Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 86 of 168
Found at i:25409031 original size:14 final size:13
Alignment explanation
Indices: 25409012--25409056 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
25409002 CCAAGTTGTG
*
25409012 AAAAAAAATTTGA
1 AAAAAAAAATTGA
25409025 AAAAAAAAATTGA
1 AAAAAAAAATTGA
25409038 AAAAAAAAATTGA
1 AAAAAAAAATTGA
25409051 AAAAAA
1 AAAAAA
25409057 GAGAGTTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:25423116 original size:21 final size:23
Alignment explanation
Indices: 25423069--25423118 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
25423059 TCATCTGCAA
*
25423069 TAAACACATTAAAATAAGTTAAT
1 TAAACACATGAAAATAAGTTAAT
*
25423092 TAAACACATGAAAA-CAGTT-AT
1 TAAACACATGAAAATAAGTTAAT
25423113 TAAACA
1 TAAACA
25423119 TAACACACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.32
22 4 0.16
23 13 0.52
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (23 bp):
TAAACACATGAAAATAAGTTAAT
Found at i:25423420 original size:29 final size:30
Alignment explanation
Indices: 25423386--25423466 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 30
25423376 AAATGCAAAT
*
25423386 TTAACTAACATGAAAGTTACATATTTAAAC
1 TTAACTAACATGAAAGTTACATATGTAAAC
* * *
25423416 -TAACTTGAC-T-TAATTTA-ATGATGTAAAC
1 TTAAC-TAACATGAAAGTTACAT-ATGTAAAC
25423444 TTAACTAACATGAAAGTTACATA
1 TTAACTAACATGAAAGTTACATA
25423467 ATGCATGAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
27 2 0.05
28 15 0.39
29 10 0.26
30 9 0.24
31 2 0.05
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (30 bp):
TTAACTAACATGAAAGTTACATATGTAAAC
Found at i:25426259 original size:15 final size:15
Alignment explanation
Indices: 25426230--25426287 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
25426220 TCCATTGAGC
*
25426230 GAGAAAAAGAAAAAAA
1 GAGAAAAA-AGAAAAA
25426246 GAGAAAAAAGAAAAA
1 GAGAAAAAAGAAAAA
**
25426261 GATTAAAAAGAAAAA
1 GAGAAAAAAGAAAAA
*
25426276 GAGAGAAAAGAA
1 GAGAAAAAAGAA
25426288 TGATGAGAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
15 28 0.78
16 8 0.22
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (15 bp):
GAGAAAAAAGAAAAA
Found at i:25426284 original size:9 final size:8
Alignment explanation
Indices: 25426230--25426286 Score: 64
Period size: 8 Copynumber: 7.2 Consensus size: 8
25426220 TCCATTGAGC
25426230 GAGAAAAA
1 GAGAAAAA
*
25426238 GAAAAAAA
1 GAGAAAAA
25426246 GAGAAAAA
1 GAGAAAAA
25426254 -AGAAAAA
1 GAGAAAAA
**
25426261 GATTAAAA
1 GAGAAAAA
25426269 -AGAAAAA
1 GAGAAAAA
25426276 GAGAGAAAA
1 GAGA-AAAA
25426285 GA
1 GA
25426287 ATGATGAGAG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
7 12 0.30
8 22 0.55
9 6 0.15
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (8 bp):
GAGAAAAA
Found at i:25436096 original size:10 final size:10
Alignment explanation
Indices: 25436081--25436142 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
25436071 TTTGAACCAT
*
25436081 TACCAATTCG
1 TACCAATTCA
*
25436091 TACCAAATACCA
1 TACC-AAT-TCA
*
25436103 TACCATTTCA
1 TACCAATTCA
25436113 TACCAATTCCA
1 TACCAATT-CA
* *
25436124 TACCATTTCG
1 TACCAATTCA
25436134 TACCAATTC
1 TACCAATTC
25436143 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:25436126 original size:21 final size:21
Alignment explanation
Indices: 25436081--25436143 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
25436071 TTTGAACCAT
* *
25436081 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
25436103 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
25436124 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
25436144 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:25437814 original size:20 final size:20
Alignment explanation
Indices: 25437791--25437837 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
25437781 GGGTTAAAAT
*
25437791 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
25437811 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
25437831 TGAGCTG
1 TGAGCTG
25437838 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:25441898 original size:22 final size:22
Alignment explanation
Indices: 25441876--25441949 Score: 103
Period size: 22 Copynumber: 3.4 Consensus size: 22
25441866 AAGAGGTGTT
**
25441876 TAACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGGC
* * *
25441898 TAACGAACTAAACCCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
25441920 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
25441942 TAACGTAC
1 TAACGTAC
25441950 AACTTTTAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGGC
Found at i:25445601 original size:29 final size:29
Alignment explanation
Indices: 25445566--25445633 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
25445556 ACAAGAACAT
25445566 ATTAAAAACATGTAATAGACTA-A-GACAA
1 ATTAAAAACATGTAATAG-CTATATGACAA
* *
25445594 ATTAAAAACATGTACTAGCTATATGACAT
1 ATTAAAAACATGTAATAGCTATATGACAA
25445623 ATT-AAAACATG
1 ATTAAAAACATG
25445634 CATTAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 3 0.08
28 26 0.72
29 7 0.19
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.26
Consensus pattern (29 bp):
ATTAAAAACATGTAATAGCTATATGACAA
Found at i:25447513 original size:18 final size:18
Alignment explanation
Indices: 25447490--25447583 Score: 87
Period size: 18 Copynumber: 5.6 Consensus size: 18
25447480 TCTTTACACG
25447490 TTTCTTTTTCAAGCTCTC
1 TTTCTTTTTCAAGCTCTC
*
25447508 TCTCTTTTTC-A-CTCAT-
1 TTTCTTTTTCAAGCTC-TC
25447524 TTTC-TTTTCAAGCTCTC
1 TTTCTTTTTCAAGCTCTC
*
25447541 TTTCCTTTTC-A-CT-TGC
1 TTTCTTTTTCAAGCTCT-C
25447557 TTTC-TTTTCAAGCTCTC
1 TTTCTTTTTCAAGCTCTC
*
25447574 TTTCCTTTTC
1 TTTCTTTTTC
25447584 TTGCTTACAT
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
15 11 0.17
16 16 0.25
17 17 0.27
18 20 0.31
ACGTcount: A:0.10, C:0.30, G:0.04, T:0.56
Consensus pattern (18 bp):
TTTCTTTTTCAAGCTCTC
Found at i:25447537 original size:33 final size:33
Alignment explanation
Indices: 25447490--25447583 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
25447480 TCTTTACACG
* * *
25447490 TTTCTTTTTCAAGCTCTCTCTCTTTTTCACTCAT
1 TTTC-TTTTCAAGCTCTCTTTCCTTTTCACTCAC
**
25447524 TTTCTTTTCAAGCTCTCTTTCCTTTTCACTTGC
1 TTTCTTTTCAAGCTCTCTTTCCTTTTCACTCAC
25447557 TTTCTTTTCAAGCTCTCTTTCCTTTTC
1 TTTCTTTTCAAGCTCTCTTTCCTTTTC
25447584 TTGCTTACAT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 51 0.93
34 4 0.07
ACGTcount: A:0.10, C:0.30, G:0.04, T:0.56
Consensus pattern (33 bp):
TTTCTTTTCAAGCTCTCTTTCCTTTTCACTCAC
Found at i:25447650 original size:17 final size:18
Alignment explanation
Indices: 25447630--25447669 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
25447620 TTTTTCGATT
25447630 TCTTTTTC-TTTCATTTC
1 TCTTTTTCATTTCATTTC
*
25447647 TCTTTTTCATTTTATTTC
1 TCTTTTTCATTTCATTTC
25447665 T-TTTT
1 TCTTTT
25447670 GACTCGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (18 bp):
TCTTTTTCATTTCATTTC
Found at i:25453681 original size:29 final size:29
Alignment explanation
Indices: 25453648--25453720 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
25453638 ATGTATTAGT
* *
25453648 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
25453677 TTAGGACATATTTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
25453706 TTAGGACATATTTAA
1 TTAGGACATATTTAA
