Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009591.1 Hibiscus syriacus cultivar Beakdansim tig00116970_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: 2451160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1449197 original size:59 final size:59
Alignment explanation
Indices: 1449123--1449531 Score: 518
Period size: 59 Copynumber: 6.9 Consensus size: 59
1449113 TTTCCCATAT
* * * * *
1449123 GGAAATTCATACACTTAGTATGAATTTCTTATCCTTTTGGCACAC-AAGGTGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAA-GTGCCCTATAC
** * * *
1449182 GGAAATTCATACACTTAAAATGAATTTCTTATCATTTTAGCACACGAAGTGACCTATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGCCCTATAC
* * *
1449241 GGAAATCCATACACTTAGTATGAATTCCTTCTTATGTTAGCACACGAAGTGCCCTATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGCCCTATAC
* * *
1449300 AGAAATTCATACACTTTGTATGAA-TTCATTCTCATGTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTTC-TTCTCATGTTAGCACACGAAGTGCCCTATAC
* * * *
1449359 GGAAATTCATACACTTGGCATGAATTCCTTCTCATGTTTA-CACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTCTCATG-TTAGCACACGAAGTGCCCTATAC
* * * * *
1449418 GGAAATTCATACACTTGGCATGAATTACTTCTCATGTTAGTACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGCCCTATAC
* * *
1449477 GGAAATTCATACACTTATTATGAATTCCTTCTCATGTTAGCACACTAAGTGCCCT
1 GGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGCCCT
1449532 TTTCGTAATC
Statistics
Matches: 313, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
58 5 0.02
59 301 0.96
60 7 0.02
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGCCCTATAC
Found at i:1449877 original size:17 final size:19
Alignment explanation
Indices: 1449855--1449891 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
1449845 GGTTCCTCAG
1449855 TATCGATACT-CCC-ACAA
1 TATCGATACTACCCTACAA
1449872 TATCGATACTACCCTACAA
1 TATCGATACTACCCTACAA
1449891 T
1 T
1449892 GGTATCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 3 0.17
19 5 0.28
ACGTcount: A:0.35, C:0.32, G:0.05, T:0.27
Consensus pattern (19 bp):
TATCGATACTACCCTACAA
Found at i:1449898 original size:22 final size:18
Alignment explanation
Indices: 1449853--1449902 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 18
1449843 TTGGTTCCTC
1449853 AGTATCGATACTCCCACA
1 AGTATCGATACTCCCACA
1449871 A-TATCGATACTACCCTACA
1 AGTATCGATACT-CCC-ACA
1449890 ATGGTATCGATAC
1 A--GTATCGATAC
1449903 CCTCTTCCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 10 0.37
18 4 0.15
19 4 0.15
22 9 0.33
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (18 bp):
AGTATCGATACTCCCACA
Found at i:1452147 original size:34 final size:35
Alignment explanation
Indices: 1452090--1452181 Score: 105
Period size: 34 Copynumber: 2.7 Consensus size: 35
1452080 AATATGTATA
1452090 TGATAACTGTAAAACATCTGATATCTATAAATATC
1 TGATAACTGTAAAACATCTGATATCTATAAATATC
* * * * *
1452125 TGATAATTGT-AATCATCTGATATCTGTATATATT
1 TGATAACTGTAAAACATCTGATATCTATAAATATC
* * *
1452159 TGATAACGGTGAAATATCTGATA
1 TGATAACTGTAAAACATCTGATA
1452182 ACTGTAAACA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 28 0.60
35 19 0.40
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (35 bp):
TGATAACTGTAAAACATCTGATATCTATAAATATC
Found at i:1452152 original size:17 final size:18
Alignment explanation
Indices: 1452090--1452189 Score: 75
Period size: 17 Copynumber: 5.7 Consensus size: 18
1452080 AATATGTATA
* *
1452090 TGATAACTGTAAAACATC
1 TGATATCTGTAAATCATC
*
1452108 TGATATCTATAAAT-ATC
1 TGATATCTGTAAATCATC
1452125 TGATAAT-TGT-AATCATC
1 TGAT-ATCTGTAAATCATC
* *
1452142 TGATATCTGTATAT-ATT
1 TGATATCTGTAAATCATC
* *
1452159 TGATAACGGTGAAAT-ATC
1 TGATATCTGT-AAATCATC
*
1452177 TGATAACTGTAAA
1 TGATATCTGTAAA
1452190 CATTTAGAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
16 5 0.08
17 32 0.48
18 29 0.44
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (18 bp):
TGATATCTGTAAATCATC
Found at i:1456952 original size:32 final size:32
Alignment explanation
Indices: 1456914--1456977 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1456904 AATCAACTTC
*
1456914 CTCTCCTTATATATAGATTAGTTGAGGGGCAA
1 CTCTCCTTATATATAGACTAGTTGAGGGGCAA
1456946 CTCTCCTTATATATAGACTAGTTGAGGGGCAA
1 CTCTCCTTATATATAGACTAGTTGAGGGGCAA
1456978 ATCTTAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (32 bp):
CTCTCCTTATATATAGACTAGTTGAGGGGCAA
Found at i:1459941 original size:55 final size:56
Alignment explanation
Indices: 1459875--1459988 Score: 194
Period size: 55 Copynumber: 2.1 Consensus size: 56
1459865 ATGTTCCCAT
1459875 TGTTTTTCTATTTAGTATGCCTGAGCTGCAAATGTCAC-TGCACTTTCACTTGATA
1 TGTTTTTCTATTTAGTATGCCTGAGCTGCAAATGTCACTTGCACTTTCACTTGATA
* * *
1459930 TGTTTTTCTATTTATTATGCCTGAGCTTCAAATGTCACTTTCACTTTCACTTGATA
1 TGTTTTTCTATTTAGTATGCCTGAGCTGCAAATGTCACTTGCACTTTCACTTGATA
1459986 TGT
1 TGT
1459989 CACAATAAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 36 0.65
56 19 0.35
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (56 bp):
TGTTTTTCTATTTAGTATGCCTGAGCTGCAAATGTCACTTGCACTTTCACTTGATA
Found at i:1464276 original size:2 final size:2
Alignment explanation
Indices: 1464269--1464296 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1464259 TGAGCATGAC
1464269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1464297 GGTTCAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1464637 original size:10 final size:10
Alignment explanation
Indices: 1464592--1464665 Score: 58
Period size: 10 Copynumber: 7.0 Consensus size: 10
1464582 GGTCTCGTTC
*
1464592 GTTCATTTAT
1 GTTCGTTTAT
** *
1464602 GTTCGTGAAC
1 GTTCGTTTAT
*
1464612 GTTCGGTTAT
1 GTTCGTTTAT
1464622 GTTCGTTTAT
1 GTTCGTTTAT
1464632 GTTCGTTCGATTAT
1 GTTCG-T---TTAT
*
1464646 GTTAGTTTAT
1 GTTCGTTTAT
1464656 GTTCGTTTAT
1 GTTCGTTTAT
1464666 TTTCATTCAT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
10 39 0.80
11 1 0.02
13 1 0.02
14 8 0.16
ACGTcount: A:0.15, C:0.11, G:0.22, T:0.53
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:1464638 original size:24 final size:24
Alignment explanation
Indices: 1464611--1464662 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1464601 TGTTCGTGAA
* *
1464611 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTAGTTTATGTT
1464635 CGTTCGATTATGTTAGTTTATGTT
1 CGTTCGATTATGTTAGTTTATGTT
1464659 CGTT
1 CGTT
1464663 TATTTTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.54
Consensus pattern (24 bp):
CGTTCGATTATGTTAGTTTATGTT
Found at i:1464656 original size:34 final size:34
Alignment explanation
Indices: 1464618--1464682 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
1464608 GAACGTTCGG
*
1464618 TTATGTTCGTTTATGTTCGTTCGA-TTATGTTAGT
1 TTATGTTCGTTTATGTTCATTC-ATTTATGTTAGT
*
1464652 TTATGTTCGTTTATTTTCATTCATTTATGTT
1 TTATGTTCGTTTATGTTCATTCATTTATGTT
1464683 TAACCCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 1 0.04
34 27 0.96
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.60
Consensus pattern (34 bp):
TTATGTTCGTTTATGTTCATTCATTTATGTTAGT
Found at i:1465700 original size:45 final size:46
Alignment explanation
Indices: 1465615--1465704 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 46
1465605 AAAAAGCCTG
* * *
1465615 AGTGCAACGATGCATGGTCTTGTGCATCGATGCATCAAATGCATTA
1 AGTGCAACGATGAATGGTCATGTGCATCGATGCATAAAATGCATTA
*
1465661 AGTGCATCGATGAATGGT-ATGTGCATCGATGCATAAAATGCATT
1 AGTGCAACGATGAATGGTCATGTGCATCGATGCATAAAATGCATT
1465705 CGATGTTTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 24 0.60
46 16 0.40
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (46 bp):
AGTGCAACGATGAATGGTCATGTGCATCGATGCATAAAATGCATTA
Found at i:1472354 original size:22 final size:21
Alignment explanation
Indices: 1472312--1472351 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1472302 GAGTTTATTT
*
1472312 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1472333 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1472352 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1474381 original size:26 final size:26
Alignment explanation
Indices: 1474334--1474386 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1474324 TGAAAAAGCC
*
1474334 TGAGTGCATCGATGCATCAAATGCAT
1 TGAGTGCATCGATGCATAAAATGCAT
**
1474360 TGAGTGCATCGATGTGTAAAATGCAT
1 TGAGTGCATCGATGCATAAAATGCAT
1474386 T
1 T
1474387 CGATGTTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (26 bp):
TGAGTGCATCGATGCATAAAATGCAT
Found at i:1474692 original size:7 final size:7
Alignment explanation
Indices: 1474680--1474757 Score: 84
Period size: 7 Copynumber: 11.1 Consensus size: 7
1474670 TTGTTTTCAA
1474680 CCTAAAC
1 CCTAAAC
*
1474687 CCTAAAA
1 CCTAAAC
1474694 CCTAAAC
1 CCTAAAC
**
1474701 TTTAAAC
1 CCTAAAC
1474708 CCTAAAC
1 CCTAAAC
1474715 CCTAAAC
1 CCTAAAC
*
1474722 CCTAAAT
1 CCTAAAC
** *
1474729 TATAAAT
1 CCTAAAC
*
1474736 CATAAAC
1 CCTAAAC
1474743 CCTAAAC
1 CCTAAAC
1474750 CCTAAAC
1 CCTAAAC
1474757 C
1 C
1474758 TTAATCTAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 59 1.00
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (7 bp):
CCTAAAC
Found at i:1474717 original size:28 final size:28
Alignment explanation
Indices: 1474680--1474761 Score: 112
Period size: 28 Copynumber: 2.9 Consensus size: 28
1474670 TTGTTTTCAA
*
1474680 CCTAAACCCTAAAACCTAAACTTTAAAC
1 CCTAAACCCTAAACCCTAAACTTTAAAC
*
1474708 CCTAAACCCTAAACCCTAAA-TTATAAAT
1 CCTAAACCCTAAACCCTAAACTT-TAAAC
* *
1474736 CATAAACCCTAAACCCTAAACCTTAA
1 CCTAAACCCTAAACCCTAAACTTTAA
1474762 TCTAATTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.04
28 45 0.94
29 1 0.02
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (28 bp):
CCTAAACCCTAAACCCTAAACTTTAAAC
Found at i:1476060 original size:22 final size:23
Alignment explanation
Indices: 1476006--1476063 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
1475996 TGAATAGAGT
1476006 TTGAATCGAGCTCAAAATTGAGC
1 TTGAATCGAGCTCAAAATTGAGC
1476029 TTGAATCGAGCTCAAAATTGAGC
1 TTGAATCGAGCTCAAAATTGAGC
1476052 TT-AATCGAGCTC
1 TTGAATCGAGCTC
1476064 GAGTCGAGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 10 0.29
23 25 0.71
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (23 bp):
TTGAATCGAGCTCAAAATTGAGC
