCAAGAGTGAATCAATGCATGGCTGTCC
Found at i:1260243 original size:11 final size:11
Alignment explanation
Indices: 1260209--1260267 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
1260199 ACCAATCTGC
*
1260209 TTGAATATATTT
1 TTGAAAATA-TT
*
1260221 TATGAAAGTATT
1 T-TGAAAATATT
1260233 TTGAAAATATT
1 TTGAAAATATT
*
1260244 TTGAATAA-GTT
1 TTGAA-AATATT
1260255 TTGAAAATATT
1 TTGAAAATATT
1260266 TT
1 TT
1260268 ATGAAAGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 2 0.05
11 25 0.64
12 6 0.15
13 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (11 bp):
TTGAAAATATT
Found at i:1260320 original size:25 final size:25
Alignment explanation
Indices: 1260292--1260389 Score: 151
Period size: 25 Copynumber: 3.9 Consensus size: 25
1260282 AATAATATTT
* *
1260292 GAATTTTGAAAAATGTTTGATAAAA
1 GAATTTTGAAGAATGTTTGATGAAA
* *
1260317 GAATTTTGAAGATTGTTTAATGAAA
1 GAATTTTGAAGAATGTTTGATGAAA
*
1260342 GAATTTTGAAGAATATTTGATGAAA
1 GAATTTTGAAGAATGTTTGATGAAA
1260367 GAATTTTGAAGAATGTTTGATGA
1 GAATTTTGAAGAATGTTTGATGA
1260390 TTTTTTTAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (25 bp):
GAATTTTGAAGAATGTTTGATGAAA
Found at i:1263253 original size:29 final size:28
Alignment explanation
Indices: 1263212--1263268 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
1263202 ACAAAAACTG
1263212 CCCTTTTTTACTAATG-TCATTCGGTGCA
1 CCCTTTTTTACTAATGCT-ATTCGGTGCA
1263240 CCCTTTTTTGACTAATGCTATTCGGTGCA
1 CCCTTTTTT-ACTAATGCTATTCGGTGCA
1263269 TTAATGCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.33
29 17 0.63
30 1 0.04
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.42
Consensus pattern (28 bp):
CCCTTTTTTACTAATGCTATTCGGTGCA
Found at i:1269637 original size:82 final size:83
Alignment explanation
Indices: 1269474--1269657 Score: 221
Period size: 82 Copynumber: 2.2 Consensus size: 83
1269464 GCGTTTCTTT
* ** *
1269474 AACAAACGCCGTGATAGAATAGTAATTTAGCGGTGTTTTTAGCATAAATATAGCAATAGGGTTCA
1 AACAAACGTCGTGATA-AATAGTAATTTAGCGGCATTTTTAGCACAAATATAGCAATAGGGTTCA
* *
1269539 TTTATAGTGGCGTTTTTCC
65 TTTATAGGGGCATTTTTCC
** * *
1269558 AACAAACGTCGTGATAAATAGTTCTTTAGCGGCATTTTTAG-ACAAATGCT-GTAATAGGGTT-A
1 AACAAACGTCGTGATAAATAGTAATTTAGCGGCATTTTTAGCACAAAT-ATAGCAATAGGGTTCA
1269620 GTTTATAGGGGCATTTTTCC
65 -TTTATAGGGGCATTTTTCC
*
1269640 AATAAACGTCGTGATAAA
1 AACAAACGTCGTGATAAA
1269658 GAGAACTGTA
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
81 1 0.01
82 49 0.56
83 22 0.25
84 15 0.17
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (83 bp):
AACAAACGTCGTGATAAATAGTAATTTAGCGGCATTTTTAGCACAAATATAGCAATAGGGTTCAT
TTATAGGGGCATTTTTCC
Found at i:1269681 original size:82 final size:82
Alignment explanation
Indices: 1269528--1269685 Score: 210
Period size: 82 Copynumber: 1.9 Consensus size: 82
1269518 TAAATATAGC
* * * ** * *
1269528 AATAGGGTTCATTTATAGTGGCGTTTTTCCAACAAACGTCGTGATAAATAGTTCTTTAGCGGCAT
1 AATAGGGTTCATTTATAGGGGCATTTTTCCAACAAACGTCGTGATAAAGAGAACTGTAGCAGCAT
*
1269593 TTTTAGACAAATGCTGT
66 TGTTAGACAAATGCTGT
* *
1269610 AATAGGGTT-AGTTTATAGGGGCATTTTTCCAATAAACGTCGTGATAAAGAGAACTGTAGCAGCG
1 AATAGGGTTCA-TTTATAGGGGCATTTTTCCAACAAACGTCGTGATAAAGAGAACTGTAGCAGCA
1269674 TTGTTAGACAAA
65 TTGTTAGACAAA
1269686 CACCACAATA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
81 1 0.02
82 64 0.98
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (82 bp):
AATAGGGTTCATTTATAGGGGCATTTTTCCAACAAACGTCGTGATAAAGAGAACTGTAGCAGCAT
TGTTAGACAAATGCTGT
Found at i:1270152 original size:20 final size:22
Alignment explanation
Indices: 1270123--1270169 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
1270113 GTGTTTTACT
*
1270123 GCTTTTGAATA-GAAAA-AACA
1 GCTTTCGAATAGGAAAATAACA
1270143 GCTTTCGAATAGGAAAATAACA
1 GCTTTCGAATAGGAAAATAACA
*
1270165 ACTTT
1 GCTTT
1270170 TGAAAATGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 5 0.22
22 8 0.35
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (22 bp):
GCTTTCGAATAGGAAAATAACA
Found at i:1272101 original size:41 final size:41
Alignment explanation
Indices: 1272052--1272251 Score: 127
Period size: 41 Copynumber: 4.9 Consensus size: 41
1272042 GTTTTAATGT
*
1272052 AAACGCCGCGATAGAGTAGCACTATAAAGGCGTTTTCATAC
1 AAACGCCGCGATAGAGTAGCACTATAGAGGCGTTTTCATAC
* * * * * * * * ** *
1272093 AAATGCCGCAAAAGAGTTGGACAATAGTGGCATTTTTTTAGT
1 AAACGCCGCGATAGAGTAGCACTATAGAGGCGTTTTCATA-C
* *
1272135 AAACGCCGCGATAGAGTAGCACTATAGAGACGTTTTCAGAC
1 AAACGCCGCGATAGAGTAGCACTATAGAGGCGTTTTCATAC
* * * * * * * *
1272176 AAACGCTGCTATCGAG-ATGGA-TAGTAGTGACGTTTT-TTAGT
