Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 71 of 198
Found at i:22170248 original size:34 final size:35
Alignment explanation
Indices: 22170210--22170279 Score: 115
Period size: 34 Copynumber: 2.0 Consensus size: 35
22170200 TGTATAAGTA
*
22170210 AATTTCTATTTTAGTACATGAAATAATAT-AAAAT
1 AATTTCTATTTTAGTACATCAAATAATATCAAAAT
*
22170244 AATTTCTATTTTATTACATCAAATAATATCAAAAT
1 AATTTCTATTTTAGTACATCAAATAATATCAAAAT
22170279 A
1 A
22170280 TTCAAAATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 27 0.82
35 6 0.18
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (35 bp):
AATTTCTATTTTAGTACATCAAATAATATCAAAAT
Found at i:22171312 original size:27 final size:27
Alignment explanation
Indices: 22171246--22171313 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
22171236 GCAAGCTGGT
*
22171246 GTACGCCAGTAGGCATGGCGAGTTGAA
1 GTACGCCAGTAGGCATGGAGAGTTGAA
** * *
22171273 GTAAACCAGTAGGCCTGGAGAGTTGTA
1 GTACGCCAGTAGGCATGGAGAGTTGAA
*
22171300 GTACGCCAATAGGC
1 GTACGCCAGTAGGC
22171314 TTAGCGAGCT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.28, C:0.19, G:0.34, T:0.19
Consensus pattern (27 bp):
GTACGCCAGTAGGCATGGAGAGTTGAA
Found at i:22177125 original size:18 final size:18
Alignment explanation
Indices: 22177102--22177136 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22177092 CAAGAATAGG
22177102 AAGCATCAAAATAGTTTC
1 AAGCATCAAAATAGTTTC
*
22177120 AAGCATGAAAATAGTTT
1 AAGCATCAAAATAGTTT
22177137 GGCATATCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (18 bp):
AAGCATCAAAATAGTTTC
Found at i:22183534 original size:6 final size:6
Alignment explanation
Indices: 22183523--22183572 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
22183513 GCTATGATGT
22183523 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA
22183571 AA
1 AA
22183573 GGTTACGACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:22184331 original size:20 final size:20
Alignment explanation
Indices: 22184306--22184348 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
22184296 AAGCTTATGC
22184306 TAAGTAAATGAAATAGA-AAG
1 TAAGTAAATGAAAT-GATAAG
*
22184326 TAAGTAAATGGAATGATAAG
1 TAAGTAAATGAAATGATAAG
22184346 TAA
1 TAA
22184349 ATGGAGTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (20 bp):
TAAGTAAATGAAATGATAAG
Found at i:22185384 original size:16 final size:16
Alignment explanation
Indices: 22185365--22185397 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
22185355 AGTTTTCTTT
22185365 AGAAGTTGTTTTAACA
1 AGAAGTTGTTTTAACA
22185381 AGAAGTTGTTTTAACA
1 AGAAGTTGTTTTAACA
22185397 A
1 A
22185398 TCTTTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (16 bp):
AGAAGTTGTTTTAACA
Found at i:22189523 original size:27 final size:27
Alignment explanation
Indices: 22189461--22189523 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
22189451 GTGGGCTGGT
* *
22189461 GTACACCAGTAGGCCTGTCGAGTTGGA
1 GTACACCAGTAGGCCTGACGAGTTAGA
*
22189488 GTACGCCAGTAGGCCTGACGAGCTTAG-
1 GTACACCAGTAGGCCTGACGAG-TTAGA
*
22189515 GTTCACCAG
1 GTACACCAG
22189524 AAATCAGGCG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.22, C:0.25, G:0.32, T:0.21
Consensus pattern (27 bp):
GTACACCAGTAGGCCTGACGAGTTAGA
Found at i:22190340 original size:30 final size:30
Alignment explanation
Indices: 22190304--22190364 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
22190294 TGTTCTTCAT
*
22190304 GTTAGTTAAGTTGGTTAACAGTATAGATAA
1 GTTAGTTAAGTTGGTTAACACTATAGATAA
*
22190334 GTTAGTTAAGTTGGTTAACACTATAGCTAA
1 GTTAGTTAAGTTGGTTAACACTATAGATAA
22190364 G
1 G
22190365 CTTTATGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (30 bp):
GTTAGTTAAGTTGGTTAACACTATAGATAA
Found at i:22191623 original size:66 final size:66
Alignment explanation
Indices: 22191540--22191669 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
22191530 TCCCCAAATC
22191540 ATACACAAGATAACTTTTCTAATATCCCATCCTTAGGAAAGAGAGAGCAAATATTCTCTAAATTA
1 ATACACAAGATAACTTTTCTAATATCCCATCCTTAGGAAAGAGAGAGCAAATATTCTCTAAATTA
22191605 T
66 T
* * *
22191606 ATACACATGATAACTTTTCTAATATCTCATCCTTGGGAAAGAGAGAGCAAATATTCTCTAAATT
1 ATACACAAGATAACTTTTCTAATATCCCATCCTTAGGAAAGAGAGAGCAAATATTCTCTAAATT
22191670 TCTTGTGTGA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.32
Consensus pattern (66 bp):
ATACACAAGATAACTTTTCTAATATCCCATCCTTAGGAAAGAGAGAGCAAATATTCTCTAAATTA
T
Found at i:22197398 original size:13 final size:13
Alignment explanation
Indices: 22197333--22197398 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
22197323 AGTTTGGCAA
*
22197333 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
*
22197346 TTCTTTTGAAAAG
1 TGCTTTTGAAAAG
* **
22197359 TGCTGTAAAAAAG
1 TGCTTTTGAAAAG
* *
22197372 TGCTTTAGAGAAG
1 TGCTTTTGAAAAG
*
22197385 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
22197398 T
1 T
22197399 TTGGTTTAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:22199149 original size:37 final size:37
Alignment explanation
Indices: 22199099--22199205 Score: 205
Period size: 37 Copynumber: 2.9 Consensus size: 37
22199089 ACATAATGCT
22199099 CCACAAGCTATAACCATATTAAATCACACACATTGCA
1 CCACAAGCTATAACCATATTAAATCACACACATTGCA
*
22199136 CCACAAGCTATAACCATATTAAATCACACACATTGCT
1 CCACAAGCTATAACCATATTAAATCACACACATTGCA
22199173 CCACAAGCTATAACCATATTAAATCACACACAT
1 CCACAAGCTATAACCATATTAAATCACACACAT
22199206 ACATATATAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.22
Consensus pattern (37 bp):
CCACAAGCTATAACCATATTAAATCACACACATTGCA
Found at i:22212677 original size:21 final size:20
Alignment explanation
Indices: 22212628--22212684 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
22212618 ATTAAATGGA
22212628 AATTGCAAATGATATTATTTG
1 AATTG-AAATGATATTATTTG
22212649 AATT-AAATGA-ATTATTGTGG
1 AATTGAAATGATATTATT-T-G
*
22212669 TATTGAAATGTATATT
1 AATTGAAATG-ATATT
22212685 GGATTGAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 6 0.20
19 7 0.23
20 4 0.13
21 9 0.30
22 1 0.03
23 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.44
Consensus pattern (20 bp):
AATTGAAATGATATTATTTG
Found at i:22213778 original size:47 final size:47
Alignment explanation
Indices: 22213664--22213823 Score: 127
Period size: 47 Copynumber: 3.5 Consensus size: 47
22213654 ATTGACGAAA
* * * *
22213664 AAGACCATGGTTGGACTATGGCAACATGTGATATGTGATTTTCGTAT
1 AAGACCATAGCTGGACTATGGCATCATGTGATATGTGATATTCGTAT
* * * * * *
22213711 AAGACCATATCCGGAATATGGCATCGGTGTGATATGTGCTATT-GTGT
1 AAGACCATAGCTGGACTATGGCATC-ATGTGATATGTGATATTCGTAT
* * *
22213758 AAGACCATAGCTGGGCTATGGCATCA----ATATGT-AAATAT-GTGT
1 AAGACCATAGCTGGACTATGGCATCATGTGATATGTGATAT-TCGTAT
*
22213800 AAGACCATAGTTGGACTATGGCAT
1 AAGACCATAGCTGGACTATGGCAT
22213824 AGAGAAAATG
Statistics
Matches: 92, Mismatches: 19, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
41 2 0.02
42 33 0.36
47 43 0.47
48 14 0.15
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (47 bp):
AAGACCATAGCTGGACTATGGCATCATGTGATATGTGATATTCGTAT
Found at i:22224860 original size:51 final size:51
Alignment explanation
Indices: 22224726--22224921 Score: 236
Period size: 51 Copynumber: 3.9 Consensus size: 51
22224716 AGTGAAAGTG
*
22224726 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * *
22224775 ATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * * *
22224826 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
* * * *
22224878 ATGGCCACATGTTTAGTACTATGTGCAGGCTACTATGTGAACCG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG
22224922 AACATCATTG
Statistics
Matches: 122, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.33
51 78 0.64
52 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTA
Found at i:22224973 original size:45 final size:45
Alignment explanation
Indices: 22224923--22225010 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
22224913 TGTGAACCGA
* *
22224923 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCT-AATTCCACCAG
1 ACATCATGGATTAATAAGGTGGTTGCTATGTGCTGAA-TCCACCAG
22224968 ACATCATGGATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
1 ACATCATGGATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
22225011 GAGTATCTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 38 0.95
46 2 0.05
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (45 bp):
ACATCATGGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
Found at i:22228251 original size:30 final size:30
Alignment explanation
Indices: 22228185--22228241 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
22228175 GTGTCTCAGT
**
22228185 CGTGTGTGACACACGACCATGTGACACAAC
1 CGTGTGTGACACACGACCATGCAACACAAC
*
22228215 CGTGTGTGACACACGGCCATGCAACAC
1 CGTGTGTGACACACGACCATGCAACAC
22228242 GATTGTGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.32, G:0.25, T:0.16
Consensus pattern (30 bp):
CGTGTGTGACACACGACCATGCAACACAAC
Found at i:22229588 original size:20 final size:20
Alignment explanation
Indices: 22229561--22229622 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
22229551 GTAATGCTAT
* *
22229561 ACAGAGGCATCGTAGTGCAA
1 ACAGAGGCACCGAAGTGCAA
* *
22229581 ATAGAGGCACCAAAGTGCAA
1 ACAGAGGCACCGAAGTGCAA
22229601 ACAGAGGCACCGAAGTGCAA
1 ACAGAGGCACCGAAGTGCAA
22229621 AC
1 AC