Found at i:1476326 original size:16 final size:16
Alignment explanation
Indices: 1476305--1476371 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
1476295 GTCTCCAACG
1476305 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
1476321 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
1476337 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
1476353 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
1476367 TTTAT
1 TTTAT
1476372 TAAATGAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1476344 original size:32 final size:32
Alignment explanation
Indices: 1476303--1476363 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1476293 GGGTCTCCAA
1476303 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
*
1476335 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
1476364 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:1476627 original size:21 final size:21
Alignment explanation
Indices: 1476602--1476646 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1476592 AATTGGGACG
1476602 AATTGAAAAATCTAGGGACTA
1 AATTGAAAAATCTAGGGACTA
* *
1476623 AATTGAAAATTTTAGGGACTA
1 AATTGAAAAATCTAGGGACTA
1476644 AAT
1 AAT
1476647 GTTATATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.29
Consensus pattern (21 bp):
AATTGAAAAATCTAGGGACTA
Found at i:1476947 original size:31 final size:31
Alignment explanation
Indices: 1476877--1476966 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
1476867 CCCAAAAGGT
* *
1476877 TACAAAATGATCATTAAAATATATCGAACTAT
1 TACAAAATGATCATTAAAAT-TATCAAACTAA
* *
1476909 TATAAAATGATCATTAAACTTATCAAACTAA
1 TACAAAATGATCATTAAAATTATCAAACTAA
*
1476940 TACAAAATGAT-ACTTAAATTTATCAAA
1 TACAAAATGATCA-TTAAAATTATCAAA
1476967 ATTTATCACT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.02
31 32 0.63
32 18 0.35
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.32
Consensus pattern (31 bp):
TACAAAATGATCATTAAAATTATCAAACTAA
Found at i:1478220 original size:20 final size:19
Alignment explanation
Indices: 1478183--1478226 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1478173 TTAAACTTTC
* *
1478183 AAAAATTATAAATTATTAT
1 AAAATTTATAAATGATTAT
*
1478202 TAAATTTATCAAATGATTAT
1 AAAATTTAT-AAATGATTAT
1478222 AAAAT
1 AAAAT
1478227 ATTCATTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATTTATAAATGATTAT
Found at i:1478223 original size:30 final size:28
Alignment explanation
Indices: 1478169--1478240 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 28
1478159 GATCGTTTCA
* *
1478169 ATTATTAAACTTTCAAAAATTATAAATT
1 ATTATTAAATTTTCAAAAATTATAAAAT
*
1478197 ATTATTAAATTTATCAAATGATTATAAAAT
1 ATTATTAAATTT-TCAAA-AATTATAAAAT
1478227 ATTCATTAAATTTT
1 ATT-ATTAAATTTT
1478241 ATTGAACTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 11 0.29
29 5 0.13
30 13 0.34
31 9 0.24
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (28 bp):
ATTATTAAATTTTCAAAAATTATAAAAT
Found at i:1478253 original size:32 final size:31
Alignment explanation
Indices: 1478183--1478303 Score: 113
Period size: 32 Copynumber: 3.9 Consensus size: 31
1478173 TTAAACTTTC
* *
1478183 AAAA-ATTATAAATTATTATTAAA-TTTA-T
1 AAAATATTATAAAATATCATTAAATTTTATT
*
1478211 CAAATGATTATAAAATATTCATTAAATTTTATT
1 AAAAT-ATTATAAAATA-TCATTAAATTTTATT
* * * *
1478244 GAACTATTATAAAACTATCATTAATTTTTATC
1 AAAATATTATAAAA-TATCATTAAATTTTATT
*
1478276 AAAATATTATAAAATGATCATTTAATTT
1 AAAATATTATAAAAT-ATCATTAAATTT
1478304 AGGCTTGATA
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
28 3 0.04
30 10 0.13
31 8 0.11
32 48 0.64
33 6 0.08
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (31 bp):
AAAATATTATAAAATATCATTAAATTTTATT
Found at i:1480827 original size:19 final size:18
Alignment explanation
Indices: 1480786--1480832 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1480776 CTCAATTAAA
*
1480786 AAAAATAAAATTTTAACT
1 AAAAATAAAATTTGAACT
*
1480804 AAAAATAAAATTTGAGCT
1 AAAAATAAAATTTGAACT
1480822 ATAAAATAAAA
1 A-AAAATAAAA
1480833 CTTGTCACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (18 bp):
AAAAATAAAATTTGAACT
Found at i:1481255 original size:27 final size:28
Alignment explanation
Indices: 1481219--1481274 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
1481209 AAATATGTTC
* *
1481219 TTTAATTATTAAAAATAT-ATCAATTAT
1 TTTAACTATTAAAAATATAATAAATTAT
*
1481246 TTTAACTATTTAAAATATAATAAATTAT
1 TTTAACTATTAAAAATATAATAAATTAT
1481274 T
1 T
1481275 ATAATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTAACTATTAAAAATATAATAAATTAT
Found at i:1481285 original size:18 final size:18
Alignment explanation
Indices: 1481259--1481297 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1481249 AACTATTTAA
*
1481259 AATATAATAAATTATTAT
1 AATAAAATAAATTATTAT
*
1481277 AATAAAATAAATTATTTT
1 AATAAAATAAATTATTAT
1481295 AAT
1 AAT
1481298 TATTGTAAAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAAAATAAATTATTAT
Found at i:1482524 original size:3 final size:3
Alignment explanation
Indices: 1482509--1482551 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1482499 TAACATTGTT
* *
1482509 TTA TTA TTT TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1482552 AGGGTTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1482787 original size:21 final size:21
Alignment explanation
Indices: 1482748--1482788 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1482738 TTTTTACTAC
*
1482748 ATTAAAATTTCAAATAAAATA
1 ATTAAAATTTCAAAAAAAATA
*
1482769 ATTAAAATTTATAAAAAAAA
1 ATTAAAATTT-CAAAAAAAA
1482789 GCACAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTAAAATTTCAAAAAAAATA
Found at i:1487001 original size:102 final size:102
Alignment explanation
Indices: 1486781--1487010 Score: 379
Period size: 102 Copynumber: 2.3 Consensus size: 102
1486771 CTTCAGCATC
*
1486781 ATCTTCCGGTTGGGGTGAATGAACTTCGGTTTTAGTGGGGTCTATTTCCATATTGGAGAGGTCAG
1 ATCTTCCGGTTGGGGTGAATGAACTTCGGTTTTAGTGGCGTCTATTTCCATATTGGAGAGGTCAG
*
1486846 CACTTCCAATCTTATTCTGCTGAGAAGCTTTGTCATG
66 CACTTCCAATCTTATGCTGCTGAGAAGCTTTGTCATG
* ** * *
1486883 ATCCTCCGGTCCGGGTGAATGAAGTTCGGTTTTAGTGGCGTCTATTTCCATATTGGAGGGGTCAG
1 ATCTTCCGGTTGGGGTGAATGAACTTCGGTTTTAGTGGCGTCTATTTCCATATTGGAGAGGTCAG
1486948 CACTTCCAATCTTATGCTGCTGAGAAGCTTTGTCATG
66 CACTTCCAATCTTATGCTGCTGAGAAGCTTTGTCATG
* *
1486985 ATCTTCCGGTTGGGGTGGAGGAACTT
1 ATCTTCCGGTTGGGGTGAATGAACTT
1487011 TTATTTCTGT
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 115 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (102 bp):
ATCTTCCGGTTGGGGTGAATGAACTTCGGTTTTAGTGGCGTCTATTTCCATATTGGAGAGGTCAG
CACTTCCAATCTTATGCTGCTGAGAAGCTTTGTCATG
Found at i:1487050 original size:102 final size:102
Alignment explanation
Indices: 1486793--1487076 Score: 259
Period size: 102 Copynumber: 2.8 Consensus size: 102
1486783 CTTCCGGTTG
* * * * * * * **
1486793 GGGTGAATGAACTTCGGTTTTAGTGGGGTCTATTTCCATATTGGAGAGGTCAGCACTTCCAATCT
1 GGGTGAAGGAACTTCGATTTTAGTGGAGTCGACTTCCATATTGAAAACATCAGCACTTCCAATCT
*
1486858 TATTCTGCTGAGAAGCTTTGTCATGATCCTCCGGTCC
66 TATGCTGCTGAGAAGCTTTGTCATGATCCTCCGGTCC
* * * * * * * ****
1486895 GGGTGAATGAAGTTCGGTTTTAGTGGCGTCTATTTCCATATTGGAGGGGTCAGCACTTCCAATCT
1 GGGTGAAGGAACTTCGATTTTAGTGGAGTCGACTTCCATATTGAAAACATCAGCACTTCCAATCT
* **
1486960 TATGCTGCTGAGAAGCTTTGTCATGATCTTCCGGTTG
66 TATGCTGCTGAGAAGCTTTGTCATGATCCTCCGGTCC
* ** * *
1486997 GGGTGGAGGAACTTTTATTTCT-GTGGAGTCGACTTCCATATTGAAAACATCAGCAGTTTCAGA-
1 GGGTGAAGGAACTTCGATTT-TAGTGGAGTCGACTTCCATATTGAAAACATCAGCACTTCCA-AT
1487060 CTTA-GTCTGCTGAGAAG
64 CTTATG-CTGCTGAGAAG
1487077 GCTCAGCATG
Statistics
Matches: 156, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
101 1 0.01
102 153 0.98
103 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (102 bp):
GGGTGAAGGAACTTCGATTTTAGTGGAGTCGACTTCCATATTGAAAACATCAGCACTTCCAATCT
TATGCTGCTGAGAAGCTTTGTCATGATCCTCCGGTCC
Found at i:1499935 original size:37 final size:36
Alignment explanation
Indices: 1499825--1499935 Score: 159
Period size: 37 Copynumber: 3.0 Consensus size: 36
1499815 TCATCCGAGC
* *
1499825 CATCTTAAGCCTTCACAAAATAGTAGTGAAACAAATT
1 CATCTTAAGCCTTCACAAAAGAGTAGTGAAGCAAA-T
* *
1499862 CATCTTAAGCATTCACTAAAGAGTAGTGAAGCAAAT
1 CATCTTAAGCCTTCACAAAAGAGTAGTGAAGCAAAT
*
1499898 CAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAAT
1 C-ATCTTAAGCCTTCACAAAAGAGTAGTGAAGCAAAT
1499935 C
1 C
1499936 CAAGATTTGA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 2 0.03
37 65 0.97
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.24
Consensus pattern (36 bp):
CATCTTAAGCCTTCACAAAAGAGTAGTGAAGCAAAT
Found at i:1500009 original size:48 final size:48
Alignment explanation
Indices: 1499934--1500069 Score: 200
Period size: 48 Copynumber: 2.8 Consensus size: 48
1499924 GTGAAGCAAA
* *
1499934 TCCAAGATTTGATATTCCTTTTAGAGTAAGCGGAACAAGTCTCTCTTC
1 TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTC
* * * *
1499982 TCCAAGATTTGATATTCCCTTCGGAGTAAGCAGAACAAATCTCTCTTT
1 TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTC
* *
1500030 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGAAACAAGT
1 TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGT
1500070 ATGCCCTAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 77 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (48 bp):
TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTCTTC
Found at i:1500172 original size:48 final size:48
Alignment explanation
Indices: 1500100--1500315 Score: 303
Period size: 48 Copynumber: 4.5 Consensus size: 48
1500090 AAATTCCTTC
*
1500100 AGATCTGATATTCCCTTCAGAGTAAGCAGAACATATCTCTCTTTTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGCAGAACAAATCTCTCTTTTCCA
* *
1500148 AGATATGATATTCCCTTCAGAGTAAGCGGAACAAATCTCTCTTTTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGCAGAACAAATCTCTCTTTTCCA
* *
1500196 AGATTTGATATTCCCTTCAGAGTAAGCAGAACAAATCTCT-TTTCCCCA
1 AGATCTGATATTCCCTTCAGAGTAAGCAGAACAAATCTCTCTTT-TCCA
*
1500244 AGATCTGATATTCCCTTCAGAGTAAGC-GAAACAGATCTC-CATATCTTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGCAG-AACAAATCTCTC-T-T-TTCCA
*
1500294 AGATTTGATATTCCCTTCAGAG
1 AGATCTGATATTCCCTTCAGAG
1500316 AAAGTGGAAC
Statistics
Matches: 152, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