1 AAACGCCGCGATAGAGTA-GCACTA-TAGAGGCGTTTTCATA-C
* *
1272217 AAACGCCGCGATATAGTAGCACTATAGAGACGTTT
1 AAACGCCGCGATAGAGTAGCACTATAGAGGCGTTT
1272252 GGTTTACAAA
Statistics
Matches: 114, Mismatches: 39, Indels: 12
0.69 0.24 0.07
Matches are distributed among these distances:
40 4 0.04
41 79 0.69
42 31 0.27
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (41 bp):
AAACGCCGCGATAGAGTAGCACTATAGAGGCGTTTTCATAC
Found at i:1272243 original size:82 final size:83
Alignment explanation
Indices: 1272050--1272251 Score: 271
Period size: 83 Copynumber: 2.4 Consensus size: 83
1272040 ATGTTTTAAT
* * * * *
1272050 GTAAACGCCGCGATAGAGTAGCACTATAAAGGCGTTTTCATACAAATGCCGCAAAAGAGTTGGAC
1 GTAAACGCCGCGATAGAGTAGCACTATAGAGACGTTTTCAGACAAACGCCGCAAAAGAGATGGAC
* *
1272115 AATAGTGGCATTTTTTTA
66 AATAGTGACAGTTTTTTA
* * ** *
1272133 GTAAACGCCGCGATAGAGTAGCACTATAGAGACGTTTTCAGACAAACGCTGCTATCGAGATGGAT
1 GTAAACGCCGCGATAGAGTAGCACTATAGAGACGTTTTCAGACAAACGCCGCAAAAGAGATGGAC
*
1272198 AGTAGTGAC-GTTTTTTA
66 AATAGTGACAGTTTTTTA
*
1272215 GTAAACGCCGCGATATAGTAGCACTATAGAGACGTTT
1 GTAAACGCCGCGATAGAGTAGCACTATAGAGACGTTT
1272252 GGTTTACAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
82 43 0.41
83 62 0.59
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (83 bp):
GTAAACGCCGCGATAGAGTAGCACTATAGAGACGTTTTCAGACAAACGCCGCAAAAGAGATGGAC
AATAGTGACAGTTTTTTA
Found at i:1282041 original size:9 final size:9
Alignment explanation
Indices: 1282027--1282139 Score: 64
Period size: 10 Copynumber: 11.8 Consensus size: 9
1282017 GGCTGCTGGA
1282027 AACCGGTTT
1 AACCGGTTT
1282036 AACCGGTTTT
1 AACCGG-TTT
1282046 CAACCGGTTCT
1 -AACCGGTT-T
*
1282057 GACCGGTTT
1 AACCGGTTT
*
1282066 GACCGGTTT
1 AACCGGTTT
*
1282075 CAACCGGTTCG
1 -AACCGGTT-T
*
1282086 AACCAGTTT
1 AACCGGTTT
* *
1282095 GACCGGTCTG
1 AACCGGT-TT
*
1282105 AATCGGTTT
1 AACCGGTTT
* *
1282114 GACCGGTCTG
1 AACCGGT-TT
*
1282124 AGCCGGTTT
1 AACCGGTTT
*
1282133 GACCGGT
1 AACCGGT
1282140 CTGACCCGAC
Statistics
Matches: 78, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
9 33 0.42
10 38 0.49
11 7 0.09
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1282072 original size:19 final size:18
Alignment explanation
Indices: 1282048--1282145 Score: 99
Period size: 19 Copynumber: 5.2 Consensus size: 18
1282038 CCGGTTTTCA
*
1282048 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTCTG
*
1282067 ACCGGTTTCAACCGGT-TCG
1 ACCGGTTT-GACCGGTCT-G
*
1282086 AACCAGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
*
1282105 AATCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
1282124 AGCCGGTTTGACCGGTCTG
1 A-CCGGTTTGACCGGTCTG
1282143 ACC
1 ACC
1282146 CGACCCGACC
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
18 5 0.07
19 55 0.81
20 8 0.12
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.28
Consensus pattern (18 bp):
ACCGGTTTGACCGGTCTG
Found at i:1282152 original size:5 final size:5
Alignment explanation
Indices: 1282142--1282182 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
1282132 TGACCGGTCT
*
1282142 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC
1282183 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:1282167 original size:22 final size:22
Alignment explanation
Indices: 1282141--1282189 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1282131 TTGACCGGTC
1282141 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
1282163 TGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCCGACCGT
1282185 TGACC
1 TGACC
1282190 GTTGACCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.10
Consensus pattern (22 bp):
TGACCCGACCCGACCCGACCGT
Found at i:1282191 original size:7 final size:7
Alignment explanation
Indices: 1282179--1282209 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1282169 GACCCGACCC
1282179 GACCGTT
1 GACCGTT
1282186 GACCGTT
1 GACCGTT
1282193 GACCGTT
1 GACCGTT
1282200 GACCGTT
1 GACCGTT
1282207 GAC
1 GAC
1282210 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:1283151 original size:32 final size:31
Alignment explanation
Indices: 1283078--1283154 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1283068 CTAATGTGAC
* *
1283078 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
** * *
1283109 TCTCGGGTAGGCCCTGCTGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
1283141 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
1283155 CATGACCCCG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:1289399 original size:9 final size:9
Alignment explanation
Indices: 1289385--1289497 Score: 73