25453721 TAATATCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:25455138 original size:22 final size:22
Alignment explanation
Indices: 25455095--25455159 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
25455085 CCTTTTTGAA
* *
25455095 CCATTTCCATTTTCGTACCAAAT
1 CCATTACCA-TTTCGTACCAAAC
**
25455118 CCATTACCATTTCGTTTCAAAC
1 CCATTACCATTTCGTACCAAAC
* * *
25455140 CCCTTACCGTTTCATACCAA
1 CCATTACCATTTCGTACCAA
25455160 TTCCCAAATA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
22 25 0.76
23 8 0.24
ACGTcount: A:0.26, C:0.34, G:0.05, T:0.35
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAC
Found at i:25464138 original size:21 final size:19
Alignment explanation
Indices: 25464095--25464139 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
25464085 GAGCTCAAAT
* *
25464095 GAGCTGAAATGAGTTCATG
1 GAGCTGAAATGAGCTAATG
25464114 GAGCTGGAAATGAGCTAATTG
1 GAGCT-GAAATGAGCTAA-TG
25464135 GAGCT
1 GAGCT
25464140 CAATGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.24
Consensus pattern (19 bp):
GAGCTGAAATGAGCTAATG
Found at i:25467476 original size:12 final size:12
Alignment explanation
Indices: 25467461--25467502 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
25467451 ATTTTTTTCT
25467461 TTTTTTTTCAAA
1 TTTTTTTTCAAA
* *
25467473 TTTTTTTT-GAT
1 TTTTTTTTCAAA
25467484 TTTTTTTTCAAA
1 TTTTTTTTCAAA
25467496 TTTTTTT
1 TTTTTTT
25467503 ACGAGTCTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:25467476 original size:13 final size:13
Alignment explanation
Indices: 25467460--25467502 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 13
25467450 AATTTTTTTC
25467460 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
*
25467473 -TTTTTTTT--GA
1 TTTTTTTTTCAAA
25467483 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
25467496 TTTTTTT
1 TTTTTTT
25467503 ACGAGTCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 1 0.04
11 8 0.32
12 8 0.32
13 8 0.32
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:25467480 original size:22 final size:23
Alignment explanation
Indices: 25467452--25467502 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
25467442 TCGTATACAA
*
25467452 TTTTTTT-CTTTTTTTTTCAAAT
1 TTTTTTTGATTTTTTTTTCAAAT
25467474 TTTTTTTGATTTTTTTTTCAAAT
1 TTTTTTTGATTTTTTTTTCAAAT
25467497 TTTTTT
1 TTTTTT
25467503 ACGAGTCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (23 bp):
TTTTTTTGATTTTTTTTTCAAAT
Found at i:25469096 original size:21 final size:19
Alignment explanation
Indices: 25469053--25469097 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
25469043 GAGCTCAAAT
* *
25469053 GAGCTGAAATGAGTTCATG
1 GAGCTGAAATGAGCTAATG
25469072 GAGCTAGAAATGAGCTAATTG
1 GAGCT-GAAATGAGCTAA-TG
25469093 GAGCT
1 GAGCT
25469098 CAATGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.24
Consensus pattern (19 bp):
GAGCTGAAATGAGCTAATG
Found at i:25472408 original size:22 final size:22
Alignment explanation
Indices: 25472377--25472441 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
25472367 ACCTTTTTGA
*
25472377 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
25472400 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
* *
25472422 TCTATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
25472442 TTCCTAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
22 34 0.89
23 4 0.11
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.29
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:25478438 original size:10 final size:11
Alignment explanation
Indices: 25478417--25478441 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25478407 CTAGACCGTA
25478417 TTCAATTTTTT
1 TTCAATTTTTT
25478428 TTCAATTTTTT
1 TTCAATTTTTT
25478439 TTC
1 TTC
25478442 TTTTCGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (11 bp):
TTCAATTTTTT
Found at i:25478451 original size:16 final size:15
Alignment explanation
Indices: 25478422--25478456 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
25478412 CCGTATTCAA
25478422 TTTTTTTTCAATTTT
1 TTTTTTTTCAATTTT
*
25478437 TTTTCTTTTCGATTTT
1 TTTT-TTTTCAATTTT
25478453 TTTT
1 TTTT
25478457 GATTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTTTTTCAATTTT
Found at i:25478456 original size:11 final size:11
Alignment explanation
Indices: 25478437--25478478 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 11
25478427 TTTCAATTTT
25478437 TTTTCTTTTCGA
1 TTTT-TTTTCGA
25478449 TTTTTTTT-GA
1 TTTTTTTTCGA
25478459 TTTTTTTTCGAA
1 TTTTTTTTCG-A
25478471 TTTTTTTT
1 TTTTTTTT
25478479 GAAACTACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.36
11 5 0.18
12 13 0.46
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.76
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:25478473 original size:22 final size:22
Alignment explanation
Indices: 25478437--25478480 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
25478427 TTTCAATTTT
25478437 TTTTCTTTTCGATTTTTTTTGA
1 TTTTCTTTTCGATTTTTTTTGA
25478459 TTTT-TTTTCGAATTTTTTTTGA
1 TTTTCTTTTCG-ATTTTTTTTGA
25478481 AACTACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.11, C:0.07, G:0.09, T:0.73
Consensus pattern (22 bp):
TTTTCTTTTCGATTTTTTTTGA
Found at i:25480364 original size:11 final size:10
Alignment explanation
Indices: 25480345--25480395 Score: 68
Period size: 10 Copynumber: 5.1 Consensus size: 10
25480335 AGACCGTATA
25480345 TAATTTTTTT
1 TAATTTTTTT
25480355 T-ATTTTTTT
1 TAATTTTTTT
*
25480364 TGATTTTTTT
1 TAATTTTTTT
*
25480374 CAATTTTTTT
1 TAATTTTTTT
25480384 TCAATTTTTTT
1 T-AATTTTTTT
25480395 T
1 T
25480396 TCACGAGTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
9 9 0.25
10 17 0.47
11 10 0.28
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (10 bp):
TAATTTTTTT
Found at i:25480398 original size:12 final size:11
Alignment explanation
Indices: 25480346--25480395 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
25480336 GACCGTATAT
25480346 AATTTTTTTT-
1 AATTTTTTTTC
25480356 -ATTTTTTTT-
1 AATTTTTTTTC
*
25480365 GA-TTTTTTTC
1 AATTTTTTTTC
25480375 AATTTTTTTTC
1 AATTTTTTTTC
25480386 AATTTTTTTT
1 AATTTTTTTT
25480396 TCACGAGTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
9 16 0.44
10 2 0.06
11 18 0.50
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (11 bp):
AATTTTTTTTC
Found at i:25481898 original size:21 final size:19
Alignment explanation
Indices: 25481855--25481899 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
25481845 GAGCTCAAAT
* *
25481855 GAGCTGAAATGAGTTCATG
1 GAGCTGAAATGAGCTAATG
25481874 GAGCTGGAAATGAGCTAATTG
1 GAGCT-GAAATGAGCTAA-TG
25481895 GAGCT
1 GAGCT
25481900 CAATGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.24
Consensus pattern (19 bp):
GAGCTGAAATGAGCTAATG
Found at i:25486613 original size:26 final size:24
Alignment explanation
Indices: 25486565--25486613 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
25486555 ACGAGATTGT
**
25486565 AAAAAAAATCAAAAAAATTTTTGA
1 AAAAAAAATCAAAAAAAAGTTTGA
25486589 AAAAAAAATTCAAAAAAAAAGTTTG
1 AAAAAAAA-TC-AAAAAAAAGTTTG
25486614 TATTCGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 2 0.10
26 11 0.52
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.22
Consensus pattern (24 bp):
AAAAAAAATCAAAAAAAAGTTTGA
Found at i:25486674 original size:18 final size:19
Alignment explanation
