Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 72 of 187
Found at i:21147383 original size:98 final size:98
Alignment explanation
Indices: 21147263--21147455 Score: 332
Period size: 98 Copynumber: 2.0 Consensus size: 98
21147253 TTAAAAATAA
* * * *
21147263 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGGCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGCGATTTC
21147328 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
21147361 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGCGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGCGATTTC
*
21147426 TTAAATCTTGGATGAGTGGATGTTCTTTTA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTA
21147456 NNNNNNNNNN
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGCGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:21151957 original size:8 final size:8
Alignment explanation
Indices: 21151944--21151985 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
21151934 TCAGATTCAA
21151944 AAAAAAAC
1 AAAAAAAC
21151952 AAAAAAAC
1 AAAAAAAC
21151960 --AAAAAC
1 AAAAAAAC
21151966 --AAAAAC
1 AAAAAAAC
21151972 AAAAAAAC
1 AAAAAAAC
21151980 AAAAAA
1 AAAAAA
21151986 TAAAAGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.38
8 20 0.62
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:21151965 original size:14 final size:13
Alignment explanation
Indices: 21151942--21151990 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 13
21151932 GTTCAGATTC
21151942 AAAAAAAAACAAA
1 AAAAAAAAACAAA
21151955 AAAACAAAAACAAA
1 AAAA-AAAAACAAA
21151969 AACAAAAAAACAAA
1 AA-AAAAAAACAAA
21151983 AAATAAAA
1 AAA-AAAA
21151991 GTGAAAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.15
14 26 0.79
15 2 0.06
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.02
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:21151971 original size:20 final size:19
Alignment explanation
Indices: 21151942--21151990 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 19
21151932 GTTCAGATTC
21151942 AAAAAAAAACAAAAAAACA
1 AAAAAAAAACAAAAAAACA
21151961 AAAACAAAAACAAAAAAACA
1 AAAA-AAAAACAAAAAAACA
21151981 AAAAATAAAA
1 AAAAA-AAAA
21151991 GTGAAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.88, C:0.10, G:0.00, T:0.02
Consensus pattern (19 bp):
AAAAAAAAACAAAAAAACA
Found at i:21154365 original size:7 final size:7
Alignment explanation
Indices: 21154353--21154414 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
21154343 CTAATTAATT
21154353 TAAACCC
1 TAAACCC
21154360 TAAACCC
1 TAAACCC
*
21154367 T-GACTCC
1 TAAAC-CC
21154374 TAAACCC
1 TAAACCC
*
21154381 TAAAGCC
1 TAAACCC
21154388 TAAACCCC
1 TAAA-CCC
21154396 T-AACCC
1 TAAACCC
*
21154402 TTAAACCT
1 -TAAACCC
21154410 TAAAC
1 TAAAC
21154415 TCCAGCCATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
6 5 0.11
7 31 0.69
8 9 0.20
ACGTcount: A:0.39, C:0.39, G:0.03, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:21154513 original size:14 final size:14
Alignment explanation
Indices: 21154496--21154546 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
21154486 TAGTATCTTT
*
21154496 TAAACCTTAAACCC
1 TAAACCATAAACCC
*
21154510 TAAACCATATACCC
1 TAAACCATAAACCC
* *
21154524 -CAACCCTAAACCC
1 TAAACCATAAACCC
*
21154537 TAAACTATAA
1 TAAACCATAA
21154547 TGATAATTAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:21154687 original size:19 final size:19
Alignment explanation
Indices: 21154663--21154796 Score: 187
Period size: 19 Copynumber: 6.8 Consensus size: 19
21154653 AATTTTTGAG
*
21154663 GATATGCAATCTTATATAT
1 GATATGCAATCTTAGATAT
*
21154682 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
21154701 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
21154722 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
21154743 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
21154762 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
21154781 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
21154797 ATATATGATT
Statistics
Matches: 106, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
19 67 0.63
21 39 0.37
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:21154708 original size:40 final size:38
Alignment explanation
Indices: 21154663--21154803 Score: 187
Period size: 40 Copynumber: 3.7 Consensus size: 38
21154653 AATTTTTGAG
* *
21154663 GATATGCAATCTTATATATGATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
21154701 GATATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATATG--ATATGCAATCTTAGATAT
* **
21154743 GATATGTAATCTTAGATATGATATATAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
21154781 GATATGCAATCTTAGA-AT-ATATG
1 GATATGCAATCTTAGATATGATATG
21154804 ATTTTGTAAT
Statistics
Matches: 92, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
36 4 0.04
37 2 0.02
38 32 0.35
40 36 0.39
42 18 0.20
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCTTAGATAT
Found at i:21154812 original size:61 final size:60
Alignment explanation
Indices: 21154663--21154819 Score: 207
Period size: 61 Copynumber: 2.6 Consensus size: 60
21154653 AATTTTTGAG
* *
21154663 GATATGCAATCTT--ATATATGATATGCAATCCTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATATGATATGTAATCTTAGATATGATATAT-CAATCTTAGATAT
21154722 GATATATGCAATCTTAG--ATATGATATGTAATCTTAGATATGATATAT-AATCTTAGATAT
1 G--ATATGCAATCTTAGATATATGATATGTAATCTTAGATATGATATATCAATCTTAGATAT
*
21154781 GATATGCAATCTTAGAATATATGATTTTGTAATCTTAGA
1 GATATGCAATCTTAG-ATATATGA-TATGTAATCTTAGA
21154820 GATTTAATTT
Statistics
Matches: 87, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
57 14 0.16
59 14 0.16
60 6 0.07
61 53 0.61
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (60 bp):
GATATGCAATCTTAGATATATGATATGTAATCTTAGATATGATATATCAATCTTAGATAT
Found at i:21155328 original size:13 final size:14
Alignment explanation
Indices: 21155305--21155336 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
21155295 TTGCAATTCA
21155305 ATTTA-GTTTTTTT
1 ATTTATGTTTTTTT
21155318 -TTTATGTTTTTTT
1 ATTTATGTTTTTTT
21155331 ATTTAT
1 ATTTAT
21155337 TTTATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 8 0.47
14 5 0.29
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (14 bp):
ATTTATGTTTTTTT
Found at i:21155594 original size:25 final size:26
Alignment explanation
Indices: 21155551--21155600 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
21155541 TGTACATGTA
21155551 TATATTTTTTTAAACGAATATTTTCC
1 TATATTTTTTTAAACGAATATTTTCC
*
21155577 TATATTTTTTT-AATGAATATTTTC
1 TATATTTTTTTAAACGAATATTTTC
21155601 ATATTTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (26 bp):
TATATTTTTTTAAACGAATATTTTCC
Found at i:21156409 original size:84 final size:84
Alignment explanation
Indices: 21156268--21156435 Score: 300
Period size: 84 Copynumber: 2.0 Consensus size: 84
21156258 TTAAAAATAA
* *
21156268 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
21156333 TTAAATCTTGGATAAGTGG
66 TTAAATCTTGGATAAGTGG
*
21156352 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
21156417 TTAAATCTTGGATGAGTGG
66 TTAAATCTTGGATAAGTGG
21156436 ATGTTCTTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (84 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGG
Found at i:21156964 original size:21 final size:20
Alignment explanation
Indices: 21156940--21156980 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
21156930 CCTAACGTCT
*
21156940 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
21156961 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
21156981 TAATCCATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:21157393 original size:41 final size:39
Alignment explanation
Indices: 21157348--21157503 Score: 150
Period size: 41 Copynumber: 3.8 Consensus size: 39
21157338 TAAAATATCT
*
21157348 TTAGCGGCGCTTTTTCAAAAACGCCACTAAAGCCAAGAGAA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAG--AAGAGAA
** * *
21157389 TTAGCGGCGCCATTTCAAAAACGCCGCTAAAGAACATAGTA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAG-A-AGAGAA
* * *
21157430 TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGAACCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGAA--GAGAA
* ** *
21157471 TTAGCAGCGCTTTTTTGAAAACGCCGTTAAAGA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGA
21157504 TCCGAAAGGT
Statistics
Matches: 94, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 2 0.02
41 91 0.97
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (39 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGAAGAGAA
Found at i:21157492 original size:82 final size:81
Alignment explanation
Indices: 21157348--21157503 Score: 188
Period size: 82 Copynumber: 1.9 Consensus size: 81
21157338 TAAAATATCT
* * *
21157348 TTAGCGGCGCTTTTTCAAAAACGCCACTAAAGCCAAGAGAATTAGCGGCGCCATTTCAAAAACGC
1 TTAGCGGCGCTTCTCCAAAAACGCCACTAAAGCC-AGAGAATTAGCAGCGCCATTTCAAAAACGC
21157413 CGCTAAAGAACATAGTA
65 CGCTAAAGAACATAGTA
* * ** **
21157430 TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGAACC-GAGCATTAGCAGCGCTTTTTTGAAAACG
1 TTAGCGGCGCTTCTCCAAAAACGCCACTAAAG--CCAGAGAATTAGCAGCGCCATTTCAAAAACG
*
21157494 CCGTTAAAGA
64 CCGCTAAAGA
21157504 TCCGAAAGGT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
82 60 0.97
84 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (81 bp):
TTAGCGGCGCTTCTCCAAAAACGCCACTAAAGCCAGAGAATTAGCAGCGCCATTTCAAAAACGCC
GCTAAAGAACATAGTA
Found at i:21157613 original size:39 final size:38
Alignment explanation
Indices: 21157560--21157676 Score: 117
Period size: 40 Copynumber: 3.0 Consensus size: 38
21157550 CGTTTTTATA
*
21157560 AAAAACGCCGCTAATGCTCATTTTTAGCGGCGTTTTTC
1 AAAAATGCCGCTAATGCTCATTTTTAGCGGCGTTTTTC
* * * * *
21157598 AGAAAATGCCACTAATGCTTGATATTTAGTGGCGATTTTC
1 A-AAAATGCCGCTAATGC-TCATTTTTAGCGGCGTTTTTC
* * *
21157638 ATAAATCGCCGCTAATGCTCGATTTTTACCGACGTTTTT
1 AAAAAT-GCCGCTAATGCTC-ATTTTTAGCGGCGTTTTT
21157677 TTCTAAGCGT
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
38 1 0.02
39 19 0.31
40 41 0.67
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (38 bp):
AAAAATGCCGCTAATGCTCATTTTTAGCGGCGTTTTTC
Found at i:21158102 original size:2 final size:2