Period size: 10 Copynumber: 11.8 Consensus size: 9
1289375 GGCTGCTGGA
1289385 AACCGGTTT
1 AACCGGTTT
1289394 AACCGGTTTT
1 AACCGG-TTT
1289404 CAACCGGTTCT
1 -AACCGGTT-T
*
1289415 GACCGGTTT
1 AACCGGTTT
*
1289424 GACCGGTTT
1 AACCGGTTT
*
1289433 CAACCGGTTCG
1 -AACCGGTT-T
1289444 AACCGGTTT
1 AACCGGTTT
* *
1289453 GACCGGTCTG
1 AACCGGT-TT
*
1289463 AATCGGTTT
1 AACCGGTTT
* *
1289472 GACCGGTCTG
1 AACCGGT-TT
*
1289482 AGCCGGTTT
1 AACCGGTTT
*
1289491 GACCGGT
1 AACCGGT
1289498 CTGACCCGAC
Statistics
Matches: 80, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
9 34 0.43
10 39 0.49
11 7 0.09
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1289430 original size:19 final size:18
Alignment explanation
Indices: 1289406--1289503 Score: 108
Period size: 19 Copynumber: 5.2 Consensus size: 18
1289396 CCGGTTTTCA
*
1289406 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTCTG
*
1289425 ACCGGTTTCAACCGGT-TCG
1 ACCGGTTT-GACCGGTCT-G
1289444 AACCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
*
1289463 AATCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
1289482 AGCCGGTTTGACCGGTCTG
1 A-CCGGTTTGACCGGTCTG
1289501 ACC
1 ACC
1289504 CGACCCAACC
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
18 5 0.07
19 56 0.80
20 9 0.13
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.28
Consensus pattern (18 bp):
ACCGGTTTGACCGGTCTG
Found at i:1289448 original size:29 final size:28
Alignment explanation
Indices: 1289386--1289490 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 28
1289376 GCTGCTGGAA
*
1289386 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
1289416 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * * *
1289444 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
*
1289473 ACCGGTCTGAGCCGGTTT
1 ACCGGTTTGA-CCGGTTT
1289491 GACCGGTCTG
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
28 10 0.15
29 43 0.65
30 13 0.20
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:1289477 original size:38 final size:38
Alignment explanation
Indices: 1289385--1289501 Score: 132
Period size: 38 Copynumber: 3.0 Consensus size: 38
1289375 GGCTGCTGGA
*
1289385 AACCGGTTTAACCGGTTTTC-AACCGGTTCTGACCGGTTTG
1 AACCGGTTTAACCGG--TTCGAACCGGTT-TGACCGGTCTG
1289425 -ACCGGTTTCAACCGGTTCGAACCGGTTTGACCGGTCTG
1 AACCGGTTT-AACCGGTTCGAACCGGTTTGACCGGTCTG
* * *
1289463 AATCGGTTTGACCGG-TCTGAGCCGGTTTGACCGGTCTG
1 AACCGGTTTAACCGGTTC-GAACCGGTTTGACCGGTCTG
1289501 A
1 A
1289502 CCCGACCCAA
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
37 2 0.03
38 38 0.55
39 23 0.33
40 6 0.09
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (38 bp):
AACCGGTTTAACCGGTTCGAACCGGTTTGACCGGTCTG
Found at i:1289525 original size:5 final size:5
Alignment explanation
Indices: 1289517--1289557 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
1289507 CCCAACCGTT
*
1289517 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCC GACC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACCC GACC
1289558 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:1289564 original size:17 final size:17
Alignment explanation
Indices: 1289499--1289547 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
1289489 TTGACCGGTC
*
1289499 TGACCCGACCCAACCGT
1 TGACCCGACCCGACCGT
1289516 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1289533 TGACCCGACCCGACC
1 TGACCCGACCCGACC
1289548 CGACCCGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.20, C:0.49, G:0.20, T:0.10
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:1289566 original size:7 final size:7
Alignment explanation
Indices: 1289554--1289584 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1289544 GACCCGACCC
1289554 GACCGTT
1 GACCGTT
1289561 GACCGTT
1 GACCGTT
*
1289568 GACCATT
1 GACCGTT
1289575 GACCGTT
1 GACCGTT
1289582 GAC
1 GAC
1289585 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:1296775 original size:9 final size:9
Alignment explanation
Indices: 1296761--1296873 Score: 73
Period size: 10 Copynumber: 11.8 Consensus size: 9
1296751 GGCTGCTGGA
1296761 AACCGGTTT
1 AACCGGTTT
1296770 AACCGGTTTT
1 AACCGG-TTT
1296780 CAACCGGTTCT
1 -AACCGGTT-T
*
1296791 GACCGGTTT
1 AACCGGTTT
*
1296800 GACCGGTTT
1 AACCGGTTT
*
1296809 CAACCGGTTCG
1 -AACCGGTT-T
**
1296820 AACCGGTCA
1 AACCGGTTT
*
1296829 AACCGGTTCG
1 AACCGGTT-T
1296839 AACCGGTTT
1 AACCGGTTT
* *
1296848 GACCGGTCTG
1 AACCGGT-TT
*
1296858 AATCGGTTT
1 AACCGGTTT
*
1296867 GACCGGT
1 AACCGGT
1296874 CTGACCCGAC
Statistics
Matches: 82, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