47 4 0.03
48 121 0.80
49 1 0.01
50 25 0.16
51 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (48 bp):
AGATCTGATATTCCCTTCAGAGTAAGCAGAACAAATCTCTCTTTTCCA
Found at i:1500457 original size:115 final size:114
Alignment explanation
Indices: 1500244--1500653 Score: 551
Period size: 115 Copynumber: 3.6 Consensus size: 114
1500234 CTTTTCCCCA
* *
1500244 AGATCTGATATTCCCTTCAGAGTAAGCGAAACAGATCTCCATATCTTCCAAGATTTGATATTCCC
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGAT-TCCCTATCTTCCAAGATTTGATATTCCC
* *
1500309 TTCAGAGAAAGTGGAACAAGTTTGCCCCGATTCAATGGATCAAACTTTTC
65 TTCAGAGTAAGTGGAACAAGTTTGCCCCAATTCAATGGATCAAACTTTTC
*
1500359 AGATATGATATTCCCTTCAGAGTAAGCGGAACAGATCTCCCTATCTTCCAAGATTTGATATTCCC
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGAT-TCCCTATCTTCCAAGATTTGATATTCCC
* *
1500424 TTCAGAGTAAGTAGAACAAGTTTTCCCCAATTCAATGGATCAAA-TTCCTTC
65 TTCAGAGTAAGTGGAACAAGTTTGCCCCAATTCAATGGATCAAACTT--TTC
* * * * * *
1500475 AGATCTAATATTCCCTTCAGAGTAAGCAGAATAAATT-TCTATTTTCC-AGATTTGATATTCCCT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGATTCCCTATCTTCCAAGATTTGATATTCCCT
* *
1500538 TCAGAGTAAGTGGAACAAGTCTGCCCCAATTCAATGGATCAAACTCCTTC
66 TCAGAGTAAGTGGAACAAGTTTGCCCCAATTCAATGGATCAAACT-TTTC
** *
1500588 TAGATCTGATATTTGCTTCAAGAAG-AAGCGGAACAGA-TCCCTATCTTCCAATATTTGATATTC
1 -AGATCTGATATTCCCTTC-AG-AGTAAGCGGAACAGATTCCCTATCTTCCAAGATTTGATATTC
1500651 CCT
63 CCT
1500654 GAGTGCTAGT
Statistics
Matches: 259, Mismatches: 27, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
113 59 0.23
114 27 0.10
115 122 0.47
116 51 0.20
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (114 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGATTCCCTATCTTCCAAGATTTGATATTCCCT
TCAGAGTAAGTGGAACAAGTTTGCCCCAATTCAATGGATCAAACTTTTC
Found at i:1501774 original size:30 final size:28
Alignment explanation
Indices: 1501706--1501771 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
1501696 GGTGAGGGAG
1501706 TTTAGAGAGAACGGAGAGCTTCTCTCTC
1 TTTAGAGAGAACGGAGAGCTTCTCTCTC
*
1501734 TTTAGAGAGAACGGAGAGTTTCTCTCTC
1 TTTAGAGAGAACGGAGAGCTTCTCTCTC
1501762 TTTAGAGAGA
1 TTTAGAGAGA
1501772 GAAGGAATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (28 bp):
TTTAGAGAGAACGGAGAGCTTCTCTCTC
Found at i:1502188 original size:10 final size:10
Alignment explanation
Indices: 1502173--1502198 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1502163 ATTTTGGTTA
1502173 TTATTTAATT
1 TTATTTAATT
1502183 TTATTTAATT
1 TTATTTAATT
1502193 TTATTT
1 TTATTT
1502199 TTTTACCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTATTTAATT
Found at i:1507329 original size:19 final size:18
Alignment explanation
Indices: 1507307--1507361 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
1507297 GTCTGTTTCC
1507307 TACAGTATGTTTTCTACAA
1 TACAGTATGTTTTCTAC-A
*
1507326 TACAGTATGTTTTCTTTC-
1 TACAGTATGTTTTC-TACA
*
1507344 TACAGTCTGTTTTCTACA
1 TACAGTATGTTTTCTACA
1507362 GCGAATCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 2 0.06
18 13 0.42
19 14 0.45
20 2 0.06
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (18 bp):
TACAGTATGTTTTCTACA
Found at i:1507349 original size:18 final size:18
Alignment explanation
Indices: 1507306--1507358 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1507296 TGTCTGTTTC
1507306 CTACAGTATGTTTTC-TA
1 CTACAGTATGTTTTCTTA
*
1507323 CAATACAGTATGTTTTCTTT
1 C--TACAGTATGTTTTCTTA
*
1507343 CTACAGTCTGTTTTCT
1 CTACAGTATGTTTTCT
1507359 ACAGCGAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 1 0.03
18 14 0.45
19 14 0.45
20 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.11, T:0.49
Consensus pattern (18 bp):
CTACAGTATGTTTTCTTA
Found at i:1509873 original size:63 final size:63
Alignment explanation
Indices: 1509798--1509918 Score: 197
Period size: 63 Copynumber: 1.9 Consensus size: 63
1509788 ACTCTGATAA
* *
1509798 AATAAAAACATCGAATGCCATTAGTGCATCGATGCATAAGTAGTGCATCGATGCACCCCATTG
1 AATAAAAACATCGAATGCCATTAGTGCACCAATGCATAAGTAGTGCATCGATGCACCCCATTG
** *
1509861 AATAAAAACATCGAATGTGATTCGTGCACCAATGCATAAGTAGTGCATCGATGCACCC
1 AATAAAAACATCGAATGCCATTAGTGCACCAATGCATAAGTAGTGCATCGATGCACCC
1509919 GTTAAAGAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (63 bp):
AATAAAAACATCGAATGCCATTAGTGCACCAATGCATAAGTAGTGCATCGATGCACCCCATTG
Found at i:1510370 original size:20 final size:20
Alignment explanation
Indices: 1510325--1510379 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
1510315 ATGATACAGA
*
1510325 TATGTGAATATTGAAAAGAAT
1 TATGTGTATA-TGAAAAGAAT
*
1510346 CATGTGTATATGAAATA-AAT
1 TATGTGTATATGAAA-AGAAT
1510366 TATGTGCTATATGA
1 TATGTG-TATATGA
1510380 GAAGTGATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (20 bp):
TATGTGTATATGAAAAGAAT
Found at i:1510506 original size:18 final size:18
Alignment explanation
Indices: 1510483--1510555 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
1510473 AGGGATATAC
1510483 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* **
1510501 AGTGGTTCTTCGAAACAAT
1 AGTGGTCCTTCGGGAC-AT
1510520 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
1510539 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1510556 AATATTGAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 4 0.09
20 13 0.28
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1511887 original size:14 final size:14
Alignment explanation
Indices: 1511864--1511927 Score: 121
Period size: 14 Copynumber: 4.6 Consensus size: 14
1511854 CAATGGAGTC
1511864 GTAC-AGTGTATGA
1 GTACGAGTGTATGA
1511877 GTACGAGTGTATGA
1 GTACGAGTGTATGA
1511891 GTACGAGTGTATGA
1 GTACGAGTGTATGA
1511905 GTACGAGTGTATGA
1 GTACGAGTGTATGA
1511919 GTACGAGTG
1 GTACGAGTG
1511928 CGAATTCAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
13 4 0.08
14 46 0.92
ACGTcount: A:0.28, C:0.08, G:0.36, T:0.28
Consensus pattern (14 bp):
GTACGAGTGTATGA
Found at i:1516700 original size:21 final size:21
Alignment explanation
Indices: 1516676--1516726 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1516666 CTGGGCTATG
1516676 TGCATCGATGCACATTCAATA
1 TGCATCGATGCACATTCAATA
1516697 TGCATCGATGCACATTCAATA
1 TGCATCGATGCACATTCAATA
1516718 TGCATCGAT
1 TGCATCGAT
1516727 ACACTATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACATTCAATA
Found at i:1516813 original size:63 final size:63
Alignment explanation
Indices: 1516739--1516859 Score: 199
Period size: 63 Copynumber: 1.9 Consensus size: 63
1516729 ACTATGATAA
*
1516739 AATAAAAACATCGAATGCCATT-AGTGCATCGATGCATAAGTAGTGCATCGATGCACCCCATTG
1 AATAAAAACATCGAATGCCATTCA-TGCACCGATGCATAAGTAGTGCATCGATGCACCCCATTG
**
1516802 AATAAAAACATCGAATGTGATTCATGCACCGATGCATAAGTAGTGCATCGATGCACCC
1 AATAAAAACATCGAATGCCATTCATGCACCGATGCATAAGTAGTGCATCGATGCACCC
1516860 GTTAAGGAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 53 0.98
64 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (63 bp):
AATAAAAACATCGAATGCCATTCATGCACCGATGCATAAGTAGTGCATCGATGCACCCCATTG
Found at i:1516898 original size:63 final size:64
Alignment explanation
Indices: 1516761--1516902 Score: 157
Period size: 63 Copynumber: 2.2 Consensus size: 64
1516751 GAATGCCATT
* * *
1516761 AGTGCATCGATGCATAAGTAGTGCATCGATGCACCCCATTGAATAAAAACATCGAATGTGATTC
1 AGTGCATCGATGCATAAGTAGTGCATCGATGCACCCCATTGAAGAAAAACATCGAATCTGATAC
* * * * *
1516825 A-TGCACCGATGCATAAGTAGTGCATCGATGCA-CCCGTT-AAGGAATACATTGATATACTG-TA
1 AGTGCATCGATGCATAAGTAGTGCATCGATGCACCCCATTGAAGAAAAACATCGA-AT-CTGATA
*
1516886 G
64 C
1516887 AGTGCATCGATGCATA
1 AGTGCATCGATGCATA
1516903 CCCTCATTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
61 10 0.15
62 9 0.14
63 45 0.69
64 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (64 bp):
AGTGCATCGATGCATAAGTAGTGCATCGATGCACCCCATTGAAGAAAAACATCGAATCTGATAC
Found at i:1517447 original size:18 final size:18
Alignment explanation
Indices: 1517424--1517496 Score: 110
Period size: 18 Copynumber: 3.9 Consensus size: 18
1517414 AGGGATATAC
1517424 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
1517442 AGTGGTTCTTCGGAACAATT
1 AGTGGTCCTTCGGGAC-A-T
1517462 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1517480 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1517497 AATACTGAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
18 32 0.65
19 2 0.04
20 15 0.31
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1517475 original size:38 final size:38
Alignment explanation
Indices: 1517424--1517497 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
1517414 AGGGATATAC
*
1517424 AGTGGTCCTTCGGGACATAGTGGTTCTTCGGAACAATT
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAATT
*
1517462 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAA
1517498 ATACTGAACG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.28
Consensus pattern (38 bp):
AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAATT
Found at i:1521642 original size:21 final size:21
Alignment explanation
Indices: 1521596--1521712 Score: 76
Period size: 23 Copynumber: 5.4 Consensus size: 21
1521586 ATAAAAAGGT
* *
1521596 AAGAAAGAAATAAATTAAAATG
1 AAGAAA-AAATAAAATAAAATA
*
1521618 AAGAAAAAATAAAATAAATTA
1 AAGAAAAAATAAAATAAAATA
* * * **
1521639 AAGATAAGAT-AAAGAAAGCA
1 AAGAAAAAATAAAATAAAATA
*
1521659 AAGATAAAATAGTAAATAAAATA
1 AAGAAAAAATA--AAATAAAATA
*
1521682 AATAAAAATATATATAA-AAAATA
1 AAGAAAAA-ATA-A-AATAAAATA
1521705 AAGAAAAA
1 AAGAAAAA
1521713 GAAGAAAAAT
Statistics
Matches: 75, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
20 16 0.21
21 20 0.27
22 6 0.08
23 28 0.37
24 5 0.07
ACGTcount: A:0.72, C:0.01, G:0.09, T:0.18
Consensus pattern (21 bp):
AAGAAAAAATAAAATAAAATA
Found at i:1521732 original size:57 final size:55
Alignment explanation
Indices: 1521671--1521802 Score: 133
Period size: 57 Copynumber: 2.3 Consensus size: 55
1521661 GATAAAATAG
*
1521671 TAAATAAAATAAATAAAAATATATATAAAAAATAAAG-AAAAAGAAGAAAAATATATA
1 TAAATAAAA-AAATAAAAAAATA-ATAAAAAA-AAAGTAAAAAGAAGAAAAATATATA
* * * * * *
1521728 TAAATAAAACAAACAAATAAAATAATAATAAAAAAGTAAAAATAATATATATATATA
1 TAAATAAAA-AAATAAA-AAAATAATAAAAAAAAAGTAAAAAGAAGAAAAATATATA
*
1521785 T-AATAAAAACATAAAAAA
1 TAAATAAAAAAATAAAAAA
1521803 TAGTAAATAT
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
