Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007938.1 Hibiscus syriacus cultivar Beakdansim tig00110348_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: 2808856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:1086352 original size:13 final size:13
Alignment explanation
Indices: 1086334--1086363 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1086324 AGGTGAATGG
1086334 CTTTATAAAGATT
1 CTTTATAAAGATT
1086347 CTTTATAAAGATT
1 CTTTATAAAGATT
1086360 CTTT
1 CTTT
1086364 CTCGTGCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (13 bp):
CTTTATAAAGATT
Found at i:1088353 original size:183 final size:183
Alignment explanation
Indices: 1088045--1088413 Score: 738
Period size: 183 Copynumber: 2.0 Consensus size: 183
1088035 AGAGTGACCA
1088045 AATAGATAGTTTACCCTAAATAAAAATATGTATGAATATGATAAGAAACTTAATATATATTGCTC
1 AATAGATAGTTTACCCTAAATAAAAATATGTATGAATATGATAAGAAACTTAATATATATTGCTC
1088110 TAATTAATATATTTTTATATATTTAATCTAATTATAATGTAATTGTTACTATAAATTAAAAAAAT
66 TAATTAATATATTTTTATATATTTAATCTAATTATAATGTAATTGTTACTATAAATTAAAAAAAT
1088175 ATATTTATTATATTAGATAAATTTTTTATTATATTTACATTAACCCAACCCAT
131 ATATTTATTATATTAGATAAATTTTTTATTATATTTACATTAACCCAACCCAT
1088228 AATAGATAGTTTACCCTAAATAAAAATATGTATGAATATGATAAGAAACTTAATATATATTGCTC
1 AATAGATAGTTTACCCTAAATAAAAATATGTATGAATATGATAAGAAACTTAATATATATTGCTC
1088293 TAATTAATATATTTTTATATATTTAATCTAATTATAATGTAATTGTTACTATAAATTAAAAAAAT
66 TAATTAATATATTTTTATATATTTAATCTAATTATAATGTAATTGTTACTATAAATTAAAAAAAT
1088358 ATATTTATTATATTAGATAAATTTTTTATTATATTTACATTAACCCAACCCAT
131 ATATTTATTATATTAGATAAATTTTTTATTATATTTACATTAACCCAACCCAT
1088411 AAT
1 AAT
1088414 TTTTTTTTGA
Statistics
Matches: 186, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 186 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (183 bp):
AATAGATAGTTTACCCTAAATAAAAATATGTATGAATATGATAAGAAACTTAATATATATTGCTC
TAATTAATATATTTTTATATATTTAATCTAATTATAATGTAATTGTTACTATAAATTAAAAAAAT
ATATTTATTATATTAGATAAATTTTTTATTATATTTACATTAACCCAACCCAT
Found at i:1094199 original size:110 final size:110
Alignment explanation
Indices: 1094006--1094229 Score: 439
Period size: 110 Copynumber: 2.0 Consensus size: 110
1093996 GCGAACTGTA
1094006 AGCAAGACTTGCTGCTTCCATAGCAGGAAGTTCATTTCATCAAGAACAACGTTGACCTTCATGTT
1 AGCAAGACTTGCTGCTTCCATAGCAGGAAGTTCATTTCATCAAGAACAACGTTGACCTTCATGTT
1094071 GGTGAAGGATTTGCCAGCGTTGACAGAGAGCTCCATTGCAAACAC
66 GGTGAAGGATTTGCCAGCGTTGACAGAGAGCTCCATTGCAAACAC
*
1094116 AGCAAGACTTGCTGCTTCCATAGCAGGAAGTTCATTTCATCAAGAACAATGTTGACCTTCATGTT
1 AGCAAGACTTGCTGCTTCCATAGCAGGAAGTTCATTTCATCAAGAACAACGTTGACCTTCATGTT
1094181 GGTGAAGGATTTGCCAGCGTTGACAGAGAGCTCCATTGCAAACAC
66 GGTGAAGGATTTGCCAGCGTTGACAGAGAGCTCCATTGCAAACAC
1094226 AGCA
1 AGCA
1094230 CGAGCAGGAA
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 113 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.25
Consensus pattern (110 bp):
AGCAAGACTTGCTGCTTCCATAGCAGGAAGTTCATTTCATCAAGAACAACGTTGACCTTCATGTT
GGTGAAGGATTTGCCAGCGTTGACAGAGAGCTCCATTGCAAACAC
Found at i:1094434 original size:24 final size:24
Alignment explanation
Indices: 1094407--1094476 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
1094397 ACAGCTATGA
*
1094407 ATAACTGAATCCTTATTACTTATC
1 ATAACTAAATCCTTATTACTTATC
1094431 ATAACTAAATCCTTATTACTTATC
1 ATAACTAAATCCTTATTACTTATC
* *
1094455 ATAAATAAATCCTTACTACTTA
1 ATAACTAAATCCTTATTACTTA
1094477 CTAACTGCGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.39, C:0.20, G:0.01, T:0.40
Consensus pattern (24 bp):
ATAACTAAATCCTTATTACTTATC
Found at i:1094650 original size:79 final size:79
Alignment explanation
Indices: 1094554--1094699 Score: 247
Period size: 79 Copynumber: 1.8 Consensus size: 79
1094544 ACAAGATGCT
* *
1094554 ATCAATGGAAACACCCTTTTGTGTCTTTAATGAAGAGATAACTTTAGGTCCTTTTTTATGTCTTA
1 ATCAATGGAAACACCCTTTTGTGTCTTTAATGAAGAGATAACCTTAGGTCCTTTTTTACGTCTTA
1094619 TGAATGTCGATGTC
66 TGAATGTCGATGTC
* * *
1094633 ATCAATGGGAACACCCTTTTGTGTCTTTAATGAAGTGATAACCTTAGGTCTTTTTTTACGTCTTA
1 ATCAATGGAAACACCCTTTTGTGTCTTTAATGAAGAGATAACCTTAGGTCCTTTTTTACGTCTTA
1094698 TG
66 TG
1094700 TCTAGTTTCA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 62 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (79 bp):
ATCAATGGAAACACCCTTTTGTGTCTTTAATGAAGAGATAACCTTAGGTCCTTTTTTACGTCTTA
TGAATGTCGATGTC
Found at i:1101698 original size:19 final size:19
Alignment explanation
Indices: 1101674--1101717 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1101664 ATTAAAATAT
*
1101674 TTTAAAACTT-AAATATCAA
1 TTTAAAACTTGAAAGAT-AA
*
1101693 TTTAAAATTTGAAAGATAA
1 TTTAAAACTTGAAAGATAA
1101712 TTTAAA
1 TTTAAA
1101718 GACATTTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (19 bp):
TTTAAAACTTGAAAGATAA
Found at i:1102126 original size:16 final size:16
Alignment explanation
Indices: 1102105--1102137 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1102095 TAATAAATAA
1102105 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1102121 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1102137 A
1 A
1102138 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1102254 original size:26 final size:26
Alignment explanation
Indices: 1102225--1102275 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1102215 AAACGAACAC
*
1102225 GAACATAAACGA-ACACGAACATAAAT
1 GAACATAAAC-ATAAACGAACATAAAT
*
1102251 GAACATGAACATAAACGAACATAAA
1 GAACATAAACATAAACGAACATAAA
1102276 CGTTGGAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.59, C:0.18, G:0.12, T:0.12
Consensus pattern (26 bp):
GAACATAAACATAAACGAACATAAAT
Found at i:1102272 original size:16 final size:16
Alignment explanation
Indices: 1102207--1102271 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
1102197 TAATAAATAA
*
1102207 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
1102223 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1102239 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
1102255 ATGAACATAAACGAAC
1 ACGAACATAAACGAAC
1102271 A
1 A
1102272 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1103392 original size:24 final size:23
Alignment explanation
Indices: 1103365--1103437 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 23
1103355 ATAAATGAAT
1103365 GAACATAAGCGAACATAACCGAAC
1 GAACATAA-CGAACATAACCGAAC
*
1103389 GAACATAAACGAACATAACCGAATA
1 GAACAT-AACGAACATAACCGAA-C
* **
1103414 TAACCGAACGAACATAACCGAAC
1 GAACATAACGAACATAACCGAAC
1103437 G
1 G
1103438 TTCACGAACG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
24 36 0.88
25 5 0.12
ACGTcount: A:0.51, C:0.25, G:0.15, T:0.10
Consensus pattern (23 bp):
GAACATAACGAACATAACCGAAC
Found at i:1103406 original size:34 final size:34
Alignment explanation
Indices: 1103365--1103436 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
1103355 ATAAATGAAT
*
1103365 GAACATAAGCGAACATAACCGAACGAACATAAAC
1 GAACATAACCGAACATAACCGAACGAACATAAAC
* *
1103399 GAACATAACCGAATATAACCGAACGAACATAACC
1 GAACATAACCGAACATAACCGAACGAACATAAAC
1103433 GAAC
1 GAAC
1103437 GTTCACGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.25, G:0.14, T:0.10
Consensus pattern (34 bp):
GAACATAACCGAACATAACCGAACGAACATAAAC
Found at i:1103436 original size:10 final size:10
Alignment explanation
Indices: 1103365--1103422 Score: 53
Period size: 10 Copynumber: 5.4 Consensus size: 10
1103355 ATAAATGAAT
*
1103365 GAACATAAGC
1 GAACATAACC
1103375 GAACATAACCGAAC
1 GAACATAA-C---C
*
1103389 GAACATAAAC
1 GAACATAACC
1103399 GAACATAACC
1 GAACATAACC
*
1103409 GAATATAACC
1 GAACATAACC
1103419 GAAC
1 GAAC
1103423 GAACATAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 30 0.77
14 9 0.23
ACGTcount: A:0.52, C:0.24, G:0.14, T:0.10
Consensus pattern (10 bp):
GAACATAACC
Found at i:1103445 original size:24 final size:24
Alignment explanation
Indices: 1103374--1103447 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
1103364 TGAACATAAG
** **
1103374 CGAACATAACCGAACGAACATAAA
1 CGAACATAACCGAACGTTCACGAA
*
1103398 CGAACATAACCGAA--TATAACCGAA
1 CGAACATAACCGAACGT-TCA-CGAA
1103422 CGAACATAACCGAACGTTCACGAA
1 CGAACATAACCGAACGTTCACGAA
1103446 CG
1 CG
1103448 TAAATGAACG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
23 1 0.03
24 36 0.90
25 2 0.05
26 1 0.03
ACGTcount: A:0.47, C:0.27, G:0.15, T:0.11
Consensus pattern (24 bp):
CGAACATAACCGAACGTTCACGAA
Found at i:1103652 original size:17 final size:17
Alignment explanation
Indices: 1103630--1103673 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
1103620 TGCGTATAAA
1103630 ATTTTAAAAATTATTTT
1 ATTTTAAAAATTATTTT
1103647 ATTTTAAAAATTATTTT
1 ATTTTAAAAATTATTTT
1103664 ATTTTAAAAA
1 ATTTTAAAAA
1103674 AATAATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAAAAATTATTTT
Found at i:1104143 original size:16 final size:16
Alignment explanation
Indices: 1104119--1104155 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1104109 AAATTTAAAA
*
1104119 TTATAAAATTAATTTT
1 TTATAAAATTAAATTT
*
1104135 TTATTAAATTAAATTT
1 TTATAAAATTAAATTT
1104151 TTATA
1 TTATA
1104156 TTCAGATTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATAAAATTAAATTT
Found at i:1104279 original size:16 final size:17
Alignment explanation
Indices: 1104254--1104287 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1104244 CTATTTTAGG
1104254 TATCCAAAATTTTCGGA