9 35 0.43
10 40 0.49
11 7 0.09
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1296806 original size:19 final size:20
Alignment explanation
Indices: 1296761--1296877 Score: 102
Period size: 19 Copynumber: 6.0 Consensus size: 20
1296751 GGCTGCTGGA
* *
1296761 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTAACCGGTTCTG
*
1296781 AACCGGTTCTGACCGGTT-TG
1 AACCGGTT-TAACCGGTTCTG
1296801 -ACCGGTTTCAACCGGTTC-G
1 AACCGGTTT-AACCGGTTCTG
**
1296820 AACCGGTCAAACCGGTTC-G
1 AACCGGTTTAACCGGTTCTG
*
1296839 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTAACCGGTTCTG
* *
1296858 AATCGGTTTGACCGG-TCTG
1 AACCGGTTTAACCGGTTCTG
1296877 A
1 A
1296878 CCCGACCCGA
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
18 3 0.04
19 57 0.69
20 15 0.18
21 8 0.10
ACGTcount: A:0.19, C:0.26, G:0.27, T:0.27
Consensus pattern (20 bp):
AACCGGTTTAACCGGTTCTG
Found at i:1296824 original size:29 final size:31
Alignment explanation
Indices: 1296761--1296836 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
1296751 GGCTGCTGGA
1296761 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
*
1296792 -ACCGGTTTGACCGG-TTTCAACCGGTTC-G
1 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
**
1296820 AACCGGTCAAACCGGTT
1 AACCGGTTTAACCGGTT
1296837 CGAACCGGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 1 0.03
29 24 0.62
30 14 0.36
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (31 bp):
AACCGGTTTAACCGGTTTTCAACCGGTTCTG
Found at i:1296842 original size:29 final size:28
Alignment explanation
Indices: 1296770--1296855 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 28
1296760 AAACCGGTTT
**
1296770 AACCGGTTTTCAACCGGTTCTGACCGGTTT
1 AACCGG-TTTCAACCGGTTC-GACCGGTCA
*
1296800 GACCGGTTTCAACCGGTTCGAACCGGTCA
1 AACCGGTTTCAACCGGTTCG-ACCGGTCA
*
1296829 AACCGG-TTCGAACCGGTTTGACCGGTC
1 AACCGGTTTC-AACCGGTTCGACCGGTC
1296856 TGAATCGGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
28 11 0.22
29 33 0.67
30 5 0.10
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.26
Consensus pattern (28 bp):
AACCGGTTTCAACCGGTTCGACCGGTCA
Found at i:1296897 original size:17 final size:17
Alignment explanation
Indices: 1296875--1296932 Score: 89
Period size: 17 Copynumber: 3.3 Consensus size: 17
1296865 TTGACCGGTC
1296875 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1296892 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
*
1296909 TGACCCGACCGTTGACCGT
1 TGACCCGACC--CGACCGT
1296928 TGACC
1 TGACC
1296933 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
17 27 0.71
19 11 0.29
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:1296913 original size:7 final size:7
Alignment explanation
Indices: 1296903--1296966 Score: 105
Period size: 7 Copynumber: 9.4 Consensus size: 7
1296893 GACCCGACCC
1296903 GACCGTT
1 GACCGTT
*
1296910 GACC--C
1 GACCGTT
1296915 GACCGTT
1 GACCGTT
1296922 GACCGTT
1 GACCGTT
1296929 GACCGTT
1 GACCGTT
1296936 GACCGTT
1 GACCGTT
1296943 GACCGTT
1 GACCGTT
1296950 GACCGTT
1 GACCGTT
1296957 GACCGTT
1 GACCGTT
1296964 GAC
1 GAC
1296967 TTTATTTGAC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
5 4 0.08
7 49 0.92
ACGTcount: A:0.16, C:0.31, G:0.28, T:0.25
Consensus pattern (7 bp):
GACCGTT
Found at i:1297920 original size:32 final size:31
Alignment explanation
Indices: 1297836--1297912 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
1297826 CTAATGTGAC
* *
1297836 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
** *
1297867 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
1297899 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
1297913 CACGGCCCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:1297938 original size:63 final size:63
Alignment explanation
Indices: 1297836--1297959 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
1297826 CTAATGTGAC
* ** * *
1297836 TCTTAGGTAGGCTCTGCGGCCCTGAGATTATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
1297899 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAAT-TATTCTCGGGTAGGCCCTCAGGCCCTAAGATGT
1297960 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 49 0.94
64 2 0.04
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:1298707 original size:58 final size:59
Alignment explanation
Indices: 1298617--1298727 Score: 181
Period size: 58 Copynumber: 1.9 Consensus size: 59
1298607 GGAGAGTTGG
*
1298617 TTAGAGCCATATTATCGAGTTTTCCATTTCATTGA-GACTAGGA-GGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCATTTCATT-ACGACTAGGAGGGTTCGATAGGACAC
*