54 3 0.05
55 5 0.08
56 11 0.17
57 39 0.62
58 5 0.08
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (55 bp):
TAAATAAAAAAATAAAAAAATAATAAAAAAAAAGTAAAAAGAAGAAAAATATATA
Found at i:1521813 original size:31 final size:32
Alignment explanation
Indices: 1521676--1521818 Score: 94
Period size: 31 Copynumber: 4.7 Consensus size: 32
1521666 AATAGTAAAT
* *
1521676 AAAATAAATAAAAATATATATAAAAAATAAAG-A
1 AAAAT-AATATAAATATATATAATAAA-AAAGTA
* *
1521709 AAAAGAAGA-AAA-ATATAT-ATAAATAAA--A
1 AAAATAATATAAATATATATAATAAA-AAAGTA
* *
1521737 CAAACAA-ATAAA-ATA-ATAATAAAAAAGTA
1 AAAATAATATAAATATATATAATAAAAAAGTA
*
1521766 AAAATAATATATATATATATAATAAAAACA-T-
1 AAAATAATATAAATATATATAATAAAAA-AGTA
1521797 AAAA-AATAGTAAATATATATAA
1 AAAATAATA-TAAATATATATAA
1521819 ATTAATAAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
27 6 0.07
28 17 0.18
29 14 0.15
30 14 0.15
31 22 0.24
32 14 0.15
33 5 0.05
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.23
Consensus pattern (32 bp):
AAAATAATATAAATATATATAATAAAAAAGTA
Found at i:1521813 original size:35 final size:36
Alignment explanation
Indices: 1521764--1521858 Score: 115
Period size: 35 Copynumber: 2.6 Consensus size: 36
1521754 AATAAAAAAG
*
1521764 TAAAAATAATATATATATATATAATAAAAACATA-AA
1 TAAAAATAACATATATATATATAAT-AAAACATATAA
* *
1521800 -AAATAGTAA-ATATATATAAATTAATAAAACATATAA
1 TAAA-AATAACATATATATATA-TAATAAAACATATAA
1521836 TAAAAATAACATATATATATATA
1 TAAAAATAACATATATATATATA
1521859 TATATATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
35 21 0.42
36 16 0.32
37 13 0.26
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (36 bp):
TAAAAATAACATATATATATATAATAAAACATATAA
Found at i:1521853 original size:2 final size:2
Alignment explanation
Indices: 1521846--1521875 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1521836 TAAAAATAAC
1521846 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1521876 GTAATCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1523323 original size:39 final size:38
Alignment explanation
Indices: 1523255--1523331 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
1523245 CTCGGGTTTG
* *
1523255 GTGTTTCAAGAGAAATATTTTCAAAGGTTTTTTGTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT-TGTGT
* *
1523294 GTGTTTCAAGAGAAACAATTTCGAGGGTTTTTTTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
1523332 TTCAAGAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 5 0.15
39 29 0.85
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (38 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTGT
Found at i:1523369 original size:36 final size:37
Alignment explanation
Indices: 1523329--1523447 Score: 172
Period size: 36 Copynumber: 3.2 Consensus size: 37
1523319 GGTTTTTTTG
*
1523329 TGTTTCAAGAGAAACTGTCTCAAGAGG-GACAAAATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGGAGACAAAATT
1523365 TGTTTCAAAAGAAACTGTCTCAAGAGAGAGACAAAACTT
1 TGTTTCAAAAGAAACTGTCTCAAGAG-GAGACAAAA-TT
*
1523404 AG-TTCTAAAAGAAACTGTCTCAAG-GGAGACAAAATT
1 TGTTTC-AAAAGAAACTGTCTCAAGAGGAGACAAAATT
1523440 TGTTTCAA
1 TGTTTCAA
1523448 GGAAAAGATA
Statistics
Matches: 75, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
36 30 0.40
37 13 0.17
38 11 0.15
39 21 0.28
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.25
Consensus pattern (37 bp):
TGTTTCAAAAGAAACTGTCTCAAGAGGAGACAAAATT
Found at i:1523578 original size:29 final size:29
Alignment explanation
Indices: 1523522--1523580 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1523512 GATTTAAATA
* * *
1523522 GTTTGTGTTTCAAGGGAAATATTTTCAAG
1 GTTTATGTTTCAAGAGAAATATTCTCAAG
1523551 GTTTATGTTTCAAGAGAAACTA-TCTCAAG
1 GTTTATGTTTCAAGAGAAA-TATTCTCAAG
1523580 G
1 G
1523581 GAGACAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (29 bp):
GTTTATGTTTCAAGAGAAATATTCTCAAG
Found at i:1523607 original size:37 final size:37
Alignment explanation
Indices: 1523556--1523628 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
1523546 TCAAGGTTTA
*
1523556 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
*
1523593 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
1523629 AATTTCAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:1523635 original size:102 final size:102
Alignment explanation
Indices: 1523529--1523764 Score: 373
Period size: 102 Copynumber: 2.3 Consensus size: 102
1523519 ATAGTTTGTG
* *
1523529 TTTCAAGGGAAATATTTTCAAGGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* *
1523594 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
66 GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
* * *
1523631 TTTCAAAGGAAATGTTTTCAATGTTTATGTTACAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* * *
1523696 GTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTA
66 GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
*
1523733 TTTTAAGGGAAATGTTTTCAATGTTTATGTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTT
1523765 TAAGGGAGAC
Statistics
Matches: 121, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 121 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
Found at i:1523642 original size:36 final size:37
Alignment explanation
Indices: 1523558--1523642 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
1523548 AAGGTTTATG
* **
1523558 TTTC-AAGAGAAACTATCTCAAGGGAGACAAAATTTTG
1 TTTCAAAG-GAAACTATCTCAAGAGAGACAAAATTTAA
*
1523595 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTAA
1 TTTCAAAGGAAACTATCTCAAGAGAGACAAAATTTAA
1523631 TTTCAAAGGAAA
1 TTTCAAAGGAAA
1523643 TGTTTTCAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 13 0.31
37 27 0.64
38 2 0.05
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.25
Consensus pattern (37 bp):
TTTCAAAGGAAACTATCTCAAGAGAGACAAAATTTAA
Found at i:1523780 original size:87 final size:87
Alignment explanation
Indices: 1523677--1523942 Score: 451
Period size: 87 Copynumber: 3.1 Consensus size: 87
1523667 AGAAACTGTC
* * * * *
1523677 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTTAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1523742 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* *
1523764 TTAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1523829 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* *
1523851 TCAAGGGAGATAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAAATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1523916 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
1523938 TCAAG
1 TCAAG
1523943 AGAAACTGTC
Statistics
Matches: 168, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 168 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
AAATGTTTTCAATGTTTATGTT
Found at i:1524386 original size:106 final size:106
Alignment explanation
Indices: 1524273--1524507 Score: 350
Period size: 106 Copynumber: 2.2 Consensus size: 106
1524263 AGTCAGCCAC
* * * *
1524273 CCCTTCGTTGTGAATTTGAGCTTGTGCTATCTTGAGTCCAATATCCTTCACTGTGAAGTTGAAAT
1 CCCTTCGTTGTGAAGTTGAACTTGTGCTATCTCGAGTCCAATATCCTTCACCGTGAAGTTGAAAT
*
1524338 TGGCTCCAAAATTGGGAAATTTTTTGTTGACAACCAGTCGT
66 TGGCTCCAAAATTGGGAAATTATTTGTTGACAACCAGTCGT
* * **
1524379 CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTTGCCGTGAAGTTGAAAT
1 CCCTTCGTTGTGAAGTTGAACTTGTGCTATCTCGAGTCCAATATCCTTCACCGTGAAGTTGAAAT
*
1524444 TGGCTCTAAAATTGGGAAATTATTTGTTGACAACCAGTCGT
66 TGGCTCCAAAATTGGGAAATTATTTGTTGACAACCAGTCGT
*
1524485 CCC-T--TTGTGGAGTTGAACTTGTG
1 CCCTTCGTTGTGAAGTTGAACTTGTG
1524508 TTGTCTTGAA
Statistics
Matches: 118, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
103 18 0.15
105 1 0.01
106 99 0.84
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (106 bp):
CCCTTCGTTGTGAAGTTGAACTTGTGCTATCTCGAGTCCAATATCCTTCACCGTGAAGTTGAAAT
TGGCTCCAAAATTGGGAAATTATTTGTTGACAACCAGTCGT
Found at i:1525165 original size:32 final size:32
Alignment explanation
Indices: 1525129--1525209 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
1525119 CTCAATATTC
**
1525129 GATGTTGAATCTCAAAAAATGTCCCAACATTT
1 GATGTTGAATCTCAAAAAATACCCCAACATTT
* *
1525161 GATGTTAAATCTAAAAAAATACCCCAACATTT
1 GATGTTGAATCTCAAAAAATACCCCAACATTT
1525193 GATGTTGAATCTTCAAA
1 GATGTTGAATC-TCAAA
1525210 GATTCCCTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 38 0.90
33 4 0.10
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATACCCCAACATTT
Found at i:1526246 original size:69 final size:69
Alignment explanation
Indices: 1526131--1526265 Score: 207
Period size: 69 Copynumber: 2.0 Consensus size: 69
1526121 TGTCTCTCTC
* * *
1526131 TTGATGCTCCATGATCTTCGAGTGGAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCGATC
1 TTGATGATCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1526196 TCAT
66 TCAT
* * * *
1526200 TTGATGATCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGATCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1526265 T
66 T
1526266 TATAGTTTGA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (69 bp):
TTGATGATCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:1526376 original size:27 final size:27
Alignment explanation
Indices: 1526340--1526393 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
1526330 TTTTTCTTCA
1526340 ATTTTCCTTTG-TTTTTTTATCTTTTT
1 ATTTTCCTTTGTTTTTTTTATCTTTTT
*
1526366 ATTTTCTCTTTGTTTTTTTTCTCTTTTT
1 ATTTTC-CTTTGTTTTTTTTATCTTTTT
1526394 CTCTTTTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 14 0.56
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.78
Consensus pattern (27 bp):
ATTTTCCTTTGTTTTTTTTATCTTTTT
Found at i:1526381 original size:26 final size:27
Alignment explanation
Indices: 1526340--1526392 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1526330 TTTTTCTTCA
1526340 ATTTTCCTTTGTTTTTTTATCT-TTTT
1 ATTTTCCTTTGTTTTTTTATCTCTTTT
1526366 ATTTTCTCTTTGTTTTTTT-TCTCTTTT
1 ATTTTC-CTTTGTTTTTTTATCTCTTTT
1526393 TCTCTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.77
Consensus pattern (27 bp):
ATTTTCCTTTGTTTTTTTATCTCTTTT
Found at i:1526385 original size:15 final size:15
Alignment explanation
Indices: 1526341--1526391 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 15
1526331 TTTTCTTCAA
1526341 TTTTC-CTTTG-TTT
1 TTTTCTCTTTGTTTT
* *
