Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 92 of 345
Found at i:30363104 original size:7 final size:7
Alignment explanation
Indices: 30363090--30363163 Score: 53
Period size: 7 Copynumber: 10.6 Consensus size: 7
30363080 TTATTTTTCG
30363090 TAAA-TT
1 TAAATTT
30363096 TAAATTT
1 TAAATTT
*
30363103 TAAAATT
1 TAAATTT
30363110 T-AATTT
1 TAAATTT
*
30363116 TTAATTT
1 TAAATTT
* *
30363123 CAAGAATT
1 TAA-ATTT
*
30363131 TAATTTT
1 TAAATTT
30363138 TAAATTT
1 TAAATTT
*
30363145 TCAGATTT
1 T-AAATTT
*
30363153 TAAAATT
1 TAAATTT
30363160 TAAA
1 TAAA
30363164 CTCAACTATT
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
6 9 0.17
7 32 0.62
8 11 0.21
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (7 bp):
TAAATTT
Found at i:30363119 original size:21 final size:22
Alignment explanation
Indices: 30363094--30363155 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
30363084 TTTTCGTAAA
30363094 TTTAAATTTTAA-AATTTAATT
1 TTTAAATTTTAAGAATTTAATT
*
30363115 TTT-AATTTCAAGAATTTAATT
1 TTTAAATTTTAAGAATTTAATT
* *
30363136 TTTAAATTTTCAGATTTTAA
1 TTTAAATTTTAAGAATTTAA
30363156 AATTTAAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.20
21 15 0.43
22 13 0.37
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (22 bp):
TTTAAATTTTAAGAATTTAATT
Found at i:30363396 original size:8 final size:8
Alignment explanation
Indices: 30363385--30363415 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
30363375 AAAAAAGGGA
30363385 AAAAAATT
1 AAAAAATT
30363393 AAAAAATT
1 AAAAAATT
30363401 AAAAAATT
1 AAAAAATT
30363409 AAAAAAT
1 AAAAAAT
30363416 AATAATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAAATT
Found at i:30372996 original size:46 final size:46
Alignment explanation
Indices: 30372769--30372996 Score: 341
Period size: 46 Copynumber: 5.0 Consensus size: 46
30372759 TTTGACATGA
* * * * * *
30372769 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* * *
30372815 TGCCATGGTATCTTTCAACCATGGTCTTACACTTTTCATGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
30372861 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
**
30372907 TGCCACAGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
30372953 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
30372997 AGAGCACACT
Statistics
Matches: 169, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 4 0.02
46 165 0.98
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:30385073 original size:27 final size:26
Alignment explanation
Indices: 30385040--30385120 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 26
30385030 TGTAATAATG
30385040 ATATATACACAATATGGTATTAAGAAT
1 ATATATACACAATATGGTATTAA-AAT
* *
30385067 ATATATATACAATATAGTATTTAAAA-
1 ATATATACACAATATGGTA-TTAAAAT
* * *
30385093 ATATATACATAAGATGGTATAAAAAT
1 ATATATACACAATATGGTATTAAAAT
30385119 AT
1 AT
30385121 GTACATGGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
25 5 0.11
26 17 0.38
27 19 0.42
28 4 0.09
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.35
Consensus pattern (26 bp):
ATATATACACAATATGGTATTAAAAT
Found at i:30385115 original size:24 final size:23
Alignment explanation
Indices: 30385069--30385193 Score: 87
Period size: 24 Copynumber: 5.2 Consensus size: 23
30385059 TTAAGAATAT
*
30385069 ATATATACAATATAG-TATTTAAAA
1 ATATATAC-ATA-AGATATATAAAA
*
30385093 ATATATACATAAGATGGTATAAAA
1 ATATATACATAAGAT-ATATAAAA
* *
30385117 ATATGTACATGGAA-ATGTATAAGAA
1 ATATATACAT--AAGATATATAA-AA
*
30385142 ATATATA-ATTAG-TAATATTAAAA
1 ATATATACATAAGAT-ATA-TAAAA
*
30385165 ATATATACATAACATATATAAAA
1 ATATATACATAAGATATATAAAA
30385188 CATATA
1 -ATATA
30385194 CAATATATAC
Statistics
Matches: 82, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
22 4 0.05
23 20 0.24
24 45 0.55
25 11 0.13
26 2 0.02
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (23 bp):
ATATATACATAAGATATATAAAA
Found at i:30385274 original size:16 final size:17
Alignment explanation
Indices: 30385243--30385277 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
30385233 AACTACTTTG
30385243 TACACTACACAAATATA
1 TACACTACACAAATATA
*
30385260 TACAC-ACACATATATA
1 TACACTACACAAATATA
30385276 TA
1 TA
30385278 TATAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (17 bp):
TACACTACACAAATATA
Found at i:30385337 original size:44 final size:43
Alignment explanation
Indices: 30385277--30385371 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 43
30385267 ACATATATAT
30385277 ATATAA-ATAATAGTATTAGAAATATACAA-T-ATAATATTAGAA
1 ATATAATATAATAGTATTA-AAATATACAACTAATAATATTA-AA
*
30385319 ATATACATATAATAGTATTAAAATATATAACTAATAATATTAAA
1 ATATA-ATATAATAGTATTAAAATATACAACTAATAATATTAAA
30385363 ATATAATAT
1 ATATAATAT
30385372 TGAAAACATA
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
42 5 0.10
43 14 0.29
44 20 0.42
45 9 0.19
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (43 bp):
ATATAATATAATAGTATTAAAATATACAACTAATAATATTAAA
Found at i:30385345 original size:22 final size:22
Alignment explanation
Indices: 30385277--30385367 Score: 109
Period size: 22 Copynumber: 4.2 Consensus size: 22
30385267 ACATATATAT
*
30385277 ATATA-AATAATAGTATTAGAA
1 ATATACAATAATAATATTAGAA
30385298 ATATACAAT-ATAATATTAGAA
1 ATATACAATAATAATATTAGAA
*
30385319 ATATACATATAATAGTATTA-AA
1 ATATACA-ATAATAATATTAGAA
*
30385341 ATATATAACTAATAATATTA-AA
1 ATATACAA-TAATAATATTAGAA
30385363 ATATA
1 ATATA
30385368 ATATTGAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
21 24 0.39
22 30 0.48
23 8 0.13
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATACAATAATAATATTAGAA
Found at i:30385539 original size:16 final size:17
Alignment explanation
Indices: 30385501--30385541 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
30385491 AAGTATATAA
*
30385501 AAAGTAA-ATATAATAT
1 AAAGTAATATATAAAAT
30385517 AATAGTAATAT-TAAAAT
1 AA-AGTAATATATAAAAT
30385534 AAAGTAAT
1 AAAGTAAT
30385542 TAAAATAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 12 0.55
18 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (17 bp):
AAAGTAATATATAAAAT
Found at i:30385586 original size:21 final size:20
Alignment explanation
Indices: 30385566--30385605 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
30385556 ATGTAAATAT
30385566 ATATACATACA-T-ATA-TA
1 ATATACATACACTAATATTA
30385583 ATATACATACACTAATATTA
1 ATATACATACACTAATATTA
30385603 ATA
1 ATA
30385606 ATAATAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 1 0.05
19 3 0.15
20 5 0.25
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (20 bp):
ATATACATACACTAATATTA
Found at i:30385588 original size:17 final size:16
Alignment explanation
Indices: 30385562--30385593 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
30385552 CTATATGTAA
30385562 ATATATATACATACAT
1 ATATATATACATACAT
30385578 ATATAATATACATACA
1 ATAT-ATATACATACA
30385594 CTAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATATATACATACAT
Found at i:30385609 original size:3 final size:3
Alignment explanation
Indices: 30385595--30385755 Score: 59
Period size: 3 Copynumber: 53.7 Consensus size: 3
30385585 ATACATACAC
* *
30385595 TAA TAT TAA TAA TAA TAA -AA CTAGA -AA TAA TAA TAA TTAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TA-A TAA TAA TAA TAA -TAA TAA TAA
* * * ** * *
30385641 TAA TACG TTA GAA -AA TAA TTAA T-A TGT TAA TAA AAA TAA TAG TAA
1 TAA TA-A TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
30385686 TGAA -AA TAA TAC TAA CAG TAA TAA TAA -AGA TAA TAA TAGA -AA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA
** *
30385731 -AA TAA TCG TAA TAA TAT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
30385756 TGTAAAAAAA
Statistics
Matches: 114, Mismatches: 28, Indels: 32
0.66 0.16 0.18
Matches are distributed among these distances:
2 13 0.11
3 89 0.78
4 11 0.10
5 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:30387604 original size:14 final size:15
Alignment explanation
Indices: 30387585--30387614 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
30387575 AATTGCATTT
30387585 TAAATATT-ATTTTA
1 TAAATATTAATTTTA
30387599 TAAATATTAATTTTA
1 TAAATATTAATTTTA
30387614 T
1 T
30387615 TCATAGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAAATATTAATTTTA
Found at i:30391272 original size:37 final size:37
Alignment explanation
Indices: 30391211--30391356 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
30391201 TACGTATGAT
* *
30391211 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
30391246 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
30391283 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
30391320 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
30391357 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:30391373 original size:46 final size:46
Alignment explanation
Indices: 30391320--30391634 Score: 398
Period size: 46 Copynumber: 6.6 Consensus size: 46
30391310 TAAGTGTAGC
* * **
30391320 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
30391366 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
30391412 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
30391458 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
30391510 CACTTATCACTTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCAC-TTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * ** *
30391557 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAG-TAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
30391608 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
30391635 GTACTCAAAT
Statistics
Matches: 246, Mismatches: 12, Indels: 23
0.88 0.04 0.08
Matches are distributed among these distances:
45 16 0.07
46 99 0.40
47 43 0.17
48 2 0.01
49 2 0.01
50 2 0.01
51 15 0.06
52 67 0.27
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:30391489 original size:52 final size:52
Alignment explanation