1 TATCCAAAATTTTCGGA
*
1104271 TATCC-AAATTTTTGGA
1 TATCCAAAATTTTCGGA
1104287 T
1 T
1104288 CGGATCGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (17 bp):
TATCCAAAATTTTCGGA
Found at i:1104668 original size:20 final size:19
Alignment explanation
Indices: 1104644--1104689 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1104634 TTTTAAAGTA
*
1104644 TTAAAATATA-AAATAAAA
1 TTAAAATATACAAATAAAT
*
1104662 TTATAAATTTACAAATAAAT
1 TTA-AAATATACAAATAAAT
1104682 TTAAAATA
1 TTAAAATA
1104690 ATGTAGGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 3 0.13
19 10 0.43
20 10 0.43
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAAAATATACAAATAAAT
Found at i:1105511 original size:27 final size:27
Alignment explanation
Indices: 1105480--1105571 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
1105470 TTATTTTTAT
1105480 ATTAATATTTAATTAATAATGAATTAA
1 ATTAATATTTAATTAATAATGAATTAA
*
1105507 ATTAATATTTAATTAATAAT--ACT-A
1 ATTAATATTTAATTAATAATGAATTAA
*
1105531 A--AACA--T-ATT-ATAATGAATTAA
1 ATTAATATTTAATTAATAATGAATTAA
1105552 ATTAATATTTAATTAATAAT
1 ATTAATATTTAATTAATAAT
1105572 ACTATTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
18 5 0.10
19 3 0.06
20 3 0.06
21 2 0.04
22 3 0.06
23 3 0.06
24 2 0.04
25 3 0.06
26 3 0.06
27 25 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (27 bp):
ATTAATATTTAATTAATAATGAATTAA
Found at i:1105519 original size:20 final size:20
Alignment explanation
Indices: 1105496--1105564 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 20
1105486 ATTTAATTAA
1105496 TAATGAATTAAATTAATATT
1 TAATGAATTAAATTAATATT
* *
1105516 TAATTAA-TAATACTAAAACATATT
1 TAATGAATTAA-A-T--TA-ATATT
1105540 ATAATGAATTAAATTAATATT
1 -TAATGAATTAAATTAATATT
1105561 TAAT
1 TAAT
1105565 TAATAATACT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 3 0.08
20 11 0.29
21 6 0.16
22 1 0.03
23 1 0.03
24 6 0.16
25 7 0.18
26 3 0.08
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
TAATGAATTAAATTAATATT
Found at i:1105567 original size:16 final size:16
Alignment explanation
Indices: 1105490--1105558 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 16
1105480 ATTAATATTT
1105490 AATTAATAATGAATTA
1 AATTAATAATGAATTA
* *
1105506 AATTAATATTTAATT-
1 AATTAATAATGAATTA
* * **
1105521 AA-TAATACTAAAACA
1 AATTAATAATGAATTA
*
1105536 TATT-ATAATGAATTA
1 AATTAATAATGAATTA
1105551 AATTAATA
1 AATTAATA
1105559 TTTAATTAAT
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
14 8 0.21
15 13 0.34
16 17 0.45
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
AATTAATAATGAATTA
Found at i:1108456 original size:3 final size:3
Alignment explanation
Indices: 1108448--1108484 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1108438 GTCCGGGTCT
*
1108448 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1108485 AATACAAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1111466 original size:17 final size:16
Alignment explanation
Indices: 1111439--1111484 Score: 74
Period size: 17 Copynumber: 2.8 Consensus size: 16
1111429 TGAAATAAAT
1111439 CATTTTGGGTAGAAAG
1 CATTTTGGGTAGAAAG
1111455 CATTTCTGGGTAGAAAG
1 CATTT-TGGGTAGAAAG
1111472 CATTTTTGGGTAG
1 CA-TTTTGGGTAG
1111485 GAATGTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.18
17 20 0.71
18 3 0.11
ACGTcount: A:0.26, C:0.09, G:0.30, T:0.35
Consensus pattern (16 bp):
CATTTTGGGTAGAAAG
Found at i:1115324 original size:37 final size:36
Alignment explanation
Indices: 1115258--1115376 Score: 132
Period size: 36 Copynumber: 3.3 Consensus size: 36
1115248 GTCTCGCTAA
* *
1115258 AGACAATTTTTCTTAAAAACAAA-TCTGTCTTGCTTG
1 AGACATTTTTTC-TAAAAACAAATTTTGTCTTGCTTG
*
1115294 AGACAGTTTTTTCTAAAAACAAATTTTGTCTCGCTTG
1 AGACA-TTTTTTCTAAAAACAAATTTTGTCTTGCTTG
* * * * **
1115331 AGACAATTTCTCTCAACACAAATTTCATCTTGCTTG
1 AGACATTTTTTCTAAAAACAAATTTTGTCTTGCTTG
1115367 AGACATTTTT
1 AGACATTTTT
1115377 CCTTTGAGAT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
36 47 0.68
37 22 0.32
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (36 bp):
AGACATTTTTTCTAAAAACAAATTTTGTCTTGCTTG
Found at i:1115647 original size:31 final size:31
Alignment explanation
Indices: 1115510--1115656 Score: 93
Period size: 31 Copynumber: 4.5 Consensus size: 31
1115500 AACTTTGGAA
* * * *
1115510 ATTGTTTCACTTGAAACATAAAACCTTTAAG
1 ATTGTTTCTCTTGAAACGTAAAATCTTTGAG
*
1115541 ATTGTTTCTCTTGAAACGTAAGAAT-ATTGAG
1 ATTGTTTCTCTTGAAACGTAA-AATCTTTGAG
* *
1115572 ATTGTTTCAT-TTGAAGC-AAAAATTTGTCTCTCTTGAG
1 ATTGTTTC-TCTTGAAACGTAAAA------TCT-TTGAG
**
1115609 ACAGTTTCTCTTGAAACGTAAAATCTTTGAG
1 ATTGTTTCTCTTGAAACGTAAAATCTTTGAG
* *
1115640 ATTGTTTCCCTCGAAAC
1 ATTGTTTCTCTTGAAAC
1115657 AAATTTTGTC
Statistics
Matches: 88, Mismatches: 16, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
29 2 0.02
30 2 0.02
31 55 0.62
32 6 0.07
35 1 0.01
36 1 0.01
37 17 0.19
38 4 0.05
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (31 bp):
ATTGTTTCTCTTGAAACGTAAAATCTTTGAG
Found at i:1115705 original size:68 final size:66
Alignment explanation
Indices: 1115544--1115826 Score: 295
Period size: 68 Copynumber: 4.2 Consensus size: 66
1115534 CTTTAAGATT
* * * * *
1115544 GTTTCTCTTGAAACGTAAGAAT-ATTGAGATTGTTTCATTTGAAGCAAAAATTTGTCTCT-CTTG
1 GTTTCTCTTGAAAC--AAAAATCTTTGAGATTGTTTCCTTTGAAAC-AAATTTTGTCT-TGCTTG
1115607 AGACA
62 AGACA
* * *
1115612 GTTTCTCTTGAAACGTAAAATCTTTGAGATTGTTTCCCTCGAAACAAATTTTGTCTTGCTTGAGA
1 GTTTCTCTTGAAAC-AAAAATCTTTGAGATTGTTTCCTTTGAAACAAATTTTGTCTTGCTTGAGA
*
1115677 CT
65 CA
* * * *
1115679 GTTTGTCTTGAAACAAAAAAATCTTTGAGTTTGTTTCCTTTGAAACAAAGTTTGT-TTCTCTTGA
1 GTTTCTCTTGAAAC--AAAAATCTTTGAGATTGTTTCCTTTGAAACAAATTTTGTCTT-GCTTGA
1115743 GACA
63 GACA
* * *
1115747 GTTTCTCTTGAAACAAAAATCTTTGAG-TCTGTTTCCATTGAAACAAGTTTTGTCTCGCTTGAGA
1 GTTTCTCTTGAAACAAAAATCTTTGAGAT-TGTTTCCTTTGAAACAAATTTTGTCTTGCTTGAGA
**
1115811 TG
65 CA
1115813 GTTTCTCTTGAAAC
1 GTTTCTCTTGAAAC
1115827 CATTATCCCT
Statistics
Matches: 182, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
65 1 0.01
66 56 0.31
67 38 0.21
68 87 0.48
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Consensus pattern (66 bp):
GTTTCTCTTGAAACAAAAATCTTTGAGATTGTTTCCTTTGAAACAAATTTTGTCTTGCTTGAGAC
A
Found at i:1115799 original size:66 final size:66
Alignment explanation
Indices: 1115594--1115826 Score: 281
Period size: 66 Copynumber: 3.5 Consensus size: 66
1115584 GAAGCAAAAA
* ** * *
1115594 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACGTAAAATCTTTGAGATTGTTTCCCTCGAAACAA
1 TTTGTCTCGCTTGAGACAGTTTCTCTTGAAACAAAAAATCTTTGAG-TTGTTTCCATTGAAACAA
*
1115659 AT
65 GT
* * * *
1115661 TTTGTCTTGCTTGAGACTGTTTGTCTTGAAACAAAAAAATCTTTGAGTTTGTTTCCTTTGAAACA
1 TTTGTCTCGCTTGAGACAGTTTCTCTTGAAAC-AAAAAATCTTTGAG-TTGTTTCCATTGAAAC-
1115726 AAG-
63 AAGT
* *
1115729 TTTGTTTCTCTTGAGACAGTTTCTCTTGAAAC-AAAAATCTTTGAGTCTGTTTCCATTGAAACAA
1 TTTGTCTCGCTTGAGACAGTTTCTCTTGAAACAAAAAATCTTTGAGT-TGTTTCCATTGAAACAA
1115793 GT
65 GT
**
1115795 TTTGTCTCGCTTGAGATGGTTTCTCTTGAAAC
1 TTTGTCTCGCTTGAGACAGTTTCTCTTGAAAC
1115827 CATTATCCCT
Statistics
Matches: 142, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
65 4 0.03
66 55 0.39
67 28 0.20
68 53 0.37
69 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (66 bp):
TTTGTCTCGCTTGAGACAGTTTCTCTTGAAACAAAAAATCTTTGAGTTGTTTCCATTGAAACAAG
T
Found at i:1121176 original size:30 final size:30
Alignment explanation
Indices: 1121064--1121158 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
1121054 TGTGGCATCA
* * *
1121064 CACGTGGATATGTC-CGTCAGTATTTAGTC
1 CACGTGCATATGCCACGTCAGCATTTAGTC
* * * *
1121093 TACGTGAATCTGCCATGTCAGCATTTAGTC
1 CACGTGCATATGCCACGTCAGCATTTAGTC
*
1121123 CACGTGCATATGCCACATCAGCATTTAGTC
1 CACGTGCATATGCCACGTCAGCATTTAGTC
1121153 CACGTG
1 CACGTG
1121159 GATTTGTTGC
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
29 10 0.19
30 44 0.81
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (30 bp):
CACGTGCATATGCCACGTCAGCATTTAGTC
Found at i:1122004 original size:23 final size:23
Alignment explanation
Indices: 1121971--1122036 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
1121961 TGCCACATAT
*
1121971 TTGTCCTGAAGAACCACATAGGA
1 TTGTCCCGAAGAACCACATAGGA
**
1121994 TTGTCCCGAAGAACCACATAGTT
1 TTGTCCCGAAGAACCACATAGGA
*
1122017 TTGTCCCGAAGGACCACATA
1 TTGTCCCGAAGAACCACATA
1122037 TAACCCTCGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.23
Consensus pattern (23 bp):
TTGTCCCGAAGAACCACATAGGA
Found at i:1130711 original size:8 final size:8
Alignment explanation
Indices: 1130692--1130729 Score: 67
Period size: 8 Copynumber: 4.6 Consensus size: 8
1130682 ACAAGTTGAA
1130692 TTTTGTTTG
1 TTTTG-TTG
1130701 TTTTGTTG
1 TTTTGTTG
1130709 TTTTGTTG
1 TTTTGTTG
1130717 TTTTGTTG
1 TTTTGTTG
1130725 TTTTG
1 TTTTG
1130730 CATGTGATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 24 0.83
9 5 0.17
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (8 bp):
TTTTGTTG
Found at i:1131169 original size:15 final size:15
Alignment explanation
Indices: 1131149--1131179 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1131139 TCGAGGTTAA
1131149 ATGGACATTCGATTT
1 ATGGACATTCGATTT
*
1131164 ATGGACATTTGATTT
1 ATGGACATTCGATTT
1131179 A
1 A
1131180 ATTTGGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (15 bp):
ATGGACATTCGATTT