1526354 TTTTATC-TT-TTTA
1 TTTTCTCTTTGTTTT
1526367 TTTTCTCTTTGTTTT
1 TTTTCTCTTTGTTTT
1526382 TTTTCTCTTT
1 TTTTCTCTTT
1526392 TTCTCTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 14 0.47
14 3 0.10
15 13 0.43
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.78
Consensus pattern (15 bp):
TTTTCTCTTTGTTTT
Found at i:1529666 original size:2 final size:2
Alignment explanation
Indices: 1529661--1529685 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1529651 AGTAAAACTA
1529661 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
1529686 ATAAATAAAA
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:1532848 original size:4 final size:4
Alignment explanation
Indices: 1532841--1532962 Score: 163
Period size: 4 Copynumber: 30.5 Consensus size: 4
1532831 CTCTCTCTCC
*
1532841 ATAT ATAT ATAT ATAT ATAT ATAT ATAA ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * *
1532889 ATAT ATAT ATAT ATGT ATGT ATGT ATGT ATAT ATAT ATAT ATAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
1532937 ATGT ATGT ATAT ATAT ATAT GTAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT AT
1532963 GTATGTATGT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 110 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:1532963 original size:28 final size:28
Alignment explanation
Indices: 1532841--1532974 Score: 187
Period size: 28 Copynumber: 4.8 Consensus size: 28
1532831 CTCTCTCTCC
* * * *
1532841 ATATATATATATATATATATATATATAA
1 ATATATATATGTATGTATGTATATATAT
* * *
1532869 ATATATATATATATATATATATATATAT
1 ATATATATATGTATGTATGTATATATAT
*
1532897 ATATATGTATGTATGTATGTATATATAT
1 ATATATATATGTATGTATGTATATATAT
1532925 ATATATATATGTATGTATGTATATATAT
1 ATATATATATGTATGTATGTATATATAT
*
1532953 ATATGTATATGTATGTATGTAT
1 ATATATATATGTATGTATGTAT
1532975 GTGTTGGTAA
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 99 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (28 bp):
ATATATATATGTATGTATGTATATATAT
Found at i:1532971 original size:8 final size:8
Alignment explanation
Indices: 1532900--1532976 Score: 73
Period size: 8 Copynumber: 9.6 Consensus size: 8
1532890 TATATATATA
1532900 TATGTATG
1 TATGTATG
1532908 TATGTATG
1 TATGTATG
* *
1532916 TATATATA
1 TATGTATG
* *
1532924 TATATATA
1 TATGTATG
1532932 TATGTATG
1 TATGTATG
*
1532940 TATGTATA
1 TATGTATG
* *
1532948 TATATATA
1 TATGTATG
* *
1532956 TGTATATG
1 TATGTATG
1532964 TATGTATG
1 TATGTATG
1532972 TATGT
1 TATGT
1532977 GTTGGTAAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.51
Consensus pattern (8 bp):
TATGTATG
Found at i:1542056 original size:90 final size:90
Alignment explanation
Indices: 1541903--1542082 Score: 360
Period size: 90 Copynumber: 2.0 Consensus size: 90
1541893 CACTCATTTT
1541903 TTCATTGATTTTACAACCTTTCTTCCACTTCTGTTTTTCATACAAAATTTGTTGATAGCAGGGGA
1 TTCATTGATTTTACAACCTTTCTTCCACTTCTGTTTTTCATACAAAATTTGTTGATAGCAGGGGA
1541968 CACATTTCCTTTTCTTTTCAATAGA
66 CACATTTCCTTTTCTTTTCAATAGA
1541993 TTCATTGATTTTACAACCTTTCTTCCACTTCTGTTTTTCATACAAAATTTGTTGATAGCAGGGGA
1 TTCATTGATTTTACAACCTTTCTTCCACTTCTGTTTTTCATACAAAATTTGTTGATAGCAGGGGA
1542058 CACATTTCCTTTTCTTTTCAATAGA
66 CACATTTCCTTTTCTTTTCAATAGA
1542083 AGCGCACAAA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (90 bp):
TTCATTGATTTTACAACCTTTCTTCCACTTCTGTTTTTCATACAAAATTTGTTGATAGCAGGGGA
CACATTTCCTTTTCTTTTCAATAGA
Found at i:1544109 original size:42 final size:40
Alignment explanation
Indices: 1544063--1544178 Score: 108
Period size: 40 Copynumber: 2.9 Consensus size: 40
1544053 ATAAGTCGAA
* * * *
1544063 TTCGCAACTCGAATTTGACATTTTTGCAACACGAATTTCTTT
1 TTCGCAACTCGAATTTGA-A-ATTCGAAACACGAATTTCATT
* * *
1544105 TTCGCAACTCGATTTTTAAATTCGAAACACGAGTTTCATT
1 TTCGCAACTCGAATTTGAAATTCGAAACACGAATTTCATT
* * *
1544145 TTCGCAACTCGATTTTCG-AATTCGCAACTCGAAT
1 TTCGCAACTCGAATTT-GAAATTCGAAACACGAAT
1544179 CTTGCTATGA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
40 45 0.73
41 1 0.02
42 16 0.26
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (40 bp):
TTCGCAACTCGAATTTGAAATTCGAAACACGAATTTCATT
Found at i:1544161 original size:20 final size:20
Alignment explanation
Indices: 1544063--1544176 Score: 86
Period size: 20 Copynumber: 5.6 Consensus size: 20
1544053 ATAAGTCGAA
*
1544063 TTCGCAACTCGAATTTGACATT
1 TTCGCAACTCG-ATTT-TCATT
* * * *
1544085 TTTGCAACACGAATTTCTTT
1 TTCGCAACTCGATTTTCATT
* **
1544105 TTCGCAACTCGATTTTTAAA
1 TTCGCAACTCGATTTTCATT
* * *
1544125 TTCGAAACACGAGTTTCATT
1 TTCGCAACTCGATTTTCATT
*
1544145 TTCGCAACTCGATTTTCGA-A
1 TTCGCAACTCGATTTTC-ATT
1544165 TTCGCAACTCGA
1 TTCGCAACTCGA
1544177 ATCTTGCTAT
Statistics
Matches: 69, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 56 0.81
21 4 0.06
22 9 0.13
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (20 bp):
TTCGCAACTCGATTTTCATT
Found at i:1544167 original size:40 final size:40
Alignment explanation
Indices: 1544090--1544178 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
1544080 ACATTTTTGC
* *
1544090 AACACGAATTTCTTTTTCGCAACTCGATTTTTAAATTCGA
1 AACACGAATTTCATTTTCGCAACTCGATTTTCAAATTCGA
* * *
1544130 AACACGAGTTTCATTTTCGCAACTCGATTTTCGAATTCGC
1 AACACGAATTTCATTTTCGCAACTCGATTTTCAAATTCGA
*
1544170 AACTCGAAT
1 AACACGAAT
1544179 CTTGCTATGA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (40 bp):
AACACGAATTTCATTTTCGCAACTCGATTTTCAAATTCGA
Found at i:1548173 original size:20 final size:20
Alignment explanation
Indices: 1548150--1548193 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1548140 ATTTCACCAC
*
1548150 ATGCAACTAAATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
* *
1548170 ATGCATCTATATGATCCTAA
1 ATGCAACTAAATGATCCTAA
1548190 ATGC
1 ATGC
1548194 GCTCTTAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Found at i:1560508 original size:218 final size:219
Alignment explanation
Indices: 1560130--1560571 Score: 796
Period size: 218 Copynumber: 2.0 Consensus size: 219
1560120 TCCCCTCAAC
* *
1560130 TCTCAGTTATCACTAATTTGCTAAAAAAATTACAACGTTCTACTGATGTGAAGGAAGTGAAAGCA
1 TCTCAGTTATCACTAATATGCTAAAAAAATTACAACGTTCTACTGATATGAAGGAAGTGAAAGCA
*
1560195 AATAGCTTGGCATGTCTGTTATGAAAAGGCAATCATCGCGAGAGCGATTATCCGACCAACCATGA
66 AATAGCTTGGCATGTCTGTTATGAAAAGGCAATCATCGCAAGAGCGATTATCCGACCAACCATGA
* *
1560260 GTCCATCAACTTTGTAGGTAATTTCAATCGAGCCAA-AAAAATCCTTACTGTAACACTTATAATG
131 GTACATCAACTTTGTAGGTAATTTCAATCGAGCCAACAAAAATCCTTACTCTAACACTTATAATG
*
1560324 TTGGATGGCGTCAACATCCTAATT
196 ATGGATGGCGTCAACATCCTAATT
1560348 TCTCAGTTATCACTAATATGCTAAAAAAATTACAACGTTCTACTGATATGAAGGAAGTGAAAGCA
1 TCTCAGTTATCACTAATATGCTAAAAAAATTACAACGTTCTACTGATATGAAGGAAGTGAAAGCA
*
1560413 AATAGCTTGGCATGTCTGTTATGAAAAGGCAATCATCGCAAGAGCGATTGTCCGACCAACCATGA
66 AATAGCTTGGCATGTCTGTTATGAAAAGGCAATCATCGCAAGAGCGATTATCCGACCAACCATGA
* *
1560478 GTATATCAACTTTGTAGGTAATTTCAATCGAGCCAACAACAATCCTTACTCTAACACTTATAATG
131 GTACATCAACTTTGTAGGTAATTTCAATCGAGCCAACAAAAATCCTTACTCTAACACTTATAATG
1560543 ATGGATGGCGTCAACATCCTAATT
196 ATGGATGGCGTCAACATCCTAATT
1560567 TCTCA
1 TCTCA
1560572 TGGGGAAATC
Statistics
Matches: 214, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
218 160 0.75
219 54 0.25
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (219 bp):
TCTCAGTTATCACTAATATGCTAAAAAAATTACAACGTTCTACTGATATGAAGGAAGTGAAAGCA
AATAGCTTGGCATGTCTGTTATGAAAAGGCAATCATCGCAAGAGCGATTATCCGACCAACCATGA
GTACATCAACTTTGTAGGTAATTTCAATCGAGCCAACAAAAATCCTTACTCTAACACTTATAATG
ATGGATGGCGTCAACATCCTAATT
Found at i:1564499 original size:19 final size:19
Alignment explanation
Indices: 1564475--1564512 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1564465 GAAATGGCAT
*
1564475 GACCAGAAACTGATGCCAC
1 GACCAGAAAATGATGCCAC
1564494 GACCAGAAAATGATGCCAC
1 GACCAGAAAATGATGCCAC
1564513 AATATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.29, G:0.21, T:0.11
Consensus pattern (19 bp):
GACCAGAAAATGATGCCAC
Found at i:1565186 original size:20 final size:22
Alignment explanation
Indices: 1565150--1565197 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
1565140 TAACTTTTTG
1565150 TTTTCTCTTTCATTC-TTAACT
1 TTTTCTCTTTCATTCTTTAACT
*
1565171 TTTTTTCTTTCA-TCTTTAACT
1 TTTTCTCTTTCATTCTTTAACT
1565192 TTTTCT
1 TTTTCT
1565198 TTTTTTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTCTCTTTCATTCTTTAACT
Found at i:1565313 original size:151 final size:151
Alignment explanation
Indices: 1565131--1565454 Score: 562
Period size: 152 Copynumber: 2.1 Consensus size: 151
1565121 TCATTTTCCC
* * *
1565131 TCTT-ATTTTTAACTTTTTGTTTTCTCTTTCATTCTTAACTTTTTTTCTTTCATCTTTAACTTTT
1 TCTTCATTTTTCA-TTTTTCTTATCTCTTTCATTCTTAACTTTTTTTCTTTCATCTTTAACTTTT
*
1565195 T-CTTTTTTTCTCTCTCATTTCTTCATCATCTTCTTTCATTTTCCTCCATAGTCGAAAATCCTTC
65 TCCTTTTTTTCTCTCTCATTTCTTCATCATCTTCTTTCATTTTCCTCCATAGTAGAAAATCCTTC
1565259 AAGTTTTTAACAACATCAAAGCT
130 AAGTTTTTAACAACATC-AAGCT
1565282 TCTTCATTTTTCATTTTTCTTATCTCTTTCATTCTTAACTTTTTTTCTTTCATCTTTAACTTTTT
1 TCTTCATTTTTCATTTTTCTTATCTCTTTCATTCTTAACTTTTTTTCTTTCATCTTTAACTTTTT
*
1565347 CCTTTTTTTCTCTCTCATTTCTTTATCATCTTCTTTCATTTTCCTCCATAGTAGAAAATCCTTCA
66 CCTTTTTTTCTCTCTCATTTCTTCATCATCTTCTTTCATTTTCCTCCATAGTAGAAAATCCTTCA
1565412 AGTTTTTAACAACATCAAGCT
131 AGTTTTTAACAACATCAAGCT
*
1565433 TCTTCGTTTTTCATTTTTCTTA
1 TCTTCATTTTTCATTTTTCTTA
1565455 CTTCAAAACC
Statistics
Matches: 165, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
151 80 0.48
152 85 0.52
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.56
Consensus pattern (151 bp):
TCTTCATTTTTCATTTTTCTTATCTCTTTCATTCTTAACTTTTTTTCTTTCATCTTTAACTTTTT
CCTTTTTTTCTCTCTCATTTCTTCATCATCTTCTTTCATTTTCCTCCATAGTAGAAAATCCTTCA
AGTTTTTAACAACATCAAGCT
Found at i:1565345 original size:20 final size:21
Alignment explanation
Indices: 1565306--1565346 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1565296 TTTTCTTATC
1565306 TCTTTCATTCTTAACTTTTTT
1 TCTTTCATTCTTAACTTTTTT
1565327 TCTTTCA-TCTTTAACTTTTT
1 TCTTTCATTC-TTAACTTTTT
1565347 CCTTTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.66
Consensus pattern (21 bp):
TCTTTCATTCTTAACTTTTTT
Found at i:1565351 original size:20 final size:21
Alignment explanation
Indices: 1565307--1565351 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1565297 TTTCTTATCT
*