Indices: 30391409--30391628 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
30391399 TAGCCGAAGC
* *
30391409 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
30391462 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
30391514 TATCAC--TT---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
30391561 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAG-TAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
30391612 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
30391629 ATCAGAGTAC
Statistics
Matches: 149, Mismatches: 12, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
47 43 0.29
49 1 0.01
50 2 0.01
51 18 0.12
52 73 0.49
53 12 0.08
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:30391535 original size:47 final size:46
Alignment explanation
Indices: 30391462--30391634 Score: 215
Period size: 47 Copynumber: 3.7 Consensus size: 46
30391452 AGCTATCACT
*
30391462 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGC
1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
30391507 TATCACTTATCACTTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
1 TATCACTTATCAC-TTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
* **
30391554 TATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAG-TAAAGC
1 TATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
30391605 TACCACTTATCACTTTGTCACTTGATCAGA
1 TATCACTTATCACTTTGTCACTTGATCAGA
30391635 GTACTCAAAT
Statistics
Matches: 113, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
45 28 0.25
47 43 0.38
48 2 0.02
49 1 0.01
51 15 0.13
52 24 0.21
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
Found at i:30391545 original size:99 final size:98
Alignment explanation
Indices: 30391320--30391634 Score: 464
Period size: 99 Copynumber: 3.3 Consensus size: 98
30391310 TAAGTGTAGC
* * **
30391320 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAC---T---TT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTT
* *
30391379 GTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
30391412 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTT
30391477 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
30391510 CACTTATCACTTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1 CACTTATCAC-TTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACT
** *
30391575 TGTCACTTGATCAGATAAGTGTAG-TAAAGCTAC
65 TGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
30391608 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
30391635 GTACTCAAAT
Statistics
Matches: 205, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
92 53 0.26
95 1 0.00
97 17 0.08
98 59 0.29
99 75 0.37
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:30394340 original size:48 final size:48
Alignment explanation
Indices: 30394269--30394461 Score: 177
Period size: 53 Copynumber: 4.0 Consensus size: 48
30394259 CTTCGTTTCT
*
30394269 CGATGCATAGTCCA-ACTATGGTCTTACACGTAATCACA-AATCACATAC
1 CGATGCATAGCCCAGA-TATGGTCTTACACG-AATCACACAATCACATAC
30394317 CGATGCCATAGCCCA-ATATGGTCTTACACGAAT--CAC-ATCAC-TAC
1 CGATG-CATAGCCCAGATATGGTCTTACACGAATCACACAATCACATAC
* * *
30394361 CGATGCCATAGCCCAGCTATGGTCTTACAAATCACATATCACACATAT-ACTTAC
1 CGATG-CATAGCCCAGATATGGTCTTAC--A-C-GA-ATCACACA-ATCACATAC
* *
30394415 CGATGCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCATAGCCCAGATATGGTCTTACAC-GAATCACACAATCACAT
30394462 GTTCACATGT
Statistics
Matches: 124, Mismatches: 7, Indels: 27
0.78 0.04 0.17
Matches are distributed among these distances:
44 18 0.15
45 18 0.15
47 4 0.03
48 22 0.18
49 20 0.16
50 4 0.03
51 1 0.01
52 3 0.02
53 24 0.19
54 10 0.08
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.24
Consensus pattern (48 bp):
CGATGCATAGCCCAGATATGGTCTTACACGAATCACACAATCACATAC
Found at i:30395773 original size:37 final size:37
Alignment explanation
Indices: 30395712--30395857 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
30395702 TACGTATGAT
* *
30395712 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
30395747 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
30395784 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
30395821 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
30395858 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:30395874 original size:46 final size:46
Alignment explanation
Indices: 30395821--30396134 Score: 421
Period size: 46 Copynumber: 6.6 Consensus size: 46
30395811 TAAGTGTAGC
* **
30395821 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
30395867 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
30395913 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
30395959 CACTTATCACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC--T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
30396010 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
30396056 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
30396108 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
30396135 AGTACTCAAA
Statistics
Matches: 244, Mismatches: 13, Indels: 22
0.87 0.05 0.08
Matches are distributed among these distances:
46 156 0.64
48 2 0.01
49 1 0.00
50 1 0.00
51 44 0.18
52 40 0.16
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:30396034 original size:97 final size:97
Alignment explanation
Indices: 30395821--30396134 Score: 476
Period size: 97 Copynumber: 3.3 Consensus size: 97
30395811 TAAGTGTAGC
* **
30395821 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAC--T---TTG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTG
* *
30395881 TCTCTTGATCAGATAAGTATAGCCGAAGCTAT
66 TCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
30395913 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTG
30395978 TCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 TCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
30396010 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT-CACTT
** *
30396075 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
65 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
30396108 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
30396135 AGTACTCAAA
Statistics
Matches: 205, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
92 54 0.26
94 1 0.00
97 89 0.43
98 61 0.30
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (97 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTG
TCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:30396086 original size:52 final size:52
Alignment explanation
Indices: 30396007--30396120 Score: 158
Period size: 52 Copynumber: 2.2 Consensus size: 52
30395997 TAGCCGAAGC
* **
30396007 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTT-TCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
* *
30396060 TATCACTTTCCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTT-CACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
30396112 TATCACTTT
1 TATCACTTT
30396121 ATCACTTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
52 44 0.80
53 11 0.20
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (52 bp):
TATCACTTTCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTACCACT
Found at i:30396100 original size:143 final size:139
Alignment explanation
Indices: 30395820--30396134 Score: 427
Period size: 143 Copynumber: 2.2 Consensus size: 139
30395810 ATAAGTGTAG
* * *
30395820 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCAC
*
30395885 TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAAGTGT-AG
66 TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAAG
**
30395949 CCGAAGCTA
131 CTAAAGCTA
* *
30395958 TCACTTATCACTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
1 CCACTTATCAC--T---TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTT
*
30396023 GTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAG
61 GTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCAC--T----TTGTCACTTGATCAG
30396088 ATAAGTGT-AGCTAAAGCTA
120 ATAAGTGTAAGCTAAAGCTA
*
30396107 CCACTTATCACTTTATCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
30396135 AGTACTCAAA
Statistics
Matches: 155, Mismatches: 11, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
138 10 0.06
140 1 0.01
143 86 0.55
144 15 0.10
145 1 0.01
147 1 0.01
149 41 0.26
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (139 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCAC
TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAAG
CTAAAGCTA
Found at i:30398402 original size:24 final size:24
Alignment explanation
Indices: 30398370--30398466 Score: 114
Period size: 24 Copynumber: 4.2 Consensus size: 24
30398360 ATATAAAAAA
30398370 AAATTTACATGGAAAAAAGTAA-TT
1 AAATTTACATGGAAAAAA-TAATTT
30398394 AAATTTACATGGAAAAAATAATTT
1 AAATTTACATGGAAAAAATAATTT
* * *
30398418 AAA-TGAAAT--AAGAAAA-AAATT
1 AAATTTACATGGAA-AAAATAATTT
30398439 AAATTTACATGGAAAAAATAATTT
1 AAATTTACATGGAAAAAATAATTT
30398463 AAAT
1 AAAT
30398467 GAAATAAGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
21 9 0.15
22 8 0.13
23 11 0.18
24 33 0.54
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (24 bp):
AAATTTACATGGAAAAAATAATTT
Found at i:30398442 original size:21 final size:21
Alignment explanation
Indices: 30398407--30398487 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 21
30398397 TTTACATGGA
30398407 AAAAATAATTTAAATGAAATAAG
1 AAAAA-AA-TTAAATGAAATAAG
* *
30398430 AAAAAAATTAAATTTACATGGAA-
1 AAAAAAATTAAA-TGAAAT--AAG
*
30398453 AAAATAATTTAAATGAAATAAG
1 AAAA-AAATTAAATGAAATAAG
30398475 AAAAAAATTAAAT
1 AAAAAAATTAAAT
30398488 TTAAATGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
21 15 0.32
22 10 0.21
23 13 0.28
24 9 0.19
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (21 bp):
AAAAAAATTAAATGAAATAAG
Found at i:30398446 original size:45 final size:45
Alignment explanation
Indices: 30398390--30398490 Score: 202