Indices: 25486640--25486676 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
25486630 TCCTTTGTGT
*
25486640 ATTCAGTATTGAAAAAAAA
1 ATTCAGAATTGAAAAAAAA
25486659 ATTCAGAATT-AAAAAAAA
1 ATTCAGAATTGAAAAAAAA
25486677 GTGATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.24
Consensus pattern (19 bp):
ATTCAGAATTGAAAAAAAA
Found at i:25488815 original size:15 final size:14
Alignment explanation
Indices: 25488779--25488833 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
25488769 TCTATTGAGC
25488779 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
25488793 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
25488807 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
25488822 GAAAGAAAAGAA
1 GAGA-AAAAGAA
25488834 TGATGAGAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:25495241 original size:27 final size:28
Alignment explanation
Indices: 25495206--25495259 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
25495196 GCTGGACTTG
*
25495206 GACATCATTAAAAACATGTAATAAAATT
1 GACATCATTAAAAACATGCAATAAAATT
* * *
25495234 GACA-CATTTATAACATGCATTAAAAT
1 GACATCATTAAAAACATGCAATAAAAT
25495260 AAAACACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (28 bp):
GACATCATTAAAAACATGCAATAAAATT
Found at i:25498636 original size:45 final size:45
Alignment explanation
Indices: 25498572--25498682 Score: 213
Period size: 45 Copynumber: 2.5 Consensus size: 45
25498562 NNNNNNNNNN
*
25498572 GATGTTGGTCAAATGCTTCCTCAAATTCTTCCATGAATTATGCAT
1 GATGTTGGTCAAATGCTTCCTCAAATTCTCCCATGAATTATGCAT
25498617 GATGTTGGTCAAATGCTTCCTCAAATTCTCCCATGAATTATGCAT
1 GATGTTGGTCAAATGCTTCCTCAAATTCTCCCATGAATTATGCAT
25498662 GATGTTGGTCAAATGCTTCCT
1 GATGTTGGTCAAATGCTTCCT
25498683 TAATTTCATG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (45 bp):
GATGTTGGTCAAATGCTTCCTCAAATTCTCCCATGAATTATGCAT
Found at i:25506194 original size:30 final size:29
Alignment explanation
Indices: 25506146--25506202 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
25506136 GAGAAAATGA
*
25506146 AAAAGAAAAAGAAGATGAG-TGTGAGATAG
1 AAAAGAAAAAGAAAATGAGAT-TGAGATAG
*
25506175 AAAAGAAAATTGAAAATGAGATTGAGAT
1 AAAAGAAAA-AGAAAATGAGATTGAGAT
25506203 TGAGAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.38
30 14 0.58
31 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (29 bp):
AAAAGAAAAAGAAAATGAGATTGAGATAG
Found at i:25506220 original size:54 final size:54
Alignment explanation
Indices: 25506162--25506285 Score: 142
Period size: 54 Copynumber: 2.3 Consensus size: 54
25506152 AAAAGAAGAT
* * * * * *
25506162 GAGTGTGAGATAGAAAAGAAAATTGAAAATGAGATTGAGATTG-AGAATAAAAAC
1 GAGTGTGAAAAAGAAAAGAAAACTAAAAAAGAGAGTGAGATTGAAGAA-AAAAAC
* *
25506216 GAGTGTGAAAAAGAAAATAAAACTAAAAAAGAGAGTGAGATTGAAGAAAGAAAC
1 GAGTGTGAAAAAGAAAAGAAAACTAAAAAAGAGAGTGAGATTGAAGAAAAAAAC
* *
25506270 GAGAGTGCAAAAGAAA
1 GAGTGTGAAAAAGAAA
25506286 TGAGTGATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 55 0.93
55 4 0.07
ACGTcount: A:0.56, C:0.03, G:0.26, T:0.15
Consensus pattern (54 bp):
GAGTGTGAAAAAGAAAAGAAAACTAAAAAAGAGAGTGAGATTGAAGAAAAAAAC
Found at i:25506622 original size:22 final size:22
Alignment explanation
Indices: 25506570--25506634 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
25506560 TATTTGGGAA
* * *
25506570 TTGGTATGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
25506592 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
25506614 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
25506635 TTCAAAAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:25510599 original size:20 final size:20
Alignment explanation
Indices: 25510574--25510620 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
25510564 AGCTCGTTTC
*
25510574 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
25510594 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
25510614 CAGCTCA
1 CAGCTCA
25510621 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:25512464 original size:14 final size:15
Alignment explanation
Indices: 25512437--25512465 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25512427 ATGCATCTTC
25512437 ACATTCATTGAATCT
1 ACATTCATTGAATCT
25512452 ACATTCA-TGAATCT
1 ACATTCATTGAATCT
25512466 GCCCACTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (15 bp):
ACATTCATTGAATCT
Found at i:25514461 original size:20 final size:20
Alignment explanation
Indices: 25514438--25514475 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25514428 TTGAGTTGAA
25514438 TTGAACTCGAATGAGCTGAC
1 TTGAACTCGAATGAGCTGAC
* *
25514458 TTGAGCTCGAGTGAGCTG
1 TTGAACTCGAATGAGCTG
25514476 GAAACGAGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (20 bp):
TTGAACTCGAATGAGCTGAC
Found at i:25519634 original size:21 final size:22
Alignment explanation
Indices: 25519608--25519666 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
25519598 TCAATTTCAA
25519608 CTCACT-TTTTCTTTTTGTTTT
1 CTCACTCTTTTCTTTTTGTTTT
*
25519629 CTCACTCTTTT-TTTCT-TTTT
1 CTCACTCTTTTCTTTTTGTTTT
25519649 C-CA-TCTTTTCTTTTTGTT
1 CTCACTCTTTTCTTTTTGTT
25519667 CCTTTGCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 6 0.18
19 6 0.18
20 7 0.21
21 10 0.30
22 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.69
Consensus pattern (22 bp):
CTCACTCTTTTCTTTTTGTTTT
Found at i:25519662 original size:20 final size:20
Alignment explanation
Indices: 25519608--25519666 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
25519598 TCAATTTCAA
25519608 CTCACTTTTTCTTTTTGTTTT
1 CTCAC-TTTTCTTTTTGTTTT
25519629 CTCACTCTTT-TTTTCT-TTTT
1 CTCACT-TTTCTTTT-TGTTTT
25519649 C-CATCTTTTCTTTTTGTT
1 CTCA-CTTTTCTTTTTGTT
25519667 CCTTTGCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
19 6 0.18
20 18 0.55
21 9 0.27
ACGTcount: A:0.05, C:0.22, G:0.03, T:0.69
Consensus pattern (20 bp):
CTCACTTTTCTTTTTGTTTT
Found at i:25519668 original size:18 final size:19
Alignment explanation
Indices: 25519610--25519668 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 19
25519600 AATTTCAACT
25519610 CACT-TTTTCTTTTTGTTTTC
1 CACTCTTTTCTTTTTG--TTC
*
25519630 TCACTCTTTT-TTTCTTTTTC
1 -CACTCTTTTCTTT-TTGTTC
25519650 CA-TCTTTTCTTTTTGTTC
1 CACTCTTTTCTTTTTGTTC
25519668 C
1 C
25519669 TTTGCCTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 12 0.36
19 5 0.15
20 3 0.09
21 7 0.21
22 6 0.18
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.68
Consensus pattern (19 bp):
CACTCTTTTCTTTTTGTTC
Found at i:25521734 original size:20 final size:19
Alignment explanation
Indices: 25521709--25521746 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
25521699 AACATTTTCG
25521709 ATTCAGCTCATTCGAGCTCA
1 ATTCAGCTCATT-GAGCTCA
25521729 ATTCAGCTCATTGAGCTC
1 ATTCAGCTCATTGAGCTC
25521747 GTTATTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (19 bp):
ATTCAGCTCATTGAGCTCA
Found at i:25523588 original size:11 final size:11
Alignment explanation
Indices: 25523572--25523610 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
25523562 TCGAGATTGT
25523572 AAAAAAA-TCA
1 AAAAAAATTCA
*
25523582 AAAAAAATTTGA
1 AAAAAAA-TTCA
25523594 AAAAAAATTCA
1 AAAAAAATTCA
25523605 AAAAAA
1 AAAAAA
25523611 GTTTGTACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 7 0.28
11 9 0.36
12 9 0.36
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:25523605 original size:23 final size:22