22229623 TCATAAAAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.40, C:0.23, G:0.27, T:0.10
Consensus pattern (20 bp):
ACAGAGGCACCGAAGTGCAA
Found at i:22230450 original size:18 final size:18
Alignment explanation
Indices: 22230416--22230457 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
22230406 TACTTCATAC
**
22230416 AACATAGGTTCGTATAAA
1 AACATAGGTTCACATAAA
*
22230434 AACATAGGTTCACATAAT
1 AACATAGGTTCACATAAA
22230452 AACATA
1 AACATA
22230458 TGTTTCCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (18 bp):
AACATAGGTTCACATAAA
Found at i:22245647 original size:23 final size:22
Alignment explanation
Indices: 22245621--22245663 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
22245611 AAATGGTTTA
22245621 TTTA-CCATTTAAGCCCATTTACC
1 TTTATCCA-TTAAG-CCATTTACC
*
22245644 TTTATTCATTAAGCCATTTA
1 TTTATCCATTAAGCCATTTA
22245664 ATCACTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 9 0.50
24 2 0.11
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (22 bp):
TTTATCCATTAAGCCATTTACC
Found at i:22260607 original size:27 final size:26
Alignment explanation
Indices: 22260440--22260612 Score: 145
Period size: 27 Copynumber: 6.4 Consensus size: 26
22260430 AACCCCATAA
* **
22260440 CAGTCATTTCATCTCCTA-GGGGTATGA
1 CAGTCATTTTA-C-CCTATGGGGTATTT
22260467 CAGTCATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTAT-GGGGTATTT
*
22260494 CAATCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTAT-GGGGTATTT
* **
22260521 C-GATCATTTTACCTTGCGGGGGTATTT
1 CAG-TCATTTTACCCT-ATGGGGTATTT
* *
22260548 CAG-CTATTTTGCCCTACGGAGGTATTT
1 CAGTC-ATTTTACCCTATGG-GGTATTT
22260575 CAGTCATTTTACCCTATGGGGCTATTT
1 CAGTCATTTTACCCTATGGGG-TATTT
**
22260602 TGGTCATTTTA
1 CAGTCATTTTA
22260613 TTGACCTCAC
Statistics
Matches: 120, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
25 4 0.03
26 6 0.05
27 108 0.90
28 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.40
Consensus pattern (26 bp):
CAGTCATTTTACCCTATGGGGTATTT
Found at i:22270323 original size:25 final size:25
Alignment explanation
Indices: 22270295--22270354 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
22270285 ATATTGTCAA
22270295 CATGAGTCATAGTATGCATGAATTT
1 CATGAGTCATAGTATGCATGAATTT
22270320 CATGAGTCATAGTATGCATGAATTT
1 CATGAGTCATAGTATGCATGAATTT
*
22270345 CA-AAGTCATA
1 CATGAGTCATA
22270355 TAGAACATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 7 0.21
25 27 0.79
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (25 bp):
CATGAGTCATAGTATGCATGAATTT
Found at i:22273240 original size:50 final size:50
Alignment explanation
Indices: 22273129--22273374 Score: 294
Period size: 50 Copynumber: 4.8 Consensus size: 50
22273119 ATTTGGGTAA
* *
22273129 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
*
22273185 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
22273235 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
22273285 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGAATGGGCACCTATATT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
22273335 AGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
22273375 TAGTACAAGA
Statistics
Matches: 169, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
50 125 0.74
53 3 0.02
55 1 0.01
56 40 0.24
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:22276418 original size:16 final size:16
Alignment explanation
Indices: 22276394--22276424 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22276384 TTCTAAATAT
*
22276394 TTATTAAAAATTAAGA
1 TTATAAAAAATTAAGA
22276410 TTATAAAAAATTAAG
1 TTATAAAAAATTAAG
22276425 GTTCTACTAA
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:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TTATAAAAAATTAAGA
Found at i:22279509 original size:9 final size:9
Alignment explanation
Indices: 22279495--22279525 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
22279485 TTTGGTTAAA
22279495 AATTAACCG
1 AATTAACCG
22279504 AATTAACCG
1 AATTAACCG
*
22279513 AATTACCCG
1 AATTAACCG
22279522 AATT
1 AATT
22279526 GAATAACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:22279605 original size:27 final size:27
Alignment explanation
Indices: 22279573--22279626 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
22279563 GAATCACTAC
22279573 ATAATTAAACATAATTCTTGAAATTAA
1 ATAATTAAACATAATTCTTGAAATTAA
22279600 ATAATTAAACATAATTCTTGAAATTAA
1 ATAATTAAACATAATTCTTGAAATTAA
22279627 CACATAGTTG
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:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (27 bp):
ATAATTAAACATAATTCTTGAAATTAA
Found at i:22279834 original size:39 final size:39
Alignment explanation
Indices: 22279755--22279865 Score: 188
Period size: 39 Copynumber: 2.9 Consensus size: 39
22279745 TAAGAGTTAA
* *
22279755 ACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGGTAG
1 ACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTTGGTAG
22279793 ACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTTGGTAG
1 ACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTTGGTAG
*
22279832 ACTTTAGTTTTAGTTTTATTGGGTTGGATAATTT
1 ACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTT
22279866 TATTTATTAA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
38 24 0.35
39 45 0.65
ACGTcount: A:0.19, C:0.03, G:0.25, T:0.53
Consensus pattern (39 bp):
ACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTTGGTAG
Found at i:22280465 original size:42 final size:41
Alignment explanation
Indices: 22280380--22280484 Score: 149
Period size: 42 Copynumber: 2.6 Consensus size: 41
22280370 ACAATATTTT
* ** *
22280380 TAGT-GGCATGCTGAACATGCAATCGGATTTATAATCAATA
1 TAGTCGGCATGCTTAACATGCAATCAAATTTATAATCAACA
*
22280420 TAGTCGGCATGCTTAACATGCGAATCAAATTTATAGTCAACA
1 TAGTCGGCATGCTTAACATGC-AATCAAATTTATAATCAACA
22280462 TAGTCGGCATGCTTAACATGCAA
1 TAGTCGGCATGCTTAACATGCAA
22280485 GTTTTATTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
40 4 0.07
41 17 0.29
42 37 0.64
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (41 bp):
TAGTCGGCATGCTTAACATGCAATCAAATTTATAATCAACA
Found at i:22282407 original size:33 final size:32
Alignment explanation
Indices: 22282370--22282437 Score: 75
Period size: 33 Copynumber: 2.1 Consensus size: 32
22282360 ATTATTTCTA
22282370 AATTT-TAGAAACTATAAAAAAATATTTTAATAT
1 AATTTATAGAAA--ATAAAAAAATATTTTAATAT
* * *
22282403 AATTTAATATAAAATATAAAATTATTTTAATAT
1 AATTT-ATAGAAAATAAAAAAATATTTTAATAT
22282436 AA
1 AA
22282438 AATATTCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
33 25 0.83
35 5 0.17
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (32 bp):
AATTTATAGAAAATAAAAAAATATTTTAATAT
Found at i:22282450 original size:16 final size:16
Alignment explanation
Indices: 22282414--22282486 Score: 53
Period size: 16 Copynumber: 4.5 Consensus size: 16
22282404 ATTTAATATA
22282414 AAATATAAAATTATTT
1 AAATATAAAATTATTT
*
22282430 TAATATAAAA-TATTCT
1 AAATATAAAATTATT-T
*
22282446 AAATATTATAATATAATTT
1 AAATA-TA-AA-ATTATTT
* *
22282465 -AATA-AAAAATACTT
1 AAATATAAAATTATTT
22282479 AAATATAA
1 AAATATAA
22282487 TTTAATATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
14 4 0.09
15 10 0.23
16 17 0.39
17 2 0.05
18 6 0.14
19 2 0.05
20 3 0.07
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATAAAATTATTT
Found at i:22282462 original size:57 final size:56
Alignment explanation
Indices: 22282389--22282532 Score: 163
Period size: 57 Copynumber: 2.6 Consensus size: 56
22282379 AACTATAAAA
* * *
22282389 AAATATTTTAATATAATTTAATATAAAATATAAAAT-TATTTTAATATAAAATATTCT
1 AAATATTATAATATAATTTAATAAAAAATATAAAATATAATTTAATATAAAAT-TT-T
* *
22282446 AAATATTATAATATAATTTAATAAAAAATACTTAAATATAATTTAATATAAACTTTT
1 AAATATTATAATATAATTTAATAAAAAATA-TAAAATATAATTTAATATAAAATTTT
*
22282503 --AT-TTGA-AATATAATTTAATAGAAAATATAA
1 AAATATT-ATAATATAATTTAATAAAAAATATAA
22282533 TTTAAATATT
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
53 2 0.03
54 22 0.29
55 3 0.04
57 29 0.38
58 7 0.09
59 14 0.18
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (56 bp):
AAATATTATAATATAATTTAATAAAAAATATAAAATATAATTTAATATAAAATTTT
Found at i:22290478 original size:20 final size:20
Alignment explanation
Indices: 22290453--22290505 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
22290443 AATAATGAAC
22290453 TGATCATTTTATTAAAAATT
1 TGATCATTTTATTAAAAATT
22290473 TGATCATTTTATTAAAAATT
1 TGATCATTTTATTAAAAATT
*
22290493 TCATTCATTTTAT
1 TGA-TCATTTTAT
22290506 GGTTAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.53
Consensus pattern (20 bp):
TGATCATTTTATTAAAAATT
Found at i:22290523 original size:22 final size:21
Alignment explanation
Indices: 22290456--22290523 Score: 86
Period size: 20 Copynumber: 3.2 Consensus size: 21
22290446 AATGAACTGA
*
22290456 TCATTTTATTAAAAATTTGA-
1 TCATTTTATTAAAAATTTCAT
22290476 TCATTTTATTAAAAATTTCAT
1 TCATTTTATTAAAAATTTCAT
*
22290497 TCATTTTATGGTTAAAATTT-AT
1 TCATTTTAT--TAAAAATTTCAT
22290519 TCATT
1 TCATT
22290524 GTACGTCAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.44
21 9 0.21
22 7 0.16
23 8 0.19
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.53
Consensus pattern (21 bp):
TCATTTTATTAAAAATTTCAT
Found at i:22292142 original size:42 final size:42