1298675 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTACGACTAGGAGGGTTCGATA
1 TTAGAGCCATATTATCGAGTTTGCCATTTCATTACGACTAGGAGGGTTCGATA
1298728 TTATCCATCT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
57 1 0.02
58 39 0.80
59 9 0.18
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTGCCATTTCATTACGACTAGGAGGGTTCGATAGGACAC
Found at i:1299565 original size:14 final size:14
Alignment explanation
Indices: 1299546--1299572 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1299536 TTAGGTTCTT
1299546 TTGTTTTCCTTGTA
1 TTGTTTTCCTTGTA
1299560 TTGTTTTCCTTGT
1 TTGTTTTCCTTGT
1299573 TTTCCAATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.15, G:0.15, T:0.67
Consensus pattern (14 bp):
TTGTTTTCCTTGTA
Found at i:1317808 original size:19 final size:19
Alignment explanation
Indices: 1317784--1317820 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1317774 ATGTGATTTA
*
1317784 ATATTTTATAATAATAACT
1 ATATTTTATAAAAATAACT
*
1317803 ATATTTTGTAAAAATAAC
1 ATATTTTATAAAAATAAC
1317821 ATTTTAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (19 bp):
ATATTTTATAAAAATAACT
Found at i:1319378 original size:16 final size:16
Alignment explanation
Indices: 1319357--1319398 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
1319347 GCTTTGGGAA
1319357 TAACATTACTGGAATG
1 TAACATTACTGGAATG
*
1319373 TAACATTACTGGAATT
1 TAACATTACTGGAATG
1319389 TAACATTACT
1 TAACATTACT
1319399 ATGGATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (16 bp):
TAACATTACTGGAATG
Found at i:1319845 original size:23 final size:23
Alignment explanation
Indices: 1319793--1319837 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1319783 TCATCCTATA
*
1319793 AAATTATAAATAGTAAAATATTG
1 AAATTAAAAATAGTAAAATATTG
1319816 AATATTAAAAATA-TAAAATATT
1 AA-ATTAAAAATAGTAAAATATT
1319838 TTAAATTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
AAATTAAAAATAGTAAAATATTG
Found at i:1338655 original size:25 final size:23
Alignment explanation
Indices: 1338605--1338656 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
1338595 CCTACAAAAG
*
1338605 AAAATAAGAAAAGACAAACACGT
1 AAAATAAGAAAAGACAAAAACGT
1338628 AAAACTAAGAAAATGACAAGAAAC-T
1 AAAA-TAAGAAAA-GACAA-AAACGT
1338653 AAAA
1 AAAA
1338657 GTTGATATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 4 0.16
24 8 0.32
25 10 0.40
26 3 0.12
ACGTcount: A:0.67, C:0.12, G:0.12, T:0.10
Consensus pattern (23 bp):
AAAATAAGAAAAGACAAAAACGT
Found at i:1341006 original size:40 final size:40
Alignment explanation
Indices: 1340951--1341112 Score: 324
Period size: 40 Copynumber: 4.0 Consensus size: 40
1340941 TGCAGGTTTA
1340951 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1340991 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1341031 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1341071 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1341111 TA
1 TA
1341113 GCACTACGGT
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 122 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1341264 original size:44 final size:47
Alignment explanation
Indices: 1341216--1341325 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
1341206 GTAACCATGC
* *
1341216 AAATAAGCTTATGAGCTTACG-GA-TT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTACGTAATTTAAATGGCAAGTATATTGGAA
* * * *
1341260 AAATAAGCTTACGAGCTTATGTAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTACGTAATTTAAATGGCAAGTATATTGGAA
1341307 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
1341326 TGGGATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 19 0.33
45 1 0.02
46 2 0.04
47 35 0.61
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTACGTAATTTAAATGGCAAGTATATTGGAA
Found at i:1343066 original size:6 final size:6
Alignment explanation
Indices: 1343055--1343085 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1343045 AAGACCCATA
1343055 GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT G
1 GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT G
1343086 ATACAAGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.35, T:0.32
Consensus pattern (6 bp):
GGTCAT
Found at i:1344176 original size:18 final size:18
Alignment explanation
Indices: 1344149--1344224 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
1344139 AATATATTAT
*
1344149 AAGAAGAAAAAAACAGAAG
1 AAGAA-AAAAAAACAGAAA
*
1344168 AAGAAAAAAAAATAGAAA
1 AAGAAAAAAAAACAGAAA
* *
1344186 AAGAAAATGAAAAC-GAGA
1 AAGAAAA-AAAAACAGAAA
*
1344204 AAGAAAAGAAAAAGAGAAA
1 AAGAAAA-AAAAACAGAAA
1344223 AA
1 AA
1344225 ATGAGAGATG