Period size: 45 Copynumber: 2.2 Consensus size: 45
30398380 GGAAAAAAGT
30398390 AATTAAATTTACATGGAAAAAATAATTTAAATGAAATAAGAAAAA
1 AATTAAATTTACATGGAAAAAATAATTTAAATGAAATAAGAAAAA
30398435 AATTAAATTTACATGGAAAAAATAATTTAAATGAAATAAGAAAAA
1 AATTAAATTTACATGGAAAAAATAATTTAAATGAAATAAGAAAAA
30398480 AATTAAATTTA
1 AATTAAATTTA
30398491 AATGAAATGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (45 bp):
AATTAAATTTACATGGAAAAAATAATTTAAATGAAATAAGAAAAA
Found at i:30398451 original size:69 final size:72
Alignment explanation
Indices: 30398370--30398574 Score: 233
Period size: 76 Copynumber: 2.8 Consensus size: 72
30398360 ATATAAAAAA
* * *
30398370 AAATTTACATGGAAAAAAGTAA-TTAAATTTACAT-GGAAAAAA-T-AATTTAAATGAAAT-A-A
1 AAATTTACATGGAAAAAA-TAATTTAAA-TGAAATAGAAAAAAATTAAATTTAAATGAAATGACA
30398429 GAAAAAAATT
64 -AAAAAAATT
30398439 AAATTTACATGGAAAAAATAATTTAAATGAAATAAGAAAAAAATTAAATTTAAATGAAATGACAA
1 AAATTTACATGGAAAAAATAATTTAAATGAAAT-AGAAAAAAATTAAATTTAAATGAAATGACAA
30398504 AAAAAATT
65 AAAAAATT
* * * *
30398512 AAATTAAAATGGGAAGATAAATAATTTAAATGAAATGAGAAAAAAAATAAACTTAAATGAAAT
1 AAATTTACAT-GGAA-A-AAATAATTTAAATGAAAT-AGAAAAAAATTAAATTTAAATGAAAT
30398575 AAAGAAAAAA
Statistics
Matches: 118, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
68 7 0.06
69 23 0.19
70 7 0.06
71 1 0.01
72 14 0.12
73 18 0.15
74 5 0.04
75 1 0.01
76 42 0.36
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.26
Consensus pattern (72 bp):
AAATTTACATGGAAAAAATAATTTAAATGAAATAGAAAAAAATTAAATTTAAATGAAATGACAAA
AAAAATT
Found at i:30398489 original size:27 final size:26
Alignment explanation
Indices: 30398451--30398594 Score: 122
Period size: 27 Copynumber: 5.6 Consensus size: 26
30398441 ATTTACATGG
30398451 AAAAAAT-AATTTAAATGAAATAAGA
1 AAAAAATAAATTTAAATGAAATAAGA
30398476 AAAAAATTAAATTTAAATGAAAT--GA
1 AAAAAA-TAAATTTAAATGAAATAAGA
* * **
30398501 CAAAAA-AAA-TTAAATTAAAATGGGA
1 AAAAAATAAATTTAAA-TGAAATAAGA
* *
30398526 AGATAAAT-AATTTAAATGAAATGAGAA
1 A-AAAAATAAATTTAAATGAAATAAG-A
*
30398553 AAAAAATAAACTTAAATGAAATAA-A
1 AAAAAATAAATTTAAATGAAATAAGA
*
30398578 GAAAAAATAAAGTTAAA
1 -AAAAAATAAATTTAAA
30398595 ACGGAAAGAA
Statistics
Matches: 98, Mismatches: 10, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
22 5 0.05
23 8 0.08
25 16 0.16
26 34 0.35
27 35 0.36
ACGTcount: A:0.66, C:0.01, G:0.10, T:0.23
Consensus pattern (26 bp):
AAAAAATAAATTTAAATGAAATAAGA
Found at i:30398553 original size:76 final size:70
Alignment explanation
Indices: 30398406--30398601 Score: 243
Period size: 76 Copynumber: 2.7 Consensus size: 70
30398396 ATTTACATGG
* *
30398406 AAAAAAT-AATTTAAATGAAATAAGAAAAAAATTAAATTTACATGGAAAAAATAATTTAAATGAA
1 AAAAAATAAATTTAAATGAAATAA-AAAAAAATTAAATTAAAATGGAAAAAATAATTTAAATGAA
30398470 ATAAGA
65 ATAAGA
30398476 AAAAAATTAAATTTAAATGAAATGACAAAAAAAATTAAATTAAAATGGGAAGATAAATAATTTAA
1 AAAAAA-TAAATTTAAATGAAAT-A-AAAAAAAATTAAATTAAAAT-GGAA-A-AAATAATTTAA
*
30398541 ATGAAATGAGAA
60 ATGAAATAAG-A
* *
30398553 AAAAAATAAACTTAAATGAAATAAAGAAAAAA-TAAAGTTAAAACGGAAA
1 AAAAAATAAATTTAAATGAAATAAA-AAAAAATTAAA-TTAAAATGGAAA
30398602 GAAAGATAAC
Statistics
Matches: 111, Mismatches: 5, Indels: 17
0.83 0.04 0.13
Matches are distributed among these distances:
70 6 0.05
71 1 0.01
72 14 0.13
73 19 0.17
74 15 0.14
75 14 0.13
76 35 0.32
77 7 0.06
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.23
Consensus pattern (70 bp):
AAAAAATAAATTTAAATGAAATAAAAAAAAATTAAATTAAAATGGAAAAAATAATTTAAATGAAA
TAAGA
Found at i:30398601 original size:28 final size:26
Alignment explanation
Indices: 30398553--30398607 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
30398543 GAAATGAGAA
* *
30398553 AAAAAATAAACTTAAATGAAATAAAG
1 AAAAAATAAACTTAAAGGAAAGAAAG
*
30398579 AAAAAATAAAGTTAAAACGGAAAGAAAG
1 AAAAAATAAACTT-AAA-GGAAAGAAAG
30398607 A
1 A
30398608 TAACTTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 12 0.50
27 3 0.12
28 9 0.38
ACGTcount: A:0.69, C:0.04, G:0.13, T:0.15
Consensus pattern (26 bp):
AAAAAATAAACTTAAAGGAAAGAAAG
Found at i:30398700 original size:23 final size:22
Alignment explanation
Indices: 30398656--30398700 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
30398646 ATTTGTATAG
*
30398656 GAAAAAAATAATAAATTTAAAT
1 GAAAAAAATAATAAATTGAAAT
30398678 GAAAAAAATTAATGAAA-TGAAAT
1 GAAAAAAA-TAAT-AAATTGAAAT
30398701 ATGAATATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 9 0.45
24 3 0.15
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (22 bp):
GAAAAAAATAATAAATTGAAAT
Found at i:30398869 original size:6 final size:6
Alignment explanation
Indices: 30398855--30398892 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
30398845 AAATAAATTT
* *
30398855 AAATG- AAATGA AAATGA AAATTA AAATAA AAATGA AAA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAA
30398893 AAAAAAGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (6 bp):
AAATGA
Found at i:30398898 original size:12 final size:12
Alignment explanation
Indices: 30398860--30398897 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
30398850 AATTTAAATG
*
30398860 AAATGAAAATGA
1 AAATGAAAATAA
*
30398872 AAATTAAAATAA
1 AAATGAAAATAA
30398884 AAATGAAAA-AA
1 AAATGAAAATAA
30398895 AAA
1 AAA
30398898 AGTTGAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 5 0.22
12 18 0.78
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAATGAAAATAA
Found at i:30398898 original size:18 final size:18
Alignment explanation
Indices: 30398860--30398898 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
30398850 AATTTAAATG
* **
30398860 AAATGAAAATGAAAATTA
1 AAATAAAAATGAAAAAAA
30398878 AAATAAAAATGAAAAAAA
1 AAATAAAAATGAAAAAAA
30398896 AAA
1 AAA
30398899 GTTGAAGTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (18 bp):
AAATAAAAATGAAAAAAA
Found at i:30399146 original size:25 final size:26
Alignment explanation
Indices: 30399100--30399149 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
30399090 ATGAGAAATT
* *
30399100 TTTTTTAATTTAAGTGAAATTTAAAA
1 TTTTGTAATGTAAGTGAAATTTAAAA
*
30399126 TTTTGTAATGTAA-TGATATTTAAA
1 TTTTGTAATGTAAGTGAAATTTAAA
30399150 TTGAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (26 bp):
TTTTGTAATGTAAGTGAAATTTAAAA
Found at i:30399256 original size:16 final size:15
Alignment explanation
Indices: 30399231--30399263 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
30399221 GAAAAAATAT
30399231 AAAATGAATTGAAAA
1 AAAATGAATTGAAAA
30399246 AAAATTGAATTGAAAA
1 AAAA-TGAATTGAAAA
30399262 AA
1 AA
30399264 GATAACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (15 bp):
AAAATGAATTGAAAA
Found at i:30399354 original size:5 final size:5
Alignment explanation
Indices: 30399344--30399555 Score: 52
Period size: 5 Copynumber: 38.4 Consensus size: 5
30399334 TAAAAAAATT
* * *
30399344 AATGA AATGA AATGTTA AATGA GATATGA ATATCA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATGA -A-ATGA A-ATGA AATGA AATG-A A-ATGA
* * * * *
30399396 AATGA ATATGA AATAA AATGA AATAA AAGTTTA AATGA AA-AA AATTATA
1 AATGA A-ATGA AATGA AATGA AATGA AA--TGA AATGA AATGA AA-T-GA
* * ** *
30399445 AATTTA AATGAA AATAAA AACTGA AATGA AAAAA AATGA AATTATA AAT-A
1 AA-TGA AATG-A AAT-GA AA-TGA AATGA AATGA AATGA AA-T-GA AATGA
* * *
30399495 AAT-A AATTTA AATGA AATGA AATGTA AACGA AATGA AATGGA AATTAA
1 AATGA AA-TGA AATGA AATGA AATG-A AATGA AATGA AAT-GA AA-TGA
30399543 AATGGA AATGA AA
1 AAT-GA AATGA AA
30399556 AAAAATAAAA
Statistics
Matches: 158, Mismatches: 26, Indels: 46
0.69 0.11 0.20
Matches are distributed among these distances:
4 10 0.06
5 74 0.47
6 49 0.31
7 25 0.16
ACGTcount: A:0.59, C:0.01, G:0.13, T:0.26
Consensus pattern (5 bp):
AATGA
Found at i:30399400 original size:35 final size:33
Alignment explanation
Indices: 30399344--30399434 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 33
30399334 TAAAAAAATT
*
30399344 AATGAAATGAAATGTTAAATGAGATATGAATATCA
1 AATGAAATGAAATGTTAAATGA-ATATGAA-ATAA
* *
30399379 AATGAAATGTAAT-TTGTAATGAATATGAAATAA
1 AATGAAATGAAATGTT-AAATGAATATGAAATAA
*
30399412 AATGAAAT-AAAAGTTTAAATGAA
1 AATGAAATGAAATG-TTAAATGAA
30399435 AAAAATTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
32 2 0.04
33 17 0.36
34 11 0.23
35 17 0.36
ACGTcount: A:0.54, C:0.01, G:0.15, T:0.30
Consensus pattern (33 bp):
AATGAAATGAAATGTTAAATGAATATGAAATAA
Found at i:30399522 original size:16 final size:16
Alignment explanation
Indices: 30399344--30399539 Score: 79
Period size: 16 Copynumber: 12.2 Consensus size: 16
30399334 TAAAAAAATT
30399344 AATGAAATGAAATGTTA
1 AATGAAATGAAATG-TA
*
30399361 AATGAGATATGAATAT-CA
1 AATGA-A-ATGAA-ATGTA
*
30399379 AATGAAATGTAATTTGT-
1 AATGAAATG-AA-ATGTA
*
30399396 AATGAATATGAAAT-AA
1 AATGAA-ATGAAATGTA
* *
30399412 AATGAAATAAAAGTTTA
1 AATGAAATGAAA-TGTA
* *
30399429 AATGAAA-AAAATTATA
1 AATGAAATGAAA-TGTA
* *
30399445 AATTTAAATGAAA-ATA
1 AA-TGAAATGAAATGTA
*
30399461 AA--AACTGAAATG-A
1 AATGAAATGAAATGTA
** *
30399474 AAAAAAATGAAATTATA
1 AATGAAATGAAA-TGTA
*
30399491 AAT-AAAT-AAATTTA
1 AATGAAATGAAATGTA
30399505 AATGAAATGAAATGTA
1 AATGAAATGAAATGTA
* *
30399521 AACGAAATGAAATGGA
1 AATGAAATGAAATGTA
30399537 AAT
1 AAT
30399540 TAAAATGGAA
Statistics
Matches: 140, Mismatches: 21, Indels: 37
0.71 0.11 0.19
Matches are distributed among these distances:
13 10 0.07
14 6 0.04
15 19 0.14
16 52 0.37
17 33 0.24
18 13 0.09
19 5 0.04
20 2 0.01
ACGTcount: A:0.59, C:0.02, G:0.13, T:0.27
Consensus pattern (16 bp):
AATGAAATGAAATGTA
Found at i:30399538 original size:11 final size:11
Alignment explanation
Indices: 30399504--30399555 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
30399494 AAATAAATTT
30399504 AAATGAAAT-G
1 AAATGAAATGG
*
30399514 AAATGTAAA-CG
1 AAATG-AAATGG
30399525 AAATGAAATGG
1 AAATGAAATGG
*
30399536 AAATTAAAATGG
1 AAA-TGAAATGG
30399548 AAATGAAA
1 AAATGAAA
30399556 AAAAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 8 0.23