Alignment explanation
Indices: 22292090--22292170 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
22292080 CCTACTTTCT
22292090 TGACTCATATAAAAAACATAACGAAACATCACATCTAATTTA
1 TGACTCATATAAAAAACATAACGAAACATCACATCTAATTTA
* * * * *
22292132 TGACTTATATAACAAACATAATGAAATATCACGTCTAAT
1 TGACTCATATAAAAAACATAACGAAACATCACATCTAAT
22292171 CACTTTCATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.28
Consensus pattern (42 bp):
TGACTCATATAAAAAACATAACGAAACATCACATCTAATTTA
Found at i:22296396 original size:14 final size:14
Alignment explanation
Indices: 22296379--22296414 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
22296369 TCCCACAGCA
22296379 TTTTCTTTTTACCT
1 TTTTCTTTTTACCT
*
22296393 TTTTCTTTTTACGT
1 TTTTCTTTTTACCT
22296407 TTTTCTTT
1 TTTTCTTT
22296415 CTTCTGCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.75
Consensus pattern (14 bp):
TTTTCTTTTTACCT
Found at i:22303345 original size:35 final size:35
Alignment explanation
Indices: 22303279--22303345 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
22303269 ACCTCAACAA
* **
22303279 TTGATTTTGTCTTTCTCTTCTTGATTACAACTTCC
1 TTGATATTGTCTTTCTCTTCTCCATTACAACTTCC
*
22303314 TTGATATTGT-TTTCCTCTTCTCCATTGCAACT
1 TTGATATTGTCTTT-CTCTTCTCCATTACAACT
22303346 CCCATCCTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 3 0.11
35 24 0.89
ACGTcount: A:0.15, C:0.24, G:0.09, T:0.52
Consensus pattern (35 bp):
TTGATATTGTCTTTCTCTTCTCCATTACAACTTCC
Found at i:22309560 original size:20 final size:20
Alignment explanation
Indices: 22309535--22309598 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
22309525 GGTATTAAGG
*
22309535 AAATCTTTAGAAATATTGCT
1 AAATCTTTAGAAATATTGGT
** *
22309555 AAATCTTTAGAAGCAATGGT
1 AAATCTTTAGAAATATTGGT
22309575 AAAT-TCTTAGAAATATTGGT
1 AAATCT-TTAGAAATATTGGT
22309595 AAAT
1 AAAT
22309599 TGTTAGATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 1 0.03
20 35 0.97
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (20 bp):
AAATCTTTAGAAATATTGGT
Found at i:22309599 original size:20 final size:20
Alignment explanation
Indices: 22309541--22309605 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
22309531 AAGGAAATCT
*
22309541 TTAGAAATATTGCTAAA-TC
1 TTAGAAATATTGGTAAATTC
** *
22309560 TTTAGAAGCAATGGTAAATTC
1 -TTAGAAATATTGGTAAATTC
*
22309581 TTAGAAATATTGGTAAATTG
1 TTAGAAATATTGGTAAATTC
22309601 TTAGA
1 TTAGA
22309606 TTTTTTTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
20 34 0.94
21 2 0.06
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (20 bp):
TTAGAAATATTGGTAAATTC
Found at i:22309646 original size:20 final size:20
Alignment explanation
Indices: 22309571--22309658 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
22309561 TTAGAAGCAA
*
22309571 TGGTAAATTCTTAGAAATAT
1 TGGTAAATTCTTAGAAATTT
* **
22309591 TGGTAAATTGTTAGATTTTT
1 TGGTAAATTCTTAGAAATTT
** * *
22309611 TTTTATATAACATTAGAAATTT
1 TGGTAAAT-TC-TTAGAAATTT
*
22309633 TGGTAAATTCTTAGATATTT
1 TGGTAAATTCTTAGAAATTT
22309653 TGGTAA
1 TGGTAA
22309659 GGAATAATAT
Statistics
Matches: 50, Mismatches: 16, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
20 36 0.72
21 1 0.02
22 13 0.26
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.48
Consensus pattern (20 bp):
TGGTAAATTCTTAGAAATTT
Found at i:22309947 original size:20 final size:20
Alignment explanation
Indices: 22309922--22310019 Score: 83
Period size: 20 Copynumber: 4.9 Consensus size: 20
22309912 AAGAAAGAAG
22309922 TTTTGGTAAATCCTTAAATA
1 TTTTGGTAAATCCTTAAATA
*
22309942 TTTTGGTATAA-CTTTAAA-A
1 TTTTGGTA-AATCCTTAAATA
* * *
22309961 TTTTTGTTAAATTCTTAGATA
1 -TTTTGGTAAATCCTTAAATA
* *
22309982 TTTTGGTAAAGCCTTAAAAA
1 TTTTGGTAAATCCTTAAATA
** *
22310002 TTTTAATAAATTCTTAAA
1 TTTTGGTAAATCCTTAAA
22310020 AATATCACTA
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
19 3 0.05
20 54 0.90
21 3 0.05
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (20 bp):
TTTTGGTAAATCCTTAAATA
Found at i:22309983 original size:40 final size:40
Alignment explanation
Indices: 22309922--22310019 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 40
22309912 AAGAAAGAAG
* * * *
22309922 TTTTGGTAAATCCTTAAATATTTTGGTATAA-CTTTAAAAT
1 TTTTGATAAATTCTTAAATATTTTGGTA-AAGCCTTAAAAA
* *
22309962 TTTTGTTAAATTCTTAGATATTTTGGTAAAGCCTTAAAAA
1 TTTTGATAAATTCTTAAATATTTTGGTAAAGCCTTAAAAA
*
22310002 TTTTAATAAATTCTTAAA
1 TTTTGATAAATTCTTAAA
22310020 AATATCACTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 2 0.04
40 47 0.96
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (40 bp):
TTTTGATAAATTCTTAAATATTTTGGTAAAGCCTTAAAAA
Found at i:22310031 original size:20 final size:20
Alignment explanation
Indices: 22309994--22310033 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
22309984 TTGGTAAAGC
* *
22309994 CTTAAAAATTTTAATAAATT
1 CTTAAAAATATCAATAAATT
*
22310014 CTTAAAAATATCACTAAATT
1 CTTAAAAATATCAATAAATT
22310034 ACCCTTTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (20 bp):
CTTAAAAATATCAATAAATT
Found at i:22310463 original size:19 final size:19
Alignment explanation
Indices: 22310421--22310588 Score: 113
Period size: 20 Copynumber: 8.6 Consensus size: 19
22310411 GACCAATACT
*
22310421 AAAATTTCTAACGAATATC
1 AAAATTTCTAACAAATATC
* * *
22310440 GAAATTTCTAACACATACC
1 AAAATTTCTAACAAATATC
* * *
22310459 AAAATATCTAACCATATATG
1 AAAATTTCTAA-CAAATATC
*
22310479 AAAATCTTCTAACAGATATC
1 AAAAT-TTCTAACAAATATC
* *
22310499 AAAATTTTGTAACAAATACC
1 AAAA-TTTCTAACAAATATC
* * *
22310519 ACATTTTTTAATCAAATATC
1 AAAATTTCTAA-CAAATATC
***
22310539 AAAATTTCTAATGGATATC
1 AAAATTTCTAACAAATATC
* *
22310558 AAAATTTGTAACCAAGTA-C
1 AAAATTTCTAA-CAAATATC
22310577 AAAAATTTCTAA
1 -AAAATTTCTAA
22310589 TGCGATATCC
Statistics
Matches: 112, Mismatches: 31, Indels: 11
0.73 0.20 0.07
Matches are distributed among these distances:
19 46 0.41
20 60 0.54
21 6 0.05
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.32
Consensus pattern (19 bp):
AAAATTTCTAACAAATATC
Found at i:22310548 original size:59 final size:57
Alignment explanation
Indices: 22310421--22310588 Score: 156
Period size: 59 Copynumber: 2.8 Consensus size: 57
22310411 GACCAATACT
* * * * *
22310421 AAAATTTCTAACGAATATCGAAATTTCTAACACATACCAAAATATCTAACCATATATG
1 AAAATTTCTAACG-ATATCAAAATTTGTAACAAATACCAAAATATCTAACCAAATATC
* * * * *
22310479 AAAATCTTCTAACAGATATCAAAATTTTGTAACAAATACCACATTTTTTAATCAAATATC
1 AAAAT-TTCTAAC-GATATCAAAA-TTTGTAACAAATACCAAAATATCTAACCAAATATC
* * * *
22310539 AAAATTTCTAATGGATATCAAAATTTGTAACCAAGTACAAAAATTTCTAA
1 AAAATTTCTAA-CGATATCAAAATTTGTAA-CAAATACCAAAATATCTAA
22310589 TGCGATATCC
Statistics
Matches: 89, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
58 12 0.13
59 45 0.51
60 32 0.36
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.32
Consensus pattern (57 bp):
AAAATTTCTAACGATATCAAAATTTGTAACAAATACCAAAATATCTAACCAAATATC
Found at i:22313374 original size:145 final size:144
Alignment explanation
Indices: 22313089--22313413 Score: 440
Period size: 145 Copynumber: 2.2 Consensus size: 144
22313079 CGGTGGTCGG
* * * *
22313089 AAATTTTT-TATTACAAAATCTAA-TTTTTCTTTTAAAAAAATCACTATTTTTTTAAAAATCAAA
1 AAATTTTTATTTTA-AAAATCTAACTTTCTCTTTTAAAAAAATAACTATTTTTTTAAAAATAAAA
*** ** *
22313152 ACTTTATTTTGAAATAATTGAAAAAGATCAAAATTTTATTTTAAAATTTTTAAAATTTTCCTTTA
65 AAAATATTTCAAAATAATTGAAAAAGATCAAAACTTTATTTTAAAATTTTTAAAATTTTCCTTTA
*
22313217 AAATGACTAAAAAAC
130 AAATGACTAAAAAAA
22313232 AAATTTTTATTTTAAAAATCTATACTTTCTCTTTTAAAAAAATAACTATTTTTCTTAAAAATAAA
1 AAATTTTTATTTTAAAAATCTA-ACTTTCTCTTTTAAAAAAATAACTATTTTT-TTAAAAATAAA
* * *
22313297 AAAAATATTTCAAAATAGTTGAAAAAGATCAAAACTTTGTTTTAAAA-TTTTAAACTTTTCCTTT
64 AAAAATATTTCAAAATAATTGAAAAAGATCAAAACTTTATTTTAAAATTTTTAAAATTTTCCTTT
*
22313361 AATATGACTAAAAAAA
129 AAAATGACTAAAAAAA
22313377 ATAGATTTTTATTTTAAAAATCTAAACTTTCTCTTTT
1 A-A-ATTTTTATTTTAAAAATCT-AACTTTCTCTTTT
22313414 TTTAAAAAAA
Statistics
Matches: 160, Mismatches: 15, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
143 16 0.10
144 5 0.03
145 57 0.36
146 50 0.31
147 31 0.19
148 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (144 bp):
AAATTTTTATTTTAAAAATCTAACTTTCTCTTTTAAAAAAATAACTATTTTTTTAAAAATAAAAA
AAATATTTCAAAATAATTGAAAAAGATCAAAACTTTATTTTAAAATTTTTAAAATTTTCCTTTAA
AATGACTAAAAAAA
Found at i:22313375 original size:146 final size:143
Alignment explanation
Indices: 22313089--22313413 Score: 431
Period size: 146 Copynumber: 2.2 Consensus size: 143
22313079 CGGTGGTCGG
* * * *
22313089 AAATTTTT-TATTACAAAATCTAA-TTTTTCTTTTAAAAAAATCACTATTTTTTTAAAAATCAAA
1 AAATTTTTATTTTA-AAAATCTAACTTTCTCTTTTAAAAAAATAACTATTTTTTTAAAAATAAAA
*** ** *
22313152 ACTTTATTTTGAAATAATTGAAAAAGATCAAAATTTTATTTTAAAATTTTTAAAATTTTCCTTTA
65 AAAATATTTCAAAATAATTGAAAAAGATCAAAACTTTATTTTAAAATTTTTAAAATTTTCCTTTA
22313217 AAATGACTAAAAAA
130 AAATGACTAAAAAA
22313231 CAAATTTTTATTTTAAAAATCTATACTTTCTCTTTTAAAAAAATAACTATTTTTCTTAAAAATAA
1 -AAATTTTTATTTTAAAAATCTA-ACTTTCTCTTTTAAAAAAATAACTATTTTT-TTAAAAATAA
* * *
22313296 AAAAAATATTTCAAAATAGTTGAAAAAGATCAAAACTTTGTTTTAAAA-TTTTAAACTTTTCCTT
63 AAAAAATATTTCAAAATAATTGAAAAAGATCAAAACTTTATTTTAAAATTTTTAAAATTTTCCTT
*
22313360 TAATATGACTAAAAAAA
128 TAAAATGACT-AAAAAA
22313377 ATAGATTTTTATTTTAAAAATCTAAACTTTCTCTTTT