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 32 0.70
19 14 0.30
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (18 bp):
AAGAAAAAAAAACAGAAA
Found at i:1344190 original size:6 final size:6
Alignment explanation
Indices: 1344149--1344223 Score: 57
Period size: 6 Copynumber: 12.3 Consensus size: 6
1344139 AATATATTAT
* *
1344149 AAGAAGA AA-AAA ACAGAAG AAGAAA AA-AAA ATAGAAA AAGAAA ATGAAA
1 AAGAA-A AAGAAA A-AGAAA AAGAAA AAGAAA A-AGAAA AAGAAA AAGAAA
* *
1344198 ACGAGA AAG-AA AAGAAA AAGAGAA AA
1 AAGAAA AAGAAA AAGAAA AAGA-AA AA
1344224 AATGAGAGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
5 10 0.18
6 32 0.58
7 13 0.24
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:1348241 original size:40 final size:40
Alignment explanation
Indices: 1348186--1348307 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
1348176 TGCAGGTTTA
1348186 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1348226 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1348266 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1348306 TA
1 TA
1348308 GCACTACGGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1348459 original size:44 final size:47
Alignment explanation
Indices: 1348411--1348520 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
1348401 GTAACCATGC
* *
1348411 AAATAAGCTTATGAGCTTACG-GA-TT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTACGTAATTTAAATGGCAAGTATATTGGAA
* * * *
1348455 AAATAAGCTTACGAGCTTATGTAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTACGTAATTTAAATGGCAAGTATATTGGAA
1348502 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
1348521 TGGGATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 19 0.33
45 1 0.02
46 2 0.04
47 35 0.61
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTACGTAATTTAAATGGCAAGTATATTGGAA
Found at i:1355254 original size:102 final size:105
Alignment explanation
Indices: 1355135--1355465 Score: 398
Period size: 112 Copynumber: 3.0 Consensus size: 105
1355125 CGAAGTTTCA
* * *
1355135 AAATGGTAATTCACCTCATTATGAATACCATGGGTGGCGCCTTTTATGCC-AAA-A-ATGTATTA
1 AAATGGTAATTTACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAACATATGCATTA
* *
1355197 AGTAAAATTGATCGATAACTTTCATACACGAAGTATGTCG
66 AGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCG
** *
1355237 AAATGGTAATTTACCTCATTACAAATACCATGGGTGGAACCTTTTATGCCAAAAAGGCACCGTTA
1 AAATGGTAATTTACCTCATTATGAATACCATGGGTGGCACCTTTTATGCC-AAAA--CA----TA
** *
1355302 TGCATTAAGCAAAATCGATCGATAACTTTCATACATAAAGTATGTTG
59 TGCATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCG
* *
1355349 AAATGGTATTTTACCTCATTATGAATACCATGGGTGACACCTTTTATGCCGAAAATACACCTTTA
1 AAATGGTAATTTACCTCATTATGAATACCATGGGTGGCACCTTTTATGCC--AAA-ACA----TA
1355414 TGCATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCG
59 TGCATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCG
1355461 AAATG
1 AAATG
1355466 CACATATAAC
Statistics
Matches: 197, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
102 45 0.23
104 3 0.02
107 1 0.01
112 143 0.73
113 4 0.02
114 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (105 bp):
AAATGGTAATTTACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAACATATGCATTA
AGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCG
Found at i:1355391 original size:112 final size:112
Alignment explanation
Indices: 1355193--1355465 Score: 422
Period size: 112 Copynumber: 2.4 Consensus size: 112
1355183 CCAAAAATGT
* *
1355193 ATTAAGTAAAATTGATCGATAACTTTCATACACGAAGTATGTCGAAATGGTAATTTACCTCATTA
1 ATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCGAAATGGTAATTTACCTCATTA
*
1355258 CAAATACCATGGGTGGAACCTTTTATGCCAAAAAGGCACCGTTATGC
66 CAAATACCATGGGTGGAACCTTTTATGCCAAAAAGACACCGTTATGC
** * *
1355305 ATTAAGCAAAATCGATCGATAACTTTCATACATAAAGTATGTTGAAATGGTATTTTACCTCATTA
1 ATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCGAAATGGTAATTTACCTCATTA
** * * *
1355370 TGAATACCATGGGT-GACACCTTTTATGCCGAAAATACACCTTTATGC
66 CAAATACCATGGGTGGA-ACCTTTTATGCCAAAAAGACACCGTTATGC
1355417 ATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCGAAATG
1 ATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCGAAATG
1355466 CACATATAAC
Statistics
Matches: 145, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
111 2 0.01
112 143 0.99
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (112 bp):
ATTAAGCAAAATCGATCGATAACTTTCATACACGAAGTATGTCGAAATGGTAATTTACCTCATTA
CAAATACCATGGGTGGAACCTTTTATGCCAAAAAGACACCGTTATGC
Found at i:1361842 original size:41 final size:41