Found at i:1136211 original size:32 final size:31
Alignment explanation
Indices: 1136175--1136234 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
1136165 ATAGAAAATT
*
1136175 TAATTAA-ATTATTATTATAATAATCAATATGA
1 TAATTAATA-TATTATTATAA-AATAAATATGA
*
1136207 TAATTAATATATTTTTATAAAATAAATA
1 TAATTAATATATTATTATAAAATAAATA
1136235 AACTTAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 7 0.28
32 17 0.68
33 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (31 bp):
TAATTAATATATTATTATAAAATAAATATGA
Found at i:1138127 original size:4 final size:4
Alignment explanation
Indices: 1138118--1138146 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1138108 AATATAGTAC
1138118 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1138147 GTTTTATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1138639 original size:16 final size:16
Alignment explanation
Indices: 1138620--1138652 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1138610 TTTATAAAAA
*
1138620 TATAAAAATATATATT
1 TATAAAAAAATATATT
1138636 TATAAAAAAATATATT
1 TATAAAAAAATATATT
1138652 T
1 T
1138653 TCTTGGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAAAAAAATATATT
Found at i:1142405 original size:24 final size:26
Alignment explanation
Indices: 1142369--1142416 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
1142359 TCATTCATAA
*
1142369 AAAAAAGATAAAAAAAGAT-AAAAGG
1 AAAAAAGAGAAAAAAAGATGAAAAGG
1142394 AAAAAAG-GAAAAAAAGATGAAAA
1 AAAAAAGAGAAAAAAAGATGAAAA
1142417 AAAAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (26 bp):
AAAAAAGAGAAAAAAAGATGAAAAGG
Found at i:1142434 original size:20 final size:20
Alignment explanation
Indices: 1142368--1142428 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
1142358 CTCATTCATA
1142368 AAAAAAAGAT--AAAAAAAG
1 AAAAAAAGATGAAAAAAAAG
* *
1142386 -ATAAAAG--G-AAAAAAGG
1 AAAAAAAGATGAAAAAAAAG
1142402 AAAAAAAGATGAAAAAAAAG
1 AAAAAAAGATGAAAAAAAAG
1142422 AAAAAAA
1 AAAAAAA
1142429 ATTGAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 7 0.21
17 12 0.35
19 1 0.03
20 14 0.41
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAAAAGATGAAAAAAAAG
Found at i:1143852 original size:75 final size:75
Alignment explanation
Indices: 1143729--1143909 Score: 245
Period size: 75 Copynumber: 2.4 Consensus size: 75
1143719 CATCAACAAG
* * * *
1143729 AAGCAAAGGTTGGGGCATGCTAAAAGCCAATTTTAATCAGAAATAGGAATCTTGACGCATTTTGA
1 AAGCAAAGGTTGGGGCATACTGAAAGCCCATTTCAATCAGAAATAGGAATCTTGACGCATTTTGA
*
1143794 ACATTCATAT
66 ACATTCATAC
* * * *
1143804 AAGCAAATGTTGGGGCACACTGAAAGCCCATTTCAATCAGAAATAGGAATGTTGACTCATTTTGA
1 AAGCAAAGGTTGGGGCATACTGAAAGCCCATTTCAATCAGAAATAGGAATCTTGACGCATTTTGA
* *
1143869 ACGTTCGTAC
66 ACATTCATAC
* *
1143879 CAGCAAAGGTTGGGGCATACTGAAGGCCCAT
1 AAGCAAAGGTTGGGGCATACTGAAAGCCCAT
1143910 ATCATCTTAT
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 91 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (75 bp):
AAGCAAAGGTTGGGGCATACTGAAAGCCCATTTCAATCAGAAATAGGAATCTTGACGCATTTTGA
ACATTCATAC
Found at i:1144201 original size:54 final size:54
Alignment explanation
Indices: 1144097--1144208 Score: 125
Period size: 54 Copynumber: 2.1 Consensus size: 54
1144087 CAATTATTGA
* * * * * * * *
1144097 GAACATCTGTGTAAAAACCATAAGAAGTGATGAATGTGTTTTTAAATGTTTTAT
1 GAACATCTATGCAAAAACCACAAGAAATGATGAATGTATTGTCAAATGTTTTAC
* * *
1144151 GAACATCTATGCAGAAACCACAAGAAATGATTAATGTATTGTCAATTGTTTTAC
1 GAACATCTATGCAAAAACCACAAGAAATGATGAATGTATTGTCAAATGTTTTAC
1144205 GAAC
1 GAAC
1144209 CAGTTATTAT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (54 bp):
GAACATCTATGCAAAAACCACAAGAAATGATGAATGTATTGTCAAATGTTTTAC
Found at i:1145412 original size:73 final size:73
Alignment explanation
Indices: 1145293--1145682 Score: 586
Period size: 73 Copynumber: 5.3 Consensus size: 73
1145283 TCAAATAAAT
* * * *
1145293 TTTATCTCATTTGAGAATGTTTTTCTTAAAAAAAACTGTTTCTCGTTGGAGAAAGTTTCACTCGA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGTTGGAGAAAGTTTCACTCGA
1145358 AATAGCAA
66 AATAGCAA
*
1145366 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTATTTCTCGTTGGAGAAAGTTTCACTCGA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGTTGGAGAAAGTTTCACTCGA
1145431 AATAGCAA
66 AATAGCAA
* * *
1145439 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGTTGTTTCTCGCTGGAGAAAGTTTCACTTGA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGTTGGAGAAAGTTTCACTCGA
*
1145504 AATAACAA
66 AATAGCAA
* * *
1145512 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGTTGTTTCTCGCTGGAGAAAGTTTCACTTGA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGTTGGAGAAAGTTTCACTCGA
1145577 AATAGCAA
66 AATAGCAA
* *
1145585 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTGTCTCGCTT-GAGACAA-TTTCACTC
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCG-TTGGAGA-AAGTTTCACTC
* *
1145648 GAAACAGAAA
64 GAAATAGCAA
* *
1145658 TTTATCTCACTCGAGATAGTTTTTC
1 TTTATCTCACTTGAGATTGTTTTTC
1145683 CCAAAGCAAA
Statistics
Matches: 295, Mismatches: 20, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
73 292 0.99
74 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (73 bp):
TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGTTGGAGAAAGTTTCACTCGA
AATAGCAA
Found at i:1146049 original size:122 final size:122
Alignment explanation
Indices: 1145829--1146159 Score: 545
Period size: 122 Copynumber: 2.7 Consensus size: 122
1145819 CACTCGATGG
* * *
1145829 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAGGAGCTCATAATGAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAA
* * *
1145894 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGTAGATATATCATC
66 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAAC
* *
1145951 ATTAACATTTCCAGAGGAGCTCATAATGAGAAGAACTCATTTGAAGAAGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAGGAGCTCATAATGAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAA
*
1146016 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACATAAGGAGATAGATCAAC
66 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAAC
* *
1146073 ATCAACATTTCCAGAGGAGCTCATAATGAGAAGAAGTCATTTGAAGAGGAATAAGAAGTTCATAA
1 ATCAACATTTCCAGAGGAGCTCATAATGAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAA
* *
1146138 TAAGAAGAACTTGTTCGACCTT
66 TGAGAAGAACTTGTTCAACCTT
1146160 AGCTTGATTC
Statistics
Matches: 194, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 194 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (122 bp):
ATCAACATTTCCAGAGGAGCTCATAATGAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAAC
Found at i:1146252 original size:139 final size:134
Alignment explanation
Indices: 1146073--1146432 Score: 429
Period size: 134 Copynumber: 2.6 Consensus size: 134
1146063 ATAGATCAAC
* * *
1146073 ATCAACATTTCCAGAGGAGCTCATAATGAGAAGAAGTCATTTGAAGAGGAATAAGAAGTTCATAA
1 ATCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAA
* * * *
1146138 TAAGAAGAACTTGTTCGACCTTAGCTTGATTCATCATC-TATGGAGTTGAATGAAAGAAGAACCT
66 TGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCA-CATATGAAGTTG-A-G--AGAA-AACCT
1146202 CACTTGA-GG
125 CACTTGAGGG
* * *
1146211 ATCAACATTTCCAGAGGAATTTCATGACGAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAGG-AGTTCATAATGAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATA
* * ** ** **
1146276 ATGAGAAGAACTTATTCAACCTTATCTTAATTCATCACATATGAAGTTGAGTTAACTCCTCTTTT
65 ATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGAAGTTGAGAGAAAACCTCACTT
1146341 GAGGG
130 GAGGG
* * *
1146346 A-CATCATTTGCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAG-AGGAGTTCATAATGAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATA
*
1146410 ATGAGAATAACTTGTTCAACCTT
65 ATGAGAAGAACTTGTTCAACCTT
1146433 TTGCCAGATT
Statistics
Matches: 192, Mismatches: 26, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
134 82 0.43
135 8 0.04
137 1 0.01
138 19 0.10
139 82 0.43
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (134 bp):
ATCAACATTTCCAGAGGAGTTCATAATGAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGAAGTTGAGAGAAAACCTCACTTG
AGGG
Found at i:1147817 original size:16 final size:17
Alignment explanation
Indices: 1147780--1147823 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1147770 AATTTCTATT
*
1147780 TTATTTCATTTTAGTCA
1 TTATTTAATTTTAGTCA
*
1147797 TTATTTAATTTT-GTTA
1 TTATTTAATTTTAGTCA
*
1147813 TTATTTTATTT
1 TTATTTAATTT
1147824 ATGAATATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (17 bp):
TTATTTAATTTTAGTCA
Found at i:1147937 original size:4 final size:4
Alignment explanation
Indices: 1147928--1147960 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1147918 AATATAGTAC
1147928 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1147961 GTTTTATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1148141 original size:2 final size:2
Alignment explanation
Indices: 1148134--1148160 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1148124 AAATAAATAA
1148134 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 A
1148161 CACTTCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1148211 original size:17 final size:17
Alignment explanation
Indices: 1148189--1148227 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1148179 TTTAAGAAAA
1148189 AATA-TTATATTATTCTT
1 AATATTTAT-TTATTCTT