Alignment explanation
Indices: 25523572--25523615 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
25523562 TCGAGATTGT
25523572 AAAAAAATCAAAAAAAATTTGA
1 AAAAAAATCAAAAAAAATTTGA
*
25523594 AAAAAAATTCAAAAAAAGTTTG
1 AAAAAAA-TCAAAAAAAATTTG
25523616 TACTCAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (22 bp):
AAAAAAATCAAAAAAAATTTGA
Found at i:25524524 original size:20 final size:21
Alignment explanation
Indices: 25524494--25524540 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
25524484 AATCTTGAAT
*
25524494 GAAATTGAGAGAAGAA-AAAAA
1 GAAA-TGAGAGAAAAAGAAAAA
25524515 GAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
25524536 GAAAT
1 GAAAT
25524541 AAATGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.09
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:25524548 original size:21 final size:21
Alignment explanation
Indices: 25524510--25524555 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
25524500 GAGAGAAGAA
*
25524510 AAAAAGAAATGAGAGAAAAAG
1 AAAAAGAAATGAAAGAAAAAG
*
25524531 AAAAAGAAAT-AAATGAAAATG
1 AAAAAGAAATGAAA-GAAAAAG
25524552 AAAA
1 AAAA
25524556 TGAGAGTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (21 bp):
AAAAAGAAATGAAAGAAAAAG
Found at i:25532973 original size:17 final size:18
Alignment explanation
Indices: 25532951--25532991 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
25532941 CATTTCTTTT
25532951 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
25532968 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
25532986 T-TTTTG
1 TCTTTTG
25532992 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:25535165 original size:11 final size:11
Alignment explanation
Indices: 25535146--25535185 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
25535136 TTCCAATTTT
25535146 TTTTCTTTTCGA
1 TTTT-TTTTCGA
25535158 TTTTTTTT--A
1 TTTTTTTTCGA
25535167 TTTTTTTTCGA
1 TTTTTTTTCGA
25535178 TTTTTTTT
1 TTTTTTTT
25535186 TCTAAGCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.35
11 13 0.50
12 4 0.15
ACGTcount: A:0.07, C:0.07, G:0.05, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:25535165 original size:20 final size:19
Alignment explanation
Indices: 25535142--25535186 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
25535132 TTTTTTCCAA
*
25535142 TTTTTTTTCTTTTCGATTT
1 TTTTTTTTTTTTTCGATTT
25535161 TTTTTATTTTTTTTCGATTT
1 TTTTT-TTTTTTTTCGATTT
25535181 TTTTTT
1 TTTTTT
25535187 CTAAGCTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.07, C:0.07, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTTTTTCGATTT
Found at i:25563739 original size:18 final size:18
Alignment explanation
Indices: 25563716--25563751 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
25563706 TATACAATTT
25563716 TTTTCTTTTCTTTT-CAAA
1 TTTTCTTTT-TTTTACAAA
25563734 TTTTCTTTTTTTTACAAA
1 TTTTCTTTTTTTTACAAA
25563752 AACAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCTTTTTTTTACAAA
Found at i:25566484 original size:20 final size:19
Alignment explanation
Indices: 25566459--25566496 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
25566449 AACATTTTCG
25566459 ATTCAGCTCATTCGAGCTCA
1 ATTCAGCTCATT-GAGCTCA
25566479 ATTCAGCTCATTGAGCTC
1 ATTCAGCTCATTGAGCTC
25566497 GTTATTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (19 bp):
ATTCAGCTCATTGAGCTCA
Found at i:25570205 original size:11 final size:11
Alignment explanation
Indices: 25570177--25570228 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
25570167 CCGTATACAA
25570177 TTTTTTTCAAT
1 TTTTTTTCAAT
**
25570188 TAATTTTTTTTAT
1 T--TTTTTTCAAT
*
25570201 TTTTTTTCGAT
1 TTTTTTTCAAT
25570212 TTTTTTTCAAT
1 TTTTTTTCAAT
25570223 TTTTTT
1 TTTTTT
25570229 CACGAATCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 25 0.74
13 9 0.26
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:25626022 original size:12 final size:12
Alignment explanation
Indices: 25626005--25626056 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
25625995 TTTTGTACTC
25626005 AAATTTTTTTTG
1 AAATTTTTTTTG
25626017 AAATTTTTTTTTCG
1 AAA-TTTTTTTT-G
*
25626031 -AATTTTTTTTC
1 AAATTTTTTTTG
*
25626042 AAATTTTTTTCG
1 AAATTTTTTTTG
25626054 AAA
1 AAA
25626057 CTATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 23 0.68
13 10 0.29
14 1 0.03
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.62
Consensus pattern (12 bp):
AAATTTTTTTTG
Found at i:25626025 original size:14 final size:13
Alignment explanation
Indices: 25626008--25626051 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
25625998 TGTACTCAAA
25626008 TTTTTTTT-GAAAT
1 TTTTTTTTCG-AAT
25626021 TTTTTTTTCGAA-
1 TTTTTTTTCGAAT
*
25626033 TTTTTTTTCAAAT
1 TTTTTTTTCGAAT
25626046 TTTTTT
1 TTTTTT
25626052 CGAAACTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 11 0.39
13 16 0.57
14 1 0.04
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.73
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:25627731 original size:13 final size:13
Alignment explanation
Indices: 25627713--25627742 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25627703 GAACTCTTCA
25627713 AGCTTAAGTAATC
1 AGCTTAAGTAATC
*
25627726 AGCTTAATTAATC
1 AGCTTAAGTAATC
25627739 AGCT
1 AGCT
25627743 GAATTGGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
AGCTTAAGTAATC
Found at i:25634852 original size:22 final size:22
Alignment explanation
Indices: 25634800--25634864 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
25634790 TATTTGGGAA
* * *
25634800 TTGGTATGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
25634822 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
25634844 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
25634865 TTCAAAAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:25647798 original size:19 final size:18
Alignment explanation
Indices: 25647776--25647811 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25647766 TCAAATTAGG
25647776 TTCGTGAATTAAAAAAAAA
1 TTCGTGAA-TAAAAAAAAA
*
25647795 TTCGTGCATAAAAAAAA
1 TTCGTGAATAAAAAAAA
25647812 GAGGTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.08, G:0.11, T:0.25
Consensus pattern (18 bp):
TTCGTGAATAAAAAAAAA
Found at i:25648751 original size:18 final size:18
Alignment explanation
Indices: 25648730--25648764 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25648720 AGAAAAGAAA
25648730 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
25648748 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
25648765 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:25668773 original size:18 final size:18
Alignment explanation
Indices: 25668728--25668779 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
25668718 CATTTTCATA
*
25668728 CTCTTTCTTTTCTTTACT
1 CTCTTTATTTTCTTTACT
* *
25668746 CATC-TCATTTTCTTTTCT
1 C-TCTTTATTTTCTTTACT
25668764 CTCTTTATTTTTCTTT
1 CTCTTTA-TTTTCTTT
25668780 GTTTTTACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 2 0.07
18 15 0.56
19 10 0.37
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.67
Consensus pattern (18 bp):
CTCTTTATTTTCTTTACT
Found at i:25695746 original size:28 final size:28
Alignment explanation
Indices: 25695714--25695768 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