11 17 0.49
12 10 0.29
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (11 bp):
AAATGAAATGG
Found at i:30400765 original size:104 final size:104
Alignment explanation
Indices: 30400623--30400812 Score: 256
Period size: 104 Copynumber: 1.8 Consensus size: 104
30400613 TTATAAATCA
* * *
30400623 TAAACAGTGAGTTATACGGCCCGAACACACGCCAATGTCATTACCTGTGTGACTCACACGGCCT-
1 TAAACAGTGAGTTACACAGCCCGAACACACGCCAATGTCATTACCCGTGTGACTCACACGGCCTA
*
30400687 GGGCACACACCCATGTTCCTGGTCATGTGGTTCTATAGTG
66 GGG-ACACACCCATGTCCCTGGTCATGTGGTTCTATAGTG
* * * * * * *
30400727 TAAATAGTGAGTTACACAGCCTGGACACACGCCCATGTCTTTACCCGTGTGGCTCACATGGCCTA
1 TAAACAGTGAGTTACACAGCCCGAACACACGCCAATGTCATTACCCGTGTGACTCACACGGCCTA
*
30400792 GGGACACGCCCATGTCCCTGG
66 GGGACACACCCATGTCCCTGG
30400813 CTATGTTGCT
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 70 0.96
105 3 0.04
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (104 bp):
TAAACAGTGAGTTACACAGCCCGAACACACGCCAATGTCATTACCCGTGTGACTCACACGGCCTA
GGGACACACCCATGTCCCTGGTCATGTGGTTCTATAGTG
Found at i:30402319 original size:20 final size:20
Alignment explanation
Indices: 30402291--30402328 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30402281 TAATTTTGAG
*
30402291 ACTTCTACTGACACAAGTCC
1 ACTTATACTGACACAAGTCC
*
30402311 ACTTATACTGATACAAGT
1 ACTTATACTGACACAAGT
30402329 ATATCTGAAA
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:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (20 bp):
ACTTATACTGACACAAGTCC
Found at i:30403134 original size:13 final size:14
Alignment explanation
Indices: 30403108--30403136 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
30403098 TAAGTTCATT
30403108 TATAAAATAATTAA
1 TATAAAATAATTAA
30403122 TATAAAA-AATTAA
1 TATAAAATAATTAA
30403135 TA
1 TA
30403137 AGATACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TATAAAATAATTAA
Found at i:30413674 original size:47 final size:47
Alignment explanation
Indices: 30413522--30413696 Score: 216
Period size: 47 Copynumber: 3.7 Consensus size: 47
30413512 TGTAACCCGC
* * * *
30413522 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGC-GTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTCACAT
30413568 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-AGTTCACAT
* * *
30413618 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTCACAT
30413662 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
30413697 AATGTTCAAC
Statistics
Matches: 111, Mismatches: 9, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
43 3 0.03
44 5 0.05
45 1 0.01
46 36 0.32
47 56 0.50
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTCACAT
Found at i:30414152 original size:30 final size:30
Alignment explanation
Indices: 30414118--30414177 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
30414108 CCTTAATACG
30414118 AACTTTGGCAAAATTATCA-TTTTACCCCTA
1 AACTTTGGCAAAATTA-CACTTTTACCCCTA
* * *
30414148 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTACCCCTA
30414178 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTACCCCTA
Found at i:30415835 original size:18 final size:18
Alignment explanation
Indices: 30415812--30415848 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
30415802 GCTAGGGCAA
*
30415812 ATGGAGAAGGAAGAAGAG
1 ATGGAGAAAGAAGAAGAG
30415830 ATGGAGAAAGAAGAAGAG
1 ATGGAGAAAGAAGAAGAG
30415848 A
1 A
30415849 AGCAAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (18 bp):
ATGGAGAAAGAAGAAGAG
Found at i:30423934 original size:25 final size:24
Alignment explanation
Indices: 30423906--30423962 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
30423896 TAATATAATA
*
30423906 ATATTATCTGATATT-TTATTAATTT
1 ATATTATCT-ATATTACTATT-ATTT
30423931 ATATTCATCTATATTACTATTATTT
1 ATATT-ATCTATATTACTATTATTT
*
30423956 AAATTAT
1 ATATTAT
30423963 TTAAAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 2 0.07
25 18 0.64
26 8 0.29
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (24 bp):
ATATTATCTATATTACTATTATTT
Found at i:30426948 original size:36 final size:36
Alignment explanation
Indices: 30426908--30426978 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
30426898 TTTAAGTTAA
*
30426908 TTAAATTATCTATCAAATATTCAAATATGTTAAATG
1 TTAAATTATCTATCAAATATTCAAATATGCTAAATG
* **
30426944 TTAAATTATCTGTCGGATATTCAAATATGCTAAAT
1 TTAAATTATCTATCAAATATTCAAATATGCTAAAT
30426979 ATTTGTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (36 bp):
TTAAATTATCTATCAAATATTCAAATATGCTAAATG
Found at i:30435235 original size:24 final size:23
Alignment explanation
Indices: 30435195--30435241 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
30435185 TTTTAATGTA
* *
30435195 TTAAGTATAATTCTTAAATATTT
1 TTAAGTATAAATATTAAATATTT
*
30435218 TTAAGTAATAAATATTAATTATTT
1 TTAAGT-ATAAATATTAAATATTT
30435242 ATAAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
TTAAGTATAAATATTAAATATTT
Found at i:30438281 original size:29 final size:28
Alignment explanation
Indices: 30438232--30438305 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
30438222 ATTTAATTAA
* * *
30438232 ATAAA-TTTAATAATATTAAAATTTAAAT
1 ATAAATTTTAA-AATATAAAAAATAAAAT
*
30438260 TTAAATTTTAAAATATAAAAAAATAAAAT
1 ATAAATTTTAAAATAT-AAAAAATAAAAT
30438289 ATAAATTCTTTAAAATA
1 ATAAA-T-TTTAAAATA
30438306 AAATTGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 9 0.24
29 18 0.49
30 1 0.03
31 9 0.24
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (28 bp):
ATAAATTTTAAAATATAAAAAATAAAAT
Found at i:30438616 original size:45 final size:46
Alignment explanation
Indices: 30438567--30438672 Score: 126
Period size: 46 Copynumber: 2.3 Consensus size: 46
30438557 CATTAGCAAT
* * *
30438567 TAATTAATTTTTTA-AAAATTATTTTTATA-ATTTTTATATTTTTAA
1 TAATTAATTATTTATAAAA-TATTTTTAAATATTTTTAAATTTTTAA
* *
30438612 TAATTTATAATTTATAAAATATTTTTAAATATTTTTAAATTTTTAA
1 TAATTAATTATTTATAAAATATTTTTAAATATTTTTAAATTTTTAA
* *
30438658 AAATTAATTAATTAT
1 TAATTAATTATTTAT
30438673 TGATGTGACC
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
45 20 0.40
46 30 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (46 bp):
TAATTAATTATTTATAAAATATTTTTAAATATTTTTAAATTTTTAA
Found at i:30438645 original size:28 final size:29
Alignment explanation
Indices: 30438602--30438659 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
30438592 TATAATTTTT
30438602 ATATTTTTAATAATTTAT-AATTTATAAA
1 ATATTTTTAATAATTTATAAATTTATAAA
* *
30438630 ATATTTTTAA-ATATTTTTAAATTTTTAAA
1 ATATTTTTAATA-ATTTATAAATTTATAAA
30438659 A
1 A
30438660 ATTAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 1 0.04
28 15 0.58
29 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATATTTTTAATAATTTATAAATTTATAAA
Found at i:30439827 original size:2 final size:2
Alignment explanation
Indices: 30439822--30439851 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
30439812 CCAATTATCA
*
30439822 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30439852 GAATATCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:30440107 original size:34 final size:35
Alignment explanation
Indices: 30440069--30440137 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
30440059 TATATATTGT
*
30440069 CTTGTGGTCC-AAAGTAGAGAAAAATATATGATGA
1 CTTGTGGTCCAAAAATAGAGAAAAATATATGATGA
*
30440103 CTTGTGGTCCAAAAATAGAGTAAAATATATGATGA
1 CTTGTGGTCCAAAAATAGAGAAAAATATATGATGA
30440138 TGACTTCAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 10 0.31
35 22 0.69
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.28
Consensus pattern (35 bp):
CTTGTGGTCCAAAAATAGAGAAAAATATATGATGA
Found at i:30446233 original size:19 final size:19
Alignment explanation
Indices: 30446209--30446253 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
30446199 GAAGTTGACT
30446209 GGAGATCTTCAATCTTGAA
1 GGAGATCTTCAATCTTGAA
30446228 GGAGATCTTCAATCTTGAA
1 GGAGATCTTCAATCTTGAA
30446247 GGAGATC
1 GGAGATC
30446254 CTACTTCTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (19 bp):
GGAGATCTTCAATCTTGAA
Found at i:30448689 original size:6 final size:6
Alignment explanation
Indices: 30448671--30448724 Score: 72
Period size: 6 Copynumber: 8.8 Consensus size: 6
30448661 AAAGTCTAGG
* * *
30448671 AAAATA CAAATA AACATA AAAATA AAAATA AAAACTA AGAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA-TA AAAATA AAAATA
30448720 AAAAT
1 AAAAT
30448725 TAAATTATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
6 36 0.88
7 5 0.12
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:30448715 original size:19 final size:18
Alignment explanation
Indices: 30448671--30448724 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 18
30448661 AAAGTCTAGG
* *
30448671 AAAATACAAATAAACATA
1 AAAATAAAAATAAAAATA
30448689 AAAATAAAAATAAAAACTA
1 AAAATAAAAATAAAAA-TA
*
30448708 AGAATAAAAATAAAAAT
1 AAAATAAAAATAAAAAT
30448725 TAAATTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.17
Consensus pattern (18 bp):
AAAATAAAAATAAAAATA
Found at i:30450356 original size:12 final size:15
Alignment explanation
Indices: 30450322--30450371 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
30450312 AAAATAAAGC
*
30450322 AATAATAA-AGAAAT
1 AATAATAATAGTAAT
*
30450336 AATTAATAAAAAG-AAT
1 AA-TAAT-AATAGTAAT
30450352 AATAATAATAGTAAT
1 AATAATAATAGTAAT
30450367 AATAA
1 AATAA
30450372 GAAGGAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.19
15 16 0.52
16 7 0.23
17 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (15 bp):
AATAATAATAGTAAT
Found at i:30452540 original size:52 final size:48
Alignment explanation
Indices: 30452521--30452723 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
30452511 TGACAAGTGG
* *
30452521 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
30452567 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
30452619 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