*
1148206 AATATTTATTTATTTTT
1 AATATTTATTTATTCTT
1148223 AATAT
1 AATAT
1148228 CAAAGAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
AATATTTATTTATTCTT
Found at i:1148389 original size:144 final size:143
Alignment explanation
Indices: 1148195--1148453 Score: 369
Period size: 144 Copynumber: 1.8 Consensus size: 143
1148185 AAAAAATATT
* * * *
1148195 ATATTATTCTTAATATTTATTTATTTTTAATATCAAAGAAATGAGTTGTCTTAAAGCAACTAGAT
1 ATATTATTATTAATATTTATTTATTTTTAATATCAAAGAAAGGAGGTGTCTTAAAGCAACTAGAA
* * * *
1148260 GTCATTTTATGATATTTTTAAATAACTAAATATCCTACTTTTATAAATTATATATATTAATTTAA
66 GTCATTTTATGATATTTCTAAATAAATAAATATCATA--TTTATAAAATATATATATTAATTTAA
1148325 TTTATTTTTAGAGAA
129 TTTATTTTTAGAGAA
* *
1148340 ATATT-TTATTAATATTTATTTATTTTTTAATAT-TAAGAAAGGGGGTGTCTTAAAGCAACTAGA
1 ATATTATTATTAATATTTATTTA-TTTTTAATATCAAAGAAAGGAGGTGTCTTAAAGCAACTAGA
* *
1148403 AGTCATTTTCTGATATTTCTAAGTAAATAAATATCATATTTATAAAATATA
65 AGTCATTTTATGATATTTCTAAATAAATAAATATCATATTTATAAAATATA
1148454 AAAAAAATAT
Statistics
Matches: 101, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
142 12 0.12
144 74 0.73
145 15 0.15
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (143 bp):
ATATTATTATTAATATTTATTTATTTTTAATATCAAAGAAAGGAGGTGTCTTAAAGCAACTAGAA
GTCATTTTATGATATTTCTAAATAAATAAATATCATATTTATAAAATATATATATTAATTTAATT
TATTTTTAGAGAA
Found at i:1150284 original size:22 final size:22
Alignment explanation
Indices: 1150258--1150322 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 22
1150248 AATTTTTTTC
1150258 TTAT-TTTTTAAAATAAAATT-
1 TTATATTTTTAAAATAAAATTA
*
1150278 TTATA-TTTTAAAATTAAATTA
1 TTATATTTTTAAAATAAAATTA
* *
1150299 TTTTCATTTTAAAAATAAAATTA
1 TTAT-ATTTTTAAAATAAAATTA
1150322 T
1 T
1150323 ATTAAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 18 0.49
21 3 0.08
22 1 0.03
23 15 0.41
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATATTTTTAAAATAAAATTA
Found at i:1154722 original size:29 final size:30
Alignment explanation
Indices: 1154655--1154728 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
1154645 GGAGGGCTAG
* *
1154655 AAACCGGTTTGACCGGTTTTTAACTAGTTC
1 AAACCGGTTTGACCGGTTTTCAACCAGTTC
** *
1154685 TGACCGGTTTGACCGG-TTTCGACCAGTTC
1 AAACCGGTTTGACCGGTTTTCAACCAGTTC
1154714 AAACCGGTTTGACCG
1 AAACCGGTTTGACCG
1154729 ATATGACCCG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (30 bp):
AAACCGGTTTGACCGGTTTTCAACCAGTTC
Found at i:1154746 original size:19 final size:18
Alignment explanation
Indices: 1154724--1154777 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
1154714 AAACCGGTTT
1154724 GACCGATATGACCCGACCC
1 GACCGAT-TGACCCGACCC
*
1154743 GACCCGACTGACCCGACCC
1 GA-CCGATTGACCCGACCC
*
1154762 AACCG-TTGACCCGACC
1 GACCGATTGACCCGACC
1154778 GTTGACCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 10 0.32
18 3 0.10
19 14 0.45
20 4 0.13
ACGTcount: A:0.24, C:0.46, G:0.20, T:0.09
Consensus pattern (18 bp):
GACCGATTGACCCGACCC
Found at i:1160551 original size:27 final size:27
Alignment explanation
Indices: 1160521--1160576 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1160511 TAAATTAATT
1160521 AAAATATGATTTAATTATTCTGAAATA
1 AAAATATGATTTAATTATTCTGAAATA
* * *
1160548 AAAATCTTATTTAATTATTCTGAATTA
1 AAAATATGATTTAATTATTCTGAAATA
1160575 AA
1 AA
1160577 TATTCATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (27 bp):
AAAATATGATTTAATTATTCTGAAATA
Found at i:1165072 original size:20 final size:20
Alignment explanation
Indices: 1165049--1165086 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1165039 CTTAAGAAAA
*
1165049 AGTATCGATACTCGGGGCTT
1 AGTATCGATACTCAGGGCTT
1165069 AGTATCGATACTCAGGGC
1 AGTATCGATACTCAGGGC
1165087 CTTGATCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
AGTATCGATACTCAGGGCTT
Found at i:1165390 original size:20 final size:21
Alignment explanation
Indices: 1165340--1165393 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
1165330 TACTTGGGGA
*
1165340 AGTATCGATACCACATGGGGG
1 AGTATCGATACCACATGGAGG
1165361 AGTA-CTGATACC-CA-GAGAGG
1 AGTATC-GATACCACATG-GAGG
1165381 AGTATCGATACCA
1 AGTATCGATACCA
1165394 TTGTGAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 1 0.04
20 16 0.57
21 11 0.39
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (21 bp):
AGTATCGATACCACATGGAGG
Found at i:1175465 original size:23 final size:23
Alignment explanation
Indices: 1175439--1175487 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
1175429 ATAAAGAACC
1175439 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAATAT-CCATT
*
1175462 AAAATAAAGTCTAAATATCCATT
1 AAAATAAACTCTAAATATCCATT
1175485 AAA
1 AAA
1175488 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAACTCTAAATATCCATT
Found at i:1182465 original size:119 final size:116
Alignment explanation
Indices: 1182341--1182558 Score: 303
Period size: 119 Copynumber: 1.9 Consensus size: 116
1182331 GTTTGTATGA
*
1182341 AATTTGACCATTTAAATTAAAACAAAAGTATAGAGTAGTGTAATTTAGCCATG-CCTATTAAAAC
1 AATTTGACCATTTAAATTAAAACAAAAGTATAGAGTAGTGTAATTTAGCCATGTCC-ACTAAAAC
* *
1182405 AAAAAACATACATTTGTCTAAAATCTAAATGGGAGAAATTATGGGGGGGTTTACG
65 -AAAAACAT-CATTTG-CTAAAATATAAATGAGAGAAATTATGGGGGGGTTTACG
* * * * *
1182460 AATTTGACCATTTACATTAAAACAAAATTATGGGGTAGTGTAATTTAGCCATGTCCACTAAAACC
1 AATTTGACCATTTAAATTAAAACAAAAGTATAGAGTAGTGTAATTTAGCCATGTCCACTAAAACA
* *
1182525 GAAACATTATTTGCTAAAATATAAATGAGAGAAA
66 AAAACATCATTTGCTAAAATATAAATGAGAGAAA
1182559 CTATAGAGGG
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
116 19 0.22
117 5 0.06
118 6 0.07
119 56 0.64
120 2 0.02
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (116 bp):
AATTTGACCATTTAAATTAAAACAAAAGTATAGAGTAGTGTAATTTAGCCATGTCCACTAAAACA
AAAACATCATTTGCTAAAATATAAATGAGAGAAATTATGGGGGGGTTTACG
Found at i:1189150 original size:20 final size:21
Alignment explanation
Indices: 1189122--1189161 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1189112 GACATATATT
1189122 TATCTAAAAGTTAATATTTAA
1 TATCTAAAAGTTAATATTTAA
1189143 TATC-AAAAGTTAATATTTA
1 TATCTAAAAGTTAATATTTA
1189162 TCGGTTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (21 bp):
TATCTAAAAGTTAATATTTAA
Found at i:1191658 original size:176 final size:177
Alignment explanation
Indices: 1191352--1191699 Score: 662
Period size: 176 Copynumber: 2.0 Consensus size: 177
1191342 TATTCAAAGG
*
1191352 AAAATCAGTTTTTAAGATACATAATACGACGTGGATCTGTCACTTGTGATGAGATGTGAATGTTT
1 AAAATCAATTTTTAAGATACATAATACGACGTGGATCTGTCACTTGTGATGAGATGTGAATGTTT
1191417 TTTTTTAAAGAAGCTACTAATTTTATTCAAAATAGAAAATATCTCAAATTATAGTGAATATTTAC
66 TTTTTTAAAGAAGCTACTAATTTTATTCAAAATAGAAAATATCTCAAATTATAGTGAATATTTAC
1191482 AATCATAATCGTAAATCTAAGATAATTTCTATAATCACTGAATATTT
131 AATCATAATCGTAAATCTAAGATAATTTCTATAATCACTGAATATTT
*
1191529 AAAATCAATTTTTAATATACATAATACGACGTGGATCTGTCACTTGTGATGAGATGTGAATG-TT
1 AAAATCAATTTTTAAGATACATAATACGACGTGGATCTGTCACTTGTGATGAGATGTGAATGTTT
1191593 TTTTTTAAAGAAGCTACTAATTTTATTCAAAATAGAAAATATCTCAAATTATAGTGAATATTTAC
66 TTTTTTAAAGAAGCTACTAATTTTATTCAAAATAGAAAATATCTCAAATTATAGTGAATATTTAC
*
1191658 AATCATAATCGTAAATCTAGGATAATTTCTATAATCACTGAA
131 AATCATAATCGTAAATCTAAGATAATTTCTATAATCACTGAA
1191700 ATAAAACTAG
Statistics
Matches: 168, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
176 108 0.64
177 60 0.36
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.37
Consensus pattern (177 bp):
AAAATCAATTTTTAAGATACATAATACGACGTGGATCTGTCACTTGTGATGAGATGTGAATGTTT
TTTTTTAAAGAAGCTACTAATTTTATTCAAAATAGAAAATATCTCAAATTATAGTGAATATTTAC
AATCATAATCGTAAATCTAAGATAATTTCTATAATCACTGAATATTT
Found at i:1192082 original size:23 final size:23
Alignment explanation
Indices: 1192052--1192119 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
1192042 ACCAAAAAAC
1192052 AGAAGAAAATATGTTATAAAGGT
1 AGAAGAAAATATGTTATAAAGGT
*** *
1192075 AGAAGAAAGCGTGTCT-TAAAGAT
1 AGAAGAAAATATGT-TATAAAGGT
* *
1192098 AGACGAAAATATGTCATAAAGG
1 AGAAGAAAATATGTTATAAAGG
1192120 CAAACTTGTT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.24, T:0.22
Consensus pattern (23 bp):
AGAAGAAAATATGTTATAAAGGT
Found at i:1193290 original size:34 final size:34
Alignment explanation
Indices: 1193244--1193318 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
1193234 ATTATATATA
* *
1193244 AACTAAAATGTTGAAAATAAATATACATAAAATT
1 AACTTAAATGTTGAAAATAAAAATACATAAAATT
1193278 AACTTAAATGTTGAAAATAAAAATACATAAAATT
1 AACTTAAATGTTGAAAATAAAAATACATAAAATT
1193312 AACTTAA
1 AACTTAA
1193319 GTATTAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (34 bp):
AACTTAAATGTTGAAAATAAAAATACATAAAATT
Found at i:1194348 original size:30 final size:28
Alignment explanation
Indices: 1194305--1194360 Score: 94
Period size: 30 Copynumber: 1.9 Consensus size: 28
1194295 TAAAGTTATA
1194305 AAATTTTAAATTAAATCAAACTTAATTT
1 AAATTTTAAATTAAATCAAACTTAATTT
1194333 AAATTTCTAAAATTAAATCAAACTTAAT
1 AAATTT-T-AAATTAAATCAAACTTAAT
1194361 GATACTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 6 0.23
29 1 0.04
30 19 0.73
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (28 bp):
AAATTTTAAATTAAATCAAACTTAATTT
Found at i:1194582 original size:73 final size:73
Alignment explanation
Indices: 1194463--1194608 Score: 274
Period size: 73 Copynumber: 2.0 Consensus size: 73
1194453 TTAGCTCTGA
*
1194463 ATGTAACATGTTGTTTGATAGTGACTCTGAATCATTCAAAATGTACTTATGTGCTGAATCATTCA