1 A-A-ATTTTTATTTTAAAAATCT-AACTTTCTCTTTT
22313414 TTTAAAAAAA
Statistics
Matches: 160, Mismatches: 14, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
143 16 0.10
144 5 0.03
145 51 0.32
146 56 0.35
147 31 0.19
148 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (143 bp):
AAATTTTTATTTTAAAAATCTAACTTTCTCTTTTAAAAAAATAACTATTTTTTTAAAAATAAAAA
AAATATTTCAAAATAATTGAAAAAGATCAAAACTTTATTTTAAAATTTTTAAAATTTTCCTTTAA
AATGACTAAAAAA
Found at i:22322137 original size:71 final size:71
Alignment explanation
Indices: 22322043--22322184 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 71
22322033 GCCATGTAAA
*
22322043 CTTTTGAATCATTTTTTGCCTTGAAACAAATGCTTATATTTAGCTTGTGAATGAAATAAGTATGT
1 CTTTTGAATCATTTTTTGCCTTGAAACAAATGCTTATATGTAGCTTGTGAATGAAATAAGTATGT
22322108 TTGATG
66 TTGATG
* * *
22322114 CTTTTGAATTATGTTTTT-TCTTGAAACAAATGCTTGTATGTAGCTTGTGAATGAAATAAGTATG
1 CTTTTGAATCAT-TTTTTGCCTTGAAACAAATGCTTATATGTAGCTTGTGAATGAAATAAGTATG
22322178 TTTGATG
65 TTTGATG
22322185 AGCTTGAATC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
71 61 0.92
72 5 0.08
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.44
Consensus pattern (71 bp):
CTTTTGAATCATTTTTTGCCTTGAAACAAATGCTTATATGTAGCTTGTGAATGAAATAAGTATGT
TTGATG
Found at i:22330016 original size:49 final size:49
Alignment explanation
Indices: 22329952--22330175 Score: 182
Period size: 50 Copynumber: 4.4 Consensus size: 49
22329942 CAAAGCTATG
* * * *
22329952 TCCCAGACATAGTCTTACATTGGATGTT-TCCTGTAC-TGCCAATGCCATA
1 TCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGTGCCAATGCCATA
* * *
22330001 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACATGGGAGTTCTCATATC-GTGCCAATGCCATA
** ** * * *
22330051 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGAGTTCTCATATC-GTGCCAATGCCATA
* * *
22330101 TCCCAGACATGGTCTTACATGGGACTTCTCATAATTTCAATAATGCCAATGCCATG
1 TCCCAGACATGGTCTTACATGGGAGTTCTCAT-A--TC----GTGCCAATGCCATA
22330157 TCCCAGACATGGTCTTACA
1 TCCCAGACATGGTCTTACA
22330176 CTGGCTCACA
Statistics
Matches: 144, Mismatches: 22, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
48 4 0.03
49 25 0.17
50 82 0.57
53 2 0.01
56 31 0.22
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (49 bp):
TCCCAGACATGGTCTTACATGGGAGTTCTCATATCGTGCCAATGCCATA
Found at i:22330056 original size:50 final size:50
Alignment explanation
Indices: 22329988--22330221 Score: 240
Period size: 50 Copynumber: 4.6 Consensus size: 50
22329978 TTTCCTGTAC
* * *
22329988 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGG
* ** * *
22330038 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGG
* **
22330088 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATAATTTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCAT-A--TC---GG
* *
22330144 TGCCAATGCCATGTCCCAGACATGGTCTTACACT-GG-C-TCACATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-TGGGACTTCTCATATCGG
* * *
22330192 TGTCGATGCCATGTCCCAAACATGGTCTTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTA
22330222 TACGAGATCG
Statistics
Matches: 155, Mismatches: 22, Indels: 16
0.80 0.11 0.08
Matches are distributed among these distances:
48 28 0.18
50 82 0.53
51 2 0.01
53 3 0.02
54 5 0.03
55 1 0.01
56 33 0.21
57 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGG
Found at i:22337134 original size:16 final size:16
Alignment explanation
Indices: 22337101--22337168 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 16
22337091 TTTAAAAACC
22337101 ATATTTTAATATAAAT
1 ATATTTTAATATAAAT
*
22337117 ATATATTTAAT-TAGAT
1 ATAT-TTTAATATAAAT
* * *
22337133 AT-TATAAATATAATT
1 ATATTTTAATATAAAT
*
22337148 ATA-TTT-ATAAAAAT
1 ATATTTTAATATAAAT
22337162 ATATTTT
1 ATATTTT
22337169 TAGTTAAATA
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
14 13 0.33
15 10 0.26
16 10 0.26
17 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (16 bp):
ATATTTTAATATAAAT
Found at i:22337148 original size:12 final size:13
Alignment explanation
Indices: 22337110--22337150 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
22337100 CATATTTTAA
22337110 TATAAATATATAT
1 TATAAATATATAT
* *
22337123 T-TAATTAGATAT
1 TATAAATATATAT
22337135 TATAAATATA-AT
1 TATAAATATATAT
22337147 TATA
1 TATA
22337151 TTTATAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (13 bp):
TATAAATATATAT
Found at i:22337331 original size:31 final size:31
Alignment explanation
Indices: 22337296--22337362 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
22337286 ATCTTATTTT
* *
22337296 TAAAATAACATACAAAT-TTAAATCTATAAAA
1 TAAAATAAAATA-AAATATTAAATCTAAAAAA
* *
22337327 TAAAATAAAATAAAATATTAATTTTAAAAAA
1 TAAAATAAAATAAAATATTAAATCTAAAAAA
22337358 TAAAA
1 TAAAA
22337363 CAAGTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (31 bp):
TAAAATAAAATAAAATATTAAATCTAAAAAA
Found at i:22337810 original size:18 final size:18
Alignment explanation
Indices: 22337787--22337822 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
22337777 AACCATCAAT
22337787 TAAATATATTTT-AATTAA
1 TAAATA-ATTTTGAATTAA
22337805 TAAATAATTTTGAATTAA
1 TAAATAATTTTGAATTAA
22337823 ATTCTAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TAAATAATTTTGAATTAA
Found at i:22339414 original size:25 final size:26
Alignment explanation
Indices: 22339376--22339427 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
22339366 CTAATATTAG
22339376 AAAATGATAAGGCAA-AACAAGAATA
1 AAAATGATAAGGCAATAACAAGAATA
*
22339401 AAAATG-TAATGGCAATTACAAGAATA
1 AAAATGATAA-GGCAATAACAAGAATA
22339427 A
1 A
22339428 TTACGCGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 3 0.12
25 11 0.46
26 10 0.42
ACGTcount: A:0.60, C:0.08, G:0.15, T:0.17
Consensus pattern (26 bp):
AAAATGATAAGGCAATAACAAGAATA
Found at i:22364674 original size:20 final size:20
Alignment explanation
Indices: 22364646--22364721 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
22364636 AAGACTATGA
*
22364646 ACCACTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
*
22364666 ACCATTCCATTTACTTAGTT
1 ACCATTCCATTTACTTACTT
* *
22364686 -CTATTTCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
*
22364705 TCCATTCCATTTACTTA
1 ACCATTCCATTTACTTA
22364722 GCATAAACTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.33
20 32 0.67
ACGTcount: A:0.24, C:0.28, G:0.01, T:0.47
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:22373374 original size:40 final size:41
Alignment explanation
Indices: 22373330--22373429 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 41
22373320 AGCAATTCCG
22373330 ACTTGTTTGAAAATAATTTTGA-TGTG-TTAAAATGATTTTA
1 ACTTGTTTGAAAATAATTTTGACT-TGATTAAAATGATTTTA
* * *
22373370 ACTTGGTTG-AAATCATTTTGACTTGATTAAAATTATTTTA
1 ACTTGTTTGAAAATAATTTTGACTTGATTAAAATGATTTTA
* *
22373410 ACTTGATTTTAAAATTATTT
1 ACTTG-TTTGAAAATAATTT
22373430 CAAAATTTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
39 13 0.26
40 27 0.54
41 2 0.04
42 8 0.16
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (41 bp):
ACTTGTTTGAAAATAATTTTGACTTGATTAAAATGATTTTA
Found at i:22373387 original size:20 final size:20
Alignment explanation
Indices: 22373356--22373417 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
22373346 TTTTGATGTG
* *
22373356 TTAAAATGATTTTAACTTGG
1 TTAAAATCATTTTAACTTGA
* *
22373376 TTGAAATCATTTTGACTTGA
1 TTAAAATCATTTTAACTTGA
*
22373396 TTAAAATTATTTTAACTTGA
1 TTAAAATCATTTTAACTTGA
22373416 TT
1 TT
22373418 TTAAAATTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.48
Consensus pattern (20 bp):
TTAAAATCATTTTAACTTGA
Found at i:22377886 original size:18 final size:18
Alignment explanation
Indices: 22377863--22377898 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
22377853 ACTTTGCCGG
22377863 TAGTCACTCTGCAAAATT
1 TAGTCACTCTGCAAAATT
22377881 TAGTCACTCTGCAAAATT
1 TAGTCACTCTGCAAAATT
22377899 GAAACTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (18 bp):
TAGTCACTCTGCAAAATT
Found at i:22380085 original size:22 final size:20
Alignment explanation
Indices: 22380037--22380076 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
22380027 ATTGATGTCC
*
22380037 TTTCATTGATTCCTCCTAAA
1 TTTCATTGATTCATCCTAAA
*
22380057 TTTCATTGATTTATCCTAAA
1 TTTCATTGATTCATCCTAAA
22380077 GATTTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTCATTGATTCATCCTAAA
Found at i:22387267 original size:24 final size:22
Alignment explanation
Indices: 22387223--22387271 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
22387213 TTTTTCCAAG
* **
22387223 AGGGAAATTGGAAAGGGAATGGA
1 AGGGAAAATGGAAAGCAAAT-GA
22387246 AGGGAAAAATGGAAAGCAAATGA
1 AGGG-AAAATGGAAAGCAAATGA
22387269 AGG
1 AGG
22387272 TTTGGAAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.49, C:0.02, G:0.39, T:0.10
Consensus pattern (22 bp):
AGGGAAAATGGAAAGCAAATGA
Found at i:22387650 original size:6 final size:6
Alignment explanation
Indices: 22387639--22387691 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
22387629 AATAAATTGG
22387639 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
22387687 ATTAA
1 ATTAA
22387692 TTATATTATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATTAAA
Found at i:22389786 original size:15 final size:17
Alignment explanation