25695704 ATTTTGAGCG
25695714 AGAAAAGAATAAAGAA-A-ATGAAAATGAA
1 AGAAAAG-A-AAAGAATATATGAAAATGAA
*
25695742 AGAAATGAAAAGAATATATGAAAATGA
1 AGAAAAGAAAAGAATATATGAAAATGA
25695769 GATTTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.25
27 2 0.08
28 16 0.67
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (28 bp):
AGAAAAGAAAAGAATATATGAAAATGAA
Found at i:25697773 original size:20 final size:20
Alignment explanation
Indices: 25697736--25697773 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25697726 AGCTCATTTC
*
25697736 CAGCTCACTTGAGCTCAAGT
1 CAGCTCACTTGAGATCAAGT
25697756 CAGCTCA-TTCGAGATCAA
1 CAGCTCACTT-GAGATCAA
25697774 TTTAGCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (20 bp):
CAGCTCACTTGAGATCAAGT
Found at i:25712062 original size:1 final size:1
Alignment explanation
Indices: 25712056--25712098 Score: 68
Period size: 1 Copynumber: 43.0 Consensus size: 1
25712046 NNNNNNNNNN
* *
25712056 AAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25712099 GAGTGCCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:25712081 original size:16 final size:16
Alignment explanation
Indices: 25712056--25712098 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
25712046 NNNNNNNNNN
25712056 AAAA-AAAAAAAAAAA
1 AAAAGAAAAAAAAAAA
25712071 AAAAGAAAAAAAAAAA
1 AAAAGAAAAAAAAAAA
25712087 AAAAGAAAAAAA
1 AAAAGAAAAAAA
25712099 GAGTGCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAAAAA
Found at i:25718722 original size:15 final size:15
Alignment explanation
Indices: 25718697--25718743 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
25718687 AGAAAAGAAT
25718697 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
25718713 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
25718728 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
25718743 A
1 A
25718744 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:25718790 original size:12 final size:12
Alignment explanation
Indices: 25718773--25718812 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
25718763 AGTGAAAAGC
25718773 AAAAAGAGATTG
1 AAAAAGAGATTG
*
25718785 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
25718797 AAAGAGAGCTTG
1 AAAAAGAGATTG
25718809 AAAA
1 AAAA
25718813 GAAATCGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.15
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:25737904 original size:15 final size:15
Alignment explanation
Indices: 25737886--25737926 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
25737876 CTTACTACCT
25737886 TCTTTTTCTTTTATC
1 TCTTTTTCTTTTATC
*
25737901 TCTTTTTCTTTTCTC
1 TCTTTTTCTTTTATC
*
25737916 TC-ATTTCTTTT
1 TCTTTTTCTTTT
25737927 TTTCTTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (15 bp):
TCTTTTTCTTTTATC
Found at i:25740746 original size:11 final size:10
Alignment explanation
Indices: 25740723--25740782 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
25740713 ATTGGGTTAA
25740723 AATTGAGCTG
1 AATTGAGCTG
*
25740733 AATTGATCTCG
1 AATTGAGCT-G
25740744 AA-TGAGCTG
1 AATTGAGCTG
* *
25740753 ACTTGAGCTC
1 AATTGAGCTG
*
25740763 AAGTGAGCTGG
1 AATTGAGCT-G
*
25740774 AAATGAGCT
1 AATTGAGCT
25740783 AAACAGAGCT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 2 0.05
10 26 0.67
11 11 0.28
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (10 bp):
AATTGAGCTG
Found at i:25740749 original size:20 final size:20
Alignment explanation
Indices: 25740726--25740782 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
25740716 GGGTTAAAAT
*
25740726 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
25740746 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
*
25740766 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
25740783 AAACAGAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.06
20 21 0.68
21 8 0.26
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:25741703 original size:80 final size:80
Alignment explanation
Indices: 25741610--25741770 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
25741600 TGATTTTGAC
25741610 TACTCGATCCAAATGGCAACGAGGGTGTTAGCATACTCAAATTCAAACAAGCAAACCCTTTAAAT
1 TACTCGATCCAAATGGCAACGAGGGTGTTAGCATACTCAAATTCAAACAAGCAAACCCTTTAAAT
25741675 TTTGTTCGAAAAGAT
66 TTTGTTCGAAAAGAT
25741690 TACTCGATCCAAATGGCAACGAGGGTGTTAGCATACTCAAATTCAAACAAGCAAACCCTTTAAAT
1 TACTCGATCCAAATGGCAACGAGGGTGTTAGCATACTCAAATTCAAACAAGCAAACCCTTTAAAT
25741755 TTTGTTCGAAAAGAT
66 TTTGTTCGAAAAGAT
25741770 T
1 T
25741771 TACGAAAACA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (80 bp):
TACTCGATCCAAATGGCAACGAGGGTGTTAGCATACTCAAATTCAAACAAGCAAACCCTTTAAAT
TTTGTTCGAAAAGAT
Found at i:25742756 original size:12 final size:12
Alignment explanation
Indices: 25742723--25742803 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
25742713 TTTCCACTCG
25742723 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
25742734 AGCTCTCTTTCA
1 ATTTCTTTTTCA
25742746 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
25742759 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
25742772 --TTCTCTTTCA
1 ATTTCTTTTTCA
25742782 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
25742794 ATCTCTTTTT
1 ATTTCTTTTT
25742804 GCTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:25742764 original size:21 final size:20
Alignment explanation
Indices: 25742738--25742793 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
25742728 TTTTCAAGCT
25742738 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
25742759 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
25742774 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
25742794 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:25742855 original size:15 final size:15
Alignment explanation
Indices: 25742832--25742878 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
25742822 TTTTGAAATC
25742832 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
25742847 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
25742862 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
25742878 T
1 T
25742879 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:25743936 original size:12 final size:13
Alignment explanation
Indices: 25743915--25743985 Score: 67
Period size: 12 Copynumber: 5.4 Consensus size: 13
25743905 CTCGCAAGAC
*
25743915 TTTTCACTTCTTT
1 TTTTTACTTCTTT
25743928 TTTTT-CTTCTTT
1 TTTTTACTTCTTT
*
25743940 TTTTTACTCCTTTT
1 TTTTTACTTC-TTT
25743954 TTTTGCTCACTTCTTT
1 TTTT--T-ACTTCTTT
25743970 TTTTT-CTT-TTT
1 TTTTTACTTCTTT
25743981 TTTTT
1 TTTTT
25743986 CGAATTTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
11 8 0.16
12 15 0.30
13 7 0.14
14 8 0.16
16 8 0.16
17 4 0.08
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (13 bp):
TTTTTACTTCTTT
Found at i:25743985 original size:13 final size:13
Alignment explanation
Indices: 25743925--25743986 Score: 63
Period size: 13 Copynumber: 4.7 Consensus size: 13
25743915 TTTTCACTTC
*
25743925 TTTTTTTTCTTCT
1 TTTTTTTTCTCCT
*
25743938 TTTTTTTACTCCT
1 TTTTTTTTCTCCT
*
25743951 TTTTTTTGCTCACT
1 TTTTTTTTCTC-CT
*
25743965 TCTTTTTTT-TCTT
1 T-TTTTTTTCTCCT
25743978 TTTTTTTTC
1 TTTTTTTTC
25743987 GAATTTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
12 7 0.17
13 23 0.56
14 5 0.12
15 6 0.15