30452665 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
30452711 AAAGTGATAAGTG
1 AAAGTGATAAGTG
30452724 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:30452575 original size:98 final size:98
Alignment explanation
Indices: 30452455--30452723 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
30452445 TTTGAGTACT
*
30452455 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
30452520 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
30452553 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
30452618 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
30452651 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
30452716 GATAAGTG
65 GAAAAGTG
30452724 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:30452731 original size:37 final size:37
Alignment explanation
Indices: 30452687--30452832 Score: 224
Period size: 37 Copynumber: 4.0 Consensus size: 37
30452677 GATAGCTTTA
*
30452687 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
30452724 GCTACACTTATCCAATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
30452761 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
30452798 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
30452833 ATCATACGTA
Statistics
Matches: 100, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 85 0.85
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:30455035 original size:43 final size:43
Alignment explanation
Indices: 30454987--30455094 Score: 164
Period size: 43 Copynumber: 2.5 Consensus size: 43
30454977 GATTAACGAG
30454987 ATGTGATTATGTGTAAGACCATGACTGGGACATTGGCATCATT
1 ATGTGATTATGTGTAAGACCATGACTGGGACATTGGCATCATT
* **
30455030 ATGTGATTATGTGTAAGACCATGTCTGGGGTATTGGCATCATT
1 ATGTGATTATGTGTAAGACCATGACTGGGACATTGGCATCATT
*
30455073 ATTTGATT-TCGTGTAAGACCAT
1 ATGTGATTAT-GTGTAAGACCAT
30455095 AGCTGGGCTA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 1 0.02
43 59 0.98
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (43 bp):
ATGTGATTATGTGTAAGACCATGACTGGGACATTGGCATCATT
Found at i:30455101 original size:43 final size:43
Alignment explanation
Indices: 30454997--30455137 Score: 153
Period size: 43 Copynumber: 3.3 Consensus size: 43
30454987 ATGTGATTAT
* *
30454997 GTGTAAGACCATGACTGGGACATTGGCATCATTATGTGATTAT-
1 GTGTAAGACCATGACTGGGATATTGGCATCATTATTTGATT-TC
* *
30455040 GTGTAAGACCATGTCTGGGGTATTGGCATCATTATTTGATTTC
1 GTGTAAGACCATGACTGGGATATTGGCATCATTATTTGATTTC
* * * *
30455083 GTGTAAGACCAT-AGCTGGGCTATCGGTATCGA-TATTTGATTAC
1 GTGTAAGACCATGA-CTGGGATATTGGCATC-ATTATTTGATTTC
*
30455126 ATGTAAGACCAT
1 GTGTAAGACCAT
30455138 ATTTGGGATA
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
42 1 0.01
43 83 0.98
44 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (43 bp):
GTGTAAGACCATGACTGGGATATTGGCATCATTATTTGATTTC
Found at i:30460119 original size:20 final size:20
Alignment explanation
Indices: 30460068--30460120 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
30460058 ACAGCCTCGG
*
30460068 ACACGTCCGTGTGACCTTCC
1 ACACGCCCGTGTGACCTTCC
* **
30460088 ATACGCTTGTGTGA-CTTCCC
1 ACACGCCCGTGTGACCTT-CC
30460108 ACACGCCCGTGTG
1 ACACGCCCGTGTG
30460121 GTATGGCCAT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.15, C:0.36, G:0.23, T:0.26
Consensus pattern (20 bp):
ACACGCCCGTGTGACCTTCC
Found at i:30463710 original size:14 final size:14
Alignment explanation
Indices: 30463688--30463730 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
30463678 AGAAGCAAAT
* *
30463688 AAAAGAAAAATTAG
1 AAAATAAAAATTAA
30463702 AAAATAAAAATTAA
1 AAAATAAAAATTAA
30463716 AAAATAAAAA-TAA
1 AAAATAAAAATTAA
30463729 AA
1 AA
30463731 TGTAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (14 bp):
AAAATAAAAATTAA
Found at i:30470570 original size:47 final size:43
Alignment explanation
Indices: 30470457--30470583 Score: 130
Period size: 47 Copynumber: 2.8 Consensus size: 43
30470447 TATTTGTGTA
*
30470457 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAG
1 CCAGAGTAAGACATGTCTGGGACATGCATCGG---CATTATGAGAG
* *
30470503 CCAGTGTAAGACCATATCTGGGACATGGCATCGGCATTGA-GACGACAG
1 CCAGAGTAAGA-CATGTCTGGGACAT-GCATCGGCATT-ATGA-G--AG
*
30470551 CTAGAGTAAGACATGTCTGGGACATGCATCGGC
1 CCAGAGTAAGACATGTCTGGGACATGCATCGGC
30470584 TACGAGATGT
Statistics
Matches: 71, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
45 6 0.08
46 21 0.30
47 26 0.37
48 18 0.25
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.20
Consensus pattern (43 bp):
CCAGAGTAAGACATGTCTGGGACATGCATCGGCATTATGAGAG
Found at i:30470628 original size:46 final size:46
Alignment explanation
Indices: 30470458--30470778 Score: 147
Period size: 48 Copynumber: 6.8 Consensus size: 46
30470448 ATTTGTGTAC
* * *
30470458 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-C-ATTATGAGAG
1 CAGTGTAAGACCATATCTGGGACATGGCATCGG-CATCGA-GACGA-AG
*
30470503 CCAGTGTAAGACCATATCTGGGACATGGCATCGGCATTGAGACGACAG
1 -CAGTGTAAGACCATATCTGGGACATGGCATCGGCATCGAGACGA-AG
* * * *
30470551 CTAGAGTAAGA-CATGTCTGGGACAT-GCATCGGC-TACGAGATG-TG
1 C-AGTGTAAGACCATATCTGGGACATGGCATCGGCAT-CGAGACGAAG
* * ** * **
30470595 TCAGTGTAAGACCATATCCGGGACATGGAATCGGCAAGTATAGAGGTGG
1 -CAGTGTAAGACCATATCTGGGACATGGCATCGGC-A-TCGAGACGAAG
* * * * *
30470644 CAATGTAAGACCGTGTCTGGGACATGGCATCGGCA-CAGATATGTGAGAG
1 CAGTGTAAGACCATATCTGGGACATGGCATCGGCATC-GAGA--CGA-AG
* * * * * * * **
30470693 CTAGTGTAAGACCATGTCTGGGATATTGCGTCAGCCTCAATTTCGATAG
1 C-AGTGTAAGACCATATCTGGGACATGGCATCGGCATCGA-GACGA-AG
*
30470742 TCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
1 -CAGTGTAAGACCATATCTGGGACATGGCATCGGCAT
30470779 TATACCCTAT
Statistics
Matches: 209, Mismatches: 45, Indels: 39
0.71 0.15 0.13
Matches are distributed among these distances:
44 9 0.04
45 14 0.07
46 32 0.15
47 30 0.14
48 54 0.26
49 39 0.19
50 29 0.14
51 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
CAGTGTAAGACCATATCTGGGACATGGCATCGGCATCGAGACGAAG
Found at i:30478081 original size:46 final size:46
Alignment explanation
Indices: 30477931--30478147 Score: 158
Period size: 46 Copynumber: 4.7 Consensus size: 46
30477921 TTATTTGTGT
** * *
30477931 GCCAGTGTAAGACATGTCTGGGACATGCATTGGCCAC-A-TTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAT-A-A
* * * * *
30477977 GCTAGTGTAAGAACATGTCTGGGACATGGCATCAGCATTGAGACGA-GA
1 GCCAGTGTAAG-ACATGTCTGGGACAT-GCATCAGCCTCGAGA-TATAA
** * *
30478025 GTTAGAGTAAGACATGTATGGGACATGCATCAGCCTCGAGATATAA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATAA
* * * *
30478071 GCCAGTGTAAGACATGTCTGGGTCATGCATC-GGCTATGAGATGT--
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCT-CGAGATATAA
*
30478115 GTCAGTGTAAGACCATGTCTGGGACATGGCATC
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
30478148 GGCACGTATA
Statistics
Matches: 136, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
44 11 0.08
45 17 0.12
46 61 0.45
47 29 0.21
48 16 0.12
49 1 0.01
51 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATAA
Found at i:30478148 original size:46 final size:46
Alignment explanation
Indices: 30477980--30478340 Score: 211
Period size: 46 Copynumber: 7.6 Consensus size: 46
30477970 TATGAGAGCT
* * * * *
30477980 AGTGTAAGAACATGTCTGGGACATGGCATCAGC-ATTGAGACGAGAGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTA-TGAGA--TGTGTC
* * * * * *
30478028 AGAGTAAGA-CATGTATGGGACAT-GCATCAGCCT-CGAGATATAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GGCTATGAGATGT--GTC
*
30478074 AGTGTAAGA-CATGTCTGGGTCAT-GCATCGGCTATGAGATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTATGAGATGTGTC
*
30478118 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTAT-AGAGGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG--C-TATGAGATGTGTC
* * * *
30478166 AGTGTAAGACCATGTCTAGGACATGGCATCGG-TACGGATATGTGAGAGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTA-TGAGATGT--G-TC
* ** **
30478215 TAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCAAATTCGAT-AATC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGG-CT---ATGAGATGTGTC
* * * * * *
30478265 AGTGTAAGATCATATCTAGGACATGGCATCGACT-TGATGGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTATGA--GATGTGTC
*
30478312 AGTGTAAGACCATGTCTAGGACATGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCAT
30478341 TGGTACTACA
Statistics
Matches: 245, Mismatches: 44, Indels: 49
0.72 0.13 0.14
Matches are distributed among these distances:
44 14 0.06
45 16 0.07
46 55 0.22
47 43 0.18
48 51 0.21
49 31 0.13
50 31 0.13
52 1 0.00
54 2 0.01
55 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTATGAGATGTGTC
Found at i:30478171 original size:48 final size:48
Alignment explanation
Indices: 30478073--30478248 Score: 202
Period size: 48 Copynumber: 3.7 Consensus size: 48
30478063 AGATATAAGC
* *
30478073 CAGTGTAAGA-CATGTCTGGGTCAT-GCATCGG--C-TATGAGATGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTAT-AGAGGTGT
30478117 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
* * * * *
30478165 CAGTGTAAGACCATGTCTAGGACATGGCATCGGTACGGATATGTGAGAG-
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATA-GAG-GTGT
*
30478214 CTAGTGTAAGACCATGTCTGGGACATGGCGTCGGC
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCGGC
30478249 CTCAAATTCG
Statistics
Matches: 114, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
44 10 0.09
45 13 0.11
46 7 0.06
48 46 0.40
49 6 0.05
50 32 0.28
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGT
Found at i:30478231 original size:98 final size:96
Alignment explanation
Indices: 30477931--30478340 Score: 257
Period size: 94 Copynumber: 4.3 Consensus size: 96
30477921 TTATTTGTGT
* * * ** *
30477931 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATTGGCCACATTATGAGA-GCT-AGTGTAAGAACA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCA-AATGAGATAATCAGTGTAAGACCA
* *
30477992 TGTCTGGGACATGGCATC-AGCATTGA-GACGA-GA
65 TATCTAGGACATGGCATCGA-CA-TGATG--GATGA