Indices: 22389756--22389790 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
22389746 ATGTAATAGA
22389756 TATATTTATAATAAAAT
1 TATATTTATAATAAAAT
22389773 TATATTTA-AA-AAAAT
1 TATATTTATAATAAAAT
22389788 TAT
1 TAT
22389791 TTTGGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 2 0.11
17 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATATTTATAATAAAAT
Found at i:22392113 original size:19 final size:18
Alignment explanation
Indices: 22392073--22392144 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 18
22392063 CAAAAGATAT
* **
22392073 CATACATGCATGGGTTTT
1 CATACATACATGGGTTCA
* *
22392091 CATACTTTCATAGGGTTCA
1 CATACATACAT-GGGTTCA
*
22392110 CATAAATACATGGGTTCA
1 CATACATACATGGGTTCA
*
22392128 CATACATATATGGGTTC
1 CATACATACATGGGTTC
22392145 GCACAATTCA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 31 0.70
19 13 0.30
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (18 bp):
CATACATACATGGGTTCA
Found at i:22392126 original size:18 final size:18
Alignment explanation
Indices: 22392103--22392165 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
22392093 TACTTTCATA
22392103 GGGTTCACATAAATACAT
1 GGGTTCACATAAATACAT
* *
22392121 GGGTTCACATACATATAT
1 GGGTTCACATAAATACAT
* * *
22392139 GGGTTCGCACAATTCACAT
1 GGGTTCACATAAAT-ACAT
22392158 GGGTTCAC
1 GGGTTCAC
22392166 TAAGTAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
18 26 0.72
19 10 0.28
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (18 bp):
GGGTTCACATAAATACAT
Found at i:22393162 original size:31 final size:31
Alignment explanation
Indices: 22393124--22393188 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
22393114 CACATAAAGA
**
22393124 CTTATCACAAAGAGCTTGCATAGAGAGCTTG
1 CTTATCACAAAGAGCTCACATAGAGAGCTTG
* *
22393155 CTTATCACAGAGAGCTCACATAGGGAGCTTG
1 CTTATCACAAAGAGCTCACATAGAGAGCTTG
22393186 CTT
1 CTT
22393189 GAAAACACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (31 bp):
CTTATCACAAAGAGCTCACATAGAGAGCTTG
Found at i:22395108 original size:10 final size:12
Alignment explanation
Indices: 22395089--22395122 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
22395079 AAATTGTAGT
22395089 TTCGAAAAAAAA
1 TTCGAAAAAAAA
22395101 -TC-AAAAAAAA
1 TTCGAAAAAAAA
22395111 TTCGAAAAAAAA
1 TTCGAAAAAAAA
22395123 AATATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.40
11 4 0.20
12 8 0.40
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.15
Consensus pattern (12 bp):
TTCGAAAAAAAA
Found at i:22395162 original size:23 final size:24
Alignment explanation
Indices: 22395118--22395162 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
22395108 AAATTCGAAA
*
22395118 AAAAAAATATATATTACGAAAATT
1 AAAAAAATATATATTACAAAAATT
*
22395142 AAAAAAAT-TATATTATAAAAA
1 AAAAAAATATATATTACAAAAA
22395163 AAGAATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAAAAATATATATTACAAAAATT
Found at i:22397359 original size:18 final size:17
Alignment explanation
Indices: 22397317--22397364 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
22397307 AAAAGAAGAA
*
22397317 AAACAAAAAAATGAGTG
1 AAACAAAAAAAAGAGTG
22397334 ATAA-AAAAAAAGAGAGTG
1 A-AACAAAAAAA-AGAGTG
22397352 AAACAAAAGAAAA
1 AAACAAAA-AAAA
22397365 AGAAAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 10 0.38
18 13 0.50
19 3 0.12
ACGTcount: A:0.71, C:0.04, G:0.17, T:0.08
Consensus pattern (17 bp):
AAACAAAAAAAAGAGTG
Found at i:22402443 original size:14 final size:15
Alignment explanation
Indices: 22402421--22402497 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
22402411 CAATCAAACA
22402421 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
22402435 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
22402450 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
22402470 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
22402484 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
22402498 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:22402462 original size:20 final size:20
Alignment explanation
Indices: 22402437--22402476 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
22402427 AATATTTTCC
*
22402437 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
22402457 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
22402477 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:22402482 original size:34 final size:35
Alignment explanation
Indices: 22402425--22402491 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
22402415 CAAACACCAG
*
22402425 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
22402460 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
22402492 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:22404989 original size:48 final size:49
Alignment explanation
Indices: 22404937--22405089 Score: 136
Period size: 52 Copynumber: 3.1 Consensus size: 49
22404927 GATTTTGTTC
*
22404937 ATTTAATTGTTTTTTAGATCT-GAT-TCTTTTAAATAAATATAGATATTT
1 ATTTAATTGTTTTTTAGATCTAG-TGTCTTTTAAATAAATATAAATATTT
* *
22404985 ATTTAATTTGTTTTTCTTAGATCTAGTGTTTTTTACATAAATATAAATATTT
1 ATTTAA-TTG-TTTT-TTAGATCTAGTGTCTTTTAAATAAATATAAATATTT
* * * **
22405037 ATTTATATTATTTGTTCAGATCT--TGT-ATTTAATATAAATATTTATATTT
1 ATTTA-ATTGTTT-TTTAGATCTAGTGTCTTTTAA-ATAAATATAAATATTT
22405086 ATTT
1 ATTT
22405090 GTTAACGTGT
Statistics
Matches: 88, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
48 10 0.11
49 24 0.27
50 4 0.05
51 19 0.22
52 30 0.34
53 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (49 bp):
ATTTAATTGTTTTTTAGATCTAGTGTCTTTTAAATAAATATAAATATTT
Found at i:22412111 original size:38 final size:38
Alignment explanation
Indices: 22412064--22412138 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
22412054 GATAACTCCA
*
22412064 CAATCCCATATTTTCCTCCTAAAATCACTCCAACACTC
1 CAATCCCATATTTCCCTCCTAAAATCACTCCAACACTC
*
22412102 CAATCCCATATTTCCCTCCTAAAATCACTCTAACACT
1 CAATCCCATATTTCCCTCCTAAAATCACTCCAACACT
22412139 GCCCTACCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (38 bp):
CAATCCCATATTTCCCTCCTAAAATCACTCCAACACTC
Found at i:22415347 original size:24 final size:24
Alignment explanation
Indices: 22415293--22415347 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
22415283 TGGCCCTCTA
*
22415293 GAGCTTCCCGATATTGGCTCGCTT
1 GAGCTTCCCGATATTGGCGCGCTT
* *
22415317 GAACTTCCTGATATTGGCGCG-TAT
1 GAGCTTCCCGATATTGGCGCGCT-T
22415341 GAGCTTC
1 GAGCTTC
22415348 ACGTTAATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.33
Consensus pattern (24 bp):
GAGCTTCCCGATATTGGCGCGCTT
Found at i:22415410 original size:25 final size:25
Alignment explanation
Indices: 22415339--22415411 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 25
22415329 ATTGGCGCGT
*
22415339 ATGAGCTTCACGTTA-ATGGCTCTC
1 ATGAGCTTCACGTTATATGGCTCAC
** * **
22415363 CGGAGCTTCTCGTTATACAGCTCAC
1 ATGAGCTTCACGTTATATGGCTCAC
*
22415388 ATGAGCTTCCCGTTATATGGCTCA
1 ATGAGCTTCACGTTATATGGCTCA
22415412 AAAGATTTTC
Statistics
Matches: 37, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
24 12 0.32
25 25 0.68
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.32
Consensus pattern (25 bp):
ATGAGCTTCACGTTATATGGCTCAC
Found at i:22416340 original size:14 final size:14
Alignment explanation
Indices: 22416321--22416347 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22416311 GTTATTGAAT
22416321 ATAACTTCACGAGC
1 ATAACTTCACGAGC
22416335 ATAACTTCACGAG
1 ATAACTTCACGAG
22416348 TTATTGAATA
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:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (14 bp):
ATAACTTCACGAGC
Found at i:22418983 original size:44 final size:43
Alignment explanation
Indices: 22418934--22419021 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 43
22418924 TATCTTTATT
*
22418934 CATGGAAATTTCCAAAAGTCCTTCATATTGAATGCCTATAAAAA
1 CATGGAAATTTCCAAAAGTCCTCCATATTGAATG-CTATAAAAA
*
22418978 CATGGAAGTTTCCAAAAGTCCTCCATATTGAATGCTATAAAAA
1 CATGGAAATTTCCAAAAGTCCTCCATATTGAATGCTATAAAAA
22419021 C
1 C
22419022 CAAAAGAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 10 0.24
44 32 0.76
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (43 bp):
CATGGAAATTTCCAAAAGTCCTCCATATTGAATGCTATAAAAA
Found at i:22420261 original size:38 final size:40
Alignment explanation
Indices: 22420204--22420288 Score: 120
Period size: 38 Copynumber: 2.2 Consensus size: 40
22420194 TGGTCTAAAC
*
22420204 TAAAGACATGTATTGAAGATGT-CTAAACTAGGACAT-AT
1 TAAAAACATGTATTGAAGATGTCCTAAACTAGGACATAAT
* * *
22420242 TCAAAACATGTATTTAAGATGTCCTAAACTATGACATAAT
1 TAAAAACATGTATTGAAGATGTCCTAAACTAGGACATAAT
22420282 TAAAAAC
1 TAAAAAC
22420289 CCTTATTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 19 0.47
39 13 0.32
40 8 0.20
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (40 bp):
TAAAAACATGTATTGAAGATGTCCTAAACTAGGACATAAT
Found at i:22420335 original size:38 final size:39
Alignment explanation
Indices: 22420252--22420359 Score: 128
Period size: 38 Copynumber: 2.8 Consensus size: 39
22420242 TCAAAACATG
* * * *
22420252 TATTTAAGATGTCCTAAACTATGACATAATTAAAAACCCT
1 TATTAAAGATGTTC-AAATTATGACATAATTAAAAACCCA
* * *
22420292 TATTAAAGATGTTCAGATTATGGCATAATT-AAAACTCA
1 TATTAAAGATGTTCAAATTATGACATAATTAAAAACCCA
*