1565307 CTTTCATTCTTAACTTTTTTT
1 CTTTCATTCTTAACTTTTTTC
1565328 CTTTCA-TCTTTAAC-TTTTTC
1 CTTTCATTC-TTAACTTTTTTC
1565348 CTTT
1 CTTT
1565352 TTTTCTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.64
Consensus pattern (21 bp):
CTTTCATTCTTAACTTTTTTC
Found at i:1575008 original size:15 final size:15
Alignment explanation
Indices: 1574985--1575014 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1574975 CTAGGATATT
1574985 TGGTCTAGATAACGA
1 TGGTCTAGATAACGA
*
1575000 TGGTTTAGATAACGA
1 TGGTCTAGATAACGA
1575015 GAGAGAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (15 bp):
TGGTCTAGATAACGA
Found at i:1578204 original size:24 final size:23
Alignment explanation
Indices: 1578148--1578273 Score: 119
Period size: 23 Copynumber: 5.4 Consensus size: 23
1578138 AAAATTTGCA
*
1578148 CCGAAGTG-CCACGTAAAATTGTC
1 CCGAA-TGACCACGTAGAATTGTC
*
1578171 CCGAATGACCGCGTAGAATTTGTC
1 CCGAATGACCACGTAGAA-TTGTC
* *
1578195 CTGAAGGACCACGTAGAATTGTC
1 CCGAATGACCACGTAGAATTGTC
** *
1578218 CCGAATGACCATATAGATTTGTC
1 CCGAATGACCACGTAGAATTGTC
* * * * *
1578241 TCGAATTACCACATAGATTTTTC
1 CCGAATGACCACGTAGAATTGTC
1578264 CCGAATGACC
1 CCGAATGACC
1578274 GCTAAAACCC
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
22 2 0.02
23 63 0.74
24 20 0.24
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (23 bp):
CCGAATGACCACGTAGAATTGTC
Found at i:1584304 original size:10 final size:9
Alignment explanation
Indices: 1584289--1584347 Score: 55
Period size: 10 Copynumber: 6.0 Consensus size: 9
1584279 CTCTTTTGAA
1584289 TTTCTTTTCT
1 TTTCTTTT-T
1584299 TTTCTTTTT
1 TTTCTTTTT
1584308 TTTCTGATTTT
1 TTTCT--TTTT
*
1584319 TCTCTTCTTT
1 TTTCTT-TTT
*
1584329 TGTCTTTTT
1 TTTCTTTTT
1584338 CTTTCTTTTT
1 -TTTCTTTTT
1584348 GCACTCCAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
9 10 0.24
10 24 0.57
11 8 0.19
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:1584632 original size:19 final size:19
Alignment explanation
Indices: 1584601--1584651 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1584591 AGGGGATAAT
1584601 AATATAAGTAATGAAATGA
1 AATATAAGTAATGAAATGA
1584620 AATATTAAG-AATGAAATGA
1 AATA-TAAGTAATGAAATGA
*
1584639 AATA-AAGAAATGA
1 AATATAAGTAATGA
1584652 TAGAGATGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.10
18 5 0.17
19 18 0.60
20 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.24
Consensus pattern (19 bp):
AATATAAGTAATGAAATGA
Found at i:1586109 original size:151 final size:152
Alignment explanation
Indices: 1585939--1586244 Score: 596
Period size: 151 Copynumber: 2.0 Consensus size: 152
1585929 AATATATATT
*
1585939 TATATGAAACTAACTATCTTATAACATATGAAATAAGCATCTATAGGTATAAAGATAGAAAGTTT
1 TATATGAAAATAACTATCTTATAACATATGAAATAAGCATCTATAGGTATAAAGATAGAAAGTTT
1586004 CTTCCCTGGAGAGGTTGG-ATAGCCATGGTAAATATGATGCTGAATTGGATCACATCAAAAATAA
66 CTTCCCTGGAGAGGTTGGAATAGCCATGGTAAATATGATGCTGAATTGGATCACATCAAAAATAA
1586068 ACCATAAAATTTTAAATCCTTA
131 ACCATAAAATTTTAAATCCTTA
1586090 TATATGAAAATAACTATCTTATAACATATGAAATAAGCATCTATAGGTATAAAGATAGAAAGTTT
1 TATATGAAAATAACTATCTTATAACATATGAAATAAGCATCTATAGGTATAAAGATAGAAAGTTT
1586155 CTTCCCTGGAGAGGTTGGAATAGCCATGGTAAATATGATGCTGAATTGGATCACATCAAAAATAA
66 CTTCCCTGGAGAGGTTGGAATAGCCATGGTAAATATGATGCTGAATTGGATCACATCAAAAATAA
1586220 ACCATAAAATTTTAAATCCTTA
131 ACCATAAAATTTTAAATCCTTA
1586242 TAT
1 TAT
1586245 TTTAGTTACT
Statistics
Matches: 153, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
151 82 0.54
152 71 0.46
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (152 bp):
TATATGAAAATAACTATCTTATAACATATGAAATAAGCATCTATAGGTATAAAGATAGAAAGTTT
CTTCCCTGGAGAGGTTGGAATAGCCATGGTAAATATGATGCTGAATTGGATCACATCAAAAATAA
ACCATAAAATTTTAAATCCTTA
Found at i:1588622 original size:20 final size:21
Alignment explanation
Indices: 1588590--1588628 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1588580 GTAATGATAA
1588590 AATAAAAACTAAATCAAATAT
1 AATAAAAACTAAATCAAATAT
1588611 AATAAAAA-TAAATCAAAT
1 AATAAAAACTAAATCAAAT
1588629 CAAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (21 bp):
AATAAAAACTAAATCAAATAT
Found at i:1590866 original size:83 final size:83
Alignment explanation
Indices: 1590756--1591244 Score: 509
Period size: 83 Copynumber: 5.9 Consensus size: 83
1590746 TTTGATATGT
* * * * *
1590756 CTGAGTGTAATCGAACTTGAAGGTCTTTGTTGACAGATAACCCTTCTATCCTTGAGTTATGTTGC
1 CTGAGTGTAGTCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGC
* *
1590821 AATTGATATGCCTTTGAG
66 AAATGATGTGCCTTTGAG
* * * * *
1590839 CTGAGTGTAGTTAAACTCAAAGGTCTTTGTCGGA-AGATAACCCTTCTAGCCTTGAGTTGTGTTG
1 CTGAGTGTAGTCAAACTCGAAGGTCTTTGT-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTG
* *
1590903 TAAATGATGTGCCTTGGAG
65 CAAATGATGTGCCTTTGAG
* * * * * *
1590922 CTGAGCT-TAGTCTAACTCAAAAGTCATTGATGACAGATAACCCTTCTCGCCTTGAGTTATGCTG
1 CTGAG-TGTAGTCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTG
*
1590986 CAAATGATGTGCCTTGGAG
65 CAAATGATGTGCCTTTGAG
* * * * * * *
1591005 TTAAGCGTAGTCGAACTCGATGGTCTTTGGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTG
1 CTGAGTGTAGTCAAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTG
1591070 CAAATGATGTGCCTTTGAG
65 CAAATGATGTGCCTTTGAG
* * * * *
1591089 CTGAGTGTAATCGAACTCGAAGGTCTTGGTTGGA-AAATAACTCTTCTAGCCTTGAGTTATGCTG
1 CTGAGTGTAGTCAAACTCGAAGGTCTTTGTT-GACAGATAACCCTTCTAGCCTTGAGTTATGCTG
* * *
1591153 TAAATTATGTGTCTTTGAG
65 CAAATGATGTGCCTTTGAG
* * * * * *
1591172 CTGAGTGTAATCAAACTCGAAGGT-TTTTTTGTTAGCAGATAGCCCTTCTTGCCTTGAGCTAAGC
1 CTGAGTGTAGTCAAACTCGAAGGTCTTTGTTG--A-CAGATAACCCTTCTAGCCTTGAGTTATGC
1591236 TGCAAATGA
63 TGCAAATGA
1591245 GCACGATATC
Statistics
Matches: 338, Mismatches: 58, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
81 1 0.00
82 6 0.02
83 225 0.67
84 77 0.23
85 29 0.09
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (83 bp):
CTGAGTGTAGTCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGC
AAATGATGTGCCTTTGAG
Found at i:1591084 original size:167 final size:166
Alignment explanation
Indices: 1590663--1591244 Score: 543
Period size: 167 Copynumber: 3.5 Consensus size: 166
1590653 GCCATGCGGT
* * * * * * * * *
1590663 TGATATGCCTATGAGCTGAATGAAATCGAACTCGAAGGTCTTTGATGTCAAATAACCCTTCTTGC
1 TGATGTGCCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGC
* ** * * ** * * *
1590728 CTTGAGCTATGCTTTAAAT--T-TG-ATAT-G-TCTGAGTGTAATCGAACTTGAAGGTCTTTGTT
66 CTTGAGTTATGCTGCAAATGATGTGCCT-TGGAGCTGAGTGTAATCGAACTCAAAAGTCTTGGAT
* * *
1590787 GACAGATAACCCTTCTATCCTTGAGTTATGTTGCAAT
130 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
* * * * * *
1590824 TGATATGCCTTTGAGCTGAGTGTAGTTAAACTCAAAGGTCTTTGTCGGAAGATAACCCTTCTAGC
1 TGATGTGCCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGC
* * * * *
1590889 CTTGAGTTGTGTTGTAAATGATGTGCCTTGGAGCTGAGCT-TAGTCTAACTCAAAAGTCATT-GA
66 CTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAG-TGTAATCGAACTCAAAAGTC-TTGGA
*
1590952 TGACAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAA
129 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
* * * * * *
1590990 TGATGTGCCTTGGAGTTAAGCGTAGTCGAACTCGATGGTCTTTGGTTGGCAGATAACCCTTCTTG
1 TGATGTGCCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTTG
* * * *
1591055 CCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTT
65 CCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCAAAAGTCTTGGAT
* * *
1591120 GGA-AAATAACTCTTCTAGCCTTGAGTTATGCTGTAAA
130 -GACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
* * * * * *
1591157 TTATGTGTCTTTGAGCTGAGTGTAATCAAACTCGAAGGTTTTTTTGTTAGCAGATAGCCCTTCTT
1 TGATGTGCCTTTGAGCTGAGTGTAGTCAAACTCGAAGG--TCTTTGTTGGCAGATAACCCTTCTT
* *
1591222 GCCTTGAGCTAAGCTGCAAATGA
64 GCCTTGAGTTATGCTGCAAATGA
1591245 GCACGATATC
Statistics
Matches: 339, Mismatches: 68, Indels: 21
0.79 0.16 0.05
Matches are distributed among these distances:
161 67 0.20
163 1 0.00
164 3 0.01
165 2 0.01
166 90 0.27
167 131 0.39
168 41 0.12
169 4 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (166 bp):
TGATGTGCCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGC
CTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCAAAAGTCTTGGATG
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
Found at i:1591680 original size:43 final size:43
Alignment explanation
Indices: 1591633--1591734 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 43
1591623 TTCGTCGTGA
**
1591633 AGTTGAAA-CTGTGGATGTGTGGGCACGATATCCTCCATTGTGG
1 AGTTGAAATC-GTGGATCCGTGGGCACGATATCCTCCATTGTGG
* * *
1591676 AGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTTGTGG
1 AGTTGAAATCGTGGATCCGTGGGCACGATATCCTCCATTGTGG
*
1591719 AGTTGAAATCATGGAT
1 AGTTGAAATCGTGGAT
1591735 GACCCCTTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 51 0.98
44 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (43 bp):
AGTTGAAATCGTGGATCCGTGGGCACGATATCCTCCATTGTGG
Found at i:1591918 original size:64 final size:64
Alignment explanation
Indices: 1591812--1591941 Score: 190
Period size: 64 Copynumber: 2.0 Consensus size: 64
1591802 GTGTTGTTTC
* *
1591812 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTGTTTGTT
1 GAGTACAATATCCTTCGTCGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTCTTTGTT
* * * *
1591876 GAGTACAATATCCTTCG-CTGTGAAGTTGAAATTGACTTTGAATGAAATTGTAAAGTTCTTTGTT
1 GAGTACAATATCCTTCGTC-GTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTCTTTGTT
1591940 GA
1 GA
1591942 CAGACGCTCC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 1 0.02
64 58 0.98
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (64 bp):
GAGTACAATATCCTTCGTCGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTCTTTGTT
Found at i:1592271 original size:32 final size:32
Alignment explanation
Indices: 1592197--1592271 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
1592187 TTGCATCAGG
* *
1592197 ATGTTGAATCCCCAAATATGCCACAATATTCA
1 ATGTTGAATCTCCAAATATGCCACAACATTCA
* *
1592229 ATGTTGAATCTCCAAATATGCCCCAACATTTA
1 ATGTTGAATCTCCAAATATGCCACAACATTCA
*
1592261 CTGTTGAATCT
1 ATGTTGAATCT
1592272 TTAAAGATGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (32 bp):
ATGTTGAATCTCCAAATATGCCACAACATTCA
Found at i:1592452 original size:22 final size:22
Alignment explanation