** * * * * * *
30478025 GTTAGAGTAAGA-CATGTATGGGACAT-GCATCAGCCTC-GA-GATATAAGCCAGTGTAAGA-CA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAATGAGATAA-TCAGTGTAAGACCA
* * * * *
30478085 TGTCTGGGTCAT-GCATCGGC-T-ATGAGATGT
65 TATCTAGGACATGGCATCGACATGATG-GATGA
* * * *
30478115 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGT-ATA-GAGGT-GTCAGTGTAAGACC
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-C-TCAAATGAGATAATCAGTGTAAGACC
*
30478177 ATGTCTAGGACATGGCATCGGTACGGAT-ATGTGA-GA
64 ATATCTAGGACATGGCATC-G-AC--ATGATG-GATGA
* * ** *
30478213 GCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCAAATTCGATAATCAGTGTAAGATCAT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAATGAGATAATCAGTGTAAGACCAT
*
30478278 ATCTAGGACATGGCATCGACTTGATGGATGA
66 ATCTAGGACATGGCATCGACATGATGGATGA
*
30478309 GCCAGTGTAAGACCATGTCTAGGACATGGCAT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCAT
30478341 TGGTACTACA
Statistics
Matches: 249, Mismatches: 44, Indels: 44
0.74 0.13 0.13
Matches are distributed among these distances:
89 3 0.01
90 13 0.05
91 16 0.06
92 24 0.10
93 26 0.10
94 49 0.20
95 4 0.02
96 36 0.14
97 5 0.02
98 37 0.15
99 36 0.14
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (96 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAAATGAGATAATCAGTGTAAGACCAT
ATCTAGGACATGGCATCGACATGATGGATGA
Found at i:30479909 original size:44 final size:44
Alignment explanation
Indices: 30479857--30479962 Score: 178
Period size: 44 Copynumber: 2.4 Consensus size: 44
30479847 AGTTGATATG
*
30479857 GCACTAAGTGTGTGAGATTGTTATAGCTTTGGCTAACCATTAAT
1 GCACTAAGTGTGTGAGATTGTTATAACTTTGGCTAACCATTAAT
* *
30479901 GCATTAAGTGTGTGAGATTGTTATAACTTTGGCTAATCATTAAT
1 GCACTAAGTGTGTGAGATTGTTATAACTTTGGCTAACCATTAAT
30479945 GCACTAAGTGTGTG-GATT
1 GCACTAAGTGTGTGAGATT
30479963 CTTAAAGTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 4 0.07
44 54 0.93
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (44 bp):
GCACTAAGTGTGTGAGATTGTTATAACTTTGGCTAACCATTAAT
Found at i:30482419 original size:46 final size:45
Alignment explanation
Indices: 30482352--30482521 Score: 159
Period size: 46 Copynumber: 3.7 Consensus size: 45
30482342 CCCGCCCCTA
* * *
30482352 AGTGAACTTGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCAT
*
30482397 GAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-T
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCAT
* * * *
30482445 CA-CGAACTGGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCAT
*
30482490 AGGTGAACTCGGACTCAACTGAACGAGTTCGG
1 A-GTGAACTCGGACTCAACTCAACGAGTTCGG
30482522 ATGCTCAACC
Statistics
Matches: 101, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 1 0.01
46 54 0.53
47 27 0.27
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCAT
Found at i:30482981 original size:14 final size:14
Alignment explanation
Indices: 30482962--30482988 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30482952 AAAAAATTAT
30482962 ACTTTTGCCCCTAA
1 ACTTTTGCCCCTAA
30482976 ACTTTTGCCCCTA
1 ACTTTTGCCCCTA
30482989 GGCTCGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.37, G:0.07, T:0.37
Consensus pattern (14 bp):
ACTTTTGCCCCTAA
Found at i:30493650 original size:136 final size:136
Alignment explanation
Indices: 30493446--30493780 Score: 541
Period size: 136 Copynumber: 2.5 Consensus size: 136
30493436 CATTTATATT
* * *
30493446 AATAAACTCAAATAACCAATTATAAAAAA-ATGCTCA-CACTTTAAATACGAAAAACCGATATAA
1 AATAAACTCAACTAACCAATTATAAAAAATATGCTCATAAC-TTAAATATGAAAAACCGATATAA
* *
30493509 CTTAAATACGAAATAATAAATAAATTAATATAACATACAATTATATTAATAAACACAATTCCCTA
65 CTTAAATACGAAATAATAAATAAATTAATATAACATACAATTACATTAATAAACACAATTCCCCA
30493574 AACATTA
130 AACATTA
* *
30493581 AATAAACTCAACTGACCAATTATAAAAAATATGCTCATAACTTAAATATGAAAAACTGATATAAC
1 AATAAACTCAACTAACCAATTATAAAAAATATGCTCATAACTTAAATATGAAAAACCGATATAAC
30493646 TTAAATACGAAATAATAAATAAATTAATATAACATACAATTACATTAATAAACACAATTCCCCAA
66 TTAAATACGAAATAATAAATAAATTAATATAACATACAATTACATTAATAAACACAATTCCCCAA
30493711 ACATTA
131 ACATTA
* * *
30493717 AATAAACTGAACTAACCAATTATAAAAAATATGC-CGATACCTTAAATATGAAAATCCGATATAA
1 AATAAACTCAACTAACCAATTATAAAAAATATGCTC-ATAACTTAAATATGAAAAACCGATATAA
30493781 GATTCTTCAA
Statistics
Matches: 185, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
135 28 0.15
136 155 0.84
137 2 0.01
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.27
Consensus pattern (136 bp):
AATAAACTCAACTAACCAATTATAAAAAATATGCTCATAACTTAAATATGAAAAACCGATATAAC
TTAAATACGAAATAATAAATAAATTAATATAACATACAATTACATTAATAAACACAATTCCCCAA
ACATTA
Found at i:30497809 original size:23 final size:23
Alignment explanation
Indices: 30497765--30497811 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
30497755 AAAAAGGTAC
30497765 TATATTTGTTGTATAATCTAATT
1 TATATTTGTTGTATAATCTAATT
30497788 TATATTT-TTGTTACTAAT-TAATT
1 TATATTTGTTG-TA-TAATCTAATT
30497811 T
1 T
30497812 TTTTAAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 3 0.14
23 15 0.68
24 4 0.18
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (23 bp):
TATATTTGTTGTATAATCTAATT
Found at i:30498188 original size:3 final size:3
Alignment explanation
Indices: 30498180--30498208 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
30498170 TAGTAATAAC
30498180 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
30498209 GATAATGAAT
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:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:30498793 original size:52 final size:52
Alignment explanation
Indices: 30498715--30498818 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
30498705 AGAACAAAAT
30498715 AGCAAATTATAAGTTCATAGGGAAACACCTTTTTAGCAAGATCAATACTATC
1 AGCAAATTATAAGTTCATAGGGAAACACCTTTTTAGCAAGATCAATACTATC
30498767 AGCAAATTATAAGTTCATAGGGAAACACCTTTTTAGCAAGATCAATACTATC
1 AGCAAATTATAAGTTCATAGGGAAACACCTTTTTAGCAAGATCAATACTATC
30498819 CCTGGGTTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (52 bp):
AGCAAATTATAAGTTCATAGGGAAACACCTTTTTAGCAAGATCAATACTATC
Found at i:30501157 original size:20 final size:20
Alignment explanation
Indices: 30501119--30501157 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30501109 AAACATACAT
* *
30501119 TTCACATACAATTTAATCAA
1 TTCAAATACAATTCAATCAA
*
30501139 TTCAAATACAATTCGATCA
1 TTCAAATACAATTCAATCA
30501158 CAACCAATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.33
Consensus pattern (20 bp):
TTCAAATACAATTCAATCAA
Found at i:30502648 original size:48 final size:48
Alignment explanation
Indices: 30502591--30502763 Score: 186
Period size: 48 Copynumber: 3.6 Consensus size: 48
30502581 CTCAGAGCCA
* * *
30502591 ATATCATGGCCTGAAGCTAAATCAATGAAGCTAACACCCAAAGTGCCG
1 ATATCATGGCCCGAAGCCAAATCAATGAAGCTAGCACCCAAAGTGCCG
* * * *
30502639 ATATCATGGCCCGAAGCCAAATCGATGTAA-CTCGCACCCAAAGTTCCA
1 ATATCATGGCCCGAAGCCAAATCAATG-AAGCTAGCACCCAAAGTGCCG
* ** * * * * * *
30502687 ATATCATGACTTGAAGCCACATCAATAAAGCTTGCACACGAAGTGCTG
1 ATATCATGGCCCGAAGCCAAATCAATGAAGCTAGCACCCAAAGTGCCG
30502735 ATATCATGGCCCGAAGCCAAATCAATGAA
1 ATATCATGGCCCGAAGCCAAATCAATGAA
30502764 TTCCCTAATG
Statistics
Matches: 99, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
47 2 0.02
48 95 0.96
49 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (48 bp):
ATATCATGGCCCGAAGCCAAATCAATGAAGCTAGCACCCAAAGTGCCG
Found at i:30512186 original size:24 final size:23
Alignment explanation
Indices: 30512142--30512187 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
30512132 CATTTTTATT
*
30512142 TTATTTTTTTGGAAATATGAAAA
1 TTATTTTTTGGGAAATATGAAAA
* *
30512165 TTATTTTTATGGGACATTTGAAA
1 TTATTTTT-TGGGAAATATGAAA
30512188 TATACAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (23 bp):
TTATTTTTTGGGAAATATGAAAA
Found at i:30514435 original size:27 final size:27
Alignment explanation
Indices: 30514397--30514566 Score: 171
Period size: 27 Copynumber: 6.3 Consensus size: 27
30514387 GCCACACGGT
* *
30514397 TTCCATTTCTTAGATAGCTACAAAGGC
1 TTCCATCTCTTAGATAGCCACAAAGGC
* **
30514424 TTTCATCTCTTAGATCA-CCATGAAGGC
1 TTCCATCTCTTAGAT-AGCCACAAAGGC
* * *
30514451 TTCCATTTCTTAGATCGCCACAAAGGA
1 TTCCATCTCTTAGATAGCCACAAAGGC
* *
30514478 TTTCATCTCTTAGATCGCCACAAAGGC
1 TTCCATCTCTTAGATAGCCACAAAGGC
* **
30514505 TTCCATCTCTTAGATTGTTACAAAGGC
1 TTCCATCTCTTAGATAGCCACAAAGGC
* ***
30514532 TTCCATCTCTTAAATCTTCACAAAGGC
1 TTCCATCTCTTAGATAGCCACAAAGGC
30514559 TTCCATCT
1 TTCCATCT
30514567 TTCTGGCATG
Statistics
Matches: 119, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
27 118 0.99
28 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (27 bp):
TTCCATCTCTTAGATAGCCACAAAGGC
Found at i:30514455 original size:54 final size:54
Alignment explanation
Indices: 30514397--30514564 Score: 219
Period size: 54 Copynumber: 3.1 Consensus size: 54
30514387 GCCACACGGT
**
30514397 TTCCATTTCTTAGATAGCTACAAAGGCTTTCATCTCTTAGATCACCATGAAGGC
1 TTCCATTTCTTAGATAGCTACAAAGGCTTTCATCTCTTAGATCACCACAAAGGC
* * * *
30514451 TTCCATTTCTTAGATCGCCACAAAGGATTTCATCTCTTAGATCGCCACAAAGGC
1 TTCCATTTCTTAGATAGCTACAAAGGCTTTCATCTCTTAGATCACCACAAAGGC
* * * * * **
30514505 TTCCATCTCTTAGATTGTTACAAAGGCTTCCATCTCTTAAATCTTCACAAAGGC
1 TTCCATTTCTTAGATAGCTACAAAGGCTTTCATCTCTTAGATCACCACAAAGGC
30514559 TTCCAT
1 TTCCAT
30514565 CTTTCTGGCA
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.33
Consensus pattern (54 bp):
TTCCATTTCTTAGATAGCTACAAAGGCTTTCATCTCTTAGATCACCACAAAGGC
Found at i:30514531 original size:81 final size:81
Alignment explanation
Indices: 30514397--30514566 Score: 196
Period size: 81 Copynumber: 2.1 Consensus size: 81
30514387 GCCACACGGT
* * * ** *
30514397 TTCCATTTCTTAGATAGCTACAAAGGCTTTCATCTCTTAGATCACCATGAAGGCTTCCATTTCTT
1 TTCCATCTCTTAGATAGCCACAAAGGCTTCCATCTCTTAGATCACCACAAAGGCTTCCATCTCTT
*
30514462 AGATCGCCACAAAGGA
66 AAATCGCCACAAAGGA
* * ****
30514478 TTTCATCTCTTAGATCGCCACAAAGGCTTCCATCTCTTAGATTGTTACAAAGGCTTCCATCTCTT