ACGTcount: A:0.03, C:0.18, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTTTTTCTCCT
Found at i:25745548 original size:20 final size:20
Alignment explanation
Indices: 25745525--25745571 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
25745515 GGGTTAAAAT
*
25745525 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
25745545 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
25745565 TGAGCTG
1 TGAGCTG
25745572 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:25747568 original size:33 final size:34
Alignment explanation
Indices: 25747531--25747602 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
25747521 GAGTTAGTTT
*
25747531 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCACCTCAAATAAGTGTTAGTA
* *
25747564 ATTAATTTTAGTTCACCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCACCTCAAATAAGTGTTAGTA
25747598 ATTAA
1 ATTAA
25747603 TTTGTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCACCTCAAATAAGTGTTAGTA
Found at i:25753723 original size:10 final size:10
Alignment explanation
Indices: 25753689--25753715 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
25753679 CTTAAAAGCT
25753689 AAGAAAAATC
1 AAGAAAAATC
25753699 AAGAAAAATC
1 AAGAAAAATC
25753709 AAGAAAA
1 AAGAAAA
25753716 TTCCAGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.07, G:0.11, T:0.07
Consensus pattern (10 bp):
AAGAAAAATC
Found at i:25754259 original size:29 final size:29
Alignment explanation
Indices: 25754225--25754297 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
25754215 ATGTATTAGT
* *
25754225 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
25754254 TTAGGACATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
25754283 TTAGGACATATTTAA
1 TTAGGACATATTTAA
25754298 TAATATCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:25757353 original size:11 final size:11
Alignment explanation
Indices: 25757339--25757377 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
25757329 TTCGACGAAA
25757339 TTTTTATTGATT
1 TTTTTATTGA-T
25757351 TTTTTATTGAT
1 TTTTTATTGAT
25757362 TTTTTATTGAT
1 TTTTTATTGAT
25757373 TTTTT
1 TTTTT
25757378 TACAATACCG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTTATTGAT
Found at i:25757356 original size:12 final size:12
Alignment explanation
Indices: 25757339--25757379 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
25757329 TTCGACGAAA
25757339 TTTTTATTGATT
1 TTTTTATTGATT
25757351 TTTTTATTGA-T
1 TTTTTATTGATT
25757362 TTTTTATTGATT
1 TTTTTATTGATT
25757374 TTTTTA
1 TTTTTA
25757380 CAATACCGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTTATTGATT
Found at i:25760528 original size:100 final size:100
Alignment explanation
Indices: 25760414--25760613 Score: 328
Period size: 100 Copynumber: 2.0 Consensus size: 100
25760404 TTGTTTTGAT
*
25760414 CATTTTCAATTTTATCAATTATGTTTCAGAAAATGTTTTCCTTTGAAGGGATCCAAGATAATAGG
1 CATTTTCAATTTTATCAATTATGTTTCAGAAAATGTTTTCCTTTGAAGGGATCCAAGACAATAGG
* *
25760479 AGAAATGAATTGTTTGTGTGTGGAAATAAAGCTAC
66 AGAAATGAACTGTTTGTGTGTGGAAACAAAGCTAC
** * **
25760514 CATTTTCAATTTTATTGATTATGTTTGAGAAAATGTTTTCCTTTGAAGGGATCCAAGACAATCTG
1 CATTTTCAATTTTATCAATTATGTTTCAGAAAATGTTTTCCTTTGAAGGGATCCAAGACAATAGG
25760579 AGAAATGAACTGTTTGTGTGTGGAAACAAAGCTAC
66 AGAAATGAACTGTTTGTGTGTGGAAACAAAGCTAC
25760614 TTTGATCAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 92 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (100 bp):
CATTTTCAATTTTATCAATTATGTTTCAGAAAATGTTTTCCTTTGAAGGGATCCAAGACAATAGG
AGAAATGAACTGTTTGTGTGTGGAAACAAAGCTAC
Found at i:25768022 original size:16 final size:16
Alignment explanation
Indices: 25768001--25768033 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25767991 ATGGCTTCTT
*
25768001 GTTCGTTGTCCATTTG
1 GTTCGTTCTCCATTTG
25768017 GTTCGTTCTCCATTTG
1 GTTCGTTCTCCATTTG
25768033 G
1 G
25768034 AACCAGTCCG
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:0.06, C:0.21, G:0.24, T:0.48
Consensus pattern (16 bp):
GTTCGTTCTCCATTTG
Found at i:25768215 original size:12 final size:12
Alignment explanation
Indices: 25768182--25768262 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
25768172 TTTCCACTCG
25768182 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
25768193 AGCTCTCTTTCA
1 ATTTCTTTTTCA
25768205 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
25768218 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
25768231 --TTCTCTTTCA
1 ATTTCTTTTTCA
25768241 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
25768253 ATCTCTTTTT
1 ATTTCTTTTT
25768263 GCTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:25768223 original size:21 final size:20
Alignment explanation
Indices: 25768197--25768252 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
25768187 TTTTCAAGCT
25768197 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
25768218 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
25768233 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
25768253 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:25768328 original size:15 final size:14
Alignment explanation
Indices: 25768290--25768336 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
25768280 ATTTTTGAAA
25768290 TCTCATTTTCATATT
1 TCTCATTTTCAT-TT
* *
25768305 TTTCTTTTTCATTT
1 TCTCATTTTCATTT
25768319 CTCTCATTTTCATTT
1 -TCTCATTTTCATTT
25768334 TCT
1 TCT
25768337 TTATTCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.66
Consensus pattern (14 bp):
TCTCATTTTCATTT
Found at i:25768333 original size:28 final size:29
Alignment explanation
Indices: 25768290--25768349 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
25768280 ATTTTTGAAA
25768290 TCTCATTTTCATATTTTTCTTT-TTCATTTC
1 TCTCATTTTCA-A-TTTTCTTTATTCATTTC
*
25768320 TCTCATTTTC-ATTTTCTTTATTCTTTTC
1 TCTCATTTTCAATTTTCTTTATTCATTTC
25768348 TC
1 TC
25768350 GCTCAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 8 0.29
28 10 0.36
30 10 0.36
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.67
Consensus pattern (29 bp):
TCTCATTTTCAATTTTCTTTATTCATTTC
Found at i:25770995 original size:20 final size:20
Alignment explanation
Indices: 25770972--25771018 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
25770962 GGGTTAAAAT
*
25770972 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
25770992 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
25771012 TGAGCTG
1 TGAGCTG
25771019 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:25773718 original size:109 final size:109
Alignment explanation
Indices: 25773585--25773803 Score: 438
Period size: 109 Copynumber: 2.0 Consensus size: 109
25773575 CTTTCAGAAC
25773585 TATTTCGAGCTGAGATGAGCTGCATGCACATATTTGAGCTTCAACCGAGCTAGAAATGATATCTT
1 TATTTCGAGCTGAGATGAGCTGCATGCACATATTTGAGCTTCAACCGAGCTAGAAATGATATCTT
25773650 AAGCTGCTGTCCATTACGTTTCCTTATGGTAAACAAAACAAACA
66 AAGCTGCTGTCCATTACGTTTCCTTATGGTAAACAAAACAAACA
25773694 TATTTCGAGCTGAGATGAGCTGCATGCACATATTTGAGCTTCAACCGAGCTAGAAATGATATCTT
1 TATTTCGAGCTGAGATGAGCTGCATGCACATATTTGAGCTTCAACCGAGCTAGAAATGATATCTT
25773759 AAGCTGCTGTCCATTACGTTTCCTTATGGTAAACAAAACAAACA
66 AAGCTGCTGTCCATTACGTTTCCTTATGGTAAACAAAACAAACA
25773803 T
1 T
25773804 GCATTAAAGT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (109 bp):
TATTTCGAGCTGAGATGAGCTGCATGCACATATTTGAGCTTCAACCGAGCTAGAAATGATATCTT