Alignment explanation
Indices: 21158095--21158119 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21158085 AAACAAGTTT
21158095 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21158120 GATCTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21159565 original size:18 final size:19
Alignment explanation
Indices: 21159542--21159586 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
21159532 AAATTTACTA
21159542 ATTAATTT-TTTGGACCAC
1 ATTAATTTCTTTGGACCAC
21159560 ATTAATTTCTTTGGACCAC
1 ATTAATTTCTTTGGACCAC
21159579 ATTAATTT
1 ATTAATTT
21159587 AAGATCTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (19 bp):
ATTAATTTCTTTGGACCAC
Found at i:21160239 original size:6 final size:6
Alignment explanation
Indices: 21160228--21160254 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
21160218 AAAAAAATTA
21160228 TCAATG TCAATG TCAATG TCAATG TCA
1 TCAATG TCAATG TCAATG TCAATG TCA
21160255 TCAATGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (6 bp):
TCAATG
Found at i:21164918 original size:3 final size:3
Alignment explanation
Indices: 21164910--21164985 Score: 109
Period size: 3 Copynumber: 25.0 Consensus size: 3
21164900 ATAGTAATGG
* *
21164910 TAA TAA TAA CT-A TAG TAA GAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21164955 TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
21164986 CATAATTAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
2 1 0.02
3 61 0.92
4 4 0.06
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:21172382 original size:54 final size:54
Alignment explanation
Indices: 21172233--21172362 Score: 206
Period size: 54 Copynumber: 2.4 Consensus size: 54
21172223 ACCCACACAG
* *
21172233 CCGTGTGTCTTAAAATAATTGAGTAACATGGTCTGAGACACGACCAATGACATGA
1 CCGTGTGTCTTAAAAT-AGTGAGTAACATGGTCTGAGACACGACCAACGACATGA
* * *
21172288 CCGTGTGTTTTAAAACAGTGAGTAACATGGTCTGAGACACGGCCAACGACATGA
1 CCGTGTGTCTTAAAATAGTGAGTAACATGGTCTGAGACACGACCAACGACATGA
21172342 CCGTGTGTCTTAAAATAGTGA
1 CCGTGTGTCTTAAAATAGTGA
21172363 CTTACACGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
54 54 0.79
55 14 0.21
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25
Consensus pattern (54 bp):
CCGTGTGTCTTAAAATAGTGAGTAACATGGTCTGAGACACGACCAACGACATGA
Found at i:21174267 original size:21 final size:21
Alignment explanation
Indices: 21174237--21174284 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
21174227 TGAACAATTC
* *
21174237 AACTAGATCAAAATCCATCTA
1 AACTAAATCAAAATCCAACTA
21174258 AACTAAATCAAAATCCAACTA
1 AACTAAATCAAAATCCAACTA
21174279 AACTAA
1 AACTAA
21174285 CCATGCCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.23, G:0.02, T:0.21
Consensus pattern (21 bp):
AACTAAATCAAAATCCAACTA
Found at i:21174754 original size:18 final size:17
Alignment explanation
Indices: 21174712--21174759 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
21174702 TGTCGTTTCT
21174712 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
21174729 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTC-A
21174748 TTTCAAAACATT
1 TTTCAAAACATT
21174760 TTTTTATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
19 4 0.16
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:21180270 original size:30 final size:30
Alignment explanation
Indices: 21180236--21180297 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
21180226 TATTTTACTA
21180236 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
* *
21180266 TTAATTTTGTTATTATTTTAGAGGTATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
21180296 TT
1 TT
21180298 TGTTAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.60
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:21187915 original size:17 final size:17
Alignment explanation
Indices: 21187890--21187929 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
21187880 TAGAATTGGG
* *
21187890 TTGAGAAAATTATTTAA
1 TTGAAAAAATTAATTAA
21187907 TTGAAAAAATTAATTAA
1 TTGAAAAAATTAATTAA
21187924 TT-AAAA
1 TTGAAAA
21187930 CTAATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (17 bp):
TTGAAAAAATTAATTAA
Found at i:21188766 original size:30 final size:31
Alignment explanation
Indices: 21188720--21188810 Score: 78
Period size: 30 Copynumber: 3.0 Consensus size: 31
21188710 ATACATATTA
* *
21188720 CATTTTCATACTTTGTATTCATTCACATTTG
1 CATTATCATACCTTGTATTCATTCACATTTG
* **
21188751 TA-TATCATACCTTGTAATT-GGTCACATTTG
1 CATTATCATACCTTGT-ATTCATTCACATTTG
* * * *
21188781 CATTTTCATACCCTGTAATCATTCATATTT
1 CATTATCATACCTTGTATTCATTCACATTT
21188811 TCACATATAT
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
30 23 0.51
31 22 0.49
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (31 bp):
CATTATCATACCTTGTATTCATTCACATTTG
Found at i:21188798 original size:31 final size:30
Alignment explanation
Indices: 21188742--21188799 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
21188732 TTGTATTCAT
* *
21188742 TCACATTTGTATATCATACCTTGTAATTGG
1 TCACATTTGCATATCATACCCTGTAATTGG
*
21188772 TCACATTTGCATTTTCATACCCTGTAAT
1 TCACATTTGCA-TATCATACCCTGTAAT
21188800 CATTCATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (30 bp):
TCACATTTGCATATCATACCCTGTAATTGG
Found at i:21194268 original size:46 final size:46
Alignment explanation
Indices: 21194134--21194273 Score: 228
Period size: 46 Copynumber: 3.0 Consensus size: 46
21194124 CCATGGAAAA
*
21194134 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTAAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
*
21194180 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* *
21194226 TTGTGAAAAGTAGGTATGGTATTTCAGTGAA-AGAAACTATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGA-AAACCATACTGAG
21194272 TT
1 TT
21194274 ATAGCATTGT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 1 0.01
46 87 0.99
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:21197139 original size:24 final size:26
Alignment explanation
Indices: 21197112--21197160 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
21197102 GCTAGGAACC
21197112 ACAAC-ATG-ACCCTTCCTGCTGAAA
1 ACAACAATGTACCCTTCCTGCTGAAA
*
21197136 ACAACAATGTTGCCCTTCCTGCTGA
1 ACAACAATG-TACCCTTCCTGCTGA
21197161 GAACGACGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
27 13 0.62
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (26 bp):
ACAACAATGTACCCTTCCTGCTGAAA
Found at i:21197582 original size:69 final size:69
Alignment explanation
Indices: 21197465--21197622 Score: 201
Period size: 69 Copynumber: 2.3 Consensus size: 69
21197455 GTGGTATTGG
* * * * *
21197465 ACCTGTGAGCCCTAAAATGACAGTTAGAAGTTTTTAGCTCTCGCTAACTGTTTGGGGCTACAATG
1 ACCTGCGAGCCATAAAATGAAAGTTAGAAGCTTTTAACTCTCGCTAACTGTTTGGGGCTACAATG
*
21197530 TTTG
66 TTTA
* * * *
21197534 ACGTGCGAGCCATAAAATGAAAGTT-GATAGCTTTTAACTCTCGTTAACTGTTTGGGGCTGCAGT
1 ACCTGCGAGCCATAAAATGAAAGTTAGA-AGCTTTTAACTCTCGCTAACTGTTTGGGGCTACAAT
21197598 GTTTA
65 GTTTA
*
21197603 ACCTGTGAGCCATAAAATGA
1 ACCTGCGAGCCATAAAATGA
21197623 CACTCGCTAA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
68 2 0.03
69 74 0.97
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (69 bp):
ACCTGCGAGCCATAAAATGAAAGTTAGAAGCTTTTAACTCTCGCTAACTGTTTGGGGCTACAATG
TTTA
Found at i:21197671 original size:52 final size:52
Alignment explanation
Indices: 21197573--21197672 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 52
21197563 GCTTTTAACT
* * * **
21197573 CTCGTTAACTGTTTGGGGCTGCAGTGTTTAACCTGTGAGCCATAAAATGACA
1 CTCGCTAACTATTTGGGGCTGCAGTGTTTAACATGCAAGCCATAAAATGACA
* * *
21197625 CTCGCTAACTATTTGGGGTTGCGGTGTTTAACATGCAAGCCTTAAAAT
1 CTCGCTAACTATTTGGGGCTGCAGTGTTTAACATGCAAGCCATAAAAT
21197673 TATAGTTGGG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 40 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (52 bp):
CTCGCTAACTATTTGGGGCTGCAGTGTTTAACATGCAAGCCATAAAATGACA
Found at i:21197740 original size:69 final size:69
Alignment explanation
Indices: 21197625--21197910 Score: 286
Period size: 69 Copynumber: 4.1 Consensus size: 69
21197615 TAAAATGACA
* * * * * * * * * **
21197625 CTCGCTAACTATTTGGGGTTGCGGTGTTTAACATGCAAGCCTTAAAATTATAGTTGGGAGCTTTT
1 CTCGCTAACTGTTTAGGGCTGCGGTGTTTAACCTGCGAGCCATAAAATGACAGCTAAGAGCTTTT
21197690 AACT
66 AACT
* * * * *
21197694 CTCGCTAATTGTTTAGGGTTGCGGTGTTCAACCTGCGAGCCATAAAATGACAGCTAAAAACTTTT
1 CTCGCTAACTGTTTAGGGCTGCGGTGTTTAACCTGCGAGCCATAAAATGACAGCTAAGAGCTTTT
21197759 AACT
66 AACT
** * * * *
21197763 CTCAATAACTGTTT-GAGGCTGCGGTGTTTAACTTGCGATCCATGAAATGACAGCTAAGAGTTTT
1 CTCGCTAACTGTTTAG-GGCTGCGGTGTTTAACCTGCGAGCCATAAAATGACAGCTAAGAGCTTT
21197827 TAACT
65 TAACT
* * * * * * **
21197832 ATCACCAATTGTTTAGGGCTGCAGTGTTTAACCTACGAGCCATAAAATGACAGCTCGGAGCTTTT
1 CTCGCTAACTGTTTAGGGCTGCGGTGTTTAACCTGCGAGCCATAAAATGACAGCTAAGAGCTTTT
21197897 AACT
66 AACT
21197901 CTCGCTAACT
1 CTCGCTAACT
21197911 ATTTTGGTTT
Statistics
Matches: 174, Mismatches: 41, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
68 1 0.01
69 172 0.99
70 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (69 bp):
CTCGCTAACTGTTTAGGGCTGCGGTGTTTAACCTGCGAGCCATAAAATGACAGCTAAGAGCTTTT
AACT
Found at i:21209219 original size:37 final size:36
Alignment explanation
Indices: 21209136--21209204 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
21209126 TAGCCTTCCA
*
21209136 TTTATTTA--TTTTTACCTTTTTAGCCTTTAAACCT
1 TTTATTTATTTTTTTACATTTTTAGCCTTTAAACCT
21209170 TTTATTTATTTTTTTCACATTTTTAGCCTTTAAAC
1 TTTATTTATTTTTTT-ACATTTTTAGCCTTTAAAC
21209205 TTGCTTTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
34 8 0.26
36 5 0.16
37 18 0.58
ACGTcount: A:0.22, C:0.16, G:0.03, T:0.59
Consensus pattern (36 bp):
TTTATTTATTTTTTTACATTTTTAGCCTTTAAACCT
Found at i:21209301 original size:30 final size:29
Alignment explanation
Indices: 21209267--21209326 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
21209257 ATTTGAATAA
21209267 ATTTTTAAAATTTTAAAAGTTATAAAAAAT
1 ATTTTTAAAATTTTAAAAGTTA-AAAAAAT
* * *
21209297 ATTTTTAATATTTTTAAATTTAAAAAAAT
1 ATTTTTAAAATTTTAAAAGTTAAAAAAAT
21209326 A
1 A
21209327 ATTAAATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
ATTTTTAAAATTTTAAAAGTTAAAAAAAT
Found at i:21216587 original size:37 final size:37