Indices: 1592418--1592479 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
1592408 CTTTTATTTT
*
1592418 CAAAAGTTCTGAAAATGTATTAA
1 CAAAAGTTTTGAAAATGT-TTAA
*
1592441 -AAGAGTTTTGAAAAATGTTTAA
1 CAAAAGTTTTG-AAAATGTTTAA
1592463 TCAAAAGTTTTGAAAAT
1 -CAAAAGTTTTGAAAAT
1592480 ATTGCCCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 12 0.36
23 12 0.36
24 9 0.27
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.34
Consensus pattern (22 bp):
CAAAAGTTTTGAAAATGTTTAA
Found at i:1597679 original size:49 final size:49
Alignment explanation
Indices: 1597618--1597716 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
1597608 TATCAAACTA
1597618 AATTATCAAATCTATAAATCATTTTTTA-AATTTTTTTATCATTTCTCTT
1 AATTATCAAATCTATAAAT-ATTTTTTAGAATTTTTTTATCATTTCTCTT
*
1597667 AATTTTCAAATCTATAAATATTTTTTAGAATTTTTTTATCATTTCTCTT
1 AATTATCAAATCTATAAATATTTTTTAGAATTTTTTTATCATTTCTCTT
1597716 A
1 A
1597717 GTCAAACACA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 8 0.17
49 40 0.83
ACGTcount: A:0.32, C:0.11, G:0.01, T:0.56
Consensus pattern (49 bp):
AATTATCAAATCTATAAATATTTTTTAGAATTTTTTTATCATTTCTCTT
Found at i:1612555 original size:38 final size:38
Alignment explanation
Indices: 1612505--1612587 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 38
1612495 TGTTCTTTCT
*
1612505 TTTTCAATGATAAAGAGATAACATTTAAACTCCCTATC
1 TTTTCAAGGATAAAGAGATAACATTTAAACTCCCTATC
*
1612543 TTTTCAAGGATAAAGAGATAATATTTAAACTCCCTATC
1 TTTTCAAGGATAAAGAGATAACATTTAAACTCCCTATC
1612581 TTTTCAA
1 TTTTCAA
1612588 TTGGCTAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (38 bp):
TTTTCAAGGATAAAGAGATAACATTTAAACTCCCTATC
Found at i:1614375 original size:18 final size:18
Alignment explanation
Indices: 1614338--1614371 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1614328 TTTTAAGATT
1614338 TTATATTCGATTTAAATA
1 TTATATTCGATTTAAATA
1614356 TTATATTCGA-TTAAAT
1 TTATATTCGATTTAAAT
1614372 TATTCAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
TTATATTCGATTTAAATA
Found at i:1614796 original size:24 final size:24
Alignment explanation
Indices: 1614719--1614797 Score: 60
Period size: 24 Copynumber: 3.5 Consensus size: 24
1614709 ACCATGTTAG
** *
1614719 GTATCGATACTACTTTACATAATA
1 GTATCGATACTACTGCACATAGTA
*
1614743 GTATCGATACTCACTGGAC---G--
1 GTATCGATACT-ACTGCACATAGTA
* *
1614763 GTTTCTATACTACTGCACATAGTA
1 GTATCGATACTACTGCACATAGTA
1614787 GTATCGATACT
1 GTATCGATACT
1614798 CTCTGGACAG
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
19 6 0.15
20 9 0.22
22 1 0.02
24 20 0.49
25 5 0.12
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (24 bp):
GTATCGATACTACTGCACATAGTA
Found at i:1614817 original size:44 final size:44
Alignment explanation
Indices: 1614719--1614817 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
1614709 ACCATGTTAG
** *
1614719 GTATCGATACTACTTTACATAATAGTATCGATACTCACTGGACG
1 GTATCGATACTACTGCACATAATAGTATCGATACTCACTGGACA
* * * *
1614763 GTTTCTATACTACTGCACATAGTAGTATCGATACTCTCTGGACA
1 GTATCGATACTACTGCACATAATAGTATCGATACTCACTGGACA
1614807 GTATCGATACT
1 GTATCGATACT
1614818 GTTGGTTTGC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (44 bp):
GTATCGATACTACTGCACATAATAGTATCGATACTCACTGGACA
Found at i:1614884 original size:22 final size:21
Alignment explanation
Indices: 1614859--1614915 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 21
1614849 TTATACAAGT
1614859 AGTATCGATACCCCTATGAAGG
1 AGTA-CGATACCCCTATGAAGG
*
1614881 AGTACTGATAACCCTATGAAGG
1 AGTAC-GATACCCCTATGAAGG
1614903 AGTACCGATACCC
1 AGTA-CGATACCC
1614916 ATACGCTCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (21 bp):
AGTACGATACCCCTATGAAGG
Found at i:1620524 original size:103 final size:103
Alignment explanation
Indices: 1620345--1620776 Score: 774
Period size: 103 Copynumber: 4.2 Consensus size: 103
1620335 GTCGAGGGTC
* * *
1620345 TATGTAGTCCTTCGGGACATATATTTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAAGTCTGGTGAGACACATAC
*
1620410 TTGATCCTTGGCATATGTATATGATTCTTAATGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1620448 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAATTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAAGTCTGGTGAGACACATAC
*
1620513 TTGATCCTTGGCATATGTATATGATTCTTAAGGACTGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
1620551 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCAAGTGTGAAGTCTGGTGAAACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAAGTCTGGTGAGACACATAC
*
1620616 TTGATCCTTGGCATATGTATATGATTCTTAAGGACTGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1620654 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAAGTCTGGTGAGACACATAC
*
1620719 TTGATCCCTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1620757 TATGTGGTCCTTCGGGACAT
1 TATGTGGTCCTTCGGGACAT
1620777 TATTATATGG
Statistics
Matches: 316, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 316 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1620819 original size:23 final size:23
Alignment explanation
Indices: 1620785--1620847 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
1620775 ATTATTATAT
*
1620785 GGCACTAC-GGTGCAATTGTACGC
1 GGCACT-CTGGTGCAATTCTACGC
*
1620808 GGCACTCTGGTGCAATTCTACGT
1 GGCACTCTGGTGCAATTCTACGC
1620831 GGCACT-TCGGTGCAATT
1 GGCACTCT-GGTGCAATT
1620848 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
22 2 0.06
23 34 0.94
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTCTGGTGCAATTCTACGC
Found at i:1626496 original size:103 final size:103
Alignment explanation
Indices: 1626317--1626645 Score: 613
Period size: 103 Copynumber: 3.2 Consensus size: 103
1626307 GTCGAGGGTC
*
1626317 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAAGTCTGGTGAGACACATAC
*
1626382 TTGATCCTTGGCATATGTATATGATTCTTATGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1626420 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAATTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAAGTCTGGTGAGACACATAC
1626485 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1626523 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAAGTCTGGTGAGACACATAC
*
1626588 TTGATCCCTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1626626 TATGTGGTCCTTCGGGACAT
1 TATGTGGTCCTTCGGGACAT
1626646 TATTATATGG
Statistics
Matches: 219, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 219 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAGCATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1626687 original size:23 final size:23
Alignment explanation
Indices: 1626654--1626716 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1626644 ATTATTATAT
1626654 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
1626677 GGCACTCCGGTACAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
1626700 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
1626717 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1629655 original size:18 final size:18
Alignment explanation
Indices: 1629634--1629668 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1629624 AATTAAAAAA
1629634 ATGTTTTTAATTTAATTG
1 ATGTTTTTAATTTAATTG
*
1629652 ATGTTTTTTATTTAATT
1 ATGTTTTTAATTTAATT
1629669 ACATTGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.66
Consensus pattern (18 bp):
ATGTTTTTAATTTAATTG
Found at i:1629678 original size:19 final size:18
Alignment explanation
Indices: 1629634--1629678 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1629624 AATTAAAAAA
*
1629634 ATGTTTTTAATTTAATTG
1 ATGTTTTTAATTTAATTC
*
1629652 ATGTTTTTTATTTAATTAC
1 ATGTTTTTAATTTAATT-C
1629671 ATTGTTTT
1 A-TGTTTT
1629679 CATGAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 16 0.70
19 1 0.04
20 6 0.26
ACGTcount: A:0.24, C:0.02, G:0.09, T:0.64
Consensus pattern (18 bp):
ATGTTTTTAATTTAATTC
Found at i:1632054 original size:24 final size:23
Alignment explanation
Indices: 1631981--1632059 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 23
1631971 ATCATGTTAG
1631981 GTATCGATACTACTTTGCA-TAGTA
1 GTATCGATACTAC--TGCACTAGTA
1632005 GTATCGATACTCACTAG-AC-A-TA
1 GTATCGATACT-ACT-GCACTAGTA
1632027 --ATCGATACTACTGCACGTAGTA
1 GTATCGATACTACTGCAC-TAGTA
1632049 GTATCGATACT
1 GTATCGATACT
1632060 CTAGGGACAA
Statistics
Matches: 46, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
18 1 0.02
19 5 0.11
20 9 0.20
21 1 0.02
22 4 0.09
23 3 0.07
24 21 0.46
25 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (23 bp):
GTATCGATACTACTGCACTAGTA
Found at i:1632075 original size:44 final size:41
Alignment explanation
Indices: 1631982--1632079 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 41
1631972 TCATGTTAGG
1631982 TATCGATACTACTTTGCATAGTAGTATCGATACTCACTAGACA
1 TATCGATACTAC-TTGCATAGTAGTATCGATACT-ACTAGACA
1632025 TAATCGATACTAC-TGCACGTAGTAGTATCGATACT-CTAGGGACAA
1 T-ATCGATACTACTTGCA--TAGTAGTATCGATACTACTA--GAC-A
1632070 TATCGATACT
1 TATCGATACT
1632080 GTTGGTTTGC
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
42 7 0.14
43 1 0.02
44 39 0.80
45 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (41 bp):
TATCGATACTACTTGCATAGTAGTATCGATACTACTAGACA
Found at i:1633211 original size:9 final size:9
Alignment explanation
Indices: 1633197--1633234 Score: 76
Period size: 9 Copynumber: 4.2 Consensus size: 9
1633187 ATTGAATTTA
1633197 TTCAAAGTT
1 TTCAAAGTT
1633206 TTCAAAGTT
1 TTCAAAGTT
1633215 TTCAAAGTT
1 TTCAAAGTT
1633224 TTCAAAGTT
1 TTCAAAGTT
1633233 TT
1 TT
1633235 AAAAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (9 bp):
TTCAAAGTT
Found at i:1639622 original size:31 final size:31
Alignment explanation
Indices: 1639569--1639972 Score: 201
Period size: 30 Copynumber: 13.5 Consensus size: 31
1639559 ATAATTTATG
1639569 TATCTTAACTTTAAAAAATATATTTCTATTTT
1 TATCTTAACTTTAAAAAATATATTT-TATTTT
** *
1639601 TATCTTAA-TTTATTAAATATATTTTATTAT
1 TATCTTAACTTTAAAAAATATATTTTATTTT
* ** * *
1639631 CAAATTAA--TTAAAAATATATATATTATTCT
1 TATCTTAACTTTAAAAA-ATATATTTTATTTT
* * **
1639661 TAT-TTTAGTTTAAAAATATATATTTTTATTAG
1 TATCTTAACTTTAAAAA-ATATA-TTTTATTTT
*
1639693 TATC-TAAC-TT-AAAAATATATTTTA-TCT
1 TATCTTAACTTTAAAAAATATATTTTATTTT
* * *
1639720 CATCTTAACTTTTAAAAATATACTTTTATTAT
1 TATCTTAACTTTAAAAAATATA-TTTTATTTT