AAGCTGCTGTCCATTACGTTTCCTTATGGTAAACAAAACAAACA
Found at i:25774867 original size:11 final size:11
Alignment explanation
Indices: 25774851--25774878 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
25774841 TTTAATTAGG
25774851 TGTTTTAAATA
1 TGTTTTAAATA
25774862 TGTTTTAAATA
1 TGTTTTAAATA
25774873 TGTTTT
1 TGTTTT
25774879 GTTAATGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (11 bp):
TGTTTTAAATA
Found at i:25775005 original size:41 final size:41
Alignment explanation
Indices: 25774944--25775051 Score: 180
Period size: 41 Copynumber: 2.6 Consensus size: 41
25774934 TTTAATATGT
* *
25774944 CGAATTTAATGCTGCCACTACATGTTATAAATGTGTCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
*
25774985 CGAATTTAATGCTGCGACTACATGTTATAAATATGCCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
*
25775026 CGAATTTAATGCTGCTACTACATGTT
1 CGAATTTAATGCTGCCACTACATGTT
25775052 TGGCCGAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (41 bp):
CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
Found at i:25778819 original size:24 final size:24
Alignment explanation
Indices: 25778787--25778848 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
25778777 CCTTTTTGAG
25778787 CCATTTCGTACCAAAAATCCCATA
1 CCATTTCGTACCAAAAATCCCATA
25778811 CCATTTCGTACCAAAAATCCCATA
1 CCATTTCGTACCAAAAATCCCATA
*
25778835 CCATTTTGTACCAA
1 CCATTTCGTACCAA
25778849 TACCCAATTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.35, C:0.32, G:0.05, T:0.27
Consensus pattern (24 bp):
CCATTTCGTACCAAAAATCCCATA
Found at i:25783106 original size:21 final size:21
Alignment explanation
Indices: 25783073--25783125 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
25783063 TACCAATTTG
*
25783073 TACCAAATACCATACCATTTCA
1 TACC-AATTCCATACCATTTCA
*
25783095 TACCAATTCCATACCATTTCC
1 TACCAATTCCATACCATTTCA
25783116 TACCAATTCC
1 TACCAATTCC
25783126 CAAATACCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30
Consensus pattern (21 bp):
TACCAATTCCATACCATTTCA
Found at i:25783109 original size:11 final size:11
Alignment explanation
Indices: 25783082--25783125 Score: 56
Period size: 10 Copynumber: 4.2 Consensus size: 11
25783072 GTACCAAATA
25783082 CCATACC-ATT
1 CCATACCAATT
*
25783092 TCATACCAATT
1 CCATACCAATT
*
25783103 CCATACCATTT
1 CCATACCAATT
25783114 CC-TACCAATT
1 CCATACCAATT
25783124 CC
1 CC
25783126 CAAATACCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 15 0.52
11 14 0.48
ACGTcount: A:0.30, C:0.39, G:0.00, T:0.32
Consensus pattern (11 bp):
CCATACCAATT
Found at i:25785070 original size:20 final size:20
Alignment explanation
Indices: 25785045--25785099 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
25785035 GCGAAAATAC
*
25785045 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
25785065 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
*
25785084 AAAAGAGAATGAAAAA
1 AAAAGA-AAAGAAAAA
25785100 AATGAGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 17 0.59
20 5 0.17
21 7 0.24
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:25785077 original size:36 final size:33
Alignment explanation
Indices: 25785026--25785101 Score: 89
Period size: 36 Copynumber: 2.2 Consensus size: 33
25785016 AATGAGAGAA
**
25785026 AAAAAAAGAGCGAAAATACAAAAGAAAAGAAAAATG
1 AAAAAAAGAAAGAAAATAC-AAA-AAAAG-AAAATG
* *
25785062 AAAAAAAGAAAGAAAATTCAAAAAAAGAGAATG
1 AAAAAAAGAAAGAAAATACAAAAAAAGAAAATG
25785095 AAAAAAA
1 AAAAAAA
25785102 TGAGAAAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 12 0.33
34 5 0.14
35 3 0.08
36 16 0.44
ACGTcount: A:0.75, C:0.04, G:0.14, T:0.07
Consensus pattern (33 bp):
AAAAAAAGAAAGAAAATACAAAAAAAGAAAATG
Found at i:25785131 original size:15 final size:16
Alignment explanation
Indices: 25785094--25785131 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
25785084 AAAAGAGAAT
*
25785094 GAAAAAAATGAGAAAA
1 GAAAAAGATGAGAAAA
*
25785110 GCAAAAGATGA-AAAA
1 GAAAAAGATGAGAAAA
25785125 GAAAAAG
1 GAAAAAG
25785132 TGATTGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.71, C:0.03, G:0.21, T:0.05
Consensus pattern (16 bp):
GAAAAAGATGAGAAAA
Found at i:25790175 original size:11 final size:11
Alignment explanation
Indices: 25790159--25790183 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25790149 GGCTTTGAAT
25790159 ACTTAGCCCAA
1 ACTTAGCCCAA
25790170 ACTTAGCCCAA
1 ACTTAGCCCAA
25790181 ACT
1 ACT
25790184 CTTTTGAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.08, T:0.20
Consensus pattern (11 bp):
ACTTAGCCCAA
Found at i:25790337 original size:28 final size:28
Alignment explanation
Indices: 25790297--25790352 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
25790287 AGGCCGGATC
25790297 GCATCACTGATGAACAAGAAAATTCTTT
1 GCATCACTGATGAACAAGAAAATTCTTT
25790325 GCATCACTGATGAACAAGAAAATTCTTT
1 GCATCACTGATGAACAAGAAAATTCTTT
25790353 TAATAAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (28 bp):
GCATCACTGATGAACAAGAAAATTCTTT
Found at i:25794062 original size:22 final size:21
Alignment explanation
Indices: 25794014--25794062 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
25794004 TTATCTTTAT
*
25794014 AAATTTATTTTTAAAATTTTA
1 AAATTTATTTTTAAAATTTCA
* *
25794035 ATATTTAGTTTTTCAAATTTCA
1 AAATTTA-TTTTTAAAATTTCA
25794057 AAATTT
1 AAATTT
25794063 CAATTCTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (21 bp):
AAATTTATTTTTAAAATTTCA
Found at i:25794171 original size:18 final size:20
Alignment explanation
Indices: 25794134--25794170 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
25794124 TTATTAATAA
25794134 TGTAATTAAAAAAATAAAAT
1 TGTAATTAAAAAAATAAAAT
*
25794154 TGTAA-TAAAAAACTAAA
1 TGTAATTAAAAAAATAAA
25794171 TAATAGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (20 bp):
TGTAATTAAAAAAATAAAAT
Found at i:25799204 original size:22 final size:20
Alignment explanation
Indices: 25799187--25799247 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
25799177 CCAAAATGAG
25799187 ATTGAGAAAAGAAAAAAAGA
1 ATTGAGAAAAGAAAAAAAGA
*
25799207 AATGAGAGAAA-AAGAAAAAGA
1 ATTGAGA-AAAGAA-AAAAAGA
25799228 CATTGA-AAAAGAAAAAAAGA
1 -ATTGAGAAAAGAAAAAAAGA
25799248 GTGAGAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 18 0.51
21 13 0.37
22 4 0.11
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.08
Consensus pattern (20 bp):
ATTGAGAAAAGAAAAAAAGA
Found at i:25799211 original size:41 final size:41
Alignment explanation
Indices: 25799165--25799247 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
25799155 TAATGCGAGA
** * *
25799165 AAATGA-ACAAATCCAAAATGAGATTGAGAAAAGAAAAAAAG
1 AAATGAGACAAAAACAAAAAGACATTGA-AAAAGAAAAAAAG
* *
25799206 AAATGAGAGAAAAAGAAAAAGACATTGAAAAAGAAAAAAAG
1 AAATGAGACAAAAACAAAAAGACATTGAAAAAGAAAAAAAG
25799247 A
1 A
25799248 GTGAGAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 20 0.57
42 15 0.43
ACGTcount: A:0.67, C:0.05, G:0.18, T:0.10
Consensus pattern (41 bp):
AAATGAGACAAAAACAAAAAGACATTGAAAAAGAAAAAAAG
Found at i:25801253 original size:22 final size:22
Alignment explanation
Indices: 25801225--25801274 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
25801215 AGTTGTAAAG
* *
25801225 TTTTATTTTTATTTA-TTTATT
1 TTTTATTTTTACTTAGTTTAAT
25801246 TGTTTATTTTTACTTAGTTTAAT
1 T-TTTATTTTTACTTAGTTTAAT
25801269 TTTTAT
1 TTTTAT