Alignment explanation
Indices: 21216546--21216621 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
21216536 ATGAAAACAT
21216546 GATTTTGAGACTAAATTGAAAAGAAGCAAAATTTATG
1 GATTTTGAGACTAAATTGAAAAGAAGCAAAATTTATG
21216583 GATTTTGAGACTAAATTGAAAAGAAGCAAAATTTATG
1 GATTTTGAGACTAAATTGAAAAGAAGCAAAATTTATG
21216620 GA
1 GA
21216622 AAAATTCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (37 bp):
GATTTTGAGACTAAATTGAAAAGAAGCAAAATTTATG
Found at i:21217397 original size:73 final size:73
Alignment explanation
Indices: 21217295--21217433 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 73
21217285 GGCTCTTCGT
* * * *
21217295 GAGCTTCTTGATTAATGGCTCTTCGGAGCTTCTCGA-TA-TGGCTCGCTTGAACTTTCCGATATA
1 GAGCTTCTTGATTAATGGCTCTTCAGAGCTACTC-ATTATTGGCTCACATGAACTTTCCGA-ATA
21217358 TGGTTATCCG
64 TGGTTATCCG
* *
21217368 GAGCTTCTTGATTAATGGCTTTTCAGAGCTACTCATTATTGGCTCACATGAGCTTTCCGAATATG
1 GAGCTTCTTGATTAATGGCTCTTCAGAGCTACTCATTATTGGCTCACATGAACTTTCCGAATATG
21217433 G
66 G
21217434 CTCTTATGAG
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
72 1 0.02
73 39 0.67
74 18 0.31
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (73 bp):
GAGCTTCTTGATTAATGGCTCTTCAGAGCTACTCATTATTGGCTCACATGAACTTTCCGAATATG
GTTATCCG
Found at i:21217445 original size:73 final size:72
Alignment explanation
Indices: 21217267--21217447 Score: 184
Period size: 73 Copynumber: 2.5 Consensus size: 72
21217257 CGCAGCTCTT
* * * * *
21217267 ATGAGCGTTCCGTTATATGGCTCTTCGTGAGCTTCTTGATTAATGGCTCTTCGGAGCTTCTCGAT
1 ATGAGCTTTCCG-AATATGGCTCTT-ATGAGCTTCTTGATTAATGGCTCTTCAGAGCTACTCGAT
*
21217332 ATGGCTCGC
64 ATGGCTCAC
* * * * *** *
21217341 TTGAACTTTCCGATATATGGTTATCCGGAGCTTCTTGATTAATGGCTTTTCAGAGCTACTC-ATT
1 ATGAGCTTTCCGA-ATATGGCTCTTATGAGCTTCTTGATTAATGGCTCTTCAGAGCTACTCGA-T
21217405 ATTGGCTCAC
64 A-TGGCTCAC
21217415 ATGAGCTTTCCGAATATGGCTCTTATGAGCTTC
1 ATGAGCTTTCCGAATATGGCTCTTATGAGCTTC
21217448 CCGTTATACA
Statistics
Matches: 84, Mismatches: 20, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
72 1 0.01
73 48 0.57
74 35 0.42
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (72 bp):
ATGAGCTTTCCGAATATGGCTCTTATGAGCTTCTTGATTAATGGCTCTTCAGAGCTACTCGATAT
GGCTCAC
Found at i:21217470 original size:25 final size:25
Alignment explanation
Indices: 21217442--21217497 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
21217432 GGCTCTTATG
* * *
21217442 AGCTTCCCGTTATACAGCCCAGATA
1 AGCTTCCCATTACACAGCCCACATA
*
21217467 AGCTTCCCATTACACAGCTCACATA
1 AGCTTCCCATTACACAGCCCACATA
21217492 AGCTTC
1 AGCTTC
21217498 ATGTTATATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.29, C:0.34, G:0.12, T:0.25
Consensus pattern (25 bp):
AGCTTCCCATTACACAGCCCACATA
Found at i:21221845 original size:16 final size:16
Alignment explanation
Indices: 21221820--21221850 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21221810 TTTATTTTTA
21221820 GATTTCTTTTAAAATT
1 GATTTCTTTTAAAATT
*
21221836 GATTTTTTTTAAAAT
1 GATTTCTTTTAAAAT
21221851 ACTATAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (16 bp):
GATTTCTTTTAAAATT
Found at i:21226210 original size:2 final size:2
Alignment explanation
Indices: 21226203--21226228 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21226193 AAGGGGGACT
21226203 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
21226229 AAGGGGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:21231573 original size:27 final size:25
Alignment explanation
Indices: 21231522--21231574 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
21231512 TGTTTTTTAT
* *
21231522 ATAAAAAATTTAAAAGAACATAATA
1 ATAAAAAATTTAAAAAAACACAATA
*
21231547 ATAAAAAATATTAAAAAAATTACAATA
1 ATAAAAAAT-TTAAAAAAA-CACAATA
21231574 A
1 A
21231575 ATGTTTCTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 9 0.39
26 8 0.35
27 6 0.26
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (25 bp):
ATAAAAAATTTAAAAAAACACAATA
Found at i:21234355 original size:113 final size:113
Alignment explanation
Indices: 21234183--21234546 Score: 561
Period size: 113 Copynumber: 3.2 Consensus size: 113
21234173 AAAATAAGCA
* *
21234183 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAACCTAAGCCCAACGACATCGTTTCCTGAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCCAACGACATCGTTTTCTGAGCTTT
*
21234247 CGGGGATTTAGCGGCGTTTCTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 CGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * *
21234295 TTAGCGGCGTTTTTGGGAAAGCGCCACAAAAAACCTAAGCCCCACGACGTCGTTTTCTGAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCCAACGACATCGTTTTCTGAGCTTT
* * *
21234360 CGGGGATTTAGCGGCATTTTTAAGAAAGTGCTGCTAATGCTCAGGGCT
66 CGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * *
21234408 TTAGCGGCGTTTTTGAGAAAGCGTCGCA-AAAAAACCTAAGCCCAATGACACCTTTTTCTGAGCT
1 TTAGCGGCGTTTTTGAGAAAGCG-C-CACAAAAAACCTAAGCCCAACGACATCGTTTTCTGAGCT
**
21234472 TTTAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
64 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
*
21234522 TTAGCGGCGTTTTTGGGAAAGCGCC
1 TTAGCGGCGTTTTTGAGAAAGCGCC
21234547 GCTAAAAATA
Statistics
Matches: 228, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
112 26 0.11
113 101 0.44
114 99 0.43
115 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (113 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCACAAAAAACCTAAGCCCAACGACATCGTTTTCTGAGCTTT
CGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:21234500 original size:114 final size:114
Alignment explanation
Indices: 21234183--21234554 Score: 570
Period size: 114 Copynumber: 3.3 Consensus size: 114
21234173 AAAATAAGCA
*
21234183 TTAGCGGCGTTTTTGAGAAAGCGCCGC--AAAAACCTAAGCCCAACGACATCGTTTCCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACATCGTTTTCTGAGCTT
*
21234246 TCGGGGATTTAGCGGCGTTTCTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * * *
21234295 TTAGCGGCGTTTTTGGGAAAGCGCCAC-AAAAAACCTAAGCCCCACGACGTCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACATCGTTTTCTGAGCTT
* * *
21234359 TCGGGGATTTAGCGGCATTTTTAAGAAAGTGCTGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* * * *
21234408 TTAGCGGCGTTTTTGAGAAAGCGTCGCAAAAAAACCTAAGCCCAATGACACCTTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACATCGTTTTCTGAGCTT
**
21234473 TTAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
* *
21234522 TTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAAA
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAA
21234555 TATTTTATCT
Statistics
Matches: 233, Mismatches: 25, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
112 25 0.11
113 102 0.44
114 106 0.45
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACATCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCT
Found at i:21234819 original size:15 final size:15
Alignment explanation
Indices: 21234799--21234829 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21234789 CATATTTTAA
21234799 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
21234814 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
21234829 G
1 G
21234830 ATTAGGGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:21235770 original size:15 final size:15
Alignment explanation
Indices: 21235750--21235779 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21235740 ACTTTTTATT
21235750 TTAATTTATAAAAAA
1 TTAATTTATAAAAAA
21235765 TTAATTTATAAAAAA
1 TTAATTTATAAAAAA
21235780 CAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAATTTATAAAAAA
Found at i:21236040 original size:52 final size:53
Alignment explanation
Indices: 21235939--21236041 Score: 206
Period size: 53 Copynumber: 1.9 Consensus size: 53
21235929 AAAAAATAAA
21235939 AACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAATTTTTTTTTG
1 AACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAATTTTTTTTTG
21235992 AACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAATTTTTTT
1 AACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAATTTTTTT
21236042 AGCATAGCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (53 bp):
AACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAATTTTTTTTTG
Found at i:21236104 original size:107 final size:107
Alignment explanation
Indices: 21235992--21236185 Score: 316
Period size: 107 Copynumber: 1.8 Consensus size: 107
21235982 TTTTTTTTTG
* *** *
21235992 AACGCCGCAAAAAATAAATCAATTTATAAAAAATAAAATAAAATTTTTTTAGCATAGCAAAACGG
1 AACGCCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAAATTTTAGAATAGCAAAACGG
*
21236057 TGTCATTTTGTTCAAAATGAAATAGCGGCGTTTTTTTATAAA
66 CGTCATTTTGTTCAAAATGAAATAGCGGCGTTTTTTTATAAA
*
21236099 AACGCCGCAAAAAATAAATCAATTTATAAAGAACAAAATAAAAAAATTTTAGAATAGCAAAACGG
1 AACGCCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAAATTTTAGAATAGCAAAACGG
*
21236164 CGTCGTTTTGTTCAAAATGAAA
66 CGTCATTTTGTTCAAAATGAAA
21236186 AAAATTTTGT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 79 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (107 bp):
AACGCCGCAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAAATTTTAGAATAGCAAAACGG
CGTCATTTTGTTCAAAATGAAATAGCGGCGTTTTTTTATAAA
Found at i:21236261 original size:25 final size:25
Alignment explanation
Indices: 21236233--21236280 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
21236223 GGTAAGCAGC
21236233 AAAAATAAATCAATTTATAAAAACA
1 AAAAATAAATCAATTTATAAAAACA
21236258 AAAAATAAATCAATTTATAAAAA
1 AAAAATAAATCAATTTATAAAAA
21236281 AGCAATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (25 bp):
AAAAATAAATCAATTTATAAAAACA
Found at i:21239107 original size:23 final size:23
Alignment explanation
Indices: 21239077--21239424 Score: 254
Period size: 23 Copynumber: 15.3 Consensus size: 23
21239067 GAAATTTGAT
21239077 AGTGCTGCAAATTGAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
*
21239100 AGTGCTGCAAATTGAAGTATTT-
1 AGTGCTGCAAATTGAAGTGTTTA
* * *
21239122 AGTTGCTGGAAATTGAGGTGTTTT
1 AG-TGCTGCAAATTGAAGTGTTTA
* * *
21239146 A-TCGCTG-TAATTGAGGTGTATA
1 AGT-GCTGCAAATTGAAGTGTTTA
* * ** *
21239168 AATGTTGTTAATT-AA-TATGTTA
1 AGTGCTGCAAATTGAAGTGT-TTA
*
21239190 AGTGCTGCAAATTTAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
* *
21239213 AATGCTGTAAATTGAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
* *
21239236 AGTGCTGCAAATTGAAATATTT-
1 AGTGCTGCAAATTGAAGTGTTTA
* *
21239258 AGTTGCTGGAAATTG-AGATGTTTT
1 AG-TGCTGCAAATTGAAG-TGTTTA
* * *
21239282 A-TCGCTG-TAATTGAGGTGTATA
1 AGT-GCTGCAAATTGAAGTGTTTA
* * **
21239304 AATGTTGTTAATTGATA-TGTTTA
1 AGTGCTGCAAATTGA-AGTGTTTA
21239327 AGTGCTGCAAATTGAAGTGTTTA
1 AGTGCTGCAAATTGAAGTGTTTA
21239350 AGTGCTGCAAATTGAAGTGTTT-
1 AGTGCTGCAAATTGAAGTGTTTA
*
21239372 AGTTGCTGCAAATTG-AGATGTTTT
1 AG-TGCTGCAAATTGAAG-TGTTTA
* *
21239396 A-TCGCTGTAAATTGAAGTGTTAA
1 AGT-GCTGCAAATTGAAGTGTTTA
21239419 AGTGCT
1 AGTGCT
21239425 ACTTTCCATT
Statistics
Matches: 262, Mismatches: 40, Indels: 46
0.75 0.11 0.13
Matches are distributed among these distances:
21 2 0.01
22 54 0.21
23 198 0.76
24 8 0.03
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (23 bp):
AGTGCTGCAAATTGAAGTGTTTA
Found at i:21239239 original size:46 final size:46
Alignment explanation
Indices: 21239079--21239424 Score: 282
Period size: 46 Copynumber: 7.6 Consensus size: 46
21239069 AATTTGATAG
* * **
21239079 TGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTATTTAGT
1 TGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAA
* * * * * *
21239125 TGCTGGAAATTGAGGTGTTTTA-TCGCTG-TAATTGAGGTGTATAAA
1 TGCTGTAAATTGAAGTGTTTAAGT-GCTGCAAATTGAAGTGTTTAAA
* * * *
21239170 TGTTGTTAATT-AA-TATGTTAAGTGCTGCAAATTTAAGTGTTTAAA
1 TGCTGTAAATTGAAGTGT-TTAAGTGCTGCAAATTGAAGTGTTTAAA
* * **
21239215 TGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATATTTAGT
1 TGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAA
* * * * *
21239261 TGCTGGAAATTG-AGATGTTTTA-TCGCTG-TAATTGAGGTGTATAAA
1 TGCTGTAAATTGAAG-TGTTTAAGT-GCTGCAAATTGAAGTGTTTAAA
* * *
21239306 TGTTGTTAATTGATA-TGTTTAAGTGCTGCAAATTGAAGTGTTTAAG
1 TGCTGTAAATTGA-AGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAA
* *
21239352 TGCTGCAAATTGAAGTGTTT-AGTTGCTGCAAATTG-AGATGTTT-TA
1 TGCTGTAAATTGAAGTGTTTAAG-TGCTGCAAATTGAAG-TGTTTAAA
*
21239397 TCGCTGTAAATTGAAGTGTTAAAGTGCT
1 T-GCTGTAAATTGAAGTGTTTAAGTGCT
21239425 ACTTTCCATT
Statistics
Matches: 232, Mismatches: 51, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
43 2 0.01
44 8 0.03
45 81 0.35
46 136 0.59
47 5 0.02
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (46 bp):
TGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAA
Found at i:21239242 original size:136 final size:137
Alignment explanation
Indices: 21239079--21239387 Score: 541
Period size: 136 Copynumber: 2.3 Consensus size: 137
21239069 AATTTGATAG
* *
21239079 TGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTATTTAGTTGCTGGAAATTGAGGTGTT
1 TGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATATTTAGTTGCTGGAAATTGAGATGTT
*
21239144 TTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTAATATG-TTAAGTGCTGCAAATTTAAGT
66 TTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTAATATGTTTAAGTGCTGCAAATTGAAGT
21239208 GTTTAAA
131 GTTTAAA
*
21239215 TGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATATTTAGTTGCTGGAAATTGAGATGTT
1 TGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATATTTAGTTGCTGGAAATTGAGATGTT
*
21239280 TTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTGAAGT
66 TTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTAATATGTTTAAGTGCTGCAAATTGAAGT
*
21239345 GTTTAAG
131 GTTTAAA
21239352 TGCTGCAAATTGAAGTGTTT-AGTTGCTGCAAATTGA
1 TGCTGCAAATTGAAGTGTTTAAG-TGCTGCAAATTGA
21239388 GATGTTTTAT
Statistics
Matches: 164, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
136 106 0.65
137 58 0.35
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (137 bp):
TGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATATTTAGTTGCTGGAAATTGAGATGTT
TTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTAATATGTTTAAGTGCTGCAAATTGAAGT
GTTTAAA
Found at i:21239342 original size:114 final size:114
Alignment explanation
Indices: 21239207--21239419 Score: 356
Period size: 114 Copynumber: 1.9 Consensus size: 114
21239197 CAAATTTAAG
* *
21239207 TGTTTAAATGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATATTTAGTTGCTGGAAATT
1 TGTTTAAATGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATATTTAGTTGCTGCAAATT
*
21239272 GAGATGTTTTATCGCTGT-AATTGAGGTGTATAAATGTTGTTAATTGATA
66 GAGATGTTTTATCGCTGTAAATTGAAGTGT-TAAATGTTGTTAATTGATA
* * *
21239321 TGTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAGTTGCTGCAAATT
1 TGTTTAAATGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATATTTAGTTGCTGCAAATT
21239386 GAGATGTTTTATCGCTGTAAATTGAAGTGTTAAA
66 GAGATGTTTTATCGCTGTAAATTGAAGTGTTAAA
21239420 GTGCTACTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
114 82 0.89
115 10 0.11
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (114 bp):
TGTTTAAATGCTGCAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATATTTAGTTGCTGCAAATT
GAGATGTTTTATCGCTGTAAATTGAAGTGTTAAATGTTGTTAATTGATA
Found at i:21239348 original size:68 final size:68
Alignment explanation
Indices: 21239125--21239348 Score: 258
Period size: 68 Copynumber: 3.3 Consensus size: 68
21239115 AGTATTTAGT
* * *
21239125 TGCTGGAAATTGAGGTGTTTTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTAATATG-TT
1 TGCTGCAAATTGAAGTGTTTTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTT
21239189 AAG
66 AAG
* * * * * * ** * *
21239192 TGCTGCAAATTTAAGTGTTTAAAT-GCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATAT
1 TGCTGCAAATTGAAGTGTTT-TATCGCTGT-AATTGAGGTGTATAAATGTTGTTAATTGATATGT
21239256 TT-AG
64 TTAAG
*
21239260 TTGCTGGAAATTG-AGATGTTTTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGT
1 -TGCTGCAAATTGAAG-TGTTTTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGT
21239324 TTAAG
64 TTAAG
21239329 TGCTGCAAATTGAAGTGTTT
1 TGCTGCAAATTGAAGTGTTT
21239349 AAGTGCTGCA
Statistics
Matches: 124, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
67 22 0.18
68 76 0.61
69 26 0.21
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (68 bp):
TGCTGCAAATTGAAGTGTTTTATCGCTGTAATTGAGGTGTATAAATGTTGTTAATTGATATGTTT
AAG
Found at i:21239371 original size:91 final size:91
Alignment explanation
Indices: 21239206--21239424 Score: 241
Period size: 91 Copynumber: 2.4 Consensus size: 91
21239196 GCAAATTTAA
* *
21239206 GTGTTTAAATGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATATTTAGTTGCTGGAAAT
1 GTGTATAAATGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATATTTAGTTGCTGCAAAT
21239271 TGAGATGTTTTATCGCTGTAATTGAG
66 TGAGATGTTTTATCGCTGTAATTGAG
* * * *
21239297 GTGTATAAATGTTGTTAATTGATA-TGTTTAAGTGCTGCAAATTGAAGTGTTTAAG-TGCTGCAA
1 GTGTATAAATGCTGTAAATTGA-AGTGTTTAAGTGCTGCAAATTGAAATATTT-AGTTGCTGCAA
* *
21239360 ATTGA-A-GTGTTTAGTTGCTGCAAATTGAG
64 ATTGAGATGT-TTTA-TCGCTG-TAATTGAG
* ** *
21239389 ATGT-TTTATCGCTGTAAATTGAAGTGTTAAAGTGCT
1 GTGTATAAAT-GCTGTAAATTGAAGTGTTTAAGTGCT
21239425 ACTTTCCATT
Statistics
Matches: 107, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
89 2 0.02
90 5 0.05
91 66 0.62
92 34 0.32
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (91 bp):
GTGTATAAATGCTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAATATTTAGTTGCTGCAAAT
TGAGATGTTTTATCGCTGTAATTGAG
Found at i:21240394 original size:43 final size:43
Alignment explanation
Indices: 21240346--21240575 Score: 311
Period size: 43 Copynumber: 5.3 Consensus size: 43
21240336 GTTTTTGGAG
* * * * * *
21240346 AAAGCGTCGCTAAAGGTCTTGTTTTTTAGCGGCGCTTCAGGGA
1 AAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGAGGGA
* * *
21240389 AAAGCGCTGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGA
1 AAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGAGGGA
21240432 AAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTA-GGA
1 AAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTG-AGGGA
* *
21240475 AAAGCGCCGCCAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGA
1 AAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGAGGGA
21240518 AAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTT-ATGGGA
1 AAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGA-GGGA
* *
21240561 AGAGCGCTGCTAAAG
1 AAAGCGCCGCTAAAG
21240576 TTAGCGACAC
Statistics
Matches: 168, Mismatches: 16, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
43 168 1.00
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26
Consensus pattern (43 bp):
AAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGAGGGA
Found at i:21240490 original size:129 final size:129
Alignment explanation
Indices: 21240326--21240575 Score: 349
Period size: 129 Copynumber: 1.9 Consensus size: 129
21240316 TTTTTGTGAC
* * * * * * *
21240326 CTTTAGTGGCGTTTTTGGAGAAAGCGTCGCTAAAGGTCTTGTTTTTTAGCGGCGCTTCAGGGAAA
1 CTTTAGCGGCGTTTTAGGAGAAAGCGCCGCCAAAGGTCCTGGTCTTTAGCGGCGCTTCAGGGAAA
* * *
21240391 AGCGCTGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGT
66 AGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGGTCCTGGT
* **
21240455 CTTTAGCGGCGTTTGTAGGA-AAAGCGCCGCCAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAA
1 CTTTAGCGGCGTTT-TAGGAGAAAGCGCCGCCAAAGGTCCTGGTCTTTAGCGGCGCTTCAGGGAA
* *
21240519 AAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTATGGGAAGAGCGCTGCTAAAG
65 AAGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTATGGGAAAAGCGCCGCTAAAG
21240576 TTAGCGACAC
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
129 101 0.96
130 4 0.04
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (129 bp):
CTTTAGCGGCGTTTTAGGAGAAAGCGCCGCCAAAGGTCCTGGTCTTTAGCGGCGCTTCAGGGAAA
AGCGCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGGTCCTGGT
Found at i:21241000 original size:15 final size:15
Alignment explanation
Indices: 21240980--21241009 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21240970 GAACGGACAA
21240980 ACTTGCAAGTTTATG
1 ACTTGCAAGTTTATG
21240995 ACTTGCAAGTTTATG
1 ACTTGCAAGTTTATG
21241010 GCTAAACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
ACTTGCAAGTTTATG
Found at i:21241379 original size:2 final size:2
Alignment explanation
Indices: 21241372--21241402 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21241362 TGAATATAGG