1 ATGTAACATGCTGTTTGATAGTGACTCTGAATCATTCAAAATGTACTTATGTGCTGAATCATTCA
1194528 GTACTGTT
66 GTACTGTT
*
1194536 ATGTAACATGCTGTTTGATAGTGGCTCTGAATCATTCAAAATGTACTTATGTGCTGAATCATTCA
1 ATGTAACATGCTGTTTGATAGTGACTCTGAATCATTCAAAATGTACTTATGTGCTGAATCATTCA
1194601 GTACTGTT
66 GTACTGTT
1194609 TTGCTGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.39
Consensus pattern (73 bp):
ATGTAACATGCTGTTTGATAGTGACTCTGAATCATTCAAAATGTACTTATGTGCTGAATCATTCA
GTACTGTT
Found at i:1194651 original size:23 final size:23
Alignment explanation
Indices: 1194587--1194652 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
1194577 TGTACTTATG
*
1194587 TGCTGAATCATTCAGTACTGTTT
1 TGCTGAATCATTCAGCACTGTTT
*
1194610 TGCTGAATCATTCAACACTGTTT
1 TGCTGAATCATTCAGCACTGTTT
*
1194633 TGTTGAATCAGTT-AGCACTG
1 TGCTGAATCA-TTCAGCACTG
1194653 AATCATTCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 36 0.95
24 2 0.05
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (23 bp):
TGCTGAATCATTCAGCACTGTTT
Found at i:1202541 original size:35 final size:37
Alignment explanation
Indices: 1202469--1202541 Score: 87
Period size: 40 Copynumber: 1.9 Consensus size: 37
1202459 TCGTTTATTT
* *
1202469 ATTAAATGAACGAACATGAACAAGATTTTGCGTTCGTTTA
1 ATTAAATGAACGAACACGAACAAGA---TGCGCTCGTTTA
1202509 ATTAAATGAACGAACACGAACAA-A-GCGCTCGTT
1 ATTAAATGAACGAACACGAACAAGATGCGCTCGTT
1202542 CGTTCATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 8 0.26
39 1 0.03
40 22 0.71
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (37 bp):
ATTAAATGAACGAACACGAACAAGATGCGCTCGTTTA
Found at i:1202884 original size:10 final size:10
Alignment explanation
Indices: 1202869--1202933 Score: 58
Period size: 10 Copynumber: 6.1 Consensus size: 10
1202859 TAGTTTATTG
1202869 TGTTCGTTTA
1 TGTTCGTTTA
1202879 TGTTCGTTTATA
1 TGTTCG-TT-TA
*
1202891 TTCGTTCGTTTG
1 -T-GTTCGTTTA
*
1202903 TGTTCATTTA
1 TGTTCGTTTA
* *
1202913 CGTACGTTTA
1 TGTTCGTTTA
1202923 TGTTCGTTTA
1 TGTTCGTTTA
1202933 T
1 T
1202934 CATTTAAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
10 29 0.67
11 3 0.07
12 3 0.07
13 3 0.07
14 5 0.12
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.57
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:1202920 original size:24 final size:24
Alignment explanation
Indices: 1202870--1202920 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1202860 AGTTTATTGT
* * *
1202870 GTTCGTTTATGTTCGTTTATATTC
1 GTTCGTTTATGTTCATTTACATAC
* *
1202894 GTTCGTTTGTGTTCATTTACGTAC
1 GTTCGTTTATGTTCATTTACATAC
1202918 GTT
1 GTT
1202921 TATGTTCGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.14, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTTACATAC
Found at i:1202921 original size:34 final size:34
Alignment explanation
Indices: 1202866--1202930 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
1202856 TGTTAGTTTA
* * *
1202866 TTGTGTTCGTTTATGTTCGTTTATATTCGTTCGT
1 TTGTGTTCATTTACGTACGTTTATATTCGTTCGT
*
1202900 TTGTGTTCATTTACGTACGTTTATGTTCGTT
1 TTGTGTTCATTTACGTACGTTTATATTCGTT
1202931 TATCATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.11, C:0.12, G:0.20, T:0.57
Consensus pattern (34 bp):
TTGTGTTCATTTACGTACGTTTATATTCGTTCGT
Found at i:1203468 original size:9 final size:8
Alignment explanation
Indices: 1203446--1203470 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1203436 AATAATTATT
1203446 AATTTTTA
1 AATTTTTA
1203454 AATTTTTA
1 AATTTTTA
1203462 AATTTTTA
1 AATTTTTA
1203470 A
1 A
1203471 TAGATAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
AATTTTTA
Found at i:1203832 original size:17 final size:17
Alignment explanation
Indices: 1203801--1203833 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1203791 AAATAATATT
1203801 TTATTATTTATTTTAAA
1 TTATTATTTATTTTAAA
1203818 TTATT-TTTATATTTAA
1 TTATTATTTAT-TTTAA
1203834 TAATATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATTTATTTTAAA
Found at i:1203861 original size:3 final size:3
Alignment explanation
Indices: 1203853--1203881 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1203843 AAAATGTCAT
1203853 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1203882 TCATAGTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1204724 original size:20 final size:20
Alignment explanation
Indices: 1204699--1204755 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1204689 ATTTTGGCTC
* *
1204699 AAATGATCAATCTCCTAGCA
1 AAATGATCGATCTCCTAACA
* *
1204719 AAATGATCGATCTCTTTAACC
1 AAATGATCGATCTC-CTAACA
1204740 AAATGATCGATCTCCT
1 AAATGATCGATCTCCT
1204756 TGAAAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.30
Consensus pattern (20 bp):
AAATGATCGATCTCCTAACA
Found at i:1204755 original size:41 final size:40
Alignment explanation
Indices: 1204698--1204775 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
1204688 AATTTTGGCT
* *
1204698 CAAATGATCAATCTCCTAGCAAAATGATCGATCTCTTTAAC
1 CAAATGATCAATCTCCTAGAAAAAAGATCGAT-TCTTTAAC
* *
1204739 CAAATGATCGATCTCCTTGAAAAAAGATCGATTCTTT
1 CAAATGATCAATCTCCTAGAAAAAAGATCGATTCTTT
1204776 GAATTCCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.31
Consensus pattern (40 bp):
CAAATGATCAATCTCCTAGAAAAAAGATCGATTCTTTAAC
Found at i:1204769 original size:20 final size:20
Alignment explanation
Indices: 1204699--1204770 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1204689 ATTTTGGCTC
* * *
1204699 AAATGATCAATCTCCTAGCA
1 AAATGATCGATCTCCTTGAA
*
1204719 AAATGATCGATCT-CTTTAA
1 AAATGATCGATCTCCTTGAA
1204738 CCAAATGATCGATCTCCTTGAA
1 --AAATGATCGATCTCCTTGAA
*
1204760 AAAAGATCGAT
1 AAATGATCGAT
1204771 TCTTTGAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 22 0.51
21 13 0.30
22 5 0.12
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (20 bp):
AAATGATCGATCTCCTTGAA
Found at i:1204819 original size:21 final size:21
Alignment explanation
Indices: 1204793--1204844 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1204783 AAAAACTTTT
1204793 GGATCGATCCCTTG-TACAAAA
1 GGATCGATCCCTTGAT-CAAAA
*
1204814 GGATCGATCCCTTGATGAAAA
1 GGATCGATCCCTTGATCAAAA
*
1204835 GGATAGATCC
1 GGATCGATCC
1204845 ATTCCCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (21 bp):
GGATCGATCCCTTGATCAAAA
Found at i:1212447 original size:32 final size:32
Alignment explanation
Indices: 1212411--1212489 Score: 133
Period size: 31 Copynumber: 2.5 Consensus size: 32
1212401 ATCGTGCACA
*
1212411 TCATCTTCAATCTCTTACTTTGGACACTACTT
1 TCATCTTCAATCTCTTACTTTAGACACTACTT
1212443 TCATCTTCAATCTC-TACTTTAGACACTACTT
1 TCATCTTCAATCTCTTACTTTAGACACTACTT
*
1212474 TTATCTTCAATCTCTT
1 TCATCTTCAATCTCTT
1212490 TCACAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 29 0.66
32 15 0.34
ACGTcount: A:0.23, C:0.28, G:0.04, T:0.46
Consensus pattern (32 bp):
TCATCTTCAATCTCTTACTTTAGACACTACTT
Found at i:1215375 original size:20 final size:20
Alignment explanation
Indices: 1215347--1215398 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1215337 AAGTATCAGA
*
1215347 AGTAACGATACTCACAAGGT
1 AGTATCGATACTCACAAGGT
1215367 AGTATCGATACTCACAAGGT
1 AGTATCGATACTCACAAGGT
1215387 AGTATCGATACT
1 AGTATCGATACT
1215399 GCCAGCATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (20 bp):
AGTATCGATACTCACAAGGT
Found at i:1215459 original size:18 final size:17
Alignment explanation
Indices: 1215432--1215466 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1215422 ATGCAAAAAT
*
1215432 GGTACTGATATCTAAAGG
1 GGTACCGATATC-AAAGG
1215450 GGTACCGATATCAAAGG
1 GGTACCGATATCAAAGG
1215467 TAATAGAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (17 bp):
GGTACCGATATCAAAGG
Found at i:1215566 original size:107 final size:107
Alignment explanation
Indices: 1215367--1215637 Score: 389
Period size: 107 Copynumber: 2.5 Consensus size: 107
1215357 CTCACAAGGT
*
1215367 AGTATCGATACTCACAAGGTAGTATCGATACTGCCAGCATTGCTCAAATTCCAGAATGCAAAAAT
1 AGTATCGATACTCACAAGGTAGTATCGATACTACCAGCATTGCTCAAATTCCAGAATGCAAAAAT
* * * * * *
1215432 GGTACTGATATCTAAAGGGGTACCGATATCAAAGGTAATAGA
66 GGTACCGATACCCAAAGAGATACCGATACCAAAGGTAATAGA
* * * *
1215474 AGTATTGATACTCACAAGTTAGCATCGATACTACCAGCATTGCTCAAATTCCATAATGCAAAAAT
1 AGTATCGATACTCACAAGGTAGTATCGATACTACCAGCATTGCTCAAATTCCAGAATGCAAAAAT
* * *
1215539 GGTACCGATACCCAAAGAGATATCGATACCAAATGTAATGGA
66 GGTACCGATACCCAAAGAGATACCGATACCAAAGGTAATAGA
* * *
1215581 AGTATCGATACTCACAAGGTAGTATCGATACTACCAACATTACTCAAATTCTAGAAT
1 AGTATCGATACTCACAAGGTAGTATCGATACTACCAGCATTGCTCAAATTCCAGAAT
1215638 AAAATATTAT
Statistics
Matches: 143, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
107 143 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (107 bp):
AGTATCGATACTCACAAGGTAGTATCGATACTACCAGCATTGCTCAAATTCCAGAATGCAAAAAT
GGTACCGATACCCAAAGAGATACCGATACCAAAGGTAATAGA
Found at i:1217021 original size:21 final size:21
Alignment explanation
Indices: 1216997--1217070 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
1216987 CGTCGCAAAT
1216997 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
1217018 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
1217038 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
1217059 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1217071 TTTCCATTTC
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:1217041 original size:41 final size:41