25801275 GTAAATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 18 0.72
23 6 0.24
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTACTTAGTTTAAT
Found at i:25810184 original size:22 final size:22
Alignment explanation
Indices: 25810130--25810186 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
25810120 ACCTTTTTGA
*
25810130 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
25810153 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
25810175 TCCATACCATTT
1 ACCATACCATTT
25810187 TGTGCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:25810194 original size:22 final size:21
Alignment explanation
Indices: 25810135--25810198 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
25810125 TTTGAACCAT
* *
25810135 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
25810157 TACCATTTCGTACCAACTTCCA
1 TACCATTTCGTACCAA-TTCCA
* *
25810179 TACCATTTTGTGCCAATTCC
1 TACCATTTCGTACCAATTCC
25810199 TAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 6 0.16
22 31 0.84
ACGTcount: A:0.30, C:0.33, G:0.06, T:0.31
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:25810527 original size:29 final size:29
Alignment explanation
Indices: 25810493--25810565 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
25810483 TTAGATATTA
* *
25810493 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
25810522 TTAAATATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
25810551 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
25810566 ACTAATACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:25819177 original size:20 final size:20
Alignment explanation
Indices: 25819152--25819194 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
25819142 AAAAGAAAAG
25819152 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
25819172 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
25819192 AAA
1 AAA
25819195 ACAAGAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:25832611 original size:11 final size:12
Alignment explanation
Indices: 25832593--25832622 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
25832583 TACGGTATTG
25832593 TAAAAAAATCAA
1 TAAAAAAATCAA
25832605 TAAAAAAATCAA
1 TAAAAAAATCAA
25832617 TAAAAA
1 TAAAAA
25832623 TTTCGTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (12 bp):
TAAAAAAATCAA
Found at i:25838634 original size:13 final size:13
Alignment explanation
Indices: 25838616--25838641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25838606 TATTCTGCAT
25838616 TTAAACAACAGCA
1 TTAAACAACAGCA
25838629 TTAAACAACAGCA
1 TTAAACAACAGCA
25838642 GCATTAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (13 bp):
TTAAACAACAGCA
Found at i:25838643 original size:16 final size:17
Alignment explanation
Indices: 25838619--25838661 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
25838609 TCTGCATTTA
*
25838619 AACAACAGCATT-AAAC
1 AACAGCAGCATTAAAAC
25838635 AACAGCAGCATTAAAAC
1 AACAGCAGCATTAAAAC
25838652 AACAGCAGCA
1 AACAGCAGCA
25838662 AAACACATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.53, C:0.26, G:0.12, T:0.09
Consensus pattern (17 bp):
AACAGCAGCATTAAAAC
Found at i:25842671 original size:18 final size:18
Alignment explanation
Indices: 25842650--25842684 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25842640 TTTTTCTTTT
25842650 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
25842668 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
25842685 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:25871700 original size:27 final size:28
Alignment explanation
Indices: 25871663--25871727 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
25871653 TGTTTTTTTA
* *
25871663 CTTTCACTTTCTTTTTC-TTTTTCATTT
1 CTTTCAATTTCTTTTTCATTGTTCATTT
*
25871690 CTTTCAATTTCTTTTTCATTGTTCGTTT
1 CTTTCAATTTCTTTTTCATTGTTCATTT
*
25871718 CTCTCAATTT
1 CTTTCAATTT
25871728 TTCCACAGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.11, C:0.22, G:0.03, T:0.65
Consensus pattern (28 bp):
CTTTCAATTTCTTTTTCATTGTTCATTT
Found at i:25873874 original size:16 final size:16
Alignment explanation
Indices: 25873853--25873896 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
25873843 AGACCGTATA
25873853 CAATTTTTTTTCTTTT
1 CAATTTTTTTTCTTTT
25873869 CAATTTTTTTTCTTTT
1 CAATTTTTTTTCTTTT
* *
25873885 GATTTTTTTTTC
1 CAATTTTTTTTC
25873897 GATTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.75
Consensus pattern (16 bp):
CAATTTTTTTTCTTTT
Found at i:25873890 original size:12 final size:12
Alignment explanation
Indices: 25873874--25873920 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
25873864 CTTTTCAATT
*
25873874 TTTTTTCTTTTGA
1 TTTTTT-TTTCGA
25873887 TTTTTTTTTCGA
1 TTTTTTTTTCGA
*
25873899 TTTTTTTTTCAAA
1 TTTTTTTTTC-GA
25873912 TTTTTTTTT
1 TTTTTTTTT
25873921 AGAAATCTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
12 15 0.48
13 16 0.52
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTCGA
Found at i:25882771 original size:52 final size:52
Alignment explanation
Indices: 25882688--25882788 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
25882678 TAAGGAAACG
* *
25882688 TAATGGACAGCAGCTTAAAATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAAACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
*
25882740 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAAACCTCATTTCTAGCTCGGTTGAAGCTCAAA
25882789 TATGTGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAAACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:25884787 original size:42 final size:42
Alignment explanation
Indices: 25884728--25884810 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
25884718 AAATTCAAAG
25884728 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
25884770 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
25884811 CACACATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (42 bp):
GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
Found at i:25887511 original size:20 final size:20
Alignment explanation
Indices: 25887486--25887532 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
25887476 AGCTCATTTC
*
25887486 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
25887506 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
25887526 CAGCTCA
1 CAGCTCA
25887533 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:25887535 original size:10 final size:10
Alignment explanation
Indices: 25887476--25887535 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
25887466 AGCTCTGTTT
*
25887476 AGCTCATTTCC
1 AGCTCAATT-C
* *
25887487 AGCTCACTTG
1 AGCTCAATTC
*
25887497 AGCTCAAGTC
1 AGCTCAATTC
25887507 AGCTC-ATTC
1 AGCTCAATTC
*
25887516 GAGATCAATTC
1 -AGCTCAATTC
25887527 AGCTCAATT
1 AGCTCAATT
25887536 TTAACCCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 3 0.08
10 24 0.62
11 12 0.31
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:25889771 original size:14 final size:15
Alignment explanation
Indices: 25889739--25889777 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
25889729 AAAAAAAATC
*
25889739 AAAAAATTTGAAAAG
1 AAAAAAATTGAAAAG
25889754 AAAAAAATTGAAAA-
1 AAAAAAATTGAAAAG
*
25889768 AAAAATATTG
1 AAAAAAATTG
25889778 CATACGGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (15 bp):
AAAAAAATTGAAAAG
Done.