21241372 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21241403 GTGTCGAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21243035 original size:88 final size:87
Alignment explanation
Indices: 21242943--21243138 Score: 214
Period size: 88 Copynumber: 2.2 Consensus size: 87
21242933 CACTGCAACT
* * * * * *
21242943 TCAGGGAGATAGGATTATTGGCTTC-GATCTGCTTCATTGCCAATACAAGAAGGCAAGATCTGCT
1 TCAGGGAGATAGG-CTAGT-GCTTCTGATCTGCTTCACTGCCAATACAAGAAGACAAGATCTACA
* * *
21243007 ATTTTCAACCTGCTCCGCTACTGC
64 ATCTTCAACCTACTCCACTACTGC
* * *
21243031 TCAGGGAGATAAGGCTGGTGCTTCTGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAA
1 TCAGGGAGAT-AGGCTAGTGCTTCTGATCTGCTTCACTGCCAATACAAGAAGACAAGATCTACAA
* **
21243096 TCTTCGACCTACTCCACTGTTGC
65 TCTTCAACCTACTCCACTACTGC
21243119 TCAGGGAGATAAGGCTAGTG
1 TCAGGGAGAT-AGGCTAGTG
21243139 GCTTAAATTT
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
87 5 0.06
88 82 0.91
89 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (87 bp):
TCAGGGAGATAGGCTAGTGCTTCTGATCTGCTTCACTGCCAATACAAGAAGACAAGATCTACAAT
CTTCAACCTACTCCACTACTGC
Found at i:21243276 original size:132 final size:132
Alignment explanation
Indices: 21243102--21243793 Score: 1028
Period size: 132 Copynumber: 5.2 Consensus size: 132
21243092 ACAATCTTCG
* * * * *
21243102 ACCTACTCCACTGTTGCTCAGGGAGATAAGGCTAGTGGCTTAAATTTGATTCCCTACTGTCTTAG
1 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* * *
21243167 GAAGATAAGATTCGCCGTCTTCGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAATTTT
66 GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
21243232 CA
131 CA
* * *
21243234 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAATGACTTAAATCTGCTTCCCTACTACCTTGG
1 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* * * *
21243299 GAAGATAAAATTCGTCGTCTTTGATCTGCTCCACTACTTCTGAGGGAGATAAGATCTGTAATTTT
66 GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
21243364 CA
131 CA
* * * *
21243366 ACCTACGCCACTGTTGCTCAGGGAGATAAGGCT-GCTGGCTTAAATCTGCTTCCTTATTGCCTTG
1 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAG-TGGCTTAAATCTGCTTCCCTACTGCCTTG
* * *
21243430 GGAAGATAAAATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTGTAATTT
65 GGAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTT
21243495 TCA
130 TCA
* * *
21243498 ACCTACTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATTTGCTTCCCTACTGTCTTGG
1 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* *
21243563 GAAGATAAAATTCGCCGTTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTT
66 GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
21243628 CA
131 CA
*
21243630 ACCTACTCCACTGCTACTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
1 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* * * * **
21243695 GAAGAT-AAGTTCGCCGTCTTTGATTTGCTCCACTACTGCTTAGGGAGATAAGATTTACAATTTT
66 GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
21243759 CA
131 CA
* * *
21243761 ACCTACTCCAGTGTTGCTCAAGGAGATAAGGCT
1 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCT
21243794 GGTATCTTCG
Statistics
Matches: 502, Mismatches: 56, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
131 82 0.16
132 419 0.83
133 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (132 bp):
ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
CA
Found at i:21243481 original size:44 final size:44
Alignment explanation
Indices: 21243433--21243614 Score: 113
Period size: 44 Copynumber: 4.1 Consensus size: 44
21243423 TGCCTTGGGA
*
21243433 AGATAAAATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAAATTCACCATCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * *
21243477 AGATAAAATCTGTA--ATTTTCAACCTACTCCACTACTGCTCAGGG
1 AGATAAAAT-T-CACCATCTTCAATCTGCTCCACTACTGCTTAGGG
*** **** * *
21243521 AGATAAGGCT-AGTGGCTTAAATTTGCTTCC-CTACTGTCTT-GGG
1 AGATAAAATTCACCATCTTCAATCTGC-TCCACTACTG-CTTAGGG
* * * *
21243564 AAGATAAAATTCGCCGTTTTCGATCTGCTCCACTACTGCTTAGGG
1 -AGATAAAATTCACCATCTTCAATCTGCTCCACTACTGCTTAGGG
21243609 AGATAA
1 AGATAA
21243615 GATATGTAAT
Statistics
Matches: 100, Mismatches: 28, Indels: 20
0.68 0.19 0.14
Matches are distributed among these distances:
41 1 0.01
43 16 0.16
44 64 0.64
45 18 0.18
46 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
AGATAAAATTCACCATCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:21243628 original size:44 final size:44
Alignment explanation
Indices: 21243454--21243659 Score: 143
Period size: 44 Copynumber: 4.7 Consensus size: 44
21243444 ACCATCTTCG
* *
21243454 ATCTGCTCCACTACTGCTTAGGGAGATAAAATCTGTAATTTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCA
* * * * *** *
21243498 ACCTACTCCACTACTGCTCAGGGAGATAAGGCTA-GT-GGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAA-GATATGTAATTTTCA
* * *** *
21243541 ATTTGCTTCC-CTACTGTCTT-GGGAAGATAAAAT-TCGCCGTTTTCG
1 ATCTGC-TCCACTACTG-CTTAGGG-AGATAAGATAT-GTAATTTTCA
21243586 ATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCA
* * * * *
21243630 ACCTACTCCACTGCTACTCAGGGAGATAAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAG
21243660 GCTAGTGGCT
Statistics
Matches: 120, Mismatches: 32, Indels: 20
0.70 0.19 0.12
Matches are distributed among these distances:
43 16 0.13
44 85 0.71
45 19 0.16
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCA
Found at i:21245440 original size:50 final size:50
Alignment explanation
Indices: 21245331--21245466 Score: 182
Period size: 50 Copynumber: 2.7 Consensus size: 50
21245321 ACATGCCAAA
* ** * *
21245331 GCCATGCCCCAGACATGGTCTTACATGGGATGTTCTTATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATATCGGTGCCCAC
** * *
21245382 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCTAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCCAC
21245432 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
21245467 TTACCCAAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 47 0.64
51 27 0.36
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCCAC
Found at i:21247961 original size:41 final size:41
Alignment explanation
Indices: 21247913--21248001 Score: 133
Period size: 41 Copynumber: 2.2 Consensus size: 41
21247903 AGCAATTCAT
* *
21247913 CTACTAGGTTTAAAGTCTAATTCAGTTCACCGGCACTTAGC
1 CTACTAGGCTTAAAGCCTAATTCAGTTCACCGGCACTTAGC
* * *
21247954 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTACTAGGCTTAAAGCCTAATTCAGTTCACCGGCACTTAGC
21247995 CTACTAG
1 CTACTAG
21248002 ACATATAGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (41 bp):
CTACTAGGCTTAAAGCCTAATTCAGTTCACCGGCACTTAGC
Found at i:21248009 original size:41 final size:41
Alignment explanation
Indices: 21247932--21248014 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
21247922 TTAAAGTCTA
* * *
21247932 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGTTCACCGGCACTTAGCCTACTAGACATATAGCCTG
*
21247973 ATTCAGTTCACCGGCACTTAGCCTACTAGACATATAGTCTG
1 ATTCAGTTCACCGGCACTTAGCCTACTAGACATATAGCCTG
21248014 A
1 A
21248015 ATAATTTCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (41 bp):
ATTCAGTTCACCGGCACTTAGCCTACTAGACATATAGCCTG
Found at i:21248024 original size:41 final size:41
Alignment explanation
Indices: 21247936--21248029 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 41
21247926 AGTCTAATTC
* * * * *
21247936 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
1 AGTTCACCGGCACTTAGCCTACTAGACATATAGCCTGAATA
*
21247977 AGTTCACCGGCACTTAGCCTACTAGACATATAGTCTGAATA
1 AGTTCACCGGCACTTAGCCTACTAGACATATAGCCTGAATA
* *
21248018 ATTTCACTGGCA
1 AGTTCACCGGCA
21248030 ATAAATCCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (41 bp):
AGTTCACCGGCACTTAGCCTACTAGACATATAGCCTGAATA
Found at i:21249810 original size:13 final size:13
Alignment explanation
Indices: 21249792--21249816 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21249782 ACCAATGATA
21249792 AAATTTTCACACG
1 AAATTTTCACACG
21249805 AAATTTTCACAC
1 AAATTTTCACAC
21249817 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:21255707 original size:50 final size:50
Alignment explanation
Indices: 21255583--21255875 Score: 397
Period size: 50 Copynumber: 5.8 Consensus size: 50
21255573 GATCATAACA
* * ** * * *
21255583 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTCTTATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * **
21255634 TGCCTATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
21255684 TGCCAACGCCGTGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
21255734 TGCCAACTCCATGTCCCATACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
21255784 TGCCAACGCCATGCCCCAGACATGGTCTTACATGGGACCTCTCGTGTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
21255834 TGCCAACGCAATGTCCTAGACATGGTCTTATATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
21255876 TTACCCAAAT
Statistics
Matches: 215, Mismatches: 27, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
50 183 0.85
51 32 0.15
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:21269633 original size:12 final size:11
Alignment explanation
Indices: 21269618--21269657 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
21269608 AAGTAAAACC
*
21269618 TAATGTAAATAA
1 TAATATAAAT-A
21269630 TAATATAAATA
1 TAATATAAATA
21269641 TAATAATAAATA
1 TAAT-ATAAATA
21269653 TAATA
1 TAATA
21269658 ATAATAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (11 bp):
TAATATAAATA
Found at i:21269658 original size:12 final size:12
Alignment explanation
Indices: 21269623--21269661 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
21269613 AAACCTAATG
21269623 TAAATAATAAT-A
1 TAAAT-ATAATAA
21269635 TAAATATAATAA
1 TAAATATAATAA
21269647 TAAATATAATAA
1 TAAATATAATAA
21269659 TAA
1 TAA
21269662 TAAACCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 5 0.19
12 21 0.81
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAATATAATAA
Found at i:21269769 original size:49 final size:49
Alignment explanation
Indices: 21269708--21269806 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
21269698 ATAAATTAAT
21269708 TTAGAACTAAAACAAAATCTCAGGGGCGAATTTGAAACAAATGTGTAAA
1 TTAGAACTAAAACAAAATCTCAGGGGCGAATTTGAAACAAATGTGTAAA
21269757 TTAGAACTAAAACAAAATCTCAGGGGCGAATTTGAAACAAATGTGTAAA