1 TTCCATCTCTTAGATAGCCACAAAGGCTTCCATCTCTTAGATCACCACAAAGGCTTCCATCTCTT
** *
30514543 AAATCTTCACAAAGGC
66 AAATCGCCACAAAGGA
30514559 TTCCATCT
1 TTCCATCT
30514567 TTCTGGCATG
Statistics
Matches: 72, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (81 bp):
TTCCATCTCTTAGATAGCCACAAAGGCTTCCATCTCTTAGATCACCACAAAGGCTTCCATCTCTT
AAATCGCCACAAAGGA
Found at i:30516002 original size:37 final size:37
Alignment explanation
Indices: 30515939--30516011 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
30515929 TACAAGCCAT
*
30515939 AATCTTTATAAGCCACATATCATGGCTATAT-ATAACG
1 AATCATTATAAGCCACATATCATGGCTA-ATCATAACG
30515976 AATCATTATAAGCCA-ATA-CATTTGGCTAATCATAAC
1 AATCATTATAAGCCACATATCA--TGGCTAATCATAAC
30516012 AACATCTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
35 2 0.06
36 5 0.16
37 25 0.78
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.32
Consensus pattern (37 bp):
AATCATTATAAGCCACATATCATGGCTAATCATAACG
Found at i:30517451 original size:43 final size:43
Alignment explanation
Indices: 30517403--30517495 Score: 141
Period size: 43 Copynumber: 2.2 Consensus size: 43
30517393 TCCGGGTTAG
*
30517403 ATCCTTTCTATATTGAGATCAACGGATTATCTGTCCAGGCTAA
1 ATCCTTTCTATATTGAGATCAACGGATTACCTGTCCAGGCTAA
* * *
30517446 ATCCTTTCTATATTGAGATCAACGGGTTACCTGTCCGGGTTAA
1 ATCCTTTCTATATTGAGATCAACGGATTACCTGTCCAGGCTAA
*
30517489 ATTCTTT
1 ATCCTTT
30517496 TCTGCAACAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (43 bp):
ATCCTTTCTATATTGAGATCAACGGATTACCTGTCCAGGCTAA
Found at i:30517739 original size:17 final size:17
Alignment explanation
Indices: 30517717--30517759 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
30517707 ATTTCAATTA
**
30517717 AAATGTCAATTTCCATC
1 AAATGTCAATTAACATC
*
30517734 AAATGTCCATTAACATC
1 AAATGTCAATTAACATC
30517751 AAAT-TCAAT
1 AAATGTCAAT
30517760 ACAATCATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.33
Consensus pattern (17 bp):
AAATGTCAATTAACATC
Found at i:30518489 original size:12 final size:12
Alignment explanation
Indices: 30518474--30518505 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
30518464 AAAATTTGGC
30518474 TTTTAATTTTGT
1 TTTTAATTTTGT
30518486 TTTTAATTTTGT
1 TTTTAATTTTGT
30518498 TTTTAATT
1 TTTTAATT
30518506 CACTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (12 bp):
TTTTAATTTTGT
Found at i:30521362 original size:33 final size:33
Alignment explanation
Indices: 30521316--30521381 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
30521306 CCTCATAATC
*
30521316 AAGTTTCGCTCTAATAAAATCTGTTTATATTAT
1 AAGTTTCGCTCTAATAAAATCTGATTATATTAT
*
30521349 AAGTTTCGTTCTAATAAAATCTGATTATATTAT
1 AAGTTTCGCTCTAATAAAATCTGATTATATTAT
30521382 CTTAATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (33 bp):
AAGTTTCGCTCTAATAAAATCTGATTATATTAT
Found at i:30524416 original size:16 final size:16
Alignment explanation
Indices: 30524395--30524435 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
30524385 CAATATTAAT
*
30524395 GTCAATCGAGTTAAAA
1 GTCAATCGAATTAAAA
30524411 GTCAATCGAATTAAAA
1 GTCAATCGAATTAAAA
*
30524427 CTCAATCGA
1 GTCAATCGA
30524436 TTTCTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (16 bp):
GTCAATCGAATTAAAA
Found at i:30526395 original size:13 final size:13
Alignment explanation
Indices: 30526377--30526406 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
30526367 ACTCACTTTT
30526377 TAATTGAAATTTA
1 TAATTGAAATTTA
30526390 TAATTGAAATTTA
1 TAATTGAAATTTA
30526403 -AATT
1 TAATT
30526407 AATCAAGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (13 bp):
TAATTGAAATTTA
Found at i:30537260 original size:2 final size:2
Alignment explanation
Indices: 30537253--30537289 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
30537243 TCATTCAAGA
30537253 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30537290 TCCTTAGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:30545657 original size:25 final size:25
Alignment explanation
Indices: 30545625--30545682 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
30545615 TCTCCACTCC
30545625 CCCTCTCTTCCTTTTTTTTTTCTTT
1 CCCTCTCTTCCTTTTTTTTTTCTTT
30545650 CCCTCTCTTCCTTTTTTTTTTCTTT
1 CCCTCTCTTCCTTTTTTTTTTCTTT
*
30545675 TCCTCTCT
1 CCCTCTCT
30545683 CAACTGACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (25 bp):
CCCTCTCTTCCTTTTTTTTTTCTTT
Found at i:30546150 original size:3 final size:3
Alignment explanation
Indices: 30546135--30546167 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
30546125 GTTATTTTCA
30546135 TAT TAT TGA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
30546168 GTATATTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.04
3 26 0.93
4 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:30546288 original size:3 final size:3
Alignment explanation
Indices: 30546280--30546304 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30546270 ATATTTCAAC
30546280 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
30546305 CCAATGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:30546832 original size:22 final size:24
Alignment explanation
Indices: 30546785--30546846 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 24
30546775 TATGTAAAGA
*
30546785 GTTTTAATATTATATTATATATAT
1 GTTTTAATATTATATTATATACAT
30546809 GTTTT-ATA-TATATTATGA-ACAT
1 GTTTTAATATTATATTAT-ATACAT
30546831 GTATTTTCAATATTAT
1 G--TTTT-AATATTAT
30546847 TAGTTAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
22 12 0.39
23 4 0.13
24 9 0.29
26 3 0.10
27 3 0.10
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (24 bp):
GTTTTAATATTATATTATATACAT
Found at i:30552411 original size:19 final size:19
Alignment explanation
Indices: 30552375--30552413 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
30552365 TTTTCATCAT
* *
30552375 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
30552394 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
30552413 A
1 A
30552414 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:30552916 original size:55 final size:56
Alignment explanation
Indices: 30552851--30552965 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
30552841 AGCATGGCTG
* *
30552851 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
30552907 CCAGA-ACAGATATATGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
30552962 CCAG
1 CCAG
30552966 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.56
56 22 0.42
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:30552928 original size:27 final size:27
Alignment explanation
Indices: 30552876--30552965 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
30552866 GTGACAGAGT
30552876 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* *
30552905 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
30552932 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
30552960 CACCAG
1 CACCAG
30552966 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:30553118 original size:28 final size:28
Alignment explanation
Indices: 30553071--30553135 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
30553061 AAATTAACCC
*
30553071 TAGGGGTATAAAGGTCATTTAGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
* *
30553099 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
30553127 TAGGGGTAT
1 TAGGGGTAT
30553136 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTAGCATACA
Found at i:30558602 original size:32 final size:32
Alignment explanation
Indices: 30558555--30558624 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
30558545 AAAATCCCGC
*
30558555 TCCCTTTACAGAGCTATCAGAATCCGTAAACTA
1 TCCC-TTACAGAGCTATCAGAACCCGTAAACTA
*
30558588 TCCCTTACGGAGCTATCAGAACCCGTAAACTA
1 TCCCTTACAGAGCTATCAGAACCCGTAAACTA
30558620 TCCCT
1 TCCCT
30558625 GAGATTGTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.89
33 4 0.11
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (32 bp):
TCCCTTACAGAGCTATCAGAACCCGTAAACTA
Found at i:30559501 original size:13 final size:13
Alignment explanation
Indices: 30559483--30559507 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30559473 TGAGTATTCC
30559483 AATTTAAACAAAT
1 AATTTAAACAAAT
30559496 AATTTAAACAAA
1 AATTTAAACAAA
30559508 CAACAGTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTTAAACAAAT
Found at i:30561599 original size:40 final size:41
Alignment explanation
Indices: 30561516--30561599 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 41
30561506 GGCCAAAGCT
*
30561516 AAATCGATTGAGAGAGGGAGAGAAGAAAAAGAGAATCGGCC
1 AAATCGATTGAGAGAGGGAGAGAAGAAAAAGAGAATCGACC
* *
30561557 AAATCGATTGAGAGAGGGAGTGAAG-CAAAGAGAATCGACC
1 AAATCGATTGAGAGAGGGAGAGAAGAAAAAGAGAATCGACC
30561597 AAA
1 AAA
30561600 ACAAAAAGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 16 0.40
41 24 0.60
ACGTcount: A:0.46, C:0.11, G:0.32, T:0.11
Consensus pattern (41 bp):
AAATCGATTGAGAGAGGGAGAGAAGAAAAAGAGAATCGACC
Found at i:30565627 original size:20 final size:20
Alignment explanation
Indices: 30565602--30565640 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30565592 GTTAAAAAAT
30565602 TTAGTAAAAAATATATAATG
1 TTAGTAAAAAATATATAATG
* *
30565622 TTAGTAAAATATATTTAAT
1 TTAGTAAAAAATATATAAT
30565641 TACTAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (20 bp):
TTAGTAAAAAATATATAATG
Found at i:30565662 original size:22 final size:22
Alignment explanation
Indices: 30565637--30565681 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
30565627 AAAATATATT
30565637 TAATTACTAAAATT-AATAAAAA
1 TAATTA-TAAAATTAAATAAAAA
**
30565659 TAATTATATTATTAAATAAAAA
1 TAATTATAAAATTAAATAAAAA
30565681 T
1 T
30565682 GAATATGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAATTATAAAATTAAATAAAAA
Found at i:30565960 original size:17 final size:17
Alignment explanation
Indices: 30565926--30565959 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