Alignment explanation
Indices: 1361777--1361868 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
1361767 TGCCAAATTG
* * * * *
1361777 GTATCGATACTGAAAACGATTATTGATACCATAGTGTAGTA
1 GTATCGATACTGAAAAAGAGTATTGATACCATAATATAGAA
*
1361818 GTATCGATACTGAGAAAAG-GTATTGGTACCATAATATAGAA
1 GTATCGATACTGA-AAAAGAGTATTGATACCATAATATAGAA
*
1361859 GTATTGATAC
1 GTATCGATAC
1361869 CATTGTAGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 39 0.91
42 4 0.09
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (41 bp):
GTATCGATACTGAAAAAGAGTATTGATACCATAATATAGAA
Found at i:1362357 original size:44 final size:44
Alignment explanation
Indices: 1362294--1362611 Score: 469
Period size: 44 Copynumber: 7.2 Consensus size: 44
1362284 AAACTGAATT
*
1362294 CATAACTGAAATGCATAATGGTGCATTAAGACATGAAAGGATGC
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
*
1362338 CATAACTGAAATGCATAATGGTGCATTAATGCATGAAAGGATGC
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
* * *
1362382 AATAATTGAAATGCATAATGCTGCATTAAGGCATGAAAGGATGC
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
** * *
1362426 CATAACTGAAATGCATAATGGAACATTAAGTCATGAAAGGATGT
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
* *
1362470 CATAACTGAAATGCATAATGGTTCATTAAGGCATGAAAGGATGT
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
*
1362514 CATAACTGAAATGCGTAATGGTGCATTAAGGCATGAATA--ATGC
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAA-AGGATGC
* * *
1362557 CATAACTGAAATGCATAACGGTGCAGTAAGGCATGAAAGGATGT
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
*
1362601 CATAAATGAAA
1 CATAACTGAAA
1362612 ATAATAGATA
Statistics
Matches: 247, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
42 1 0.00
43 37 0.15
44 208 0.84
45 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.24
Consensus pattern (44 bp):
CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
Found at i:1375734 original size:23 final size:23
Alignment explanation
Indices: 1375688--1375735 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1375678 GAGAAGTTTG
**
1375688 TAAAGAAAATGAAAGATTTAATT
1 TAAAGAAAATGAAAGAAATAATT
1375711 TAAAGAAAAT-AAAGAAATAGATT
1 TAAAGAAAATGAAAGAAATA-ATT
1375734 TA
1 TA
1375736 CATAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.27
Consensus pattern (23 bp):
TAAAGAAAATGAAAGAAATAATT
Found at i:1376516 original size:20 final size:20
Alignment explanation
Indices: 1376491--1376531 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1376481 TCAAATTTAA
*
1376491 TCCTAAAAATAAAAGATAAT
1 TCCTAAAAACAAAAGATAAT
1376511 TCCTAAAAACAAAAGATAAT
1 TCCTAAAAACAAAAGATAAT
1376531 T
1 T
1376532 TTAATTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.12, G:0.05, T:0.24
Consensus pattern (20 bp):
TCCTAAAAACAAAAGATAAT
Found at i:1377165 original size:19 final size:20
Alignment explanation
Indices: 1377141--1377178 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1377131 AAAGATATAT
1377141 TTATT-AAAATAATATTTAG
1 TTATTAAAAATAATATTTAG
*
1377160 TTATTAAAAATAATTTTTA
1 TTATTAAAAATAATATTTA
1377179 AATGGTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTATTAAAAATAATATTTAG
Found at i:1377310 original size:18 final size:18
Alignment explanation
Indices: 1377287--1377329 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1377277 GGTAATTTTA
1377287 AAATGGTTCTAGAAGCTT
1 AAATGGTTCTAGAAGCTT
1377305 AAATGGTTCTAGAAGCTT
1 AAATGGTTCTAGAAGCTT
1377323 AAATGGT
1 AAATGGT
1377330 GTGATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (18 bp):
AAATGGTTCTAGAAGCTT
Found at i:1388478 original size:22 final size:22
Alignment explanation
Indices: 1388417--1388467 Score: 84
Period size: 23 Copynumber: 2.3 Consensus size: 22
1388407 CGATTCCCCT
*
1388417 AGGGGGAATCAGTTTCCCTTCAA
1 AGGGGGAATCAGTTCCCCTTC-A
1388440 AGGGGGAATCAGTTCCCCTTCA
1 AGGGGGAATCAGTTCCCCTTCA
1388462 AGGGGG
1 AGGGGG
1388468 TATCGATTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.22
Consensus pattern (22 bp):
AGGGGGAATCAGTTCCCCTTCA
Found at i:1407350 original size:12 final size:12
Alignment explanation
Indices: 1407317--1407350 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1407307 TCCTCATCAC
*
1407317 ATCATTATCATT
1 ATCATTATCCTT
1407329 ATCATTATCCTT
1 ATCATTATCCTT
*
1407341 ATTATTATCC
1 ATCATTATCC
1407351 ATTCAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (12 bp):
ATCATTATCCTT
Found at i:1412924 original size:18 final size:19
Alignment explanation
Indices: 1412897--1412932 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1412887 TATTGAAAAC