1 TTAGAACTAAAACAAAATCTCAGGGGCGAATTTGAAACAAATGTGTAAA
21269806 T
1 T
21269807 GACCAAATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.23
Consensus pattern (49 bp):
TTAGAACTAAAACAAAATCTCAGGGGCGAATTTGAAACAAATGTGTAAA
Found at i:21270031 original size:17 final size:18
Alignment explanation
Indices: 21269991--21270031 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
21269981 ACAATATAAA
*
21269991 AGACAGATGGACCTATTG
1 AGACAAATGGACCTATTG
*
21270009 CG-CAAATGGACC-ATTG
1 AGACAAATGGACCTATTG
21270025 AGACAAA
1 AGACAAA
21270032 ACGCGCGGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 5 0.26
17 13 0.68
18 1 0.05
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (18 bp):
AGACAAATGGACCTATTG
Found at i:21274704 original size:33 final size:33
Alignment explanation
Indices: 21274644--21274707 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
21274634 TACGTTCCTA
* **
21274644 AAAATATGACATTCTGATTTGGTATATGTTTTG
1 AAAATATGACATTCTGATCTGACATATGTTTTG
21274677 AAAATATGACATTCTGATCTGACATATGTTT
1 AAAATATGACATTCTGATCTGACATATGTTT
21274708 CTGTTAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (33 bp):
AAAATATGACATTCTGATCTGACATATGTTTTG
Found at i:21276857 original size:43 final size:43
Alignment explanation
Indices: 21276809--21276902 Score: 143
Period size: 43 Copynumber: 2.2 Consensus size: 43
21276799 CACATAAATG
* * *
21276809 CCGCTAAAGAACATGACCTTTAGCGGCTCTTTTATCACGAACA
1 CCGCTAAAGAACATGACCTTTAGCGACGCTTTTATCACAAACA
* *
21276852 CCGCTAAAGAACATGACCTTTAGCGACGCTTTTTTCACAAACG
1 CCGCTAAAGAACATGACCTTTAGCGACGCTTTTATCACAAACA
21276895 CCGCTAAA
1 CCGCTAAA
21276903 AGTACCATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (43 bp):
CCGCTAAAGAACATGACCTTTAGCGACGCTTTTATCACAAACA
Found at i:21279182 original size:20 final size:21
Alignment explanation
Indices: 21279157--21279203 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
21279147 TATCCATACT
21279157 AATATAGGTTAT-ATATTAAA
1 AATATAGGTTATAATATTAAA
* *
21279177 AATATAGGTTTTAATATTTAA
1 AATATAGGTTATAATATTAAA
21279198 AATATA
1 AATATA
21279204 ATATTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (21 bp):
AATATAGGTTATAATATTAAA
Found at i:21279322 original size:122 final size:120
Alignment explanation
Indices: 21279086--21279513 Score: 671
Period size: 122 Copynumber: 3.5 Consensus size: 120
21279076 GTATTTCAAC
* *
21279086 ATTTATAATTATGTATAAAATTTAAAAAGTTATTAGTAATGAATTTGAAATATAGGTTACATATC
1 ATTTATAATTATGTTTAAAATTTAAAAAGTTATTAGTAATGAATTTGAAATATAGGTTATATATC
21279151 CATACTAATATAGGTTATATATTAAAAATATAGGTTTTAATATTTAAAATATAAT
66 CATACTAATATAGGTTATATATTAAAAATATAGGTTTTAATATTTAAAATATAAT
* *
21279206 ATTTATAATTATGTTTAAAATTTAAAAAAAGTTATTAGTAATGAATTTGAAATATATGTAATATA
1 ATTTATAATTATGTTTAAAATTT--AAAAAGTTATTAGTAATGAATTTGAAATATAGGTTATATA
*
21279271 TCCATACTAATATAGGTGATATATTAAAAA-ATAGGTTTTAATATTTAAAAATATAA-
64 TCCATACTAATATAGGTTATATATTAAAAATATAGGTTTTAATATTT-AAAATATAAT
** *
21279327 ATAAATAATTATGTTTAAAATTTAAAAAGTTATTAGTAATGAATTTAAAATATAGGTTATATATC
1 ATTTATAATTATGTTTAAAATTTAAAAAGTTATTAGTAATGAATTTGAAATATAGGTTATATATC
* *
21279392 CAAACTAATATAGGTTATATATTAAAAATATAGGTTTTAAGTTTTTTTAAAATATAAT
66 CATACTAATATAGGTTATATATTAAAAATATAGGTTTTAA---TATTTAAAATATAAT
* * *
21279450 AATTATAATTATTTTTAAAATTTAAAAACTTATTAGTAATGAATTTGAAATATAGGTTATATAT
1 ATTTATAATTATGTTTAAAATTTAAAAAGTTATTAGTAATGAATTTGAAATATAGGTTATATAT
21279514 TAATAATATA
Statistics
Matches: 281, Mismatches: 19, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
119 65 0.23
120 33 0.12
121 37 0.13
122 84 0.30
123 62 0.22
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (120 bp):
ATTTATAATTATGTTTAAAATTTAAAAAGTTATTAGTAATGAATTTGAAATATAGGTTATATATC
CATACTAATATAGGTTATATATTAAAAATATAGGTTTTAATATTTAAAATATAAT
Found at i:21279590 original size:100 final size:100
Alignment explanation
Indices: 21279398--21279592 Score: 345
Period size: 100 Copynumber: 1.9 Consensus size: 100
21279388 TATCCAAACT
* *
21279398 AATATAGGTTATATATTAAAAATATAGGTTTTAAGTTTTTTTAAAATATAATAATTATAATTATT
1 AATATAGGTTATATATTAAAAATATAGGTTTTAAGTTATTTAAAAATATAATAATTATAATTATT
21279463 TTTAAAATTTAAAAACTTATTAGTAATGAATTTGA
66 TTTAAAATTTAAAAACTTATTAGTAATGAATTTGA
* *
21279498 AATATAGGTTATATATTAATAATATAGGTTTTAAGTTATTTAAAAATATAATATTTATAATTATT
1 AATATAGGTTATATATTAAAAATATAGGTTTTAAGTTATTTAAAAATATAATAATTATAATTATT
*
21279563 TTTAAAATTTAAAAATTTATTAGTAATGAA
66 TTTAAAATTTAAAAACTTATTAGTAATGAA
21279593 AAATCAAAGG
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 90 1.00
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.46
Consensus pattern (100 bp):
AATATAGGTTATATATTAAAAATATAGGTTTTAAGTTATTTAAAAATATAATAATTATAATTATT
TTTAAAATTTAAAAACTTATTAGTAATGAATTTGA
Found at i:21280862 original size:125 final size:125
Alignment explanation
Indices: 21280707--21281113 Score: 539
Period size: 125 Copynumber: 3.3 Consensus size: 125
21280697 AATTTTATAA
* * * * *
21280707 CTTTTGCAGCGTTT-TCAGCAAAAACGCCACTAAAAAATTAATTTCCTATAACGAAACAACACCG
1 CTTTTGCGGCGTTTCTGAG-AAAAACGCCACTAAAAAATTAATTTCCTGTAACCAAACAACGCCG
* ** * *
21280771 TTTTGCACAATTTTTAATACACAGTTGCGGCGGTTTTAGACCAAACGCCACTATTGCTTAC
65 TTTTGTACAATTTTTAATACATTGTTGCGGCGTTTTTAGACCAAACGCCGCTATTGCTTAC
* * * * *
21280832 CTTTTGCGGCATTTCTGAGAAAAACACCACTAAAAATTTAATTTCCTGTAACTAAACAATGCCGT
1 CTTTTGCGGCGTTTCTGAGAAAAACGCCACTAAAAAATTAATTTCCTGTAACCAAACAACGCCGT
*
21280897 TTTGTACAATTTTTAATACATTGTTGCGACGTTTTTAGACCAAACGCCGCTATTGCTTAC
66 TTTGTACAATTTTTAATACATTGTTGCGGCGTTTTTAGACCAAACGCCGCTATTGCTTAC
** * * * * **
21280957 CTTTTGCAACGTTTTTGAGAAAAATGCCACT-AAAAATTAAATTCATGTAACCAAACGGCGCCGT
1 CTTTTGCGGCGTTTCTGAGAAAAACGCCACTAAAAAATTAATTTCCTGTAACCAAACAACGCCGT
* * *
21281021 CTTGTACAATTTTTAATACATTGTTGCGGCGTTTTTTGTCCAAACGCCGCTATTGCTTAC
66 TTTGTACAATTTTTAATACATTGTTGCGGCGTTTTTAGACCAAACGCCGCTATTGCTTAC
*
21281081 CTTTTGCGGCGTTTCTGAGAAAAACGCCGCTAA
1 CTTTTGCGGCGTTTCTGAGAAAAACGCCACTAA
21281114 CGATTGACTT
Statistics
Matches: 243, Mismatches: 37, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
124 108 0.44
125 132 0.54
126 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (125 bp):
CTTTTGCGGCGTTTCTGAGAAAAACGCCACTAAAAAATTAATTTCCTGTAACCAAACAACGCCGT
TTTGTACAATTTTTAATACATTGTTGCGGCGTTTTTAGACCAAACGCCGCTATTGCTTAC
Found at i:21281988 original size:18 final size:18
Alignment explanation
Indices: 21281920--21281991 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
21281910 TGTCACTATG
* * *
21281920 TATTTTGAAATTAAAAAA
1 TATTTTAAAAATAAAAAT
* *
21281938 TATATTAAATATAAAAAT
1 TATTTTAAAAATAAAAAT
***
21281956 ATGATTTTTTTAATAAAAAT
1 -T-ATTTTAAAAATAAAAAT
21281976 TATTTTAAAAATAAAA
1 TATTTTAAAAATAAAA
21281992 TGTGAAATTG
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
18 25 0.64
19 2 0.05
20 12 0.31
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
TATTTTAAAAATAAAAAT
Found at i:21282604 original size:9 final size:9
Alignment explanation
Indices: 21282587--21282623 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
21282577 TATAGTTTGA
*
21282587 TATTTGAAT
1 TATTCGAAT
21282596 TATTCGAAT
1 TATTCGAAT
*
21282605 TATTCGAGT
1 TATTCGAAT
21282614 TATTCGAAT
1 TATTCGAAT
21282623 T
1 T
21282624 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:21282859 original size:7 final size:7
Alignment explanation
Indices: 21282847--21282930 Score: 80
Period size: 7 Copynumber: 12.1 Consensus size: 7
21282837 AAAAAAACCT
21282847 CCTAAAC
1 CCTAAAC
21282854 CCTAAA-
1 CCTAAAC
21282860 CCTAAAC
1 CCTAAAC
*
21282867 CGTAAAC
1 CCTAAAC
*
21282874 ACTAAAC
1 CCTAAAC
* *
21282881 TCTTAAC
1 CCTAAAC
* *
21282888 ACTAAAT
1 CCTAAAC
* *
21282895 CATAAAT
1 CCTAAAC
21282902 CCTAAAC
1 CCTAAAC
21282909 CCTAAAC
1 CCTAAAC
21282916 CCTAAAC
1 CCTAAAC
*
21282923 CTTAAAC
1 CCTAAAC
21282930 C
1 C
21282931 TCAAACCATA
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
6 6 0.10
7 57 0.90
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.20
Consensus pattern (7 bp):
CCTAAAC
Found at i:21282880 original size:14 final size:13
Alignment explanation
Indices: 21282847--21282942 Score: 77
Period size: 14 Copynumber: 7.0 Consensus size: 13
21282837 AAAAAAACCT
*
21282847 CCTAAACCCTAAA
1 CCTAAACCATAAA
*
21282860 CCTAAACCGTAAA
1 CCTAAACCATAAA
*
21282873 CACTAAACTC-TTAA
1 C-CTAAAC-CATAAA
*
21282887 CACTAAATCATAAA
1 C-CTAAACCATAAA
*
21282901 TCCTAAACCCTAAA
1 -CCTAAACCATAAA
*
21282915 CCCTAAACCTTAAA
1 -CCTAAACCATAAA
21282929 CCTCAAACCATAAA
1 CCT-AAACCATAAA
21282943 TATACACCCT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
13 17 0.25
14 50 0.72
15 2 0.03
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.20
Consensus pattern (13 bp):
CCTAAACCATAAA
Found at i:21282920 original size:28 final size:28
Alignment explanation
Indices: 21282846--21282942 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
21282836 GAAAAAAACC
*
21282846 TCCTAAACCCTAAA-CCTAAACCGTAAA
1 TCCTAAACCCTAAACCCTAAACCATAAA
* * * *
21282873 -CACTAAACTCTTAACACTAAATCATAAA
1 TC-CTAAACCCTAAACCCTAAACCATAAA
*
21282901 TCCTAAACCCTAAACCCTAAACCTTAAA
1 TCCTAAACCCTAAACCCTAAACCATAAA
*
21282929 -CCTCAAACCATAAA
1 TCCT-AAACCCTAAA
21282943 TATACACCCT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
26 1 0.02
27 13 0.24
28 40 0.73
29 1 0.02
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (28 bp):
TCCTAAACCCTAAACCCTAAACCATAAA
Found at i:21282921 original size:21 final size:20
Alignment explanation
Indices: 21282847--21282962 Score: 90
Period size: 21 Copynumber: 5.7 Consensus size: 20
21282837 AAAAAAACCT
21282847 CCTAAACCCTAAACCTAAAC
1 CCTAAACCCTAAACCTAAAC
* * *
21282867 CGTAAACACTAAACTCTTAAC
1 CCTAAACCCTAAAC-CTAAAC
* * *
21282888 ACTAAATCATAAATCCTAAAC
1 CCTAAACCCTAAA-CCTAAAC
21282909 CCTAAACCCTAAACCTTAAA-
1 CCTAAACCCTAAACC-TAAAC
* ** *
21282929 CCTCAAACCATAAATATACAC
1 CCT-AAACCCTAAACCTAAAC
*
21282950 CCTAAACCTTAAA
1 CCTAAACCCTAAA
21282963 TATATATATT
Statistics
Matches: 74, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
20 29 0.39
21 44 0.59
22 1 0.01
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.21
Consensus pattern (20 bp):
CCTAAACCCTAAACCTAAAC
Found at i:21282931 original size:7 final size:6