22420330 TATTAATGATGTTCAAATTATGACATAATT
1 TATTAAAGATGTTCAAATTATGACATAATT
22420360 TAATACTTAA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 33 0.57
39 13 0.22
40 12 0.21
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (39 bp):
TATTAAAGATGTTCAAATTATGACATAATTAAAAACCCA
Found at i:22423120 original size:21 final size:21
Alignment explanation
Indices: 22423094--22423133 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
22423084 TTCGATGAGA
22423094 TGGGACTGAGGAGTGTGCCGG
1 TGGGACTGAGGAGTGTGCCGG
22423115 TGGGACTGAGGAGTGTGCC
1 TGGGACTGAGGAGTGTGCC
22423134 ATAGGAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.50, T:0.20
Consensus pattern (21 bp):
TGGGACTGAGGAGTGTGCCGG
Found at i:22424456 original size:19 final size:19
Alignment explanation
Indices: 22424432--22424468 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
22424422 AGAAGAGTCT
22424432 ACATTAGCTATAGATGCAA
1 ACATTAGCTATAGATGCAA
22424451 ACATTAGCTATAGATGCA
1 ACATTAGCTATAGATGCA
22424469 GACTTACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (19 bp):
ACATTAGCTATAGATGCAA
Found at i:22428853 original size:11 final size:12
Alignment explanation
Indices: 22428833--22428933 Score: 76
Period size: 11 Copynumber: 9.2 Consensus size: 12
22428823 CGTAACCATT
22428833 CAGATA-AGATG
1 CAGATACAGATG
22428844 CAGA-ACAGAT-
1 CAGATACAGATG
*
22428854 CATATACAGATG
1 CAGATACAGATG
*
22428866 CAGA-ACAGATT
1 CAGATACAGATG
22428877 C-GATACAGATG
1 CAGATACAGATG
*
22428888 CAGA-ACAAAT-
1 CAGATACAGATG
* *
22428898 CAAATAAAGATG
1 CAGATACAGATG
*
22428910 AAGA-ACAGAT-
1 CAGATACAGATG
*
22428920 CAAATACAGATG
1 CAGATACAGATG
22428932 CA
1 CA
22428934 ATTTCCTACC
Statistics
Matches: 68, Mismatches: 13, Indels: 17
0.69 0.13 0.17
Matches are distributed among these distances:
10 11 0.16
11 48 0.71
12 9 0.13
ACGTcount: A:0.50, C:0.16, G:0.19, T:0.16
Consensus pattern (12 bp):
CAGATACAGATG
Found at i:22428867 original size:22 final size:22
Alignment explanation
Indices: 22428839--22428933 Score: 129
Period size: 22 Copynumber: 4.3 Consensus size: 22
22428829 CATTCAGATA
*
22428839 AGATGCAGAACAGATCATATAC
1 AGATGCAGAACAGATCAAATAC
*
22428861 AGATGCAGAACAGATTC-GATAC
1 AGATGCAGAACAGA-TCAAATAC
* *
22428883 AGATGCAGAACAAATCAAATAA
1 AGATGCAGAACAGATCAAATAC
*
22428905 AGATGAAGAACAGATCAAATAC
1 AGATGCAGAACAGATCAAATAC
22428927 AGATGCA
1 AGATGCA
22428934 ATTTCCTACC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.03
22 59 0.94
23 2 0.03
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (22 bp):
AGATGCAGAACAGATCAAATAC
Found at i:22428889 original size:44 final size:45
Alignment explanation
Indices: 22428830--22428933 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 45
22428820 TATCGTAACC
* * * *
22428830 ATTCAGATA-AGATGCAGAACAGATCATATACAGATGCAGAACAG
1 ATTCAGATACAGATGCAGAACAAATCAAATAAAGATGAAGAACAG
22428874 ATTC-GATACAGATGCAGAACAAATCAAATAAAGATGAAGAACAG
1 ATTCAGATACAGATGCAGAACAAATCAAATAAAGATGAAGAACAG
*
22428918 A-TCAAATACAGATGCA
1 ATTCAGATACAGATGCA
22428934 ATTTCCTACC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
43 6 0.11
44 47 0.89
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.17
Consensus pattern (45 bp):
ATTCAGATACAGATGCAGAACAAATCAAATAAAGATGAAGAACAG
Found at i:22429637 original size:63 final size:63
Alignment explanation
Indices: 22429536--22429657 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
22429526 ACACAACCAT
* * * * *
22429536 GTCCTTAACCCATGTTACCCTAAATAAAAAATAATGAGTTACACGGCCTGTACGCACGCTCGC
1 GTCCTTAACCCATGTGACCCTAAACAAAAAATAATGAGTCACACGGCCTGGACACACGCTCGC
* * * * *
22429599 GTCCTTAGCCCGTGTGACCCTAAACCACAAATAGTGAGTCACACGGCCTGGACACACGC
1 GTCCTTAACCCATGTGACCCTAAACAAAAAATAATGAGTCACACGGCCTGGACACACGC
22429658 CCGTGTGACT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (63 bp):
GTCCTTAACCCATGTGACCCTAAACAAAAAATAATGAGTCACACGGCCTGGACACACGCTCGC
Found at i:22429681 original size:50 final size:50
Alignment explanation
Indices: 22429606--22429713 Score: 162
Period size: 50 Copynumber: 2.2 Consensus size: 50
22429596 CGCGTCCTTA
*
22429606 GCCCGTGTGACCCTAAACCACAAATAGTGAGTCACACGGCCTGGACACAC
1 GCCCGTGTGACCCTAAACCACAAATAGTGAGTCACACGACCTGGACACAC
* * * *
22429656 GCCCGTGTGACTCTAAATCACAAATAGTGAGTTACATGACCTGGACACAC
1 GCCCGTGTGACCCTAAACCACAAATAGTGAGTCACACGACCTGGACACAC
*
22429706 ACCCGTGT
1 GCCCGTGT
22429714 CCCTGGCATG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.19
Consensus pattern (50 bp):
GCCCGTGTGACCCTAAACCACAAATAGTGAGTCACACGACCTGGACACAC
Found at i:22435515 original size:22 final size:22
Alignment explanation
Indices: 22435476--22435537 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
22435466 TAATATGTAG
* * *
22435476 AACATATCAGTTATAGATGCAA
1 AACAGATCAGATACAGATGCAA
* *
22435498 AACAGATTC-GATACAGATGTAG
1 AACAGA-TCAGATACAGATGCAA
22435520 AACAGATCAGATACAGAT
1 AACAGATCAGATACAGAT
22435538 ACAGTTTCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.23
Consensus pattern (22 bp):
AACAGATCAGATACAGATGCAA
Found at i:22436313 original size:63 final size:63
Alignment explanation
Indices: 22436191--22436679 Score: 387
Period size: 63 Copynumber: 7.8 Consensus size: 63
22436181 CGCGTCCTTG
* * * * * * * **
22436191 GCCCATGTGACCTTAAATAACAAAT-GTGAGTTACACAGTCTAGACACACGTCCGCGTCCCTA
1 GCCCGTGTGACCCTAAATCACAAATAGTGAGTTACACAGCCTGGACACAAGCCCATGTCCCTA
** * * * * *
22436253 GTTCATGTAACCCTAAATCACAAACAGTGAGTTACAGAGCCTGGACAGAAGCCCATGTCCCTA
1 GCCCGTGTGACCCTAAATCACAAATAGTGAGTTACACAGCCTGGACACAAGCCCATGTCCCTA
* * * ** *
22436316 GCCCGTGTGACCGTAAATCACAAATAGTGAGTTACATAGCCTGGACACAGGCCTGTGTCCCTG
1 GCCCGTGTGACCCTAAATCACAAATAGTGAGTTACACAGCCTGGACACAAGCCCATGTCCCTA
* * **
22436379 GCCCGTGTGACCCTAAATCACAAATAGAGAGTTACACAGCCTGGTCACACA-CCTGTGTCCCT-
1 GCCCGTGTGACCCTAAATCACAAATAGTGAGTTACACAGCCTGGACACA-AGCCCATGTCCCTA
** * * * * * ** *
22436441 GTCCTATGCGACTCTAAATCACAAATAGCGAGTTACACGGCCTGGTCACACA-CCTGTGTCCCTG
1 G-CCCGTGTGACCCTAAATCACAAATAGTGAGTTACACAGCCTGGACACA-AGCCCATGTCCCTA
* * ** * * * *
22436505 GCCCGTGTGACTCTAAATCATAAATAACGAGTTACACGGCCTGGACACACA-CCCGTGTCCTTG
1 GCCCGTGTGACCCTAAATCACAAATAGTGAGTTACACAGCCTGGACACA-AGCCCATGTCCCTA
** * * *
22436568 GCCCGTGTGACTTTAAATCACAAATAGCGAGTTACACAGCCTGGACACATA-CCCGTGTCCCTG
1 GCCCGTGTGACCCTAAATCACAAATAGTGAGTTACACAGCCTGGACACA-AGCCCATGTCCCTA
*** * * *
22436631 GCCCGTGTGATTTTAAATCACAAACAGTAAGTTACACGGCCTGGCACAC
1 GCCCGTGTGACCCTAAATCACAAATAGTGAGTTACACAGCCTGG-ACAC
22436680 GACCGTGTGA
Statistics
Matches: 366, Mismatches: 56, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
62 20 0.05
63 341 0.93
64 5 0.01
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (63 bp):
GCCCGTGTGACCCTAAATCACAAATAGTGAGTTACACAGCCTGGACACAAGCCCATGTCCCTA
Found at i:22436511 original size:189 final size:188
Alignment explanation
Indices: 22436174--22436688 Score: 525
Period size: 189 Copynumber: 2.7 Consensus size: 188
22436164 TGGCGTCGAT
* * * * * * * * *
22436174 ACACGCCCGCGTCCTTGGCCCATGTGACCTTAAATAACAAAT-GTGAGTTACACAGTCTAGACAC
1 ACACACCCGTGTCCCTGGCCCGTGTGACCCTAAATCACAAATAGAGAGTTACACAGCCTGGACAC
** * * ** ** *
22436238 ACGTCCGCGTCCCTAGTTCATGTAACCCTAAATCACAAACAGTGAGTTACA-GAGCCTGG-ACAG
66 ACACCCGTGTCCCTGGCCCATGCGACTCTAAATCACAAACAGTGAGTTACACG-GCCTGGCACA-
* ** ** *
22436301 AAGCCCATGTCCCTAGCCCGTGTGAC-CGTAAATCACAAATAGTGAGTTACATAGCCTGGAC
129 CA-CCTGTGTCCCTAGCCCGTGTGACTC-TAAATCACAAATAACGAGTTACACAGCCTGGAC
** * *
22436362 ACAGGCCTGTGTCCCTGGCCCGTGTGACCCTAAATCACAAATAGAGAGTTACACAGCCTGGTCAC
1 ACACACCCGTGTCCCTGGCCCGTGTGACCCTAAATCACAAATAGAGAGTTACACAGCCTGGACAC
* * * * *
22436427 ACACCTGTGTCCCTGTCCTATGCGACTCTAAATCACAAATAGCGAGTTACACGGCCTGGTCACAC
66 ACACCCGTGTCCCTGGCCCATGCGACTCTAAATCACAAACAGTGAGTTACACGGCCTGG-CACAC
* * *
22436492 ACCTGTGTCCCTGGCCCGTGTGACTCTAAATCATAAATAACGAGTTACACGGCCTGGAC
130 ACCTGTGTCCCTAGCCCGTGTGACTCTAAATCACAAATAACGAGTTACACAGCCTGGAC
* ** *
22436551 ACACACCCGTGTCCTTGGCCCGTGTGACTTTAAATCACAAATAGCGAGTTACACAGCCTGGACAC
1 ACACACCCGTGTCCCTGGCCCGTGTGACCCTAAATCACAAATAGAGAGTTACACAGCCTGGACAC
* * * * * *
22436616 ATACCCGTGTCCCTGGCCCGTGTGATTTTAAATCACAAACAGTAAGTTACACGGCCTGGCACACG
66 ACACCCGTGTCCCTGGCCCATGCGACTCTAAATCACAAACAGTGAGTTACACGGCCTGGCACAC-
22436681 ACCGTGTG
130 ACC-TGTG
22436689 ACACACACGG
Statistics
Matches: 267, Mismatches: 53, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
188 40 0.15
189 217 0.81
190 7 0.03
191 3 0.01
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (188 bp):
ACACACCCGTGTCCCTGGCCCGTGTGACCCTAAATCACAAATAGAGAGTTACACAGCCTGGACAC
ACACCCGTGTCCCTGGCCCATGCGACTCTAAATCACAAACAGTGAGTTACACGGCCTGGCACACA
CCTGTGTCCCTAGCCCGTGTGACTCTAAATCACAAATAACGAGTTACACAGCCTGGAC
Found at i:22442210 original size:7 final size:7
Alignment explanation
Indices: 22442171--22442195 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
22442161 TTCTTATTTC
22442171 TATTTAT
1 TATTTAT
22442178 TATTTAT
1 TATTTAT
22442185 TATTTAT
1 TATTTAT
22442192 TATT
1 TATT
22442196 CCCCATTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTAT
Found at i:22442799 original size:59 final size:59
Alignment explanation
Indices: 22442721--22442832 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 59
22442711 AATACAAGAA
* ** *