Alignment explanation
Indices: 1216996--1217094 Score: 198
Period size: 41 Copynumber: 2.4 Consensus size: 41
1216986 GCGTCGCAAA
1216996 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1217037 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1217078 TTCGCGTTGCGATAGTT
1 TTCGCGTTGCGATAGTT
1217095 ATGATAGTTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
Found at i:1217043 original size:20 final size:20
Alignment explanation
Indices: 1217018--1217090 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1217008 TAGTTGAAAA
1217018 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
1217038 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
1217059 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
1217079 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1217091 AGTTATGATA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:1217356 original size:21 final size:21
Alignment explanation
Indices: 1217269--1217356 Score: 90
Period size: 21 Copynumber: 4.2 Consensus size: 21
1217259 ACCATTTTTT
1217269 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * *
1217290 GAA-AATCGCAACGAC-AACTG
1 CAACTATCGCAACG-CGAAATG
** *
1217310 CAGACTATCGCAACGCGATTTT
1 CA-ACTATCGCAACGCGAAATG
1217332 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
1217353 CAAC
1 CAAC
1217357 GCGAATTTGC
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
20 14 0.27
21 25 0.48
22 13 0.25
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:1218860 original size:44 final size:44
Alignment explanation
Indices: 1218809--1218898 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
1218799 AATAGGTAAT
1218809 AACAATTATAATGTTAATGAACAACATATAAAAAATCTCACCAA
1 AACAATTATAATGTTAATGAACAACATATAAAAAATCTCACCAA
*
1218853 AACAATTATAATGTTAATGAACAACATATAAATAATCTCACCAA
1 AACAATTATAATGTTAATGAACAACATATAAAAAATCTCACCAA
1218897 AA
1 AA
1218899 ATATATCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.26
Consensus pattern (44 bp):
AACAATTATAATGTTAATGAACAACATATAAAAAATCTCACCAA
Found at i:1218887 original size:24 final size:24
Alignment explanation
Indices: 1218816--1218888 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
1218806 AATAACAATT
1218816 ATAATGTTAATGAACAACATATAA
1 ATAATGTTAATGAACAACATATAA
* * * ** *
1218840 AAAAT-CTCACCAA-AACA-AT-T
1 ATAATGTTAATGAACAACATATAA
1218860 ATAATGTTAATGAACAACATATAA
1 ATAATGTTAATGAACAACATATAA
1218884 ATAAT
1 ATAAT
1218889 CTCACCAAAA
Statistics
Matches: 33, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 4 0.12
21 6 0.18
22 8 0.24
23 6 0.18
24 9 0.27
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.27
Consensus pattern (24 bp):
ATAATGTTAATGAACAACATATAA
Found at i:1225065 original size:20 final size:21
Alignment explanation
Indices: 1225011--1225073 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1225001 GATTCCCCTG
1225011 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1225035 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1225055 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1225074 TGCACCAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1228846 original size:21 final size:21
Alignment explanation
Indices: 1228822--1228863 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1228812 GAGTTTTTTT
*
1228822 TCATTTTTCA-ATTTTGAAATA
1 TCATTTTT-ATATTTTAAAATA
1228843 TCATTTTTATATTTTAAAATA
1 TCATTTTTATATTTTAAAATA
1228864 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
TCATTTTTATATTTTAAAATA
Found at i:1231550 original size:20 final size:20
Alignment explanation
Indices: 1231525--1231587 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
1231515 ATTCGCAACA
*
1231525 CGATTACGTAAATCGTAATG
1 CGATTACGTAAATCGCAATG
1231545 CGATTACGTAAATCGCAATG
1 CGATTACGTAAATCGCAATG
*
1231565 CGATTACATAAATCGCAATG
1 CGATTACGTAAATCGCAATG
1231585 CGA
1 CGA
1231588 ATCTGACTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (20 bp):
CGATTACGTAAATCGCAATG
Found at i:1234929 original size:20 final size:19
Alignment explanation
Indices: 1234904--1234997 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 19
1234894 GACATTCATT
1234904 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAA-A
1234924 TGACTATCGCAACATG-GAAA
1 TGACTATCGCAAC--GCGAAA
* * *
1234944 TGACTATCGCAATGTGGAAT
1 TGACTATCGCAACG-CGAAA
1234964 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGC-GAAA
1234984 TGACTATCGCAACG
1 TGACTATCGCAACG
1234998 AGAGAATCGC
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
18 1 0.02
20 59 0.92
21 3 0.05
22 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (19 bp):
TGACTATCGCAACGCGAAA
Found at i:1234968 original size:40 final size:40
Alignment explanation
Indices: 1234904--1234997 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
1234894 GACATTCATT
*
1234904 TGACTATCGCAACGCGAATATGACTATCGCAACATGGAAA
1 TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
* * *
1234944 TGACTATCGCAATGTGGAAT-TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACG-CGAATATGACTATCGCAACACGGAAA
1234984 TGACTATCGCAACG
1 TGACTATCGCAACG
1234998 AGAGAATCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 44 0.92
41 4 0.08
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (40 bp):
TGACTATCGCAACGCGAATATGACTATCGCAACACGGAAA
Found at i:1235029 original size:19 final size:19
Alignment explanation
Indices: 1235002--1235100 Score: 93
Period size: 19 Copynumber: 5.4 Consensus size: 19
1234992 GCAACGAGAG
1235002 AATCGCAATGCAGAATGAA
1 AATCGCAATGCAGAATGAA
* *
1235021 AATCACAATGCAAAATGAA
1 AATCGCAATGCAGAATGAA
*
1235040 AATCGCAATG-TGAAATGAA
1 AATCGCAATGCAG-AATGAA
*
1235059 AATCGCAA--C-GAGTG--
1 AATCGCAATGCAGAATGAA
*
1235073 AATCGCAATGCGAAAATGAA
1 AATCGCAATGC-AGAATGAA
1235093 AATCGCAA
1 AATCGCAA
1235101 CGCGAAACTA
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
14 8 0.12
16 4 0.06
17 1 0.02
18 3 0.05
19 40 0.62
20 8 0.12
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCAGAATGAA
Found at i:1235174 original size:33 final size:34
Alignment explanation
Indices: 1235117--1235188 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
1235107 ACTAATTTCG
*
1235117 CGTTACGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* *
1235151 CGTTGCGATTTTCA-TTTCGCATTGCTATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1235184 CGTTG
1 CGTTG
1235189 TGATAGTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 22 0.63
34 13 0.37
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:1235199 original size:33 final size:33
Alignment explanation
Indices: 1235132--1235201 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1235122 CGATTTTCAT
**
1235132 TTTCGCATTGCGATTCACTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCACTCGTTGCGATAGTCA
* * *
1235165 TTTCGCATTGCTATTCTCTCGTTGTGATAGTCA
1 TTTCGCATTGCGATTCACTCGTTGCGATAGTCA
1235198 TTTC
1 TTTC
1235202 CACGTTGCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTCACTCGTTGCGATAGTCA
Found at i:1235394 original size:34 final size:34
Alignment explanation
Indices: 1235351--1235445 Score: 140
Period size: 32 Copynumber: 2.9 Consensus size: 34
1235341 ATTAGTTTCG
1235351 CGTTGCGATTTTCATTTTTGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTTGCATTGCGATTCACT
*
1235385 CGTTGCGATTTTCA--TTTGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTTGCATTGCGATTCACT
** *
1235417 CGTTGCGATAGTCATTTTTGCGTTGCGAT
1 CGTTGCGATTTTCATTTTTGCATTGCGAT
1235446 AGTCTGTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
32 29 0.53
34 26 0.47
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTTGCATTGCGATTCACT
Found at i:1235491 original size:233 final size:234
Alignment explanation
Indices: 1235083--1235550 Score: 816
Period size: 233 Copynumber: 2.0 Consensus size: 234
1235073 AATCGCAATG
1235083 CGAAAATGAAAATCGCAACGCGAAACTAATTTCGCGTTACGATTTTCATTTTCGCATTGCGATTC
1 CGAAAATGAAAATCGCAACGCGAAACTAATTTCGCGTTACGATTTTCATTTTCGCATTGCGATTC
* *
1235148 ACTCGTTGCGATTTTCATTTCGCATTGCTATTCTCTCGTTGTGATAGTCATTTCCACGTTGCGAT
66 ACTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCACGTTGCGAT
1235213 AGTCTGTTTTGCATTCAACATAATGCAGATTGAAATCAACAAATCAACTATTACA-TTCAATCAA
131 AGTCTGTTTTGCATTCAACATAATGCAGATTGAAATCAACAAATCAACTA-TACATTTCAATCAA
1235277 TTAAACAAGCAC-AATATATGTACACATCAATTAAACAAAT
195 TTAAACAAGCACAAATAT-TGTACACATCAATTAAACAAAT
* * * *
1235317 CGAAAATGAAAATCGCAACGCGAAATTAGTTTCGCGTTGCGATTTTCATTTTTGCATTGCGATTC
1 CGAAAATGAAAATCGCAACGCGAAACTAATTTCGCGTTACGATTTTCATTTTCGCATTGCGATTC
***
1235382 ACTCGTTGCGATTTTCATTT-GCATTGCGATTCTCTCGTTGCGATAGTCATTTTTGCGTTGCGAT
66 ACTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCACGTTGCGAT
1235446 AGTCTGTTTTGCATTCAACATAATGCAGATTGAAATCAACAAATCAACTATACATTTCAATCAAT
131 AGTCTGTTTTGCATTCAACATAATGCAGATTGAAATCAACAAATCAACTATACATTTCAATCAAT
1235511 TAAACAAGCACAAATATTGTACACATCAATTAAACAAAT
196 TAAACAAGCACAAATATTGTACACATCAATTAAACAAAT
1235550 C
1 C
1235551 AACATTTACA
Statistics
Matches: 223, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
232 4 0.02
233 133 0.60
234 86 0.39
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (234 bp):
CGAAAATGAAAATCGCAACGCGAAACTAATTTCGCGTTACGATTTTCATTTTCGCATTGCGATTC
ACTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCACGTTGCGAT
AGTCTGTTTTGCATTCAACATAATGCAGATTGAAATCAACAAATCAACTATACATTTCAATCAAT
TAAACAAGCACAAATATTGTACACATCAATTAAACAAAT
Found at i:1235563 original size:14 final size:14
Alignment explanation
Indices: 1235544--1235580 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1235534 CATCAATTAA
1235544 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1235558 ACAAATCATCTTTT
1 ACAAATCAACATTT
1235572 ACAAATCAA
1 ACAAATCAA
1235581 TTAAACATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1236978 original size:21 final size:22
Alignment explanation
Indices: 1236928--1237030 Score: 65
Period size: 21 Copynumber: 4.9 Consensus size: 22
1236918 AATGTTGGGA
* *
1236928 GGGACCTCTTCAAC-GATGACAG
1 GGGA-CTCTTGAACGGATGAGAG
* *
1236950 TGGCCTCTTGAACGG-TGAGAG
1 GGGACTCTTGAACGGATGAGAG
* *
1236971 GGGACTCTTG-AGGGATGATAG
1 GGGACTCTTGAACGGATGAGAG
* *
1236992 GGGCCTCTTGAAC-GAT-AGGG
1 GGGACTCTTGAACGGATGAGAG
*
1237012 GAGGCCTCTTGAAC-GATGA
1 G-GGACTCTTGAACGGATGA
1237031 CAGGTGAGTC
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
20 6 0.09
21 53 0.83
22 5 0.08
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (22 bp):
GGGACTCTTGAACGGATGAGAG
Found at i:1237021 original size:42 final size:42
Alignment explanation
Indices: 1236942--1237034 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1236932 CCTCTTCAAC
* *
1236942 GATGACAGTGGCCTCTTGAACGGTGAGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGAGAGGGGACTCTTGAGG
* * * **
1236984 GATGATAGGGGCCTCTTGAACGAT-AGGGGAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGATGAGAGG-GGACTCTTGAGG
1237026 GATGACAGG
1 GATGACAGG
1237035 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGAGAGGGGACTCTTGAGG
Found at i:1237536 original size:20 final size:20
Alignment explanation
Indices: 1237513--1237581 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
1237503 GAAACTTAAA
1237513 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1237533 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
** **
1237553 ATCGCAATACGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1237573 ATCGCAACG
1 ATCGCAACG
1237582 AGAGAATCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1237645 original size:20 final size:20
Alignment explanation
Indices: 1237620--1237668 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1237610 CAACAACAAA
1237620 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1237640 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1237660 ATCGCAACG
1 ATCGCAACG
1237669 AGGGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1237741 original size:20 final size:20
Alignment explanation
Indices: 1237713--1237929 Score: 280
Period size: 20 Copynumber: 11.5 Consensus size: 20
1237703 GATTCTTTCG
* **
1237713 TTGCTATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1237733 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
1237753 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1237773 TTGCGATAGTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1237792 TTGCGAT--TC----TCTCA
1 TTGCGATAGTCATTTTCGCA
1237806 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1237826 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1237846 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1237866 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
1237880 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1237900 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1237920 TTGCGATAGT
1 TTGCGATAGT
1237930 AAACTATTCT
Statistics
Matches: 175, Mismatches: 10, Indels: 24
0.84 0.05 0.11
Matches are distributed among these distances:
14 18 0.10
16 8 0.05
17 2 0.01
18 6 0.03
19 14 0.08
20 127 0.73
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1237773 original size:40 final size:40
Alignment explanation
Indices: 1237675--1237929 Score: 280
Period size: 40 Copynumber: 6.9 Consensus size: 40
1237665 AACGAGGGAA
* **
1237675 TCGCAATGCGATTTTCA-TTTCGCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
* **
1237710 TCG--TTGCTATAGTCAAATTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
1237748 TTGCATTGCGATAGTCATTTTCGCATTGCGATAGTCA-TT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
1237787 TCGCATTGCGAT--TC----TCTCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1237821 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
1237861 TCGCATTGCGAT--TC--TCTCG--TTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
*
1237895 TCGCGTTGCGATAGTCATTTTCGCATTGCGATAGT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
1237930 AAACTATTCT
Statistics
Matches: 185, Mismatches: 15, Indels: 35
0.79 0.06 0.15
Matches are distributed among these distances:
33 24 0.13
34 53 0.29
35 3 0.02
36 10 0.05
37 2 0.01
38 10 0.05
39 13 0.07
40 70 0.38
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.40
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
Found at i:1237795 original size:93 final size:93
Alignment explanation
Indices: 1237675--1237872 Score: 315
Period size: 93 Copynumber: 2.1 Consensus size: 93
1237665 AACGAGGGAA
* ** * * *
1237675 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCTATAGTCAAATTCGCATTGCGAT
1 TCGCATTGCGATAGTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGAT
*
1237740 AGTCATTTTTGCATTGCGATAGTCATTT
66 AGTCATTTTCGCATTGCGATAGTCATTT
**
1237768 TCGCATTGCGATAGTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCATTTTCGCATTGCGAT
1 TCGCATTGCGATAGTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGAT
1237833 AGTCATTTTCGCATTGCGATAGTCATTT
66 AGTCATTTTCGCATTGCGATAGTCATTT
1237861 TCGCATTGCGAT
1 TCGCATTGCGAT
1237873 TCTCTCGTTG
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 96 1.00
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (93 bp):
TCGCATTGCGATAGTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCAAATTCGCATTGCGAT
AGTCATTTTCGCATTGCGATAGTCATTT
Found at i:1237897 original size:74 final size:73
Alignment explanation
Indices: 1237731--1237929 Score: 362
Period size: 74 Copynumber: 2.7 Consensus size: 73
1237721 GTCAAATTCG
*
1237731 CATTGCGATAGTCATTTTTGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTCGCATTGC
1 CATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTCGCATTGC
1237796 GATTCTCT
66 GATTCTCT
1237804 CATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTG
1 CATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCA-TTTCGCATTG
1237869 CGATTCTCT
65 CGATTCTCT
* *
1237878 CGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATAGT
1 CATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGT
1237930 AAACTATTCT
Statistics
Matches: 122, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
73 53 0.43
74 69 0.57
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (73 bp):
CATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTTCGCATTGC
GATTCTCT
Found at i:1239762 original size:18 final size:19
Alignment explanation
Indices: 1239741--1239778 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
1239731 TTCGAACTTT
1239741 AAATCGCAAC-CGAAAATG
1 AAATCGCAACACGAAAATG
1239759 AAATCGCAACACGAAAATG
1 AAATCGCAACACGAAAATG
1239778 A
1 A
1239779 CTATCACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.53, C:0.21, G:0.16, T:0.11
Consensus pattern (19 bp):
AAATCGCAACACGAAAATG
Found at i:1239793 original size:20 final size:20
Alignment explanation
Indices: 1239743--1239810 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
1239733 CGAACTTTAA
*
1239743 ATCGCAAC-CGAAAATGA-A
1 ATCGCAACGCGAAAATGACT
*
1239761 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
1239781 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1239801 ATCGCAACGC
1 ATCGCAACGC
1239811 AAGAATCGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.19
19 9 0.21
20 25 0.60
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1239838 original size:19 final size:19
Alignment explanation
Indices: 1239741--1239839 Score: 59
Period size: 20 Copynumber: 5.4 Consensus size: 19
1239731 TTCGAACTTT
1239741 AAATCGCAAC-CGAAAATG-
1 AAATCGCAACGCG-AAATGA
*
1239759 AAATCGCAACACGAAAATGA
1 AAATCGCAACGCG-AAATGA
** * *
1239779 CTATCACAACGCGAATTTGA
1 AAATCGCAACGCGAA-ATGA
**
1239799 CTATCGCAACGC--AA-G-
1 AAATCGCAACGCGAAATGA
1239814 -AATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAATGA
1239832 AAATCGCA
1 AAATCGCA
1239840 TTGCGATTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.15
16 3 0.05
17 1 0.02
18 11 0.17
19 17 0.26
20 23 0.35
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.14
Consensus pattern (19 bp):
AAATCGCAACGCGAAATGA
Found at i:1239878 original size:20 final size:20
Alignment explanation
Indices: 1239853--1239899 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1239843 CGATTTCTCG
1239853 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
1239873 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
1239893 TTGCGAT
1 TTGCGAT
1239900 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:1240274 original size:22 final size:22
Alignment explanation
Indices: 1240213--1240274 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
1240203 TGACCGTGAA
* *
1240213 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
1240235 TG-TTATCGTC---G-TGGGGAC