Alignment explanation
Indices: 21282847--21282942 Score: 66
Period size: 7 Copynumber: 14.0 Consensus size: 6
21282837 AAAAAAACCT
* *
21282847 CCTAAA CCCTAAA CCTAAA CCGTAAA CACTAAA CTCTTAA CACTAAA TCATAAA
1 CCTAAA -CCTAAA CCTAAA CC-TAAA C-CTAAA C-CTAAA C-CTAAA -CCTAAA
21282901 TCCTAAA CCCTAAA CCCTAAA CCTTAAA CCTCAAA CCATAAA
1 -CCTAAA -CCTAAA -CCTAAA CC-TAAA CCT-AAA CC-TAAA
21282943 TATACACCCT
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
6 11 0.14
7 62 0.82
8 3 0.04
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.20
Consensus pattern (6 bp):
CCTAAA
Found at i:21284887 original size:21 final size:23
Alignment explanation
Indices: 21284863--21284905 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21284853 ATAAATTTTC
21284863 TATT-AATTAA-ATAAGATTTAA
1 TATTAAATTAATATAAGATTTAA
*
21284884 TATTAAATTAATATAATATTTA
1 TATTAAATTAATATAAGATTTA
21284906 TCAAGTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TATTAAATTAATATAAGATTTAA
Found at i:21285707 original size:27 final size:27
Alignment explanation
Indices: 21285675--21285728 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21285665 GTAAAATTAG
21285675 CATGTAAATAAGTAAGATTACAAATTT
1 CATGTAAATAAGTAAGATTACAAATTT
21285702 CATGTAAATAAGTAAGATTACAAATTT
1 CATGTAAATAAGTAAGATTACAAATTT
21285729 AACTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.33
Consensus pattern (27 bp):
CATGTAAATAAGTAAGATTACAAATTT
Found at i:21286004 original size:25 final size:25
Alignment explanation
Indices: 21285970--21286020 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
21285960 TTACATATTG
*
21285970 CTTCAAGACTTAAGACACTTAAAAT
1 CTTCAAGACTTAAGACACCTAAAAT
21285995 CTTCAAGACTTAAGACACCTAAAAT
1 CTTCAAGACTTAAGACACCTAAAAT
21286020 C
1 C
21286021 GAGCTTTCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (25 bp):
CTTCAAGACTTAAGACACCTAAAAT
Found at i:21289986 original size:23 final size:23
Alignment explanation
Indices: 21289956--21290001 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
21289946 CAACCAATTT
*
21289956 ATAGCTATTAACTAGTTATAGTC
1 ATAGCTATGAACTAGTTATAGTC
*
21289979 ATAGCTATGAATTAGTTATAGTC
1 ATAGCTATGAACTAGTTATAGTC
21290002 TTTTTGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (23 bp):
ATAGCTATGAACTAGTTATAGTC
Found at i:21290930 original size:32 final size:32
Alignment explanation
Indices: 21290892--21290953 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
21290882 CCCGTTTTTT
* **
21290892 AAATAAATACCAAAAATTTATTTTAAAAATTA
1 AAATAAAAACCAAAAAAGTATTTTAAAAATTA
**
21290924 AAATAAAAATTAAAAAAGTATTTTAAAAAT
1 AAATAAAAACCAAAAAAGTATTTTAAAAAT
21290954 ATTTTAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (32 bp):
AAATAAAAACCAAAAAAGTATTTTAAAAATTA
Found at i:21290987 original size:40 final size:40
Alignment explanation
Indices: 21290910--21291059 Score: 189
Period size: 40 Copynumber: 3.7 Consensus size: 40
21290900 ACCAAAAATT
21290910 TATTTTAAAAATTAAAATAAAAATT-AAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAAGTATTTTAAAAA
21290953 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
* *
21290993 AATTTTAAAATTAAAAAAATTTAAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAA-TT-AAAAAAAGTATTTTAAAAA
* *
21291035 TATTTTTAAGTT-AAAAAA-TAAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAA
21291060 TAAAAATAAA
Statistics
Matches: 99, Mismatches: 5, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
38 6 0.06
39 8 0.08
40 38 0.38
41 8 0.08
42 33 0.33
43 6 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:21291029 original size:31 final size:31
Alignment explanation
Indices: 21290968--21291033 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
21290958 TAAAATTAAA
**
21290968 AAAATTAAAAAAAGTATTTTAAAAAAATTTT
1 AAAATTAAAAAAAGTATTAAAAAAAAATTTT
21290999 AAAATTAAAAAAA-T-TTAAAAAAAAGTATTTT
1 AAAATTAAAAAAAGTATTAAAAAAAA--ATTTT
21291030 AAAA
1 AAAA
21291034 GTATTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 8 0.26
30 1 0.03
31 22 0.71
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (31 bp):
AAAATTAAAAAAAGTATTAAAAAAAAATTTT
Found at i:21300004 original size:16 final size:16
Alignment explanation
Indices: 21299985--21300017 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21299975 AAATCAATAA
21299985 TATAA-TATAATATATT
1 TATAATTATAA-ATATT
21300001 TATAATTATAAATATT
1 TATAATTATAAATATT
21300017 T
1 T
21300018 TCTTAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATAATTATAAATATT
Found at i:21304302 original size:6 final size:7
Alignment explanation
Indices: 21304285--21304310 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21304275 AATTAACTCT
21304285 TTTTTTC
1 TTTTTTC
21304292 TTTTTTC
1 TTTTTTC
21304299 TTTTTTC
1 TTTTTTC
21304306 TTTTT
1 TTTTT
21304311 ACAATCGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:21305369 original size:30 final size:32
Alignment explanation
Indices: 21305319--21305387 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 32
21305309 CGGCTCGATC
*
21305319 AAAATTTAATTTAAAATAT-AAAAATATTTTT
1 AAAATTTAAATTAAAATATAAAAAATATTTTT
*
21305350 AAAA-TTAAATTAAATTATAAAAAATA-TTTT
1 AAAATTTAAATTAAAATATAAAAAATATTTTT
21305380 AAATATTT
1 AAA-ATTT
21305388 TATTAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 19 0.58
31 12 0.36
32 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AAAATTTAAATTAAAATATAAAAAATATTTTT
Found at i:21305393 original size:31 final size:30
Alignment explanation
Indices: 21305319--21305379 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
21305309 CGGCTCGATC
*
21305319 AAAATTTAATTTAAAATATAAAAATATTTTT
1 AAAA-TTAAATTAAAATATAAAAATATTTTT
*
21305350 AAAATTAAATTAAATTATAAAAAATATTTT
1 AAAATTAAATTAAAATAT-AAAAATATTTT
21305380 AAATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
AAAATTAAATTAAAATATAAAAATATTTTT
Found at i:21307535 original size:58 final size:57
Alignment explanation
Indices: 21307436--21307618 Score: 165
Period size: 58 Copynumber: 3.2 Consensus size: 57
21307426 TGGAAGATGT
* * * **
21307436 TAGATATGTTGCTATATATTATAAATTTTATTATCCATATAAAATGTTGTTATATAAA
1 TAGATATGTTGGTATATATTATAGATTTTAGTAT-TTTATAAAATGTTGTTATATAAA
* * * * *
21307494 TAGATATGTTGGTATATATTATAGATTTTAGTATTTGTATAAAATATTATCATTTAAG
1 TAGATATGTTGGTATATATTATAGATTTTAGTATTT-TATAAAATGTTGTTATATAAA
* * * **
21307552 TAGATATGCT-GT-TATAATA-AGATTTTGGTAGTTATTATAAAAATGTTGTTATATATT
1 TAGATATGTTGGTATATATTATAGATTTTAGTA-TT-TTAT-AAAATGTTGTTATATAAA
21307609 TAGATATGTT
1 TAGATATGTT
21307619 ATATATTATA
Statistics
Matches: 101, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
55 10 0.10
56 11 0.11
57 24 0.24
58 56 0.55
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.48
Consensus pattern (57 bp):
TAGATATGTTGGTATATATTATAGATTTTAGTATTTTATAAAATGTTGTTATATAAA
Found at i:21307787 original size:43 final size:39
Alignment explanation
Indices: 21307726--21307827 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 39
21307716 TATTGAAATT
* *
21307726 CCAACTTTGTAACTAAATACT-TTGTAATTGTGCGTAGGTGTAC
1 CCAACTTTGTAACCAAATACTATT-T-A-TATGCG-A-GTGTAC
*
21307769 CCAACTTTATAACCAAATACTCATTTATATGCGAGTGTAC
1 CCAACTTTGTAACCAAATACT-ATTTATATGCGAGTGTAC
21307809 CCAACTTTGTAACCAAATA
1 CCAACTTTGTAACCAAATA
21307828 GTAAAATTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 24 0.45
41 1 0.02
42 5 0.09
43 20 0.38
44 1 0.02
45 2 0.04
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (39 bp):
CCAACTTTGTAACCAAATACTATTTATATGCGAGTGTAC
Found at i:21307857 original size:38 final size:39
Alignment explanation
Indices: 21307807--21307904 Score: 137
Period size: 38 Copynumber: 2.5 Consensus size: 39
21307797 ATGCGAGTGT
21307807 ACCCAACTTTGTAACCAAATAGTAAAATT-TCTACTG-AA
1 ACCCAACTTTGTAACCAAATAGTAAAATTCT-TACTGAAA
** * *
21307845 ATTCAACTTTGTAACCAAATATTAAAATTCTTATTGAAA
1 ACCCAACTTTGTAACCAAATAGTAAAATTCTTACTGAAA
21307884 ACCCAACTTTGTAACCAAATA
1 ACCCAACTTTGTAACCAAATA
21307905 CTTTGTAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
38 30 0.58
39 22 0.42
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (39 bp):
ACCCAACTTTGTAACCAAATAGTAAAATTCTTACTGAAA
Found at i:21308574 original size:80 final size:81
Alignment explanation
Indices: 21308440--21308639 Score: 233
Period size: 80 Copynumber: 2.5 Consensus size: 81
21308430 CAAAGTTAAG
* * *
21308440 TTTCCAATAGAAATTTTAG-TTTTCGGTTATAAAGTTGGACACAGTCACACACAATTACAAAGTA
1 TTTCCAATA-AAAATTTAGTTTTTC-GTTACAAAGTTGGACACACTCACACACAATTACAAAGTA
*** *
21308504 TTTGGTTACAAACTT-GA
64 TTCAATTACAAAATTGGA
* *
21308521 TTTCCAATAAAAATTTAGTTTTTCGTTACAAAGTTGGATACACTCACGCACAATTACAAAGTATT
1 TTTCCAATAAAAATTTAGTTTTTCGTTACAAAGTTGGACACACTCACACACAATTACAAAGTATT
*
21308586 CAATTACAAAATTGGG
66 CAATTACAAAATTGGA
* * * *
21308602 TCTCCAATAGAAACTTAGTTTTTTTGTTACAAAGTTGG
1 TTTCCAATAAAAATTTAG-TTTTTCGTTACAAAGTTGG
21308640 GTTTCCAATA
Statistics
Matches: 102, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
80 54 0.53
81 30 0.29
82 18 0.18
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (81 bp):
TTTCCAATAAAAATTTAGTTTTTCGTTACAAAGTTGGACACACTCACACACAATTACAAAGTATT
CAATTACAAAATTGGA
Found at i:21323106 original size:46 final size:46
Alignment explanation
Indices: 21323039--21323134 Score: 183
Period size: 46 Copynumber: 2.1 Consensus size: 46
21323029 ACATCGATCA
21323039 CAAAAGCCTTAAGTATCTGTTGACTTAAAAGGAGTTGAACCTTAAG
1 CAAAAGCCTTAAGTATCTGTTGACTTAAAAGGAGTTGAACCTTAAG
*
21323085 CAAAAGCCTTAAGTATCTGTTGACTTAAAAGGAGTTGAACCTTAGG
1 CAAAAGCCTTAAGTATCTGTTGACTTAAAAGGAGTTGAACCTTAAG
21323131 CAAA
1 CAAA
21323135 GTAAATGGAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (46 bp):
CAAAAGCCTTAAGTATCTGTTGACTTAAAAGGAGTTGAACCTTAAG
Found at i:21323241 original size:39 final size:39
Alignment explanation
Indices: 21323180--21323257 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
21323170 ACTATAGAGT
* *
21323180 ACCATCCCGATAAGACTCATATTGTGGCTGATGCTCTTA
1 ACCATCCCGATAAGACTAATATTGTGGCTGATACTCTTA
*
21323219 ACCATCCCGATAAGGCTAATATTGTGGCTGATACTCTTA
1 ACCATCCCGATAAGACTAATATTGTGGCTGATACTCTTA
21323258 GTCGTAGAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (39 bp):
ACCATCCCGATAAGACTAATATTGTGGCTGATACTCTTA