22442721 TTTATGATTTAATTGCTTATGATTGATGGTATAAATCTGTGAATGATTTTATAATTGCT
1 TTTATGATATAATCACTTATGATTGATGGTATAAATCTGTGAATGATTATATAATTGCT
* * * * *
22442780 TTTATGATATAATCACTTATGATTGTTTGTTTAAATTTGTGAATTATTATATA
1 TTTATGATATAATCACTTATGATTGATGGTATAAATCTGTGAATGATTATATA
22442833 TATTTATTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 44 1.00
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.51
Consensus pattern (59 bp):
TTTATGATATAATCACTTATGATTGATGGTATAAATCTGTGAATGATTATATAATTGCT
Found at i:22442965 original size:16 final size:15
Alignment explanation
Indices: 22442940--22442969 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
22442930 ATAATGATAT
22442940 TGATTGATTGCATTA
1 TGATTGATTGCATTA
22442955 TGATTGCATTGCATT
1 TGATTG-ATTGCATT
22442970 GCATTTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.47
Consensus pattern (15 bp):
TGATTGATTGCATTA
Found at i:22443603 original size:37 final size:36
Alignment explanation
Indices: 22443540--22443639 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 36
22443530 TACCATATGG
** *
22443540 AATTGATTGATATGTGAAACCATTTGTTATCATGT-TA
1 AATTGATTGATATGTGAAACTGTTTGTCAT--TGTATA
*
22443577 AATTGATTGATATGTGAAACTGTTTGTCATTGTAGTG
1 AATTGATTGATATGTGAAACTGTTTGTCATTGTA-TA
* *
22443614 AATAGATTGATATGTGAAATTGTTTG
1 AATTGATTGATATGTGAAACTGTTTG
22443640 ATATTATTGT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 3 0.05
37 52 0.95
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (36 bp):
AATTGATTGATATGTGAAACTGTTTGTCATTGTATA
Found at i:22443642 original size:17 final size:17
Alignment explanation
Indices: 22443540--22443643 Score: 52
Period size: 17 Copynumber: 5.8 Consensus size: 17
22443530 TACCATATGG
22443540 AATTGATTGATATGTGAA
1 AATTGATTGATATGTG-A
*
22443558 ACCATTTG-TT-ATCATGTTA
1 A--A-TTGATTGAT-ATGTGA
22443577 AATTGATTGATATGTGA
1 AATTGATTGATATGTGA
* * *
22443594 AACTGTTTG-TCATTGTAGTG
1 AATTGATTGAT-A-TGT-G-A
*
22443614 AATAGATTGATATGTGA
1 AATTGATTGATATGTGA
*
22443631 AATTGTTTGATAT
1 AATTGATTGATAT
22443644 TATTGTACAG
Statistics
Matches: 64, Mismatches: 11, Indels: 23
0.65 0.11 0.23
Matches are distributed among these distances:
16 4 0.06
17 27 0.42
18 7 0.11
19 8 0.12
20 14 0.22
21 4 0.06
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (17 bp):
AATTGATTGATATGTGA
Found at i:22450685 original size:13 final size:13
Alignment explanation
Indices: 22450667--22450691 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22450657 TTCAAAAATA
22450667 TTATTTATTTAAT
1 TTATTTATTTAAT
22450680 TTATTTATTTAA
1 TTATTTATTTAA
22450692 AATTAAATTG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTATTTAAT
Found at i:22462319 original size:3 final size:3
Alignment explanation
Indices: 22462311--22462353 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
22462301 ACAAAGACAT
*
22462311 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TAA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
22462354 AATGGTCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:22463579 original size:21 final size:21
Alignment explanation
Indices: 22463553--22463592 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
22463543 TGATGTAGCT
*
22463553 AAGTTCATTT-ATTTTTTCCCC
1 AAGTTC-TTTCATTTGTTCCCC
22463574 AAGTTCTTTCATTTGTTCC
1 AAGTTCTTTCATTTGTTCC
22463593 AAGGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.17, C:0.23, G:0.07, T:0.53
Consensus pattern (21 bp):
AAGTTCTTTCATTTGTTCCCC
Found at i:22468792 original size:17 final size:17
Alignment explanation
Indices: 22468770--22468881 Score: 82
Period size: 17 Copynumber: 6.5 Consensus size: 17
22468760 TCAAACATCT
*
22468770 GTTCATATAAAATAACA
1 GTTCATACAAAATAACA
*
22468787 GTTCATACACCAAATGACA
1 GTTCATACA--AAATAACA
* * *
22468806 GCTCATGCAAAATAATA
1 GTTCATACAAAATAACA
* ** *
22468823 GTTTATATGAAATATCA
1 GTTCATACAAAATAACA
**
22468840 GTTCATACCGAATAACTA
1 GTTCATACAAAATAAC-A
*
22468858 -TTCATGCAAAATAACA
1 GTTCATACAAAATAACA
22468874 GTTCATAC
1 GTTCATAC
22468882 TCTATCATAA
Statistics
Matches: 69, Mismatches: 22, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
16 1 0.01
17 53 0.77
18 1 0.01
19 14 0.20
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.29
Consensus pattern (17 bp):
GTTCATACAAAATAACA
Found at i:22469602 original size:36 final size:36
Alignment explanation
Indices: 22469534--22469603 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
22469524 AATTAATATC
*
22469534 GTTCGCCATATTAATACAAATCACCAAATTAACACA
1 GTTCGCCATAATAATACAAATCACCAAATTAACACA
* * * *
22469570 GTTCGCCATAATAATATAATTCGCCAAGTTAACA
1 GTTCGCCATAATAATACAAATCACCAAATTAACA
22469604 TGGTTCACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.41, C:0.23, G:0.09, T:0.27
Consensus pattern (36 bp):
GTTCGCCATAATAATACAAATCACCAAATTAACACA
Found at i:22469879 original size:25 final size:27
Alignment explanation
Indices: 22469845--22469980 Score: 117
Period size: 29 Copynumber: 5.1 Consensus size: 27
22469835 ACTCATCCAT
*
22469845 ATATATATATTATA-A-AACAAGACCC
1 ATATATATATTATAGATAACAAAACCC
*
22469870 ATATATATATTAT--ATAACAAAACTC
1 ATATATATATTATAGATAACAAAACCC
*
22469895 ACT-CATATATTATAGATAACAAAACCC
1 A-TATATATATTATAGATAACAAAACCC
*
22469922 ATGCATATAT-TTAATATATAACAAAACCC
1 AT--ATATATATT-ATAGATAACAAAACCC
22469951 ATACATATATATTAT-GCATAAC-AAACCC
1 AT--ATATATATTATAG-ATAACAAAACCC
22469979 AT
1 AT
22469981 GCATGTATAT
Statistics
Matches: 93, Mismatches: 8, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
24 1 0.01
25 31 0.33
26 2 0.02
27 12 0.13
28 10 0.11
29 35 0.38
30 2 0.02
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.30
Consensus pattern (27 bp):
ATATATATATTATAGATAACAAAACCC
Found at i:22469901 original size:29 final size:28
Alignment explanation
Indices: 22469841--22469992 Score: 131
Period size: 27 Copynumber: 5.5 Consensus size: 28
22469831 CAAAACTCAT
* *
22469841 CCAT-ATATATATATTATAAAACAAGA-
1 CCATCATATATATATTATATAACAAAAC
22469867 CC--CATATATATATTATATAACAAAAC
1 CCATCATATATATATTATATAACAAAAC
* *
22469893 TCACTCATATAT-TA-TAGATAACAAAAC
1 CCA-TCATATATATATTATATAACAAAAC
* *
22469920 CCATGCATATATTTAATATATAACAAAAC
1 CCAT-CATATATATATTATATAACAAAAC
*
22469949 CCAT-ACATATATATTATGCATAAC-AAAC
1 CCATCATATATATATTAT--ATAACAAAAC
*
22469977 CCATGCATGTATATAT
1 CCAT-CATATATATAT
22469993 AGTATATATA
Statistics
Matches: 103, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
25 20 0.19
26 4 0.04
27 31 0.30
28 12 0.12
29 28 0.27
30 8 0.08
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (28 bp):
CCATCATATATATATTATATAACAAAAC
Found at i:22476587 original size:18 final size:19
Alignment explanation
Indices: 22476564--22476604 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
22476554 TGCAGGATTT
*
22476564 TATTTCATT-TTGTATTAC
1 TATTTCATTCTTATATTAC
*
22476582 TATTTCCTTCTTATATTAC
1 TATTTCATTCTTATATTAC
22476601 TATT
1 TATT
22476605 ATATATTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.22, C:0.15, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTTCATTCTTATATTAC
Found at i:22480706 original size:16 final size:17
Alignment explanation
Indices: 22480682--22480715 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
22480672 TAGTCTTTCT
22480682 TTTTATTTTTT-TCTTC
1 TTTTATTTTTTGTCTTC
*
22480698 TTTTCTTTTTTGTCTTC
1 TTTTATTTTTTGTCTTC
22480715 T
1 T
22480716 CTTCGACTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTTGTCTTC
Found at i:22489774 original size:14 final size:14
Alignment explanation
Indices: 22489755--22489782 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22489745 TAAACACTAT
22489755 TGGATACTCAATAA
1 TGGATACTCAATAA
22489769 TGGATACTCAATAA
1 TGGATACTCAATAA
22489783 CAATTCTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
TGGATACTCAATAA
Found at i:22491083 original size:40 final size:40
Alignment explanation
Indices: 22491020--22491095 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
22491010 TCTCAACTTC
* * *
22491020 ATACTTGATGATTAATCTTAGTGCATTATGTTGGAACATT
1 ATACTTGATAATTAATCTAAGTGCATTATGGTGGAACATT
*
22491060 ATACTTGATAATTCATCTAAGTGCATTATGGTGGAA
1 ATACTTGATAATTAATCTAAGTGCATTATGGTGGAA
22491096 TATAAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (40 bp):
ATACTTGATAATTAATCTAAGTGCATTATGGTGGAACATT
Found at i:22504976 original size:7 final size:7
Alignment explanation
Indices: 22504964--22504999 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
22504954 TGCAAGGAGA
22504964 TGAAAGG
1 TGAAAGG
22504971 TGAAAGG
1 TGAAAGG
22504978 TGAAAGG
1 TGAAAGG
*
22504985 TCAAAGG
1 TGAAAGG
*
22504992 TCAAAGG
1 TGAAAGG
22504999 T
1 T
22505000 TGAGGAAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.42, C:0.06, G:0.36, T:0.17
Consensus pattern (7 bp):
TGAAAGG
Found at i:22506273 original size:36 final size:37
Alignment explanation
Indices: 22506232--22506311 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 37
22506222 TATATATATC
* *
22506232 AATTTTTAT-ATTTTTTAAATTTGTAATATATTTAT-A
1 AATTTTTATGAGTTTTTAAATTTCTAAT-TATTTATAA
* *
22506268 TATTTTT-TGAGTTTTTAATTTTCTAATTATTTATAA
1 AATTTTTATGAGTTTTTAAATTTCTAATTATTTATAA
22506304 AATTTTTA
1 AATTTTTA
22506312 CATATACTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
35 8 0.22