30565916 TAAAAAAATA
30565926 TAAATATAAATTAATTT
1 TAAATATAAATTAATTT
*
30565943 TAAATATATA-TAATTT
1 TAAATATAAATTAATTT
30565959 T
1 T
30565960 TTAGGCAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATATAAATTAATTT
Found at i:30569378 original size:206 final size:206
Alignment explanation
Indices: 30569024--30569442 Score: 820
Period size: 206 Copynumber: 2.0 Consensus size: 206
30569014 CACTCTGCGC
30569024 AAAGAACTTTCTCAATGTACCCCTTCTGACTTAGGTACAATTTACTTGCTTTTCTATCTCTGAGA
1 AAAGAACTTTCTCAATGTACCCCTTCTGACTTAGGTACAATTTACTTGCTTTTCTATCTCTGAGA
*
30569089 ATCTCCATACCAAGTATCTTCTTTGCTGGTCCTAAATCTTTCATCTCAAATTCTTCACTTAGTTG
66 ATCTCCATACCAAGTATCTTCTTTGCTGGTCCTAAATCTTTCATCTCAAATTATTCACTTAGTTG
30569154 GGCTTTAACCTTTCTTATCTCTCCTTTATCTTTTGCTGCTATCAACATGTCATCAACATAAAGAA
131 GGCTTTAACCTTTCTTATCTCTCCTTTATCTTTTGCTGCTATCAACATGTCATCAACATAAAGAA
30569219 GTAGATACACA
196 GTAGATACACA
30569230 AAAGAACTTTCTCAATGTACCCCTTCTGACTTAGGTACAATTTACTTGCTTTTCTATCTCTGAGA
1 AAAGAACTTTCTCAATGTACCCCTTCTGACTTAGGTACAATTTACTTGCTTTTCTATCTCTGAGA
*
30569295 ATCTCCATACCAAGTATCTTCTTTGCTGGTCCTAAATCTTTCATCTCAAATTATTCGCTTAGTTG
66 ATCTCCATACCAAGTATCTTCTTTGCTGGTCCTAAATCTTTCATCTCAAATTATTCACTTAGTTG
30569360 GGCTTTAACCTTTCTTATCTCTCCTTTATCTTTTGCTGCTATCAACATGTCATCAACATAAAGAA
131 GGCTTTAACCTTTCTTATCTCTCCTTTATCTTTTGCTGCTATCAACATGTCATCAACATAAAGAA
30569425 GTAGATACACA
196 GTAGATACACA
30569436 AAAGAAC
1 AAAGAAC
30569443 CATCACTGTT
Statistics
Matches: 211, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
206 211 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (206 bp):
AAAGAACTTTCTCAATGTACCCCTTCTGACTTAGGTACAATTTACTTGCTTTTCTATCTCTGAGA
ATCTCCATACCAAGTATCTTCTTTGCTGGTCCTAAATCTTTCATCTCAAATTATTCACTTAGTTG
GGCTTTAACCTTTCTTATCTCTCCTTTATCTTTTGCTGCTATCAACATGTCATCAACATAAAGAA
GTAGATACACA
Found at i:30573734 original size:25 final size:27
Alignment explanation
Indices: 30573685--30573735 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
30573675 ACATTATTTT
30573685 AATGTAATAGAATAATAATGTATAAAAA
1 AATGTAATAGAATAAT-ATGTATAAAAA
*
30573713 AATGTGATAGAATAAT-TG-ATAAA
1 AATGTAATAGAATAATATGTATAAA
30573736 TTTATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 2 0.09
28 15 0.68
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (27 bp):
AATGTAATAGAATAATATGTATAAAAA
Found at i:30574931 original size:69 final size:68
Alignment explanation
Indices: 30574831--30574995 Score: 161
Period size: 69 Copynumber: 2.4 Consensus size: 68
30574821 TCACTAAAGT
* * * * * * * * * * ** * *
30574831 AGTTAACGAGAGTAAAGCTCCTAGCTATAAAATTAAGGTTCACAGGTGAAGAGTCGTGACCTCTA
1 AGTTAGCGAGAGCAAAGCTCCCAACTGTAAAATCAAAGTTCACAAGTGAAAAGCCACGACCCCCA
30574896 ACA
66 ACA
*
30574899 CAGTTAGCGAGAGCAAAGCTCCCAACTGTAAAATCAAAGTTCGCAAGTGAAAAGCCACGACCCCC
1 -AGTTAGCGAGAGCAAAGCTCCCAACTGTAAAATCAAAGTTCACAAGTGAAAAGCCACGACCCCC
30574964 AACA
65 AACA
* *
30574968 A-TTAGTGAGAGCAAAGCTCCCATCTGTA
1 AGTTAGCGAGAGCAAAGCTCCCAACTGTA
30574996 GTGCCAAGGT
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
67 25 0.32
68 1 0.01
69 53 0.67
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (68 bp):
AGTTAGCGAGAGCAAAGCTCCCAACTGTAAAATCAAAGTTCACAAGTGAAAAGCCACGACCCCCA
ACA
Found at i:30577360 original size:43 final size:43
Alignment explanation
Indices: 30577266--30577366 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 43
30577256 CCGAGATATG
* * * *
30577266 ATTATATGTAAGACCGTGTCTGGGACATTGGAATTGTATTGAT
1 ATTATGTGTAAGACCATGTCTGGGACATTGGAATCGTATCGAT
* *
30577309 ATTATGTGTAAGATCATGTCTGGGACATTGGCATCGTTAATCGAT
1 ATTATGTGTAAGACCATGTCTGGGACATTGGAATCG-T-ATCGAT
30577354 -TT-TGTGTAAGACC
1 ATTATGTGTAAGACC
30577367 CTATTTGGGA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
43 41 0.84
44 3 0.06
45 5 0.10
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.37
Consensus pattern (43 bp):
ATTATGTGTAAGACCATGTCTGGGACATTGGAATCGTATCGAT
Found at i:30580782 original size:16 final size:16
Alignment explanation
Indices: 30580761--30580792 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
30580751 CACCTATAAG
30580761 TATGGTGAGCTAAAGA
1 TATGGTGAGCTAAAGA
30580777 TATGGTGAGCTAAAGA
1 TATGGTGAGCTAAAGA
30580793 CCTCGCGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.31, T:0.25
Consensus pattern (16 bp):
TATGGTGAGCTAAAGA
Found at i:30586664 original size:46 final size:46
Alignment explanation
Indices: 30586592--30586865 Score: 334
Period size: 46 Copynumber: 6.0 Consensus size: 46
30586582 GGTTTTTGAA
* **
30586592 ATGAAATGTGTAAGACCATTGTTGAAAGATATAATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
30586638 ATGATATGTGTAAGACAATGGTTGAAACATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
30586684 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * ** *
30586730 ATGAAAAGTGTAAGACCATGGTTGAAAGATACCATGGAAATGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * * * *
30586776 ATGAAATGAATAAGACCATGGTTGAAATATATCACGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
30586822 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
30586866 TCGAAGATAA
Statistics
Matches: 196, Mismatches: 31, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
45 1 0.01
46 195 0.99
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:30586969 original size:13 final size:13
Alignment explanation
Indices: 30586949--30586991 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
30586939 CCAGATGGCG
30586949 AATGGTTATATGA
1 AATGGTTATATGA
* **
30586962 ATTGGTTATACAA
1 AATGGTTATATGA
*
30586975 AATGGTTGTATGA
1 AATGGTTATATGA
30586988 AATG
1 AATG
30586992 TTTACAAGAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.37
Consensus pattern (13 bp):
AATGGTTATATGA
Found at i:30587006 original size:26 final size:26
Alignment explanation
Indices: 30586949--30587043 Score: 70
Period size: 26 Copynumber: 3.6 Consensus size: 26
30586939 CCAGATGGCG
*
30586949 AATGGTTATATGAATTGGTTATACAA
1 AATGGTTATATGAAATGGTTATACAA
*
30586975 AATGGTTGTATGAAAT-GTT-TACAA
1 AATGGTTATATGAAATGGTTATACAA
* * *
30586999 GAATTGGTCATATGGAAAT-ATATTTACAA
1 -AA-TGGTTATAT-GAAATGGT-TATACAA
* *
30587028 AATAGTTGTATGAAAT
1 AATGGTTATATGAAAT
30587044 AATTAAGAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
24 5 0.09
25 5 0.09
26 26 0.46
27 12 0.21
28 3 0.05
29 5 0.09
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (26 bp):
AATGGTTATATGAAATGGTTATACAA
Found at i:30588202 original size:22 final size:22
Alignment explanation
Indices: 30588148--30588206 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
30588138 TACGGGACCT
** *
30588148 TAGCACATAAGTGCTCTCCGTT
1 TAGCACATTTGTGCTCTCCGTA
*
30588170 TAGCACATTTGTGCTCTCTGTA
1 TAGCACATTTGTGCTCTCCGTA
*
30588192 TAGCACTTTTGTGCT
1 TAGCACATTTGTGCT
30588207 TTTTGTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.39
Consensus pattern (22 bp):
TAGCACATTTGTGCTCTCCGTA
Found at i:30591902 original size:21 final size:21
Alignment explanation
Indices: 30591877--30591948 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
30591867 TTTTCTGAAA
30591877 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* * * *
30591898 TGAAAGATATCATAAGAACATGAT
1 TG-AA-ATGT-GTAAGACCATGGT
*
30591922 ATGATATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
30591944 TGAAA
1 TGAAA
30591949 GATACCATGG
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
21 6 0.16
22 12 0.32
23 6 0.16
24 11 0.30
25 2 0.05
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:30591933 original size:46 final size:46
Alignment explanation
Indices: 30591876--30592195 Score: 446
Period size: 46 Copynumber: 7.0 Consensus size: 46
30591866 TTTTTCTGAA
* *
30591876 ATGAAATGTGTAAGACCATGGTTGAAAGATATCATAAG-AACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCAT-GGCAACATGAT
*
30591922 ATGATATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
30591968 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAGATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
30592014 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * ** *
30592060 ATTAAAAGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** *
30592106 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * * *
30592152 A-GAAAATGAGTAAGATCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
30592196 TCAAAGATAA
Statistics
Matches: 249, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
45 2 0.01
46 247 0.99
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:30595455 original size:69 final size:69
Alignment explanation
Indices: 30595338--30595692 Score: 356
Period size: 69 Copynumber: 5.1 Consensus size: 69
30595328 ATTTATCGTT
* * * * * * *
30595338 TGTAAAATTAAGGTTTGCAGGCGAAGTGCCGCAACCTCTAATACAGTTAGTTAGAGTAAAGCTTC
1 TGTAAAATCAAGGTTCGCAGGCGAAGAGTCGCGACCTCTAACACAGTTAGTGAGAGTAAAGCTTC
30595403 CAGA
66 CAGA
* * * * * *
30595407 TGTAAAATCAAGGCTCGCAGGCGAAGAGCCGTGACCTCTAACATAGTTAGCGAGAGTAAAAC-TC
1 TGTAAAATCAAGGTTCGCAGGCGAAGAGTCGCGACCTCTAACACAGTTAGTGAGAGTAAAGCTTC
*
30595471 CTAGC
66 C-AGA
* * * ** *
30595476 TGTAAAATCAAGGCTCACAGGCTAAGAGTCGCGACCTCTAACACAGTTAGCAAGAGTAAAGCTCC
1 TGTAAAATCAAGGTTCGCAGGCGAAGAGTCGCGACCTCTAACACAGTTAGTGAGAGTAAAGCTTC
30595541 CA-A
66 CAGA
* * * * **
30595544 CTGTAAAATCAAGGTTCGCAGGTGAAGAGTCGCAAACACTAACACAGTTAGTGAGAACAAAGC-T
1 -TGTAAAATCAAGGTTCGCAGGCGAAGAGTCGCGACCTCTAACACAGTTAGTGAGAGTAAAGCTT
30595608 CCTAGA
65 CC-AGA
* * * * * * *
30595614 TGTAAAATTAAGGTTCGTAGGTGAAAAGTCGCGACCTCTAACACAGTTAATGAGAGCAAAGTTTC
1 TGTAAAATCAAGGTTCGCAGGCGAAGAGTCGCGACCTCTAACACAGTTAGTGAGAGTAAAGCTTC
*
30595679 CAGT
66 CAGA
30595683 TGTAAAATCA
1 TGTAAAATCA
30595693 TAGTTCGTAA
Statistics
Matches: 236, Mismatches: 44, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
68 5 0.02
69 225 0.95
70 6 0.03
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (69 bp):
TGTAAAATCAAGGTTCGCAGGCGAAGAGTCGCGACCTCTAACACAGTTAGTGAGAGTAAAGCTTC
CAGA
Done.