1412897 TTATAAAAAAAT-TAAATT
1 TTATAAAAAAATATAAATT
*
1412915 TTATACAAAAATATAAAT
1 TTATAAAAAAATATAAAT
1412933 AAAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TTATAAAAAAATATAAATT
Found at i:1413223 original size:90 final size:90
Alignment explanation
Indices: 1413124--1413304 Score: 344
Period size: 90 Copynumber: 2.0 Consensus size: 90
1413114 TTTGTATTTA
1413124 AATATAATTAGGAAACATAAATTTTTTTGTATCAATACACACATCTAATCATACTTCGAACAATT
1 AATATAATTAGGAAACATAAATTTTTTTGTATCAATACACACATCTAATCATACTTCGAACAATT
1413189 TTAAGGATTATTTGTAAACCCTTGC
66 TTAAGGATTATTTGTAAACCCTTGC
*
1413214 AATATAATTAGGAAACATAATTTTTTTTGTATCAATACACACATCTAATCATACTTCGAACAATT
1 AATATAATTAGGAAACATAAATTTTTTTGTATCAATACACACATCTAATCATACTTCGAACAATT
*
1413279 TTAAGGATTATTTGTAAACCTTTGC
66 TTAAGGATTATTTGTAAACCCTTGC
1413304 A
1 A
1413305 CATCTATAAA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (90 bp):
AATATAATTAGGAAACATAAATTTTTTTGTATCAATACACACATCTAATCATACTTCGAACAATT
TTAAGGATTATTTGTAAACCCTTGC
Found at i:1414393 original size:34 final size:32
Alignment explanation
Indices: 1414316--1414581 Score: 127
Period size: 34 Copynumber: 8.0 Consensus size: 32
1414306 ATCAAAATAG
* **
1414316 ATATTTTTAATATTCAAATA-TAAATGGATAATAA
1 ATATTTTTAAT-TTGAAATATTAAAAAGAT-AT-A
1414350 ATATCTTTTAATTTGAAATATTAAAAAGATATA
1 ATAT-TTTTAATTTGAAATATTAAAAAGATATA
* * * *
1414383 GATATGTTTTAATATTCAAA-CTTAAAGAGATAACA
1 -ATAT-TTTTAAT-TTGAAATATTAAAAAGAT-ATA
* *
1414418 TATATATTTTAATTTGAAATACTCAAAATGATATA
1 -ATAT-TTTTAATTTGAAATA-TTAAAAAGATATA
* * * * *
1414453 ATTTTTTTTA-TTCAAAT-TTAAATAGATAAAA
1 ATATTTTTAATTTGAAATATTAAAAAGAT-ATA
* *
1414484 ATACATTTTAATTTGAAATATTCAAAAGA-ATA
1 ATA-TTTTTAATTTGAAATATTAAAAAGATATA
*
1414516 AT-TTTCCTACTAATATT-AAA-ATTAAAGAGATA-A
1 ATATTT--T--TAAT-TTGAAATATTAAAAAGATATA
*
1414549 ATATCTTTTAATTTGGAATATTAAAAAGGATAT
1 ATAT-TTTTAATTTGAAATATTAAAAA-GATAT
1414582 GGATTTAATT
Statistics
Matches: 174, Mismatches: 35, Indels: 46
0.68 0.14 0.18
Matches are distributed among these distances:
30 11 0.06
31 10 0.06
32 23 0.13
33 28 0.16
34 57 0.33
35 38 0.22
36 7 0.04
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (32 bp):
ATATTTTTAATTTGAAATATTAAAAAGATATA
Found at i:1414551 original size:65 final size:64
Alignment explanation
Indices: 1414319--1414581 Score: 243
Period size: 69 Copynumber: 4.0 Consensus size: 64
1414309 AAAATAGATA
1414319 TTTTTAATATTC-AAATATAAATG-GATAATAAATATCTTTTAATTTGAAATATTAAAAAGATAT
1 TTTTTAATATTCAAAAT-TAAA-GAGAT-A-AAATATCTTTTAATTTGAAATATTAAAAAGATAT
1414382 AGAT
62 A-AT
* * * *
1414386 ATGTTTTAATATTCAAACTTAAAGAGATAACATATATATTTTAATTTGAAATACTCAAAATGATA
1 -T-TTTTAATATTCAAAATTAAAGAGATAA-A-ATATCTTTTAATTTGAAATA-TTAAAAAGATA
1414451 TAAT
61 TAAT
* * * *
1414455 TTTTT-TTATTCAAATTTAAATAGATAAAA-ATACATTTTAATTTGAAATATTCAAAAGA-ATAA
1 TTTTTAATATTCAAAATTAAAGAGATAAAATAT-C-TTTTAATTTGAAATATTAAAAAGATATAA
1414517 T
64 T
*
1414518 TTTCCTACTAATATT-AAAATTAAAGAGAT-AAATATCTTTTAATTTGGAATATTAAAAAGGATA
1 TTT--T--TAATATTCAAAATTAAAGAGATAAAATATCTTTTAATTTGAAATATTAAAAA-GATA
1414581 T
61 T
1414582 GGATTTAATT
Statistics
Matches: 163, Mismatches: 16, Indels: 33
0.77 0.08 0.16
Matches are distributed among these distances:
63 10 0.06
64 7 0.04
65 37 0.23
66 25 0.15
67 22 0.13
68 9 0.06
69 39 0.24
70 14 0.09
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (64 bp):
TTTTTAATATTCAAAATTAAAGAGATAAAATATCTTTTAATTTGAAATATTAAAAAGATATAAT
Found at i:1427365 original size:29 final size:28
Alignment explanation
Indices: 1427299--1427366 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
1427289 GAGGTTTTAT
*
1427299 TTGAGTTACTTTTAATGTTTTATCATAAT
1 TTGAGTTA-TTTTAATGTTTTATCATAAC
*
1427328 TATGA-TTATTTTAATTGTTTTAT-ATCACC
1 T-TGAGTTATTTTAA-TGTTTTATCAT-AAC
1427357 TTGAGTTATT
1 TTGAGTTATT
1427367 ACTGCCTCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
28 11 0.33
29 19 0.58
30 3 0.09
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.56
Consensus pattern (28 bp):
TTGAGTTATTTTAATGTTTTATCATAAC
Found at i:1431921 original size:8 final size:8
Alignment explanation
Indices: 1431908--1431950 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
1431898 GAAAATTTTG
1431908 ATTTTATT
1 ATTTTATT
1431916 ATTTTATT
1 ATTTTATT
*
1431924 ATTTGATT
1 ATTTTATT
1431932 A-TTTATT
1 ATTTTATT
1431939 ATATTTATT
1 AT-TTTATT
1431948 ATT
1 ATT
1431951 ATTTCTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 6 0.19
8 17 0.55
9 8 0.26
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (8 bp):
ATTTTATT
Done.