36 28 0.78
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (37 bp):
AATTTTTATGAGTTTTTAAATTTCTAATTATTTATAA
Found at i:22506310 original size:35 final size:36
Alignment explanation
Indices: 22506243--22506310 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
22506233 ATTTTTATAT
* * *
22506243 TTTTTAAATTTGTAATATATTTATATATTTTTTGAG
1 TTTTTAAATTTCTAATATATTTATAAAATTTTTGAG
*
22506279 TTTTTAATTTTCTAAT-TATTTATAAAATTTTT
1 TTTTTAAATTTCTAATATATTTATAAAATTTTT
22506311 ACATATACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 14 0.50
36 14 0.50
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (36 bp):
TTTTTAAATTTCTAATATATTTATAAAATTTTTGAG
Found at i:22507187 original size:1 final size:1
Alignment explanation
Indices: 22507183--22507207 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
22507173 GTTCAGCGGT
22507183 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
22507208 CTCAAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22514426 original size:24 final size:25
Alignment explanation
Indices: 22514397--22514446 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
22514387 AAATCGAGTT
*
22514397 TCTTTTCTCAGTTAAACTCT-ATTA
1 TCTTTTCTCAATTAAACTCTAATTA
*
22514421 TCTTTTCTCAATTAAAGTCTAATTA
1 TCTTTTCTCAATTAAACTCTAATTA
22514446 T
1 T
22514447 TCTAGGGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.50
Consensus pattern (25 bp):
TCTTTTCTCAATTAAACTCTAATTA
Found at i:22524073 original size:85 final size:83
Alignment explanation
Indices: 22523967--22524250 Score: 311
Period size: 85 Copynumber: 3.3 Consensus size: 83
22523957 CTTTGAATGT
** * * *
22523967 AAGGGGTTGCTAAGTGCTGATTCCCCAAATTATTGACTCTAAAGGTGGTTGCTAAGTGTTGATCC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGA-T-TAAAGGTGGTTGCTAAGTGCTGATTC
** *
22524032 CACCGTATTTTTTATTGTGA
64 CACCGTATCCTTGATTGTGA
* * * *
22524052 ATGGGGTTGCTAAGTGTTGATTTCCCGTATCACTTAATATAAAGGTGGTTGCTAAGTGCTGATTC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCA-TTGAT-TAAAGGTGGTTGCTAAGTGCTGATTC
22524117 CACCGTATCCTTGATTGTGA
64 CACCGTATCCTTGATTGTGA
* *
22524137 AAGGGGTTGTTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA-AAGGTGGTTGCTAAGTGCTGATTCC
* ***
22524202 ACCGGGATCCTTTGAACATG-
65 ACC-GTATCC-TTGATTGTGA
22524222 -AGGTGGTTGCTAAGTGCTGATTCCACCGT
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGT
22524251 GTAACGGTTA
Statistics
Matches: 168, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
83 2 0.01
84 35 0.21
85 118 0.70
86 13 0.08
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (83 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAAAGGTGGTTGCTAAGTGCTGATTCCA
CCGTATCCTTGATTGTGA
Found at i:22524102 original size:42 final size:43
Alignment explanation
Indices: 22523962--22524250 Score: 210
Period size: 42 Copynumber: 6.8 Consensus size: 43
22523952 GGATTCTTTG
** *
22523962 AATGT-AAGG-GGTTGCTAAGTGCTGATTCC-CCAAATTA-TT
1 AATGTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTT
* * * * ***
22524001 GACTCTAAAGGTGGTTGCTAAGTGTTGATCCCACCGTATTTTTT
1 -AATGTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTT
* * * *
22524045 ATTGTGAATGG-GGTTGCTAAGTGTTGATTTC-CCGTATCACTT
1 AATGT-AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTT
*
22524087 AATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATC-CTT
1 AATGTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTT
* * *
22524129 GATTGTGAAAGG-GGTTGTTATGTGCTGATTCC-CCGTATCA-TT
1 -AATGT-AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTT
* *
22524171 GAT-TATAAGGTGGTTGCTAAGTGCTGATTCCACCGGGATC-CTT
1 AATGTA-AAGGTGGTTGCTAAGTGCTGATTCCACC-GTATCACTT
*
22524214 --TGAACATGAGGTGGTTGCTAAGTGCTGATTCCACCGT
1 AATGTA-A--AGGTGGTTGCTAAGTGCTGATTCCACCGT
22524251 GTAACGGTTA
Statistics
Matches: 199, Mismatches: 32, Indels: 33
0.75 0.12 0.12
Matches are distributed among these distances:
39 1 0.01
40 8 0.04
41 28 0.14
42 63 0.32
43 61 0.31
44 38 0.19
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (43 bp):
AATGTAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCACTT
Found at i:22524232 original size:44 final size:42
Alignment explanation
Indices: 22524009--22524250 Score: 215
Period size: 43 Copynumber: 5.7 Consensus size: 42
22523999 TTGACTCTAA
* * ** * *
22524009 AGGTGGTTGCTAAGTGTTGATCCCACCGTATTTTTTATTGTG
1 AGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG
* * * *
22524051 AATGG-GGTTGCTAAGTGTTGATTTC-CCGTATCACTT-AATATAA
1 -A-GGTGGTTGCTAAGTGCTGATTCCACCGTATC-CTTGATTAT-G
*
22524094 AGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTG
1 AGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG
* * * *
22524136 AAAGG-GGTTGTTATGTGCTGATTCC-CCGTATCATTGATTATA
1 --AGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG
* **
22524178 AGGTGGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAACATG
1 AGGTGGTTGCTAAGTGCTGATTCCACC-GTATCC-TTGATTATG
22524222 AGGTGGTTGCTAAGTGCTGATTCCACCGT
1 AGGTGGTTGCTAAGTGCTGATTCCACCGT
22524251 GTAACGGTTA
Statistics
Matches: 162, Mismatches: 25, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
40 3 0.02
41 20 0.12
42 47 0.29
43 54 0.33
44 38 0.23
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (42 bp):
AGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG
Found at i:22528120 original size:23 final size:25
Alignment explanation
Indices: 22527978--22528120 Score: 73
Period size: 24 Copynumber: 5.9 Consensus size: 25
22527968 ATCCAGGTTG
* ***
22527978 TATAACGGGAAGCTCATAAGAGCCA
1 TATATCGGGAAGCTCCGGAGAGCCA
* ** *
22528003 TA-ATCAGGAAGCTCATGCGAGCCA
1 TATATCGGGAAGCTCCGGAGAGCCA
* * * *
22528027 -ATAACGGGTAGCTCCGAAAAGCCA
1 TATATCGGGAAGCTCCGGAGAGCCA
* *
22528051 T-TCA-CGGGAAGCTTCGGATAGCCA
1 TAT-ATCGGGAAGCTCCGGAGAGCCA
* ** *
22528075 TATATCGGGAAGTTCAAGTGAGCCA
1 TATATCGGGAAGCTCCGGAGAGCCA
22528100 TAT-T-GGGAAGCTCCGGAGAGC
1 TATATCGGGAAGCTCCGGAGAGC
22528121 GATTACTCAA
Statistics
Matches: 87, Mismatches: 26, Indels: 12
0.70 0.21 0.10
Matches are distributed among these distances:
23 14 0.16
24 52 0.60
25 21 0.24
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (25 bp):
TATATCGGGAAGCTCCGGAGAGCCA
Found at i:22535992 original size:9 final size:9
Alignment explanation
Indices: 22535978--22536008 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
22535968 GTTAAATGAA
22535978 TCGAGTTAT
1 TCGAGTTAT
*
22535987 TCGAGTTAA
1 TCGAGTTAT
22535996 TCGAGTTAT
1 TCGAGTTAT
22536005 TCGA
1 TCGA
22536009 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:22537099 original size:5 final size:5
Alignment explanation
Indices: 22537089--22537124 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
22537079 TTCGAAAATT
* *
22537089 TTCGA TTCGA TTCAA TTCGA TTCAA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
22537125 CGAATACTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:22539482 original size:27 final size:25
Alignment explanation
Indices: 22539440--22539490 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
22539430 TTATTTTCAT
22539440 AAATATTAAAATATAATAATTATTTC
1 AAATATTAAAATATAA-AATTATTTC
*
22539466 AAATAATTATAAA-ATAAATTTATTT
1 AAAT-ATTA-AAATATAAAATTATTT
22539491 ATAATTACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 11 0.50
27 8 0.36
28 3 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATATTAAAATATAAAATTATTTC
Found at i:22539543 original size:16 final size:16
Alignment explanation
Indices: 22539522--22539556 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
22539512 CACTGGAATA
* *
22539522 GAATAGGGTTGTAATG
1 GAATAGGGCTATAATG
22539538 GAATAGGGCTATAATG
1 GAATAGGGCTATAATG
22539554 GAA
1 GAA
22539557 CAAAACTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (16 bp):
GAATAGGGCTATAATG
Found at i:22539622 original size:46 final size:42
Alignment explanation
Indices: 22539563--22539650 Score: 113
Period size: 46 Copynumber: 2.0 Consensus size: 42
22539553 GGAACAAAAC
* *
22539563 TGTAATGAAATAGAGTTGTAATCAGTGATTCAATTGTTTGGTTGAA
1 TGTAATGAAATAGAATTGTAAT-AAT-ATT--ATTGTTTGGTTGAA
*
22539609 TGTAATGGAATAGAATTGTAATAATATTATTGTTTGGTTGAA
1 TGTAATGAAATAGAATTGTAATAATATTATTGTTTGGTTGAA
22539651 AGGAATAGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
42 14 0.36
44 3 0.08
45 2 0.05
46 20 0.51
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (42 bp):
TGTAATGAAATAGAATTGTAATAATATTATTGTTTGGTTGAA
Found at i:22540962 original size:21 final size:19
Alignment explanation
Indices: 22540916--22540967 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
22540906 TAAGGTAATC
22540916 TTCTATTAATTTAAATAGA
1 TTCTATTAATTTAAATAGA
*
22540935 -T-TA-TAATTTAAATATTA
1 TTCTATTAATTTAAATA-GA
22540952 TTTCTATTAATTTAAA
1 -TTCTATTAATTTAAA
22540968 AATGGATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 1 0.04
19 1 0.04
20 2 0.07
21 9 0.33
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (19 bp):
TTCTATTAATTTAAATAGA
Found at i:22541091 original size:2 final size:2
Alignment explanation
Indices: 22541079--22541110 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
22541069 AGACCTTGTA
22541079 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22541111 AAATGTGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.