1 TGATT-TCGTCGGAGATGGGGAC
1240253 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1240275 GGATGTCGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 13 0.41
19 3 0.09
21 3 0.09
22 13 0.41
ACGTcount: A:0.18, C:0.16, G:0.39, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:1240476 original size:20 final size:20
Alignment explanation
Indices: 1240451--1240502 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1240441 GCTATGTAAA
1240451 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
* *
1240471 TCGCATTGGGATAGTTAGAT
1 TCGCATTGCGATAGTCAGAT
*
1240491 TCACATTGCGAT
1 TCGCATTGCGAT
1240503 TTACGTATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAGAT
Found at i:1240512 original size:20 final size:20
Alignment explanation
Indices: 1240489--1240545 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
1240479 GGATAGTTAG
*
1240489 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1240509 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1240529 AATCGCATTGCGATTTA
1 ATTCGCATTGCGATTTA
1240546 GGAAAATCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1241289 original size:65 final size:65
Alignment explanation
Indices: 1241179--1241491 Score: 581
Period size: 65 Copynumber: 4.8 Consensus size: 65
1241169 CTAGTCTTTA
*
1241179 ATACTCTTCCTACACATTTGTGTCAAAATTTATACTATTTGCATTAGCCTTTAGTACTCTACCTA
1 ATACT-TTCCTACACATTTGTGTCAAAATTTCTACTATTTGCATTAGCCTTTAGTACTCTACCTA
1241244 C
65 C
1241245 ATACTTTCCTACACATTTGTGTCAAAATTTCTACTATTTGCATTAGCCTTTAGTACTCTACCTAC
1 ATACTTTCCTACACATTTGTGTCAAAATTTCTACTATTTGCATTAGCCTTTAGTACTCTACCTAC
*
1241310 ATACTTTCCTACACATTTGTGTCAAAATTTCTACTATTTGCATTAGCCTTTAGTACTCTACCTAT
1 ATACTTTCCTACACATTTGTGTCAAAATTTCTACTATTTGCATTAGCCTTTAGTACTCTACCTAC
*
1241375 GTACTTTCCTACACATTTGTGTCAAAATTTCTACTATTTGCATTAGCCTTTAGTACTCTACCTAC
1 ATACTTTCCTACACATTTGTGTCAAAATTTCTACTATTTGCATTAGCCTTTAGTACTCTACCTAC
*
1241440 GTACTTTCCTACACATTTGTGTCAAAATTTCTACTATTTGCATTAGCCTTTA
1 ATACTTTCCTACACATTTGTGTCAAAATTTCTACTATTTGCATTAGCCTTTA
1241492 TTTTATTTAT
Statistics
Matches: 243, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
65 238 0.98
66 5 0.02
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (65 bp):
ATACTTTCCTACACATTTGTGTCAAAATTTCTACTATTTGCATTAGCCTTTAGTACTCTACCTAC
Found at i:1241617 original size:22 final size:22
Alignment explanation
Indices: 1241576--1241617 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1241566 AGTGAAAAGC
*
1241576 TAAAATACATGTAGTATTATAG
1 TAAAATACATGTACTATTATAG
*
1241598 TAAAATACATGTACTTTTAT
1 TAAAATACATGTACTATTAT
1241618 GAATAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (22 bp):
TAAAATACATGTACTATTATAG
Found at i:1247509 original size:21 final size:21
Alignment explanation
Indices: 1247483--1247538 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1247473 TACAGTGTTG
1247483 TAGGATTTTCAGCAATGGCTA
1 TAGGATTTTCAGCAATGGCTA
*
1247504 TAGGATTTTCAACAATGGCTA
1 TAGGATTTTCAGCAATGGCTA
1247525 TAGGATTTTCAGCA
1 TAGGATTTTCAGCA
1247539 GGTTTTGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (21 bp):
TAGGATTTTCAGCAATGGCTA
Found at i:1252959 original size:19 final size:19
Alignment explanation
Indices: 1252935--1252981 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
1252925 ATGAACTATC
1252935 TATAAAAGTCAACGTCGAA
1 TATAAAAGTCAACGTCGAA
*
1252954 TATAAAAGTCAACGTCGAT
1 TATAAAAGTCAACGTCGAA
*
1252973 TATTAAAGT
1 TATAAAAGT
1252982 TGATACTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (19 bp):
TATAAAAGTCAACGTCGAA
Found at i:1253976 original size:15 final size:15
Alignment explanation
Indices: 1253909--1253984 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
1253899 GTCTGATCTG
*
1253909 ATTCGAATAACACA-
1 ATTCGAATAACATAT
* *
1253923 ATCCGAATAAAATAT
1 ATTCGAATAACATAT
* *
1253938 A-TCTAAATAACACAT
1 ATTC-GAATAACATAT
*
1253953 A-TCTTAATAACATAT
1 ATTC-GAATAACATAT
1253968 ATTCGAATAACATAT
1 ATTCGAATAACATAT
1253983 AT
1 AT
1253985 CCAAATTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
14 12 0.24
15 35 0.71
16 2 0.04
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (15 bp):
ATTCGAATAACATAT
Found at i:1253977 original size:30 final size:30
Alignment explanation
Indices: 1253909--1253986 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
1253899 GTCTGATCTG
1253909 ATTCGAATAACACA-ATCCGAATAAAATAT
1 ATTCGAATAACACATATCCGAATAAAATAT
* ** *
1253938 A-TCTAAATAACACATATCTTAATAACATAT
1 ATTC-GAATAACACATATCCGAATAAAATAT
*
1253968 ATTCGAATAACATATATCC
1 ATTCGAATAACACATATCC
1253987 AAATTATGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.05
29 10 0.26
30 25 0.64
31 2 0.05
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.29
Consensus pattern (30 bp):
ATTCGAATAACACATATCCGAATAAAATAT
Found at i:1255678 original size:23 final size:23
Alignment explanation
Indices: 1255632--1255679 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1255622 AGCTTGTATA
* * * *
1255632 AAATGCATCGAAGTGCCGCGTAG
1 AAATGCACCAAAGTGCCACATAG
1255655 AAATGCACCAAAGTGCCACATAG
1 AAATGCACCAAAGTGCCACATAG
1255678 AA
1 AA
1255680 TGTCCCAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.15
Consensus pattern (23 bp):
AAATGCACCAAAGTGCCACATAG
Found at i:1255744 original size:23 final size:21
Alignment explanation
Indices: 1255662--1255744 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 21
1255652 TAGAAATGCA
1255662 CCAAAGTG-CCACATAGAATGTC
1 CCAAAG-GACCACATAG-ATGTC
*
1255684 CCAAAGGACCACATATATGTC
1 CCAAAGGACCACATAGATGTC
* * *
1255705 CCGAAGTACCACGTAGAGTTGTC
1 CCAAAGGACCACATAGA--TGTC
*
1255728 CCAAAGGACTACATAGA
1 CCAAAGGACCACATAGA
1255745 ACCCTCAACT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 19 0.39
22 13 0.27
23 17 0.35
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (21 bp):
CCAAAGGACCACATAGATGTC
Found at i:1268133 original size:16 final size:16
Alignment explanation
Indices: 1268101--1268142 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1268091 TTTGAAGGTA
1268101 AAATAGTATTTTAATAT
1 AAATA-TATTTTAATAT
1268118 AAATATA-TTTATATAT
1 AAATATATTTTA-ATAT
1268134 AAATA-ATTT
1 AAATATATTT
1268143 GATTAGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.22
16 13 0.57
17 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AAATATATTTTAATAT
Found at i:1274098 original size:19 final size:19
Alignment explanation
Indices: 1274074--1274110 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1274064 AAAGATTCAA
1274074 TAAAATAATATTTTATAAT
1 TAAAATAATATTTTATAAT
*
1274093 TAAAATATTATTTTATAA
1 TAAAATAATATTTTATAA
1274111 ATTTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAAATAATATTTTATAAT
Found at i:1275255 original size:23 final size:23
Alignment explanation
Indices: 1275205--1275254 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1275195 ATTTTTAGGT
*
1275205 AAAATAATTAAATATTATTTTAA
1 AAAATAATTAAATATTAATTTAA
* *
1275228 AAAATAATTATGATTTTAATTTAA
1 AAAATAATTA-AATATTAATTTAA
1275252 AAA
1 AAA
1275255 TTAGGTGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAATAATTAAATATTAATTTAA
Found at i:1277496 original size:130 final size:130
Alignment explanation
Indices: 1277197--1277661 Score: 531
Period size: 130 Copynumber: 3.5 Consensus size: 130
1277187 GGTCGTCTAA
* ** *
1277197 GGGTGACATGACTCCTACGTGATGAGGAGA-CATGGTCAACG-GATGACACTACTCATACGTGAT
1 GGGTGACACGACTCCTACGTGATGAGGAGATCA-GGTC-GGGTGATGACACGACTCATACGTGAT
* * * * *
1277260 GAAGAGTTCTTGGTCATCTTTAGAAAGGTTGATAATACAATTCCTACGCGATGAGGACGACTGGT
64 GAAGAGTT-TTGGCCATCTTT---AAGGATGATAACACAGTTCCTACGTGATGAGGACGACTGGT
1277325 TATCTAG
125 TATCT-G
* *
1277332 GGGTGACACGACTCATACGTGATGAGGAGATCAGGTCGGGTGATGATACGACTCATACGTGATGA
1 GGGTGACACGACTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGACTCATACGTGATGA
* * *
1277397 AGAGTTTTGGCCATCTTTAAGGATGATAACACGGTTTCTACGTGATGAGGATGACTGGTTATCTG
66 AGAGTTTTGGCCATCTTTAAGGATGATAACACAGTTCCTACGTGATGAGGACGACTGGTTATCTG
* * *
1277462 GGGTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGAGACGACTCATACGTGATAA
1 GGGTGACACGACTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGACTCATACGTGATGA
* * * * * ** * * *
1277527 ACAATTATGGCCATATTTAAGGATGATCACATTGTCCCTACGTGATGAGGACGGCTGATTATCTG
66 AGAGTTTTGGCCATCTTTAAGGATGATAACACAGTTCCTACGTGATGAGGACGACTGGTTATCTG
* * * * * *
1277592 AGGTTGACACAACTTCTATGTGATGAGGAGATAATGTCGGGTGATGACAC-AGCTCATACGTGAT
1 -GGGTGACACGACTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGA-CTCATACGTGAT
1277656 GAAGAG
64 GAAGAG
1277662 ATCTTGAAGA
Statistics
Matches: 285, Mismatches: 41, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
130 116 0.41
131 95 0.33
134 12 0.04
135 60 0.21
136 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (130 bp):
GGGTGACACGACTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGACTCATACGTGATGA
AGAGTTTTGGCCATCTTTAAGGATGATAACACAGTTCCTACGTGATGAGGACGACTGGTTATCTG
Found at i:1289481 original size:19 final size:19
Alignment explanation
Indices: 1289457--1289501 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1289447 TTAAAATATG
*
1289457 ATTAATTT-ATTGAATATTA
1 ATTAATTTGATTCAA-ATTA
*
1289476 ATTAATTTGCTTCAAATTA
1 ATTAATTTGATTCAAATTA
1289495 ATTAATT
1 ATTAATT
1289502 AGAGAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (19 bp):
ATTAATTTGATTCAAATTA
Done.