* * * * * *
1639752 CATTTTAACTTTTAAAAATGTATTGTATTCT
1 TATCTTAACTTTAAAAAATATATTTTATTTT
* ** *
1639783 TA-CTTTAA-ATTATTAAATATATTTTATTTA
1 TATC-TTAACTTTAAAAAATATATTTTATTTT
* * * * *
1639813 TATATTTAC-TT--AAAAGATA-TTTAATCT
1 TATCTTAACTTTAAAAAATATATTTTATTTT
* * * *
1639840 TATTTTAA-TTTAAACAATATACTTTATTAT
1 TATCTTAACTTTAAAAAATATATTTTATTTT
*
1639870 TATCTTAAC-TTAAAAATATATATTTTATTCT
1 TATCTTAACTTTAAAAA-ATATATTTTATTTT
* *
1639901 TATTTTAAC-TT-AAACATGCATATTTTA----
1 TATCTTAACTTTAAAAAAT--ATATTTTATTTT
*
1639928 T-TCTTAA-ATTAAAAAATATATTTTATTTT
1 TATCTTAACTTTAAAAAATATATTTTATTTT
1639957 TATCTTAA-TTTAAAAA
1 TATCTTAACTTTAAAAA
1639973 TAACTTTAAT
Statistics
Matches: 286, Mismatches: 58, Indels: 58
0.71 0.14 0.14
Matches are distributed among these distances:
25 8 0.03
26 7 0.02
27 23 0.08
28 15 0.05
29 24 0.08
30 92 0.32
31 76 0.27
32 41 0.14
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (31 bp):
TATCTTAACTTTAAAAAATATATTTTATTTT
Found at i:1639709 original size:62 final size:58
Alignment explanation
Indices: 1639582--1639972 Score: 241
Period size: 62 Copynumber: 6.6 Consensus size: 58
1639572 CTTAACTTTA
* * **
1639582 AAAAATATATTTCTATTTTTATCTTAATTTATTAAATATA-TTTTATTATCAAAT-TAA-TT
1 AAAAATATATTT-TATTCTTATTTTAATTTAAAAAATATATTTTTATTAT---ATCTAACTT
*
1639641 AAAAATATATATATTATTCTTATTTTAGTTTAAAAATATATATTTTTATTAGTATCTAACTT
1 AAAAATATAT-T-TTATTCTTATTTTAATTTAAAAA-ATATATTTTTATTA-TATCTAACTT
* * * * *
1639703 AAAAATATATTTTA-TCTCATCTTAACTTTTAAAAATATACTTTTATTATCATTTTAACTTTT
1 AAAAATATATTTTATTCTTATTTTAA-TTTAAAAAATATATTTTTATTAT-A-TCTAAC--TT
* * * * ** * *
1639765 AAAAATGTATTGTATTCTTACTTTAAATTATTAAATATA-TTTTATTTATATATTTACTT
1 AAAAATATATTTTATTCTTATTTTAATTTAAAAAATATATTTTTA-TTATAT-CTAACTT
* * * *
1639824 -AAAAGATA-TTTAATCTTATTTTAATTTAAACAATATA-CTTTATTATTATCTTAACTT
1 AAAAATATATTTTATTCTTATTTTAATTTAAAAAATATATTTTTATTA-TATC-TAACTT
* * * *
1639881 AAAAATATATATTTTATTCTTATTTTAACTT-AAACATGCATA-TTTTA-T-TCT-TAAATT
1 -AAAA-ATATATTTTATTCTTATTTTAATTTAAAAAAT--ATATTTTTATTATATCTAACTT
* *
1639938 AAAAAATATATTTTATTTTTATCTTAATTTAAAAA
1 -AAAAATATATTTTATTCTTATTTTAATTTAAAAA
1639973 TAACTTTAAT
Statistics
Matches: 263, Mismatches: 45, Indels: 50
0.73 0.13 0.14
Matches are distributed among these distances:
56 25 0.10
57 47 0.18
58 7 0.03
59 39 0.15
60 44 0.17
61 38 0.14
62 54 0.21
63 9 0.03
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.52
Consensus pattern (58 bp):
AAAAATATATTTTATTCTTATTTTAATTTAAAAAATATATTTTTATTATATCTAACTT
Found at i:1639737 original size:30 final size:31
Alignment explanation
Indices: 1639570--1639780 Score: 138
Period size: 32 Copynumber: 6.9 Consensus size: 31
1639560 TAATTTATGT
* * *
1639570 ATCTTAACTTTAAAAAATATATTTCTATTTTT
1 ATCTTAACTTTTAAAAATATATTT-TATTATC
*
1639602 ATCTTAA--TTTATTAAATATATTTTATTATC
1 ATCTTAACTTTTA-AAAATATATTTTATTATC
** * *
1639632 AAATTAA---TTAAAAATATATATATTATTCTT
1 ATCTTAACTTTTAAAAATATAT-T-TTATTATC
* * *
1639662 AT-TTTAGTTTAAAAATATATATTTTTATTAGT-
1 ATCTTAACTTTTAAAA-ATATA-TTTTATTA-TC
*
1639694 ATC-TAAC--TTAAAAATATATTTTA-TCTC
1 ATCTTAACTTTTAAAAATATATTTTATTATC
1639721 ATCTTAACTTTTAAAAATATACTTTTATTATC
1 ATCTTAACTTTTAAAAATATA-TTTTATTATC
* * *
1639753 ATTTTAACTTTTAAAAATGTATTGTATT
1 ATCTTAACTTTTAAAAATATATTTTATT
1639781 CTTACTTTAA
Statistics
Matches: 142, Mismatches: 21, Indels: 33
0.72 0.11 0.17
Matches are distributed among these distances:
26 1 0.01
27 4 0.03
28 17 0.12
29 12 0.08
30 36 0.25
31 21 0.15
32 43 0.30
33 7 0.05
34 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (31 bp):
ATCTTAACTTTTAAAAATATATTTTATTATC
Found at i:1639841 original size:57 final size:56
Alignment explanation
Indices: 1639731--1639888 Score: 135
Period size: 57 Copynumber: 2.7 Consensus size: 56
1639721 ATCTTAACTT
* * *
1639731 TTAAA-AATATACTTTTATTATCATTTTAACTTTTAAAAATGTATTGTATTCTTACTTTAAA
1 TTAAACAATATAC-TTTATTATTATCTTAAC--TTAAAAA--TATT-TAATCTTACTTTAAA
* * * *
1639792 TTATTA-AATATATTTTATTTATATAT-TT-ACTTAAAAGATATTTAATCTTATTTTAAT
1 TTA-AACAATATACTTTA-TTAT-TATCTTAACTTAAAA-ATATTTAATCTTACTTTAAA
1639849 TTAAACAATATACTTTATTATTATCTTAACTTAAAAATAT
1 TTAAACAATATACTTTATTATTATCTTAACTTAAAAATAT
1639889 ATATTTTATT
Statistics
Matches: 82, Mismatches: 8, Indels: 19
0.75 0.07 0.17
Matches are distributed among these distances:
55 3 0.04
56 11 0.13
57 33 0.40
58 4 0.05
59 6 0.07
60 1 0.01
61 9 0.11
62 13 0.16
63 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (56 bp):
TTAAACAATATACTTTATTATTATCTTAACTTAAAAATATTTAATCTTACTTTAAA
Found at i:1639954 original size:56 final size:57
Alignment explanation
Indices: 1639864--1639970 Score: 155
Period size: 56 Copynumber: 1.9 Consensus size: 57
1639854 CAATATACTT
* *
1639864 TATTATTATCTTAACTTAAAAATATATATTTTATTCTTATTTTAACTTAAACATGCA
1 TATTATTATCTTAAATTAAAAATATATATTTTATTCTTATCTTAACTTAAACATGCA
* *
1639921 TATT-TTATTCTTAAATTAAAAA-ATATATTTTATTTTTATCTTAATTTAAA
1 TATTATTA-TCTTAAATTAAAAATATATATTTTATTCTTATCTTAACTTAAA
1639971 AATAACTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
56 28 0.62
57 17 0.38
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (57 bp):
TATTATTATCTTAAATTAAAAATATATATTTTATTCTTATCTTAACTTAAACATGCA
Found at i:1639964 original size:25 final size:26
Alignment explanation
Indices: 1639864--1639964 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 26
1639854 CAATATACTT
* *
1639864 TATTATTA-TCTTAACTTAAAAATATA
1 TATT-TTATTCTTATCTTAAAAACATA
*
1639890 TATTTTATTCTTATTTTAACTTAAACATGCA
1 TATTTTATTCTTATCTTAA---AAACAT--A
**
1639921 TATTTTATTCTTAAATTAAAAA-ATA
1 TATTTTATTCTTATCTTAAAAACATA
*
1639946 TATTTTATTTTTATCTTAA
1 TATTTTATTCTTATCTTAA
1639965 TTTAAAAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
25 20 0.33
26 13 0.21
27 2 0.03
28 3 0.05
29 5 0.08
31 18 0.30
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (26 bp):
TATTTTATTCTTATCTTAAAAACATA
Found at i:1640049 original size:32 final size:31
Alignment explanation
Indices: 1639980--1640079 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 31
1639970 AAATAACTTT
*
1639980 AATATATATTTAATAAGTTAAAATAAGAACA
1 AATATATATTTAATAAGTTAAAATAAGAAAA
**
1640011 AA-ATATATTTAATAAGTTAATGTAAGAATAA
1 AATATATATTTAATAAGTTAAAATAAGAA-AA
* * *
1640042 AATATATATTTGGAATAGATTTAAATTAAGACAA
1 AATATATATTT--AATA-AGTTAAAATAAGAAAA
1640076 AATA
1 AATA
1640080 AAATAGATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
30 24 0.42
31 5 0.09
32 8 0.14
34 10 0.18
35 10 0.18
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (31 bp):
AATATATATTTAATAAGTTAAAATAAGAAAA
Found at i:1640120 original size:29 final size:29
Alignment explanation
Indices: 1640061--1640203 Score: 132
Period size: 29 Copynumber: 4.9 Consensus size: 29
1640051 TTGGAATAGA
* *
1640061 TTTAAA-TTAAGACAAAATAAAATAGATT
1 TTTAAATTTAAGATAAAATAAAATATATT
*
1640089 TTTAAAATTTAAGATAGAATAAAATATATT
1 TTT-AAATTTAAGATAAAATAAAATATATT
* *
1640119 TTTAAGTTATAATA-AAAATAAAATATATT
1 TTTAAATT-TAAGATAAAATAAAATATATT
*
1640148 TTT-AAGTTAAGATAATAATAAAATAAGTATT
1 TTTAAATTTAAGATAA-AATAAAAT-A-TATT
* *
1640179 TTTAAA-TTAAAATAATAATGAAATA
1 TTTAAATTTAAGATAA-AATAAAATA
1640204 ATCAAGTATA
Statistics
Matches: 96, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
27 4 0.04
28 7 0.07
29 32 0.33
30 28 0.29
31 23 0.24
32 2 0.02
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (29 bp):
TTTAAATTTAAGATAAAATAAAATATATT
Found at i:1640203 original size:60 final size:57
Alignment explanation
Indices: 1640061--1640203 Score: 153
Period size: 60 Copynumber: 2.4 Consensus size: 57
1640051 TTGGAATAGA
* * *
1640061 TTTAAATTAAGACAAAATAAAATAGATTTTTAAAATTTAAGATAGAATAAAATATATT
1 TTTAAATTAAAATAAAATAAAATAGATTTTT-AAAGTTAAGATAGAATAAAATATATT
* * * *
1640119 TTTAAGTTATAATAAAAATAAAATATATTTTT-AAGTTAAGATAATAATAAAATAAGTATT
1 TTTAAATTAAAAT-AAAATAAAATAGATTTTTAAAGTTAAGAT-AGAATAAAAT-A-TATT
*
1640179 TTTAAATTAAAATAATAATGAAATA
1 TTTAAATTAAAATAA-AATAAAATA
1640204 ATCAAGTATA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
57 9 0.13
58 18 0.26
59 20 0.29
60 23 0.33
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (57 bp):
TTTAAATTAAAATAAAATAAAATAGATTTTTAAAGTTAAGATAGAATAAAATATATT
Found at i:1644225 original size:107 final size:107
Alignment explanation
Indices: 1644026--1644248 Score: 315
Period size: 107 Copynumber: 2.1 Consensus size: 107
1644016 TCGTTGAACC
* *
1644026 AAACAATTACGTATCACTAAATCTATTCTAATAACACGAGTGATCATCTTGTTCACTGATAGTAC
1 AAACAATTACATATCACTAAATCTATTCTAATAACACGAGTGATCATCTTGCTCACTGATAGTAC
*
1644091 ATAAAATAATATATCGTCAGTCCATATCGGTATTTCACTCAT
66 ATAAAATAATATATCGTCAGTCCATATCGATATTTCACTCAT
*
1644133 AAACAATTACATATCACTAAATC-AGTTCTAATAACACGAGTGATCATCTTGCTCACTGATAGTG
1 AAACAATTACATATCACTAAATCTA-TTCTAATAACACGAGTGATCATCTTGCTCACTGATAGTA
* * * * * *
1644197 CATAAAGTTATATA-CAGTCATTCGATATCGATATTTCATTCGT
65 CATAAAATAATATATC-GTCAGTCCATATCGATATTTCACTCAT
*
1644240 AAAAAATTA
1 AAACAATTA
1644249 AACCAACCAA
Statistics
Matches: 103, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
106 2 0.02
107 101 0.98
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (107 bp):
AAACAATTACATATCACTAAATCTATTCTAATAACACGAGTGATCATCTTGCTCACTGATAGTAC
ATAAAATAATATATCGTCAGTCCATATCGATATTTCACTCAT
Found at i:1645054 original size:20 final size:20
Alignment explanation
Indices: 1645023--1645077 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1645013 TATATTATTT
*
1645023 AATTATTA-AAAATATAGTA
1 AATTATTATAAAATATAATA
1645042 AATTATTATAAAATATAATA
1 AATTATTATAAAATATAATA
*
1645062 AATGATTAT-AAATATA
1 AATTATTATAAAATATA
1645078 TCATTATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (20 bp):
AATTATTATAAAATATAATA
Found at i:1648765 original size:20 final size:20
Alignment explanation
Indices: 1648736--1648796 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
1648726 TTATGAATAG
*
1648736 TACC-ATACTGAATGAACAA
1 TACCGATACTGTATGAACAA
* *
1648755 TACTGATACTGTATGAATAA
1 TACCGATACTGTATGAACAA
*
1648775 TACCGATACTGTGTGAACAA
1 TACCGATACTGTATGAACAA
1648795 TA
1 TA
1648797 ATGAACAGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
19 3 0.09
20 32 0.91
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (20 bp):
TACCGATACTGTATGAACAA
Done.