Found at i:21325935 original size:29 final size:29
Alignment explanation
Indices: 21325902--21325967 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
21325892 ATGTGATGAG
*
21325902 CCACACGGCCATGTGCCAGGTCTTGTGGA
1 CCACACGGCCATGTGCCAGGTCTTGTGAA
* * * *
21325931 CCACATGACCGTGTGCTAGGTCTTGTGAA
1 CCACACGGCCATGTGCCAGGTCTTGTGAA
*
21325960 CTACACGG
1 CCACACGG
21325968 GCCAGCCATC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.23
Consensus pattern (29 bp):
CCACACGGCCATGTGCCAGGTCTTGTGAA
Found at i:21327780 original size:23 final size:24
Alignment explanation
Indices: 21327769--21327825 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
21327759 ATTTTTAATT
21327769 TTTAATTAAATAAA-TTATATGTA
1 TTTAATTAAATAAATTTATATGTA
21327792 TTTAATTAAATATAATTTAT-T-TA
1 TTTAATTAAATA-AATTTATATGTA
21327815 TTTAA-TAAATA
1 TTTAATTAAATA
21327826 TTTTTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.19
23 19 0.59
24 3 0.09
25 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
TTTAATTAAATAAATTTATATGTA
Found at i:21334168 original size:17 final size:17
Alignment explanation
Indices: 21334132--21334163 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
21334122 GTGTCTTATA
21334132 AAATATAATAAAATATT
1 AAATATAATAAAATATT
21334149 AAATA-AAT-AAATATT
1 AAATATAATAAAATATT
21334164 TTAAAAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAATAAAATATT
Found at i:21338351 original size:10 final size:11
Alignment explanation
Indices: 21338339--21338368 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
21338329 ATTTTATACG
21338339 AAATAAAACGA
1 AAATAAAACGA
21338350 AAATAAAA-GA
1 AAATAAAACGA
21338360 AAATAAAAC
1 AAATAAAAC
21338369 ACATATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (11 bp):
AAATAAAACGA
Found at i:21339037 original size:5 final size:5
Alignment explanation
Indices: 21339027--21339056 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
21339017 TGATTTTAAA
21339027 TAATT TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT TAATT
21339057 ACGCATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:21341895 original size:57 final size:57
Alignment explanation
Indices: 21341825--21341945 Score: 170
Period size: 57 Copynumber: 2.1 Consensus size: 57
21341815 TAAACGCAAC
* * * *
21341825 CACGATAAGTAAATAAAATATTTTCTAAATTCAGTGACTATAATAAATTACATAAAA
1 CACGATAAATAAATAAAATATTCTCTAAATTCAATCACTATAATAAATTACATAAAA
* * * *
21341882 CATGATAAATAAATAAAATGTTCTCTAAATTCAATCACTGTAATAAATTACTTAAAA
1 CACGATAAATAAATAAAATATTCTCTAAATTCAATCACTATAATAAATTACATAAAA
21341939 CACGATA
1 CACGATA
21341946 CGGTAAGAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (57 bp):
CACGATAAATAAATAAAATATTCTCTAAATTCAATCACTATAATAAATTACATAAAA
Found at i:21342528 original size:19 final size:20
Alignment explanation
Indices: 21342490--21342528 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
21342480 AAAAAGAAAG
**
21342490 TTCAAAAAATTATGAGATAA
1 TTCAAAAAATTAACAGATAA
21342510 TTCAAAAAATTAACA-ATAA
1 TTCAAAAAATTAACAGATAA
21342529 AAAATGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (20 bp):
TTCAAAAAATTAACAGATAA
Found at i:21343090 original size:24 final size:24
Alignment explanation
Indices: 21343058--21343114 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
21343048 TATTCTCTTA
*
21343058 AGTTAAACTCCTTTATCTTTTCCT
1 AGTTGAACTCCTTTATCTTTTCCT
21343082 AGTTGAACTCCTTTATCTTTTCCT
1 AGTTGAACTCCTTTATCTTTTCCT
21343106 AGTTGAACT
1 AGTTGAACT
21343115 TTGATATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.21, C:0.23, G:0.09, T:0.47
Consensus pattern (24 bp):
AGTTGAACTCCTTTATCTTTTCCT
Found at i:21343124 original size:21 final size:23
Alignment explanation
Indices: 21343058--21343124 Score: 57
Period size: 24 Copynumber: 2.9 Consensus size: 23
21343048 TATTCTCTTA
* * *
21343058 AGTTAAACTCCTTTATCTTTTCCT
1 AGTTGAACT-CTTGATCATTTCCT
* *
21343082 AGTTGAACTCCTTTATCTTTTCCT
1 AGTTGAACT-CTTGATCATTTCCT
21343106 AGTTGAACT-TTGAT-ATTTC
1 AGTTGAACTCTTGATCATTTC
21343125 AATCAAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
21 4 0.10
22 4 0.10
24 32 0.80
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (23 bp):
AGTTGAACTCTTGATCATTTCCT
Found at i:21345941 original size:12 final size:13
Alignment explanation
Indices: 21345918--21345944 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
21345908 TAAAAAGGAG
21345918 AAAATTCAAAAAA
1 AAAATTCAAAAAA
21345931 AAAATTCAAAAAA
1 AAAATTCAAAAAA
21345944 A
1 A
21345945 TTTAACAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATTCAAAAAA
Found at i:21346082 original size:17 final size:17
Alignment explanation
Indices: 21346060--21346092 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21346050 AAAAATTGTA
21346060 AAAAAATTCA-AAAAAAT
1 AAAAAA-TCATAAAAAAT
21346077 AAAAAATCATAAAAAA
1 AAAAAATCATAAAAAA
21346093 AATGAAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAAATCATAAAAAAT
Found at i:21346100 original size:28 final size:28
Alignment explanation
Indices: 21346046--21346100 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
21346036 GTAAAAAAGT
** *
21346046 AATAAAAAATTGTAAAAAAATTCAAAAA
1 AATAAAAAATCATAAAAAAAATCAAAAA
*
21346074 AATAAAAAATCATAAAAAAAATGAAAA
1 AATAAAAAATCATAAAAAAAATCAAAA
21346101 GCTTTAAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (28 bp):
AATAAAAAATCATAAAAAAAATCAAAAA
Found at i:21359234 original size:51 final size:51
Alignment explanation
Indices: 21359071--21359255 Score: 205
Period size: 51 Copynumber: 3.6 Consensus size: 51
21359061 GAAGTTGCTA
* * *
21359071 GGTCACGTGTGTAGTACTATGTGCAGACTACTACGTGTACCAGAATG-ATA-
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAG-ATGAAAAT
* * ** * ***
21359121 GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCATACCGGAT-AGCTT
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATGAAAAT
* * *
21359171 CGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGAAAAT
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATGAAAAT
21359223 GGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTA
21359256 TATGAACCGG
Statistics
Matches: 108, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
49 2 0.02
50 36 0.33
51 68 0.63
52 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATGAAAAT
Found at i:21359296 original size:102 final size:101
Alignment explanation
Indices: 21359073--21359256 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 101
21359063 AGTTGCTAGG
* * *
21359073 TCACGTGTGTAGTACTATGTGCAGACTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTATGTGCAGACTACTACGTGTACCAGAATGAAAGGTCACATGTGTAGTAC
21359138 TATGTGCAGGCTACTATGCATACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCATACCGGATAGCTTCGA
* * *
21359174 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAG-ATGAAAATGGTCACATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAGACTACTACGTGTACCAGAATG-AAA-GGTCACATGTGTAGT
21359238 ACTATGTGCAGGCTACTAT
64 ACTATGTGCAGGCTACTAT
21359257 ATGAACCGGG
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 3 0.04
101 41 0.53
102 33 0.43
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGTGCAGACTACTACGTGTACCAGAATGAAAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCATACCGGATAGCTTCGA
Found at i:21366821 original size:17 final size:17
Alignment explanation
Indices: 21366795--21366830 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21366785 TAAACATCTT
21366795 ATTAAAATAATATTTTA
1 ATTAAAATAATATTTTA
* *
21366812 ATTAAGATAATTTTTTA
1 ATTAAAATAATATTTTA
21366829 AT
1 AT
21366831 AAATTATAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTAAAATAATATTTTA
Found at i:21369936 original size:19 final size:19
Alignment explanation
Indices: 21369887--21370124 Score: 134
Period size: 19 Copynumber: 11.9 Consensus size: 19
21369877 GGCGCCAATG
*
21369887 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
*
21369906 GTAACTTTTTGTGTGAATATT
1 GTAA--TTTTGTATGAATATT
*
21369927 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
21369946 GTAATTATT-T-T--ATAAT
1 GTAATT-TTGTATGAATATT
*
21369962 -TAATTTTGTATTTATAGTTATT
1 GTAATTTTGTA-TGA-A--TATT
21369984 GATTAGTATTTTGTATGAATATT
1 G--TA--ATTTTGTATGAATATT
*
21370007 GTAATTTTGAATGAATATT
1 GTAATTTTGTATGAATATT
*
21370026 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
21370049 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
21370069 GTAA-TTTGTATGAATATT
1 GTAATTTTGTATGAATATT
21370087 GTAATTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
21370108 GTAATTTTGTATGAATA
1 GTAATTTTGTATGAATA
21370125 NNNNNNNNNN
Statistics
Matches: 171, Mismatches: 18, Indels: 60
0.69 0.07 0.24
Matches are distributed among these distances:
14 2 0.01
15 6 0.04
16 4 0.02
17 6 0.04
18 7 0.04
19 61 0.36
20 13 0.08
21 39 0.23
22 7 0.04
23 9 0.05
24 3 0.02
25 4 0.02
26 2 0.01
27 8 0.05
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:21370015 original size:80 final size:80
Alignment explanation
Indices: 21369912--21370113 Score: 334
Period size: 80 Copynumber: 2.5 Consensus size: 80
21369902 TATTGTAACT
* *
21369912 TTTTGTGTGAATATTATAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAT
21369977 AGTTATT-GATTAGTA
66 AGTT-TTGGATTAGTA
*
21369992 TTTTGTATGAATATTGTAATTTTGAATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAT
21370057 AGTTTTGGATTAGTA
66 AGTTTTGGATTAGTA
*
21370072 ATTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAA--TTTTGTATGAATATTGTAATT
21370114 TTGTATGAAT
Statistics
Matches: 114, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
79 2 0.02
80 92 0.81
82 20 0.18
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.55
Consensus pattern (80 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTAT
AGTTTTGGATTAGTA
Found at i:21370456 original size:15 final size:16
Alignment explanation
Indices: 21370420--21370456 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
21370410 CTCATTTAAT
21370420 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
*
21370436 TTTTATATTATGTAA-
1 TTTTATATAATGTAAC
21370451 TTTTAT
1 TTTTAT
21370457 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Done.